软甲纲动物和星虫动物线粒体基因组特征及分子进化研究
|
摘要
在过去的几十年间,利用线粒体基因组序列探讨后生动物深层次的系统发育关系已取得初步进展。这主要得益于,线粒体基因组与其它分子标记相比具备诸多优势。迄今为止,超过1,200个后生动物的线粒体基因组已被测定,然而所获得的数据分布极不均衡。
软甲纲历来是甲壳动物分类学和系统发育学研究的重要类群,在形态学特征和分子生物学各方面取得广泛的发展。尽管软甲纲本身作为单系群已得到大多数甲壳动物学家认可,但是软甲纲内部各个类群之间的系统发育关系迄今仍颇有争议。本文报道了凡纳滨对虾Litopenaeus vannamei、中国明对虾Fenneropenaeus chinensis、脊尾白虾Exopalaemon carinicauda、太平洋磷虾Euphausia pacifica和采自南极普里兹湾南极磷虾Euphausia superba的线粒体基因组,其长度分别为15,989 bp、16,004 bp、15,730 bp、16,898 bp和15,498 bp以上(部分非编码区没有测定)。
本研究发现凡纳滨对虾、中国明对虾、脊尾白虾和太平洋磷虾的线粒体基因组包含后生动物线粒体基因组典型的基因组成(13个蛋白质编码基因、22个转运RNA、2个核糖体RNA和一个非编码的AT富含区);然而,南极磷虾与后生动物线粒体基因组典型的基因组成相比,存在1个trnN基因的重复。与泛甲壳动物线粒体基因组的原始排列相比,凡纳滨对虾和中国明对虾线粒体基因组的基因排列完全一致;脊尾白虾的线粒体基因组发生罕见的trnP和trnH易位,从而说明在真虾下目中线粒体基因组的基因排列并不保守;太平洋磷虾线粒体基因组的基因排列出现3个转运RNA的重排(trnL1、trnL2和trnW);南极磷虾线粒体基因组的基因排列除了出现太平洋磷虾具有的这3个转运RNA重排之外,还有1个trnN的重复和1个trnI基因的重排。另外,在太平洋磷虾线粒体基因组最大的非编码区中存在一个154 bp×4.7的串连重复区域,如此大片段的串联重复区域(>150 bp)在软甲纲动物线粒体基因组中是首次报道。
目前所获得的线粒体基因组数据强有力地支持口足目、对虾科、真虾下目和短尾下目为单系群。通过比较基因排列及蛋白质编码基因核苷酸和氨基酸序列的系统发育分析得知真虾类和龙虾类为腹胚亚目的原始类群,并支持“((Penaeus+Fenneropenaeus)+Litopenaeus)+Marsupenaeus”的系统发育关系。此外,线粒体基因组的数据也强有力地支持磷虾目为单系群。但对于磷虾目在软甲纲中的分类地位及与其它类群的系统发育关系存在一些分歧:基于蛋白质编码基因核苷酸和氨基酸数据的贝叶斯分析强有力地支持磷虾目和十足目近缘,这个结果和传统的分类系统完全一致;然而,基于核苷酸序列的邻接法、氨基酸序列的邻接法和最大似然法均强有力地支持磷虾类和对虾类亲缘关系较近,从而破坏了十足目的单系性,与传统的认识并不一致,但由于自展值的支持率非常高,所以深层次的分析需要进一步加强。
星虫动物属于海洋生物中的一个小门类,自1555年被记载以来,其在后生动物中的分类地位就备受争议。本研究测定了星虫动物门的第一条线粒体基因组:革囊星虫Phascolosoma esculenta的线粒体基因组,全长为15,494 bp,包含13个蛋白质编码基因、22个转运RNA、2个核糖体RNA和1个非编码的AT富含区,所有37个基因在同一条链上编码。与后生动物线粒体基因组的典型组成相比,存在一个trnR基因的缺失和一个trnM基因的重复。比较星虫动物和其它后生动物的线粒体基因组,可以得到以下结论:1)星虫动物和环节动物(包括螠虫动物)的线粒体基因组有相近的基因排列,而且所有基因都在同一链上编码;2)基于蛋白质编码基因的系统发育分析强有力地支持星虫动物和环节动物(包括螠虫动物)组成一个单系群,而将软体动物排除在外。因此,本研究认为以前许多星虫动物和软体动物“共享”的特征,包括发育特征和缺乏分节等,需要重新考虑。
Over the past decades, inference of a deeper phylogenetic relationship of metazoan with whole mitochondrial genome sequences has gained popularity. This resulted from many advantages offered over other molecular markers for phylogenetic analysis. Although more than one thousand and two hundreds mitochondrial genome sequences have been determined to date, the taxonomic sampling is still highly biased.
Malacostracans have been the subject of a huge number of classificatory and phylogenetic studies employing morphological characters and molecular characters. Though Malacostraca itself is widely regarded as a monophyletic grouping, the relationships among the various groups of the Malacostraca are still controversial. In this paper, we report the mitochondrial genomes from the Litopenaeus vannamei Boone 1931, Fenneropenaeus chinensis Osbeck 1765, Exopalaemon carinicauda Holthuis 1950, Euphausia pacifica Hansen 1911 and Euphausia superba Dana 1852 (sampling from Prydz Bay, Antarctic). The mitochondrial genomes of them is 15, 989 bp, 16, 004 bp, 15, 730 bp, 16, 898 bp and more than 15, 498 bp in length (partial non-coding region was not determined), respectively.
As seen in other metazoans, the genomes of L. vannamei, F. chinensis, Exopalaemon carinicauda and Euphausia pacifica contain a standard set of 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes and an AT-rich non-coding region. However, the mitochondrial genome of Euphausia superba has an extra trnN gene compared with standard set of metazoan mitochondrial genomes. The gene arrangements of L. vannamei and F. chinensis mitochondrial genoms are consistent with the pancrustacean ground pattern. Unusual translocation of trnP and trnH was found when comparing with the pancrustacean ground pattern, which indicating gene order is not conserved among Caridea. Translocation of three tRNAs (trnL1, trnL2 and trnW) was found in the mitochondrial genome of Euphausia pacifica when comparing with the pancrustacean ground pattern. Besides the translocation of above three tRNAs, the duplication of trnN and translocation of trnI were founded in the mitochondrial genome of Euphausia superba. The largest non-coding region in the mitochondrial genome of Euphausia pacifica contains one section with tandem repeats (4.7×154 bp), which is the first report of largest tandem repeats (>150 bp) founded in the malacostracan mitochondrial genomes.
All analyses based on nucleotide and amino acid data strongly support the monophyly of Stomatopoda, Penaeidae, Caridea and Brachyura. Both the pattern of gene rearrangements and phylogenomic analyses using concatenated nucleic acid and amino acid sequences of the 13 mitochondrial PCGs strengthened the support that Caridea and Palinura are primitive members of Pleocyemata and that (((Penaeus+Fenneropenaeus)+Litopenaeus)+Marsupenaeus). The Euphausiacea clade was also recovered as monophyletic with strong statistical support. However, the taxonomic position and phylogenetic relationship of Euphausiacea within Malacostraca is unstable. The Bayesian analysis based on nucleotide and amino acid data strongly support the close relationship between Euphausiacea and Decapoda, which is coincidence with traditional views. The Neighbor-Joining approach based on nucleotide and amino acid data and Maximum-Likelihood analysis based on amino acid data strongly support the close relationship between Euphausiacea and Penaeidae, which destroy the monophyly of Decapoda and not coincidence with traditional classification. Nevertheless, the bootstrap value is very high, so the deeper analyses are needed.
Sipunculans form a minor phylum of marine animals. Although the group was first documented in 1555, their taxonomic position within Metazoan is controversial. In this paper, we present here the sequence of Phascolosoma esculenta mitochondrial genome, the first one from phylum Sipuncula. The mitochondrial genome of the P. esculenta is 15, 494 bp in length and contains 13 PCGs, 22 transfer RNA genes, 2 ribosomal RNA genes and a non-coding AT-rich region. All of the 37 identified genes are transcribed from the same DNA strand. In comparison to typical metazoan mitochondrial genomes, sipunculid mitochondrial genome lacks trnR but has an extra trnM. From the analyses of mitochondrial genome of P. esculenta and other metazoan, we make the following conclusion: First, sipunculans and annelids (including echiurans) share similar gene order in the mitochondrial genome, with all 37 genes located on the same strand; Second, phylogenetic analyses based on concatenated protein sequences also provide strong evidence that Sipuncula and Annelida (including echiurans) form a monophyletic clade to the exclusion of the Mollusca. Thus, many characteristics that have been hypothesized to link sipunculans with molluscs, including their developmental pattern and lack of segmentation, should be reevaluated.
软甲纲历来是甲壳动物分类学和系统发育学研究的重要类群,在形态学特征和分子生物学各方面取得广泛的发展。尽管软甲纲本身作为单系群已得到大多数甲壳动物学家认可,但是软甲纲内部各个类群之间的系统发育关系迄今仍颇有争议。本文报道了凡纳滨对虾Litopenaeus vannamei、中国明对虾Fenneropenaeus chinensis、脊尾白虾Exopalaemon carinicauda、太平洋磷虾Euphausia pacifica和采自南极普里兹湾南极磷虾Euphausia superba的线粒体基因组,其长度分别为15,989 bp、16,004 bp、15,730 bp、16,898 bp和15,498 bp以上(部分非编码区没有测定)。
本研究发现凡纳滨对虾、中国明对虾、脊尾白虾和太平洋磷虾的线粒体基因组包含后生动物线粒体基因组典型的基因组成(13个蛋白质编码基因、22个转运RNA、2个核糖体RNA和一个非编码的AT富含区);然而,南极磷虾与后生动物线粒体基因组典型的基因组成相比,存在1个trnN基因的重复。与泛甲壳动物线粒体基因组的原始排列相比,凡纳滨对虾和中国明对虾线粒体基因组的基因排列完全一致;脊尾白虾的线粒体基因组发生罕见的trnP和trnH易位,从而说明在真虾下目中线粒体基因组的基因排列并不保守;太平洋磷虾线粒体基因组的基因排列出现3个转运RNA的重排(trnL1、trnL2和trnW);南极磷虾线粒体基因组的基因排列除了出现太平洋磷虾具有的这3个转运RNA重排之外,还有1个trnN的重复和1个trnI基因的重排。另外,在太平洋磷虾线粒体基因组最大的非编码区中存在一个154 bp×4.7的串连重复区域,如此大片段的串联重复区域(>150 bp)在软甲纲动物线粒体基因组中是首次报道。
目前所获得的线粒体基因组数据强有力地支持口足目、对虾科、真虾下目和短尾下目为单系群。通过比较基因排列及蛋白质编码基因核苷酸和氨基酸序列的系统发育分析得知真虾类和龙虾类为腹胚亚目的原始类群,并支持“((Penaeus+Fenneropenaeus)+Litopenaeus)+Marsupenaeus”的系统发育关系。此外,线粒体基因组的数据也强有力地支持磷虾目为单系群。但对于磷虾目在软甲纲中的分类地位及与其它类群的系统发育关系存在一些分歧:基于蛋白质编码基因核苷酸和氨基酸数据的贝叶斯分析强有力地支持磷虾目和十足目近缘,这个结果和传统的分类系统完全一致;然而,基于核苷酸序列的邻接法、氨基酸序列的邻接法和最大似然法均强有力地支持磷虾类和对虾类亲缘关系较近,从而破坏了十足目的单系性,与传统的认识并不一致,但由于自展值的支持率非常高,所以深层次的分析需要进一步加强。
星虫动物属于海洋生物中的一个小门类,自1555年被记载以来,其在后生动物中的分类地位就备受争议。本研究测定了星虫动物门的第一条线粒体基因组:革囊星虫Phascolosoma esculenta的线粒体基因组,全长为15,494 bp,包含13个蛋白质编码基因、22个转运RNA、2个核糖体RNA和1个非编码的AT富含区,所有37个基因在同一条链上编码。与后生动物线粒体基因组的典型组成相比,存在一个trnR基因的缺失和一个trnM基因的重复。比较星虫动物和其它后生动物的线粒体基因组,可以得到以下结论:1)星虫动物和环节动物(包括螠虫动物)的线粒体基因组有相近的基因排列,而且所有基因都在同一链上编码;2)基于蛋白质编码基因的系统发育分析强有力地支持星虫动物和环节动物(包括螠虫动物)组成一个单系群,而将软体动物排除在外。因此,本研究认为以前许多星虫动物和软体动物“共享”的特征,包括发育特征和缺乏分节等,需要重新考虑。
Over the past decades, inference of a deeper phylogenetic relationship of metazoan with whole mitochondrial genome sequences has gained popularity. This resulted from many advantages offered over other molecular markers for phylogenetic analysis. Although more than one thousand and two hundreds mitochondrial genome sequences have been determined to date, the taxonomic sampling is still highly biased.
Malacostracans have been the subject of a huge number of classificatory and phylogenetic studies employing morphological characters and molecular characters. Though Malacostraca itself is widely regarded as a monophyletic grouping, the relationships among the various groups of the Malacostraca are still controversial. In this paper, we report the mitochondrial genomes from the Litopenaeus vannamei Boone 1931, Fenneropenaeus chinensis Osbeck 1765, Exopalaemon carinicauda Holthuis 1950, Euphausia pacifica Hansen 1911 and Euphausia superba Dana 1852 (sampling from Prydz Bay, Antarctic). The mitochondrial genomes of them is 15, 989 bp, 16, 004 bp, 15, 730 bp, 16, 898 bp and more than 15, 498 bp in length (partial non-coding region was not determined), respectively.
As seen in other metazoans, the genomes of L. vannamei, F. chinensis, Exopalaemon carinicauda and Euphausia pacifica contain a standard set of 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes and an AT-rich non-coding region. However, the mitochondrial genome of Euphausia superba has an extra trnN gene compared with standard set of metazoan mitochondrial genomes. The gene arrangements of L. vannamei and F. chinensis mitochondrial genoms are consistent with the pancrustacean ground pattern. Unusual translocation of trnP and trnH was found when comparing with the pancrustacean ground pattern, which indicating gene order is not conserved among Caridea. Translocation of three tRNAs (trnL1, trnL2 and trnW) was found in the mitochondrial genome of Euphausia pacifica when comparing with the pancrustacean ground pattern. Besides the translocation of above three tRNAs, the duplication of trnN and translocation of trnI were founded in the mitochondrial genome of Euphausia superba. The largest non-coding region in the mitochondrial genome of Euphausia pacifica contains one section with tandem repeats (4.7×154 bp), which is the first report of largest tandem repeats (>150 bp) founded in the malacostracan mitochondrial genomes.
All analyses based on nucleotide and amino acid data strongly support the monophyly of Stomatopoda, Penaeidae, Caridea and Brachyura. Both the pattern of gene rearrangements and phylogenomic analyses using concatenated nucleic acid and amino acid sequences of the 13 mitochondrial PCGs strengthened the support that Caridea and Palinura are primitive members of Pleocyemata and that (((Penaeus+Fenneropenaeus)+Litopenaeus)+Marsupenaeus). The Euphausiacea clade was also recovered as monophyletic with strong statistical support. However, the taxonomic position and phylogenetic relationship of Euphausiacea within Malacostraca is unstable. The Bayesian analysis based on nucleotide and amino acid data strongly support the close relationship between Euphausiacea and Decapoda, which is coincidence with traditional views. The Neighbor-Joining approach based on nucleotide and amino acid data and Maximum-Likelihood analysis based on amino acid data strongly support the close relationship between Euphausiacea and Penaeidae, which destroy the monophyly of Decapoda and not coincidence with traditional classification. Nevertheless, the bootstrap value is very high, so the deeper analyses are needed.
Sipunculans form a minor phylum of marine animals. Although the group was first documented in 1555, their taxonomic position within Metazoan is controversial. In this paper, we present here the sequence of Phascolosoma esculenta mitochondrial genome, the first one from phylum Sipuncula. The mitochondrial genome of the P. esculenta is 15, 494 bp in length and contains 13 PCGs, 22 transfer RNA genes, 2 ribosomal RNA genes and a non-coding AT-rich region. All of the 37 identified genes are transcribed from the same DNA strand. In comparison to typical metazoan mitochondrial genomes, sipunculid mitochondrial genome lacks trnR but has an extra trnM. From the analyses of mitochondrial genome of P. esculenta and other metazoan, we make the following conclusion: First, sipunculans and annelids (including echiurans) share similar gene order in the mitochondrial genome, with all 37 genes located on the same strand; Second, phylogenetic analyses based on concatenated protein sequences also provide strong evidence that Sipuncula and Annelida (including echiurans) form a monophyletic clade to the exclusion of the Mollusca. Thus, many characteristics that have been hypothesized to link sipunculans with molluscs, including their developmental pattern and lack of segmentation, should be reevaluated.
引文
1. Abele, L. G. 1991. Comparison of morphological and molecular phylogeny of the Decapoda. Memoirs of the Queensland Museum. 31:101-108.
2. Abele, L. G., Felgenhauer, B. E. 1986. Phylogenetic and phenetic relationships among the lower Decapoda. J. Crust. Biol. 6:385-400.
3. Aguinaldo, A. M., Turbeville, J. M., Linford, L. S., Rivera, M. C., Garey, J. R., Raff, R. A., Lake, J. A. 1997. Evidence for a clade of nematodes, arthropods and other moulting animals. Nature. 387:489-493.
4. ?kesson, B. 1958. A study of the nervous system of the Sipunculoideae, with some remarks on the development of the two species Phascolion strombi Montagu and Golfingia minuta Keferstein. Unders ?resund. 38:1-249.
5. Altekar, G., Dwarkadas, S., Huelsenbeck, J. P., Ronquist, F. 2004. Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics. 20:407-415.
6. Avise, J. C. 2000. Phylogeography: the history and formation of species. Harvard University Press, Cambridge, Mass.
7. Avise, J. C., Arnold, J., Ball, R. M., Bermingham, E., Lamb, T., Neigel, J. E., Reeb, C. A., Saunders, N. C. 1987. Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annu. Rev. Ecol. Syst. 18:489-522.
8. Ax, P. 1999. Das System der Metazoa: ein Lehrbuch der phylogenetischen Systematik. Vol.
2. Gustav Fischer, Stuttgart.
9. Backeljau, T., Winnepenninckx, B., Bruyn, L. D. 1993. Cladistic analysis of metazoan relationships: a reappraisal. Cladistics. 9:167-181.
10. Baldwin, J. D., Bass, A. L., Bowen, B. W., Clark, W. H. 1998. Molecular phylogeny and biogeography of the marine shrimp Penaeus. Mol. Phylogenet. Evol. 10:399-407.
11. Bayona-Bafaluy, M. P., Muller, S., Moraes, C. T. 2005. Fast adaptive coevolution of nuclear and mitochondrial subunits of ATP synthetase in orangutan. Mol. Biol. Evol. 22:716-724.
12. Beagley, C. T., Okimoto, R., Wolstenholme, D. R. 1998. The mitochondrial genome of the sea anemone Metridium senile (Cnidaria): introns, a paucity of tRNA genes, and a near-standard genetic code. Genetics. 148:1091-1108.
13. Benson, G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27:573-580.
14. Black, W. C. t., Roehrdanz, R. L. 1998. Mitochondrial gene order is not conserved in arthropods: prostriate and metastriate tick mitochondrial genomes. Mol. Biol. Evol. 15:1772-1785.
15. Blanchette, M., Kunisawa, T., Sankoff, D. 1999. Gene order breakpoint evidence in animal mitochondrial phylogeny. J. Mol. Evol. 49:193-203.
16. Bleidorn, C., Podsiadlowski, L., Bartolomaeus, T. 2006. The complete mitochondrial genome of the orbiniid polychaete Orbinia latreillii (Annelida, Orbiniidae)--A novel gene order for Annelida and implications for annelid phylogeny. Gene. 370:96-103.
17. Bleidorn, C., Vogt, L., Bartolomaeus, T. 2003. New insights into polychaete phylogeny (Annelida) inferred from 18S rDNA sequences. Mol. Phylogenet. Evol. 29:279-288.
18. Bliss, D. E., Abele, L. G. 1982. The Biology of Crustacea. Vol.1, Systematics, the fossil record, and biogeography. Academic Press, New York; London.
19. Blumer, M. J. F. 1997. The larval ocelli of Golfingia misakiana (Sipuncula, Golfingiidae) and of a pelagosphera of another unidentified species. Zoomorphology. 117:115-120.
20. Boas, J. E. V. 1880. Studier over Decapodernes Slaegtskabsforhold.
21. Boore, J. L. 1999. Animal mitochondrial genomes. Nucleic Acids Res. 27:1767-1780.
22. Boore, J. L. The duplication/random loss model for gene rearrangement exemplified by mitochondrial genomes of deuterostome animals. In: D. Sankoff, J. Nadeau, Eds.), Computational biology, Vol. 1. Kluwer Academic Publishers, Dordrecht, The Netherlands, 2000, pp. 133-147.
23. Boore, J. L. 2004. Complete mitochondrial genome sequence of Urechis caupo, a representative of the phylum Echiura. BMC Genomics. 5:67.
24. Boore, J. L. 2006. The complete sequence of the mitochondrial genome of Nautilus macromphalus (Mollusca: Cephalopoda). BMC Genomics. 7:182.
25. Boore, J. L., Brown, W. M. 1994. Complete DNA sequence of the mitochondrial genomeof the black chiton, Katharina tunicata. Genetics. 138:423-443.
26. Boore, J. L., Brown, W. M. 1995. Complete sequence of the mitochondrial DNA of the annelid worm Lumbricus terrestris. Genetics. 141:305-319.
27. Boore, J. L., Brown, W. M. 1998. Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Curr. Opin. Genet. Dev. 8:668-674.
28. Boore, J. L., Brown, W. M. 2000. Mitochondrial genomes of Galathealinum, Helobdella, and Platynereis: sequence and gene arrangement comparisons indicate that Pogonophora is not a phylum and Annelida and Arthropoda are not sister taxa. Mol. Biol. Evol. 17:87-106.
29. Boore, J. L., Collins, T. M., Stanton, D., Daehler, L. L., Brown, W. M. 1995. Deducing the pattern of arthropod phylogeny from mitochondrial DNA rearrangements. Nature. 376:163-165.
30. Boore, J. L., Lavrov, D. V., Brown, W. M. 1998. Gene translocation links insects and crustaceans. Nature. 392:667-668.
31. Boore, J. L., Macey, J. R., Medina, M. 2005. Sequencing and comparing whole mitochondrial genomes of animals. Meth. Enzymol. 395:311-348.
32. Boore, J. L., Medina, M., Rosenberg, L. A. 2004. Complete sequences of the highly rearranged molluscan mitochondrial genomes of the Scaphopod Graptacme eborea and the Bivalve Mytilus edulis. Mol. Biol. Evol. 21:1492-1503.
33. Boore, J. L., Staton, J. L. 2002. The mitochondrial genome of the Sipunculid Phascolopsis gouldii supports its association with Annelida rather than Mollusca. Mol. Biol. Evol. 19:127-137.
34. Borradaile, B. 1907. On the classification of the decapod crustaceans. Ann. Mag. Nat. Hist. 19:457-486.
35. Bouvier, E. n.-L. 1940. Décapodes marcheurs. Paris.
36. Bremer, K. 1988. The limits of amino acid sequence data in Angiosperm phylogenetic reconstruction. Evolution. 42:795-803.
37. Bridge, D., Cunningham, C. W., Schierwater, B., DeSalle, R., Buss, L. W. 1992. Class-level relationships in the phylum Cnidaria: evidence from mitochondrial genome structure. Proc. Natl. Acad. Sci. U.S.A. 89:8750-8753.
38. Brusca, R. C., Brusca, G. J. 1990. Invertebrates. Sinauer Associates, Sunderland, Mass.
39. Brusca, R. C., Brusca, G. J. 2003. Invertebrates. Sinauer Associates, Sunderland, Mass.
40. Burkenroad, M. D. 1963. The evolution of the eucarida (Crustacea, Eumalacostraca), in relation to the fossil record. Tulane Studies in Geology. 2:1-17.
41. Burkenroad, M. D. 1981. The higher taxonomy and evolution of Decapoda (Crustacea). San Diego Society of Natural History, San Diego, Calif.
42. Calman, W. T. 1904. On the classification of the Crustacea Malacostraca. Ann. Mag. Nat. Hist. 1904:144-158.
43. Calman, W. T. 1909. A Treatise on Zoology, 7: Appendiculata, Crustacea. Adam and Charles Black, London.
44. Castresana, J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17:540-552.
45. Castresana, J., Feldmaier-Fuchs, G., Yokobori, S., Satoh, N., Paabo, S. 1998. The mitochondrial genome of the hemichordate Balanoglossus carnosus and the evolution of deuterostome mitochondria. Genetics. 150:1115-1123.
46. Charlebois, R. L., Beiko, R. G., Ragan, M. A. 2003. Microbial phylogenomics: Branching out. Nature. 421:217.
47. Cheng, S., Chang, S. Y., Gravitt, P., Respess, R. 1994. Long PCR. Nature. 369:684-685.
48. Clary, D. O., Wolstenholme, D. R. 1985. The mitochondrial DNA molecular of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code. J. Mol. Evol. 22:252-271.
49. Claus, C. 1888. Ueber den Organismus der Nebaliden und die systematische Stellung der Leptostraken. Arb. Zool. Inst. Wien. 1-148.
50. Coelho, P. S., Bryan, A. C., Kumar, A., Shadel, G. S., Snyder, M. 2002. A novel mitochondrial protein, Tar1p, is encoded on the antisense strand of the nuclear 25S rDNA. Genes Dev. 16:2755-2760.
51. Cohen, W. D. 1985. Blood cells of marine invertebrates: experimental systems in cell biology and comparative physiology. A.R. Liss, New York.
52. Cook, C. E. 2005. The complete mitochondrial genome of the stomatopod crustacean Squilla mantis. BMC Genomics. 6:105.
53. Cook, C. E., Yue, Q., Akam, M. 2005. Mitochondrial genomes suggest that hexapods andcrustaceans are mutually paraphyletic. Proc. Biol. Sci. 272:1295-1304.
54. Crandall, K. A., Harris, D. J., Fetzner, J. W., Jr. 2000. The monophyletic origin of freshwater crayfish estimated from nuclear and mitochondrial DNA sequences. Proc. Biol. Sci. 267:1679-1686.
55. Crease, T. J. 1999. The complete sequence of the mitochondrial genome of Daphnia pulex (Cladocera: Crustacea). Gene. 233:89-99.
56. Cummings, M. P., Otto, S. P., Wakeley, J. 1995. Sampling properties of DNA sequence data in phylogenetic analysis. Mol. Biol. Evol. 12:814-822.
57. Curole, J. P., Kocher, T. D. 1999. Mitogenomics: digging deeper with complete mitochondrial genomes. Trends Ecol. Evol. 14:394-398.
58. Cusimano, N., Zhang, L. B., Renner, S. S. 2008. Reevaluation of the cox1 group I intron in Araceae and angiosperms indicates a history dominated by loss rather than horizontal transfer. Mol. Biol. Evol. 25:265-276.
59. Cutler, E. B. 1994. The Sipuncula: their systematics, biology and evolution. Cornell University Press, New York.
60. Cutler, E. B., Dean, H. K., Saiz-Salinas, J. I. 2001. Sipuncula from Antarctic waters. Proc. Biol. Soc. Wash. 114:861-880.
61. Davis, G. K., Patel, N. H. 1999. The origin and evolution of segmentation. Trends Cell Biol. 9:M68-72.
62. de Rosa, R., Grenier, J. K., Andreeva, T., Cook, C. E., Adoutte, A., Akam, M., Carroll, S. B., Balavoine, G. 1999. Hox genes in brachiopods and priapulids and protostome evolution. Nature. 399:772-776.
63. DeJong, R. J., Emery, A. M., Adema, C. M. 2004. The mitochondrial genome of Biomphalaria glabrata (Gastropoda: Basommatophora), intermediate host of Schistosoma mansoni. J. Parasitol. 90:991-997.
64. Dellaporta, S. L., Xu, A., Sagasser, S., Jakob, W., Moreno, M. A., Buss, L. W., Schierwater, B. 2006. Mitochondrial genome of Trichoplax adhaerens supports placozoa as the basal lower metazoan phylum. Proc. Natl. Acad. Sci. U.S.A. 103:8751-8756.
65. Delle-Chiaje, S. 1823. Memorie sulla storia e notomina degli animali senza vertebre del Regno di Napoli, Vol. I. Fratelli Fernandes. Naples.
66. Delsuc, F., Brinkmann, H., Philippe, H. 2005. Phylogenomics and the reconstruction of the tree of life. Nat. Rev. Genet. 6:361-375.
67. Desper, R., Gascuel, O. 2004. Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting. Mol. Biol. Evol. 21:587-598.
68. Dixon, C. J., Ahyong, S. T., Schram, F. R. 2003. A new hypothesis of decapod phylogeny. Crustaceana. 76:935-976.
69. Dohle, W. 2001. Are the insects terrestrial crustaceans? A discussion of some new facts and arguments and the proposal of the proper name ‘Tetraconata’ for the monophyletic unit Crustacea + Hexapoda. Annls Soc. Entomol. Fr. (N.S.). 37:85-104.
70. Dreyer, H., Steiner, G. 2006. The complete sequences and gene organisation of the mitochondrial genomes of the heterodont bivalves Acanthocardia tuberculata and Hiatella arctica - and the first record for a putative Atpase subunit 8 gene in marine bivalves. Front. Zool. 3:13-26.
71. Dunn, C. W., Hejnol, A., Matus, D. Q., Pang, K., Browne, W. E., Smith, S. A., Seaver, E., Rouse, G. W., Obst, M., Edgecombe, G. D., Sorensen, M. V., Haddock, S. H., Schmidt-Rhaesa, A., Okusu, A., Kristensen, R. M., Wheeler, W. C., Martindale, M. Q., Giribet, G. 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature. 452:745-749.
72. Edmonds, S. J. Phylum Sipuncula. Polychaetes and Allies: The Southern Synthesis. Fauna of Australia, Vol. 4A. CSIRO Publishing, Melbourne, 2000, pp. 375-400.
73. Eernisse, D. J., Albert, J. S., Anderson, F. E. 1992. Annelida and Arthropoda are not sister taxa: a phylogenetic analysis of spiralian metazoan morphology. Syst. Biol. 41:305-330.
74. Eisen, J. A., Fraser, C. M. 2003. Phylogenomics: intersection of evolution and genomics. Science. 300:1706-1707.
75. Erber, A., Riemer, D., Bovenschulte, M., Weber, K. 1998. Molecular phylogeny of metazoan intermediate filament proteins. J. Mol. Evol. 47:751-762.
76. Evans, M. J., Gurer, C., Loike, J. D., Wilmut, I., Schnieke, A. E., Schon, E. A. 1999. Mitochondrial DNA genotypes in nuclear transfer-derived cloned sheep. Nat. Genet. 23:90-93.
77. Ewing, B., Green, P. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8:186-194.
78. Ewing, B., Hillier, L., Wendl, M. C., Green, P. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8:175-185.
79. Feldmann, R. M. 2003. The Decapoda: New initiatives and novel approaches. J. Paleontol. 77:1021-1039.
80. Felgenhauer, B. E., Abele, L. G. Phylogenetic relationships among shrimp-like decapods. In: F. R. Schram, (Ed.), Crustacean Phylogeny, Vol. 1, Balkema, Netherlands, 1983, pp. 291-311.
81. Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
82. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 39:783-791.
83. Folmer, O., Black, M., Hoeh, W., Lutz, R., Vrijenhoek, R. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Marine Biol. Biotechnol. 3:294-299.
84. Friedrich, M., Tautz, D. 1995. Ribosomal DNA phylogeny of the major extant arthropod classes and the evolution of myriapods. Nature. 376:165-167.
85. Fritzsch, G., Schlegel, M., Stadler, P. F. 2006. Alignments of mitochondrial genome arrangements: applications to metazoan phylogeny. J. Theor. Biol. 240:511-520.
86. Garey, J. R., Schmidt-Rhaesa, A. 1998. The essential role of "Minor" Phyla in molecular studies of animal evolution. Amer. Zool. 38:907-917.
87. Giribet, G., Distel, D. L., Polz, M., Sterrer, W., Wheeler, W. C. 2000. Triploblastic relationships with emphasis on the acoelomates and the position of Gnathostomulida, Cycliophora, Plathelminthes, and Chaetognatha: a combined approach of 18S rDNA sequences and morphology. Syst. Biol. 49:539-562.
88. Giribet, G., Wheeler, W. C. 2002. On bivalve phylogeny: a high-level analysis of the Bivalvia (Mollusca) based on combined morphology and DNA sequence data. Invertebr. Biol. 121:271-324.
89. Gissi, C., Iannelli, F., Pesole, G. 2004. Complete mtDNA of Ciona intestinalis revealsextensive gene rearrangement and the presence of an atp8 and an extra trnM gene in ascidians. J. Mol. Evol. 58:376-389.
90. Glaessner, M. F. Decapoda. In: R. C. Moore, (Ed.), Arthropoda 4. Part R, vol. 2. Treatise on Invertebrate Paleontology. Geological Society of America and University of Kansas Press, Lawrence, 1969.
91. Glenner, H., Hansen, A. J., Sorensen, M. V., Ronquist, F., Huelsenbeck, J. P., Willerslev, E. 2004. Bayesian inference of the metazoan phylogeny; a combined molecular and morphological approach. Curr. Biol. 14:1644-1649.
92. Goloboff, P. A. 2003. Parsimony, likelihood, and simplicity. Cladistics. 19:91-103.
93. Gordon, D., Abajian, C., Green, P. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8:195-202.
94. Grande, C., Templado, J., Zardoya, R. 2008. Evolution of gastropod mitochondrial genome arrangements. BMC Evol. Biol. 8:61.
95. Guindon, S., Gascuel, O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704.
96. Guralnick, R. 2002. A recapitulation of the rise and fall of the cell lineage research program: the evolutionary developmental relationship of cleavage to homology, body plans and life history. J. Hist. Biol. 35:537-567.
97. Guralnick, R. P., Lindberg, D. R. 2001. Reconnecting cell and animal lineages: what do cell lineages tell us about the evolution and development of Spiralia? Evolution. 55:1501-1519.
98. Gusm?o, J., Lazoski, C., Solé-Cava, A. M. 2000. A new species of Penaeus (Crustacea: Penaeidae) revealed by allozyme and cytochrome oxidase I analyses. Mar. Biol. 137:435-446.
99. Haechel, E. 1866. Generelle Morphologie der Organismen. Georg Riemer, Berlin.
100. Halanych, K. M., Bacheller, J. D., Aguinaldo, A. M., Liva, S. M., Hillis, D. M., Lake, J. A. 1995. Evidence from 18S ribosomal DNA that the lophophorates are protostome animals. Science. 267:1641-1643.
101. Halanych, K. M., Dahlgren, T. G., McHugh, D. 2002. Unsegmented Annelids? Possible origins of four lophotrochozoan worm taxa. Integr. Comp. Biol. 42:678-684.
102. Hansen, H. J. 1893. Zur Morphologie der Gliedmassen und Mundtheile bei Crustaceen und Insecten. Zool. Anz. . 16:193-212.
103. Hasegawa, M., Kishino, H., Saitou, N. 1991. On the maximum likelihood method in molecular phylogenetics. J. Mol. Evol. 32:443-445.
104. Hebert, P. D., Stoeckle, M. Y., Zemlak, T. S., Francis, C. M. 2004. Identification of birds through DNA barcodes. PLoS Biol. 2:e312.
105. Helfenbein, K. G., Brown, W. M., Boore, J. L. 2001. The complete mitochondrial genome of the articulate brachiopod Terebratalia transversa. Mol. Biol. Evol. 18:1734-1744.
106. Helfenbein, K. G., Fourcade, H. M., Vanjani, R. G., Boore, J. L. 2004. The mitochondrial genome of Paraspadella gotoi is highly reduced and reveals that chaetognaths are a sister group to protostomes. Proc. Natl. Acad. Sci. U.S.A. 101:10639-10643.
107. Hendy, M. D., Penny, D. 1989. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38:297-309.
108. Hessling, R. 2002. Metameric organisation of the nervous system in developmental stages of Urechis caupo (Echiura) and its phylogenetic implications. Zoomorphology. 121:221-234.
109. Hessling, R. 2003. Novel aspects of the nervous system of Bonellia viridis (Echiura) revealed by the combination of immunohistochemistry, confocal laser-scanning microscopy and three-dimensional reconstruction. Hydrobiologia. 496:225-239.
110. Hessling, R., Westheide, W. 2002. Are Echiura derived from a segmented ancestor? Immunohistochemical analysis of the nervous system in developmental stages of Bonellia viridis. J. Morphol. 252:100-113.
111. Hickerson, M. J., Cunningham, C. W. 2000. Dramatic mitochondrial gene rearrangements in the hermit crab Pagurus longicarpus (Crustacea, anomura). Mol. Biol. Evol. 17:639-644.
112. Hillis, D. M. 1998. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst. Biol. 47:3-8.
113. Hillis, D. M., Bull, J. J. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42:182-192.
114. Hillis, D. M., Pollock, D. D., McGuire, J. A., Zwickl, D. J. 2003. Is sparse taxon samplinga problem for phylogenetic inference? Syst. Biol. 52:124-126.
115. Holder, M., Lewis, P. O. 2003. Phylogeny estimation: traditional and Bayesian approaches. Nat. Rev. Genet. 4:275-284.
116. Huang, D. Y., Chen, J. Y., Vannier, J., Saiz Salinas, J. I. 2004. Early Cambrian sipunculan worms from southwest China. Proc. R. Soc. Lond., B, Biol. Sci. 271:1671-1676.
117. Huelsenbeck, J. P. 1995. Performance of phylogenetic methods in simulation. Syst. Biol. 44:17-48.
118. Huelsenbeck, J. P., Larget, B., Miller, R. E., Ronquist, F. 2002. Potential applications and pitfalls of Bayesian inference of phylogeny. Syst. Biol. 51:673-688.
119. Huelsenbeck, J. P., Ronquist, F., Nielsen, R., Bollback, J. P. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science. 294:2310-2314.
120. Hurst, L. D. 2002. The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends Genet. 18:486-487.
121. Hwang, U. W., Friedrich, M., Tautz, D., Park, C. J., Kim, W. 2001. Mitochondrial protein phylogeny joins myriapods with chelicerates. Nature. 413:154-157.
122. Hyman, L. H. The protostomatous coelomates-Phylum Sipunculida. The Invertebrates. McGraw-Hill Press, New York, 1959, pp. 610-696.
123. Ivey, J. L., Santos, S. R. 2007. The complete mitochondrial genome of the Hawaiian anchialine shrimp Halocaridina rubra Holthuis, 1963 (Crustacea: Decapoda: Atyidae). Gene. 394:35-44.
124. Jennings, R. M., Halanych, K. M. 2005. Mitochondrial genomes of Clymenella torquata (Maldanidae) and Riftia pachyptila (Siboglinidae): evidence for conserved gene order in annelida. Mol. Biol. Evol. 22:210-222.
125. Jukes, T., Cantor, C. Evolution of protein molecules. In: M. HN, (Ed.), Mammalian Protein Metabolism. Academic Press, New York, 1969, pp. 21-132.
126. Kilpert, F., Podsiadlowski, L. 2006. The complete mitochondrial genome of the common sea slater, Ligia oceanica (Crustacea, Isopoda) bears a novel gene order and unusual control region features. BMC Genomics. 7:241.
127. Kim, J. 1996. General inconsistency conditions for maximum parsimony: effects of branch lengths and increasing numbers of taxa. Syst. Biol. 45:363-374.
128. Kjer, K. M. 2004. Aligned 18S and insect phylogeny. Syst. Biol. 53:506-514.
129. Knoll, A. H., Carroll, S. B. 1999. Early animal evolution: emerging views from comparative biology and geology. Science. 284:2129-2137.
130. Knudsen, B., Kohn, A. B., Nahir, B., McFadden, C. S., Moroz, L. L. 2006. Complete DNA sequence of the mitochondrial genome of the sea-slug, Aplysia californica: conservation of the gene order in Euthyneura. Mol. Phylogenet. Evol. 38:459-469.
131. Kumar, S., Tamura, K., Nei, M. 2004. MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief. Bioinformatics. 5:150-163.
132. Larget, B., Simon, D. L. 1999. Markov Chasin Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16:750-759.
133. Larget, B., Simon, D. L., Kadane, J. B., Sweet, D. 2005. A bayesian analysis of metazoan mitochondrial genome arrangements. Mol. Biol. Evol. 22:486-495.
134. Lavery, S., Chan, T. Y., Tam, Y. K., Chu, K. H. 2004. Phylogenetic relationships and evolutionary history of the shrimp genus Penaeus s.l. derived from mitochondrial DNA. Mol. Phylogenet. Evol. 31:39-49.
135. Lavrov, D. V., Brown, W. M., Boore, J. L. 2000. A novel type of RNA editing occurs in the mitochondrial tRNAs of the centipede Lithobius forficatus. Proc. Natl. Acad. Sci. U.S.A. 97:13738-13742.
136. Lavrov, D. V., Brown, W. M., Boore, J. L. 2004. Phylogenetic position of the Pentastomida and (pan)crustacean relationships. Proc. Biol. Sci. 271:537-544.
137. Lavrov, D. V., Forget, L., Kelly, M., Lang, B. F. 2005. Mitochondrial genomes of two demosponges provide insights into an early stage of animal evolution. Mol. Biol. Evol. 22:1231-1239.
138. Lavrov, D. V., Lang, B. F. 2005. Poriferan mtDNA and animal phylogeny based on mitochondrial gene arrangements. Syst. Biol. 54:651-659.
139. Lee, Y. S., Oh, J., Kim, Y. U., Kim, N., Yang, S., Hwang, U. W. 2008. Mitome: dynamic and interactive database for comparative mitochondrial genomics in metazoan animals. Nucleic Acids Res. 36:D938-942.
140. Lewis, D. L., Farr, C. L., Farquhar, A. L., Kaguni, L. S. 1994. Sequence, organization, and evolution of the A+T region of Drosophila melanogaster mitochondrial DNA. Mol. Biol.Evol. 11:523-538.
141. Lewis, D. L., Farr, C. L., Kaguni, L. S. 1995. Drosophila melanogaster mitochondrial DNA: completion of the nucleotide sequence and evolutionary comparisons. Insect Mol. Biol. 4:263-278.
142. Li, W. H. 1986. Evolutionary change of restriction cleavage sites and phylogenetic inference. Genetics. 113:187-213.
143. Lim, J. T., Hwang, U. W. 2006. The complete mitochondrial genome of Pollicipes mitella (Crustacea, Maxillopoda, Cirripedia): non-monophylies of maxillopoda and crustacea. Mol. Cells. 22:314-322.
144. Linnaeus, C. 1767. Systema naturae per regna tria naturae, secundum classes, ordines, genera, species cum characteribus, differentiis, synonymis, locis. Vindobonae.
145. Liu, L., Pearl, D. K. 2007. Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst. Biol. 56:504-514.
146. Liu, Z. Q., Wang, Y. Q., Su, B. 2005. The mitochondrial genome organization of the rice frog, Fejervarya limnocharis (Amphibia: Anura): a new gene order in the vertebrate mtDNA. Gene. 346:145-151.
147. Lohse, M., Drechsel, O., Bock, R. 2007. OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr. Genet. 52:267-274.
148. Lowe, T. M., Eddy, S. R. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955-964.
149. Macey, J. R., Papenfuss, T. J., Kuehl, J. V., Fourcade, H. M., Boore, J. L. 2004. Phylogenetic relationships among amphisbaenian reptiles based on complete mitochondrial genomic sequences. Mol. Phylogenet. Evol. 33:22-31.
150. Macey, J. R., Schulte, J. A., 2nd, Larson, A. 2000. Evolution and phylogenetic information content of mitochondrial genomic structural features illustrated with acrodont lizards. Syst. Biol. 49:257-277.
151. Machida, R. J., Miya, M. U., Nishida, M., Nishida, S. 2002. Complete mitochondrial DNA sequence of Tigriopus japonicus (Crustacea: Copepoda). Mar. Biotechnol. 4:406-417.
152. Machida, R. J., Miya, M. U., Yamauchi, M. M., Nishida, M., Nishida, S. 2004. Organization of the mitochondrial genome of Antarctic krill Euphausia superba (Crustacea: Malacostraca). Mar. Biotechnol. 6:238-250.
153. Mackey, L. Y., Winnepenninckx, B., De Wachter, R., Backeljau, T., Emschermann, P., Garey, J. R. 1996. 18S rRNA suggests that Entoprocta are protostomes, unrelated to Ectoprocta. J. Mol. Evol. 42:552-559.
154. Maggioni, R., Rogers, A. D., Maclean, N., D'Incao, F. 2001. Molecular phylogeny of western Atlantic Farfantepenaeus and Litopenaeus shrimp based on mitochondrial 16S partial sequences. Mol. Phylogenet. Evol. 18:66-73.
155. Martin, J. W., Abele., L. G. 1986. Notes on male pleopod morphology in the brachyuran crab family Panopeidae Ortmann, 1893, sensu Guinot (1978) (Decapoda). Crustaceana. 50:182-198.
156. Martin, J. W., Davis, G. E. 2001. An updated classification of the recent crustacea. Natural History Museum of Los Angeles County, Los Angeles, California.
157. Maxmen, A. B., King, B. F., Cutler, E. B., Giribet, G. 2003. Evolutionary relationships within the protostome phylum Sipuncula: a molecular analysis of ribosomal genes and histone H3 sequence data. Mol. Phylogenet. Evol. 27:489-503.
158. Maynard, B. T., Kerr, L. J., McKiernan, J. M., Jansen, E. S., Hanna, P. J. 2005. Mitochondrial DNA sequence and gene organization in the [corrected] Australian blacklip [corrected] abalone Haliotis rubra (leach). Mar. Biotechnol. 7:645-658.
159. McHugh, D. 1997. Molecular evidence that echiurans and pogonophorans are derived annelids. Proc. Natl. Acad. Sci. U.S.A. 94:8006-8009.
160. McHugh, D. 2000. Molecular phylogeny of the Annelida. Can. J. Zool. 78:1873.
161. Meglitsch, P. A., Schram, F. R. 1991. Invertebrate Zoology. Oxford University Press, London.
162. Miller, A. D., Austin, C. M. 2006. The complete mitochondrial genome of the mantid shrimp Harpiosquilla harpax, and a phylogenetic investigation of the Decapoda using mitochondrial sequences. Mol. Phylogenet. Evol. 38:565-574.
163. Miller, A. D., Murphy, N. P., Burridge, C. P., Austin, C. M. 2005. Complete mitochondrial DNA sequences of the decapod crustaceans Pseudocarcinus gigas (Menippidae) andMacrobrachium rosenbergii (Palaemonidae). Mar. Biotechnol. 7:339-349.
164. Miller, A. D., Nguyen, T. T., Burridge, C. P., Austin, C. M. 2004. Complete mitochondrial DNA sequence of the Australian freshwater crayfish, Cherax destructor (Crustacea: Decapoda: Parastacidae): a novel gene order revealed. Gene. 331:65-72.
165. Nardi, F., Carapelli, A., Fanciulli, P. P., Dallai, R., Frati, F. 2001. The complete mitochondrial DNA sequence of the basal hexapod Tetrodontophora bielanensis: evidence for heteroplasmy and tRNA translocations. Mol. Biol. Evol. 18:1293-1304.
166. Nardi, F., Spinsanti, G., Boore, J. L., Carapelli, A., Dallai, R., Frati, F. 2003. Hexapod origins: monophyletic or paraphyletic? Science. 299:1887-1889.
167. Naylor, G. J., Brown, W. M. 1998. Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences. Syst. Biol. 47:61-76.
168. Nei, M. 1996. Phylogenetic analysis in molecular evolutionary genetics. Annu. Rev. Genet. 30:371-404.
169. Nei, M., Kumar, S. 2000. Molecular evolution and phylogenetics. Oxford University Press, Oxford; New York.
170. Nicol, S., Endo, Y., Food and Agriculture Organization of the United, N. 1997. Krill fisheries of the world. Food and Agriculture Organization of the United Nations, Rome.
171. Nielsen, C. 1995. Animal Evolution: Interrelationships of the Living Phyla. Oxford University Press, Oxford.
172. Nielsen, C. 2001. Animal Evolution: Interrelationships of the Living Phyla. Oxford University Press, Oxford.
173. Nielsen, C. 2003. Proposing a solution to the Articulata-Ecdysozoa controversy. Zool. Scr. 32:475-482.
174. Nielsen, C., Scharff, N., Eibye-Jacobsen, D. 1996. Cladistic analyses of the animal kingdom. Biol. J. Linn. Soc. Lond. 57:385-410.
175. Nielsen, R., Yang, Z. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics. 148:929-936.
176. Nikaido, M., Rooney, A. P., Okada, N. 1999. Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: hippopotamuses are the closest extant relatives of whales. Proc. Natl. Acad. Sci. U.S.A. 96:10261-10266.
177. Noguchi, Y., Endo, K., Tajima, F., Ueshima, R. 2000. The mitochondrial genome of the brachiopod Laqueus rubellus. Genetics. 155:245-259.
178. Ojala, D., Montoya, J., Attardi, G. 1981. tRNA punctuation model of RNA processing in human mitochondria. Nature. 290:470-474.
179. Ono, T., Isobe, K., Nakada, K., Hayashi, J. I. 2001. Human cells are protected from mitochondrial dysfunction by complementation of DNA products in fused mitochondria. Nat. Genet. 28:272-275.
180. Orrhage, L., Müller, M. 2005. Morphology of the nervous system of Polychaeta (Annelida). Hydrobiologia. 535-536:79-111.
181. Pakendorf, B., Stoneking, M. 2005. Mitochondrial DNA and human evolution. Annu. Rev. Genomics Hum. Genet. 6:165-183.
182. Paland, S., Lynch, M. 2006. Transitions to asexuality result in excess amino acid substitutions. Science. 311:990-992.
183. Palumbi, S. R. 1991. The simple fool's guide to PCR. Dept. of Zoology and Kewalo Marine Laboratory, University of Hawaii, Honolulu, HI.
184. Papillon, D., Perez, Y., Caubit, X., Le Parco, Y. 2004. Identification of Chaetognaths as Protostomes is supported by the analysis of their mitochondrial genome. Mol. Biol. Evol. 21:2122-2129.
185. Parker, S. P. 1982. Synopsis and classification of living organisms. McGraw-Hill, New York.
186. Passamaneck, Y., Halanych, K. M. 2006. Lophotrochozoan phylogeny assessed with LSU and SSU data: evidence of lophophorate polyphyly. Mol. Phylogenet. Evol. 40:20-28.
187. Pearson, W. R., Robins, G., Zhang, T. 1999. Generalized neighbor-joining: more reliable phylogenetic tree reconstruction. Mol. Biol. Evol. 16:806-816.
188. Penny, D. 1982. Towards a basis for classification: the incompleteness of distance measures, incompatibility analysis and phenetic classification. J. Theor. Biol. 96:129-142.
189. Pérez-Farfante, I., Kensley, B. 1997. Penaeoid and sergestoid shrimps and prawns of the world. Editions du Muséum National d’Histoire Naturelle, Paris, France.
190. Perna, N. T., Kocher, T. D. 1995. Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J. Mol. Evol. 41:353-358.
191. Peterson, K. J., Eernisse, D. J. 2001. Animal phylogeny and the ancestry of bilaterians: inferences from morphology and 18S rDNA gene sequences. Evol. Dev. 3:170-205.
192. Philippe, H., Brinkmann, H., Martinez, P., Riutort, M., Baguna, J. 2007. Acoel flatworms are not platyhelminthes: evidence from phylogenomics. PLoS ONE. 2:e717.
193. Place, A. R., Feng, X., Steven, C. R., Fourcade, H. M., Boore, J. L. 2005. Genetic markers in blue crabs (Callinectes sapidus) II. Complete mitochondrial genome sequence and characterization of genetic variation. J. Exp. Mar. Biol. Ecol. 319:15-27.
194. Podsiadlowski, L., Braband, A. 2006. The complete mitochondrial genome of the sea spider Nymphon gracile (Arthropoda: Pycnogonida). BMC Genomics. 7:284.
195. Pollock, D. D., Zwickl, D. J., McGuire, J. A., Hillis, D. M. 2002. Increased Taxon Sampling Is Advantageous for Phylogenetic Inference. Syst. Biol. 51:664-671.
196. Porter, M. L., Perez-Losada, M., Crandall, K. A. 2005. Model-based multi-locus estimation of decapod phylogeny and divergence times. Mol. Phylogenet. Evol. 37:355-369.
197. Posada, D. 2006. ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online. Nucleic Acids Res. 34:W700-703.
198. Posada, D., Crandall, K. A. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics. 14:817-818.
199. Purschke, G., Hessling, R., Westheide, W. 2000. The phylogenetic position of the Clitellata and the Echiura - on the problematic assessment of absent characters. J. Zoolog. Syst. Evol. Res. 38:165-173.
200. Quan, J., Zhuang, Z., Deng, J., Dai, J., Zhang, Y. P. 2004. Phylogenetic relationships of 12 penaeoidea shrimp species deduced from mitochondrial DNA sequences. Biochem. Genet. 42:331-345.
201. Quatrefages, A. d. 1847. études sur les types inférieurs de l’embranchement des Annelés. Mémoire sur l'échiure de Gaertner (Echiurus gaertnerii NOB). Ann. Sci. Nat. Zool. (Paris). 7:307-343.
202. Rannala, B., Yang, Z. 1996. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 43:304-311.
203. Regier, J. C., Shultz, J. W. 1997. Molecular phylogeny of the major arthropod groups indicates polyphyly of crustaceans and a new hypothesis for the origin of hexapods. Mol.Biol. Evol. 14:902-913.
204. Regier, J. C., Shultz, J. W. 1998. Molecular phylogeny of Arthropods and the significance of the Cambrian "Explosion" for molecular systematics. Amer. Zool. 38:918-928.
205. Regier, J. C., Shultz, J. W., Kambic, R. E. 2005. Pancrustacean phylogeny: hexapods are terrestrial crustaceans and maxillopods are not monophyletic. Proc. Biol. Sci. 272:395-401.
206. Rice, M. E. 1970. Asexual reproduction in a Sipunculan worm. Science. 167:1618-1620.
207. Rice, M. E. Sipuncula: developmental evidence for phylogenetic inference. In: S. C. Morris, et al., Eds.), The Origins and Relationships of Lower Invertebrates. Oxford University Press, Oxford, 1985, pp. 274-296.
208. Richter, S. 2002. The Tetraconata concept: hexapod-crustacean relationships and the phylogeny of Crustacea. Org. Divers. Evol. 2:217-237.
209. Richter, S., Scholtz, G. 2001. Phylogenetic analysis of the Malacostraca (Crustacea). J. Zoolog. Syst. Evol. Res. 39:113-136.
210. Roehrdanz, R. L., Degrugillier, M. E., Black, W. C. t. 2002. Novel rearrangements of arthropod mitochondrial DNA detected with long-PCR: applications to arthropod phylogeny and evolution. Mol. Biol. Evol. 19:841-849.
211. Ronquist, F., Huelsenbeck, J. P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 19:1572-1574.
212. Rousset, V., Pleijel, F., Rouse, G. W., Erseus, C., Siddall, M. E. 2007. A molecular phylogeny of annelids. Cladistics. 23:41-63.
213. Rozas, J., Sanchez-DelBarrio, J. C., Messeguer, X., Rozas, R. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics. 19:2496-2497.
214. Rzhetsky, A., Nei, M. 1993. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol. Biol. Evol. 10:1073-1095.
215. Saitou, N., Imanishi, T. 1989. Relative efficiencies of the Fitch-Margoliash, maximum-parsimony, maximum-likelihood, minimum-evolution, and neighbor-joining methods of phylogenetic tree construction in obtaining the correct tree. Mol. Biol. Evol. 6: 514-525.
216. Saitou, N., Nei, M. 1987. The neighbor-joining method: a new method for reconstructingphylogenetic trees. Mol. Biol. Evol. 4:406-425.
217. Scheltema, A. H. 1993. Aplacophora as progenetic aculiferans and the coelomate origin of mollusks as the sister taxon of Sipuncula. Biol. Bull. 184:57-78.
218. Scheltema, A. H. Phylogenetic position of Sipuncula, Mollusca and the progenetic Aplacophora. In: J. Taylor, (Ed.), Origin and Evolutionary Radiation of the Mollusca. Oxford University Press, Oxford, 1996, pp. 53-58.
219. Schindel, D. E., Miller, S. E. 2005. DNA barcoding a useful tool for taxonomists. Nature. 435:17.
220. Schmidt, T. R., Wu, W., Goodman, M., Grossman, L. I. 2001. Evolution of nuclear- and mitochondrial-encoded subunit interaction in cytochrome c oxidase. Mol. Biol. Evol. 18:563-569.
221. Scholtz, G., Richter, S. 1995. Phylogenetic systematics of the reptantian Decapoda (Crustacea, Malacostraca). Zool. J. Linn. Soc. 113:289-328.
222. Schram, F. R. 2001. Phylogeny of decapods: moving towards a consensus. Hydrobiologia. 449:1-20.
223. Schulze, A., Cutler, E., Giribet, G. 2005. Reconstructing the phylogeny of the Sipuncula. Hydrobiologia. 535-536:277-296.
224. Schulze, A., Cutler, E. B., Giribet, G. 2007. Phylogeny of sipunculan worms: A combined analysis of four gene regions and morphology. Mol. Phylogenet. Evol. 42:171-192.
225. Segawa, R. D., Aotsuka, T. 2005. The mitochondrial genome of the Japanese freshwater crab, Geothelphusa dehaani (Crustacea: Brachyura): evidence for its evolution via gene duplication. Gene. 355:28-39.
226. Seifert, K. A., Samson, R. A., Dewaard, J. R., Houbraken, J., Levesque, C. A., Moncalvo, J. M., Louis-Seize, G., Hebert, P. D. 2007. Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case. Proc. Natl. Acad. Sci. U.S.A. 104:3901-3906.
227. Serb, J. M., Lydeard, C. 2003. Complete mtDNA sequence of the North American freshwater mussel, Lampsilis ornata (Unionidae): an examination of the evolution and phylogenetic utility of mitochondrial genome organization in Bivalvia (Mollusca). Mol. Biol. Evol. 20:1854-1866.
228. Shen, X., Ren, J. F., Cui, Z. X., Sha, Z. L., Wang, B., Xiang, J. H., Liu, B. 2007. The complete mitochondrial genomes of two common shrimps(Litopenaeus vannamei and Fenneropenaeus chinensis)and their phylogenomic considerations. Gene. 403:98-109.
229. Shultz, J. W., Regier, J. C. 2000. Phylogenetic analysis of arthropods using two nuclear protein-encoding genes supports a crustacean + hexapod clade. Proc. Biol. Sci. 267:1011-1019.
230. Snir, S., Warnow, T., Rao, S. 2008. Short quartet puzzling: a new quartet-based phylogeny reconstruction algorithm. J. Comput. Biol. 15:91-103.
231. S?rensen, M. V., Funch, P., Willerslev, E., Hansen, A. J., Olesen, J. 2000. On the phylogeny of Metazoa in the light of Cycliophora and Micrognathozoa. Zool. Anz. 239:297-318.
232. Staton, J. L. 2003. Phylogenetic analysis of the mitochondrial cytochrome c oxidase subunit 1 gene from 13 sipunculan genera: Intra- and interphylum relationships. Invertebr. Biol. 122:252-264.
233. Staton, J. L., Daehler, L. L., Brown, W. M. 1997. Mitochondrial gene arrangement of the horseshoe crab Limulus polyphemus L.: conservation of major features among arthropod classes. Mol. Biol. Evol. 14:867-874.
234. Stechmann, A., Schlegel, M. 1999. Analysis of the complete mitochondrial DNA sequence of the brachiopod Terebratulina retusa places Brachiopoda within the protostomes. Proc. R. Soc. Lond., B, Biol. Sci. 266:2043-2043.
235. Steel, M., Penny, D. 2000. Parsimony, likelihood, and the role of models in molecular phylogenetics. Mol. Biol. Evol. 17:839-850.
236. Steinauer, M. L., Nickol, B. B., Broughton, R., Orti, G. 2005. First sequenced mitochondrial genome from the phylum Acanthocephala (Leptorhynchoides thecatus) and its phylogenetic position within Metazoa. J. Mol. Evol. 60:706-715.
237. Stephen, A. C. 1965. A revision of the phylum Sipuncula. Ann. Mag. Nat. Hist. 137:457-462.
238. Stephen, A. C., Edmonds, S. J. 1972. The Phyla Sipuncula and Echiura. Trustees of the British Museum (Natural History), London.
239. Strimmer, K., Von Haeseler, A. 1996. Quartet puzzling: A quartet maximum-likelihoodmethod for reconstructing tree topologies. Mol. Biol. Evol. 13:964-969.
240. Struck, T. H., Schult, N., Kusen, T., Hickman, E., Bleidorn, C., McHugh, D., Halanych, K. M. 2007. Annelid phylogeny and the status of Sipuncula and Echiura. BMC Evol. Biol. 7:57-67.
241. Su, X., Wu, X. B., Yan, P., Cao, S. Y., Hu, Y. L. 2007. Rearrangement of a mitochondrial tRNA gene of the concave-eared torrent frog, Amolops tormotus. Gene. 394:25-34.
242. Sun, H., Zhou, K., Song, D. 2005. Mitochondrial genome of the Chinese mitten crab Eriocheir japonica sinenesis (Brachyura: Thoracotremata: Grapsoidea) reveals a novel gene order and two target regions of gene rearrangements. Gene. 349:207-217.
243. Suzuki, Y., Glazko, G. V., Nei, M. 2002. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Natl. Acad. Sci. U.S.A. 99:16138-16143.
244. Tamura, K., Dudley, J., Nei, M., Kumar, S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599.
245. Tateno, Y., Takezaki, N., Nei, M. 1994. Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site. Mol. Biol. Evol. 11:261-277.
246. Telford, M. J. 2007. Phylogenomics. Curr. Biol. 17:R945-946.
247. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., Higgins, D. G. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
248. Tjensvoll, K., Hodneland, K., Nilsen, F., Nylund, A. 2005. Genetic characterization of the mitochondrial DNA from Lepeophtheirus salmonis (Crustacea; Copepoda). A new gene organization revealed. Gene. 353:218-230.
249. Tong, J. G., Chan, T. Y., Chu, K. H. 2000. A preliminary phylogenetic analysis of Metapenaeopsis (Decapoda: Penacidae) based on mitochondrial DNA sequences of selected species from the Indo-West Pacific. J. Crust. Biol. 20:541-549.
250. Valles, Y., Boore, J. L. 2006. Lophotrochozoan mitochondrial genomes. Integr. Comp. Biol. 46:544-557.
251. Vázquez-Bader, A. R., Carrero, J. C., Gárcia-Varela, M., Grcia, A., Laclette, J. P. 2004. Molecular phylogeny of superfamily Penaeoidea Rafinesque-Schmaltz, 1815, based onmitochondrial 16S partial sequence analysis. J. Shellfish Res. 23:911-917.
252. von Nickisch-Rosenegk, M., Brown, W. M., Boore, J. L. 2001. Complete sequence of the mitochondrial genome of the tapeworm Hymenolepis diminuta: gene arrangements indicate that Platyhelminths are Eutrochozoans. Mol. Biol. Evol. 18:721-730.
253. Waeschenbach, A., Telford, M. J., Porter, J. S., Littlewood, D. T. 2006. The complete mitochondrial genome of Flustrellidra hispida and the phylogenetic position of Bryozoa among the Metazoa. Mol. Phylogenet. Evol. 40:195-207.
254. Wang, B., Li, F., Dong, B., Zhang, X., Zhang, C., Xiang, J. 2006. Discovery of the genes in response to white spot syndrome virus (WSSV) infection in Fenneropenaeus chinensis through cDNA microarray. Mar. Biotechnol. 8:491-500.
255. Wanninger, A., Koop, D., Bromham, L., Noonan, E., Degnan, B. M. 2005. Nervous and muscle system development in Phascolion strombus (Sipuncula). Dev. Genes. Evol. 215:509-518.
256. Wilcox, T. P., Zwickl, D. J., Heath, T. A., Hillis, D. M. 2002. Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Mol. Phylogenet. Evol. 25:361-371.
257. Wilson, K., Cahill, V., Ballment, E., Benzie, J. 2000. The complete sequence of the mitochondrial genome of the crustacean Penaeus monodon: are malacostracan crustaceans more closely related to insects than to branchiopods? Mol. Biol. Evol. 17:863-874.
258. Winkworth, R. C., Bell, C. D., Donoghue, M. J. 2008. Mitochondrial sequence data and Dipsacales phylogeny: Mixed models, partitioned Bayesian analyses, and model selection. Mol. Phylogenet. Evol. 46:830-843.
259. Winnepenninckx, B., Backeljau, T., De Wachter, R. 1995. Phylogeny of protostome worms derived from 18S rRNA sequences. Mol. Biol. Evol. 12:641-649.
260. Wolstenholme, D. R. 1992. Animal mitochondrial DNA: structure and evolution. Int. Rev. Cytol. 141:173-216.
261. Wu, W., Schmidt, T. R., Goodman, M., Grossman, L. I. 2000. Molecular evolution of cytochrome c oxidase subunit I in primates: is there coevolution between mitochondrial and nuclear genomes? Mol. Phylogenet. Evol. 17:294-304.
262. Wyman, S. K., Jansen, R. K., Boore, J. L. 2004. Automatic annotation of organellargenomes with DOGMA. Bioinformatics. 20:3252-3255.
263. Yamauchi, M., Miya, M., Nishida, M. 2002. Complete mitochondrial DNA sequence of the Japanese spiny lobster, Panulirus japonicus (Crustacea: Decapoda). Gene. 295:89-96.
264. Yamauchi, M. M., Miya, M. U., Machida, R. J., Nishida, M. 2004. PCR-based approach for sequencing mitochondrial genomes of decapod crustaceans, with a practical example from kuruma prawn (Marsupenaeus japonicus). Mar. Biotechnol. 6:419-429.
265. Yamauchi, M. M., Miya, M. U., Nishida, M. 2003. Complete mitochondrial DNA sequence of the swimming crab, Portunus trituberculatus (Crustacea: Decapoda: Brachyura). Gene. 311:129-135.
266. Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556.
267. Yang, Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24:1586-1591.
268. Yang, Z., Nielsen, R. 2000. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17:32-43.
269. Yang, Z., Rannala, B. 1997. Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo method. Mol. Biol. Evol. 14:717-724.
270. Zhang, H., Yan, J., Zhang, G., Zhou, K. 2008. Phylogeography and demographic history of Chinese black-spotted frog populations (Pelophylax nigromaculata): evidence for independent refugia expansion and secondary contact. BMC Evol. Biol. 8:21.
271. Zhang, P., Chen, Y. Q., Liu, Y. F., Zhou, H., Qu, L. H. 2003a. The complete mitochondrial genome of the Chinese giant salamander, Andrias davidianus (Amphibia: Caudata). Gene. 311:93-98.
272. Zhang, P., Chen, Y. Q., Zhou, H., Liu, Y. F., Wang, X. L., Papenfuss, T. J., Wake, D. B., Qu, L. H. 2006a. Phylogeny, evolution, and biogeography of Asiatic Salamanders (Hynobiidae). Proc. Natl. Acad. Sci. U.S.A. 103:7360-7365.
273. Zhang, P., Chen, Y. Q., Zhou, H., Wang, X. L., Qu, L. H. 2003b. The complete mitochondrial genome of a relic salamander, Ranodon sibiricus (Amphibia: Caudata) and implications for amphibian phylogeny. Mol. Phylogenet. Evol. 28:620-626.
274. Zhang, P., Zhou, H., Chen, Y. Q., Liu, Y. F., Qu, L. H. 2005a. Mitogenomic perspectiveson the origin and phylogeny of living amphibians. Syst. Biol. 54:391-400.
275. Zhang, P., Zhou, H., Liang, D., Liu, Y. F., Chen, Y. Q., Qu, L. H. 2005b. The complete mitochondrial genome of a tree frog, Polypedates megacephalus (Amphibia: Anura: Rhacophoridae), and a novel gene organization in living amphibians. Gene. 346:133-143.
276. Zhang, W., Sun, Z. 2008. Random local neighbor joining: A new method for reconstructing phylogenetic trees. Mol. Phylogenet. Evol. 117-128.
277. Zhang, Z., Li, J., Yu, J. 2006b. Computing Ka and Ks with a consideration of unequal transitional substitutions. BMC Evol. Biol. 6:44.
278. Zhang, Z., Li, J., Zhao, X. Q., Wang, J., Wong, G. K., Yu, J. 2006c. KaKs_Calculator: calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics. 4:259-263.
279. Zhou, M., Dorland, R. D. 2004. Aggregation and vertical migration behavior of Euphausia superba. Deep sea research. 51:2119-2137.
280. Zrzavy, J., Mihulka, S., Kepka, P., Bezdek, A., Tietz, D. 1998. Phylogeny of the Metazoa based on morphological and 18S ribosomal DNA evidence. Cladistics. 14:249-285.
281. 兰国宝, 杨素芳, 谢体三, 石德顺 2007. 星虫动物门系统发生研究进展. 广西科学. 14:186-192.
282. 李凤鲁, 周红, 王玮 1992. 中国沿海星虫动物门名录. 青岛海洋大学学报. 22:72-87.
283. 李新正, 刘瑞玉, 梁象秋 2003. 中国长臂虾总科的动物地理学特点. 生物多样性. 11:393-406.
284. 刘瑞玉 《现生甲壳动物(Crustacea)最新分类系统》简介. In: 中国甲壳动物学会, (Ed.), 中国甲壳动物学论文集. 科学出版社, 北京, 2003.
285. 吕宝忠, 钟杨, 高莉萍等译 2002. 分子进化与系统发育. 高等教育出版社, 北京.
286. 孙红英, 周开亚, 宋大祥 2003. 节肢动物线粒体基因组与系统发生重建. 动物学研究. 24:467-479.
287. 孙松 2002. 南极磷虾. 世界科技研究与发展. 24:57-60.
288. 孙松, 严小军 2001. 南极大磷虾的生物活性物质及其用途研究进展. 极地研究. 13:213-216.
289. 王荣, 陈亚瞿, 左涛, 王克 2003. 黄、东海春秋季磷虾的数量分布及其与水文环境的关系. 水产学报. 27:31-38.
290. 杨德渐, 孙世春 2005. 海洋无脊椎动物学. 中国海洋大学出版社, 青岛.
291. 于黎 食肉目哺乳动物(Carnivora)的分子进化研究. 中国科学院昆明动物研究所, Vol. 博士, 昆明, 2005.
292. 于黎, 张亚平 2006. 系统发育基因组学——重建生命之树的一条迷人途径. 遗传. 28:1445-1450.
2. Abele, L. G., Felgenhauer, B. E. 1986. Phylogenetic and phenetic relationships among the lower Decapoda. J. Crust. Biol. 6:385-400.
3. Aguinaldo, A. M., Turbeville, J. M., Linford, L. S., Rivera, M. C., Garey, J. R., Raff, R. A., Lake, J. A. 1997. Evidence for a clade of nematodes, arthropods and other moulting animals. Nature. 387:489-493.
4. ?kesson, B. 1958. A study of the nervous system of the Sipunculoideae, with some remarks on the development of the two species Phascolion strombi Montagu and Golfingia minuta Keferstein. Unders ?resund. 38:1-249.
5. Altekar, G., Dwarkadas, S., Huelsenbeck, J. P., Ronquist, F. 2004. Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics. 20:407-415.
6. Avise, J. C. 2000. Phylogeography: the history and formation of species. Harvard University Press, Cambridge, Mass.
7. Avise, J. C., Arnold, J., Ball, R. M., Bermingham, E., Lamb, T., Neigel, J. E., Reeb, C. A., Saunders, N. C. 1987. Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annu. Rev. Ecol. Syst. 18:489-522.
8. Ax, P. 1999. Das System der Metazoa: ein Lehrbuch der phylogenetischen Systematik. Vol.
2. Gustav Fischer, Stuttgart.
9. Backeljau, T., Winnepenninckx, B., Bruyn, L. D. 1993. Cladistic analysis of metazoan relationships: a reappraisal. Cladistics. 9:167-181.
10. Baldwin, J. D., Bass, A. L., Bowen, B. W., Clark, W. H. 1998. Molecular phylogeny and biogeography of the marine shrimp Penaeus. Mol. Phylogenet. Evol. 10:399-407.
11. Bayona-Bafaluy, M. P., Muller, S., Moraes, C. T. 2005. Fast adaptive coevolution of nuclear and mitochondrial subunits of ATP synthetase in orangutan. Mol. Biol. Evol. 22:716-724.
12. Beagley, C. T., Okimoto, R., Wolstenholme, D. R. 1998. The mitochondrial genome of the sea anemone Metridium senile (Cnidaria): introns, a paucity of tRNA genes, and a near-standard genetic code. Genetics. 148:1091-1108.
13. Benson, G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27:573-580.
14. Black, W. C. t., Roehrdanz, R. L. 1998. Mitochondrial gene order is not conserved in arthropods: prostriate and metastriate tick mitochondrial genomes. Mol. Biol. Evol. 15:1772-1785.
15. Blanchette, M., Kunisawa, T., Sankoff, D. 1999. Gene order breakpoint evidence in animal mitochondrial phylogeny. J. Mol. Evol. 49:193-203.
16. Bleidorn, C., Podsiadlowski, L., Bartolomaeus, T. 2006. The complete mitochondrial genome of the orbiniid polychaete Orbinia latreillii (Annelida, Orbiniidae)--A novel gene order for Annelida and implications for annelid phylogeny. Gene. 370:96-103.
17. Bleidorn, C., Vogt, L., Bartolomaeus, T. 2003. New insights into polychaete phylogeny (Annelida) inferred from 18S rDNA sequences. Mol. Phylogenet. Evol. 29:279-288.
18. Bliss, D. E., Abele, L. G. 1982. The Biology of Crustacea. Vol.1, Systematics, the fossil record, and biogeography. Academic Press, New York; London.
19. Blumer, M. J. F. 1997. The larval ocelli of Golfingia misakiana (Sipuncula, Golfingiidae) and of a pelagosphera of another unidentified species. Zoomorphology. 117:115-120.
20. Boas, J. E. V. 1880. Studier over Decapodernes Slaegtskabsforhold.
21. Boore, J. L. 1999. Animal mitochondrial genomes. Nucleic Acids Res. 27:1767-1780.
22. Boore, J. L. The duplication/random loss model for gene rearrangement exemplified by mitochondrial genomes of deuterostome animals. In: D. Sankoff, J. Nadeau, Eds.), Computational biology, Vol. 1. Kluwer Academic Publishers, Dordrecht, The Netherlands, 2000, pp. 133-147.
23. Boore, J. L. 2004. Complete mitochondrial genome sequence of Urechis caupo, a representative of the phylum Echiura. BMC Genomics. 5:67.
24. Boore, J. L. 2006. The complete sequence of the mitochondrial genome of Nautilus macromphalus (Mollusca: Cephalopoda). BMC Genomics. 7:182.
25. Boore, J. L., Brown, W. M. 1994. Complete DNA sequence of the mitochondrial genomeof the black chiton, Katharina tunicata. Genetics. 138:423-443.
26. Boore, J. L., Brown, W. M. 1995. Complete sequence of the mitochondrial DNA of the annelid worm Lumbricus terrestris. Genetics. 141:305-319.
27. Boore, J. L., Brown, W. M. 1998. Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Curr. Opin. Genet. Dev. 8:668-674.
28. Boore, J. L., Brown, W. M. 2000. Mitochondrial genomes of Galathealinum, Helobdella, and Platynereis: sequence and gene arrangement comparisons indicate that Pogonophora is not a phylum and Annelida and Arthropoda are not sister taxa. Mol. Biol. Evol. 17:87-106.
29. Boore, J. L., Collins, T. M., Stanton, D., Daehler, L. L., Brown, W. M. 1995. Deducing the pattern of arthropod phylogeny from mitochondrial DNA rearrangements. Nature. 376:163-165.
30. Boore, J. L., Lavrov, D. V., Brown, W. M. 1998. Gene translocation links insects and crustaceans. Nature. 392:667-668.
31. Boore, J. L., Macey, J. R., Medina, M. 2005. Sequencing and comparing whole mitochondrial genomes of animals. Meth. Enzymol. 395:311-348.
32. Boore, J. L., Medina, M., Rosenberg, L. A. 2004. Complete sequences of the highly rearranged molluscan mitochondrial genomes of the Scaphopod Graptacme eborea and the Bivalve Mytilus edulis. Mol. Biol. Evol. 21:1492-1503.
33. Boore, J. L., Staton, J. L. 2002. The mitochondrial genome of the Sipunculid Phascolopsis gouldii supports its association with Annelida rather than Mollusca. Mol. Biol. Evol. 19:127-137.
34. Borradaile, B. 1907. On the classification of the decapod crustaceans. Ann. Mag. Nat. Hist. 19:457-486.
35. Bouvier, E. n.-L. 1940. Décapodes marcheurs. Paris.
36. Bremer, K. 1988. The limits of amino acid sequence data in Angiosperm phylogenetic reconstruction. Evolution. 42:795-803.
37. Bridge, D., Cunningham, C. W., Schierwater, B., DeSalle, R., Buss, L. W. 1992. Class-level relationships in the phylum Cnidaria: evidence from mitochondrial genome structure. Proc. Natl. Acad. Sci. U.S.A. 89:8750-8753.
38. Brusca, R. C., Brusca, G. J. 1990. Invertebrates. Sinauer Associates, Sunderland, Mass.
39. Brusca, R. C., Brusca, G. J. 2003. Invertebrates. Sinauer Associates, Sunderland, Mass.
40. Burkenroad, M. D. 1963. The evolution of the eucarida (Crustacea, Eumalacostraca), in relation to the fossil record. Tulane Studies in Geology. 2:1-17.
41. Burkenroad, M. D. 1981. The higher taxonomy and evolution of Decapoda (Crustacea). San Diego Society of Natural History, San Diego, Calif.
42. Calman, W. T. 1904. On the classification of the Crustacea Malacostraca. Ann. Mag. Nat. Hist. 1904:144-158.
43. Calman, W. T. 1909. A Treatise on Zoology, 7: Appendiculata, Crustacea. Adam and Charles Black, London.
44. Castresana, J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17:540-552.
45. Castresana, J., Feldmaier-Fuchs, G., Yokobori, S., Satoh, N., Paabo, S. 1998. The mitochondrial genome of the hemichordate Balanoglossus carnosus and the evolution of deuterostome mitochondria. Genetics. 150:1115-1123.
46. Charlebois, R. L., Beiko, R. G., Ragan, M. A. 2003. Microbial phylogenomics: Branching out. Nature. 421:217.
47. Cheng, S., Chang, S. Y., Gravitt, P., Respess, R. 1994. Long PCR. Nature. 369:684-685.
48. Clary, D. O., Wolstenholme, D. R. 1985. The mitochondrial DNA molecular of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code. J. Mol. Evol. 22:252-271.
49. Claus, C. 1888. Ueber den Organismus der Nebaliden und die systematische Stellung der Leptostraken. Arb. Zool. Inst. Wien. 1-148.
50. Coelho, P. S., Bryan, A. C., Kumar, A., Shadel, G. S., Snyder, M. 2002. A novel mitochondrial protein, Tar1p, is encoded on the antisense strand of the nuclear 25S rDNA. Genes Dev. 16:2755-2760.
51. Cohen, W. D. 1985. Blood cells of marine invertebrates: experimental systems in cell biology and comparative physiology. A.R. Liss, New York.
52. Cook, C. E. 2005. The complete mitochondrial genome of the stomatopod crustacean Squilla mantis. BMC Genomics. 6:105.
53. Cook, C. E., Yue, Q., Akam, M. 2005. Mitochondrial genomes suggest that hexapods andcrustaceans are mutually paraphyletic. Proc. Biol. Sci. 272:1295-1304.
54. Crandall, K. A., Harris, D. J., Fetzner, J. W., Jr. 2000. The monophyletic origin of freshwater crayfish estimated from nuclear and mitochondrial DNA sequences. Proc. Biol. Sci. 267:1679-1686.
55. Crease, T. J. 1999. The complete sequence of the mitochondrial genome of Daphnia pulex (Cladocera: Crustacea). Gene. 233:89-99.
56. Cummings, M. P., Otto, S. P., Wakeley, J. 1995. Sampling properties of DNA sequence data in phylogenetic analysis. Mol. Biol. Evol. 12:814-822.
57. Curole, J. P., Kocher, T. D. 1999. Mitogenomics: digging deeper with complete mitochondrial genomes. Trends Ecol. Evol. 14:394-398.
58. Cusimano, N., Zhang, L. B., Renner, S. S. 2008. Reevaluation of the cox1 group I intron in Araceae and angiosperms indicates a history dominated by loss rather than horizontal transfer. Mol. Biol. Evol. 25:265-276.
59. Cutler, E. B. 1994. The Sipuncula: their systematics, biology and evolution. Cornell University Press, New York.
60. Cutler, E. B., Dean, H. K., Saiz-Salinas, J. I. 2001. Sipuncula from Antarctic waters. Proc. Biol. Soc. Wash. 114:861-880.
61. Davis, G. K., Patel, N. H. 1999. The origin and evolution of segmentation. Trends Cell Biol. 9:M68-72.
62. de Rosa, R., Grenier, J. K., Andreeva, T., Cook, C. E., Adoutte, A., Akam, M., Carroll, S. B., Balavoine, G. 1999. Hox genes in brachiopods and priapulids and protostome evolution. Nature. 399:772-776.
63. DeJong, R. J., Emery, A. M., Adema, C. M. 2004. The mitochondrial genome of Biomphalaria glabrata (Gastropoda: Basommatophora), intermediate host of Schistosoma mansoni. J. Parasitol. 90:991-997.
64. Dellaporta, S. L., Xu, A., Sagasser, S., Jakob, W., Moreno, M. A., Buss, L. W., Schierwater, B. 2006. Mitochondrial genome of Trichoplax adhaerens supports placozoa as the basal lower metazoan phylum. Proc. Natl. Acad. Sci. U.S.A. 103:8751-8756.
65. Delle-Chiaje, S. 1823. Memorie sulla storia e notomina degli animali senza vertebre del Regno di Napoli, Vol. I. Fratelli Fernandes. Naples.
66. Delsuc, F., Brinkmann, H., Philippe, H. 2005. Phylogenomics and the reconstruction of the tree of life. Nat. Rev. Genet. 6:361-375.
67. Desper, R., Gascuel, O. 2004. Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting. Mol. Biol. Evol. 21:587-598.
68. Dixon, C. J., Ahyong, S. T., Schram, F. R. 2003. A new hypothesis of decapod phylogeny. Crustaceana. 76:935-976.
69. Dohle, W. 2001. Are the insects terrestrial crustaceans? A discussion of some new facts and arguments and the proposal of the proper name ‘Tetraconata’ for the monophyletic unit Crustacea + Hexapoda. Annls Soc. Entomol. Fr. (N.S.). 37:85-104.
70. Dreyer, H., Steiner, G. 2006. The complete sequences and gene organisation of the mitochondrial genomes of the heterodont bivalves Acanthocardia tuberculata and Hiatella arctica - and the first record for a putative Atpase subunit 8 gene in marine bivalves. Front. Zool. 3:13-26.
71. Dunn, C. W., Hejnol, A., Matus, D. Q., Pang, K., Browne, W. E., Smith, S. A., Seaver, E., Rouse, G. W., Obst, M., Edgecombe, G. D., Sorensen, M. V., Haddock, S. H., Schmidt-Rhaesa, A., Okusu, A., Kristensen, R. M., Wheeler, W. C., Martindale, M. Q., Giribet, G. 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature. 452:745-749.
72. Edmonds, S. J. Phylum Sipuncula. Polychaetes and Allies: The Southern Synthesis. Fauna of Australia, Vol. 4A. CSIRO Publishing, Melbourne, 2000, pp. 375-400.
73. Eernisse, D. J., Albert, J. S., Anderson, F. E. 1992. Annelida and Arthropoda are not sister taxa: a phylogenetic analysis of spiralian metazoan morphology. Syst. Biol. 41:305-330.
74. Eisen, J. A., Fraser, C. M. 2003. Phylogenomics: intersection of evolution and genomics. Science. 300:1706-1707.
75. Erber, A., Riemer, D., Bovenschulte, M., Weber, K. 1998. Molecular phylogeny of metazoan intermediate filament proteins. J. Mol. Evol. 47:751-762.
76. Evans, M. J., Gurer, C., Loike, J. D., Wilmut, I., Schnieke, A. E., Schon, E. A. 1999. Mitochondrial DNA genotypes in nuclear transfer-derived cloned sheep. Nat. Genet. 23:90-93.
77. Ewing, B., Green, P. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8:186-194.
78. Ewing, B., Hillier, L., Wendl, M. C., Green, P. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8:175-185.
79. Feldmann, R. M. 2003. The Decapoda: New initiatives and novel approaches. J. Paleontol. 77:1021-1039.
80. Felgenhauer, B. E., Abele, L. G. Phylogenetic relationships among shrimp-like decapods. In: F. R. Schram, (Ed.), Crustacean Phylogeny, Vol. 1, Balkema, Netherlands, 1983, pp. 291-311.
81. Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
82. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 39:783-791.
83. Folmer, O., Black, M., Hoeh, W., Lutz, R., Vrijenhoek, R. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Marine Biol. Biotechnol. 3:294-299.
84. Friedrich, M., Tautz, D. 1995. Ribosomal DNA phylogeny of the major extant arthropod classes and the evolution of myriapods. Nature. 376:165-167.
85. Fritzsch, G., Schlegel, M., Stadler, P. F. 2006. Alignments of mitochondrial genome arrangements: applications to metazoan phylogeny. J. Theor. Biol. 240:511-520.
86. Garey, J. R., Schmidt-Rhaesa, A. 1998. The essential role of "Minor" Phyla in molecular studies of animal evolution. Amer. Zool. 38:907-917.
87. Giribet, G., Distel, D. L., Polz, M., Sterrer, W., Wheeler, W. C. 2000. Triploblastic relationships with emphasis on the acoelomates and the position of Gnathostomulida, Cycliophora, Plathelminthes, and Chaetognatha: a combined approach of 18S rDNA sequences and morphology. Syst. Biol. 49:539-562.
88. Giribet, G., Wheeler, W. C. 2002. On bivalve phylogeny: a high-level analysis of the Bivalvia (Mollusca) based on combined morphology and DNA sequence data. Invertebr. Biol. 121:271-324.
89. Gissi, C., Iannelli, F., Pesole, G. 2004. Complete mtDNA of Ciona intestinalis revealsextensive gene rearrangement and the presence of an atp8 and an extra trnM gene in ascidians. J. Mol. Evol. 58:376-389.
90. Glaessner, M. F. Decapoda. In: R. C. Moore, (Ed.), Arthropoda 4. Part R, vol. 2. Treatise on Invertebrate Paleontology. Geological Society of America and University of Kansas Press, Lawrence, 1969.
91. Glenner, H., Hansen, A. J., Sorensen, M. V., Ronquist, F., Huelsenbeck, J. P., Willerslev, E. 2004. Bayesian inference of the metazoan phylogeny; a combined molecular and morphological approach. Curr. Biol. 14:1644-1649.
92. Goloboff, P. A. 2003. Parsimony, likelihood, and simplicity. Cladistics. 19:91-103.
93. Gordon, D., Abajian, C., Green, P. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8:195-202.
94. Grande, C., Templado, J., Zardoya, R. 2008. Evolution of gastropod mitochondrial genome arrangements. BMC Evol. Biol. 8:61.
95. Guindon, S., Gascuel, O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704.
96. Guralnick, R. 2002. A recapitulation of the rise and fall of the cell lineage research program: the evolutionary developmental relationship of cleavage to homology, body plans and life history. J. Hist. Biol. 35:537-567.
97. Guralnick, R. P., Lindberg, D. R. 2001. Reconnecting cell and animal lineages: what do cell lineages tell us about the evolution and development of Spiralia? Evolution. 55:1501-1519.
98. Gusm?o, J., Lazoski, C., Solé-Cava, A. M. 2000. A new species of Penaeus (Crustacea: Penaeidae) revealed by allozyme and cytochrome oxidase I analyses. Mar. Biol. 137:435-446.
99. Haechel, E. 1866. Generelle Morphologie der Organismen. Georg Riemer, Berlin.
100. Halanych, K. M., Bacheller, J. D., Aguinaldo, A. M., Liva, S. M., Hillis, D. M., Lake, J. A. 1995. Evidence from 18S ribosomal DNA that the lophophorates are protostome animals. Science. 267:1641-1643.
101. Halanych, K. M., Dahlgren, T. G., McHugh, D. 2002. Unsegmented Annelids? Possible origins of four lophotrochozoan worm taxa. Integr. Comp. Biol. 42:678-684.
102. Hansen, H. J. 1893. Zur Morphologie der Gliedmassen und Mundtheile bei Crustaceen und Insecten. Zool. Anz. . 16:193-212.
103. Hasegawa, M., Kishino, H., Saitou, N. 1991. On the maximum likelihood method in molecular phylogenetics. J. Mol. Evol. 32:443-445.
104. Hebert, P. D., Stoeckle, M. Y., Zemlak, T. S., Francis, C. M. 2004. Identification of birds through DNA barcodes. PLoS Biol. 2:e312.
105. Helfenbein, K. G., Brown, W. M., Boore, J. L. 2001. The complete mitochondrial genome of the articulate brachiopod Terebratalia transversa. Mol. Biol. Evol. 18:1734-1744.
106. Helfenbein, K. G., Fourcade, H. M., Vanjani, R. G., Boore, J. L. 2004. The mitochondrial genome of Paraspadella gotoi is highly reduced and reveals that chaetognaths are a sister group to protostomes. Proc. Natl. Acad. Sci. U.S.A. 101:10639-10643.
107. Hendy, M. D., Penny, D. 1989. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38:297-309.
108. Hessling, R. 2002. Metameric organisation of the nervous system in developmental stages of Urechis caupo (Echiura) and its phylogenetic implications. Zoomorphology. 121:221-234.
109. Hessling, R. 2003. Novel aspects of the nervous system of Bonellia viridis (Echiura) revealed by the combination of immunohistochemistry, confocal laser-scanning microscopy and three-dimensional reconstruction. Hydrobiologia. 496:225-239.
110. Hessling, R., Westheide, W. 2002. Are Echiura derived from a segmented ancestor? Immunohistochemical analysis of the nervous system in developmental stages of Bonellia viridis. J. Morphol. 252:100-113.
111. Hickerson, M. J., Cunningham, C. W. 2000. Dramatic mitochondrial gene rearrangements in the hermit crab Pagurus longicarpus (Crustacea, anomura). Mol. Biol. Evol. 17:639-644.
112. Hillis, D. M. 1998. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst. Biol. 47:3-8.
113. Hillis, D. M., Bull, J. J. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42:182-192.
114. Hillis, D. M., Pollock, D. D., McGuire, J. A., Zwickl, D. J. 2003. Is sparse taxon samplinga problem for phylogenetic inference? Syst. Biol. 52:124-126.
115. Holder, M., Lewis, P. O. 2003. Phylogeny estimation: traditional and Bayesian approaches. Nat. Rev. Genet. 4:275-284.
116. Huang, D. Y., Chen, J. Y., Vannier, J., Saiz Salinas, J. I. 2004. Early Cambrian sipunculan worms from southwest China. Proc. R. Soc. Lond., B, Biol. Sci. 271:1671-1676.
117. Huelsenbeck, J. P. 1995. Performance of phylogenetic methods in simulation. Syst. Biol. 44:17-48.
118. Huelsenbeck, J. P., Larget, B., Miller, R. E., Ronquist, F. 2002. Potential applications and pitfalls of Bayesian inference of phylogeny. Syst. Biol. 51:673-688.
119. Huelsenbeck, J. P., Ronquist, F., Nielsen, R., Bollback, J. P. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science. 294:2310-2314.
120. Hurst, L. D. 2002. The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends Genet. 18:486-487.
121. Hwang, U. W., Friedrich, M., Tautz, D., Park, C. J., Kim, W. 2001. Mitochondrial protein phylogeny joins myriapods with chelicerates. Nature. 413:154-157.
122. Hyman, L. H. The protostomatous coelomates-Phylum Sipunculida. The Invertebrates. McGraw-Hill Press, New York, 1959, pp. 610-696.
123. Ivey, J. L., Santos, S. R. 2007. The complete mitochondrial genome of the Hawaiian anchialine shrimp Halocaridina rubra Holthuis, 1963 (Crustacea: Decapoda: Atyidae). Gene. 394:35-44.
124. Jennings, R. M., Halanych, K. M. 2005. Mitochondrial genomes of Clymenella torquata (Maldanidae) and Riftia pachyptila (Siboglinidae): evidence for conserved gene order in annelida. Mol. Biol. Evol. 22:210-222.
125. Jukes, T., Cantor, C. Evolution of protein molecules. In: M. HN, (Ed.), Mammalian Protein Metabolism. Academic Press, New York, 1969, pp. 21-132.
126. Kilpert, F., Podsiadlowski, L. 2006. The complete mitochondrial genome of the common sea slater, Ligia oceanica (Crustacea, Isopoda) bears a novel gene order and unusual control region features. BMC Genomics. 7:241.
127. Kim, J. 1996. General inconsistency conditions for maximum parsimony: effects of branch lengths and increasing numbers of taxa. Syst. Biol. 45:363-374.
128. Kjer, K. M. 2004. Aligned 18S and insect phylogeny. Syst. Biol. 53:506-514.
129. Knoll, A. H., Carroll, S. B. 1999. Early animal evolution: emerging views from comparative biology and geology. Science. 284:2129-2137.
130. Knudsen, B., Kohn, A. B., Nahir, B., McFadden, C. S., Moroz, L. L. 2006. Complete DNA sequence of the mitochondrial genome of the sea-slug, Aplysia californica: conservation of the gene order in Euthyneura. Mol. Phylogenet. Evol. 38:459-469.
131. Kumar, S., Tamura, K., Nei, M. 2004. MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief. Bioinformatics. 5:150-163.
132. Larget, B., Simon, D. L. 1999. Markov Chasin Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16:750-759.
133. Larget, B., Simon, D. L., Kadane, J. B., Sweet, D. 2005. A bayesian analysis of metazoan mitochondrial genome arrangements. Mol. Biol. Evol. 22:486-495.
134. Lavery, S., Chan, T. Y., Tam, Y. K., Chu, K. H. 2004. Phylogenetic relationships and evolutionary history of the shrimp genus Penaeus s.l. derived from mitochondrial DNA. Mol. Phylogenet. Evol. 31:39-49.
135. Lavrov, D. V., Brown, W. M., Boore, J. L. 2000. A novel type of RNA editing occurs in the mitochondrial tRNAs of the centipede Lithobius forficatus. Proc. Natl. Acad. Sci. U.S.A. 97:13738-13742.
136. Lavrov, D. V., Brown, W. M., Boore, J. L. 2004. Phylogenetic position of the Pentastomida and (pan)crustacean relationships. Proc. Biol. Sci. 271:537-544.
137. Lavrov, D. V., Forget, L., Kelly, M., Lang, B. F. 2005. Mitochondrial genomes of two demosponges provide insights into an early stage of animal evolution. Mol. Biol. Evol. 22:1231-1239.
138. Lavrov, D. V., Lang, B. F. 2005. Poriferan mtDNA and animal phylogeny based on mitochondrial gene arrangements. Syst. Biol. 54:651-659.
139. Lee, Y. S., Oh, J., Kim, Y. U., Kim, N., Yang, S., Hwang, U. W. 2008. Mitome: dynamic and interactive database for comparative mitochondrial genomics in metazoan animals. Nucleic Acids Res. 36:D938-942.
140. Lewis, D. L., Farr, C. L., Farquhar, A. L., Kaguni, L. S. 1994. Sequence, organization, and evolution of the A+T region of Drosophila melanogaster mitochondrial DNA. Mol. Biol.Evol. 11:523-538.
141. Lewis, D. L., Farr, C. L., Kaguni, L. S. 1995. Drosophila melanogaster mitochondrial DNA: completion of the nucleotide sequence and evolutionary comparisons. Insect Mol. Biol. 4:263-278.
142. Li, W. H. 1986. Evolutionary change of restriction cleavage sites and phylogenetic inference. Genetics. 113:187-213.
143. Lim, J. T., Hwang, U. W. 2006. The complete mitochondrial genome of Pollicipes mitella (Crustacea, Maxillopoda, Cirripedia): non-monophylies of maxillopoda and crustacea. Mol. Cells. 22:314-322.
144. Linnaeus, C. 1767. Systema naturae per regna tria naturae, secundum classes, ordines, genera, species cum characteribus, differentiis, synonymis, locis. Vindobonae.
145. Liu, L., Pearl, D. K. 2007. Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst. Biol. 56:504-514.
146. Liu, Z. Q., Wang, Y. Q., Su, B. 2005. The mitochondrial genome organization of the rice frog, Fejervarya limnocharis (Amphibia: Anura): a new gene order in the vertebrate mtDNA. Gene. 346:145-151.
147. Lohse, M., Drechsel, O., Bock, R. 2007. OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr. Genet. 52:267-274.
148. Lowe, T. M., Eddy, S. R. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955-964.
149. Macey, J. R., Papenfuss, T. J., Kuehl, J. V., Fourcade, H. M., Boore, J. L. 2004. Phylogenetic relationships among amphisbaenian reptiles based on complete mitochondrial genomic sequences. Mol. Phylogenet. Evol. 33:22-31.
150. Macey, J. R., Schulte, J. A., 2nd, Larson, A. 2000. Evolution and phylogenetic information content of mitochondrial genomic structural features illustrated with acrodont lizards. Syst. Biol. 49:257-277.
151. Machida, R. J., Miya, M. U., Nishida, M., Nishida, S. 2002. Complete mitochondrial DNA sequence of Tigriopus japonicus (Crustacea: Copepoda). Mar. Biotechnol. 4:406-417.
152. Machida, R. J., Miya, M. U., Yamauchi, M. M., Nishida, M., Nishida, S. 2004. Organization of the mitochondrial genome of Antarctic krill Euphausia superba (Crustacea: Malacostraca). Mar. Biotechnol. 6:238-250.
153. Mackey, L. Y., Winnepenninckx, B., De Wachter, R., Backeljau, T., Emschermann, P., Garey, J. R. 1996. 18S rRNA suggests that Entoprocta are protostomes, unrelated to Ectoprocta. J. Mol. Evol. 42:552-559.
154. Maggioni, R., Rogers, A. D., Maclean, N., D'Incao, F. 2001. Molecular phylogeny of western Atlantic Farfantepenaeus and Litopenaeus shrimp based on mitochondrial 16S partial sequences. Mol. Phylogenet. Evol. 18:66-73.
155. Martin, J. W., Abele., L. G. 1986. Notes on male pleopod morphology in the brachyuran crab family Panopeidae Ortmann, 1893, sensu Guinot (1978) (Decapoda). Crustaceana. 50:182-198.
156. Martin, J. W., Davis, G. E. 2001. An updated classification of the recent crustacea. Natural History Museum of Los Angeles County, Los Angeles, California.
157. Maxmen, A. B., King, B. F., Cutler, E. B., Giribet, G. 2003. Evolutionary relationships within the protostome phylum Sipuncula: a molecular analysis of ribosomal genes and histone H3 sequence data. Mol. Phylogenet. Evol. 27:489-503.
158. Maynard, B. T., Kerr, L. J., McKiernan, J. M., Jansen, E. S., Hanna, P. J. 2005. Mitochondrial DNA sequence and gene organization in the [corrected] Australian blacklip [corrected] abalone Haliotis rubra (leach). Mar. Biotechnol. 7:645-658.
159. McHugh, D. 1997. Molecular evidence that echiurans and pogonophorans are derived annelids. Proc. Natl. Acad. Sci. U.S.A. 94:8006-8009.
160. McHugh, D. 2000. Molecular phylogeny of the Annelida. Can. J. Zool. 78:1873.
161. Meglitsch, P. A., Schram, F. R. 1991. Invertebrate Zoology. Oxford University Press, London.
162. Miller, A. D., Austin, C. M. 2006. The complete mitochondrial genome of the mantid shrimp Harpiosquilla harpax, and a phylogenetic investigation of the Decapoda using mitochondrial sequences. Mol. Phylogenet. Evol. 38:565-574.
163. Miller, A. D., Murphy, N. P., Burridge, C. P., Austin, C. M. 2005. Complete mitochondrial DNA sequences of the decapod crustaceans Pseudocarcinus gigas (Menippidae) andMacrobrachium rosenbergii (Palaemonidae). Mar. Biotechnol. 7:339-349.
164. Miller, A. D., Nguyen, T. T., Burridge, C. P., Austin, C. M. 2004. Complete mitochondrial DNA sequence of the Australian freshwater crayfish, Cherax destructor (Crustacea: Decapoda: Parastacidae): a novel gene order revealed. Gene. 331:65-72.
165. Nardi, F., Carapelli, A., Fanciulli, P. P., Dallai, R., Frati, F. 2001. The complete mitochondrial DNA sequence of the basal hexapod Tetrodontophora bielanensis: evidence for heteroplasmy and tRNA translocations. Mol. Biol. Evol. 18:1293-1304.
166. Nardi, F., Spinsanti, G., Boore, J. L., Carapelli, A., Dallai, R., Frati, F. 2003. Hexapod origins: monophyletic or paraphyletic? Science. 299:1887-1889.
167. Naylor, G. J., Brown, W. M. 1998. Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences. Syst. Biol. 47:61-76.
168. Nei, M. 1996. Phylogenetic analysis in molecular evolutionary genetics. Annu. Rev. Genet. 30:371-404.
169. Nei, M., Kumar, S. 2000. Molecular evolution and phylogenetics. Oxford University Press, Oxford; New York.
170. Nicol, S., Endo, Y., Food and Agriculture Organization of the United, N. 1997. Krill fisheries of the world. Food and Agriculture Organization of the United Nations, Rome.
171. Nielsen, C. 1995. Animal Evolution: Interrelationships of the Living Phyla. Oxford University Press, Oxford.
172. Nielsen, C. 2001. Animal Evolution: Interrelationships of the Living Phyla. Oxford University Press, Oxford.
173. Nielsen, C. 2003. Proposing a solution to the Articulata-Ecdysozoa controversy. Zool. Scr. 32:475-482.
174. Nielsen, C., Scharff, N., Eibye-Jacobsen, D. 1996. Cladistic analyses of the animal kingdom. Biol. J. Linn. Soc. Lond. 57:385-410.
175. Nielsen, R., Yang, Z. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics. 148:929-936.
176. Nikaido, M., Rooney, A. P., Okada, N. 1999. Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: hippopotamuses are the closest extant relatives of whales. Proc. Natl. Acad. Sci. U.S.A. 96:10261-10266.
177. Noguchi, Y., Endo, K., Tajima, F., Ueshima, R. 2000. The mitochondrial genome of the brachiopod Laqueus rubellus. Genetics. 155:245-259.
178. Ojala, D., Montoya, J., Attardi, G. 1981. tRNA punctuation model of RNA processing in human mitochondria. Nature. 290:470-474.
179. Ono, T., Isobe, K., Nakada, K., Hayashi, J. I. 2001. Human cells are protected from mitochondrial dysfunction by complementation of DNA products in fused mitochondria. Nat. Genet. 28:272-275.
180. Orrhage, L., Müller, M. 2005. Morphology of the nervous system of Polychaeta (Annelida). Hydrobiologia. 535-536:79-111.
181. Pakendorf, B., Stoneking, M. 2005. Mitochondrial DNA and human evolution. Annu. Rev. Genomics Hum. Genet. 6:165-183.
182. Paland, S., Lynch, M. 2006. Transitions to asexuality result in excess amino acid substitutions. Science. 311:990-992.
183. Palumbi, S. R. 1991. The simple fool's guide to PCR. Dept. of Zoology and Kewalo Marine Laboratory, University of Hawaii, Honolulu, HI.
184. Papillon, D., Perez, Y., Caubit, X., Le Parco, Y. 2004. Identification of Chaetognaths as Protostomes is supported by the analysis of their mitochondrial genome. Mol. Biol. Evol. 21:2122-2129.
185. Parker, S. P. 1982. Synopsis and classification of living organisms. McGraw-Hill, New York.
186. Passamaneck, Y., Halanych, K. M. 2006. Lophotrochozoan phylogeny assessed with LSU and SSU data: evidence of lophophorate polyphyly. Mol. Phylogenet. Evol. 40:20-28.
187. Pearson, W. R., Robins, G., Zhang, T. 1999. Generalized neighbor-joining: more reliable phylogenetic tree reconstruction. Mol. Biol. Evol. 16:806-816.
188. Penny, D. 1982. Towards a basis for classification: the incompleteness of distance measures, incompatibility analysis and phenetic classification. J. Theor. Biol. 96:129-142.
189. Pérez-Farfante, I., Kensley, B. 1997. Penaeoid and sergestoid shrimps and prawns of the world. Editions du Muséum National d’Histoire Naturelle, Paris, France.
190. Perna, N. T., Kocher, T. D. 1995. Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J. Mol. Evol. 41:353-358.
191. Peterson, K. J., Eernisse, D. J. 2001. Animal phylogeny and the ancestry of bilaterians: inferences from morphology and 18S rDNA gene sequences. Evol. Dev. 3:170-205.
192. Philippe, H., Brinkmann, H., Martinez, P., Riutort, M., Baguna, J. 2007. Acoel flatworms are not platyhelminthes: evidence from phylogenomics. PLoS ONE. 2:e717.
193. Place, A. R., Feng, X., Steven, C. R., Fourcade, H. M., Boore, J. L. 2005. Genetic markers in blue crabs (Callinectes sapidus) II. Complete mitochondrial genome sequence and characterization of genetic variation. J. Exp. Mar. Biol. Ecol. 319:15-27.
194. Podsiadlowski, L., Braband, A. 2006. The complete mitochondrial genome of the sea spider Nymphon gracile (Arthropoda: Pycnogonida). BMC Genomics. 7:284.
195. Pollock, D. D., Zwickl, D. J., McGuire, J. A., Hillis, D. M. 2002. Increased Taxon Sampling Is Advantageous for Phylogenetic Inference. Syst. Biol. 51:664-671.
196. Porter, M. L., Perez-Losada, M., Crandall, K. A. 2005. Model-based multi-locus estimation of decapod phylogeny and divergence times. Mol. Phylogenet. Evol. 37:355-369.
197. Posada, D. 2006. ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online. Nucleic Acids Res. 34:W700-703.
198. Posada, D., Crandall, K. A. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics. 14:817-818.
199. Purschke, G., Hessling, R., Westheide, W. 2000. The phylogenetic position of the Clitellata and the Echiura - on the problematic assessment of absent characters. J. Zoolog. Syst. Evol. Res. 38:165-173.
200. Quan, J., Zhuang, Z., Deng, J., Dai, J., Zhang, Y. P. 2004. Phylogenetic relationships of 12 penaeoidea shrimp species deduced from mitochondrial DNA sequences. Biochem. Genet. 42:331-345.
201. Quatrefages, A. d. 1847. études sur les types inférieurs de l’embranchement des Annelés. Mémoire sur l'échiure de Gaertner (Echiurus gaertnerii NOB). Ann. Sci. Nat. Zool. (Paris). 7:307-343.
202. Rannala, B., Yang, Z. 1996. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 43:304-311.
203. Regier, J. C., Shultz, J. W. 1997. Molecular phylogeny of the major arthropod groups indicates polyphyly of crustaceans and a new hypothesis for the origin of hexapods. Mol.Biol. Evol. 14:902-913.
204. Regier, J. C., Shultz, J. W. 1998. Molecular phylogeny of Arthropods and the significance of the Cambrian "Explosion" for molecular systematics. Amer. Zool. 38:918-928.
205. Regier, J. C., Shultz, J. W., Kambic, R. E. 2005. Pancrustacean phylogeny: hexapods are terrestrial crustaceans and maxillopods are not monophyletic. Proc. Biol. Sci. 272:395-401.
206. Rice, M. E. 1970. Asexual reproduction in a Sipunculan worm. Science. 167:1618-1620.
207. Rice, M. E. Sipuncula: developmental evidence for phylogenetic inference. In: S. C. Morris, et al., Eds.), The Origins and Relationships of Lower Invertebrates. Oxford University Press, Oxford, 1985, pp. 274-296.
208. Richter, S. 2002. The Tetraconata concept: hexapod-crustacean relationships and the phylogeny of Crustacea. Org. Divers. Evol. 2:217-237.
209. Richter, S., Scholtz, G. 2001. Phylogenetic analysis of the Malacostraca (Crustacea). J. Zoolog. Syst. Evol. Res. 39:113-136.
210. Roehrdanz, R. L., Degrugillier, M. E., Black, W. C. t. 2002. Novel rearrangements of arthropod mitochondrial DNA detected with long-PCR: applications to arthropod phylogeny and evolution. Mol. Biol. Evol. 19:841-849.
211. Ronquist, F., Huelsenbeck, J. P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 19:1572-1574.
212. Rousset, V., Pleijel, F., Rouse, G. W., Erseus, C., Siddall, M. E. 2007. A molecular phylogeny of annelids. Cladistics. 23:41-63.
213. Rozas, J., Sanchez-DelBarrio, J. C., Messeguer, X., Rozas, R. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics. 19:2496-2497.
214. Rzhetsky, A., Nei, M. 1993. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol. Biol. Evol. 10:1073-1095.
215. Saitou, N., Imanishi, T. 1989. Relative efficiencies of the Fitch-Margoliash, maximum-parsimony, maximum-likelihood, minimum-evolution, and neighbor-joining methods of phylogenetic tree construction in obtaining the correct tree. Mol. Biol. Evol. 6: 514-525.
216. Saitou, N., Nei, M. 1987. The neighbor-joining method: a new method for reconstructingphylogenetic trees. Mol. Biol. Evol. 4:406-425.
217. Scheltema, A. H. 1993. Aplacophora as progenetic aculiferans and the coelomate origin of mollusks as the sister taxon of Sipuncula. Biol. Bull. 184:57-78.
218. Scheltema, A. H. Phylogenetic position of Sipuncula, Mollusca and the progenetic Aplacophora. In: J. Taylor, (Ed.), Origin and Evolutionary Radiation of the Mollusca. Oxford University Press, Oxford, 1996, pp. 53-58.
219. Schindel, D. E., Miller, S. E. 2005. DNA barcoding a useful tool for taxonomists. Nature. 435:17.
220. Schmidt, T. R., Wu, W., Goodman, M., Grossman, L. I. 2001. Evolution of nuclear- and mitochondrial-encoded subunit interaction in cytochrome c oxidase. Mol. Biol. Evol. 18:563-569.
221. Scholtz, G., Richter, S. 1995. Phylogenetic systematics of the reptantian Decapoda (Crustacea, Malacostraca). Zool. J. Linn. Soc. 113:289-328.
222. Schram, F. R. 2001. Phylogeny of decapods: moving towards a consensus. Hydrobiologia. 449:1-20.
223. Schulze, A., Cutler, E., Giribet, G. 2005. Reconstructing the phylogeny of the Sipuncula. Hydrobiologia. 535-536:277-296.
224. Schulze, A., Cutler, E. B., Giribet, G. 2007. Phylogeny of sipunculan worms: A combined analysis of four gene regions and morphology. Mol. Phylogenet. Evol. 42:171-192.
225. Segawa, R. D., Aotsuka, T. 2005. The mitochondrial genome of the Japanese freshwater crab, Geothelphusa dehaani (Crustacea: Brachyura): evidence for its evolution via gene duplication. Gene. 355:28-39.
226. Seifert, K. A., Samson, R. A., Dewaard, J. R., Houbraken, J., Levesque, C. A., Moncalvo, J. M., Louis-Seize, G., Hebert, P. D. 2007. Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case. Proc. Natl. Acad. Sci. U.S.A. 104:3901-3906.
227. Serb, J. M., Lydeard, C. 2003. Complete mtDNA sequence of the North American freshwater mussel, Lampsilis ornata (Unionidae): an examination of the evolution and phylogenetic utility of mitochondrial genome organization in Bivalvia (Mollusca). Mol. Biol. Evol. 20:1854-1866.
228. Shen, X., Ren, J. F., Cui, Z. X., Sha, Z. L., Wang, B., Xiang, J. H., Liu, B. 2007. The complete mitochondrial genomes of two common shrimps(Litopenaeus vannamei and Fenneropenaeus chinensis)and their phylogenomic considerations. Gene. 403:98-109.
229. Shultz, J. W., Regier, J. C. 2000. Phylogenetic analysis of arthropods using two nuclear protein-encoding genes supports a crustacean + hexapod clade. Proc. Biol. Sci. 267:1011-1019.
230. Snir, S., Warnow, T., Rao, S. 2008. Short quartet puzzling: a new quartet-based phylogeny reconstruction algorithm. J. Comput. Biol. 15:91-103.
231. S?rensen, M. V., Funch, P., Willerslev, E., Hansen, A. J., Olesen, J. 2000. On the phylogeny of Metazoa in the light of Cycliophora and Micrognathozoa. Zool. Anz. 239:297-318.
232. Staton, J. L. 2003. Phylogenetic analysis of the mitochondrial cytochrome c oxidase subunit 1 gene from 13 sipunculan genera: Intra- and interphylum relationships. Invertebr. Biol. 122:252-264.
233. Staton, J. L., Daehler, L. L., Brown, W. M. 1997. Mitochondrial gene arrangement of the horseshoe crab Limulus polyphemus L.: conservation of major features among arthropod classes. Mol. Biol. Evol. 14:867-874.
234. Stechmann, A., Schlegel, M. 1999. Analysis of the complete mitochondrial DNA sequence of the brachiopod Terebratulina retusa places Brachiopoda within the protostomes. Proc. R. Soc. Lond., B, Biol. Sci. 266:2043-2043.
235. Steel, M., Penny, D. 2000. Parsimony, likelihood, and the role of models in molecular phylogenetics. Mol. Biol. Evol. 17:839-850.
236. Steinauer, M. L., Nickol, B. B., Broughton, R., Orti, G. 2005. First sequenced mitochondrial genome from the phylum Acanthocephala (Leptorhynchoides thecatus) and its phylogenetic position within Metazoa. J. Mol. Evol. 60:706-715.
237. Stephen, A. C. 1965. A revision of the phylum Sipuncula. Ann. Mag. Nat. Hist. 137:457-462.
238. Stephen, A. C., Edmonds, S. J. 1972. The Phyla Sipuncula and Echiura. Trustees of the British Museum (Natural History), London.
239. Strimmer, K., Von Haeseler, A. 1996. Quartet puzzling: A quartet maximum-likelihoodmethod for reconstructing tree topologies. Mol. Biol. Evol. 13:964-969.
240. Struck, T. H., Schult, N., Kusen, T., Hickman, E., Bleidorn, C., McHugh, D., Halanych, K. M. 2007. Annelid phylogeny and the status of Sipuncula and Echiura. BMC Evol. Biol. 7:57-67.
241. Su, X., Wu, X. B., Yan, P., Cao, S. Y., Hu, Y. L. 2007. Rearrangement of a mitochondrial tRNA gene of the concave-eared torrent frog, Amolops tormotus. Gene. 394:25-34.
242. Sun, H., Zhou, K., Song, D. 2005. Mitochondrial genome of the Chinese mitten crab Eriocheir japonica sinenesis (Brachyura: Thoracotremata: Grapsoidea) reveals a novel gene order and two target regions of gene rearrangements. Gene. 349:207-217.
243. Suzuki, Y., Glazko, G. V., Nei, M. 2002. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Natl. Acad. Sci. U.S.A. 99:16138-16143.
244. Tamura, K., Dudley, J., Nei, M., Kumar, S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599.
245. Tateno, Y., Takezaki, N., Nei, M. 1994. Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site. Mol. Biol. Evol. 11:261-277.
246. Telford, M. J. 2007. Phylogenomics. Curr. Biol. 17:R945-946.
247. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., Higgins, D. G. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
248. Tjensvoll, K., Hodneland, K., Nilsen, F., Nylund, A. 2005. Genetic characterization of the mitochondrial DNA from Lepeophtheirus salmonis (Crustacea; Copepoda). A new gene organization revealed. Gene. 353:218-230.
249. Tong, J. G., Chan, T. Y., Chu, K. H. 2000. A preliminary phylogenetic analysis of Metapenaeopsis (Decapoda: Penacidae) based on mitochondrial DNA sequences of selected species from the Indo-West Pacific. J. Crust. Biol. 20:541-549.
250. Valles, Y., Boore, J. L. 2006. Lophotrochozoan mitochondrial genomes. Integr. Comp. Biol. 46:544-557.
251. Vázquez-Bader, A. R., Carrero, J. C., Gárcia-Varela, M., Grcia, A., Laclette, J. P. 2004. Molecular phylogeny of superfamily Penaeoidea Rafinesque-Schmaltz, 1815, based onmitochondrial 16S partial sequence analysis. J. Shellfish Res. 23:911-917.
252. von Nickisch-Rosenegk, M., Brown, W. M., Boore, J. L. 2001. Complete sequence of the mitochondrial genome of the tapeworm Hymenolepis diminuta: gene arrangements indicate that Platyhelminths are Eutrochozoans. Mol. Biol. Evol. 18:721-730.
253. Waeschenbach, A., Telford, M. J., Porter, J. S., Littlewood, D. T. 2006. The complete mitochondrial genome of Flustrellidra hispida and the phylogenetic position of Bryozoa among the Metazoa. Mol. Phylogenet. Evol. 40:195-207.
254. Wang, B., Li, F., Dong, B., Zhang, X., Zhang, C., Xiang, J. 2006. Discovery of the genes in response to white spot syndrome virus (WSSV) infection in Fenneropenaeus chinensis through cDNA microarray. Mar. Biotechnol. 8:491-500.
255. Wanninger, A., Koop, D., Bromham, L., Noonan, E., Degnan, B. M. 2005. Nervous and muscle system development in Phascolion strombus (Sipuncula). Dev. Genes. Evol. 215:509-518.
256. Wilcox, T. P., Zwickl, D. J., Heath, T. A., Hillis, D. M. 2002. Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Mol. Phylogenet. Evol. 25:361-371.
257. Wilson, K., Cahill, V., Ballment, E., Benzie, J. 2000. The complete sequence of the mitochondrial genome of the crustacean Penaeus monodon: are malacostracan crustaceans more closely related to insects than to branchiopods? Mol. Biol. Evol. 17:863-874.
258. Winkworth, R. C., Bell, C. D., Donoghue, M. J. 2008. Mitochondrial sequence data and Dipsacales phylogeny: Mixed models, partitioned Bayesian analyses, and model selection. Mol. Phylogenet. Evol. 46:830-843.
259. Winnepenninckx, B., Backeljau, T., De Wachter, R. 1995. Phylogeny of protostome worms derived from 18S rRNA sequences. Mol. Biol. Evol. 12:641-649.
260. Wolstenholme, D. R. 1992. Animal mitochondrial DNA: structure and evolution. Int. Rev. Cytol. 141:173-216.
261. Wu, W., Schmidt, T. R., Goodman, M., Grossman, L. I. 2000. Molecular evolution of cytochrome c oxidase subunit I in primates: is there coevolution between mitochondrial and nuclear genomes? Mol. Phylogenet. Evol. 17:294-304.
262. Wyman, S. K., Jansen, R. K., Boore, J. L. 2004. Automatic annotation of organellargenomes with DOGMA. Bioinformatics. 20:3252-3255.
263. Yamauchi, M., Miya, M., Nishida, M. 2002. Complete mitochondrial DNA sequence of the Japanese spiny lobster, Panulirus japonicus (Crustacea: Decapoda). Gene. 295:89-96.
264. Yamauchi, M. M., Miya, M. U., Machida, R. J., Nishida, M. 2004. PCR-based approach for sequencing mitochondrial genomes of decapod crustaceans, with a practical example from kuruma prawn (Marsupenaeus japonicus). Mar. Biotechnol. 6:419-429.
265. Yamauchi, M. M., Miya, M. U., Nishida, M. 2003. Complete mitochondrial DNA sequence of the swimming crab, Portunus trituberculatus (Crustacea: Decapoda: Brachyura). Gene. 311:129-135.
266. Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556.
267. Yang, Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24:1586-1591.
268. Yang, Z., Nielsen, R. 2000. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17:32-43.
269. Yang, Z., Rannala, B. 1997. Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo method. Mol. Biol. Evol. 14:717-724.
270. Zhang, H., Yan, J., Zhang, G., Zhou, K. 2008. Phylogeography and demographic history of Chinese black-spotted frog populations (Pelophylax nigromaculata): evidence for independent refugia expansion and secondary contact. BMC Evol. Biol. 8:21.
271. Zhang, P., Chen, Y. Q., Liu, Y. F., Zhou, H., Qu, L. H. 2003a. The complete mitochondrial genome of the Chinese giant salamander, Andrias davidianus (Amphibia: Caudata). Gene. 311:93-98.
272. Zhang, P., Chen, Y. Q., Zhou, H., Liu, Y. F., Wang, X. L., Papenfuss, T. J., Wake, D. B., Qu, L. H. 2006a. Phylogeny, evolution, and biogeography of Asiatic Salamanders (Hynobiidae). Proc. Natl. Acad. Sci. U.S.A. 103:7360-7365.
273. Zhang, P., Chen, Y. Q., Zhou, H., Wang, X. L., Qu, L. H. 2003b. The complete mitochondrial genome of a relic salamander, Ranodon sibiricus (Amphibia: Caudata) and implications for amphibian phylogeny. Mol. Phylogenet. Evol. 28:620-626.
274. Zhang, P., Zhou, H., Chen, Y. Q., Liu, Y. F., Qu, L. H. 2005a. Mitogenomic perspectiveson the origin and phylogeny of living amphibians. Syst. Biol. 54:391-400.
275. Zhang, P., Zhou, H., Liang, D., Liu, Y. F., Chen, Y. Q., Qu, L. H. 2005b. The complete mitochondrial genome of a tree frog, Polypedates megacephalus (Amphibia: Anura: Rhacophoridae), and a novel gene organization in living amphibians. Gene. 346:133-143.
276. Zhang, W., Sun, Z. 2008. Random local neighbor joining: A new method for reconstructing phylogenetic trees. Mol. Phylogenet. Evol. 117-128.
277. Zhang, Z., Li, J., Yu, J. 2006b. Computing Ka and Ks with a consideration of unequal transitional substitutions. BMC Evol. Biol. 6:44.
278. Zhang, Z., Li, J., Zhao, X. Q., Wang, J., Wong, G. K., Yu, J. 2006c. KaKs_Calculator: calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics. 4:259-263.
279. Zhou, M., Dorland, R. D. 2004. Aggregation and vertical migration behavior of Euphausia superba. Deep sea research. 51:2119-2137.
280. Zrzavy, J., Mihulka, S., Kepka, P., Bezdek, A., Tietz, D. 1998. Phylogeny of the Metazoa based on morphological and 18S ribosomal DNA evidence. Cladistics. 14:249-285.
281. 兰国宝, 杨素芳, 谢体三, 石德顺 2007. 星虫动物门系统发生研究进展. 广西科学. 14:186-192.
282. 李凤鲁, 周红, 王玮 1992. 中国沿海星虫动物门名录. 青岛海洋大学学报. 22:72-87.
283. 李新正, 刘瑞玉, 梁象秋 2003. 中国长臂虾总科的动物地理学特点. 生物多样性. 11:393-406.
284. 刘瑞玉 《现生甲壳动物(Crustacea)最新分类系统》简介. In: 中国甲壳动物学会, (Ed.), 中国甲壳动物学论文集. 科学出版社, 北京, 2003.
285. 吕宝忠, 钟杨, 高莉萍等译 2002. 分子进化与系统发育. 高等教育出版社, 北京.
286. 孙红英, 周开亚, 宋大祥 2003. 节肢动物线粒体基因组与系统发生重建. 动物学研究. 24:467-479.
287. 孙松 2002. 南极磷虾. 世界科技研究与发展. 24:57-60.
288. 孙松, 严小军 2001. 南极大磷虾的生物活性物质及其用途研究进展. 极地研究. 13:213-216.
289. 王荣, 陈亚瞿, 左涛, 王克 2003. 黄、东海春秋季磷虾的数量分布及其与水文环境的关系. 水产学报. 27:31-38.
290. 杨德渐, 孙世春 2005. 海洋无脊椎动物学. 中国海洋大学出版社, 青岛.
291. 于黎 食肉目哺乳动物(Carnivora)的分子进化研究. 中国科学院昆明动物研究所, Vol. 博士, 昆明, 2005.
292. 于黎, 张亚平 2006. 系统发育基因组学——重建生命之树的一条迷人途径. 遗传. 28:1445-1450.