Further support for the clades obtained by multiple molecular phylogenies in the acanthomorph bush

Several recent molecular studies have begun to clarify the phylogeny of Acanthomorpha (Teleostei), a wide clade of teleost fishes. However, different molecular datasets do not agree on a single history of the taxa, probably because of marker-specific biases. The 'total-evidence' approach maximizes character congruence, but may be biased by a single robust, but non-phylogenetic constraint from one dataset. We have therefore taken the approach to analyse also each dataset separately prior to their combination, and detect repeated groups: signal common to markers is more probably a reflection of shared ancestry than marker-specific signal. Partial sequences (678+527 base pairs) of exons of the MLL gene (Mixed Lineage Leukaemia-like) gene were used, as well as the datasets of Chen et al. (ribosomal 28S, rhodopsin gene, mitochondrial 12S and 16S). Most of the repeated clades of Chen et al. are supported by the new dataset. Some new groups were repeatedly found: a Scarus-Labrus group (clade M), the presence of Gasterosteidae as a sister taxon or within the clade Zoarcoidei-Cottoidei (clade Is), Polymixia as a sister-group to the clade Zeoidei-Gadiformes (clade O), the clade Q grouping Mugiloidei, Cichlidae, Atherinomorpha, Blennioidei and Gobiesocoidei; and the interesting clade N, reducing potential sister-groups to Tetraodontiformes to either Caproidei, Lophiiformes, Acanthuroidei, Drepanidae, Chaetodontidae, and Pomacanthidae.     

Phylogeny of the grass family (Poaceae) from rpl16 intron sequence data

DNA sequence data from the chloroplast noncoding rpl16 intron are used to address phylogenetic relationships among the major lineages of the grass family, with particular emphasis on the highly heterogeneous subfamily Bambusoideae and the basal lineages. Thirty-five grass sequences representing all six currently recognized major groups of the family and one outgroup sequence were analyzed using both parsimony and distance methods. The phylogenetic analyses indicated: (1) Puelia, a traditionally isolated bambusoid genus, is the most basal lineage in the BOP clade (Bambusoideae, Oryzoideae, and Pooideae); (2) the bambusoid clade is a sister group to the pooid clade; and (3) the monophyletic oryzoid clade is well separated from the bambusoid clade. The study further confirmed the recognition of two primary groups in the grass family: the BOP clade and the PACC clade (Panicoideae, Arundinoideae, Chloridoideae, and Centothecoideae); it also provided further evidence that the traditional subfamily Bambusoideae is highly heterogeneous and phylogenetically unacceptable. The data support Streptochaeteae, Anomochloeae, and Phareae as the most basal lineages among the extant grasses. Within the BOP clade, oryzoids and pooids are confirmed as two monophyletic clades, but the bambusoid clade, including only the woody bamboo tribe Bambuseae and the herbaceous bamboo tribe Olyreae, is relatively weakly supported. The study also indicated that the chloroplast noncoding region sequence data could be useful in phylogenetic analysis at relatively high taxonomic levels.     

Molecular phylogeny of gill monogeneans (Platyhelminthes, Monogenea, Dactylogyridae) and colonization of Indo-West Pacific butterflyfish hosts (Perciformes, Chaetodontidae)

We investigated the phylogenetic relationships among monogenean parasites of the Chaetodontidae (butterflyfishes) from the Indo-West Pacific Ocean. Molecular phylogenies of selected taxa within the Dactylogyridae, including the ancyrocephaline parasites of butterflyfishes, based on two nuclear and one mitochondrial gene fragments (complete 18S rDNA, partial 28S rDNA (D1-D3), and partial 16S rDNA) were reconstructed using parsimony, maximum likelihood and Bayesian inference methods. Our results show the non-monophyletic nature of the monogenean fauna of butterflyfishes. The group is divided into two independent lineages. The first clade contains species of the genera Aliatrema and Euryhaliotrematoides , which parasitize Chaetodontidae exclusively. The second contains species of Haliotrema , a generalist group of parasites. The positions of several other species of the Ancyrocephalinae, including freshwater species, at the base of the two clades, provide strong evidence that the monogenean fauna did not result from a single colonization event, but rather that they have colonized their butterflyfish hosts independently at least twice.     

Molecular systematics of the South American caviomorph rodents: relationships among species and genera in the family Octodontidae

Nucleotide sequences from mitochondrial (12S rRNA) and nuclear (growth hormone receptor) genes were used to investigate phylogenetic relationships among South American hystricognath rodents of the superfamily Octodontoidea, with special emphasis on the family Octodontidae. Relationships among most taxa were well resolved by a combined analysis of both genes, and the molecular phylogeny was used to address several long-standing phylogenetic problems. The family Abrocomidae was the most basal lineage within the superfamily Octodontoidea, sensu stricto, and the family Ctenomyidae was sister to the family Octodontidae, followed by a monophyletic group containing the families Myocastoridae and Echimyidae. A basic dichotomy was observed within the family Octodontidae. The Argentine desert specialists, Tympanoctomys and Octomys, grouped separate from Octodontomys, which was sister to a clade containing a monophyletic Octodon and a clade represented by species of Aconaemys and Spalacopus. Aconaemys was paraphyletic relative to Spalacopus. The phylogeny was used as an interpretive framework for an examination of variation in several non-molecular characters. The primitive diploid number for most of the octodontoids was determined to be between 46 and 56, and the primitive genome size 8.2 pg. Members of the Octodontidae appeared to be derived from an ancestral stock occupying lower elevations in scrub habitat. Furthermore, estimates of divergence time from the molecular data provided a temporal perspective for changes in plant communities, which demonstrated turnover and diversification in response to climatic and geologic events occurring in the Miocene through the Pleistocene.     

The phylogeny of the superfamily Coccoidea (Hemiptera: Sternorrhyncha) based on the morphology of extant and extinct macropterous males

Currently, 49 families of scale insects are recognised, 33 of which are extant. Despite more than a decade of DNA sequence‐based phylogenetic studies of scales insects, little is known with confidence about relationships among scale insects families. Multiple lines of evidence support the monophyly of a group of 18 scale insect families informally referred to as the neococcoids. Among neococcoid families, published DNA sequence‐based estimates have supported Eriococcidae paraphyly with respect to Beesoniidae, Dactylopiidae, and Stictococcidae. No other neococcoid interfamily relationship has been strongly supported in a published study that includes exemplars of more than ten families. Likewise, no well‐supported relationships among the 15 extant scale insect families that are not neococcoids (usually referred to as ‘archaeococcoids’) have been published. We use a Bayesian approach to estimate the scale insect phylogeny from 162 adult male morphological characters, scored from 269 extant and 29 fossil species representing 43/49 families. The result is the most taxonomically comprehensive, most resolved and best supported estimate of phylogenetic relationships among scale insect families to date. Notable results include strong support for (i) Ortheziidae sister to Matsucoccidae, (ii) a clade comprising all scale insects except for Margarodidae s.s., Ortheziidae and Matsucoccidae, (iii) Coelostomidiidae paraphyletic with respect to Monophlebidae, (iv) Eriococcidae paraphyletic with respect to Stictococcidae and Beesoniidae, and (v) Aclerdidae sister to Coccidae. We recover strong support for a clade comprising Phenacoleachiidae, Pityococcidae, Putoidae, Steingeliidae and the neococcoids, along with a sister relationship between this clade and Coelostomidiidae + Monophlebidae. In addition, we recover strong support for Pityococcidae + Steingeliidae as sister to the neococcoids. Data from fossils were incomplete, and the inclusion of extinct taxa in the data matrix reduced support and phylogenetic structure. Nonetheless, these fossil data will be invaluable in DNA sequence‐based and total evidence estimates of phylogenetic divergence times.     

Nuclear gene phylogeny of narrow-mouthed toads (Family: Microhylidae) and a discussion of competing hypotheses concerning their biogeographical origins

The family Microhylidae has a large circumtropic distribution and contains about 400 species in a highly subdivided taxonomy. Relationships among its constituent taxa remained controversial due to homoplasy in morphological characters, resulting in conflicting phylogenetic hypotheses. A phylogeny based on four nuclear genes (rag-1, rag-2, tyrosinase, BDNF) and one mitochondrial gene (CO1) of representatives of all currently recognized subfamilies uncovers a basal polytomy between several subfamilial clades. A sister group relationship between the cophylines and scaphiophrynines is resolved with moderate support, which unites these endemic Malagasy taxa for the first time. The American members of the subfamily Microhylinae are resolved to form a clade entirely separate from the Asian members of that subfamily. Otophryne is excluded from the subfamily Microhylinae, and resolved as a basal taxon. The placement of the Asian dyscophine Calluella nested within the Asian Microhyline clade rather than with the genus Dyscophus is corroborated by our data. Bayesian estimates of the divergence time of extant Microhylidae (47-90 Mya) and among the subclades within the family are discussed in frameworks of alternative possible biogeographic scenarios.     

A phylogenetic reconstruction of the Ichneumonoidea (Hymenoptera) based on the D2 variable region of 28S ribosomal RNA

The D2 variable region of 28S rRNA was sequenced in a wide range of Ichneumonoidea to provide the first comprehensive phylogenetic reconstruction of this superfamily. The two constituent families (Braconidae and Ichneumonidae) were each found to contain a single well-supported clade dominated by the more plesiomorphic life history strategies (idiobiosis, ectoparasitism and attacking endoephytic hosts). In the Braconidae this clade corresponds to the morphologically-defined group called the cyclostomes. In the Ichneumonidae the clade unites for the first time the pimpliformes ( sensu Wahl) with most of the phygadeuontoid subfamilies and several small taxa including Adelognathus and Euceros . Relationships among the remaining, more biologically-derived, subfamilies were less well resolved, but included among the Braconidae a well-supported microgastroid clade and strong evidence for a sister group relationship between the Agathidinae and Sigalphinae.     

Phylogenetic investigations of the stephanoberyciformes and beryciformes, particularly whalefishes (Euteleostei: Cetomimidae), based on partial 12S rDNA and 16S rDNA sequences

DNA data were collected from a number of acanthomorph fishes for 12S rDNA (30 sequences) and 16S rDNA (39 sequences) to investigate the phylogenetic relationships of genera within Cetomimidae (whalefishes) and of this family within the Stephanoberyciformes/Beryciformes assemblage. The Cetomimidae are apparently monophyletic. Within the family, species of Gyrinomimus and Cetomimus form a clade but the former genus is paraphyletic with respect to the latter. Cetostoma is sister to Ditropichthys rather than to Gyrinomimus plus Cetomimus as suggested by morphological analyses. Rondeletiidae + Cetomimidae + Barbourisiidae are shown, as expected from morphological analyses, as a monophyletic group in the 12S rDNA analyses, but not in the 16S rDNA or combined analyses, although the shortest trees showing the group require only one extra step in each case. These three families plus Melamphaidae (our sample of Stephanoberyciformes) are not shown as a group in any analysis, with Melamphaidae being sister to Berycidae in the 16S and combined analyses, but dispersed in the 12S analyses. Maximum-parsimony trees without imposed constraints are notably shorter than trees constrained to show ordinal groupings or either of the two main current hypotheses of Stephanoberyciformes/Beryciformes relationships. The length difference is highly significant for most comparisons using either 12S or 16S rDNA sets or their combination, and significant or nearly so for all comparisons. In particular, the Beryciformes is unlikely to be monophyletic. The Holocentridae are included, with high bootstrap and Bremer support, in a clade of non-beryciforms comprising the Gempylidae, Zeidae, and Atheriniformes (the only higher acanthomorphs sampled) and not with other Beryciform families. In these data, the Berycidae are the sister to the Melamphaidae, a stephanoberyciform family.     

Pleistocene diversification of living squirrel monkeys (Saimiri spp.) inferred from complete mitochondrial genome sequences

In order to enhance our understanding of the evolutionary history of squirrel monkeys (Saimiri spp.), we newly sequenced and analyzed data from seven complete mitochondrial genomes representing six squirrel monkey taxa. While previous studies have lent insights into the taxonomy and phylogeny of the genus, phylogenetic relationships and divergence date estimates among major squirrel monkey clades remain unclear. Using maximum likelihood and Bayesian procedures, we inferred a highly resolved phylogenetic tree with strong support for a sister relationship between Saimiri boliviensis and all other Saimiri, for monophyly of Saimiri oerstedii and Saimiri sciureus sciureus, and for Saimiri sciureus macrodon as the sister lineage to the S. oerstedii/S. s. sciureus clade. We inferred that crown lineages for extant squirrel monkeys diverged around 1.5 million years ago (MYA) in the Pleistocene Epoch, with other major clades diverging between 0.9 and 1.1 MYA. Our results suggest a relatively recent timeline of squirrel monkey evolution and challenge previous conceptions about the diversification of the genus and its expansion into Central America.     

Polyphyly across oceans: a molecular phylogeny of the Chromodorididae (Mollusca, Nudibranchia)

The Chromodorididae is a large and colourful family of nudibranch sea slugs distributed across the world's oceans. Most diversity is centred in the Indo-Pacific, but several genera are present in multiple ocean basins, or across regions separated by biogeographical barriers. The monophyly of these widespread genera had not been tested previously. We used 18S rDNA, 16S rDNA and COI sequence data to generate a molecular phylogeny for this group. We recovered evidence of paraphyly or polyphyly in all of the widespread genera examined ( Hypselodoris , Mexichromis , Chromodoris and Glossodoris ). East Atlantic Hypselodoris and west Atlantic + east Pacific Mexichromis species were more closely related to each other than they were to their Indo-Pacific congeners. The addition of Southern Ocean species of Digidentis demonstrated an interesting alternative to this relationship, becoming the sister group for the east Atlantic Hypselodoris on the basis of 16S and 18S data, but not COI data. Sister group relationships were recovered for most monotypic or enigmatic genera. Ardeadoris is linked to Glossodoris , as is Diversidoris ; Pectenodoris is sister to the Indo-Pacific Mexichromis clade, and Verconia is the sister to Noumea haliclona . Controversy surrounding the placement of the three most basal genera was only partially resolved. Using Actinocyclus to root the mitochondrial trees, Cadlinella was the unsupported sister to the Chromodorididae (excluding Cadlina ), and Tyrinna occupied a relatively basal position, although this also did not receive significant statistical support. Adding nuclear 18S data gave support for Cadlina as the sister group to the rest of the Chromodorididae s.s. Otherwise, like previous molecular studies, mitochondrial genes supported an alternative position for Cadlina (with other dorid genera).     

Relationships among characiform fishes inferred from analysis of nuclear and mitochondrial gene sequences

Suprafamilial relationships among characiform fishes and implications for the taxonomy and biogeographic history of the Characiformes were investigated by parsimony analysis of four nuclear and two mitochondrial genes across 124 ingroup and 11 outgroup taxa. Simultaneous analysis of 3660 aligned base pairs from the mitochondrial 16S and cytochrome b genes and the nuclear recombination activating gene (RAG2), seven in absentia (sia), forkhead (fkh), and alpha-tropomyosin (trop) gene loci confirmed the non-monophyly of the African and Neotropical assemblages and corroborated many suprafamilial groups proposed previously on the basis of morphological features. The African distichodontids plus citharinids were strongly supported as a monophyletic Citharinoidei that is the sistergroup to all other characiforms, which form a monophyletic Characoidei composed of two large clades. The first represents an assemblage of both African and Neotropical taxa, wherein a monophyletic African Alestidae is sister to a smaller clade comprised of the Neotropical families Ctenolucidae, Lebiasinidae, and the African Hepsetidae, with that assemblage sister to a strictly Neotropical clade comprised of the Crenuchidae and Erythrinidae. The second clade within the Characoidei is strictly Neotropical and includes all other Characiformes grouped into two well supported major clades. The first, corresponding to a traditional definition of the Characidae, is congruent with some groupings previously supported by morphological evidence. The second clade comprises a monophyletic Anostomoidea that is sister to a clade formed by the families Hemiodontidae, Parodontidae, and Serrasalmidae, with that assemblage, in turn, the sistergroup of the Cynodontidae. Serrasalmidae, traditionally regarded as a subfamily of Characidae, was recovered as the sistergroup of (Anostomoidea (Parodontidae+Hemiodontidae)) and the family Cynodontidae was recovered with strong support as the sistergroup to this assemblage. Our results reveal three instances of trans-continental sistergroup relationships and, in light of the fossil evidence, suggest that marine dispersal cannot be ruled out a priori and that a simple model of vicariance does not readily explain the biogeographic history of the characiform fishes.     

Phylogeny of Vestimentifera (Siboglinidae, Annelida) inferred from morphology

Vestimentifera, formerly considered a phylum, are here included in the annelid clade Siboglinidae which also encompasses Frenulata and Sclerolinum . All Siboglinidae inhabit reducing habitats, mostly in the deep sea. Vestimentifera are known from hydrothermal vents and cold seeps. Cladistic analyses of vestimentiferan relationships are performed on three levels: (1) among the vestimentiferan species, (2) among the reconstructed ancestral vestimentiferan and other siboglinids and (3) on the level of the families included in the annelidan clade Sabellida. The monophyly of vestimentiferans is confirmed in all analyses. A group of exclusively vent-inhabiting species forms a derived monophyletic clade. The sister group to the vent clade is the Escarpia complex. Lamellibrachia appears to be paraphyletic. Except for the paraphyly of Lamellibrachia , the reconstructed pattern agrees with the molecular phylogeny based on cytochrome c oxidase subunit I. Ancient ridge systems can be invoked to explain modern day geographical distributions. The Pacific Kula Ridge that spanned the Pacific in an east–west direction during the Early Tertiary, may have been a pathway for the ancestor of the vent clade to reach the eastern Pacific. The biogeography is consistent with the recent divergence of Vestimentifera as inferred from molecular data. The reconstructed phylogeny of the Siboglinidae supports the monophyly of the Frenulata and within those, the Thecanephria and Athecanephria. In contrast to molecular and other morphological analyses, Sclerolinum appears as the sister group to the Frenulata. The family level analysis supports the sister group relationship of the Siboglinidae to a clade formed by Sabellariidae, Sabellidae and Serpulidae. Hypothesized homologies of the vestimentiferan obturaculum and vestimentum to structures in related taxa need further investigation.     

Symbiodinium diversity among host clionaid sponges from Caribbean and Pacific reefs: Evidence of heteroplasmy and putative host-specific symbiont lineages

Among the Porifera, symbiosis with Symbiodinium spp. (i.e., zooxanthellae) is largely restricted to members of the family Clionaidae. We surveyed the diversity of zooxanthellae associated with sponges from the Caribbean and greater Indo-Pacific regions using chloroplast large subunit (cp23S) domain V sequences. We provide the first report of Clade C Symbiodinium harbored by a sponge (Cliona caesia), and the first report of Clade A Symbiodinium from an Indo-Pacific sponge (C. jullieni). Clade A zooxanthellae were also identified in sponges from the Caribbean, which has been reported previously. Sponges that we examined from the Florida Keys all harbored Clade G Symbiodinium as did C. orientalis from the Indo-Pacific, which also supports earlier work with sponges. Two distinct Clade G lineages were identified in our phylogenetic analysis; Symbiodinium extracted from clionaid sponges formed a monophyletic group sister to Symbiodinium found in foraminiferans. Truncated and 'normal' length variants of 23S rDNA sequences were detected simultaneously in all three morphotypes of C. varians providing the first evidence of chloroplast-based heteroplasmy in a sponge. None of the other sponge species examined showed evidence of heteroplasmy. As in previous work, length variation in cp23S domain V sequences was found to correspond in a highly precise manner to finer resolution of phylogenetic topology among Symbiodinium clades. On a global scale, existing data indicate that members of the family Clionaidae that host zooxanthellae can form symbiotic associations with at least four Symbiodinium clades. The majority of sponge hosts appear to harbor only one cladal type of symbiont, but some species can harbor more than one clade of zooxanthellae concurrently. The observed differences in the number of partners harbored by sponges raise important questions about the degree of coevolutionary integration and specificity of these symbioses. Although our sample sizes are small, we propose that one of the Clade G lineages identified in this study is comprised of sponge-specialist zooxanthellae. These zooxanthellae are common in Caribbean sponges, but additional work in other geographic regions is necessary to test this idea. Sponges from the Indo-Pacific region harbor zooxanthellae from Clades A, C, and G, but more sponges from this region should be examined.     

The sequence of the largest subunit of RNA polymerase II is a useful marker for inferring seed plant phylogeny

We used RT-PCR to sequence approximately 3 kb of the gene coding for the largest subunit of RNA polymerase II (rpb1) from nine land plants. Our results show that plant rpb1 genes all have a similar GC-content and that their amino acid sequences evolve at a similar rate in most species we examined, except for the Arabidopsis thaliana and rice sequences which evolve faster. This gene also exists as a single copy in most species and contains enough phylogenetically informative sites to resolve the evolutionary relationships among seed plants. Protein maximum parsimony, as well as neighbor-joining and maximum likelihood analyses of DNA and protein sequences, all generated identical tree topologies with similar strong support values at each node. The angiosperms are a clade comprising Amborella as a sister group to all other angiosperms, followed by Nymphaea, Magnolia, Arabidopsis, and a monocot clade containing maize and rice. The gymnosperms also form a monophyletic clade with Welwitschia and pine grouped together and sister to a Cycas and Zamia clade. These findings concur with recent studies that refute the Anthophyte Hypothesis and place Amborella at the base of the angiosperm tree. These rpb1 sequences also give a more consistent picture of seed plant relationships than similar analyses performed on data sets made of 18S rDNA, atpB, and rbcL sequences from the same species. These sequences therefore show great promise to help further resolve the phylogenetic relationships of seed plants.     

Phylogenetic studies of Ophioglossaceae: evidence from rbcL and trnL-F plastid DNA sequences and morphology

Ophioglossaceae are a putatively ancient lineage of ferns in which the aerial portion of the plant is composed of a single leaf. The simplicity of foliar morphology has limited the number of characters available for constructing classifications and contributed to taxonomic difficulties at nearly every level of classification within the family. Analysis of plastid DNA rbcL sequences from 36 species representing the diversity of Ophioglossaceae supported the monophyly of the family. Intrafamilial relationships were examined using rbcL and trnL-F plastid DNA sequences and morphological data. Individual and combined analyses of the three data sets revealed two main clades within the family, here termed ophioglossoid and botrychioid. In the botrychioid clade, Helminthostachys was sister to a broadly defined Botrychium, within which Botrychium in the narrow sense of some authors and Sceptridium were sister. Botrypus was paraphyletic, with Botrypus virginianus sister to Botrychium plus Sceptridium, and with Botrypus strictus sister to all other botrychioid species except Helminthostachys. In the ophioglossoid clade, Ophioglossum in the narrow sense was sister to Cheiroglossa plus Ophioderma, but relationships within Ophioglossum were not well supported.     

The evolutionary position of Lestoniidae revealed by molecular autapomorphies in the secondary structure of rRNA besides phylogenetic reconstruction (Insecta: Hemiptera: Heteroptera)

Pentatomoidea (stink bugs and their relatives) is the third largest superfamily in Heteroptera, or the true bugs. The phylogenetic relationships among the families within Pentatomoidea remain controversial. The family Lestoniidae is morphologically highly specialized, currently including only two species endemic to Australia. Previous researchers have suggested a close relationship of Lestoniidae to either Plataspidae or Acanthosomatidae, based on morphological characters. In this study, phylogenetic tree reconstruction revealed that Lestoniidae and Acanthosomatidae form a monophyletic clade. In addition, in comparisons of the secondary structures of 18S and 28S rRNAs representing 15 families of Pentatomoidea, four length‐variable regions in 18S and 28S rRNAs that can serve as autapomorphies for the clade Lestoniidae + Acanthosomatidae were recognized. Among them, E in 18S rRNA and D3‐1 and D5‐1 in 28S rRNA are unique in length in Lestoniidae and Acanthosomatidae. Based on the new molecular evidence and morphological evidence published by previous authors, Lestoniidae is suggested to be a highly specialized group derived from a common ancestor with Acanthosomatidae.     

基于13 个内含子的序列探讨鲸目的系统发育关系

本文基于实验室筛选得到的13 对内含子标记,在鲸偶蹄目的15 个物种中进行有效扩增,并重建了这15
个物种的系统发育关系。结果表明,抹香鲸总科(Physeteroidea) 位于齿鲸亚目(Odontoceti)的基部,从而支
持了传统的齿鲸亚目的单系性。在海豚总科(Delphinoidea)内部,贝斯分析结果支持了鼠海豚科(Phocoenidae)
和一角鲸科(Monodontidae)的姐妹群关系,而后再与海豚科(Delphinidae)相聚。系统发育分析同时还
强烈支持了海豚科的四个属(Sousa,Tursiops,Stenella,Delphinus)组成一个单系的“复合体”。另外,我们的分
析结果并不支持瓶鼻海豚属(Tursiops)和原海豚属(Stenella)的单系性。基于松散分子钟的分歧时间估算与以
往文献中的结果没有明显差异。这些研究结果提示,核基因内含子序列有希望解决一些长期存在的鲸类系统发
育问题。     

Molecular phylogenetics of the butterflyfishes (Chaetodontidae): taxonomy and biogeography of a global coral reef fish family

Marine butterflyfishes (10 genera, 114 species) are conspicuously beautiful and abundant animals found on coral reefs worldwide, and are well studied due to their ecological importance and commercial value. Several phylogenies based on morphological and molecular data exist, yet a well-supported molecular phylogeny at the species level for a wide range of taxa remains to be resolved. Here we present a molecular phylogeny of the butterflyfishes, including representatives of all genera (except Parachaetodon) and at least one representative of all commonly cited subgenera of Chaetodon (except Roa sensuBlum, 1988). Genetic data were collected for 71 ingroup and 13 outgroup taxa, using two nuclear and three mitochondrial genes that total 3332 nucleotides. Bayesian inference, parsimony, and maximum likelihood methods produced a well-supported phylogeny with strong support for a monophyletic Chaetodontidae. The Chaetodon subgenera Exornator and Chaetodon were found to be polyphyletic, and the genus Amphichaetodon was not the basal sister group to the rest of the family as had been previously proposed. Molecular phylogenetic analysis of data from 5 genes resolved some clades in agreement with previous phylogenetic studies, however the topology of relationships among major butterflyfish groups differed significantly from previous hypotheses. The analysis recovered a clade containing Amphichaetodon, Coradion, Chelmonops, Chelmon, Forcipiger, Hemitaurichthys, Johnrandallia, and Heniochus. Prognathodes was resolved as the sister to all Chaetodon, as in previous hypotheses, although the topology of subgeneric clades differed significantly from hypotheses based on morphology. We use the species-level phylogeny for the butterflyfishes to resolve long-standing questions regarding the use of subgenera in Chaetodon, to reconstruct molecular rates and estimated dates of diversification of major butterflyfish clades, and to examine global biogeographic patterns.     

GENETIC VARIATION OF KOGIA SPP. WITH PRELIMINARY EVIDENCE FOR TWO SPECIES OF KOGIA SIMA

Concordance between mitochondrial DNA (mtDNA) markers and morphologically based species identifications was examined for the two currently recognized Kogia species. We sequenced 406 base pairs of the control region and 398 base pairs of the cytochrome b gene from 108 Kogia breviceps and 47 K. sima samples. As expecred, the two sister species were reciprocally monophyletic to each other in phylogenetic reconstructions, but within K. sima , we unexpectedly observed another reciprocally monophyletic relationship. The two K. sima clades resolved were phylogeographically concordant with all of the haplotypes in one clade observed solely among specimens sampled from the Atlantic Ocean and with those in the other clade observed solely among specimens sampled from the Indo-Pacific Ocean. These apparently allopatric clades were observed in all phylogenetic reconstructions using the maximum parsimony, maximum likelihood, and neighborjoining algorithms, with the mtDNA gene sequences analyzed separately and combined. The nucleotide diversity for the combined gene sequence haplotypes of the two K. sima clades resolved in our analyses was 0.58% and 1.03% for the Atlantic and Indo-Pacific, respectively, whereas for the two recognized sister species, nucleotide diversity was 1.65% and 4.02% for K. breviceps and K. sima , respectively. The combined gene sequence haplotypes have accumulated 44 fixed base pair differences between the two K. sima clades compared to 20 fixed base pair differences between the two recognized sister species. Although our results are consistent with species-level differences between the two K. sima clades, recognition of a third Kogia species awaits supporting evidence that these two apparently allopatric clades represent reproductively isolated groups of animals.