The Complete Mitochondrial Genome of Aix galericulata and Tadorna ferruginea: Bearings on Their Phylogenetic Position in the Anseriformes

Aix galericulata and Tadorna ferruginea are two Anatidae species representing different taxonomic groups of Anseriformes. We used a PCR-based method to determine the complete mtDNAs of both species, and estimated phylogenetic trees based on the complete mtDNA alignment of these and 14 other Anseriforme species, to clarify Anseriform phylogenetics. Phylogenetic trees were also estimated using a multiple sequence alignment of three mitochondrial genes (Cyt b, ND2, and COI) from 68 typical species in GenBank, to further clarify the phylogenetic relationships of several groups among the Anseriformes. The new mtDNAs are circular molecules, 16,651 bp (Aix galericulata) and 16,639 bp (Tadorna ferruginea) in length, containing the 37 typical genes, with an identical gene order and arrangement as those of other Anseriformes. Comparing the protein-coding genes among the mtDNAs of 16 Anseriforme species, ATG is generally the start codon, TAA is the most frequent stop codon, one of three, TAA, TAG, and T-, commonly observed. All tRNAs could be folded into canonical cloverleaf secondary structures except for tRNASer (AGY) and tRNALeu (CUN), which are missing the "DHU" arm.Phylogenetic relationships demonstrate that Aix galericula and Tadorna ferruginea are in the same group, the Tadorninae lineage, based on our analyses of complete mtDNAs and combined gene data. Molecular phylogenetic analysis suggests the 68 species of Anseriform birds be divided into three families: Anhimidae, Anatidae, and Anseranatidae. The results suggest Anatidae birds be divided into five subfamilies: Anatinae, Tadorninae, Anserinae, Oxyurinae, and Dendrocygninae. Oxyurinae and Dendrocygninae should not belong to Anserinae, but rather represent independent subfamilies. The Anatinae includes species from the tribes Mergini, Somaterini, Anatini, and Aythyini. The Anserinae includes species from the tribes Anserini and Cygnini.     

The complete mitochondrial genomes of the whistling duck (<Emphasis Type="Italic">Dendrocygna javanica</Emphasis>) and black swan (<Emphasis Type="Italic">Cygnus atratus</Emphasis>): dating evolutionary divergence in Galloanserae

Galloanserae is an ancient and diverse avian group, for which comprehensive molecular evidence relevant to phylogenetic analysis in the context of molecular chronology is lacking. In this study, we present two additional mitochondrial genome sequences of Galloanserae (the whistling duck, Dendrocygna javanica, and the black swan, Cygnus atratus) to broaden the scope of molecular phylogenetic reconstruction. The lengths of the whistling duck’s and black swan’s mitochondrial genomes are 16,753 and 16,748 bases, respectively. Phylogenetic analyses suggest that Dendrocygna is more likely to be in a basal position of the branch consisting of Anatinae and Anserinae, an affiliation that does not conform to its traditional classification. Bayesian approaches were employed to provide a rough timescale for Galloanserae evolution. In general, a narrow range of 95% confidence intervals gave younger estimates than those based on limited genes and estimated that at least two lineages originated before the Coniacian epoch around 90 MYA, well before the Cretaceous-Tertiary boundary. In addition, these results, which were compatible with estimates from fossil evidence, also imply that the origin of numerous genera in Anseriformes took place in the late Oligocene to early Miocene. Taken together, the results presented here provide a working framework for future research on Galloanserae evolution, and they underline the utility of whole mitochondrial genome sequences for the resolution of deep divergence.     

Phylogeny of swallows (Aves: Hirundinidae) estimated from nuclear and mitochondrial DNA sequences

The phylogeny of swallows was reconstructed by comparing segments of three genes, nuclear beta-fibrinogen intron 7 (betafib7), mitochondrial cytochrome b (cytb), and mitochondrial ND2, in a variety of combinations using maximum likelihood and Bayesian methods. betafib7 was sequenced for 47 species, cytb for 74 species, and ND2 for 61 species to yield comparisons among 75 of the 84 currently recognized swallow species. The family Hirundinidae was confirmed to consist of two clades, Pseudochelidoninae (river martins) and Hirundininae (typical swallows). The Hirundininae is further divided into mud nesters (Hirundo sensu lato), core martins (Phedina, Riparia, and New World endemic genera), and basal relicts (Psalidoprocne, Cheramoeca, and Pseudhirundo). We did not resolve the hierarchy among these three hirundinine groups, but discovered many relationships within them. Mud-nesting genera have the following relationships: (Hirundo sensu stricto, Ptyonoprogne), (Delichon, (Petrochelidon, Cecropis)). Core martins have the following topology: (Phedina, Riparia cincta), (Riparia sensu stricto, Tachycineta, ((Stelgidopteryx, Progne), (Neotropical endemic genera))). Interspecific relationships among the Neotropical endemics were resolved completely; Atticora and Notiochelidon are paraphyletic, and all Neotropical endemics probably should be lumped into one or two genera. The final group of hirundinines, the basal relicts, consists of a sister pair, the Australian Cheramoeca and African Pseudhirundo. The African saw-wings (Psalidoprocne) are their likely sister group.     

Use of mitogenomic information in teleostean molecular phylogenetics: a tree-based exploration under the maximum-parsimony optimality criterion

We explored the phylogenetic utility and limits of the individual and concatenated mitochondrial genes for reconstructing the higher-level relationships of teleosts, using the complete (or nearly complete) mitochondrial DNA sequences of eight teleosts (including three newly determined sequences), whose relative phylogenetic positions were noncontroversial. Maximum-parsimony analyses of the nucleotide and amino acid sequences of 13 protein-coding genes from the above eight teleosts, plus two outgroups (bichir and shark), indicated that all of the individual protein-coding genes, with the exception of ND5, failed to recover the expected phylogeny, although unambiguously aligned sequences from 22 concatenated transfer RNA (tRNA) genes (stem regions only) recovered the expected phylogeny successfully with moderate statistical support. The phylogenetic performance of the 13 protein-coding genes in recovering the expected phylogeny was roughly classified into five groups, viz. very good (ND5, ND4, COIII, COI), good (COII, cyt b), medium (ND3, ND2), poor (ND1, ATPase 6), and very poor (ND4L, ND6, ATPase 8). Although the universality of this observation was unclear, analysis of successive concatenation of the 13 protein-coding genes in the same ranking order revealed that the combined data sets comprising nucleotide sequences from the several top-ranked protein-coding genes (no 3rd codon positions) plus the 22 concatenated tRNA genes (stem regions only) best recovered the expected phylogeny, with all internal branches being supported by bootstrap values >90%. We conclude that judicious choice of mitochondrial genes and appropriate data weighting, in conjunction with purposeful taxonomic sampling, are prerequisites for resolving higher-level relationships in teleosts under the maximum-parsimony optimality criterion.     

A recent chicken repeat 1 retrotransposition confirms the Coscoroba-Cape Barren goose clade

Chicken repeat 1 (CR1) is a member of the non-long terminal repeat class of retrotransposons. We have isolated a truncated CR1 element within the third intron of the lactate dehydrogenase B gene of the coscoroba and the Cape Barren goose (Anseriformes; Coscoroba coscoroba, Cereopsis novaehollandiae). Because the element was absent in orthologous loci within mallard (Anas platyrhynchos), snow goose (Anser caerulescens), and tundra swan (Cygnus columbianus), it provides strong support to the recent novel proposal by Donne-Goussé et al. [Donne-Goussé, C., Laudet, V., H?nni, C., 2002. A molecular phylogeny of anseriformes based on mitochondrial DNA analysis. Mol. Phylogenet. Evol. 23, 339-356] that Cape Barren goose is the sister taxon to coscoroba. The time of insertion was approximately 10.5 Mya or less estimated from mitochondrial DNA sequence information. Because this is a recent event, the DNA sequence of this CR1 should be close to that existing at the time of its insertion. This is reflected by the consistency of several structural features expected in a new CR1 copy such as the unaltered flanking target site duplication and inverted repeats that lie 22 bp apart near the 3' end of the element. Hybridization experiments show that numerous copies of sequences closely related to the coscoroba CR1 element are dispersed throughout the genomes of tested Anseriformes, but none were detected in representatives of Galliformes and Struthioniformes.     

A phylogeny of the megapodes (Aves: Megapodiidae) based on nuclear and mitochondrial DNA sequences

DNA sequences from the first intron of the nuclear gene rhodopsin (RDP1) and from the mitochondrial gene ND2 were used to construct a phylogeny of the avian family Megapodiidae. RDP1 sequences evolved about six times more slowly than ND2 and showed less homoplasy, substitution bias, and rate heterogeneity across sites. Analysis of RDP1 produced a phylogeny that was well resolved at the genus level, but RDP1 did not evolve rapidly enough for intrageneric comparisons. The ND2 phylogeny resolved intrageneric relationships and was congruent with the RDP1 phylogeny except for a single node: this node was the only aspect of tree topology sensitive to weighting in parsimony analyses. Despite differences in sequence evolution, RDP1 and ND2 contained congruent phylogenetic signal and were combined to produce a phylogeny that reflects the resolving power of both genes. This phylogeny shows an early split within the megapodes, leading to two major clades: (1) Macrocephalon and the mound-building genera Talegalla, Leipoa, Aepypodius, and Alectura, and (2) Eulipoa and Megapodius. It differs significantly from previous hypotheses based on morphology but is consistent with affiliations suggested by a recent study of parasitic chewing lice.     

Assessing phylogenetic resolution among mitochondrial, nuclear, and morphological datasets in Nothonotus darters (Teleostei: Percidae)

External morphological characters are the basis of our understanding of diversity and species relationships in many darter clades. The past decade has seen the publication of many studies utilizing mtDNA sequence data to investigate darter phylogenetics, but only recently have nuclear genes been used to investigate darter relationships. Despite a long tradition of use in darter systematics few studies have examined the phylogenetic utility of external morphological characters in estimating relationships among species in darter clades. We present DNA sequence data from the mitochondrial cytochrome b (cytb) gene, the nuclear encoded S7 intron 1, and discretely coded external morphological characters for all 20 species in the darter clade Nothonotus. Bayesian phylogenetic analyses result in phylogenies that are in broad agreement with previous studies. The cytb gene tree is well resolved, while the nuclear S7 gene tree lacks phylogenetic resolution, node support, and is characterized by a lack of reciprocal monophyly for many of the Nothonotus species. The phylogenies resulting from analysis of the morphological dataset lack resolution, but nodes present are found in the cytb and S7 gene trees. The highest resolution and node support is found in the Bayesian combined data phylogeny. Based on our results we propose continued exploration of the phylogenetic utility of external morphological characters in other darter clades. Given the extensive lack of reciprocal monophyly of species observed in the S7 gene tree we predict that nuclear gene sequences may have limited utility in intraspecific phylogeographic studies of Nothonotus darters.     

Data set incongruence and correlated character evolution: an example of functional convergence in the hind-limbs of stifftail diving ducks

The unwitting inclusion of convergent characters in phylogenetic estimates poses a serious problem for efforts to recover phylogeny. Convergence is not inscrutable, however, particularly when one group of characters tracks phylogeny and another set tracks adaptive history. In such cases, convergent characters may be correlated with one or a few functional anatomical units and readily identifiable by using comparative methods. Stifftail ducks (Oxyurinae) offer one such opportunity to study correlated character evolution and function in the context of phylogenetic reconstruction. Morphological analyses place stifftail ducks as part of a large clade of diving ducks that includes the sea ducks (Mergini), Hymenolaimus, Merganetta, and Tachyeres, and possibly the pochards (Aythyini). Molecular analyses, on the other hand, place stifftails far from other diving ducks and suggest, moreover, that stifftails are polyphyletic. Mitochondrial cytochrome b gene sequences of eight stifftail species traditionally supposed to form a clade were compared with each other and with sequences from 50 other anseriform and galliform species. Stifftail ducks are not the sister group of sea ducks but lie outside the typical ducks (Anatinae). Of the four traditional stifftail genera, monophyly of Oxyura and its sister group relationship with Nomonyx are strongly supported. Heteronetta probably is the sister group of that clade, but support is weak. Biziura is not a true stifftail. Within Oxyura, Old World species (O. australis, O. leucocephala, O. maccoa) appear to form a clade, with New World species (O. jamaicensis, O. vittata) branching basally. Incongruence between molecules and morphology is interpreted to be the result of adaptive specialization and functional convergence in the hind limbs of Biziura and true stifftails. When morphological characters are divided into classes, only hind-limb characters are significantly in conflict with the molecular tree. Likewise, null models of synonymous and nonsynonymous substitution based on patterns of codon-degeneracy and chemical dissimilarity indicate that the nucleotide and amino acid changes postulated by the molecular tree are more plausible than those postulated by the morphological tree. These findings teach general lessons about the utility of highly adaptive characters (in particular those related to foraging ecology) and underscore the problems that convergence can pose for attempts to recover phylogeny. They also demonstrate how the concept of natural data partitions and simple models of evolution (e.g., parsimony, likelihood, neutrality) can be used to test the accuracy of independent phylogenetic estimates and provide arguments in favor of one tree topology over another.     

A mitochondrial phylogeny of the rainforest skink genus Saproscincus, Wells and Wellington (1984)

The phylogenetic relationships and historical biogeography of 10 currently described rainforest skinks in the genus Saproscincus were investigated using mitochondrial protein-coding ND4 and ribosomal RNA 16S genes. A robust phylogeny is inferred using both maximum likelihood and Bayesian analysis, with all inter-specific nodes strongly supported when datasets are combined. The phylogeny supports the recognition of two major lineages (northern and southern), each of which comprises two divergent clades. Both northern and southern lineages have comparably divergent representatives in mid-east Queensland (MEQ), providing further molecular evidence for the importance of two major biogeographic breaks, the St. Lawrence gap and Burdekin gap separating MEQ from southern and northern counterparts respectively. Vicariance associated with the fragmentation and contraction of temperate rainforest during the mid-late Miocene epoch underpins the deep divergence between morphologically conservative lineages in at least three instances. In contrast, one species, Saproscincus oriarus, shows very low sequence divergence but distinct morphological and ecological differentiation from its allopatric sister clade within Saproscincus mustelinus. These results suggest that while vicariance has played a prominent role in diversification and historical biogeography of Saproscincus, divergent selection may also be important.     

Complete mitochondrial genome sequence of the Korean water deer Hydropotes inermis argyropus (Cervidae, Capreolinae)

The complete mitochondrial genome sequence of Hydropotes inermis argyropus consists of 13 protein-coding, 22 tRNA, and two rRNA genes, and 1 control region (CR). Three overlaps among the 13 protein-coding genes were found: ATP8/ATP6, ND4L/ND4, and ND5/ND6. The CR was located between the tRNA-Pro and tRNA-Phe genes and is 928 bp in length. The typical conserved domains, such as TAS and CSB, were identified in the CR.     

Phylogeny and evolution of the Drosophila nasuta subgroup based on mitochondrial ND4 and ND4L gene sequences

The sequences of the mitochondrial ND4 gene (1339 bp) and the ND4L gene (290 bp) were determined for all the 14 extant taxa of the Drosophila nasuta subgroup. The average A + T content of ND4 genes is 76.5% and that of ND4L genes is 83.5%. A total of 114 variable sites were scored. The ND4 gene sequence divergence ranged from 0 to 5.4% within the subgroup. The substitution rate of the ND4 gene is about 1.25% per million years. The base substitution of the genes is strongly transition biased. Neighbor-joining and parsimony were used to construct a phylogeny based on the resultant sequence data set. According to these trees, five distinct mtDNA clades can be identified. D. niveifrons represents the most diverged lineage. D. sulfurigaster bilimbata and D. kepulauana form two independent lineages. The other two clades are the kohkoa complex and the albomicans complex. The kohkoa complex consists of D. sulfurigaster sulfurigaster, D. pulaua, D. kohkoa, and Taxon-F. The albomicans complex can be divided into two groups: D. nasuta, D. sulfurigaster neonasuta, D. sulfurigaster albostrigata, and D. albomicans from Chiangmai form one group; and D. pallidifrons, Taxon-I, Taxon-J, and D. albomicans from China form the other group. High genetic differentiation was found among D. albomicans populations. Based on our phylogenetic results, we hypothesize that D. niveifrons diverged first from the D. nasuta subgroup in Papua New Guinea about 3.5 Mya. The ancestral population spread to the north and when it reached Borneo, it diversified sequentially into the kohkoa complex, D. s. bilimbata, and D. kepulauana. About 1 Mya, another radiation occurred when the ancestral populations reached the Indo-China Peninsula, forming the albomicans complex. Discrepancy between morphological groupings and phylogenetic results suggests that the male morphological traits may not be orthologous.     

Evolution of mitochondrial and ribosomal gene sequences in anophelinae (Diptera: Culicidae): implications for phylogeny reconstruction

In this study, two mitochondrial genes, cyt b and ND5, and the D2 expansion segment of the 28S nuclear ribosomal gene were used to reconstruct a phylogeny of the mosquito subfamily Anophelinae. The ingroup consisted of all three genera of Anophelinae and five of six subgenera of Anopheles. Six genera of Culicinae were used as the outgroup. Extreme conservation at the protein level coupled with rapid saturation of synonymous positions probably accounted for the lack of meaningful phylogenetic signal in the cyt b gene. In contrast, abundant variation at all codon positions of the ND5 gene allowed recovery of the basal and most of the recent relationships. Phylogenetic analysis of D2 produced results consistent with those of ND5. Combined analysis indicated well-supported monophyletic Anophelinae (with Chagasia basal), Anopheles + Bironella, and subgeneric clades within the genus Anopheles. Moreover, subgenera Nyssorhynchus and Kerteszia were supported as a monophyletic lineage. The Kishino-Hasegawa test could not reject the monophyly of Anopheles, whereas the recently proposed hypothesis of close affinity of Bironella to the subgenus Anopheles was rejected by the analyses of ND5 and combined data sets. The lack of resolution of Bironella and Anopheles clades, or basal relationships among subgeneric clades within Anopheles, suggests their rapid diversification. Recovery of relationships consistent with morphology and previous molecular studies provides evidence of substantial phylogenetic signal in D2 and ND5 genes at levels of divergence from closely related species to subfamily in mosquitoes.     

A molecular phylogeny of tortoises (Testudines: Testudinidae) based on mitochondrial and nuclear genes

Although tortoises of the family Testudinidae represent a familiar and widely distributed group of turtles, their phylogenetic relationships have remained contentious. In this study, we included 32 testudinid species (all genera and subgenera, and all species of Geochelone, representing 65% of the total familial species diversity), and both mitochondrial (12S rRNA, 16S rRNA, and cytb) and nuclear (Cmos and Rag2) DNA data with a total of 3387 aligned characters. Using diverse phylogenetic methods (Maximum Parsimony, Maximum Likelihood, and Bayesian Analysis) congruent support is found for a well-resolved phylogeny. The most basal testudinid lineage includes a novel sister relationship between Asian Manouria and North American Gopherus. In addition, this phylogeny supports two other major testudinid clades: Indotestudo+Malacochersus+Testudo; and a diverse clade including Pyxis, Aldabrachelys, Homopus, Chersina, Psammobates, Kinixys, and Geochelone. However, we find Geochelone rampantly polyphyletic, with species distributed in at least four independent clades. Biogeographic analysis based on this phylogeny is consistent with an Asian origin for the family (as supported by the fossil record), but rejects the long-standing hypothesis of South American tortoises originating in North America. By contrast, and of special significance, our results support Africa as the ancestral continental area for all testudinids except Manouria and Gopherus. Based on our systematic findings, we also propose modifications concerning Testudinidae taxonomy.     

Phylogeny of the Gadidae (sensu Svetovidov, 1948) based on their morphology and two mitochondrial genes

Although Codfishes are probably one of the most studied groups of all teleost fishes worldwide owing to their great importance to fisheries, their phylogeny and classification are still far from being firmly established. In this study, we present phylogenetic relationships of 19 out of 22 genera traditionally included in the Gadidae based on the analysis of entire cytochrome b and partial cytochrome oxidase I genes (1530 bp). Maximum Parsimony, Maximum Likelihood, and Bayesian analyses all recovered five main clades that correspond to traditionally recognized groupings within Gadoids. The same clades were recovered with MP analysis based on 30 morphological characters (collected from the literature). Given these findings, we propose a revised provisional classification of Gadoids: one suborder Gadoidei containing two families, the Merlucciidae (1 genus) and the Gadidae (21 genera) distributed into four subfamilies: the Gadinae (12 genera), the Lotinae (3 genera), the Gaidropsarinae (3 genera), and the Phycinae (3 genera). Lastly, nuclear inserts of mitochondrial DNA (Numts) were identified in two species, i.e., Gadiculus argenteus and Melanogrammus aeglefinus.     

Nuclear and mtDNA-based phylogeny of southern African sand lizards, Pedioplanis (Sauria: Lacertidae)

The diversity of lacertid lizards in Africa is highest in the southern African subcontinent, where over two-thirds of the species are endemic. With eleven currently recognized species, Pedioplanis is the most diverse among the southern African genera. In this study we use 2200 nucleotide positions derived from two mitochondrial markers (ND2 and 16S rRNA) and one nuclear gene (RAG-1) to (i) assess the phylogeny of Pedioplanis and (ii) estimate divergence time among lineages using the relaxed molecular clock method. Individual analyses of each gene separately supported different nodes in the phylogeny and the combined analysis yielded more well supported relationships. We present the first, well-resolved gene tree for the genus Pedioplanis and this is largely congruent with a phylogeny derived from morphology. Contrary to previous suggestions Heliobolus/Nucras are sister to Pedioplanis. The genus Pedioplanis is monophyletic, with P. burchelli/P. laticeps forming a clade that is sister to all the remaining congeners. Two distinct geographic lineages can be identified within the widespread P. namaquensis; one occurs in Namibia, while the other occurs in South Africa. The P. undata species complex is monophyletic, but one of its constituent species, P. inornata, is paraphyletic. Relationships among the subspecies of P. lineoocellata are much more complex than previously documented. An isolated population previously assigned to P. l. pulchella is paraphyletic and sister to the three named subspecies. The phylogeny identifies two biogeographical clades that probably diverged during the mid-Miocene, after the development of the Benguella Current. This probably led to habitat changes associated with climate and, in conjunction with physical barriers (Great Escarpment), contributed towards speciation within the genus Pedioplanis.     

Phylogeography and introgressive hybridization of the ground beetle Carabus yamato in Japan based on mitochondrial gene sequences

To study the phylogeography of the ground beetle Carabus yamato in Japan, we compared 1,020-bp sequences of the mitochondrial NADH dehydrogenase subunit 5 (ND5) gene from 373 specimens from 37 localities with those of three parapatric species (C. albrechti, C. kimurai, and C. japonicus) that might share mitochondrial lineages with C. yamato through introgressive hybridization. We found 81 haplotypes from C. yamato. Of these, 17 haplotypes were considered to be of an introgressed lineage from C. albrechti, based on the phylogeny and geographic distribution. In addition, one haplotype of C. kimurai was likely an introgressant from C. yamato. Putative introgression events among the four species were restricted to these two directional cases. We analyzed the phylogeography of C. yamato using nested clade phylogeographical analysis and population genetic parameters. The mitochondrial lineages of C. yamato were estimated to have diverged no more than approximately 1.12 million years ago, implying that the estimated historical events occurred after the Early Pleistocene. Carabus yamato was inferred to have experienced a contraction of its distribution range, followed by recent range expansion. Populations in the western and eastern regions, segregated by Ise Bay and the Nobi and Okazaki Plains, diverged in the mitochondrial clades. The northern and most western populations possessed one clade only (except an introgressed lineage), whereas eastern and some southwestern populations possessed several diverged clades, which were considered to be ancestral; these populations may have been associated with refugia during glacial periods.     

Phylogenetic inference of calyptrates,with the first mitogenomes for Gasterophilinae (Diptera: Oestridae) and Paramacronychiinae (Diptera: Sarcophagidae)

The complete mitogenome of the horse stomach bot fly Gasterophilus pecorum (Fabricius) and a near-complete mitogenome of Wohlfahrt''s wound myiasis fly Wohlfahrtia magnifica (Schiner) were sequenced. The mitogenomes contain the typical 37 mitogenes found in metazoans, organized in the same order and orientation as in other cyclorrhaphan Diptera. Phylogenetic analyses of mitogenomes from 38 calyptrate taxa with and without two non-calyptrate outgroups were performed using Bayesian Inference and Maximum Likelihood. Three sub-analyses were performed on the concatenated data: (1) not partitioned; (2) partitioned by gene; (3) 3rd codon positions of protein-coding genes omitted. We estimated the contribution of each of the mitochondrial genes for phylogenetic analysis, as well as the effect of some popular methodologies on calyptrate phylogeny reconstruction. In the favoured trees, the Oestroidea are nested within the muscoid grade. Relationships at the family level within Oestroidea are (remaining Calliphoridae (Sarcophagidae (Oestridae, Pollenia + Tachinidae))). Our mito-phylogenetic reconstruction of the Calyptratae presents the most extensive taxon coverage so far, and the risk of long-branch attraction is reduced by an appropriate selection of outgroups. We find that in the Calyptratae the ND2, ND5, ND1, COIII, and COI genes are more phylogenetically informative compared with other mitochondrial protein-coding genes. Our study provides evidence that data partitioning and the inclusion of conserved tRNA genes have little influence on calyptrate phylogeny reconstruction, and that the 3rd codon positions of protein-coding genes are not saturated and therefore should be included.     

Molecular phylogeny of grouse: individual and combined performance of W-linked,autosomal, and mitochondrial loci

The phylogeny of grouse (Aves: Tetraoninae) was reconstructed using four noncoding loci: two were W-linked, one was autosomal, and one was the mitochondrial control region (CR). The rapidly evolving CR provided resolution throughout the tree, whereas the slowly evolving nuclear loci failed to resolve deeper nodes. The tree based on all four loci combined was almost identical to the CR tree and did not improve resolution or bootstrap support. The stemminess and imbalance of the trees were good determinants of the quality of the phylogenetic signal. The skewness of the tree score distribution (g(1)) behaved contrary to prediction; loci that had a more symmetric tree score distribution produced trees that had greater stemminess and balance. The quality of the phylogenetic signal was related to the evolutionary rate. Four clades of grouse were discovered. Two of these clades corresponded to currently recognized genera Bonasa and Lagopus. Bonasa was the sister to other grouse and Lagopus was the sister to the other two non-Bonasa clades. The third clade included Falcipennis, Tetrao, and Lyrurus. The fourth clade included the genera Centrocercus, Dendragapus, and Tympanuchus. The data support recognition of Falcipennis canadensis franklinii and Dendragapus obscurus fuliginosus as species.     

A molecular phylogenetic analysis of the Octocorallia (Cnidaria: Anthozoa) based on mitochondrial protein-coding sequences

Despite their abundance and ecological importance in a wide variety of shallow and deep water marine communities, octocorals (soft corals, sea fans, and sea pens) are a group whose taxonomy and phylogenetic relationships remain poorly known and little studied. The group is currently divided into three orders (O: Alcyonacea, Pennatulacea, and Helioporacea); the large O. Alcyonacea (soft corals and sea fans) is further subdivided into six sub-ordinal groups on the basis of skeletal composition and colony growth form. We used 1429bp of two mitochondrial protein-coding genes, ND2 and msh1, to construct a phylogeny for 103 octocoral genera representing 28 families. In agreement with a previous 18S rDNA phylogeny, our results support a division of Octocorallia into two major clades plus a third, minor clade. We found one large clade (Holaxonia-Alcyoniina) comprising the sea fan sub-order Holaxonia and the majority of soft corals, and a second clade (Calcaxonia-Pennatulacea) comprising sea pens (O. Pennatulacea) and the sea fan sub-order Calcaxonia. Taxa belonging to the sea fan group Scleraxonia and the soft coral family Alcyoniidae were divided among the Holaxonia-Alcyoniina clade and a third, small clade (Anthomastus-Corallium) whose relationship to the two major clades was unresolved. In contrast to the previous studies, we found sea pens to be monophyletic but nested within Calcaxonia; our analyses support the sea fan family Ellisellidae as the sister taxon to the sea pens. We are unable to reject the hypothesis that the calcaxonian and holaxonian skeletal axes each arose once and suggest that the skeletal axis of sea pens is derived from that of Calcaxonia. Topology tests rejected the monophyly of sub-ordinal groups Alcyoniina, Scleraxonia, and Stolonifera, as well as 9 of 14 families for which we sampled multiple genera. The much broader taxon sampling and better phylogenetic resolution afforded by our study relative to the previous efforts greatly clarify the relationships among families and sub-ordinal groups within each of the major clades. The failure of these mitochondrial genes as well as previous 18S rDNA studies to resolve many of the deeper nodes within the tree (including its root) suggest that octocorals underwent a rapid radiation and that large amounts of sequence data will be required in order to resolve the basal relationships within the clade.