Correlation of functional domains and rates of nucleotide substitution in cytochrome b

A Molecular Evaluation of the North American “Grassland” Sparrow Clade

Because they share several morphological and ecological characters, the North American sparrow (Emberizidae) genera Ammodramus, Passerculus, and Xenospiza have historically been considered members of a well-defined “grassland” sparrow assemblage. Relationships among the 11 members of this group have been the subject of much taxonomic debate, yet no comprehensive molecular assessment of relationships has been done. We investigated these relationships using mitochondrial DNA sequence data that included complete cytochrome-b and ND2 genes. Phylogenetic reconstructions derived via parsimony, likelihood, and Bayesian methods were congruent. The grassland sparrows, as presently configured, are polyphyletic. Pooecetes gramineus, Amphispiza belli (but not A. quinquestriata and A. bilineata), Oriturus superciliosus, and all three species of Melospiza are included in a reconfigured clade, whereas the traditional forms of Ammodramus savannarum, humeralis, and aurifons are placed well outside of these. Within the clade of interest, Ammodramus remains polyphyletic, with leconteii, maritimus, nelsoni, and caudacutus forming a well-resolved clade apart from henslowii and bairdii. The latter are in another strongly supported clade that also includes Passerculus and a Xenospiza-Melozpiza sister pairing. Pooecetes, Amphispiza (belli), and Oriturus represent early lineages in this clade that today have no close living relatives. The polyphyly of the genus Ammodramus is likely the result of morphological convergence attributable to similar adaptive responses to the occupation of similar habitats. In general, the morphological and ecological factors that have defined the grassland sparrows are poor indicators of relatedness. Taxonomic revisions are suggested.

Evaluación Molecular del Clado de Gorriones de Pastizales de Norte América

Phylogeny of the genus Aphis Linnaeus, 1758 (Homoptera: Aphididae) inferred from mitochondrial DNA sequences

Aphis is the largest aphid genus in the world and contains several of the most injurious aphid pests. It is also the most reluctant aphid genus to any comprehensive taxonomic treatment: while most species are easily classified into "species groups" that form well defined entities, numerous species within these groups are difficult to tell apart morphologically and identification keys remain ambiguous and mostly rely on host plant affiliation. In this paper, we used partial sequences of COI/COII and CytB genes to reconstruct the first phylogeny of Aphis and discuss the present systematics. The monophyly of the subgenus Bursaphis and of the tree major species groups, Black aphid, Black backed aphid and frangulae-like species was recovered by all phylogenetic analyses. However our data suggested that the nominal subgenus was not monophyletic. Relationships between major species groups were often ambiguous but "Black" and "Black backed" species groups appeared as sister clades. The most striking result of this study was that our molecular data met the same limits as the morphological characters used in classifications: mitochondrial DNA did not allow the differentiation of species that are difficult to identify. Further, interspecies relationships within groups of species for which taxonomic treatment is difficult stayed unresolved. This suggests that species delineation in the genus Aphis is often ambiguous and that diversification might have been a rapid process.

Phylogenetic relationships within parrots (Psittacidae) inferred from mitochondrial cytochrome-b gene sequences

Blood and tissue samples of 40 individuals including 27 parrot species (15 genera; 3 subfamilies) were collected in Indonesia. Their phylogenetic relationships were inferred from 907 bp of the mitochondrial cytochrome-b gene, using the maximum-parsimony method, the maximum-likelihood method and the neighbor-joining method with Kimura two-parameter distance. The phylogenetic analysis revealed that (1) cockatoos (subfamily Cacatuinae) form a monophyletic sister group to other parrot groups; (2) within the genus Cacatua, C. goffini and C. sanguinea form a sister group to a clade containing other congeners; (3) subfamily Psittacinae emerged as paraphyletic, consisting of three clades, with a clade of Psittaculirostris grouping with subfamily Loriinae rather than with other Psittacinae; (4) lories and lorikeets (subfamily Loriinae) emerged as monophyletic, with Charmosyna placentis a basal sister group to other Loriinae, which comprised the subclades Lorius; Trichoglossus+Eos; and Chalcopsitta+ Pseudeos.

Molecular phylogeny of silk-producing insects based on 16S ribosomal RNA and cytochrome oxidase subunit I genes

We have examined the molecular-phylogenetic relationships between nonmulberry and mulberry silkworm species that belong to the families Saturniidae, Bombycidae and Lasiocampidae using 16S ribosomal RNA (16S rRNA) and cytochrome oxidase subunit I (coxI) gene sequences. Aligned nucleotide sequences of 16S rRNA and coxI from 14 silk-producing species were used for construction of phylogenetic trees by maximum likelihood and maximum parsimony methods. The tree topology on the basis of 16S rRNA supports monophyly for members of Saturniidae and Bombycidae. Weighted parsimony analysis weighted towards transversions relative to transitions (ts, tv4) for coxI resulted in more robust bootstrap support over unweighted parsimony and favours the 16S rRNA tree topology. Combined analysis reflected clear biogeographic pattern, and agrees with morphological and cytological data.

Multiple data sets, high homoplasy, and the phylogeny of softshell turtles (Testudines: Trionychidae)

We present a phylogenetic hypothesis and novel, rank-free classification for all extant species of softshell turtles (Testudines:Trionychidae). Our data set included DNA sequence data from two mitochondrial protein-coding genes and a approximately 1-kb nuclear intron for 23 of 26 recognized species, and 59 previously published morphological characters for a complimentary set of 24 species. The combined data set provided complete taxonomic coverage for this globally distributed clade of turtles, with incomplete data for a few taxa. Although our taxonomic sampling is complete, most of the modern taxa are representatives of old and very divergent lineages. Thus, due to biological realities, our sampling consists of one or a few representatives of several ancient lineages across a relatively deep phylogenetic tree. Our analyses of the combined data set converge on a set of well-supported relationships, which is in accord with many aspects of traditional softshell systematics including the monophyly of the Cyclanorbinae and Trionychinae. However, our results conflict with other aspects of current taxonomy and indicate that most of the currently recognized tribes are not monophyletic. We use this strong estimate of the phylogeny of softshell turtles for two purposes: (1) as the basis for a novel rank-free classification, and (2) to retrospectively examine strategies for analyzing highly homoplasious mtDNA data in deep phylogenetic problems where increased taxon sampling is not an option. Weeded and weighted parsimony, and model-based techniques, generally improved the phylogenetic performance of highly homoplasious mtDNA sequences, but no single strategy completely mitigated the problems of associated with these highly homoplasious data. Many deep nodes in the softshell turtle phylogeny were confidently recovered only after the addition of largely nonhomoplasious data from the nuclear intron.

Molecular phylogeny of Vipera Laurenti, 1768 and the related genera Macrovipera (Reuss, 1927) and Daboia (Gray, 1842), with comments about neurotoxic Vipera aspis aspis populations

We used mtDNA sequences (cytochrome b and NADH dehydrogenase subunit 2) to reconstruct molecular phylogenies of Vipera sensu lato, Vipera sensu stricto, and Vipera aspis. Three major clades were identified within the Vipera s.l. group: (1) the European vipers, (2) the oriental vipers, consisting of Montivipera (Vipera 2) plus Macrovipera lebetina, and (3) a group of Asian and North African vipers consisting of Daboia russelii, V. palaestinae, and Macrovipera mauritanica. We also distinguished three clades within the monophyletic European Vipera group: V. ammodytes, V. aspis, and V. latastei, and Pelias with monophyly of Vipera 1 uncertain. Within V. aspis, the specimens collected in France formed the sister group of an Italian clade. The "neurotoxic" French population of V. aspis, which has a specific venom profile, separated from other French V. aspis early in the history of this group.

Mitochondrial evidence for the origin of hamadryas baboons

Baboons (Mammalia: Primates, Papio) are found primarily on the continent of Africa, but the range of hamadryas baboons (Papio hamadryas) extends to the Arabian Peninsula, and the origin of Arabian populations is unclear. To estimate the timing of the divergence between Arabian and African hamadryas populations we analyzed mitochondrial DNA (mtDNA) sequences from individuals of Arabian and African origin, and from representatives of the other major baboon taxa. The oldest hamadryas mitochondrial lineages in the Arabian Peninsula form an ancient trichotomy with the two major African lineages. This suggests that Arabia was colonized by hamadryas very soon after the appearance of the distinctive hamadryas phenotype, both events perhaps coinciding with a mid-Pleistocene stage of dry climate and low sea-level. The most closely related Arabian and African mtDNA haplotypes coalesce at approximately 35 ka, suggesting that no gene flow between African and Arabian baboons has occurred since the end of the last ice age, when a land bridge at the southern sill of the Red Sea was submerged. The mitochondrial paraphyly of Ethiopian hamadryas and anubis (P. anubis) baboons suggests an extensive and complex history of sex-specific introgression.

Phylogeny of the Falconidae (Aves): a comparison of the efficacy of morphological, mitochondrial, and nuclear data

We sequenced 2800+ bp of the RAG-1 exon for representatives of all the currently recognized genera in the avian family Falconidae. A phylogenetic analysis of these data was compared to prior analyses of mitochondrial (cytochrome-b) and morphological (syringeal) data. The nuclear RAG-1 sequences produced results that were in agreement with the morphological results, but differed from the mitochondrial results with regard to monophyly of the genus Micrastur. A reanalysis of the cytochrome-b (cyt-b) data suggested that this result was due to heterogeneity in base composition. Comparisons of data quality and quantity across the three data sets indicate that the nuclear DNA sequences and the morphological data have similar consistency and retention indices as well as noise distributions that are superior to those of cyt-b. However, the RAG-1 data identify more nodes with high bootstrap support indices than do either morphology or mitochondrial sequences. In the final assessment, RAG-1 sequences were superior in phylogenetic utility both to syringeal morphology (because of sheer number of characters) and to cyt-b sequences (because of reduced noise and homogeneity of base composition, but in spite of having many fewer characters).

Phylogeny of Titmice (Paridae): II. Species Relationships Based on Sequences of the Mitochondrial Cytochrome-B Gene

We present a phylogenetic hypothesis for 40 species in the bird family Paridae, based on comparisons of nucleotide sequences of the mitochondrial cytochrome-b gene. Parids, including tits and chickadees, are an older group than their morphological stereotypy suggests. The longest cytochrome-b distances between species reach 12% in uncorrected divergence. With the exception of one thrasher-like terrestrial tit species of the Tibetan plateau (Pseudopodoces humilis), morphological and ecological stasis have prevailed since the initial parid radiation in the Old World during the mid-Tertiary.

All trees support monophyly of the family Paridae, which includes Parus (sensu lato) and the monotypic Oriental genera Sylviparus, Melanochlora, and Pseudopodoces. Within the clade of chickadees and gray tits (Parus, subgenus Poecile), three Old World species, Parus lugubris of the eastern Mediterranean and Balkan regions, P. superciliosus of high elevations in the Himalayas of western China, and P. varius of the Orient are sisters to all other species. The Eurasian crested titmice (subgenus Lophophanes) and North American crested titmice (subgenus Baeolophus) are sister groups. Our data suggest two colonizations of the New World by parids in the late Tertiary. The ancestor of modern Baeolophus colonized North America 4 mya, and the ancestor of all North American chickadees colonized North America 3.5 mya.

Phylogénie chez la mésange (Paridés): II. Relations entre les espèces basées sur des séquences du gène mitochondrial cytochrome-b

Physicochemical Evolution and Molecular Adaptation of the Cetacean and Artiodactyl Cytochrome b Proteins

Cetaceans have most likely experienced metabolic shifts since evolutionarily diverging from their terrestrial ancestors, shifts that may be reflected in the proteins such as cytochrome b that are responsible for metabolic efficiency. However, accepted statistical methods for detecting molecular adaptation are largely biased against even moderately conservative proteins because the primary criterion involves a comparison of nonsynonymous and synonymous substitution rates (dN/dS); they do not allow for the possibility that adaptation may come in the form of very few amino acid changes. We apply the MM01 model to the possible molecular adaptation of cytochrome b among cetaceans because it does not rely on a dN/dS ratio, instead evaluating positive selection in terms of the amino acid properties that comprise protein phenotypes that selection at the molecular level may act upon. We also apply the codon-degeneracy model (CDM), which focuses on evaluating overall patterns of nucleotide substitution in terms of base exchange, codon position, and synonymy to estimate the overall effect of selection. Using these relatively new models, we characterize the molecular adaptation that has occurred in the cetacean cytochrome b protein by comparing revealed amino acid replacement patterns to those found among artiodactyls, the modern terrestrial mammals found to be most closely related to cetaceans. Our findings suggest that several regions of the cetacean cytochrome b protein have experienced molecular adaptation. Also, these adaptations are spatially associated with domain structure, protein function, and the structure and function of the cytochrome bc(1) complex and its constituents. We also have found a general correlation between the results of the analytical software programs TreeSAAP (which implements the MM01 model) and CDM (which implements the codon-degeneracy model).

The origin and evolution of seahorses (genus Hippocampus): a phylogenetic study using the cytochrome b gene of mitochondrial DNA

Phylogenetic relationships among 93 specimens of 22 species of seahorses (genus Hippocampus) from the Atlantic and Indo-Pacific Oceans were analysed using cytochrome b gene sequence data. A maximum sequence divergence of 23.2% (Kimura 2-parameter model) suggests a pre-Tethyan origin for the genus. Despite a greater number of seahorse species in the Indo-Pacific than in the Atlantic Ocean, there was no compelling genetic evidence to support an Indo-Pacific origin for the genus Hippocampus. The phylogenetic data suggest that high diversity in the Indo-Pacific results from speciation events dating from the Pleistocene to the Miocene, or earlier. Both vicariance and dispersal events in structuring the current global distribution of seahorses. The results suggested that several species designations need re-evaluating, and further phylogeographic studies are required to determine patterns and processes of seahorse dispersal.

A molecular phylogeny of aquatic gastropods provides a new perspective on biogeographic history of the Snake River Region

Mitochondrial DNA sequences of aquatic gastropods of the subgenus Pyrgulopsis (Natricola) were analyzed to test a commonly accepted hypothesis concerning the early history of the Snake River in the northwestern US. Distributions of Natricola and other regional biota were previously used to infer that the Snake River flowed to the Pacific through southeastern Oregon and northern California during the Neogene prior to its capture by the Columbia River in the late Pliocene (2 Ma). A molecular phylogeny based on partial sequences of COI and NDI (1149 bp) indicates that the Natricola clade is restricted to the modern Snake-Columbia River Basin and the Oregon Lakes region whereas northern California populations previously assigned to this subgenus belong to other lineages. The Natricola clade is not deeply subdivided into Oregon Lakes and Snake River Basin units consistent with late Pliocene fragmentation of the hypothesized paleodrainage, but instead is shallowly structured and contains multiple transitions among these two geographic areas. The strongly supported sister relationship between Natricola and a species from northwest Nevada (P. imperialis) is consistent with a recent proposal that the ancestral Snake River did not flow through southeast Oregon but instead flowed south to the Humboldt River. Within the context of this hypothesis, the multiple transitions between the Snake River Basin and the Oregon Lakes region that occurred within Natricola may be attributed to a late Pleistocene connection between these areas that was unrelated to the early course of the Snake River.

Sciurid phylogeny and the paraphyly of Holarctic ground squirrels (Spermophilus)

The squirrel family, Sciuridae, is one of the largest and most widely dispersed families of mammals. In spite of the wide distribution and conspicuousness of this group, phylogenetic relationships remain poorly understood. We used DNA sequence data from the mitochondrial cytochrome b gene of 114 species in 21 genera to infer phylogenetic relationships among sciurids based on maximum parsimony and Bayesian phylogenetic methods. Although we evaluated more complex alternative models of nucleotide substitution to reconstruct Bayesian phylogenies, none provided a better fit to the data than the GTR+G+I model. We used the reconstructed phylogenies to evaluate the current taxonomy of the Sciuridae. At essentially all levels of relationships, we found the phylogeny of squirrels to be in substantial conflict with the current taxonomy. At the highest level, the flying squirrels do not represent a basal divergence, and the current division of Sciuridae into two subfamilies is therefore not phylogenetically informative. At the tribal level, the Neotropical pygmy squirrel, Sciurillus, represents a basal divergence and is not closely related to the other members of the tribe Sciurini. At the genus level, the sciurine genus Sciurus is paraphyletic with respect to the dwarf squirrels (Microsciurus), and the Holarctic ground squirrels (Spermophilus) are paraphyletic with respect to antelope squirrels (Ammospermophilus), prairie dogs (Cynomys), and marmots (Marmota). Finally, several species of chipmunks and Holarctic ground squirrels do not appear monophyletic, indicating a need for reevaluation of alpha taxonomy.

Molecular evidence of speciation between island and continental populations of Anopheles (Cellia) sundaicus (Diptera: Culicidae), a principal malaria vector taxon in Southeast Asia

Anopheles sundaicus s.l. is a principal malaria vector taxon on islands and along the coastal areas of Southeast Asia. It has a wide geographical distribution and exhibits a high level of ecological and behavioral variability. Study of this taxon is crucial for understanding its biology and implementing effectise vector control measures. We compared populations of An. sundaicus from Vietnam, Thailand, and Malaysian Borneo by using two mitochondrial DNA markers: cytochrome oxidase I and cytochrome b. Genetic divergence, geographic separation, and cladistic analysis of relationships revealed the presence of two cryptic species: Anopheles sundaicus s.s. on Malaysian Borneo and An. sundaicus species A in coastal areas of Thailand and Vietnam. A polymerase chain reaction (PCR) assay was developed to easily identify these two species throughout their geographic distributions. The assay was based on sequence characterized amplified region derived from random amplified polymorphic DNA. This PCR identification method needs to be validated and adapted for the recognition of other possible species in the Sundaicus Complex.

Phylogeny of the endemic Baikalian Sergentia (Chironomidae, Diptera)

Fragments of two mitochondrial genes, cytochrome b (CytB) and Cytochrome c oxidase subunit I (COI) have been used as phylogenetic markers in Sergentia (Chironomidae, Diptera). The concatenated (1241 bp) sequences from both genes were used to infer the phylogenetic relationships among seven Sergentia species. Five of the species belong to the endemic fauna of Lake Baikal. Alignments of the nucleotide sequences were used for the construction of trees using Neighbor-Joining and maximum parsimony methods. Both methods yielded similar results. Monophyly of both Sergentia and the Baikalian endemic species was well supported. The date of origin of the endemic group of Sergentia was estimated as 25.7 MYA which closely coincides with the start of geological changes in the Baikal area. A cytological tree, based on 12 chromosomal characteristics, for the same set of Sergentia species showed a great similarity to the molecular phylogeny.

Mitochondrial DNA sequences reveal extensive cryptic diversity within a western American springsnail

We analysed cytochrome c oxidase subunit I and NADH dehydrogenase subunit I sequence variation among 29 populations of a widely ranging southwestern springsnail (Pyrgulopsis micrococcus) and 18 regional congeners. Cladistic analyses of these sequences depict P. micrococcus as a polyphyletic composite of five well-supported clades. Sequence divergences among these clades and subclades imply the possible occurrence of as many as seven or eight cryptic species in addition to P. micrococcus. Our finding that P. micrococcus contains multiple, genetically distinct and geographically restricted lineages suggests that diversification within this highly speciose aquatic genus has been structured in large part by the operation of terrestrial barriers to gene flow. However, these sequence data also indicate that recent dispersal among hydrographically separated areas has occurred within one of these lineages, which we attribute to passive transport on migratory waterbirds.

Novel Intron Phylogeny Supports Plumage Convergence in Orioles (Icterus)

A recent study of New World orioles (Icterus spp.), which traced a large number of plumage characters onto a mitochondrial DNA phylogeny, reported high frequencies of evolutionary convergence and reversal of plumage characters (Omland and Lanyon 2000). Although those results are consistent with other smaller scale studies that have documented plumage homoplasy, the mitochondrial genome is inherited as a single linkage group, so mitochondrial data represent only one gene tree. The mitochondrial (mt) DNA tree may not reflect the true evolutionary history of a lineage; therefore, it remains possible that the plumage characters could reflect the true species phylogeny. Other rapidly evolving regions of DNA can provide independent phylogenetic hypotheses useful for evaluating mitochondrial gene trees. A novel phylogenetic marker, a region of the nuclear gene ornithine decarboxylase (ODC) spanning from exon 6 to exon 8, was sequenced in 10 oriole species. The resultant nuclear gene tree reconstructs the same three major oriole clades as the mtDNA tree (Omland et al. 1999), supporting the conclusion that plumage evolution in the New World orioles has been highly homoplastic. Although most phylogenetic studies that have employed introns report greatest resolution at the genus or family level, ODC appears to offer some degree of phylogenetic resolution for infrageneric analyses. However, that intron has clearly not sorted to monophyly within or between closely related species.

Molecular phylogeography of the Amazonian Chagas disease vectors Rhodnius prolixus and R. robustus

The phylogeographical structure of the closely related species Rhodnius prolixus and R. robustus is presented based on a 663-base pair (bp) fragment of the mitochondrial cytochrome b gene. Twenty haplotypes were recovered from 84 samples examined, representing 26 populations from seven Latin American countries. The resulting phylogenetic tree is composed of five major reciprocally monophyletic clades, one representing R. prolixus and four representing R. robustus. While R. prolixus is a very homogeneous assemblage, R. robustus has deeper clades and is paraphyletic, with the clade comprising R. robustus from Venezuela (Orinoco region) more closely related to the R. prolixus clade than to the other R. robustus populations from the Amazon region. The R. robustus paraphyly was supported further by the analysis of a nuclear gene (D2 region of the 28S RNA) for a subset of specimens. The data support the view that R. robustus represents a species complex. Levels of sequence divergence between clades within each region are compatible with a Pleistocene origin. Nucleotide diversity (pi) for all R. prolixus populations was extremely low (0.0008), suggesting that this species went through a recent bottleneck, and was subsequently dispersed by man.

Longspurs and snow buntings: phylogeny and biogeography of a high-latitude clade (Calcarius)

Using complete cytochrome b sequence data, we determined that the genus Calcarius, as presently recognized, is paraphyletic. Calcarius plus Plectrophenax form a highly supported clade composed of two subclades, a "snow bunting" clade comprised of Plectrophenax plus Calcarius mccownii (formerly in the monotypic genus Rhynchophanes), and a "collared" longspur clade of Calcarius lapponicus, ornatus, and pictus. Contrary to conventional thought, Calcarius is not phylogenetically close to either Calamospiza or Emberiza. Unlike these two genera, the taxonomic affinities of Calcarius appear to lie outside of the sparrow (tribe Emberizini) assemblage. Calcarius appears to be a relatively old songbird lineage, originating between 4.2 and 6.2 million years ago. Within Calcarius, pictus and ornatus form a closely related sister pair (2.9% divergent), as do Calcarius nivalis and hyperboreus (0.18% divergent). The group (Calcarius, sensu lato) is inferred to have its origins at relatively high latitudes in the New World.

Molecular systematics and biogeography of the Neotropical monkey genus, Alouatta

We take advantage of the broad distribution of howler monkeys from Mexico to Argentina to provide a historical biogeographical analysis on a regional scale that encompasses the entire Neotropics. The phylogenetic relationships among 9 of the 10 recognized Alouatta species were inferred using three mitochondrial and two nuclear genes. The nuclear gene regions provided no phylogenetic resolution among howler monkey species, and were characterized by very low levels of sequence divergence between Alouatta and the Ateles outgroup. The mtDNA genes, on the other hand, produced a well-resolved phylogeny, which indicated that the earliest split among howler monkeys separated cis- and trans-Andean clades. Eight monophyletic mtDNA haplotype clades were identified, representing six named species in South America, including Alouatta seniculus, Alouatta sara, Alouatta macconelli, Alouatta caraya, Alouatta belzebul, and Alouatta guariba, and two in Mesoamerica, Alouatta pigra and Alouatta palliata. Molecular clock-based estimates of branching times indicated that contemporary howler monkey species originated in the late Miocene and Pliocene, not the Pleistocene. The causes of Alouatta diversification were more difficult to pin down, although we posit that the initial cis-, trans-Andean split in the genus was caused by the late Miocene completion of the northern Andes. Riverine barriers to dispersal and putative forest refuges can neither be discounted nor distinguished as causes of speciation in many cases, and one, the other or both have likely played a role in the diversification of South American howler monkeys. Finally, we estimated the separation of Mesoamerican A. pigra and A. palliata at 3Ma, which corresponds to the completion date of the Panama Isthmus promoting a role for this earth history event in the speciation of Central American howler monkeys.

Structure and evolution of the avian mitochondrial control region

The structural and evolutionary characteristics of the mitochondrial control region were studied by using control region sequences of 68 avian species. The distribution of the variable nucleotide positions within the control region was found to be genus specific and not dependant on the level of divergence, as suggested before. Saturation was shown to occur at the level of divergence of 10% in pairwise comparisons of the control region sequences, as has also been reported for the third codon positions in ND2 and cytochrome b genes of mtDNA. The ratio of control region vs cytochrome b divergence in pairwise comparisons of the sequences was shown to vary from 0.13 to 21.65, indicating that the control region is not always the most variable region of the mtDNA, but also that there are differences in the rate of divergence among the lineages. Only two of the conserved sequence blocks localized earlier for other species, D box and CSB-1, were found to show a considerable amount of sequence conservation across the avian and mammalian sequences. Additionally, a novel avian-specific sequence block was found.

Phylogenetic relationships of the Cochliopinae (Rissooidea: Hydrobiidae): an enigmatic group of aquatic gastropods

Phylogenetic analysis based on a partial sequence of the mitochondrial cytochrome c oxidase subunit I gene was performed for 26 representatives of the aquatic gastropod subfamily Cochliopinae, 6 additional members of the family Hydrobiidae, and outgroup species of the families Rissoidae and Pomatiopsidae. Maximum-parsimony analysis yielded a single shortest tree which resolved two monophyletic groups: (1) a clade containing all cochliopine taxa with the exception of Antroselates and (2) a clade composed of Antroselates and the hydrobiid genus Amnicola. The clade containing both of these monophyletic groups was depicted as more closely related to members of the family Pomatiopsidae than to other hydrobiid snails which were basally positioned in our topology. New anatomical evidence supports recognition of the cochliopine and Antroselates-Amnicola clades, and structure within the monophyletic group of cochliopines is largely congruent with genitalic characters. However, the close relationship between the Pomatiopsidae and these clades is in conflict with commonly accepted classifications and suggests that a widely accepted scenario for genitalic evolution in these snails is in need of further study.

Phylogenetic relationships among megachiropteran species from the two major islands of the Philippines, deduced from DNA sequences of the cytochrome b gene

Complete cytochrome b gene sequences (1140 base pairs) in species of Megachiroptera were ascertained in order to deduce their phylogenetic relationships, using samples of Cynopterus brachyotis, Eonycteris spelaea, Ptenochirus jagori, Pteropus vampyrus, and Rousettus amplexicaudatus collected from the islands of Luzon and Mindanao in the Philippines. Genetic divergence between samples of R. amplexicaudatus, E. spelaea, and C. brachyotis was very small. On the other hand, a large genetic distance was detected between species of Megachiroptera. The phylogenetic tree using neighbor-joining, parsimony, and maximum-likelihood methods generated similar topologies, reflecting the evolutionary associations among megachiropteran species. We estimated that Megachiroptera separated from Microchiroptera 50.2 million years ago (MYA), and split further approximately 32.4 MYA, forming three lineages: E. spelaea, R. amplexicaudatus, and P. vampyrus and the P. jagori – C. brachyotis cluster. The third lineage, composed of P. vampyrus and the P. jagori – C. brachyotis cluster, branched out 31.9 MYA. We hypothesize that R. amplexi caudatus diverged from the three members of the subfamily Pteropodinae examined, and its phylogenetic relationship with E. spelaea remains unclear.

Molecular phylogenetics of Australo-Papuan possums and gliders (family Petauridae)

Phylogenetic relationships within the possums of the family Petauridae, including their affinities with the family Pseudocheiridae, were inferred from DNA sequences obtained for the mitochondrial ND2 gene (1040 bp) combined with previously published partial 12S rDNA sequences. Short, deep internodes characterize some of the divergences obtained. The robustness of these nodes was assessed by several methods such as exclusion of taxa and partitioning of characters. In all analyses a monophyletic Pseudocheiridae was evident, whereas a monophyletic Petauridae was not as well supported. Within the Petauridae, Gymnobelideus was more closely related to Dactylopsila-Dactylonax than to Petaurus. This supports the results obtained from microcomplement fixation of albumin and DNA-DNA hybridization studies but conflicts with morphological data.

Utility and evolution of cytochrome b in insects

Cytochrome b (cyt-b) is widely used in molecular phylogenetic studies of vertebrate, but not invertebrate, taxa. To determine whether this situation is an historical accident or reflects the utility of cyt-b, we compared the abilities of cyt-b, COI, and one nuclear ribosomal gene region (D1 of 28S) to recover intergeneric relationships within the tiger moth tribes Ctenuchini and Euchromiini. Additionally, we compared the rate of sequence and amino acid evolution of cyt-b across insects. Cytochrome b had the same level of sequence variation and A/T bias as COI, but was less useful for recovering intergeneric relationships. The total evidence tree casts doubt on the traditional taxonomy of the group. For the class Insecta, we found that functional conservation of amino acids occurs for the same regions as those found in vertebrates with the exception of Mallophaga (lice). Lice have an accelerated rate of nonsynonymous substitutions. Accelerated rate of cyt-b nucleotide and amino acid evolution in Apidae (bees) may be correlated with increased metabolic rates associated with facultative endothermy (= heterothermy).

Estimating the influence of selection on the variable amino acid sites of the cytochrome B protein functional domains

We evaluated the effects of selection on the molecular evolution of the functional domains of the mammalian cytochrome b gene as it relates to physicochemical properties shown to correlate with rates of amino acid replacement. Two groups of mammals were considered: pocket gophers of the rodent family Geomyidae, and cetaceans and ungulates of the monophyletic taxon Cetartopdactyla. Several characteristics of cytochrome b evolution were common to both mammal groups. The evolution of the matrix domain reflected the region's relative lack of function. Goodness of fit to neutral expectations indicated that external influences have had very little effect on the evolution of the matrix, although in some cases conservative and moderate changes have been favored. Although rates of synonymous nucleotide substitution have been relatively high, the transmembrane domain exhibited poor goodness of fit to neutral expectations. However, the evolution of the transmembrane domain has been constrained by negative selection, allowing a preponderance of conservative and moderate amino acid replacements. We hypothesize that a high rate of substitution is maintained in spite of negative selection because the codons of the transmembrane coding region are predisposed to conservative changes in all amino acid properties. The evolutionary patterns of the intermembrane domain in pocket gophers and cetartiodactyls, however, were very different. Changes inferred from the pocket gopher phylogenetic tree exhibited a significant fit to neutral expectations for each of the amino acid properties. Changes inferred from the cetartiodactyl tree exhibited significant fit to neutral expectations for polarity and isoelectric point, but not for composition, molecular volume, polar requirement, or hydropathy. In each case, lack of fit was due to selection that promoted conservative or moderate change, with the noteworthy exception of polar requirement. We detected an unexpectedly large change in polar requirement (from aspartic acid to threonine) in two separate lineages (Camelus bactrianus and all cetaceans) at amino acid position 159. This inferred change occurred in a region of the cyt-b protein that directly interacts with external surface proteins of the cytochrome bc(1) complex and resulted in a reversion to a more common character state in vertebrates.

Historical biogeography and a mitochondrial DNA phylogeny of grouse and ptarmigan

We sequenced 2690 nucleotides of mitochondrial DNA (mtDNA) including the entire control region (CR), partial 12S and 16S ribosomal RNAs, NADH dehydrogenase subunit 2, and cytochrome b genes from representatives of all the 17 living species of grouse and ptarmigan (Aves; Galliformes; subfamily Tetraoninae). Substitution rates and phylogenetic signals were variable among genes, with the CR being more informative than protein-coding and rRNA genes. Phylogenetic trees, computed with the CR or the concatenated sequences, indicate that: (1) genus Bonasa is monophyletic and basal within the subfamily, (2) all the other currently recognized genera of Tetraoninae are monophyletic, except Dendragapus; (3) D. obscurus is related to Centrocercus urophasianus and divergent from former D. canadensis and D. falcipennis, which, accordingly, may be ascribed to the distinct genus Falcipennis; (4) Tympanuchus, Dendragapus, and Centrocercus form a clade comprising taxa distributed exclusively in North America; and (5) the North American species of Bonasa (B. umbellus) and Lagopus (L. leucurus) are basal to their Eurasian and Holarctic congeneric species. These findings, and a dispersal-vicariance analysis, support a North American origin of the subfamily and of all the genera of Tetraoninae, with the possible exception of Tetrao. Present species distributions might have been attained by at least three dispersal events from North America to Eurasia, involving the ancestors to Palearctic Bonasa, the ancestors to circumpolar Lagopus mutus/L. lagopus, and the clade leading to Tetrao/Falcipennis. According to a "standard calibration" of the mtDNA molecular clock (2% sequence divergence per million years), Bonasa split about 5-6 million years ago, the other genera diverged during the upper Pliocene, and most of the congeneric species with North American and Eurasian distributions (Bonasa, Lagopus, and Falcipennis) originated during the lower Pleistocene, well before the last interruption of the Beringian land bridge.

Higher-level phylogeny of new world vireos (aves: vireonidae) based on sequences of multiple mitochondrial DNA genes

Interfamilial relationships of the New World songbird family Vireonidae are uncertain. Thus, we sequenced 3069 bp of four mitochondrial genes (cyt b, ND2, ND3, COI) from 19 taxa in five families and two outgroups, to examine higher-level alliances with proposed relatives. We also sequenced cyt b and ND2 from an additional five vireonids to examine intergeneric relationships within the Vireonidae and incorporated 14 sequences of cyt b from GenBank to test the effects of taxon sampling on gene tree resolution. Families appeared monophyletic in all analyses, and the affinity of vireonids to Old World corvoids was corroborated. However, relationships among the Vireonidae and other families were not resolved. Sequences of vireonids revealed high levels of divergence within and between genera, with either Cyclarhis or Vireolanius positioned basally, depending on the analysis. On the basis of mitochondrial DNA and biogeographic evidence, vireonids represent a deep lineage derived from an Old World ancestor that colonized the New World, most likely via Beringia, with subsequent radiation in the Middle American tropics. We hypothesize postcolonization dispersal of the ancestor into Middle America, followed by extinction of the ancestor in North America. This extinction event left the North Temperate Zone unoccupied by any vireonid until northward reinvasion by some species of Vireo. Although the closest living relative of vireonids remains unidentified, broad-scale sequencing of additional extant corvoids with multiple molecular markers should further elucidate Old World alliances.

Evolution of the mitochondrial DNA control region and cytochrome b genes and the inference of phylogenetic relationships in the avian genus Lophura (Galliformes)

The entire mitochondrial DNA control region (mtDNA CR) and cytochrome b (cyt b) genes were sequenced in 10 of the 11 extant species of gallopheasants (Lophura). The cyt b from L. diardi and L. ignita showed unusual leucine-coding codons at the expected terminal 3' end of the gene. Presence of conserved functional motifs in the inferred amino acid sequences, conserved secondary structures of the flanking tRNA(Pro) and tRNA(Thr), and Southern hybridization concordantly suggest that these cyt b represent functional mitochondrial genes and not nuclear transpositions. Functional stop codons can be generated by RNA editing of the primary transcripts from these sequences. Despite strong site and domain substitution rate heterogeneity, CR and cyt b diverged at similar rates, on average, and expressed congruent phylogenetic signals. Phylogenetic analyses of the concatenated sequences split Lophura into five clades including (1) L. bulweri, (2) L. diardi-L. ignita, (3) L. erythrophthalma-L. inornata, (4) L. leucomelanos-L. nycthemera, and (5) L. swinhoii-L. edwardsi-L. hatinhensis. Basal relationships among these clades, which include species distributed in continental South East Asia and the Sundaland archipelago, were weakly resolved, suggesting the occurrence of rapid cladogenic events in the early evolutionary history of Lophura. A conventional calibration of mtDNA sequence divergence indicates a mid to late Pliocene evolution of the main clades in Lophura, which could have diversified in allopatry in continental South East Asia. Sundaland could have been colonized lately and independently by the different clades. Consequently, cyclic changes in late Pleistocene climate and landscape might not have increased rates of speciation in genus Lophura in Sundaland.

Phylogeny of the genus Chironomus (Diptera) inferred from DNA sequences of mitochondrial cytochrome b and cytochrome oxidase I

Two mitochondrial genes, Cytochrome b (Cytb) and Cytochrome c oxidase subunit I (COI), have been used as phylogenetic markers in Chironomids. The nucleotide sequences of 685 bp from Cytb and 596 bp from COI have been determined for 36 Chironomus species from the Palearctic, or Holarctic, and Australasia. The concatenated sequence of 1281 bp from both genes was used to investigate the phylogenetic relationships among these species. The nucleotide sequence alignments were used for construction of phylogenetic trees based on maximum-parsimony and neighbor-joining methods. Both techniques produced similar phylogenies. Monophyly of the genus Chironomus is supported by a bootstrap value of 100% at the basal branch. Six clusters of species have been revealed with high bootstrap values supporting both monophyly of each cluster and the validity of the branching order within each cluster. Four species, C. circumdatus, C. nepeanensis, C. dorsalis, and C. crassiforceps, cannot be placed into any cluster. Cytological phylogenies were constructed using the same set of species, except for C. biwaprimus. These trees showed many similarities to that obtained from the mitochondrial (mt) sequence analysis, but also a number of significant differences. When compared with the tree constructed from the sequence of 23 species available for one of the globin genes, globin 2b (gb2b), there was better support for the mt tree than for the cytological trees. An intron, which varies in its occurrence and position in gb2b, was also investigated and the distribution of the introns supports the phylogenetic history of the genus Chironomus obtained with mt data. The differences observed in the cytological trees seem to be attributable more to the retention of the same chromosome banding sequence across several species, rather than convergent evolutionary events. An important question is the determination of the position of the subgenus Camptochironomus in relation to the representatives of the nominal subgenus Chironomus, since it has been suggested that this is a separate genus. The Camptochironomus species are internal to the trees and have arisen more recently than some of the species of the subgenus Chironomus, indicating that they are not sufficiently differentiated to be considered more than a subgenus.

Speciation, introgressive hybridization and nonlinear rate of molecular evolution in flycatchers

Evolutionary history of Muscicapidae flycatchers is inferred from nuclear and mitochondrial DNA (mtDNA) sequence comparisons and population genetic analysis of nuclear and mtDNA markers. Phylogenetic reconstruction based on sequences from the two genomes yielded similar trees with respect to the order at which the species split off. However, the genetic distances fitted a nonlinear, polynomial model reflecting diminishing divergence rate of the mtDNA sequences compared to the nuclear DNA sequences. This could be explained by Haldane's rule because genetic isolation might evolve more rapidly on the mitochondrial rather than the nuclear genome in birds. This is because hybrid sterility of the heterogametic sex (females) would predate that of the homogametic sex (males), leading to sex biased introgression of nuclear genes. Analyses of present hybrid zones of pied (Ficedula hypoleuca) and collared flycatchers (F. albicollis) may indicate a slight sexual bias in rate of introgression, but the introgression rates were too low to allow proper statistical analyses. It is suggested, however, that the observed deviation from linearity can be explained by a more rapid mutational saturation of the mtDNA sequences than of the nuclear DNA sequences, as supported by analyses of third codon position transversions at two protein coding mtDNA genes. A phylogeographic scenario for the black and white flycatcher species is suggested based on interpretation of the genetic data obtained. Four species appear to have diverged from a common ancestor relatively simultaneously during the Pleistocene. After the last glaciation period, pied and collared flycatchers expanded their breeding ranges and eventually came into secondary contact in Central and Eastern Europe and on the Baltic Isles.

Speciation and population structure in the morphospecies Lutzomyia longipalpis (Lutz & Neiva) as derived from the mitochondrial ND4 gene

Recent studies have suggested that the phlebotomine sand fly Lutzomyia longipalpis (Diptera: Psychodidae), the principal vector of visceral leishmaniasis in the Neotropics, may consist of several allopatric sibling species. Phylogenetic and population genetic analyses of nucleotide variation in a 618-bp fragment of the mitochondrial ND4 gene were carried out on specimens of Lu. longipalpis from several locations in Central and South America. The analyses were concordant with previous findings, indicating that certain allopatric populations of Lu. longipalpis have become sufficiently differentiated as to represent sibling species. Phylogenetic analyses revealed deep genetic divisions between four clades represented by specimens from northern South America, Brazil, Central America, and an isolated Colombian population. Strong differentiation also was observed between certain populations within the first two clades. Partitioning of genetic diversity within and between Central American populations did not show the presence of more than one species in the region. However, distance, even within the 70-km range of the Honduran collection sites, was found to have a remarkably strong effect on gene flow. The highly subdivided population structure may be due to the patchiness of their distribution. F(ST) values comparing a Guatemalan population with several Honduran populations revealed a level of differentiation associated with a negligible rate of gene flow.

Mitochondrial DNA phylogeography of the polytypic North American rat snake (Elaphe obsoleta): a critique of the subspecies concept

Subspecies have been considered artificial subdivisions of species, pattern classes, or incipient species. However, with more data and modern phylogenetic techniques, some subspecies may be found to represent true species. Mitochondrial DNA analysis of the polytypic snake, Elaphe obsoleta, yields well-supported clades that do not conform to any of the currently accepted subspecies. Complete nucleotide sequences of the cytochrome b gene and the mitochondrial control region produced robust maximum-parsimony and maximum-likelihood trees that do not differ statistically. Both trees were significantly shorter than a most parsimonious tree in which each subspecies was constrained to be monophyletic. Thus, the subspecies of E. obsoleta do not represent distinct genetic lineages. Instead, the evidence points to three well-supported mitochondrial DNA clades confined to particular geographic areas in the eastern United States. This research underscores the potential problems of recognizing subspecies based on one or a few characters.

Testing the hypothesis of a recombinant origin of human immunodeficiency virus type 1 subtype E

The human immunodeficiency virus type 1 (HIV-1) epidemic in Southeast Asia has been largely due to the emergence of clade E (HIV-1E). It has been suggested that HIV-1E is derived from a recombinant lineage of subtype A (HIV-1A) and subtype E, with multiple breakpoints along the E genome. We obtained complete genome sequences of clade E viruses from Thailand (93TH057 and 93TH065) and from the Central African Republic (90CF11697 and 90CF4071), increasing the total number of HIV-1E complete genome sequences available to seven. Phylogenetic analysis of complete genomes showed that subtypes A and E are themselves monophyletic, although together they also form a larger monophyletic group. The apparent phylogenetic incongruence at different regions of the genome that was previously taken as evidence of recombination is shown to be not statistically significant. Furthermore, simulations indicate that bootscanning and pairwise distance results, previously used as evidence for recombination, can be misleading, particularly when there are differences in substitution or evolutionary rates across the genomes of different subtypes. Taken jointly, our analyses suggest that there is inadequate support for the hypothesis that subtype E variants are derived from a recombinant lineage. In contrast, many other HIV strains claimed to have a recombinant origin, including viruses for which only a single parental strain was employed for analysis, do indeed satisfy the statistical criteria we propose. Thus, while intersubtype recombinant HIV strains are indeed circulating, the criteria for assigning a recombinant origin to viral structures should include statistical testing of alternative hypotheses to avoid inappropriate assignments that would obscure the true evolutionary properties of these viruses.

The impact of parsimony weighting schemes on inferred relationships among toucans and neotropical barbets (Aves: piciformes)

The development of new schemes for weighting DNA sequence data for phylogenetic analysis continues to outpace the development of consensus on the most appropriate weights. The present study is an exploration of the similarities and differences between results from 22 character weighting schemes when applied to a study of barbet and toucan (traditional avian families Capitonidae and Ramphastidae) phylogenetic relationships. The dataset comprises cytochrome b sequences for representatives of all toucan and Neotropical barbet genera, as well as for several genera of Paleotropical barbets. The 22 weighting schemes produced conflicting patterns of relationship among taxa, often with conflicting patterns each receiving strong bootstrap support. Use of multiple weighting schemes helped to identify the source within the dataset (codon position, transitions, transversions) of the various putative phylogenetic signals. Importantly, some phylogenetic hypotheses were consistently supported despite the wide range of weights employed. The use of phylogenetic frameworks to summarize the results of these multiple analyses proved very informative. Relationships among barbets and toucans inferred from these data support the paraphyly of the traditional Capitonidae. Additionally, these data support paraphyly of Neotropical barbets, but rather than indicating a relationship between Semnornis and toucans, as previously suggested by morphological data, most analyses indicate a basal position of Semnornis within the Neotropical radiation. The cytochrome b data also allow inference of relationships among toucans. Supported hypotheses include Ramphastos as the sister to all other toucans, a close relationship of Baillonius and Pteroglossus with these two genera as the sister group to an (Andigena, Selenidera) clade, and the latter four genera as a sister group to Aulacorhynchus.