Complete Mitochondrial Cytochrome Research Articles

Phylogeny and biogeography of wood-feeding cockroaches, genus Salganea Stål (Blaberidae: Panesthiinae), in Southeast Asia based on mitochondrial DNA sequences.

Molecular phylogenetic relationships among 25 species of the wood-feeding cockroach belonging to the genus Salganea Stål (Panesthiinae; Blaberidae) in Southeast Asia were analyzed based on the DNA sequence of the complete mitochondrial cytochrome oxidase II (COII) gene. Most basal relationships among species of Salganea are poorly resolved by both neighbor-joining and nonweighted parsimony analyses, suggesting the possibility of a hard polytomy due to a rapid and potentially simultaneous radiation early in the history of the genus. For more apical relationships, however, some interesting phylogenetic relationships were recognized. The monophyly of the two species groups, morio and foveolata, the former of which is distributed mainly in the Sunda lands (containing the Malay Peninsula, Sumatra, Java, and Borneo), whereas the latter is Sulawesi endemic, was strongly supported. Based on the inferred phylogenetic patterns and recent palaeogeographic scenario for Southeast Asia, it is suggested that a radiation of Salganea species occurred in Southeast Asia presumably in the early Tertiary, and several barriers against dispersal and gene flow, such as the formation of straits or high mountains, have arisen from the middle Tertiary.

Recurrent amplifications and deletions of satellite DNA accompanied chromosomal diversification in South American tuco-tucos (genus Ctenomys, Rodentia: Octodontidae): a phylogenetic approach.

We investigated the relationship between satellite copy number and chromosomal evolution in tuco-tucos (genus Ctenomys), a karyotypically diverse clade of rodents. To explore phylogenetic relationships among 23 species and 5 undescribed forms, we sequenced the complete mitochondrial cytochrome b genes of 27 specimens and incorporated 27 previously published sequences. We then used quantitative dot-blot techniques to assess changes in the copy number of the major Ctenomys satellite DNA (satDNA), named RPCS. Our analysis of the relationship between variation in copy number of RPCS and chromosomal changes employed a maximum-likelihood approach to infer the copy number of the satellite RPCS in the ancestors of each clade. We found that amplifications and deletions of RPCS were associated with extensive chromosomal rearrangements even among closely related species. In contrast, RPCS copy number stability was observed within clades characterized by chromosomal stability. This example reinforces the suspected role of amplification, deletion, and intragenomic movement of satDNA in promoting extensive chromosomal evolution.

Molecular Phylogeny of the Chipmunks Inferred from Mitochondrial Cytochrome b and Cytochrome Oxidase II Gene Sequences

There are currently 25 recognized species of the chipmunk genus Tamias. In this study we sequenced the complete mitochondrial cytochrome b (cyt b) gene of 23 Tamias species. We analyzed the cyt b sequence and then analyzed a combined data set of cyt b along with a previous data set of cytochrome oxidase subunit II (COII) sequence. Maximum-likelihood was used to further test the fit of models of evolution to the cyt b data. Other sciurid cyt b sequence was added to examine the evolution of Tamias in the context of other sciurids. Relationships among Tamias species are discussed, particularly the possibility of a current sorting event among taxa of the southwestern United States and the extreme divergences among the three subgenera (Neotamias, Eutamias, and Tamias).

A molecular phylogeny of the peacock-pheasants (Galliformes: Polyplectron spp.) indicates loss and reduction of ornamental traits and display behaviours

The South-east Asian pheasant genus Polyplectron is comprised of six or seven species which are characterized by ocelli (ornamental eye-spots) in all but one species, though the sizes and distribution of ocelli vary among species. All Polyplectron species have lateral displays, but species with ocelli also display frontally to females, with feathers held erect and spread to clearly display the ocelli. The two least ornamented Polyplectron species, one of which completely lacks ocelli, have been considered the primitive members of the genus, implying that ocelli are derived. We examined this hypothesis phylogenetically using complete mitochondrial cytochrome b and control region sequences, as well as sequences from intron G in the nuclear ovomucoid gene, and found that the two least ornamented species are in fact the most recently evolved. Thus, the absence and reduction of ocelli and other ornamental traits in Polyplectronare recent losses. The only variable that may correlate with the reduction in ornamentation is habitat, as the two less-ornamented species inhabit montane regions, while the ornamented species inhabit lowland regions. The implications of these findings are discussed in light of models of sexual selection. The phylogeny is not congruent with current geographical distributions, and there is little evidence that Pleistocene sea level changes promoted speciation in this genus. Maximum likelihood and maximum parsimony analyses of cytochrome b sequences suggest that the closest relatives of Polyplectron are probably the peafowl and the argus pheasants.

A molecular phylogeny of the peacock-pheasants (Galliformes Polyplectron spp.) indicates loss and reduction of ornamental traits and display behaviours

The South-east Asian pheasant genus Polyplectron is comprised of six or seven species which are characterized by ocelli (ornamental eye-spots) in all but one species, though the sizes and distribution of ocelli vary among species. All Polyplectron species have lateral displays, but species with ocelli also display frontally to females, with feathers held erect and spread to clearly display the ocelli. The two least ornamented Polyplectron species, one of which completely lacks ocelli, have been considered the primitive members of the genus, implying that ocelli are derived. We examined this hypothesis phylogenetically using complete mitochondrial cytochrome b and control region sequences, as well as sequences from intron G in the nuclear ovomucoid gene, and found that the two least ornamented species are in fact the most recently evolved. Thus, the absence and reduction of ocelli and other ornamental traits in Polyplectronare recent losses. The only variable that may correlate with the reduction in ornamentation is habitat, as the two less-ornamented species inhabit montane regions, while the ornamented species inhabit lowland regions. The implications of these findings are discussed in light of models of sexual selection. The phylogeny is not congruent with current geographical distributions, and there is little evidence that Pleistocene sea level changes promoted speciation in this genus. Maximum likelihood and maximum parsimony analyses of cytochrome b sequences suggest that the closest relatives of Polyplectron are probably the peafowl and the argus pheasants.

Phylogenetic divergence in leatherside chub (Gila copei) inferred from mitochondrial cytochrome b sequences

We examined intra-specific phylogenetic relationships in leatherside chub, Gila copei. The complete mitochondrial (mt) cytochrome b gene (1140 bp) was sequenced for 30 individuals from 10 populations that span the geographical distribution of this species. Traditional phylogenetic analyses revealed two deeply divergent and evolutionarily distinct mtDNA clades that are geographically separated in northern and southern drainage basins. Interpopulation sequence variation between clades ranged from 7.7 to 8.1%. The northern clade was genetically more similar and phylogenetically more closely related to the selected out-group Lepidomeda m. mollispinus than to the southern clade, suggesting that the taxonomy of this species may require revision. Sequence variation among populations within clades ranged from 0 to 0.3% in the north and from 0 to 0.7% in the south. Statistical parsimony was used to construct phylogenetic networks of haplotypes within clades. Nested clade analysis revealed that geographical fragmentation has played an important role in genetic structuring within northern and southern clades.

Utility of the Mitochondrial Cytochrome Oxidase II Gene for Resolving Relationships among Black Flies (Diptera: Simuliidae)

The complete mitochondrial cytochrome oxidase II gene was sequenced from 17 black flies, representing 13 putative species, and used to infer phylogenetic relationships. A midge (Paratanytarsus sp.) and three mosquitoes (Aedes aegypti, Anopheles quadrimaculatus, and Culex quinquefasciatus) were used as outgroup taxa. All outgroup taxa were highly divergent from black flies. Phylogenetic trees based on weighted parsimony (a priori and a posteriori), maximum likelihood, and neighbor-joining (log-determinant distances) differed topologically, with deeper nodes being the least well-supported. All analyses supported current classification into species groups but relationships among those groups were poorly resolved. The majority of phylogenetic signal came from closely related sister taxa. The CO-II gene may be useful for exploring relationships at or below the subgeneric level, but is of questionable value at higher taxonomic levels. The weighting method employed gave phylogenetic results similar to those reported by other authors for other insect CO-II data sets. A best estimate of phylogenetic relationships based on the CO-II gene is presented and discussed in relation to current black fly classification.

Intrageneric Diversity of the CytochromebGene and Phylogeny of Eurasian Species of the Genus Mustela (Mustelidae, Carnivora)

To illuminate molecular phylogenetic relationships among Eurasian species of the genus Mustela (Mustelidae, Carnivora), we determined nucleotide sequences of the complete mitochondrial cytochrome b gene region (1,140 base pairs). Molecular phylogenetic trees, constructed using the neighbor-joining and the maximum likelihood methods, showed the common topology of species relationships to each other. The American mink M. vison first branched off and was positioned very remotely from the other species of Mustela. Excluding M. vison, the ermine M. erminea first split from the rest of the species. Two small body-sized weasels, the least weasel M. nivalis and the mountain weasel M. altaica, comprised one cluster (named "the small weasel group"). The other species formed another cluster, where the remarkably close relationships among the domestic ferret M. furo, the European polecat M. putorius, and the steppe polecat M. eversmanni were noticed with 87-94% bootstrap values (named "the ferret group"), supporting the history that the ferret was domesticated from M. putorius and/or M. eversmanni. The European mink M. lutreola was the closest to the ferret group. The genetic distance between the Siberian weasel M. sibirica and the Japanese weasel M. itatsi corresponded to differences of interspecific level, while the two species were relatively close to M. lutreola and the ferret group. These results provide invaluable insight for understanding the evolution of Mustela as well as for investigating the hybridization status between native and introduced species for conservation.

Use of mitochondrial DNA sequences to test the Ceratomorpha (Perissodactyla:Mammalia) hypothesis

Wood (J. Mamm. 18, 106–118; 1937) united the superfamilies Tapiroidea sensu stricto and Rhinocerotoidea in the suborder Ceratomorpha and aligned the Ceratomorpha with the suborder Hippomorpha within the order Perissodactyla. Although the monophyly of the Ceratomorpha appears now well-supported in paleontological and morphological analyses, the molecular relationship among the three extant superfamilies Tapiroidea, Rhinocerotoidea, and Equoidea has not yet been examined due to the limited amount of molecular information on tapirs. In the present study, we examined the phylogenetic position of Tapiroidea, represented by the complete mitochondrial cytochrome b gene (1140 bp) of a lowland tapir (Tapirus terrestris), and a Indian tapir (Tapirus indicus), relative to modern horses, zebras, donkeys, and rhinoceroses. The phylogenetic analyses using standard parsimony, neighbour-joining and maximum likelihood algorithms revealed monophyly of the Perissodactyla and three clearly distinct lineages: the modern horses, tapirs, and rhinoceroses. However, the sister-taxon relationship of the tapirs to either the rhinoceroses or the horses was not resolved conclusively in the bootstrap analysis. Spectral analysis, in which phylogenetic information is displayed independently of any selected tree, revealed that the DNA sequences available do not contain enough phylogenetic signal for any of the alternative hypotheses on the basal diversification of perissodactyls. The short branch lengths among the three perissodactyl lineages suggest that they diverged within a relatively short period, a finding consistent with molecular divergence datings and the fossil evidence that indicates a major radiation of the early perissodactyls approximately 54–50 million years ago.

The Tribal Radiation of the Family Bovidae (Artiodactyla) and the Evolution of the Mitochondrial Cytochrome b Gene

The nucleotide sequence of the complete mitochondrial cytochrome b gene has been determined and compared for 51 species of the family Bovidae and 10 potential pecoran and tragulid outgroups. A detailed saturation analysis at each codon position relative to the maximum parsimony procedure indicates that all transitions on third codon positions do not accumulate in a similar fashion: C-T are more saturated than A-G substitutions. The same trend is observed for second positions but not for first positions where A-G and C-T transitions exhibit roughly the same levels of saturation. Maximum parsimony reconstructions were weighted according to these observations. Maximum parsimony, maximum likelihood, and distance phylogenetic reconstructions all depict a major split within Bovidae. The subfamily Bovinae includes four multifurcating tribes and subtribes: Boselaphini, Tragelaphini, cattle-Bovini (Bos and Bison), and buffalo-Bovini (Bubalus and Syncerus). Its sister group is the subfamily Antilopinae, i.e., all non-Bovinae taxa, represented by seven lineages: Antilopini (including Saiga), Caprini sensu lato (i.e., Caprinae including Pantholops), Hippotragini, Alcelaphini, Reduncini (including Pelea), Aepyceros possibly linked to Neotragus, and Cephalophini possibly linked to Oreotragus (the suni and the klipspringer being members of a polyphyletic Neotragini). These various tribes and major lineages were produced by two noteworthy explosive radiations, which occurred simultaneously between 12.0 and 15.3 MY (Middle Miocene) in the subfamilies Bovinae and Antilopinae.

Molecular Phylogeny and Geographic Distribution of Wood-Feeding Cockroaches in East Asian Islands

Molecular phylogenetic relationships of the wood-feeding cockroach genera Salganea and Panesthia (Blaberidae; Panesthiinae) in East Asian Islands (Ryukyu archipelago and Taiwan Island) were analyzed based on the DNA sequence of the complete mitochondrial cytochrome oxidase II gene. Unweighted parsimony analysis resulted in high bootstrap support for relationships within Panesthia taxa; however, some nodes were unresolved between members of Salganea. Comparison of the number of transitions and transversions with genetic distance at each codon position suggested that saturation of third-codon substitutions has occurred between certain pairs of taxa. Consequently, differential weighting of substitutions at these sites was performed, which resulted in a substantial increase in resolution of Salganea relationships. The inferred phylogenies for both genera displayed good correspondence to the geographical locations of populations but however did not agree with previous subspecies designations based on morphological characters. It appears that both cockroach genera invaded the Ryukyu archipelago from the Taiwan region via a land-bridge present in the Miocene period. Invasion of the main islands of Japan by these cockroaches most likely occurred before the formation of the Tokara Tectonic Strait. Our study suggests that several barriers to gene flow have arisen and persisted over the past ∼10 million years, which have caused segregation and vicariant speciation of the cockroach taxa of this region.

Cytochrome b evolution in birds and mammals: an evaluation of the avian constraint hypothesis.

Patterns of molecular evolution in birds have long been considered anomalous. Compared with other vertebrates, birds have reduced levels of genetic divergence between groups of similar taxonomic ranks for a variety of nuclear and mitochondrial markers. This observation led to the avian constraint hypothesis, which identifies increased functional constraint on avian proteins as the cause for the reduction in genetic divergence. Subsequent investigations provided additional support for the avian constraint hypothesis when rates of molecular evolution were found to be slower in birds than in mammals in a variety of independent calibrations. It is possible to test the avian constraint hypothesis as an explanation for this avian slowdown by comparing DNA sequence data from protein-coding regions in birds and homologous regions in mammals. The increased selective constraints should lead to a reduction in the proportion of amino acid replacement substitutions. To test for such a decrease, we calculated the numbers of amino acid replacement substitutions per replacement site (dN) and silent substitutions per silent site (dS) for the complete mitochondrial cytochrome b gene using 38 avian and 43 mammalian comparisons that were phylogenetically independent. We find that dN/dS is significantly smaller in birds than in mammals. This difference cannot be explained by differences in codon bias affecting dS values. We suggest that the avian slowdown can be explained, at least in part, by a decreased tolerance for amino acid substitutions in avian species relative to mammalian species.

Phylogenetic Relationships of Greek Cyprinidae: Molecular Evidence for at Least Two Origins of the Greek Cyprinid Fauna

A phylogeny of the main cyprinid species that live in Greece was based on the complete mitochondrial cytochrome b gene (1140 bp). The great diversity of the Greek cyprinid fauna, with at least 4 different lineages of barbins, 1 of gobionins, and 10 of leuciscinids, was confirmed. The validity and composition of the genera Tropidophoxinellus and Pachychilon were demonstrated. Likewise, the close phylogenetic relationships of genera Vimba, Blicca, and Abramis, as well as Telestes, Chondrostoma, and Phoxinellus, were established. Moreover, Pseudophoxinus beoticus was found to be closely related to Phoxinellus rather than to other Pseudophoxinus species. The most interesting outcome of our analyses was the existence of at least two different origins of the Greek cyprinid fauna. Most of the Greek cyprinids were directly related to the Danubian (i.e., central European) ichthyofauna. However, we found at least four cases of a close phylogenetic relationship between Greek and Iberian endemic species.

Phylogenetic Relationships among Fantail Darters (Percidae: Etheostoma: Catonotus): Total Evidence Analysis of Morphological and Molecular Data

Results of a phylogenetic analysis of the complete mitochondrial cytochrome b gene (1140 base pairs) for all species of Catonotus are presented along with a synthesis and phylogenetic analysis of published morphological data. The two datasets are combined in a total evidence analysis, and results from the molecular, morphological, and total evidence datasets are compared with each other and with previously published hypotheses. Phylogenetic relationships suggested by morphological data are similar to those from previous studies. The cytochrome b and total evidence analyses also produced trees that are generally congruent with previous hypotheses. The monophyly of the Etheostoma squamiceps group and the monophyly of a clade including members of the E. virgatum and E. flabellare groups are well supported. However, in contrast to traditional classification, E. barbouri usually clustered with the E. flabellare group, and E. percnurum usually clustered with the E. virgatum group. Etheostoma percnurum and E. barbouri possess many autapomorphies, and it is possible that they share fewer cytochrome b characters with close relatives than they share with other species due to homoplasy resulting from accelerated rates of evolution. Also, in contrast to earlier hypotheses, the molecular and total evidence analyses suggested that E. squamiceps, E. crossopterum, and E. olivaceum are closely related. An earlier hypothesis based on morphology suggested that E. olivaceum was basal to other members of the E. squamiceps group and that E. squamiceps was related to E. chienense, E. pseudovulatum, E. oophylax, and E. neopterum. Etheostoma olivaceum has been considered basal because it lacks putative synapomorphies of all other members of the E. squamiceps group. Although reversals (in E. olivaceum) and convergence (in E. squamiceps) in character states are possible, a test of the two hypotheses of relationship requires additional data.

Phylogenetic Study of Complete Cytochrome b Genes in Musk Deer (Genus Moschus) Using Museum Samples

As an endangered animal group, musk deer (genus Moschus) are not only a great concern of wildlife conservation, but also of special interest to evolutionary studies due to long-standing arguments on the taxonomic and phylogenetic associations in this group. Using museum samples, we sequenced complete mitochondrial cytochrome b genes (1140 bp) of all suggested species of musk deer in order to reconstruct their phylogenetic history through molecular information. Our results showed that the cytochrome b gene tree is rather robust and concurred for all the algorithms employed (parsimony, maximum likelihood, and distance methods). Further, the relative rate test indicated a constant sequence substitution rate among all the species, permitting the dating of divergence events by molecular clock. According to the molecular topology, M. moschiferus branched off the earliest from a common ancestor of musk deer (about 700,000 years ago); then followed the bifurcation forming the M. berezovskii lineage and the lineage clustering M. fuscus, M. chrysogaster, and M. leucogaster (around 370,000 years before present). Interestingly, the most recent speciation event in musk deer happened rather recently (140,000 years ago), which might have resulted from the diversified habitats and geographic barriers in southwest China caused by gigantic movements of the Qinghai–Tibetan Plateau in history. Combining the data of current distributions, fossil records, and molecular data of this study, we suggest that the historical dispersion of musk deer might be from north to south in China. Additionally, in our further analyses involving other pecora species, musk deer was strongly supported as a monophyletic group and a valid family in Artiodactyla, closely related to Cervidae.

Evolutionary affinities of the enigmatic saola (Pseudoryx nghetinhensis) in the context of the molecular phylogeny of Bovidae.

To elucidate the systematic status of the enigmatic saola (Pseudoryx nghetinhensis), a new bovid genus recently discovered in Vietnam, and to investigate phylogenetic relationships within the family Bovidae, four distinct DNA markers were sequenced. Complete mitochondrial cytochrome b (1143 bp) and 12S rRNA (956 bp) genes and non-coding regions from the nuclear genes for aromatase cytochrome P-450 (199 bp) and lactoferrin (338 bp) have been compared for 25 bovid species and three Cervidae and Antilocapridae outgroups. Independent and/or combined analyses of the four nucleotide matrices through maximum parsimony and maximum-likelihood methods indicated that Bovidae consists of two major lineages, i.e. Bovinac which contains the tribes Bovini, Boselaphini and Tragelaphini, and Antilopinae which encompasses all other bovids. Within Bovinae, the tribe Bovini is divided into buffalo Bovini (Bubalus and Syncerus) and cattle Bovini (Bos and Bison) and Tragelaphini are possibly related to Boselaphini. Pseudoryx is shown to be (i) robustly nested within Bovinae; (ii) strongly associated with Bovini; and (iii) tentatively sharing a sister-group relationship with cattle Bovini. Within Antilopinae, three robust clades are in evidence: (i) Hippotragus and Damaliscus are linked to Ovis; (ii) Aepyceros joins Neotragus; and (iii) Cephalophus clusters with Oreotragus.

Sorting out tigers (Panthera tigris): mitochondrial sequences, nuclear inserts, systematics, and conservation genetics

AbstractSequences from complete mitochondrial cytochrome b genes of 34 tigers support the hypothesis that Sumatran tigers are diagnostically distinct from mainland populations. None of the latter, including Bengals, Siberians, or Indochinese tigers, were found to have fixed diagnostic characters. Phylogenetic analysis of these sequences confirms these results. Within the framework of a phylogenetic species concept, current evidence thus supports the recognition of two distinct taxa, and within the context of this definition they could be ranked at the species level. This paper also documents a previously unrecognized nuclear insert of mitochondrial DNA that includes, minimally, mitochondrial homologues of a control region that lacks the feline mitochondrial repeat sequences, a complete cytochrome b gene, and complete tRNAThr and tRNAsurPro genes. In a phylogenetic analysis of the nuclear cytochrome b‐like sequences and various feline mitochondrial sequences, the nuclear insert clusters with lion mitochondrial cytochrome b sequences, which suggests the insert is at least as old as the split between lions and tigers. The results of this study emphasize the importance of doing more to conserve Sumatran tigers. Because they are underrepresented in zoos relative to Bengals and Siberians, an effort should be made to increase captive breeding stocks of Sumatrans. That Sumatrans are a distinct taxonomic entity relative to mainland populations can be used in educational programs to increase conservation efforts within Indonesia.

Phylogenetic Relationships Between the Orders Artiodactyla and Cetacea: A Combined Assessment of Morphological and Molecular Evidence

A character analysis of selected conservative morphological traits from extant and fossil artiodactyls and cetaceans was combined with a similar analysis of conservative nucleotide positions from the complete mitochondrial cytochrome b sequences of available extant artiodactyls, cetaceans, sirenians, perissodactyls, and other mammals. This combined analysis focuses on the evidence that supports conflicting hypotheses of artiodactyl monophyly, including the affinities of hippopotamids and the monophyly or paraphyly of odontocete cetaceans. Highly conserved morphological traits of the astragalus and deciduous dentition provide strong corroboration of artiodactyl monophyly, including extant and fossil hippopotamids. In contrast, cytochrome b gene sequences are incapable of confirming this monophyly, due to excessive homoplasy of nucleotide and amino acid traits within extant Eutheria. In like manner, highly conserved and uniquely derived morphological features of the skull and auditory regions provide robust corroboration of Odontoceti monophyly, including extant and fossil physeteroids. Several nucleotide similarities do exist between physeteroids and mysticetes; however, most are either silent third-position transversions or occur also in two or more odontocete families. We suggest that increased taxon sampling, combined with functional considerations of amino acids and their secondary structure in protein-coding genes, are essential requirements for the phylogenetic interpretations of molecules at higher taxonomic levels, especially when they conflict with well-supported hypotheses of mammalian phylogeny, corroborated by uniquely derived morphological traits from extant and fossil taxa.

Molecular Systematics of the Subfamily Caprinae (Artiodactyla, Bovidae) as Determined from Cytochrome b Sequences

We have sequenced the complete mitochondrial DNA cytochrome b gene from 18 species of the subfamily Caprinae and two outgroup taxa. Additional sequences retrieved from the literature were used to constitute a data set of 32 cytochrome b sequences comprising all genera usually included within the Caprinae. Phylogenetic relationships were assessed by PAUP using three new weighting schemes based on homoplasy analyses. Each type of substitution considered at each of the three codon positions was weighted according to its homoplasy level, as measured by the consistency index (CI), the slope of saturation (S), or their product (CIS). These differentially weighted parsimony analyses indicate that (1) the subfamily Caprinae is monophyletic, but only with the exclusion of Saiga from the group; (2) there is no support for monophyly of the four tribes currently recognized (Caprini, Rupicaprini, Ovibovini, and Saigini), suggesting relationships different from those traditionally accepted; (3) the caprine group consists of three major clades corresponding to (a) Budorcas and Ovis, (b) Capricornis, Ovibos, and Naemorhedus, and (c) Capra, Hemitragus, and Pseudois; and (4) the basal branching pattern is very weakly supported by bootstrap or branch support values except for the sister-group relationship of Pantholops with all other caprines, and the phylogenetic positions of Ammotragus, Oreamnos, and Rupicapra remain unclear.

Phylogeny of 6 Sciurus aberti Subspecies Based On Nucleotide Sequences of Cytochrome b

The tassel-eared squirrel, Sciurus aberti, is separated into six subspecies which occupy restricted and comparable habitats in ponderosa pine forests in the southwestern United States and Mexico. These forests and squirrel populations are currently isolated by large arid areas and, as such, S. aberti appears to offer an example of incipient speciation. We sequenced the complete mitochondrial cytochrome b gene to construct a molecular phylogeny for S. aberti and to determine whether subspecific genetic structure and geographic patterns are correlative. Twenty alleles were identified among 612 squirrels throughout the species′ range. Nucleotide divergence between alleles ranged from 0.009 to 0.0233, whereas average sequence divergence between S. aberti and an outgroup species, Sciurus niger, was 0.1823. Neighbor-joining and maximum parsimony analyses identified three major genetic assemblages composed of the following subspecies groups: (1) barberi and durangi; (2) aberti and kaibabensis; and (3) ferreus. The chuscensis samples were the only population with divergent sequences; one sequence was identical to an aberti sequence and a second unique sequence clustered with the ferreus sequences. The presence of divergent sequences in the chuscensis population, coupled with its central geographic position between aberti and ferreus, suggests a relatively recent influx of aberti mtDNA. Estimates of the times separating sequences in subspecies within different groups ranged from 0.94 to 1.52 × 10 6 years, based on a rate estimate of 7.15 × 10 −9 substitutions/year/site. The limited divergence observed between (1) aberti and kaibabensis as well as (2) barberi and durangi suggests relatively recent separations of subspecies within each assemblage. In fact, populations defined morphologically and geographically as ferreus exhibited greater sequence divergence than the aforementioned groups, identifying ferreus as the subspecies with the greatest genetic substructuring. The levels of cytochrome b divergence observed for the three distinct groups argues against a significant role for late Pleistocene glaciation in dispersal of this particular species; however, the proposed intermixing of aberti and chuscensis populations may well have been associated with such glacial events. Nucleotide diversity within subspecies ranked chuscensis ⪢ aberti > barberi ≍ kaibabensis ≍ ferreus subpopulations; the relatively high level of diversity of chuscensis samples likely results from the apparent introgression of an aberti haplotype. The comparative levels of diversity in the aberti, barberi, kaibabensis, and ferreus sample populations do not correlate with respective habitat size (and presumably population size), suggesting that relatively recent forces, e.g., glaciation and inconsistent timber harvests, may have influenced diversity in these populations without apparent alterations in population size.