Phylogenetic relationships of the African bush-shrikes and helmet-shrikes (Passeriformes: Malaconotidae)

The African bush-shrikes and helmet-shrikes (Malaconotidae sensu [A Complete Checklist of the Birds of the World, third ed., Helm Editions, London, 2003]) include 10 genera and 52 species of predatory passerine birds for which monophyly, sister-group, and inter-generic relationships are disputed. To resolve their relationships, we analyzed 2313 bp of sequence data obtained from two nuclear introns (myoglobin intron-2, beta-fibrinogen intron-5) and a mitochondrial protein-coding gene (ND2) using parsimony, maximum likelihood, and Bayesian inference. A strongly supported clade that included representatives of the Malaconotidae, Platysteiridae, and Vangidae was found in all analyses. Three main groups emerged within this clade but relationships between these three groups were always poorly supported. The first group included the helmet-shrikes (Prionops), flycatcher-shrikes (Bias and Megabyas), and vangas (Cyanolanius and Pseudobias), currently placed in the families Malaconotidae, Platysteiridae, and Vangidae, respectively. The second group consisted of four Platysteiridae genera (Lanioturdus, Batis, Platysteira, and Dyaphorophyia), with the remaining Malaconotidae genera ('core malaconotids') forming the last group. Two main clades emerged within the 'core malaconotids,' with the position of the genus Nilaus being variable. The first clade included Malaconotus, Dryoscopus, Bocagia, and Tchagra and the second Chlorophoneus, Laniarius, Rhodophoneus, and Telophorus. Monophyly of the genus Chlorophoneus was never recovered, a result that is consistent with morphological data.     

Molecular systematics of the western rattlesnake, Crotalus viridis (Viperidae), with comments on the utility of the D-loop in phylogenetic studies of snakes.

Crotalus viridis, the western rattlesnake, ranges throughout western North America and has been divided into at least eight subspecies. However, the validity of and relationships among these subspecies and the monophyly of C. viridis as a whole are questionable. We used mitochondrial DNA sequence data from the D-loop region and ND2 gene to examine the relationships among 26 populations of C. viridis and to test the monophyly of this species. These data were analyzed separately and combined using maximum-likelihood and maximum-parsimony. The C. viridis group was monophyletic in all combined analyses, consisting of two strongly divergent clades. We recommend that these clades be recognized as two distinct evolutionary species: C. viridis and C. oreganus. Crotalus viridis should be restricted to the subspecies viridis and nuntius and the remaining subspecies be assigned to the species C. oreganus. Our data do not allow strong evaluation of the validity of the subspecies. We found that the ND2 gene had greater sequence divergences among closely related individuals than the D-loop region, but this relationship reversed at higher levels of divergence. This pattern is apparently due to: (1) ND2 third positions evolving faster than the D-loop but becoming saturated at higher levels of divergence, and (2) the D-loop evolving faster than ND2 second (and possibly first) positions. Our results suggest that the ND2 gene is preferable for examining intraspecific relationships and the D-loop may better resolve relationships between species of snakes. The latter result is contrary to the common perception of the phylogenetic utility of the D-loop. Another unusual result is that the 145 bp spacer region, adjacent to the 5' end of the light strand of the D-loop, provides greater phylogenetic resolution than the 1030 bp D-loop.     

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.     

Complex biogeographic history of the cuckoo-shrikes and allies (Passeriformes: Campephagidae) revealed by mitochondrial and nuclear sequence data

The Campephagidae (minivets, cuckoo-shrikes and trillers, seven genera and 81 species) represents an Old World corvid clade of tropical birds with a mixed diet that forage in different manners, i.e., flycatching, foliage-gleaning or shriking. This family has never been the focus of any phylogenetic survey, so their phylogenetic relationships and biogeographic history remain largely unknown. To address these questions, we sequenced four loci (ND2, myoglobin intron-2, GAPDH intron-11 and c-mos) for 27 species of Campephagidae. Our analyses suggest that Coracina consists of five unrelated lineages and that Lalage is paraphyletic. Our dating analyses, using a Bayesian relaxed-clock method, indicate that the split between the Indo-Malayan genus Pericrocotus and the remaining Campephagidae occurred synchronously with other splits involving Indo-Malayan corvid lineages, suggesting that several lineages of Indo-Malayan birds were isolated at the same time from their closest relatives. The African stock of cuckoo-shrikes is likely the result of three independent trans-oceanic dispersals from Australasia.     

Phylogeography of the greenside darter complex, Etheostoma blennioides (Teleostomi: Percidae): a wide-ranging polytypic taxon

The greenside darter, Etheostoma blennioides (Teleostomi: Percidae), is a wide-ranging polytypic taxon that occurs throughout eastern North America. A previous morphological study recognized four subspecies (blennioides, newmanii, gutselli, and pholidotum), several morphological races, and three zones of morphological intergradation. We generated complete cytochrome b (1140bp) sequence data for 51 individuals from across the range of the greenside darter inclusive of all of the currently recognized taxa to assess genetic variation and taxonomic boundaries. Both maximum parsimony and mixed model Bayesian analyses resulted in two strongly supported deeply divergent clades including (1) a Tennessee River drainage clade, and (2) an Ohio River and Great Lakes basins, Interior Highlands, and Atlantic slope clade. Etheostoma blennius, a closely related congener, nested within the Tennessee River clade of E. blennioides, rendering the complex paraphyletic. Test of alternative topologies failed to support the current taxonomic designations. The inclusion of nuclear sequence data from intron 1 of the S7 ribosomal protein (523bp) from a subset of the populations was included to independently test whether the currently recognized taxa conform to distinct evolutionary lineages and also to clarify potential issues associated with ancestral hybridization. Although the nuclear data was less variable than the mitochondrial data, the monophyly of several of the subspecies could not be rejected.     

Genetic analysis and uncertain taxonomic status of threatened Foskett Spring speckled dace

Foskett Spring is a small isolated desert spring in the Warner Basin of Oregon containing an undescribed subspecies of speckled dace protected under the US Endangered Species Act. Uncertainty regarding the taxonomic status of Foskett dace has raised questions about their evolutionary relationship to other more abundant populations in the Warner Basin. To address these questions, we sequenced 1,982 base pairs (bp) of the ND2 and cyt-b genes of mitochondrial DNA (mtDNA) for 85 fish from Foskett Spring, the surrounding Warner Basin, and the adjacent Goose Lake Basin. We observed 58 unique mtDNA haplotypes defined by 96 bp substitutions in both genes. MtDNA sequences were highly divergent and reciprocally monophyletic between dace from the Warner and Goose Lake Basins, with sequence divergences (5 and 3% at ND2 and cyt-b, respectively) in the range usually observed between fish species. In contrast, mean sequence divergence between Foskett dace and other Warner Basin populations was less than 1%, with no evidence of reciprocal monophyly among mtDNA lineages. These results indicate that Foskett dace and other populations in the Warner Basin are approximately equally diverged from one another evolutionarily, suggesting similar times of divergence since the late Pleistocene. We believe further studies are needed to determine if rapid evolution of novel traits have occurred in dace inhabiting the unique ecological setting of Foskett Spring during the past 10,000 years.     

Speciation in chestnut-shouldered fairy-wrens (Malurus spp.) and rapid phenotypic divergence in variegated fairy-wrens (Malurus lamberti): a multilocus approach

The chestnut-shouldered fairy-wrens comprise a subgroup of four species in the genus Malurus (Passeriformes: Maluridae). Collectively, they are widespread across the Australian continent but phenotypic variation is strongly structured geographically in just one species, M. lamberti. Earlier phylogenetic analyses of this group have been limited to one or two individuals for each species and have not represented all currently recognised subspecies of M. lamberti. Historically, the taxonomy and nomenclature of the M. lamberti complex has been debated, in part because of morphological similarities among its subspecies and another member of the group, M. amabilis. We reconstructed the phylogeny of all four species of chestnut-shouldered fairy-wrens including all four subspecies of M. lamberti using a mitochondrial gene (ND2), five anonymous nuclear loci and three nuclear introns. Phylogenetic analysis of the mitochondrial ND2 gene nests M. amabilis within M. lamberti rendering the latter paraphyletic. Individual nuclear gene trees failed to reliably resolve each of the species boundaries or the phylogenetic relationships found in the mtDNA tree. When combined, however, a strongly supported overall topology was resolved supporting the monophyly of M. lamberti and its sister species relationship to M. amabilis. Current subspecific taxonomy of M. lamberti was not concordant with all evolutionary lineages of M. lamberti, nominotypical M. l. lamberti being the only subspecies recovered as a monophyletic group from mtDNA. Some genetic structuring is evident and potential barriers to gene flow are discussed.     

Delimiting shades of gray: phylogeography of the Northern Fulmar,Fulmarus glacialis

The Northern Fulmar (Fulmarus glacialis) is a common tube‐nosed seabird with a disjunct Holarctic range. Taxonomic divisions within the Northern Fulmar have historically been muddled by geographical variation notably including highly polymorphic plumage. Recent molecular analyses (i.e., DNA barcoding) have suggested that genetic divergence between Atlantic and Pacific populations could be on par with those typically observed between species. We employ a multigene phylogenetic analysis to better explore the level of genetic divergence between these populations and to test an old hypothesis on the origin of the modern distribution of color morphs across their range. Additionally, we test whether mutations in the melanocortin‐1 receptor gene (MC1R) are associated with dark plumage in the Northern Fulmar. We confirmed that mitochondrial lineages in the Atlantic and Pacific populations are highly divergent, but nuclear markers revealed incomplete lineage sorting. Genetic divergence between these populations is consistent with that observed between many species of Procellariiformes and we recommend elevating these two forms to separate species. We also find that MC1R variation is not associated with color morph but rather is better explained by geographical divergence.     

A molecular assessment of phylogenetic relationships and lineage accumulation rates within the family Salamandridae (Amphibia, Caudata)

We examine phylogenetic relationships among salamanders of the family Salamandridae using approximately 2700 bases of new mtDNA sequence data (the tRNALeu, ND1, tRNAIle, tRNAGln, tRNAMet, ND2, tRNATrp, tRNAAla, tRNAAsn, tRNACys, tRNATyr, and COI genes and the origin for light-strand replication) collected from 96 individuals representing 61 of the 66 recognized salamandrid species and outgroups. Phylogenetic analyses using maximum parsimony and Bayesian analysis are performed on the new data alone and combined with previously reported sequences from other parts of the mitochondrial genome. The basal phylogenetic split is a polytomy of lineages ancestral to (1) the Italian newt Salamandrina terdigitata, (2) a strongly supported clade comprising the "true" salamanders (genera Chioglossa, Mertensiella, Lyciasalamandra, and Salamandra), and (3) a strongly supported clade comprising all newts except S. terdigitata. Strongly supported clades within the true salamanders include monophyly of each genus and grouping Chioglossa and Mertensiella as the sister taxon to a clade comprising Lyciasalamandra and Salamandra. Among newts, genera Echinotriton, Pleurodeles, and Tylototriton form a strongly supported clade whose sister taxon comprises the genera Calotriton, Cynops, Euproctus, Neurergus, Notophthalmus, Pachytriton, Paramesotriton, Taricha, and Triturus. Our results strongly support monophyly of all polytypic newt genera except Paramesotriton and Triturus, which appear paraphyletic, and Calotriton, for which only one of the two species is sampled. Other well-supported clades within newts include (1) Asian genera Cynops, Pachytriton, and Paramesotriton, (2) North American genera Notophthalmus and Taricha, (3) the Triturus vulgaris species group, and (4) the Triturus cristatus species group; some additional groupings appear strong in Bayesian but not parsimony analyses. Rates of lineage accumulation through time are evaluated using this nearly comprehensive sampling of salamandrid species-level lineages. Rate of lineage accumulation appears constant throughout salamandrid evolutionary history with no obvious fluctuations associated with origins of morphological or ecological novelties.     

Phylogeny of hoplocercine lizards (Squamata: Iguania) with estimates of relative divergence times

Hoplocercine lizards form a clade of 11 currently recognized species traditionally placed in three genera (Enyalioides, Hoplocercus, and Morunasaurus) that occur in the lowlands on both sides of the Andes between Panama and the Brazilian Cerrado. We analyze 11 mitochondrial and two nuclear loci using probabilistic methods and different partitioning strategies to (1) infer the phylogenetic relationships among species of Hoplocercinae, (2) examine amounts of inter- and intraspecific sequence divergence, (3) address monophyly of four species, (4) test previous phylogenetic hypotheses, and (5) estimate divergence times. Our preferred hypothesis places H. spinosus as the sister taxon to all other species of hoplocercines, with M. annularis nested within Enyalioides. Species with multiple samples are monophyletic except for Enyalioides oshaughnessyi, which is paraphyletic relative to an undescribed species of Enyalioides. All previously published phylogenetic hypotheses for hoplocercines are rejected. Monophyly of Enyalioides cannot be rejected and, consequently, the position of Morunasaurus remains unclear. The most recent common ancestor of Hoplocercinae probably occurred east of the Andes; western taxa included in our analyses originated from at least two separate colonizations whether pre- or post-dating vicariance resulting from uplift of the Andes.     

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.     

Molecular systematics of sponges (Porifera)

The first application of molecular systematics to sponges was in the 1980s, using allozyme divergence to dis-criminate between conspecific and congeneric sponge populations. Since this time, a fairly large database has been accumulated and, although the first findings seemed to indicate that sponge species were genetically more divergent than those of other marine invertebrates, a recent review of the available dataset indicates that levels of interspecific gene identities in most sponges fall within the normal range found between species of other invertebrates. Nevertheless, some sponge genera have species that are extremely divergent from each other, suggesting a possible polyphyly of these genera. In the 1990s, molecular studies comparing sequences of ribosomal RNA have been used to reappraise the phylogenetic relationships among sponge genera, families, orders and classes. Both the 18S small subunit and the 28S large subunit rRNA genes have been sequenced (41 complete or partial and 75 partial sequences, respectively). Sequences of 18S rRNA show good support for Porifera being true Metazoa, but they are not informative for resolving relationships among genera, families or orders. 28S rRNA domains D1 and D2 appear to be more informative for the terminal nodes and provide resolution for internal topologies in sufficiently closely related species, but the deep nodes between orders or classes cannot be resolved using this molecule. Recently, a more conserved gene, Hsp70, has been used to try to resolve the relationships in the deep nodes. Metazoan monophyly is very well supported. Nevertheless, the divergence between the three classes of Porifera, as well as the divergence between Porifera, Cnidaria and Ctenophora, is not resolved. Research is in progress using other genes such as those of the homeodomain, the tyrosine kinase domain, and those coding for the aggregation factor. For the moment the dataset for these genes is too restricted to resolve the phylogenetic relationships of these phyla. However, whichever the genes, the phylogenies obtained suggest that Porifera could be paraphyletic and that the phylogenetic relationships of most of the families and orders of the Demospongiae have to be reassessed. The Calcarea and Hexactinellida are still to be studied at the molecular level.     

Phylogeography and conservation genetics of the hellbender salamander (Cryptobranchus alleganiensis)

We investigated hellbender phylogeography through phylogenetic analyses of individuals sampled from 16 locations throughout their range in the eastern United States. Analyses were conducted on concatenated cytochrome-oxidase I (COI), cytochrome-b (Cytb) and NADH dehydrogenase subunit 4 (ND4) mtDNA sequence, totaling 2160 nucleotides. Hellbender haplotypes differed by 0.1 to 5.8% maximum likelihood (ML) corrected sequence divergence. Phylogenetic analyses reveal that hellbenders are separated into 8 reciprocally monophyletic populations or clades differentiated by a minimum of 0.7 to 5.4% sequence divergence, each of which constitutes a separate Management Unit (MU). High among population divergence and reciprocal monophyly suggest that female-mediated gene flow is severely restricted or non-existent among each MU. Hellbenders are currently divided into two subspecies, Cryptobranchus alleganiensis alleganiensis and C. a. bishopi based on morphological characters. The phylogenetic analyses presented here strongly indicate that these subspecies are paraphyletic. Management priorities for the hellbender should be reconsidered in light of these new molecular data. Results from Bayesian rooting indicate the root of the hellbender mtDNA tree lies on the branch leading to hellbender haplotypes from the Current, Eleven Point and New Rivers. The rooted tree suggests that a common ancestor in the southern Ozarks and/or southern Appalachians gave rise to northern hellbender populations, consistent with a Pleistocene refuge hypothesis.     

Weak large‐scale population genetic structure in a philopatric seabird,the European Shag Phalacrocorax aristotelis

Quantifying population genetic structure is fundamental to testing hypotheses regarding gene flow, population divergence and dynamics across large spatial scales. In species with highly mobile life‐history stages, where it is unclear whether such movements translate into effective dispersal among discrete philopatric breeding populations, this approach can be particularly effective. We used seven nuclear microsatellite loci and mitochondrial DNA (ND2) markers to quantify population genetic structure and variation across 20 populations (447 individuals) of one such species, the European Shag, spanning a large geographical range. Despite high breeding philopatry, rare cross‐sea movements and recognized subspecies, population genetic structure was weak across both microsatellites and mitochondrial markers. Furthermore, although isolation‐by‐distance was detected, microsatellite variation provided no evidence that open sea formed a complete barrier to effective dispersal. These data suggest that occasional long‐distance, cross‐sea movements translate into gene flow across a large spatial scale. Historical factors may also have shaped contemporary genetic structure: cluster analyses of microsatellite data identified three groups, comprising colonies at southern, mid‐ and northern latitudes, and similar structure was observed at mitochondrial loci. Only one private mitochondrial haplotype was found among subspecies, suggesting that this current taxonomic subdivision may not be mirrored by genetic isolation.     

A molecular phylogeny of the New World orioles (Icterus): the importance of dense taxon sampling.

We sequenced 2005 bp of the mitochondrial ND2 and cytochrome b genes from the 25 recognized species of New World orioles (Icterus). Our data confirmed the monophyly of Icterus and produced a well-resolved phylogeny showing three main clades of orioles. We also sequenced multiple subspecies for most polytypic taxa. Our findings demonstrated the importance of dense taxon sampling below the species level in two ways. First, we found evidence that two species are polyphyletic, I. galbula (Northern oriole) and I. dominicensis (Black-cowled oriole). Choosing different subspecies from either of these taxa would lead to different species-level phylogenies. Second, adding subspecies even to monophyletic groups produced a bootstrap tree with significantly more support. Of the two genes that we used, ND2 provided more resolution than did cytochrome b. ND2 evolved up to 40% faster than cytochrome b, yet shows a higher saturation threshold. Our findings suggest that ND2 may be superior to cytochrome b for resolving species-level phylogenies in passerine birds.     

Differentiation of the dragonfly genus Davidius (Odonata: Gomphidae) in Japan inferred from mitochondrial and nuclear gene genealogies

To infer the differentiation of Japanese Davidius dragonflies, we investigated the genealogies of the mitochondrial cytochrome oxidase subunit I gene (COI) and the nuclear ribosomal RNA gene region encompassing 18S, ITS1, 5.8S, and ITS2 sequences for three species endemic to Japan--Davidius nanus, D. fujiama, and D. moiwanus--as well as D. lunatus from the Korean Peninsula. According to the mitochondrial and nuclear gene genealogies, D. nanus and D. moiwanus are closely related and are sister to the continental species D. lunatus, whereas D. fujiama differentiated from an ancestor of the other three species. Although the mitochondrial DNA data did not resolve the relationships between D. nanus and three D. moiwanus subspecies, the nuclear DNA data indicate the monophyly of D. moiwanus and its subspecies. The nuclear gene genealogy suggests that isolated wetlands used by larval D. moiwanus derive from the ancestral riverine habitats of D. nanus and other Davidius species. The COI sequence divergence among local populations was much greater in D. moiwanus than in D. nanus, which may be the result of differences in the dispersal ranges associated with the habitat types of these species.     

Applications of ecological niche modeling for species delimitation: a review and empirical evaluation using day geckos (Phelsuma) from Madagascar

Although the systematic utility of ecological niche modeling is generally well known (e.g., concerning the recognition and discovery of areas of endemism for biogeographic analyses), there has been little discussion of applications concerning species delimitation, and to date, no empirical evaluation has been conducted. However, ecological niche modeling can provide compelling evidence for allopatry between populations, and can also detect divergent ecological niches between candidate species. Here we present results for two taxonomically problematic groups of Phelsuma day geckos from Madagascar, where we integrate ecological niche modeling with mitochondrial DNA and morphological data to evaluate species limits. Despite relatively modest levels of genetic and morphological divergence, for both species groups we find divergent ecological niches between closely related species and parapatric ecological niche models. Niche models based on the new species limits provide a better fit to the known distribution than models based upon the combined (lumped) species limits. Based on these results, we elevate three subspecies of Phelsuma madagascariensis to species rank and describe a new species of Phelsuma from the P. dubia species group. Our phylogeny continues to support a major endemic radiation of Phelsuma in Madagascar, with dispersals to Pemba Island and the Mascarene Islands. We conclude that ecological niche modeling offers great potential for species delimitation, especially for taxonomic groups exhibiting low vagility and localized endemism and for groups with more poorly known distributions. In particular, niche modeling should be especially sensitive for detecting recent parapatric speciation driven by ecological divergence, when the environmental gradients driving speciation are represented within the ecological niche models.     

Large sequence divergence of mitochondrial DNA genotypes of the control region within populations of the african antelope, kob (Kobus kob)

The genetic differentiation among kob populations (Kobus kob) representing two recognized subspecies was examined using mitochondrial control region sequences. Two distinct lineages (estimated sequence divergence of 9.8%) exhibited different geographical distributions and do not coincide with previously recognized ranges of subspecies. The presence of the two lineages was further supported with sequences of mitochondrial cytochrome b gene. One lineage was predominant in the west and southern ranges of the populations studied and the other was commonly found in a more northern distribution (Murchison populations) in Uganda. Murchison and the geographically intermediate Toro populations (Uganda) represented the area of overlap. The existence of the two lineages in the area of overlap is hypothesized to have resulted from a range expansion and secondary contact of the two lineages of kob that evolved in allopatry. The existence of the kob during the Pleistocene offers a plausible explanation for the observed biogeographic pattern. Our mitochondrial data reveal two examples of discordance between a gene tree and presumed species tree as: (i) the two lineages co-occur in the kob subspecies, Kobus kob thomasi (Uganda kob); and (ii) the puku, which was included in the analysis because of its controversial taxonomic status (currently recognized as a distinct species from the kob), is paraphyletic with respect to the kob. Significant degrees of heterogeneity were detected between populations. Relatively high genetic variation was observed in the populations, however, the inclusion of distinct lineages influences the population structure and nucleotide diversity of the kob populations.     

Evolutionary history of woodpeckers and allies (Aves: Picidae): placing key taxa on the phylogenetic tree

We analyzed 2995 base pairs of nucleotide sequence data (nuclear beta-fibrinogen intron 7 and mitochondrial cytochrome b and ND2 genes), using parsimony and model-based approaches to infer phylogenetic relationships of the woodpeckers and allies, yielding novel hypotheses for several critical gaps in the knowledge of picid phylogeny. We tested the monophyly of sub-families within the Picidae, and sampled from widely distributed and diverse genera (Celeus, Colaptes, Dryocopus, Melanerpes, Picoides, Picumnus, Sasia, Piculus, and Picus). Relationships of three poorly known Southeast Asian genera (Dinopium, Reinwardtipicus, and Blythipicus) were also examined, revealing unexpected sister relationships. All phylogenetic approaches recovered largely congruent topologies, supporting a monophyletic Picinae and paraphyletic Picumninae, with the monotypic piculet, Nesoctites micromegas, as sister to the Picinae. We report paraphyly for Celeus and Piculus, whereas the broadly distributed genera Picumnus and Dryocopus were supported as monophyletic. Our phylogenetic results indicate a complex geographic history for the Picidae, with multiple disjunct sister lineages distributed between the New World and Asia. The relationships and geographic distribution of basal picid lineages indicates an Old World origin of the Picidae; however, the geographic origin of the Picinae remains equivocal, as the sister relationship between the Caribbean N. micromegas and the true woodpeckers presents the possibility of a New World origin for the Picinae.     

Allozyme and morphological variation in two subspecies of Dryas octopetala (Rosaceae)in Alaska

The Alaskan endemic shrub Dryas octopetala ssp. alaskensis and its circumpolar conspecific ssp. octopetala are adapted to closely adjacent habitats in alpine areas of Alaska. These alpine areas form geographically disjunct "islands" among which there are limited opportunities for gene flow. Allozyme electrophoresis and a common garden experiment were used to examine genetic variation between subspecies and among disjunct populations of each subspecies. Overall, allozyme variation in D. octopetala is low with little differentiation among populations or between subspecies. Morphological differences, however, are greater between subspecies than among populations within subspecies. Divergence for a few morphological and life-history characters has apparently occurred in response to strong selection, but without divergence at allozyme loci. The ancestors of both subspecies of D. octopetala in Alaska were isolated during the Pleistocene in the glacial refugia of Alaska and Yukon, which may explain low overall variation. Dryas. o. alaskensis is thought to be a Pleistocene derivative of ssp. octopetala, which may account for the low allozyme divergence between subspecies. Recent restriction to alpine areas may explain the low differentiation among disjunct populations.