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

Bilateral gynandromorphy in a White-ruffed Manakin (Corapipo altera)

We report bilateral gynandromorphy in a White-ruffed Manakin (Corapipo altera) collected near Santa Fé, Panamá in 2004. The specimen had an oviduct and ovary on the left side and a single testis on the right. The plumage was phenotypically female on the right side and male on the left. The weight and genetic affinity of the specimen were characteristically female. Both Z and W chromosomes were detected in genetic samples from multiple tissue types and toe pads from both feet. This report is a novel record of gynandromorphy in a suboscine passerine

A phylogeographic and population genetic analysis of a widespread, sedentary North American bird: The Hairy Woodpecker (Picoides villosus)

The Hairy Woodpecker (Picoides villosus) has one of the broadest breeding distributions of any North American bird and is also one of the most morphologically variable with as many as 21 described subspecies. This wide distribution and high degree of phenotypic diversity suggests the presence of underlying genetic structure. We used ND2 sequence from 296 individuals from 89 localities throughout the Hairy Woodpecker distribution to address this question and to explore this species’ evolutionary history. Phylogenetic analyses identified three main Hairy Woodpecker clades, each ~1.5% divergent from one another. One clade was comprised of birds from boreal and eastern zones of North America (N&E); the second, of birds from western and southwestern North America (S&W), and the third included only birds from a disjunct population in Costa Rica and Panama. Population genetic analyses and climatic niche models indicated that the N&E and S&W clades have very different recent evolutionary histories. Populations in the N&E are characterized by a lack of genetic structure and a genetic signature of recent population expansion. In contrast, S&W populations are highly structured and relative population stability was inferred. The S&W clade is further structured into three additional geographically and genetically isolated groups: Pacific Coast ranges, interior ranges, and southern Mexico. The continental scale patterns of genetic variation observed suggest that the complex topography of the montane west has probably been more important than latitude in generating phylogenetic diversity within this species

Testing hypotheses of Pleistocene population history using coalescent simulations: phylogeography of the pygmy nuthatch (Sitta pygmaea)

In this paper, we use mitochondrial NADH dehydrogenase subunit 2 sequences to test Pleistocene refugial hypotheses for the pygmy nuthatch (Sitta pygmaea). Pygmy nuthatches are a common resident of long-needle pine forests in western North America and demonstrate a particular affinity with ponderosa pine (Pinus ponderosa). Palaeoecological and genetic data indicate that ponderosa pine was isolated in two Pleistocene refugia corresponding to areas in the southern Sierra Nevada in the west and southern Arizona and New Mexico in the east. We use coalescent simulations to test the hypothesis that pygmy nuthatches tracked the Pleistocene history of their preferred habitat and persisted in two refugia during the periods of glacial maxima. Coalescent simulation of population history does not support the hypothesis of two Pleistocene refugia for the pygmy nuthatch. Instead, our data are consistent with a single refuge model. Nucleotide diversity is greatest in the western populations of southern and coastal California. We suggest that the pygmy nuthatch expanded from a far western glacial refuge into its current distribution since the most recent glacial maximum

Phylogeography of the White-Breasted Nuthatch (Sitta carolinensis), Diversification in North American pine and oak woodlands

Pine and oak woodlands are common North American floral communities with distinct regional species composition. The white-breasted nuthatch (Aves: Sitta carolinensis) is a common resident bird of North American pine and oak woodlands, and is distributed continentally across the highly disjunct distribution of these woodlands. We propose three historical hypotheses to explain the evolution of the white-breasted nuthatch in its principal habitat. (i) The species evolved in situ in the regional pine–oak communities and the isolation of populations in these regions is captured in cryptic genetic variation. (ii) Migration of individuals between regions is frequent enough to maintain the widespread distributions and prevent regional divergence. (iii) The species have recently expanded to occupy their current distributions and an insufficient amount of time has passed for divergence to occur. Phylogenetic analysis of mitochondrial DNA (ND2 gene) variation (N = 216) in the white-breasted nuthatch reveals four reciprocally monophyletic clades concordant with the distribution of the regional North American pine and oak woodlands, and supports hypothesis 1 of in situ evolution of populations in the regional pine and oak communities. Within-clade population structure and demographic history are also discussed

A molecular phylogenetic analysis of the “true thrushes” (Aves: Turdinae)

The true thrushes (Passeriformes: Muscicapidae, subfamily Turdinae) are a speciose and widespread avian lineage presumed to be of Old World origin. Phylogenetic relationships within this assemblage were investigated using mitochondrial DNA (mtDNA) sequence data that included the cytochrome b and ND2 genes. Our ingroup sampling included 54 species representing 17 of 20 putative turdine genera. Phylogenetic trees derived via maximum parsimony and maximum likelihood were largely congruent. Most of the Turdine taxa sampled can be placed into one of six well supported clades. Our data indicate a polyphyletic Zoothera which can be divided into at least two (Afro-Asian and Austral-Asian) main clades. The genus Turdus, as presently recognized, is paraphyletic but forms a well supported clade with the addition of three mostly monotypic genera (Platycichla, Nesocichla, and Cichlherminia). We identify an exclusively New World clade that includes a monophyletic Catharus, Hylocichla, Cichlopsis, Entomodestes, Ridgwayia, and Ixoreus. Members of the morphologically and behaviorally distinct genera Sialia, Myadestes, and Neocossyphus unexpectedly form a basal clade. Using multiple outgroup choices, we show that this group is distantly related, but unequivocally the sister group to the remaining Turdines sampled. The Turdinae appear to be a relatively old songbird lineage, originating in the mid to late Miocene. If the Turdinae are indeed Old World in origin, our data indicate a minimum of three separate invasions of the New World

Defining a monophyletic Cardinalini: A molecular perspective

Within the New World nine-primaried oscine assemblage, feeding morphology and behavior have long been used as a guideline for assigning membership to subgroups. For example, birds with stout, conical bills capable of crushing heavy seeds have generally been placed within the tribe Cardinalini (cardinal-grosbeaks). Many workers have tried to characterize this group more definitively, using a variety of morphological characters; however, the characters used often conflicted with one another. Previous molecular studies addressing the monophyly of Cardinalini have had only limited sampling within the group. In this study, we analyze mtDNA sequence data from all genera and 34 of the 42 Cardinalini species (sensu [Sibley, C.G., Monroe, B.L., 1990. Distribution and Taxonomy of the Birds of the World, Yale University Press, New Haven, CT]) to address the monophyly of the group and to reconstruct the most complete phylogeny of this tribe published to date. We found strong support for a redefined Cardinalini that now includes some members previously placed within Thraupini (tanagers; the genera Piranga, Habia, Chlorothraupis, and Amaurospiza) and some members previously placed within the Parulini (wood-warblers; the genus Granatellus). In addition, some genera traditionally considered members of the Cardinalini are shown to have affinities with other groups (the genera Porphyrospiza, Parkerthraustes, and Saltator). Our redefined Cardinalini contains 48 species, six more than are listed in Sibley and Monroe’s (1990) taxonomy of the group. Within the nine-primaried oscine assemblage, the Cardinalini are more closely related to the Thraupini (tanagers) than they are to the Emberizini (sparrows), Parulini (wood-warblers), or Icterini (blackbirds), consistently forming a monophyletic group with Thraupini across all analyses. The reconfigured Cardinalini is comprised of five well-supported, major clades: (1) a ‘‘masked’’ clade (Piranga, Cardinalis, Caryothraustes, Periporphyrus, and Rhodothraupis), (2) a ‘‘blue’’ clade (Amaurospiza, Cyanocompsa, Cyanoloxia, Passerina, and Spiza), (3) a clade containing the genera Habia and Chlorothraupis, (4) a clade containing all species of Granatellus, and (5) a clade containing only species of Pheucticus. Diversification of these five lineages from one another occurred relatively rapidly during the mid-Pliocene, around 5 or 8 million years ago. Each of these major clades includes both North and South American species; thus, a complex biogeographic history is inferred for the group

Cryptic diversity in a widespread North American songbird: Phylogeography of the Brown Creeper (Certhia americana)

The identification of species via morphological characteristics has traditionally left cryptic species undescribed in taxa under selection for morphological conservation (or a lack of selection for morphological change). Treecreepers (Genus: Certhia) have a conserved morphological appearance, making it difficult to ascertain relationships in the genus based on morphology alone. Recent genetic and song structure studies of Eurasian Treecreepers identified cryptic species within Old World Certhia that were previously undescribed using morphological characteristics. Here, we use mtDNA to investigate cryptic diversity and patterns of diversification in the Brown Creeper (Certhia americana), the single described Certhia species in the Americas. Phylogenetic analyses identified six well-supported geographically-structured clades; the basal divergence separates a northern and a southern lineage in the Brown Creeper, likely cryptic species previously characterized as many subspecies. Sympatry is prevalent between clades in western North America, where possible contact zones warrant further investigation. Allopatry appears to be the primary driver of deep phylogeographic structure within the Brown Creeper; however, within clade diversity is highly correlated with the life history traits of the populations that comprise the geographically structured phylogroups

Phylogeography of the Mountain Chickadee (Poecile gambeli): diversification, introgression, and expansion in response to Quaternary climate change

Since the late 1990s, molecular techniques have fuelled debate about the role of Pleistocene glacial cycles in structuring contemporary avian diversity in North America. The debate is still heated; however, there is widespread agreement that the Pleistocene glacial cycles forced the repeated contraction, fragmentation, and expansion of the North American biota. These demographic processes should leave genetic ‘footprints’ in modern descendants, suggesting that detailed population genetic studies of contemporary species provide the key to elucidating the impact of the late Quaternary (late Pleistocene–Holocene). We present an analysis of mitochondrial DNA (mtDNA) variation in the mountain chickadee (Poecile gambeli) in an attempt to examine the genetic evidence of the impact of the late Quaternary glacial cycles. Phylogenetic analyses reveal two strongly supported clades of P. gambeli: an Eastern Clade (Rocky Mountains and Great Basin) and a Western Clade (Sierra Nevada and Cascades). Post-glacial introgression is apparent between these two clades in the Mono Lake region of Central California. Within the Eastern Clade there is evidence of isolation-by-distance in the Rocky Mountain populations, and of limited gene flow into and around the Great Basin. Coalescent analysis of genetic variation in the Western Clade indicates that northern (Sierra Nevada/Cascades) and southern (Transverse/Peninsular Ranges) populations have been isolated and evolving independently for nearly 60 000 years