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

New World nine-primaried oscine relationships: constructing a molecular framework

Historically, a paucity of comparative morphological characters has led to much debate regarding relationships within and among the major lineages of New World nine-primaried oscines. More recently, DNA-DNA hybridization studies have provided novel and testable hypotheses of relationships, although no consensus has been reached. For 40 songbird taxa, we obtained 1,929 base pairs (bp) of DNA sequence from the mitochondrial cytochrome-b (894 bp) and NADH dehydrogenase subunit 2 (1,035 bp) genes. Phylogenetic analyses confirm the monophyly of this assemblage as traditionally defined. The lineages delineated historically on morphological grounds are retained; finches (Fringillinae) are sister to a well-supported clade (Emberizinae) containing blackbirds (Icterini), sparrows (Emberizini), wood-warblers (Parulini), tanagers (Thraupini), and cardinal-grosbeaks (Cardinalini). However, each tribe individually is either paraphyletic or polyphyletic with respect to most recent songbird classifications. Our results suggest that Euphonia is not a tanager but perhaps represents a derived form of cardueline finch. Piranga, traditionally considered a typical tanager, is a cardinaline in all of our analyses. Calcarius falls outside the sparrow lineage in all of our analyses, but its true affinities remain unclear. Elements of four different AOU families are represented in our clade Thraupini. The inclusion of several “tanager-finches” (Haplospiza, Diglossa, Tiaris, Volatinia, Sporophila) and a nectarivore (Coereba) in this clade is consistent with findings from other molecular phylogenies in suggesting that convergence in feeding specializations among some lineages has confounded traditional morphological classifications. We obtained a novel arrangement of relationships among tribes in our “best” topology; Cardinalini is sister to the rest of the Emberizinae assemblage (as defined by Sibley and Ahlquist [1990]), and Thraupini is sister to a clade containing Icterini, Emberizini, and Parulini. Despite nearly 2,000 bp of sequence for each taxon, and a high degree of stability across most weighting schemes and analytical methods, most nodes lack strong bootstrap support. The ND2 gene provided higher resolution than did cytochrome b, but combining genes provided the most highly supported and resolved topology. We consider the phylogeny a working hypothesis to be used as a guide for further studies within the nine-primaried oscine assemblage

Botteri\u27s Sparrow (Peucaea botterii) occurs in Northern Coahuila, Mexico

Botteri’s Sparrow (Peucaea botterii) occurs widely in the shrub-grasslands of southern North America. We report a breeding population of the species in the Sierra de la Encantada of northern Coahuila, Mexico, ~80 km from the Big Bend area of Texas and \u3e300 km from the nearest previously known breeding range in southern Coahuila and central Chihuahua. We captured three individuals, which show a mostly gray dorsal coloration, suggestive of the texana subspecies, occurring from southern Texas to northern Veracruz. The exact affinity of the northern Coahuila population still needs to be ascertained. The presence of Botteri’s Sparrow in northern Coahuila may have been overlooked previously or may be part of a (temporary) range expansion. More work is needed to map the occurrence of Botteri’s Sparrow in northcentral Mexico grasslands

A Cytochrome-b Perspective on Passerina Bunting Relationships

We sequenced the complete mitochondrial cytochrome-b gene (1,143 nucleotides) for representatives of each species in the cardinalid genera Passerina (6 species), Guiraca (1 species), and Cyanocompsa (3 species), and used a variety of phylogenetic methods to address relationships within and among genera. We determined that Passerina, as presently recognized, is paraphyletic. Lazuli Bunting (P. amoena) is sister to the much larger Blue Grosbeak (Guiraca caerulea). Indigo Bunting (P. cyanea) and Lazuli Bunting are not sister taxa as generally thought. In all weighted parsimony trees and for the gamma-corrected HKY tree, Indigo Bunting is the sister of two sister groups, a “blue” (Lazuli Bunting and Blue Grosbeak) and a “painted” (Rosita\u27s Bunting [P. rositae], Orange-breasted Bunting [P. leclancherii], Varied Bunting [P. versicolor], and Painted Bunting [P. ciris]) clade. The latter two species form a highly supported sister pair of relatively more recent origin. Uncorrected (p) distances for ingroup (Passerina and Guiraca) taxa range from 3.0% (P. versicolor–P. ciris) to 7.6% (P. cyanea–P. leclancherii) and average 6.5% overall. Assuming a molecular clock, a bunting “radiation” between 4.1 and 7.3 Mya yielded four lineages. This timing is consistent with fossil evidence and coincides with a late-Miocene cooling during which a variety of western grassland habitats evolved. A reduction in size at that time may have allowed buntings to exploit that new food resource (grass seeds). We speculate that the Blue Grosbeak subsequently gained large size and widespread distribution as a result of ecological character displacement

Evolutionary patterns of morphometrics, allozymes and mitochondrial DNA in thrashers (Genus Toxostoma)

We examined patterns of variation in skeletal morphometrics (29 characters), allozymes (34 loci), mitochondrial DNA (mtDNA) restriction sites (n = 74) and fragments (n = 395), and mtDNA sequences (1,739 bp from cytochrome b, ND2, ND6, and the control region) among all species of Toxostoma. The phenetic pattern of variation in skeletal morphometrics generally matched traditional taxonomic groupings (based on plumage patterns) with the exceptions of T. redivivum, which because of its large size clusters outside of its proper evolutionary group (lecontei), and T. occelatum, which did not cluster with T. curvirostre. Skull characters contributed highly to species discrimination, suggesting that unique feeding adaptations arose in different species groups. Although genetic variation was detected at isozyme loci (average heterozygosity = 3.6%), these data yielded little phylogenetic resolution. Similarly, mtDNA restriction sites were relatively uninformative; hence, phylogenetic conclusions were based on sequence data. Phylogenetic analyses confirmed the monophyly of these traditionally recognized assemblages: rufum group (T. rufum, T. longirostre, and T. guttatum), lecontei group (T. lecontei, T. crissale, and T. redivivum), and cinereum group (T. bendirei and T. cinereum). The cinereum and lecontei groups appear to be sister lineages. Monophyly of the curvirostre group (which also includes T. occelatum) was not confirmed. Sequence data suggest that T. occelatum and T. curvirostre, which differ by 7.7% sequence divergence, are probably most closely related to the rufum group. Toxostoma rufum and T. longirostre have similar external appearances and differ by 5.0%. Toxostoma guttatum is restricted to Cozumel Island and often is considered a subspecies of T. longirostre; it differs by more than 5% from the other two members of the rufum group and is a distinct species constituting the basal member of this group. The phenotypically distinctive T. bendirei and T. cinereum differ in sequence divergence by only 1.6%. Overall, mtDNA distances computed from coding genes (mean 8.5%) exceeded distances computed from the control region (mean 7.6%), contrary to expectation. Because neither allozymes nor mtDNA could unambiguously resolve the placement of T. occelatum and T. curvirostre, a scenario involving contemporaneous speciation is suggested. Application of a molecular clock suggested that most speciation occurred in the late Pliocene or early Pleistocene

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

Recolonization of the Flicker and other notes from Isla Guadalupe, Mexico

During a visit to Isla Guadalupe from 31 May to 3 June 1996, we documented three species new to the island, the Barn Owl, Swainson\u27s Thrush, and Hooded Oriole, and established first breeding records for the European Starling and Western Meadowlark. Red-shafted Flickers are now breeding on the island, representing a recent recolonization from the mainland following the extinction of the endemic population. We investigated the validity of Colaptes auratus rufipileus and concluded that it doesn’t meet the standard for phylogenetic species but differs from C. a. collaris at the 75% level usually associated with subspecific rank. Damage to the cypress forest by goats continues, and all species dependent on these trees are threatened by loss of habitat

Evidence supporting the recent origin and species status of the Timberline Sparrow

The Timberline Sparrow (Spizella taverneri), although originally described as a species, is currently classified as a subspecies of the more widespread Brewer\u27s Sparrow (S. breweri). We investigated the taxonomic status and recent evolutionary history of these species by comparison of both morphological and molecular characters. Morphometric comparisons using 6 external and 18 skeletal measurements show that S. taverneri specimens from two widely separated populations (Yukon and southwestern Alberta, Canada) are indistinguishable with respect to size yet are significantly larger (by 3%) than representatives of several breweri populations. Analysis of 1,413 base pairs of mitochondrial DNA (mtDNA) for 10 breweri and 5 taverneri samples representing widely scattered breeding populations revealed a maximum divergence among any breweri-taverneri pair of 0.21% and an overall average of 0.13%. In contrast, the average (± SE) pairwise distance among the other Spizella species is 5.7 ± 0.5%. We discovered that breweri and taverneri could be distinguished on the basis of a single, fixed nucleotide difference. Of an additional 11 taverneri and 8 breweri surveyed for this diagnostic site, a single bird (morphologically a taverneri) from northwest British Columbia did not sort to type. Overall, 18 of 18 breweri and 15 of 16 taverneri were diagnosable. We interpret these results to suggest that gene flow does not currently occur between these two forms and that each is on an independent, albeit recently derived, evolutionary course. The molecular data are consistent with theoretical expectations of a Late Pleistocene speciation event. We believe that for passerine birds, this is the first empirical validation of this widely accepted evolutionary model. The data presented corroborate plumage, vocal, and ecological evidence suggesting that these taxa are distinct. As such, we suggest that Spizella taverneri be recognized as a species

The taxonomic rank of Spizella taverneri: A response to Mayr and Johnson

Mayr and Johnson suggest that Spizella taverneri should be a subspecies of the biological species S. breweri, because it is possibly not reproductively isolated. We originally concluded that evidence from mitochondrial DNA sequences, habitat preferences, timing of breeding, vocalizations, and morphology supported the recognition of S. taverneri as a phylogenetic and biological species. Nothing in the commentary by Mayr and Johnson causes us to change that conclusion. We believe that it is probable that these two allopatric taxa are isolated. Contrary to Mayr and Johnson, we believe that more information is given by ranking S. taverneri as a species, because it reveals the fact that they are independently evolving taxa. The classification of Spizella should convey the sister-species status of S. taverneri and S. breweri, without regard for balancing the degree of sequence divergence among species, as suggested by Mayr and Johnson