Jeff G. Groth

A phylogenetic hypothesis for passerine birds: taxonomic and biogeographic implications of an analysis of nuclear DNA sequence data.

Passerine birds comprise over half of avian diversity, but have proved difficult to classify. Despite a long history of work on this group, no comprehensive hypothesis of passerine family–level relationships was available until recent analyses of DNA–DNA hybridization data. Unfortunately, given the value of such a hypothesis in comparative studies of passerine ecology and behaviour, the DNA–hybridization results have not been well tested using independent data and analytical approaches. Therefore, we analysed nucleotide sequence variation at the nuclear RAG–1 and c–mos genes from 69 passerine taxa, including representatives of most currently recognized families. In contradiction to previous DNA–hybridization studies, our analyses suggest paraphyly of suboscine passerines because the suboscine New Zealand wren Acanthisitta was found to be sister to all other passerines. Additionally, we reconstructed the parvorder Corvida as a basal paraphyletic grade within the oscine passerines. Finally, we found strong evidence that several family–level taxa are misplaced in the hybridization results, including the Alaudidae, Irenidae, and Melanocharitidae. The hypothesis of relationships we present here suggests that the oscine passerines arose on the Australian continental plate while it was isolated by oceanic barriers and that a major northern radiation of oscines (i.e. the parvorder Passerida) originated subsequent to dispersal from the south.

RAG-1 sequences resolve phylogenetic relationships within Charadriiform birds.

The Charadriiformes is a large and diverse order of shorebirds currently classified into 19 families, including morphologically aberrant forms that are of uncertain phylogenetic placement within non-passerine birds in general. Recent attempts using morphological characters have failed to recover a well-supported phylogeny depicting higher level relationships within Charadriiformes and the limits to the order, primarily because of inconsistency and homoplasy in these data. Moreover, these trees are incongruent with the relationships presented in the DNA hybridization tapestry of, including the location of the root and the branching order of major clades within the shorebirds. To help clarify this systematic confusion we therefore sequenced the large RAG-1 nuclear exon (2850 bp) from 36 species representing 17 families of shorebirds for which DNA was available. Trees built with maximum parsimony, maximum likelihood or Bayesian methods are topologically identical and fully resolved, with high support at basal nodes. This further attests to the phylogenetic utility of the RAG-1 sequences at higher taxonomic levels within birds. The RAG-1 tree is topologically similar to the DNA hybridization tree in depicting three major subordinal clades of shorebirds, the Charadrii (thick-knees, sheathbills, plovers, oystercatchers, and allies), Scolopaci (sandpipers and jacanas) and the Lari (coursers, pratincoles, gulls, terns, skimmers, and skuas). However, the basal split in the RAG-1 tree is between Charadrii and (Scolopaci+Lari), whereas in the DNA hybridization tree Scolopaci is the sister group to the (Charadrii+Lari). Thus in both of these DNA-based trees the Alcidae (auks, murres, and allies) are not basal among shorebirds as hypothesized in morphological trees, but instead are placed as a tip clade within Lari. The enigmatic buttonquails (Turnicidae), variously hypothesized as being allied to either the Galliformes, Gruiformes, or Charadriiformes, are shown to be a basal lineage in the more conventional Lari clade. Divergence times estimated with rate-smoothing methods and minimum time constraints imposed at nodes with key fossils suggest that Charadriiformes originated in Gondwanaland.

Phylogeographic structure, gene flow and species status in blue grouse (Dendragapus obscurus)

We investigated the genetic population structure and species status of a relatively sedentary bird that is a permanent resident of western North American forests, the blue grouse (Dendragapus obscurus). Phylogenetic analysis of complete mitochondrial control region DNA sequences resulted in the identification of three basal clades of haplotypes that were largely congruent with well‐known biogeographical regions. These clades corresponded to the parapatric sooty (D. o. fuliginosus) and dusky (D. o. obscurus) subspecies groups of blue grouse plus a previously unrecognized division between northern and southern dusky grouse populations; the latter does not correspond closely to any currently recognized subspecies boundary. Approximately 66% of the total genetic variation was distributed among these three regions. Maximum likelihood estimates of gene flow between the regions were low or asymmetric; gene flow has been insufficient to prevent genetic divergence between dusky and sooty grouse. Estimates of gene flow among populations within sooty grouse were large except across the Columbia River valley. Among populations of dusky grouse, estimates of gene flow were heterogeneous and asymmetrical, reflecting large‐scale fragmentation of the distribution due to landscape features and associated vegetation. Genetic, morphological and behavioural evidence suggest that sooty and dusky grouse are species‐level taxa; the specific status of a third clade remains ambiguous.

GENETIC STRUCTURE OF MEXICAN SPOTTED OWL (STRIX OCCIDENTALIS LUCIDA) POPULATIONS IN A FRAGMENTED LANDSCAPE

Abstract We used mitochondrial DNA control-region sequences to investigate the genetic structure of Mexican Spotted Owl (Strix occidentalis lucida) populations in the southwestern United States. This subspecies is federally listed as threatened, and its preferred habitat is naturally fragmented. We found that intrapopulation genetic diversity was high in all but the southeastern Arizona “sky island” populations, where it was variable. Genetic variance partitioning indicated that ≈17% of the variation was distributed among populations and 7.5% was distributed among physiographic regions. Patterns of genetic correlation with geographic distance indicated that gene flow was substantial among populations within the relatively continuous habitat zone of the Mogollon Rim-Upper Gila Mountains in central Arizona and west-central New Mexico. However, there was significant isolation-by-distance elsewhere, and estimates of genetic divergence increased exponentially with geographic distance among fragmented populations on the scale of a few hundreds of kilometers; this implies that gene flow is restricted among those habitat fragments. Genetic heterogeneity among southeastern Arizona populations suggest that they have regularly received immigrants from the central Arizona populations. The Colorado population either was larger than thought or, more likely, has continuously received immigrants from elsewhere and is not a self-sustaining population. Estructura Genética de las Poblaciones de Strix occidentalis lucida en un Paisaje Fragmentado

Phylogeography of the Barred Owl (Strix varia): Species limits, multiple refugia, and range expansion

ABSTRACT. The Barred Owl (Strix varia) is a common nonmigratory owl distributed across southern Canada, south to California in the west, and to Texas and Florida in the east, with isolated populations in central Mexico. We examined the genetic structure of Barred Owl populations throughout their range using 500–600 base pairs each of one nuclear and three mitochondrial genes. In 75% of the shortest trees and 64% of the bootstrapped trees, Barred Owls were not monophyletic; rather, S. v. sartorii of Mexico was separated from the remaining taxa of S. varia by S. fulvescens of Central America. Consequently, the Barred Owls of Mexico are a species-level taxon. There was a large component (32%) of genetic variance distributed among population samples from the United States and Canada because of the occurrence of two clades of haplotypes (4.8% sequence divergence) with differing geographic distributions. One clade was predominant along the Atlantic Coast and the second in the south-central United States. The two clades co-occurred from the central Gulf Coast to the Upper Midwest, and across Canada to the Pacific. Nucleotide diversity was greatest where the clades overlapped in occurrence; mismatch distributions possessed the signatures of population expansion from the southern and eastern states to northern and western locations. These results suggest two Pleistocene refugia for northern populations of Barred Owls. Diversity within populations and divergence between haplotype clades varied by an order of magnitude among the three mitochondrial genes, but each recovered the overall phylogeographic pattern. The nuclear sequences showed much less variation and differentiation.

The Hybrid Zone between Northern and California Spotted Owls in the Cascade—Sierran Suture Zone

Abstract. Both the geographic center and the shape of the hybrid zone between the Northern Spotted Owl (Strix occidentalis caurina) and California Spotted Owl (S. o. occidentalis) have been unknown because of a lack of samples from the transition zone between Mt. Shasta and Lassen Peak in northern California. However, the position of the boundary between these taxa, and their associated taxonomic rank, have important biogeographical, management, and political implications. We used sequences of the mtDNA control region from owls captured in that region to infer the quantitative structure of this contact zone. The proportion of Northern Spotted Owl haplotypes to total haplotypes fell below 50% approximately 24 km south of the Pit River; the 95% confidence interval for this transition extended from just south of the Pit River to just north of Lassen Peak. We estimated the standard width (20%–80%) of the hybrid zone, which appeared symmetrical, to be 94 km. We rejected the prior hypothesis that the boundary between Northern and California Spotted Owls was the Pit River; rather, the center of the zone did not appear to be closely associated with any obvious physical barrier to gene flow. This is the first described instance of a secondary contact zone between avian taxa that is clearly associated with Remingtons Cascade—Sierran suture zone. This hybrid zone was too narrow to be consistent with neutral introgression; it is likely that there is a selective, behavioral, or demographic barrier to gene flow across the Pit River region.

The Phylogenetic Relationships of the Endemic Genera of Australo-Papuan Hawks

Abstract Six genera of accipitrids (Erythrotriorchis, Hamirostra, Harpyopsis, Henicopernis, Lophoictinia, and Megatriorchis), composed of a total of eight species, are endemic to the Australo-Papuan region. Traditionally, these were assigned to four subfamilies in the Accipitridae; however, a recent hypothesis suggested they together comprise an endemic radiation of closely related genera and species. We investigated these alternatives using phylogenetic analysis of DNA sequences of the slowly evolving nuclear RAG-1 exon. Bootstrapped maximum likelihood trees and a permutation likelihood ratio test provide robust evidence that these genera represent four clades placed in three divergent higher taxa of accipitrids: (1) Hamirostra, Henicopernis, and Lophoictinia comprise a monophyletic clade of pernine kites, (2) Harpyopsis is a harpy eagle, and (3) Erythrotriorchis and Megatriorchis represent two unrelated clades of accipiters. Parsimony and Bayesian analyses confirmed these results. The hypothesis that the six genera are monophyletic was firmly rejected. The data are consistent with a southeast Asian or Australo-Papuan origin for each of the four clades. These six genera each include only one or two species and are closely related to other monotypic taxa; an efficient classification would place most of these genera in synonymy. RELACIONES FILOGENÉTICAS DE GÉNEROS ENDÉMICOS DE HALCONES AUSTRALO-PAPUANOS Seis géneros de accipítridos (Erythrotriorchis, Hamirostra, Harpyopsis, Henicopernis, Lophoictinia y Megatriorchis), compuestos por un total de ocho especies, son endémicos de la región Australo-Papuana. Tradicionalmente, estos géneros fueron asignados a cuatro subfamilias en Accipitridae; sin embargo, hipótesis recientes sugirieron que juntos comprenden una radiación endémica de géneros y especies relacionados cercanamente. Investigamos estas alternativas usando análisis filogenéticos de secuencias de ADN del exón nuclear de evolución lenta RAG-1. Árboles de máxima probabilidad de bootstrap y una prueba de radio de probabilidad de permutación proporcionaron evidencia robusta de que estos géneros representan cuatro clados ubicados en tres taxa divergentes más elevados de accipítridos: (1) Hamirostra, Henicopernis y Lophoictinia comprenden un clado monofilético de milanos perninos, (2) Harpyopsis es un águila harpía y (3) Erythrotriorchis y Megatriorchis representan dos clados de accipítridos no relacionados. Análisis de parsimonia y bayesianos confirmaron estos resultados. La hipótesis de que los seis géneros son monofiléticos fue firmemente rechazada. Los datos son consistentes con un origen del sureste asiático o Australo-Papuano para cada uno de los cuatro clados. Estos seis géneros sólo incluyen una o dos especies y están cercanamente relacionados con otros taxa monotípicos; una clasificación eficiente ubicaría a la mayoría de estos géneros en sinonimia.

The Mitochondrial Genome of Allonautilus (Mollusca: Cephalopoda): Base Composition, Noncoding-Region Variation, and Phylogenetic Divergence

ABSTRACT We used next-generation methods to sequence the mitochondrial genome of Allonautilus scrobiculatus from two large, overlapping amplicons generated by PCR. The genome was circular, 16,132 base pairs in length, and possessed the same sequence and orientation of genes as the previously sequenced mitogenome of Nautilus macromphalus. These two mitogenomes were approximately 8% divergent overall, but differentiation varied greatly among genes: some tRNA sequences were identical between the two taxa, whereas ATP8 differed by over 15%. The largest of the noncoding regions of the genome included a 62 base pair repeat that was essentially identical between the two genera; however, this repeat was present as six copies in N. macromphalus, but varied between four and five among individuals of Allonautilus. A 146 base pair deletion (in Allonautilus compared to Nautilus) included one copy of the repeat plus an adjacent 84 bp; because of this indel, the “CA” microsatellite in N. macromphalus was missing from Allonautilus. Base composition varied along the Allonautilus sequence, and was correlated with the strand on which genes coded. Base composition also varied within the largest noncoding region. A phylogeny of 24 extant cephalopods indicates that there is less molecular divergence between Allonautilus and Nautilus than there is among congeneric species of Octopus and Sepia.

Phylogeography and geographic variation in the Red-bellied Woodpecker (Melanerpes carolinus): characterization of mtDNA and plumage hybrid zones

ABSTRACT We used sequences of the mitochondrial ND2 gene, the nuclear TGFB-2 intron-5, and differences in plumage pattern to assay geographic variation in the Red-bellied Woodpecker (Melanerpes carolinus). Ten population samples from throughout its range indicated that ∼23% of the mitochondrial genetic variation was distributed among populations, largely due to the occurrence of a clade of haplotypes restricted to the Florida peninsula with a local frequency of 82%. In a hierarchical analysis, 37% of the mtDNA genetic variance was distributed between the Florida peninsula and elsewhere. A strong signal of population growth was detected in the non-peninsular portion of the range. Otherwise, geographic variation in haplotype frequencies was minor, with no evidence of isolation-by-distance. Nuclear intron data showed little variation among populations (Fst = 0.007). These results suggest recent secondary contact of 2 differentiated taxa following expansion from allopatric Pleistocene refugia. We modeled the transition in haplotype frequencies along the Florida peninsula as a zone of neutral introgression; the estimated width of that zone was 435 km, and its center was near present day Ocala. Variation in plumage pattern along the peninsula previously had been used to describe a subspecific taxon, M. c. perplexus. We used variation in the forehead pattern of adult males from along the east coast of the United States to model this phenotypic transition; the zone had an estimated width of >2,500 km and an approximate center in the Florida Keys. Taken together, the geographic patterns in mtDNA and plumage variation suggest the populations of Red-bellied Woodpeckers on the Florida peninsula differentiated from those elsewhere during isolation; they are now in secondary contact in a well-known suture zone and represent 2 phylogenetic species connected by wide molecular and morphological zones of introgression.

Settling the name Diomedea exulans Linnaeus, 1758 for the Wandering Albatross by neotypification

On-going conflict in use of the name Diomedea exulans Linnaeus, 1758 for different taxa of the great albatrosses (Wandering Albatross complex) is resolved by neotypification, fixing the name to the large subantarctic form formerly often known as D. chionoptera Salvin, 1896. Application of all scientific names in the complex is reviewed, an annotated synonymy for the large subantarctic form is provided, available names for smaller, temperate-zone forms are listed, and unavailable and otherwise invalid names referable to the complex are identified. Syntypes of D. chionoptera and D. spadicea J.F. Gmelin, 1789 are lectotypified as well, fixing their names as synonyms of D. exulans to prevent possible disturbance to in-use names for the smaller, temperate-zone forms.