Shannon J. Hackett

A phylogenomic study of birds reveals their evolutionary history.

Deep avian evolutionary relationships have been difficult to resolve as a result of a putative explosive radiation. Our study examined ∼32 kilobases of aligned nuclear DNA sequences from 19 independent loci for 169 species, representing all major extant groups, and recovered a robust phylogeny from a genome-wide signal supported by multiple analytical methods. We documented well-supported, previously unrecognized interordinal relationships (such as a sister relationship between passerines and parrots) and corroborated previously contentious groupings (such as flamingos and grebes). Our conclusions challenge current classifications and alter our understanding of trait evolution; for example, some diurnal birds evolved from nocturnal ancestors. Our results provide a valuable resource for phylogenetic and comparative studies in birds.

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10,000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G10KCOS), will assemble and allocate a biospecimen collection of some 16,203 representative vertebrate species spanning evolutionary diversity across living mammals, birds, nonavian reptiles, amphibians, and fishes (ca. 60,000 living species). In this proposal, we present precise counts for these 16,203 individual species with specimens presently tagged and stipulated for DNA sequencing by the G10KCOS. DNA sequencing has ushered in a new era of investigation in the biological sciences, allowing us to embark for the first time on a truly comprehensive study of vertebrate evolution, the results of which will touch nearly every aspect of vertebrate biological enquiry.

PHYLOGENETIC RELATIONSHIPS AND MORPHOLOGICAL DIVERSITY IN DARWIN'S FINCHES AND THEIR RELATIVES

Abstract Despite the importance of Darwins finches to the development of evolutionary theory, the origin of the group has only recently been examined using a rigorous, phylogenetic methodology that includes many potential outgroups. Knowing the evolutionary relationships of Darwins finches to other birds is important for understanding the context from which this adaptive radiation arose. Here we show that analysis of mitochondrial DNA sequence data from the cytochrome b gene confirm that Darwins finches are monophyletic. In addition, many taxa previously proposed as the sister taxon to Darwins finches can be excluded as their closest living relative. Darwins finches are part of a well‐supported monophyletic group of species, all of which build a domed nest. All but two of the non‐Darwins finches included in this clade occur on Caribbean islands and most are Caribbean endemics. These close relatives of Darwins finches show a diversity of bill types and feeding behaviors similar to that observed among Darwins finches themselves. Recent studies have shown that adaptive evolution in Darwins finches occurred relatively quickly. Our data show that among the relatives of Darwins finches, the evolution of bill diversity was also rapid and extensive.

Phylogenomic evidence for multiple losses of flight in ratite birds

Ratites (ostriches, emus, rheas, cassowaries, and kiwis) are large, flightless birds that have long fascinated biologists. Their current distribution on isolated southern land masses is believed to reflect the breakup of the paleocontinent of Gondwana. The prevailing view is that ratites are monophyletic, with the flighted tinamous as their sister group, suggesting a single loss of flight in the common ancestry of ratites. However, phylogenetic analyses of 20 unlinked nuclear genes reveal a genome-wide signal that unequivocally places tinamous within ratites, making ratites polyphyletic and suggesting multiple losses of flight. Phenomena that can mislead phylogenetic analyses, including long branch attraction, base compositional bias, discordance between gene trees and species trees, and sequence alignment errors, have been eliminated as explanations for this result. The most plausible hypothesis requires at least three losses of flight and explains the many morphological and behavioral similarities among ratites by parallel or convergent evolution. Finally, this phylogeny demands fundamental reconsideration of proposals that relate ratite evolution to continental drift.

Historical relationships among Neotropical lowland forest areas of endemism as determined by mitochondrial DNA sequence variation within the Wedge-billed Woodcreeper (Aves: Dendrocolaptidae: Glyphorynchus spirurus)

Studies of the distribution of South American taxa have identified several areas of endemism that may have contributed to the historical diversification of the region. We constructed a phylogeny of Glyphorynchus spirurus (Aves: Dendrocolaptidae) populations using mtDNA sequence data from portions of cytochrome b, NADH dehydrogenase subunit II (ND2), and complete NADH dehydrogenase subunit III (ND3). Using this phylogeny we evaluate five previous hypotheses of area-relationships, two based on phylogenetic studies of morphological characters in birds and three based on parsimony analysis of endemism in birds and primates. Maximum likelihood and maximum parsimony analyses recovered two phylogenetic hypotheses that differed in the placement of one of the areas. Within each of the areas of endemism, the two analyses support the same clades. Neither of the phylogenetic hypotheses for Glyphorynchus exactly matches any of the five previous hypotheses of area-relationships, although ambiguous support exists for one of them. Five areas-Central America, Inambari, Napo, Pará, and Rondônia-are supported as composites with component taxa having phylogenetic affinities with more than one area. Data reported here also indicate high levels of sequence divergence within Glyphorynchus. Genetic breaks within Glyphorynchus are only partially congruent with subspecific taxonomy. The regional sampling design used makes this study the largest scale genetic assay of a widespread Neotropical avian taxon published to date.

High levels of mitochondrial DNA differentiation in two lineages of antbirds (Drymophila and Hypocnemis)

We assessed levels of genetic differentiation based on mitochondrial DNA sequences (portions of the cytochrome-b and ND2 genes) at several taxonomic levels in thamnophilid antbirds. Our focus was to investigate genetic differentiation among populations of two species in the genus Drymophila and to identify the sister genus to Drymophila. In addition, we present evidence of high levels of population subdivision in Hypocnemis cantator (Warbling Antbird). This widespread Amazonian taxon co-occurs, on a local scale, with D. devillei (Striated Antbird). Sequence divergences among populations of D. devillei and D. caudata (Long-tailed Antbird), two bamboo-specialists, often exceeded 2% between populations. Divergences within H. cantator, a species with more generalized habitat requirements and a more continuous distribution, were even higher, including 5.7% divergence between samples separated by 350 km of apparently continuous Amazonian forest. At higher taxonomic levels, genetic distances suggest that antbird genera and biological species are old. Genetic divergence between the two species that comprise the genus Hypocnemis was 9.3%, and divergence between D. devillei and D. caudata averaged 7.2%. Weighted parsimony and maximum-likelihood analyses supported Hypocnemis as the sister taxon to Drymophila; the genus Myrmotherula was not monophyletic, supporting previous allozyme analyses. In addition to the protein-coding sequences, we found that spacer regions between genes also provided phylogenetically informative characters from the level of suboscine families to within the biological species that we studied. Received 31 March 1998, accepted 7 April 1999.

SYSTEMATICS AND BIOGEOGRAPHY OF DOUBLE-COLLARED SUNBIRDS FROM THE EASTERN ARC MOUNTAINS, TANZANIA

Abstract The double-collared sunbirds of the Eastern Arc Mountains of Tanzania and southeastern Kenya are characterized by regional variation in morphology and plumage. That variation has resulted in considerable dispute over their taxonomic status and delineation of range boundaries. It has been suggested that Moreaus Sunbird (Nectarinia Moreaui) is an atypical phenotype that has arisen from a hybridization event between the more widely distributed Eastern Double-collared Sunbird (N. mediocris) and the narrowly distributed Loveridges Sunbird (N. loveridgei). A discriminant analysis of six standard morphological characters indicates that Moreaus Sunbird is intermediate in shape and size between the Eastern Double-collared and Loveridges sunbirds. There is greater overlap between female Moreaus and Eastern Double-collared sunbirds than between males; Loveridges Sunbird shows little overlap with the other taxa. Discrete plumage characters separate all three taxa. Molecular analyses of 728 base pairs of mitochondrial DNA (NADH3 and control region) suggest that Moreaus Sunbird is a valid taxon and the sister species to Loveridges Sunbird. Eastern Double-collared Sunbird haplotypes can be divided into three distinct clades, separated from each other by substantial genetic divergence (approximately 8–10% sequence divergence). We propose species status for each of those clades and suggest the following three taxa: N. mediocris Shelley 1855, N. usambarica Gröte 1922, and N. fuelleborni Reichenow 1899. Finally, we propose a biogeographical hypothesis of speciation events within the N. mediocris species complex.

Comment on "The Latitudinal Gradient in Recent Speciation and Extinction Rates of Birds and Mammals"

Weir and Schluter (Reports, 16 March 2007, p. 1574) used variation in the age distribution of sister species to estimate that recent rates of speciation decline toward the tropics. However, this conclusion may be undermined by taxonomic biases, sampling artifacts, and the sister-species method, all of which tend to underestimate diversification rates at low latitudes.

Diversification and the adaptive radiation of the vangas of Madagascar.

The vangas of Madagascar exhibit extreme diversity in morphology and ecology. Recent studies have shown that several other Malagasy species also are part of this endemic radiation, even as the monophyly of the clade remains in question. Using DNA sequences from 13 genes and representatives of all 15 vanga genera, we find strong support for the monophyly of the Malagasy vangids and their inclusion in a family along with six aberrant genera of shrike-like corvoids distributed in Asia and Africa. Biogeographic reconstructions of these lineages include both Asia and Africa as possible dispersal routes to Madagascar. To study patterns of speciation through time, we introduce a method that can accommodate phylogenetically non-random patterns of incomplete taxon sampling in diversification studies. We demonstrate that speciation rates in vangas decreased dramatically through time following the colonization of Madagascar. Foraging strategies of these birds show remarkable congruence with phylogenetic relationships, indicating that adaptations to feeding specializations played a role in the diversification of these birds. Vangas fit the model of an ‘adaptive radiation’ in that they show an explosive burst of speciation soon after colonization, increased diversification into novel niches and extraordinary ecomorphological diversity.

Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals

Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions.