Frederick H. Sheldon

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.

Whole-genome analyses resolve early branches in the tree of life of modern birds

To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.

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.

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.

PHYLOGENY OF TITMICE (PARIDAE): II. SPECIES RELATIONSHIPS BASED ON SEQUENCES OF THE MITOCHONDRIAL CYTOCHROME-B GENE

Abstract We present a phylogenetic hypothesis for 40 species in the bird family Paridae, based on comparisons of nucleotide sequences of the mitochondrial cytochrome-b gene. Parids, including tits and chickadees, are an older group than their morphological stereotypy suggests. The longest cytochrome-b distances between species reach 12% in uncorrected divergence. With the exception of one thrasher-like terrestrial tit species of the Tibetan plateau (Pseudopodoces humilis), morphological and ecological stasis have prevailed since the initial parid radiation in the Old World during the mid-Tertiary. All trees support monophyly of the family Paridae, which includes Parus (sensu lato) and the monotypic Oriental genera Sylviparus, Melanochlora, and Pseudopodoces. Within the clade of chickadees and gray tits (Parus, subgenus Poecile), three Old World species, Parus lugubris of the eastern Mediterranean and Balkan regions, P. superciliosus of high elevations in the Himalayas of western China, and P. varius of the Orient are sisters to all other species. The Eurasian crested titmice (subgenus Lophophanes) and North American crested titmice (subgenus Baeolophus) are sister groups. Our data suggest two colonizations of the New World by parids in the late Tertiary. The ancestor of modern Baeolophus colonized North America 4 mya, and the ancestor of all North American chickadees colonized North America 3.5 mya. Phylogénie chez la mésange (Paridés): II. Relations entre les espèces basées sur des séquences du gène mitochondrial cytochrome-b

DNA-DNA HYBRIDIZATION EVIDENCE OF PHYLOGENETIC-RELATIONSHIPS AMONG MAJOR LINEAGES OF PARUS

DNA-DNA hybrids were formed among 2 outgroups and 12 taxa of titmice and chickadees to estimate the genealogical relationships of the main Parus lineages. A complete matrix of reciprocal comparisons among seven parids and the Verdin (Auriparus flaviceps) indicated that the Blue Tit (P. caeruleus) and Great Tit (P. major) together form the sister group of the rest of the genus, and that the Bridled Titmouse (P. wollweberi) is more closely related to North American titmice than to the Old World crested tits. The DNA-hybridization data complement information from allozyme and mtDNA studies of closely related parids and provide historical insight into patterns of tit behavior.

Use of an exotic tree plantation by Bornean lowland forest birds

ABsTRAcr.-During May to July 1982, we surveyed birds in primary forest and in differentaged groves of the exotic tree Albizia falcataria at Sabah Softwoods, a lowland tree plantation in Sabah, East Malaysia (formerly British North Borneo). We found that the Albizia was in general attractive to many native birds. About 60% of primary-forest species used the plantation, and the frequency at which individuals were observed in the oldest groves was almost twice that of nearby primary forest. The Albizia attracted birds because, as an extremely fastgrowing legume with thin leaves, it permitted the rapid development of a well-structured secondary forest. It also was heavily infested with pest insects, which provided an abundant food source. Despite its apparent richness, however, the Albizia lacked several important features of natural forest (e.g. canopy fruits and nest holes). As a result, some primary-forest bird groups were poorly represented (e.g. large canopy frugivores and flycatchers) and others could make only limited use of the plantation (e.g. woodpeckers). In addition, the Albizia is expected to lose its diversity as the plantation as a whole ages. Many of the plantation birds were transients from nearby forest that visited daily to feed, and some probably had been displaced by intense logging. The number of daily transients should decrease as primary forest recedes due to logging and development. Refugee species diversity should suffer from attrition as the plantation is cropped and predation and age take their toll. Received 9 March 1992, accepted 20 November 1992.

Intergeneric Phylogenetic Relationships of Swallows Estimated by DNA-DNA Hybridization

-The phylogeny of the subfamily Hirundininae was estimated by hybridizing single-copy nuclear DNAs of 21 swallow species, representing 19 former and current genera, and a Tufted Titmouse (Parus bicolor) as outgroup. The phylogeny, which was unusually well resolved, consisted of three fundamental clades: Hirundo and allies, core martins, and African sawwings. The clade of Hirundo and allies comprised Hirundo rustica, Ptyonoprogne fuligula, Delichon urbica, Cecropis semirufa, Petrochelidon pyrrhonota, and P. spilodera. The sister-group of Hirundo and allies was the core martin clade, which consisted largely of endemic New World taxa (Pygochelidon cyanoleuca, Neochelidon tibialis, Atticora fasciata, Phaeoprogne tapera, Progne chalybea, Haplochelidon andecola, Stelgidopteryx ruficollis, and Tachycineta bicolor) and some basally branching Old World groups (Riparia riparia, R. cincta, Phedina borbonica, Pseudhirundo griseopyga, and Cheramoeca leucosternus). The African sawwings (represented by Psalidoprocne holomelas) formed the sister group of the core martins and Hirundo and allies. Among some interesting discoveries, we found a close relationship between the monotypic African and Australian genera Pseudhirundo and Cheramoeca. We also found that Delichon, which has persisted in the nomenclature as a genus separate from Hirundo, is monophyletic with taxa that are commonly considered to be members of Hirundo. On the other hand, Haplochelidon andecola, which is often considered to be a Hirundo or Petrochelidon, is not closely related to those genera, but instead lies among the New World members of the core martin clade. Received 1 July 1992, accepted 25 November 1992. PERHAPS NO FAMILY of passerines is as uniform morphologically and diverse generically as the swallows (Hirundinidae). All swallow species conform to a fundamental body plan that includes long and pointed wings, medium length tails, short legs, and bills that are short and wide. This uniformity is the likely result of adaptation to a strictly aerial insectivorous lifestyle. Apparently because of this uniformity, systematists have been loath to attempt a phylogenetic reconstruction of the swallow family as a whole. While there have been many classifications of the Hirundinidae (e.g. Sharpe 1885, Peters 1960, Turner and Rose 1989, Sibley and Monroe 1990) and many discussions of the systematics of individual species or small groups of taxa, only one published paper has considered the familywide relationships of swallows based on evolutionary or phylogenetic logic. This is the 50-year-old study of Mayr and Bond

REVISITING WALLACE'S HAUNT: COALESCENT SIMULATIONS AND COMPARATIVE NICHE MODELING REVEAL HISTORICAL MECHANISMS THAT PROMOTED AVIAN POPULATION DIVERGENCE IN THE MALAY ARCHIPELAGO.

Sundaland, a biogeographic region of Southeast Asia, is a major biodiversity hotspot. However, little is known about the relative importance of Pleistocene habitat barriers and rivers in structuring populations and promoting diversification here. We sampled 16 lowland rainforest bird species primarily from peninsular Malaysia and Borneo to test the long‐standing hypothesis that animals on different Sundaic landmasses intermixed extensively when lower sea‐levels during the Last Glacial Maximum (LGM) exposed land‐bridges. This hypothesis was rejected in all but five species through coalescent simulations. Furthermore, we detected a range of phylogeographic patterns; Bornean populations are often genetically distinct from each other, despite their current habitat connectivity. Environmental niche modeling showed that the presence of unsuitable habitats between western and eastern Sundaland during the LGM coincided with deeper interpopulation genetic divergences. The location of this habitat barrier had been hypothesized previously based on other evidence. Paleo‐riverine barriers are unlikely to have produced such a pattern, but we cannot rule out that they acted with habitat changes to impede population exchanges across the Sunda shelf. The distinctiveness of northeastern Borneo populations may be underlied by a combination of factors such as rivers, LGM expansion of montane forests and other aspects of regional physiography.

Phylogeny of titmice (Paridae): I. Estimate of relationships among subgenera based on DNA-DNA hybridization

The phylogenetic relationships of titmice and chickadees (Passeriformes: Paridae) were estimated by DNA-DNA hybridization. Fifteen species of parids (representing all six subgenera) and two outgroups, Penduline Tit Remiz pendulinus and Whitebreasted Nuthatch Sitta carolinensis, were radiolabeled and compared pairwise to produce a complete reciprocal set of distance measures. The resulting phylogeny supported the traditional allocation of species to subgenera, except that Parus wollweberi clustered with the North American crested tits (subgenus Baeolophus) rather than the Old World crested tits (Lophophanes). The interrelationships of most subgenera remained unresolved. Nevertheless, a major subdivision in the family was strongly indicated: i.e., the great tits (subgenus Parus) and the blue tits (subgenus Cyanistes) formed a clade that is the sister taxon of the rest of the family. This bifurcation has important ecological, physiological, and morphological ramifications, as it correlates exactly with seed-caching and flocking habits, hippocampal development, and leg-muscle character distributions. These DNA-hybridization results corroborate or complement the phylogenetic relationships among parids supported by other molecular data sets (viz., allozyme, restriction site, and preliminary DNA hybridization analyses).