Evolutionary history of a prominent North American warbler clade: The Oporornis–Geothlypis complex

Extreme elevational migration spurred cryptic speciation in giant hummingbirds

The ecoevolutionary drivers of species niche expansion or contraction are critical for biodiversity but challenging to infer. Niche expansion may be promoted by local adaptation or constrained by physiological performance trade-offs. For birds, evolutionary shifts in migratory behavior permit the broadening of the climatic niche by expansion into varied, seasonal environments. Broader niches can be short-lived if diversifying selection and geography promote speciation and niche subdivision across climatic gradients. To illuminate niche breadth dynamics, we can ask how "outlier" species defy constraints. Of the 363 hummingbird species, the giant hummingbird (Patagona gigas) has the broadest climatic niche by a large margin. To test the roles of migratory behavior, performance trade-offs, and genetic structure in maintaining its exceptional niche breadth, we studied its movements, respiratory traits, and population genomics. Satellite and light-level geolocator tracks revealed an >8,300-km loop migration over the Central Andean Plateau. This migration included a 3-wk, ~4,100-m ascent punctuated by upward bursts and pauses, resembling the acclimatization routines of human mountain climbers, and accompanied by surging blood-hemoglobin concentrations. Extreme migration was accompanied by deep genomic divergence from high-elevation resident populations, with decisive postzygotic barriers to gene flow. The two forms occur side-by-side but differ almost imperceptibly in size, plumage, and respiratory traits. The high-elevation resident taxon is the world's largest hummingbird, a previously undiscovered species that we describe and name here. The giant hummingbirds demonstrate evolutionary limits on niche breadth: when the ancestral niche expanded due to evolution (or loss) of an extreme migratory behavior, speciation followed.

The evolutionary history of "suboptimal" migration routes

Migratoriness in birds is evolutionary labile, with many examples of increasing or decreasing migration distances on the timescale of modern ornithology. In contrast, shifts of migration to more nearby wintering grounds seem to be a slow process. We examine the history of how Palearctic migratory landbirds have expanded their wintering ranges to include both tropical Africa and Asia, a process that has involved major shifts in migratory routes. We found that species with shorter migration distances and with resident populations in the Palearctic more often winter in both Africa and Asia. Our results suggest that changes in wintering grounds are not by long-distance migrant populations per se, but through historic intermediate populations that were less migratory from which long-distance migration evolved secondarily. The failure of long-distance migrants to shift migration direction to more nearby winter quarters indicates that major modifications to the migratory program may be difficult to evolve.

Explosive radiation and spatial expansion across the cold environments of the Old World in an avian family

Our objective was to elucidate the biogeography and speciation patterns in an entire avian family, which shows a complex pattern of overlapping and nonoverlapping geographical distributions, and much variation in plumage, but less in size and structure. We estimated the phylogeny and divergence times for all of the world's species of Prunella based on multiple genetic loci, and analyzed morphometric divergence and biogeographical history. The common ancestor of Prunella was present in the Sino‐Himalayan Mountains or these mountains and Central Asia–Mongolia more than 9 million years ago (mya), but a burst of speciations took place during the mid‐Pliocene to early Pleistocene. The relationships among the six primary lineages resulting from that differentiation are unresolved, probably because of the rapid radiation. A general increase in sympatry with increasing time since divergence is evident. With one exception, species in clades younger than c. 3.7 my are allopatric. Species that are widely sympatric, including the most recently diverged (2.4 mya) sympatric sisters, are generally more divergent in size/structure than allo‐/parapatric close relatives. The distributional pattern and inferred ages suggest divergence in allopatry and substantial waiting time until secondary contact, likely due to competitive exclusion. All sympatrically breeding species are ecologically segregated, as suggested by differences in size/structure and habitat. Colonizations of new areas were facilitated during glacial periods, followed by fragmentation during interglacials—contrary to the usual view that glacial periods resulted mainly in fragmentations.

Extensive gene flow characterizes the phylogeography of a North American migrant bird: Black-headed Grosbeak (Pheucticus melanocephalus)

We describe range-wide phylogeographic variation in the Black-headed Grosbeak (Pheucticus melanocephalus), a songbird that is widely distributed across North American scrublands and forests. Phylogenetic analysis of mitochondrial DNA (mtDNA, n=424) revealed three geographically structured clades. One widespread clade occurs throughout the Rocky Mountains, Great Basin, and Mexican Plateau, a second clade is found on the Pacific coast and in coastal ranges; and, a third in the Sierra Madre del Sur of Oaxaca and Guerrero. Some geographical structuring occurs in Mexican Plateau and Sierra Madre Oriental mtDNA clade, presumably because these populations have been more stable over time than northern populations. Multiple mitochondrial groups are found sympatrically in the Okanogan River Valley in Washington, the eastern Sierra Nevada, and the Transvolcanic Belt across central Mexico, indicating that there is a potential for introgression. Analyses of 12 nuclear loci did not recover the same geographically structured clades. Population analyses show high levels of gene flow in nucDNA from the Interior into the Sierra Madre del Sur and Pacific population groups, possibly indicating expansion of the Interior population at the expense of peripheral populations.

Gene trees, species trees and Earth history combine to shed light on the evolution of migration in a model avian system

The evolution of migration in birds has fascinated biologists for centuries. In this study, we performed phylogenetic-based analyses of Catharus thrushes, a model genus in the study of avian migration, and their close relatives. For these analyses, we used both mitochondrial and nuclear genes, and the resulting phylogenies were used to trace migratory traits and biogeographic patterns. Our results provide the first robust assessment of relationships within Catharus and relatives and indicate that both mitochondrial and autosomal genes contribute to overall support of the phylogeny. Measures of phylogenetic informativeness indicated that mitochondrial genes provided more signal within Catharus than did nuclear genes, whereas nuclear loci provided more signal for relationships between Catharus and close relatives than did mitochondrial genes. Insertion and deletion events also contributed important support across the phylogeny. Across all taxa included in the study, and for Catharus, possession of long-distance migration is reconstructed as the ancestral condition, and a North American (north of Mexico) ancestral area is inferred. Within Catharus, sedentary behaviour evolved after the first speciation event in the genus and is geographically and temporally correlated with Central American distributions and the final closure of the Central American Seaway. Migratory behaviour subsequently evolved twice in Catharus and is geographically and temporally correlated with a recolonization of North America in the late Pleistocene. By temporally linking speciation events with changes in migratory condition and events in Earth history, we are able to show support for several competing hypotheses relating to the geographic origin of migration.

An Update of Wallace’s Zoogeographic Regions of the World

Modern attempts to produce biogeographic maps focus on the distribution of species, and the maps are typically drawn without phylogenetic considerations. Here, we generate a global map of zoogeographic regions by combining data on the distributions and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals. We identify 20 distinct zoogeographic regions, which are grouped into 11 larger realms. We document the lack of support for several regions previously defined based on distributional data and show that spatial turnover in the phylogenetic composition of vertebrate assemblages is higher in the Southern than in the Northern Hemisphere. We further show that the integration of phylogenetic information provides valuable insight on historical relationships among regions, permitting the identification of evolutionarily unique regions of the world.

DNA Barcodes of Arabian Partridge and Philby's Rock Partridge: Implications for Phylogeny and Species Identification

Recently, DNA barcoding based on mitochondrial cytochrome c oxidase subunit I (COI) has gained wide attention because of simplicity and robustness of these barcodes for species identification including birds. The current GenBank records show the COI barcodes of only one species, chukar partridge (Alectoris chukar), of the Alectoris genus. In this study, we sequenced the 694 bp segment of COI gene of the two species including, Arabian partridge (Alectoris melanocephala) and Philby's rock partridge (Alectoris philbyi) of the same genus. We also compared these sequences with earlier published barcodes of chukar partridge. The pair-wise sequence comparison showed a total of 53 variable sites across all the 9 sequences from 3 species. Within-species variable sites were found to be 4 (Alectoris chukar), 0 (Alectoris philbyi) and 3 (Alectoris melanocephala). The genetic distances among the 9 individuals varied from 0.000 to 0.056. Phylogenetic analysis using COI barcodes clearly discriminated the 3 species, while Alectoris chukar was found to be more closely related to Alectoris philbyi. Similar differentiation was also observed using 1155 bp mitochondrial control region (CR) sequences suggesting the efficiency of COI gene for phylogenetic reconstruction and interspecific identification. This is the first study reporting the barcodes of Arabian partridge and Philby's rock partridge.

A comprehensive multilocus phylogeny for the wood-warblers and a revised classification of the Parulidae (Aves)

The birds in the family Parulidae-commonly termed the New World warblers or wood-warblers-are a classic model radiation for studies of ecological and behavioral differentiation. Although the monophyly of a 'core' wood-warbler clade is well established, no phylogenetic hypothesis for this group has included a full sampling of wood-warbler species diversity. We used parsimony, maximum likelihood, and Bayesian methods to reconstruct relationships among all genera and nearly all wood-warbler species, based on a matrix of mitochondrial DNA (5840 nucleotides) and nuclear DNA (6 loci, 4602 nucleotides) characters. The resulting phylogenetic hypotheses provide a highly congruent picture of wood-warbler relationships, and indicate that the traditional generic classification of these birds recognizes many non-monophyletic groups. We recommend a revised taxonomy in which each of 14 genera (Seiurus, Helmitheros, Mniotilta, Limnothlypis, Protonotaria, Parkesia, Vermivora, Oreothlypis, Geothlypis, Setophaga, Myioborus, Cardellina, Basileuterus, Myiothlypis) corresponds to a well-supported clade; these nomenclatural changes also involve subsuming a number of well-known, traditional wood-warbler genera (Catharopeza, Dendroica, Ergaticus, Euthlypis, Leucopeza, Oporornis, Parula, Phaeothlypis, Wilsonia). We provide a summary phylogenetic hypothesis that will be broadly applicable to investigations of the historical biogeography, processes of diversification, and evolution of trait variation in this well studied avian group.