Habitat shifts in the evolutionary history of a Neotropical flycatcher lineage from forest and open landscapes

<p>Abstract</p> <p>Background</p> <p>Little is known about the role ecological shifts play in the evolution of Neotropical radiations that have colonized a variety of environments. We here examine habitat shifts in the evolutionary history of <it>Elaenia </it>flycatchers, a Neotropical bird lineage that lives in a range of forest and open habitats. We evaluate phylogenetic relationships within the genus based on mitochondrial and nuclear DNA sequence data, and then employ parsimony-based and Bayesian methods to reconstruct preferences for a number of habitat types and migratory behaviour throughout the evolutionary history of the genus. Using a molecular clock approach, we date the most important habitat shifts.</p> <p>Results</p> <p>Our analyses resolve phylogenetic relationships among <it>Elaenia </it>species and confirm several species associations predicted by morphology while furnishing support for other taxon placements that are in conflict with traditional classification, such as the elevation of various <it>Elaenia </it>taxa to species level. While savannah specialism is restricted to one basal clade within the genus, montane forest was invaded from open habitat only on a limited number of occasions. Riparian growth may have been favoured early on in the evolution of the main <it>Elaenia </it>clade and subsequently been deserted on several occasions. Austral long-distance migratory behaviour evolved on several occasions.</p> <p>Conclusion</p> <p>Ancestral reconstructions of habitat preferences reveal pronounced differences not only in the timing of the emergence of certain habitat preferences, but also in the frequency of habitat shifts. The early origin of savannah specialism in <it>Elaenia </it>highlights the importance of this habitat in Neotropical Pliocene and late Miocene biogeography. While forest in old mountain ranges such as the Tepuis and the Brazilian Shield was colonized early on, the most important colonization event of montane forest was in conjunction with Pliocene Andean uplift. Riparian habitats may have played an important role in facilitating habitat shifts by birds expanding up the mountains along streams and adapting to newly emerging montane forest habitat.</p

Rampant polyphyly indicates cryptic diversity in a clade of Neotropical flycatchers (Aves: Tyrannidae)

Polyphyletic arrangements in DNA phylogenies are often indicators of cryptic species diversity masked by erroneous taxonomic treatments that are frequently based on morphological data. Although mitochondrial (mt)DNA polyphyly is detected relatively rarely in phylogenetic studies, it has recently been found in a variety of tyrant-flycatcher (Tyrannidae) groups. In the present study, we provide a DNA phylogeny for a mitochondrial and a nuclear locus with a complete species sampling in Zimmerius flycatchers, showing that the genus is characterized by multiple mtDNA polyphyly. Based on phylogenetic and life-history information, we suggest the elevation of a number of taxa to species status, leading to a doubling of Zimmerius species-level diversity compared to taxonomic treatments conducted before 2001. © 2013 The Linnean Society of London

NEW AND SIGNIFICANT ISLAND RECORDS, RANGE EXTENSIONS AND ELEVATIONAL EXTENSIONS OF BIRDS IN EASTERN SULAWESI, ITS NEARBY SATELLITES, AND TERNATE

The Wallacean Region continues to be widely unexplored even in such relatively well-known animal groups as birds (Aves). We report on the results of an ornithological expedition from late Nov 2013 through early Jan 2014 to eastern Sulawesi and a number of satellite islands (Togian, Peleng, Taliabu) as well as Ternate. The expedition targeted and succeeded with the collection of 7–10 bird taxa previously documented by us and other researchers but still undescribed to science. In this contribution, we provide details on numerous first records of bird species outside their previously known geographic or elevational ranges observed or otherwise recorded during this expedition. We also document what appears to be a genuinely new taxon, possibly at the species level of kingfisher from Sulawesi that has been overlooked by previous ornithologists. Our results underscore our fragmentary knowledge of the composition of the avifauna of eastern Indonesia, and demonstrate that there continues to be a high degree of cryptic, undescribed avian diversity on these islands more than a century and a half after they were visited by Alfred Russel Wallace and other collectors

Genome-wide data reveal cryptic diversity and genetic introgression in an Oriental cynopterine fruit bat radiation

Sampling details consisting of information about number of individuals typed for each marker. Populations with mutiple sampling points are represented by one representative coordinate. FA = forearm length, EL = ear length and TIB = tibia length. All morphological measurements are recorded in millimeters (mm). (XLSX 13 kb

Two New Genera of Songbirds Represent Endemic Radiations from the Shola Sky Islands of the Western Ghats, India

A long-standing view of Indian biodiversity is that while rich in species, there are few endemics or in-situ radiations within the subcontinent. One exception is the Western Ghats biodiversity hotspot, an isolated mountain range with many endemic species. Understanding the origins of the montane-restricted species is crucial to illuminate both taxonomic and environmental history

A New Species of Muscicapa Flycatcher from Sulawesi, Indonesia

The Indonesian island of Sulawesi, a globally important hotspot of avian endemism, has been relatively poorly studied ornithologically, to the extent that several new bird species from the region have been described to science only recently, and others have been observed and photographed, but never before collected or named to science. One of these is a new species of Muscicapa flycatcher that has been observed on several occasions since 1997. We collected two specimens in Central Sulawesi in 2012, and based on a combination of morphological, vocal and genetic characters, we describe the new species herein, more than 15 years after the first observations. The new species is superficially similar to the highly migratory, boreal-breeding Gray-streaked Flycatcher Muscicapa griseisticta, which winters in Sulawesi; however, the new species differs strongly from M. griseisticta in several morphological characters, song, and mtDNA. Based on mtDNA, the new species is only distantly related to M. griseisticta, instead being a member of the M. dauurica clade. The new species is evidently widely distributed in lowland and submontane forest throughout Sulawesi. This wide distribution coupled with the species' apparent tolerance of disturbed habitats suggests it is not currently threatened with extinction.This project was funded by the National Geographic Society (NGS CRE 8919-11; granted to PCR), the Loke Wan Tho Memorial Foundation (granted to DLY), and an EIPR scholarship at the University of Adelaide (granted to JBCH). Labwork for this project was co-funded by a National University of Singapore Faculty of Science start-up grant to FER (WBS R-154-000-570-133). We thank RISTEK for issuing the national research permits (for 2011, 0215/SIP/FRP/VI/2011; for 2012, 183/SIP/FRP/SM/VI/2012) and Lore Lindu National Park for permit letters. The Research Centre for Biology-LIPI supported DMP and DDP in their field research and provided facilities for laboratory analysis. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Historic and modern genomes unveil a domestic introgression gradient in a wild red junglefowl population

The red junglefowl Gallus gallus is the ancestor of the domestic chicken and arguably the most important bird species on Earth. Continual gene flow between domestic and wild populations has compromised its gene pool, especially since the last century when human encroachment and habitat loss would have led to increased contact opportunities. We present the first combined genomic and morphological admixture assessment of a native population of red junglefowl, sampled from recolonized parts of its former range in Singapore, partly using whole genomes resequenced from dozens of individuals. Crucially, this population was genomically anchored to museum samples from adjacent Peninsular Malaysia collected ~110–150 years ago to infer the magnitude of modern domestic introgression across individuals. We detected a strong feral–wild genomic continuum with varying levels of domestic introgression in different subpopulations across Singapore. Using a trait scoring scheme, we determined morphological thresholds that can be used by conservation managers to successfully identify individuals with low levels of domestic introgression, and selected traits that were particularly useful for predicting domesticity in genomic profiles. Our study underscores the utility of combined genomic and morphological approaches in population management and suggests a way forward to safeguard the allelic integrity of wild red junglefowl in perpetuity.© 2020 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited

Conflict between Genetic and Phenotypic Differentiation: The Evolutionary History of a ‘Lost and Rediscovered’ Shorebird

Understanding and resolving conflicts between phenotypic and genetic differentiation is central to evolutionary research. While phenotypically monomorphic species may exhibit deep genetic divergences, some morphologically distinct taxa lack notable genetic differentiation. Here we conduct a molecular investigation of an enigmatic shorebird with a convoluted taxonomic history, the White-faced Plover (Charadrius alexandrinus dealbatus), widely regarded as a subspecies of the Kentish Plover (C. alexandrinus). Described as distinct in 1863, its name was consistently misapplied in subsequent decades until taxonomic clarification ensued in 2008. Using a recently proposed test of species delimitation, we reconfirm the phenotypic distinctness of dealbatus. We then compare three mitochondrial and seven nuclear DNA markers among 278 samples of dealbatus and alexandrinus from across their breeding range and four other closely related plovers. We fail to find any population genetic differentiation between dealbatus and alexandrinus, whereas the other species are deeply diverged at the study loci. Kentish Plovers join a small but growing list of species for which low levels of genetic differentiation are accompanied by the presence of strong phenotypic divergence, suggesting that diagnostic phenotypic characters may be encoded by few genes that are difficult to detect. Alternatively, gene expression differences may be crucial in producing different phenotypes whereas neutral differentiation may be lagging behind