Genomics and Population History of Black-headed Bulbul (Brachypodius atriceps) Color Morphs

Intraspecific polymorphism in birds, especially color polymorphism, is an area of active research in evolutionary biology. In this dissertation, I applied WGS to uncover the potential genetic underpinnings of color polymorphism in the Black-headed Bulbul (Brachypodius atriceps) of Southeast Asia. This species was selected because of the heterogeneous dispersion of two morphs across its range: a yellow form predominating on mainland Asia and the Greater Sunda Islands and a gray morph on two islands—Bawean and Maratua. I approached this project from three angles. First, I reconstructed the phylogeny of the bulbul family, Pycnonotidae, to examine patterns of coloration among all species and infer the commonality of color changes relevant to B. atriceps. To build the phylogenetic tree, I used a super-matrix approach, which allowed the inclusion of 121 of the 130 known species of bulbuls. Using the tree, I determined the most appropriate outgroups for comparison with B. atriceps in subsequent genomic study. Next, I generated a high-quality reference genome of a yellow individual of B. atriceps and, subsequently, sequenced low-coverage genomes of multiple gray and yellow individuals, and three outgroup taxa. I compared Fst values between genomes of gray and yellow individuals to locate peaks of divergence and identify potential candidate loci for the color polymorphism. I also tested the protein-coding genes between yellow and gray birds for signs of selection. Among genes potentially responsible for the color polymorphism, several involved in lipid uptake, transport, and deposition—processes fundamental to carotenoid expression. In the final chapter, I assessed characteristics among B. atriceps populations across the species range in Sundaland with an emphasis on Bawean and Maratua islands. The Bawean population was barely discernable genetically from that on mainland Borneo. The Maratua population, however, was notably divergent from the mainland Bornean and other populations. Therefore, I modelled its demographic parameters and used the information to gain a better idea of the historical processes that have led to its unique, singular coloration. The Maratua population was originally isolated from other Sundaic populations c. 1.9 Ma, but c. 1000 years ago began to experience a small amount of gene flow

Ornithological observations from Maratua and Bawean Islands, Indonesia

Indonesia’s many islands, large and small, make it an important center of avian diversity and endemism. Current biogeographic understanding, however, is limited by the lack of modern genetic samples for comparative analyses from most of these islands, and conservation efforts are hampered by the paucity of recent information from small islands peripheral to major, more commonly visited  islands. In November and December 2016, we visited Maratua, an oceanic coral atoll 50 km east of Borneo, and Bawean, a volcanic island on the Sunda continental shelf 150 km north of Java, to survey birds and collect specimens for morphological and genetic analysis. We detected many of the birds on Maratua’s historical lists and added several new resident and migratory species. Notably, we did not detect the Maratua White-rumped Shama (Copsychus malabaricus barbouri). On Bawean, we found the forests to be nearly silent and detected remarkably few resident land-bird species overall. The           severe population reduction of C. m. barbouri on Maratua and the drastic reduction of forest birds on Bawean probably result from overexploitation by the cage-bird trade in the first case and a combination of the cage-bird trade and pellet-gun hunting in the second

Opening the door to greater phylogeographic inference in Southeast Asia: Comparative genomic study of five codistributed rainforest bird species using target capture and historical DNA

Indochina and Sundaland are biologically diverse, interconnected regions of Southeast Asia with complex geographic histories. Few studies have examined phylogeography of bird species that span the two regions because of inadequate population sampling. To determine how geographic barriers/events and disparate dispersal potential have influenced the population structure, gene flow, and demographics of species that occupy the entire area, we studied five largely codistributed rainforest bird species: Arachnothera longirostra, Irena puella, Brachypodius atriceps, Niltava grandis, and Stachyris nigriceps. We accomplished relatively thorough sampling and data collection by sequencing ultraconserved elements (UCEs) using DNA extracted from modern and older (historical) specimens. We obtained a genome-wide set of 753–4,501 variable loci and 3,919–18,472 single nucleotide polymorphisms. The formation of major within-species lineages occurred within a similar span of time (0.5–1.5 mya). Major patterns in population genetic structure are largely consistent with the dispersal potential and habitat requirements of the study species. A population break across the Isthmus of Kra was shared only by the two hill/submontane insectivores (N. grandis and S. nigriceps). Across Sundaland, there is little structure in B. atriceps, which is a eurytopic and partially frugivorous species that often utilizes forest edges. Two other eurytopic species, A. longirostra and I. puella, possess highly divergent populations in peripheral Sunda Islands (Java and/or Palawan) and India. These species probably possess intermediate dispersal abilities that allowed them to colonize new areas, and then remained largely isolated subsequently. We also observed an east–west break in Indochina that was shared by B. atriceps and S. nigriceps, species with very different habitat requirements and dispersal potential. By analyzing high-throughput DNA data, our study provides an unprecedented comparative perspective on the process of avian population divergence across Southeast Asia, a process that is determined by geography, species characteristics, and the stochastic nature of dispersal and vicariance events

Ornithological expeditions to Sarawak, Malaysian Borneo, 2007-2017

Louisiana State University, the University of Kansas, and the Universiti Malaysia Sarawak undertook collaborative research on the evolution and ecology of Bornean birds starting in 2005. This collaboration included a series of expeditions from 2007–2017 to collect and study birds at \u3e30 sites in Sarawak, Malaysian Borneo. Here we provide information on the study-sites and summarize the main discoveries resulting from the collaboration

Tapping the woodpecker tree for evolutionary insight

Molecular phylogenetic studies of woodpeckers (Picidae) have generally focused on relationships within specific clades or have sampled sparsely across the family. We compared DNA sequences of six loci from 203 of the 217 recognized species of woodpeckers to construct a comprehensive tree of intrafamilial relationships. We recovered many known, but also numerous unknown, relationships among clades and species. We found, for example, that the three picine tribes are related as follows (Picini, (Campephilini, Melanerpini)) and that the genus Dinopium is paraphyletic. We used the tree to analyze rates of diversification and biogeographic patterns within the family. Diversification rate increased on two occasions during woodpecker history. We also tested diversification rates between temperate and tropical species but found no significant difference. Biogeographic analysis supported an Old World origin of the family and identified at least six independent cases of New World-Old World sister relationships. In light of the tree, we discuss how convergence, mimicry, and potential cases of hybridization have complicated woodpecker taxonomy

Genomic investigation of colour polymorphism and phylogeographic variation among populations of black-headed bulbul (Brachypodius atriceps) in insular southeast Asia

Intraspecific polymorphism in birds, especially plumage colour polymorphism, and the mechanisms that control it are an area of active research in evolutionary biology. The black-headed bulbul (Brachypodius atriceps) is a polymorphic species with two distinct morphs, yellow and grey. This species inhabits the mainland and virtually all continental islands of Southeast Asia where yellow morphs predominate, but on two islands in the Sunda region, Bawean and Maratua, grey morphs are common or exclusive. Here, we generated a high-quality reference genome of a yellow individual and resequenced genomes of multiple individuals of both yellow and grey morphs to study the genetic basis of coloration and population history of the species. Using PCA and STRUCTURE analysis, we found the Maratua Island population (which is exclusively grey) to be distinct from all other B. atriceps populations, having been isolated c. 1.9 million years ago (Ma). In contrast, Bawean grey individuals (a subset of yellow and grey individuals on that island) are embedded within an almost panmictic Sundaic clade of yellow birds. Using F and d to compare variable genomic segments between Maratua and yellow individuals, we located peaks of divergence and identified candidate loci involved in the colour polymorphism. Tests of selection among coding-proteins in high F regions, however, did not indicate selection on the candidate genes. Overall, we report on some loci that are potentially responsible for the grey/yellow polymorphism in a species that otherwise shows little genetic diversification across most of its range

Neo-sex chromosome evolution and phenotypic differentiation across an elevational gradient in horned larks (Eremophila alpestris)

Genetic structure and phenotypic variation among populations are affected by both geographic distance and environmental variation across species\u27 distributions. Understanding the relative contributions of isolation by distance (IBD) and isolation by environment (IBE) is important for elucidating population dynamics across habitats and ecological gradients. In this study, we compared phenotypic and genetic variation among Horned Lark (Eremophila alpestris) populations from 10 sites encompassing an elevational gradient from low-elevation desert scrub in Death Valley (285 a.s.l.) to high-elevation meadows in the White Mountains of the Sierra Nevada of California (greater than 3000 m a.s.l.). Using a ddRAD data set of 28,474 SNPs aligned to a high-quality reference genome, we compared genetic structure with elevational, environmental, and spatial distance to quantify how different aspects of the landscape drive genomic and phenotypic differentiation in Horned Larks. We found larger-bodied birds were associated with sites that had less seasonality and higher annual precipitation, and longer spurs occurred in soils with more clay and silt content, less sand, and finer fragments. Larks have large neo-sex chromosomes, and we found that associations with elevation and environmental variation were much stronger among neo-sex chromosomes compared to autosomes. Furthermore, we found that putative chromosomal translocations, fusions, and inversions were associated with elevation and may underlie local adaptation across an elevational gradient in Horned Larks. Our results suggest that genetic variation in Horned Larks is affected more by IBD than IBE, but specific phenotypes and genomic regions-particually on neo-sex chromosomes-bear stronger associations with the environment

Sundaland’s east–west rain forest population structure : variable manifestations in four polytypic bird species examined using RAD-Seq and plumage analyses

Aim: A current model of rain forest population diversification in Sundaland specifieseast–west vicariance into refugia during the early Pleistocene. In some taxa, thisdivision was followed by dispersal and apparent secondary contact on Borneo in thelate Pleistocene. To investigate genetic, morphological, spatial and temporal charac-teristics of the model, we compared genomic population and plumage variationamong four bird species with east–west mtDNA and plumage structure. Location: Borneo and western Sundaland (Sumatra and the Malay Peninsula).Methods: We quantified plumage patterns among populations of two muscicapids(Copsychus saularis and Kittacincla malabarica) and two timaliids (Mixornis gularis andTrichastoma malaccense), and compared them with population genetic patternsdetermined from (1) SNPs produced by RAD-Seq and (2) previously sequencedmtDNA. Results: All four species exhibit east–west variation in morphological and somegenetic characters, but patterns are idiosyncratic. Copsychus saularis’ mtDNA andplumage change gradually across Borneo, but RAD-Seq comparisons indicate nopopulation structure. In K. malabarica, all three characteristics change abruptly andconcurrently on Borneo. In M. gularis, the main east–west break occurs betweenBorneo and western Sundaland, with marginal mtDNA, plumage and RAD-Seq struc-ture on Borneo. T. malaccense exhibits two distinct mtDNA and genomic transitions,an early Pleistocene break between western Sundaland and Borneo, and a Pliocenebreak between the north-east and the rest of Borneo. Despite this deep geneticdivision, its plumage changes clinally across Borneo.Main conclusions: MtDNA, plumage and RAD-Seq patterns may vary depending onsuch factors as pre-Pleistocene distribution, habitat requirements and dispersalpropensity, differential introgression among the three character types, selection onplumage and phylogenetic relationships

History, Annotated Gazetteer, and Bibliography of Sarawak Ornithology

Sarawak is Malaysia’s largest state, covering most of northern Borneo. It has a remarkable history of scientific bird study, starting in the 1840s and growing ever since. To set the stage for the gazetteer, which is the core of this paper, we start with a review of this history and discuss various forces that have influenced the direction of bird research in the state. Following this introduction comes the gazetteer, which is an annotated list of c. 865 sites in Sarawak where birds have been collected, studied, or regularly observed. The gazetteer provides the latitude, longitude, and elevation of each site, and it lists publications, reports, and museum collections associated with each site. The purpose of the gazetteer is to help interested parties locate sites and investigate their research history. It is also intended to help museum curators geolocate specimens for various kinds of studies, including the assessment of bird distributions in relation to habitat change over time. A notable byproduct of the historical review and gazetteer is a bibliography of c. 750 references related to Sarawak ornithology. Another is the identification of areas in Sarawak where birds are better known and areas where they are not