Integrating Sequence Capture and Restriction Site-Associated DNA Sequencing to resolve Recent Radiations of Pelagic Seabirds

The diversification of modern birds has been shaped by a number of radiations. Rapid diversification events make reconstructing the evolutionary relationships among taxa challenging due to the convoluted effects of incomplete lineage sorting (ILS) and introgression. Phylogenomic datasets have the potential to detect patterns of phylogenetic incongruence, and to address their causes. However, the footprints of ILS and introgression on sequence data can vary between different phylogenomic markers at different phylogenetic scales depending on factors such as their evolutionary rates or their selection pressures. We show that combining phylogenomic markers that evolve at different rates, such as paired-end double-digest restriction site-associated DNA (PE-ddRAD) and ultraconserved elements (UCEs), allows a comprehensive exploration of the causes of phylogenetic discordance associated with short internodes at different timescales. We used thousands of UCE and PE-ddRAD markers to produce the first well-resolved phylogeny of shearwaters, a group of medium-sized pelagic seabirds that are among the most phylogenetically controversial and endangered bird groups. We found that phylogenomic conflict was mainly derived from high levels of ILS due to rapid speciation events. We also documented a case of introgression, despite the high philopatry of shearwaters to their breeding sites, which typically limits gene flow. We integrated state-of-the-art concatenated and coalescent-based approaches to expand on previous comparisons of UCE and RAD-Seq datasets for phylogenetics, divergence time estimation and inference of introgression, and we propose a strategy to optimise RAD-Seq data for phylogenetic analyses. Our results highlight the usefulness of combining phylogenomic markers evolving at different rates to understand the causes of phylogenetic discordance at different timescales

Evolutionary history of sympatric rainbow skinks from the australian monsoonal tropics

Tese de doutoramento, Biologia (Biologia Evolutiva), Universidade de Lisboa, Faculdade de Ciências, 2018How speciation, range shifting and reticulation through climatic oscillations combine to shape current patterns of local and regional diversity remains a key question in evolutionary biology. This can be investigated by using multi-scale analyses of closely related species assemblages in diverse communities, such as the lizards of Australia’s tropical savannas. An example of these is the understudied group of rainbow skinks (Carlia) that are broadly co-distributed across the Australian Monsoonal Tropics (AMT) region, and that stands out from most well-studied Carlia species occurring along the Australian east coast. The aims of this thesis were to: i) identify lineage diversity between two sympatric and closely related skinks and to use an integrative taxonomic approach to statistically test major lineages as species; ii) compare past responses of species with different climatic niche breadth that experienced the same climatic fluctuations; iii) infer the phylogenetic relationships of the rainbow skinks in a collaborative study; and iv) explore the occurrence of introgression in a group of six species that broadly cooccur in the AMT, using a dataset by target exon capture (>1000 loci). The investigation of lineage diversity discovered cryptic lineages mostly in the Kimberley region (north west of Australia). In an integrative taxonomic approach, these lineages were then statistically validated as new species using multispecies coalescent methods and morphological analyses, and subsequently described as C. insularis sp. nov and C. isostriacantha sp. nov. with genetic and morphological characters. The exploration of how concordant were the species responses with late Pleistocene climatic changes, identified contrasting responses by species with different climatic niches, suggesting that the narrow climatic specialist species was more sensitive to these changes. In addition, using multiple phylogenomic approaches, it contributed to a much improved and well-supported phylogeny for the rainbow skinks in comparison with a previous, poorly resolved tree. The new tree showed that the six Carlia species that co-occur in the AMT are actually closely related. Lastly, the analysis for the presence of introgression between the AMT sympatric species did not detect evidence of recent admixture, but identified patterns of ancestral introgression before the divergence of sister species, and some instances of introgression in the more climatic unstable Kimberley region. It also showed that by accounting for reticulated evolution with phylogenetic networks methods, a distinct topology from the overall well supported species tree can be observed, in this case with the clade inferred as introgressed appearing as more ancestral in the phylogeny. The results of this thesis have implications for the understanding of the processes driving cryptic species diversity and responses to past climatic change across this richm and understudied Australian Monsoonal Tropics biome

Behavioral, morphological, and genomic analyses of population structure in brood parasitic indigobirds (Vidua spp.)

The African indigobirds (Vidua spp.) are exceptional among avian brood parasites in that mimicry of host vocalizations plays an integral role in their social behaviors and evolutionary history. Young indigobirds imprint on the vocalizations of their hosts during development, adult males include mimicry of these vocalizations in their own repertoire, and adult females use these songs to choose both their mates and the nests they parasitize. Imprinting on the host during development therefore results in assortative mating and host fidelity, but also provides a mechanism for rapid, sympatric speciation via host shift. Host shifts require some degree of host infidelity, however, and the same behavioral mechanisms may thus lead to hybridization if eggs are laid in the nest of a host species already "occupied" by another indigobird species. Thus, it is not clear if the morphological and genetic similarity of most indigobird species is due to recent common ancestry or ongoing hybridization. I addressed this uncertainty by studying indigobirds in East Africa, a region that was colonized by West African ancestors in the late Pleistocene and is currently home to four indigobird species. I analyzed variation among species in: vi1) the responses of territorial males to playbacks of conspecific and heterospecific vocalizations; 2) temporal and frequency traits of chatter calls and complex non-mimicry songs; 3) morphological characters; and 4) genomic polymorphisms. The playback experiment shows that host mimicry is an important cue in species recognition, and suggests that it may contribute to species cohesion when juveniles or adults disperse beyond the boundaries of their dialect neighborhood. Analyses of both non-mimetic vocalizations and morphological characters (i.e., plumage color and body size) reveal that they are shaped by divergence among species as well as local ecology. Analyses of thousands of "double-digest" restriction site-associated DNA (ddRAD) loci scattered across the genome indicate that both species identity and geographic divergence contribute to population structure. Taken together, the results show that the tempo of speciation and morphological divergence among indigobirds associated with different hosts is likely variable, depending on geographic context, and the breeding ecology and morphology of alternative hosts