4 research outputs found

    Phylogenomics of Rapid Avian Radiations

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    I use data from sequence capture of ultraconserved elements to resolve three rapid radiations in the avian tree of life and in the process gain insights on applying analytical strategies with gene tree-based coalescent methods (GCM). In Chapter 1, I explore analytical strategies that can be employed with GCMs to increase phylogenetic resolution and minimize highly supported conflicting results, including subsampling taxa to increase the number of gene trees analyzed, trimming sequences to eliminate sequence length heterogeneity, and filtering loci based on information content. These strategies are used to reconstruct a highly resolved and consistent phylogenetic hypothesis for the relatively young avian family, Zosteropidae. I show how conflicting results from different GCMs can arise from biases introduced by sequence length heterogeneity and uninformative loci that can lead to strongly supported incorrect estimates of phylogeny. In Chapter 2, I examine higher-level relationships in the enigmatic core Corvoidea group of Oscine passerines. A highly resolved phylogeny of core Corvoidea is recovered, with a majority of nodes receiving high support from both ML and coalescent analyses. I show that short sequence lengths do not bias species tree estimates of GCMs if informative sites are present in these sequences. In contrast, some samples that have longer sequence lengths compared to most taxa but shorter sequence lengths compared to taxa in its clade can also bias species tree estimates of GCMs. In Chapter 3, I develop a hypothesis on the origins of the trogons (Trogonidae) based on a robust dated phylogeny estimated from thousands of genome-wide loci. I recover the first well-supported hypothesis of relationships among trogon genera. This topology, combined with the trogon fossil record, geologic, and climatic data, suggests an Old World origin in the Late Oligocene/Early Miocene for the crown group. In this iii chapter, I show that in some datasets in which loci have high information content, exclusion of less informative loci in analysis can lead to lower bootstrap support of species tree estimates of GCMs

    Molecular Systematics and Diversification of African Zosteropidae (Aves: Passeriformes)

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    The hyper-diverse avian family Zosteropidae (~100 species) is renowned for its exceptional colonising ability and rapid recent diversification. The genus Zosterops dominates within the family, including over 70% of all recognised species, and is notorious for the phenotypic uniformity that has traditionally made designation of taxon boundaries within the genus difficult. While the last decade has seen an abundance of research focusing on colonisation abilities and speciation patterns of insular taxa, relationships between continental forms, specifically mainland African taxa, remain subject to great uncertainty. This thesis focuses on uncovering the relationships, origin and evolutionary history of African Zosteropidae. Chapter 1 introduces the family Zosteropidae, reviews the current literature that is based predominantly on insular systems. In introducing the African Zosteropidae complex, this chapter highlights questions associated with this group and presents the aims of the thesis. Chapter 2 focuses in on one of the most geographically complex areas within the African system, to explore the relative importance of past climatic fluctuations as a driver of diversification in Zosterops endemic to the isolated montane massifs of East Africa. Results provide the first molecular assessment of mainland African Zosteropidae and are used to examine alternative models of speciation. A dated molecular phylogeny demonstrates that divergence within African Zosteropidae is very recent (<5Ma) coinciding with periods of climatic instability during the Plio-Pleistocene. Furthermore, the non-monophyly of mainland taxa, specifically the polyphyletic nature of Z. poliogaster, leads to the rejection of a widely held assumption that the montane endemics of East Africa are relics of a previously widespread population. Instead results provide evidence for evolutionary model based on ancestrally adaptive populations. Chapter 3 attempts to further investigate relationships within the East African Zosterops and explores the usefulness of amplified fragment length polymorphism (AFLPs) in revealing inter- and intra-specific relationships. Resolution of relationships across the AFLP phylogeny is generally poor which is attributed to the low information content of the AFLP matrix generated. Bayesian hypothesis testing failed to provide support for various topological constraints tested and consequently this study was unable to confirm or reject the non-monophyly of East African montane endemics. Chapter 4 builds upon the molecular phylogeny of Chapter 2, by substantially increasing the taxonomic sampling of African species using DNA obtained from museum specimens. The use of both archive and fresh material enabled the largest genetic assessment of western Zosteropidae to date. Extensive sampling across Sub-Saharan Africa, the Indian Ocean region, the Arabian Peninsula and the Gulf of Guinea region reveals six major clades within the African Zosteropidae complex. Results confirm the widespread non-monophyly of mainland African species rendering current taxonomic arrangements invalid. GMYC (General mixed Yule-coalescent) analysis recovers 14 distinct evolutionary lineages within the African Zosteropidae system and provides a framework for further work using model-based species delimitation approaches. Finally, Chapter 5 draws together key findings from Chapters 2-4, and reviews how this work advances our understanding of the African Zosteropidae system. This chapter also highlights new gaps in our understanding of the western Zosteropidae and discusses several areas for future research

    Invasive Birds: Global Trends and Impacts

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    This 381-paged book covers the biology, ecology, impact and management of 34 common alien invasive species, with reviews on the history and context of avian introductions and invasions in five major regions (Oceania, Africa, Europe (including the Middle East, Asia and South America)), as well as management challenges and the potential of citizen science for monitoring alien birds. The book pitches at the introductory level and is ideal for readers to gain a quick and comprehensive view of the current status of global avian invasions. It has brought the records and research of avian invasion one step ahead of other alien invasive animal taxa. Many chapters contain distribution maps and data tables on the diet and morphology of the species, providing a good reference for the species and its management issues. Each chapter also contains a rich list of references that could help readers dive further into the topic

    The Systematic Position of the Bird Genus Apalopteron

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    Volume: 108Start Page: 133End Page: 13
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