Phylogenetic relationships in the southern African genus Drosanthemum (Ruschioideae, Aizoaceae)

Background. Drosanthemum, the only genus of the tribe Drosanthemeae, is widespread over the Greater Cape Floristic Region in southern Africa. With 114 recognized species, Drosanthemum together with the highly succulent and species-rich tribe Ruschieae constitute the 'core ruschioids' in Aizoaceae. Within Drosanthemum, nine subgenera have been described based on flower and fruit morphology. Their phylogenetic relationships, however, have not yet been investigated, hampering understanding of monophyletic entities and patterns of geographic distribution. Methods. Using chloroplast and nuclear DNA sequence data, we performed network- and tree-based phylogenetic analyses of 73 species of Drosanthemum with multiple accessions for widespread species. A well-curated, geo-referenced occurrence data set comprising the 134 genetically analysed and 863 further accessions was used to describe the distributional ranges of intrageneric lineages and the genus as a whole. Results. Phylogenetic inference supports nine clades within Drosanthemum, seven of which group in two major clades, while the remaining two show ambiguous affinities. The nine clades are generally congruent to previously described subgenera within Drosanthemum, with exceptions such as (pseudo-) cryptic species. In-depth analyses of sequence patterns in each gene region were used to reveal phylogenetic affinities inside the retrieved clades in more detail. We observe a complex distribution pattern including widespread, species-rich clades expanding into arid habitats of the interior (subgenera Drosanthemum p.p., Vespertina, Xamera) that are genetically and morphologically diverse. In contrast, less species-rich, genetically less divergent, and morphologically unique lineages are restricted to the central Cape region and more mesic conditions (Decidua, Necopina, Ossicula, Quastea, Quadrata, Speciosa). Our results suggest that the main lineages arose from an initial rapid radiation, with subsequent diversification in some clades.Raw data, code, analysis output, and species occurrence The zip file contains a ReadMe file and 4 folders: 1_main_data_and_results (the files used to produce the figures in the main text); 2_ML_phylogenetics (raw data, code, and analysis output of ML phylogenetic analyses); 3_MJ_networks (raw data [SNP/sequence motive recoded DNA alignment matrices], and output of median-joining network analyses)

Towards a new online species-information system for legumes

The need for scientists to exchange, share and organise data has resulted in a proliferation of biodiversity research-data portals over recent decades. These cyber-infrastructures have had a major impact on taxonomy and helped the discipline by allowing faster access to bibliographic information, biological and nomenclatural data, and specimen information. Several specialised portals aggregate particular data types for a large number of species, including legumes. Here, we argue that, despite access to such data-aggregation portals, a taxon-focused portal, curated by a community of researchers specialising on a particular taxonomic group and who have the interest, commitment, existing collaborative links, and knowledge necessary to ensure data quality, would be a useful resource in itself and make important contributions to more general data providers. Such an online species-information system focused on Leguminosae (Fabaceae) would serve useful functions in parallel to and different from international data-aggregation portals. We explore best practices for developing a legume-focused portal that would support data sharing, provide a better understanding of what data are available, missing, or erroneous, and, ultimately, facilitate cross-analyses and direct development of novel research. We present a history of legume-focused portals, survey existing data portals to evaluate what is available and which features are of most interest, and discuss how a legume-focused portal might be developed to respond to the needs of the legume-systematics research community and beyond. We propose taking full advantage of existing data sources, informatics tools and protocols to develop a scalable and interactive portal that will be used, contributed to, and fully supported by the legume-systematics community in the easiest manner possible

Evolution and ecology of two iconic Australian clades: the Meliphagidae (birds) and the Hakeinae (plants)

The first part of this dissertation explores the evolution of two iconic groups of species through Australian climate space: the Meliphagidae, or honeyeaters, which are primarily nectar-feeding birds, and the Hakeinae, a section of the plant family Proteaceae. Both groups are inferred to have had their origins in Gondwanan rainforests that were widespread across Australia 45 million years ago and then diversified into more arid environments as the continent’s climate became more arid. Accordingly, dry environments are inhabited by closely related (phylogenetically clustered) sets of species, although, in contrast to the honeyeaters, Hakeinae communities are characterized by more localized diversification. The impressive and rapid Hakeinae diversification may have been driven by specialization onto a variety of highly weathered, nutrient-poor soil types on the ancient Australian landmass. The second part of this dissertation reviews a variety of methods to assess the phylogenetic structure of communities, such as local assemblages of honeyeaters and Hakeinae. Many published methods were found to be redundant, and some of the truly unique approaches do not measure what they purport to. Accordingly, only a small subset of phylogenetic community structure methods have merit. In the third part of the dissertation, observations on foraging by 74 of 75 Australian honeyeater species are used to explore patterns of community assembly. Australian honeyeater communities reflect both stochastic and deterministic processes. Co-occurring species exhibit substantial overlap in foraging niche space, in contrast to predictions from assembly theory based on competition. At the same time, species tend to occupy characteristic portions of niche space and available niche space is smaller in the arid regions of the continent. Within this smaller available niche space, arid-zone species tend to be more widely separated in niche space than species in more mesic environments

New horizons for female birdsong : evolution, culture and analysis tools : a thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Ecology at Massey University, Auckland, New Zealand

Published papers appear in Appendix 7.1. and 7.2 respectively under a CC BY 4.0 and CC BY licence: Webb, W. H., Brunton, D. H., Aguirre, J. D., Thomas, D. B., Valcu, M., & Dale, J. (2016). Female song occurs in songbirds with more elaborate female coloration and reduced sexual dichromatism. Frontiers in Ecology and Evolution, 4(22). https://doi.org/10.3389/fevo.2016.00022 Yukio Fukuzawa, Wesley Webb, Matthew Pawley, Michelle Roper, Stephen Marsland, Dianne Brunton, & Andrew Gilman. (2020). Koe: Web-based software to classify acoustic units and analyse sequence structure in animal vocalisations. Methods in Ecology and Evolution, 11(3). https://doi.org/10.1111/2041-210X.13336As a result of male-centric, northern-hemisphere-biased sexual selection theory, elaborate female traits in songbirds have been largely overlooked as unusual or non-functional by-products of male evolution. However, recent research has revealed that female song is present in most surveyed songbirds and was in fact the ancestral condition to the clade. Additionally, a high proportion of songbird species have colourful females, and both song and showy colours have demonstrated female-specific functions in a growing number of species. We have much to learn about the evolution and functions of elaborate female traits in general, and female song in particular. This thesis extends the horizons of female birdsong research in three ways: (1) by revealing the broad-scale evolutionary relationship of female song and plumage elaboration across the songbirds, (2) by developing new accessible tools for the measurement and analysis of song complexity, and (3) by showing—through a detailed field study on a large natural metapopulation—how vocal culture operates differentially in males and females. First, to understand the drivers of elaborate female traits, I tested the evolutionary relationship between female song presence and plumage colouration across the songbirds. I found strong support for a positive evolutionary correlation between traits, with female song more prevalent amongst species with elaborated female plumage. These results suggest that contrary to the idea of trade-off between showy traits, female plumage colouration and female song likely evolved together under similar selection pressures and that their respective functions are reinforcing. Second, I introduce new bioacoustics software, Koe, designed to meet the need for detailed classification and analysis of song complexity. The program enables visualisation, segmentation, rapid classification and analysis of song structure. I demonstrate Koe with a case study of New Zealand bellbird Anthornis melanura song, showcasing the capabilities for large-scale bioacoustics research and its application to female song. Third, I conducted one of the first detailed field-based analyses of female song culture, studying an archipelago metapopulation of New Zealand bellbirds. Comparing between male and female sectors of each population, I found equal syllable diversity, largely separate repertoires, and contrasting patterns of sharing between sites—revealing female dialects and pronounced sex differences in cultural evolution. By combining broad-scale evolutionary approaches, novel song analysis tools, and a detailed field study, this thesis demonstrates that female song can be as much an elaborate signal as male song. I describe how future work can build on these findings to expand understanding of elaborate female traits

Morphological evolution and modularity of the amphibian skull

Lissamphibia, the only extant, non-amniote tetrapod clade, are morphologically incredibly diverse. However, to date, studies of morphological evolution, phenotypic integration (covariation) and modularity (the division of a structure into sets of integrated traits) have concentrated overwhelmingly on amniotes. In this thesis I quantified cranial morphological variation across two lissamphibian clades, with representative specimens from every extant genus (caecilians) and family (frogs). Shape was captured in detail, using a high-dimensional surface-based geometric morphometric approach, to test alternative models of cranial organisation and reconstruct cranial evolution across caecilians and frogs. I found both frog and caecilian crania are highly modular, and the pattern of cranial integration is strongly conserved across the clades. Of particular interest is the highly integrated, fast-evolving jaw suspensorium region of both frogs and caecilians, suggesting feeding mechanics may be driving cranial evolution in these clades. In addition, ecology exerts a stronger influence on morphology than developmental strategy for both clades. Fossorial, semi-fossorial, and aquatic species are the most disparate and fastest-evolving among frogs, while aquatic caecilian species are the fastest-evolving for that clade. Ossification sequence timing significantly influences integration, evolutionary rate, and disparity across frogs, and there is no simple relationship between integration and evolutionary rate or disparity. Finally, to extend the study of morphological evolution into deep time, I investigated influences on cranial morphology for fossil and extant frogs from the Early Cretaceous to the Recent. Given the extremely dorso-ventrally compressed nature of fossil frogs, I collected two-dimensional cranial outline data for 42 fossil and 93 extant frogs. Phylogeny exerts the strongest influence on cranial morphology, with allometry and developmental strategy acting as only weak influences on cranial outlines. This thesis represents a significant advance in the study of cranial modularity and morphological evolution across frogs and caecilians, unrivalled in shape description, in taxonomic sampling, and in the in-depth exploration of hypotheses of modularity and macroevolutionary patterns

Characterising macroevolutionary patterns within crocodylomorpha

Crocodylians today comprise only 24 recognised species, and are often regarded as morphologically conservative. However, the fossil record of crocodylomorphs, which includes the extinct relatives of crocodylians, is much richer and extends over the last ~220 million years. This great biodiversity is reflected in their morphological disparity, with crocodylomorph species occupying a much wider range of ecological niches. Research effort has concentrated mostly on the description of new taxa and on placing them within the crocodylomorph evolutionary tree, and has greatly contributed to our understanding of crocodylomorph phylogeny and diversity. Nevertheless, another fundamental aspect of crocodylomorph macroevolution, morphological disparity, has only recently been the subject of quantitative scrutiny, with the focus often limited to specific subgroups rather than the entire clade. In this thesis, crocodylomorph morphological disparity is quantitatively assessed using distinct types of data. Body size patterns, characterised via a model-fitting approach, provide new insights into the adaptive landscape of crocodylomorphs. Patterns of cranial shape variation suggest an important link between ecological diversification and morphological disparity. Finally, the action of heterochrony, underlying remarkable cranial modifications in the crocodylomorph clade Notosuchia, is tested using geometric morphometrics. Together, these results represent a significant contribution to better understanding crocodylomorph phenotypic evolution

Tools O' the Times : understanding the common proporties of species interaction networks across space

Le domaine de l’écologie des réseaux est encore limité dans sa capacité à faire des inférences mondiales à grande échelle. Ce défi est principalement dû à la difficulté d’échantillonnage des interactions sur le terrain, entraînant de nombreuses « lacunes » en ce qui concerne la couverture mondiale des données. Cette thèse adopte une approche « centrée sur les méthodes » de l’écologie des réseaux et se concentre sur l’idée de développer des outils pour aider à combler les lacunes en matière de données en présentant la prédiction comme une alternative accessible à l’échantillonnage sur le terrain et introduit deux « outils » différents qui sont prêts à poser des questions à l’échelle mondiale. Le chapitre 1 présente les outils que nous pouvons utiliser pour faire des prédictions de réseaux et est motivé par l’idée selon laquelle avoir la capacité de prédire les interactions entre les espèces grâce à l’utilisation d’outils de modélisation est impératif pour une compréhension plus globale des réseaux écologiques. Ce chapitre comprend une preuve de concept (dans laquelle nous montrons comment un simple modèle de réseau neuronal est capable de faire des prédictions précises sur les interactions entre espèces), une évaluation des défis et des opportunités associés à l’amélioration des prédictions d’interaction et une feuille de route conceptuelle concernant l’utilisation de modèles prédictifs pour les réseaux écologiques. Les chapitres 2 et 3 sont étroitement liés et se concentrent sur l’utilisation de l’intégration de graphiques pour la prédiction de réseau. Essentiellement, l’intégration de graphes nous permet de transformer un graphe (réseau) en un ensemble de vecteurs, qui capturent une propriété écologique du réseau et nous fournissent une abstraction simple mais puissante d’un réseau d’interaction et servent de moyen de maximiser les informations disponibles. dispo- nibles à partir des réseaux d’interactions d’espèces. Parce que l’intégration de graphes nous permet de « décoder » les informations au sein d’un réseau, elle est conçue comme un outil de prédiction de réseau, en particulier lorsqu’elle est utilisée dans un cadre d’apprentissage par transfert. Elle s’appuie sur l’idée que nous pouvons utiliser les connaissances acquises en résolvant un problème connu. et l’utiliser pour résoudre un problème étroitement lié. Ici, nous avons utilisé le métaweb européen (connu) pour prédire un métaweb pour les espèces canadiennes en fonction de leur parenté phylogénétique. Ce qui rend ce travail particulière- ment passionnant est que malgré le faible nombre d’espèces partagées entre ces deux régions, nous sommes capables de récupérer la plupart (91%) des interactions. Le chapitre 4 approfondit la réflexion sur la complexité des réseaux et les différentes ma- nières que nous pourrions choisir de définir la complexité. Plus spécifiquement, nous remet- tons en question les mesures structurelles plus traditionnelles de la complexité en présentant l’entropie SVD comme une mesure alternative de la complexité. Adopter une approche phy- sique pour définir la complexité nous permet de réfléchir aux informations contenues dans un réseau plutôt qu’à leurs propriétés émergentes. Il est intéressant de noter que l’entropie SVD révèle que les réseaux bipartites sont très complexes et ne sont pas nécessairement conformes à l’idée selon laquelle la complexité engendre la stabilité. Enfin, je présente le package Julia SpatialBoundaries.jl. Ce package permet à l’utili- sateur d’implémenter l’algorithme de wombling spatial pour des données disposées de manière uniforme ou aléatoire dans l’espace. Étant donné que l’algorithme de wombling spatial se concentre à la fois sur le gradient et sur la direction du changement pour un paysage donné, il peut être utilisé à la fois pour détecter les limites au sens traditionnel du terme ainsi que pour examiner de manière plus nuancée la direction des changements. Cette approche pourrait être un moyen bénéfique de réfléchir aux questions liées à la détection des limites des réseaux et à leur relation avec les limites environnementales.The field of network ecology is still limited in its ability to make large-scale, global inferences. This challenge is primarily driven by the difficulty of sampling interactions in the field, leading to many ‘gaps’ with regards to global coverage of data. This thesis takes a ’methods-centric’ approach to network ecology and focuses on the idea of developing tools to help with filling in the the data gaps by presenting prediction as an accessible alternative to sampling in the field and introduces two different ’tools’ that are primed for asking questions at global scales. Chapter 1 maps out tools we can use to make network predictions and is driven by the idea that having the ability to predict interactions between species through the use of modelling tools is imperative for a more global understanding of ecological networks. This chapter includes a proof-of-concept (where we show how a simple neural network model is able to make accurate predictions about species interactions), an assessment of the challenges and opportunities associated with improving interaction predictions, and providing a conceptual roadmap concerned with the use of predictive models for ecological networks. Chapters 2 and 3 are closely intertwined and are focused on the use of graph embedding for network prediction. Essentially graph embedding allows us to transform a graph (net- work) into a set of vectors, which capture an ecological property of the network and provides us with a simple, yet powerful abstraction of an interaction network and serves as a way to maximise the available information available from species interaction networks. Because graph embedding allows us to ’decode’ the information within a network it is primed as a tool for network prediction, specifically when used in a transfer learning framework, this builds on the idea that we can take the knowledge gained from solving a known problem and using it to solve a closely related problem. Here we used the (known) European metaweb to predict a metaweb for Canadian species based on their phylogenetic relatedness. What makes this work particularly exciting is that despite the low number of species shared between these two regions we are able to recover most (91%) of interactions. Chapter 4 delves into thinking about the complexity of networks and the different ways we might choose to define complexity. More specifically we challenge the more traditional structural measures of complexity by presenting SVD entropy as an alternative measure of complexity. Taking a physical approach to defining complexity allows us to think about the information contained within a network as opposed to their emerging properties. Interest- ingly, SVD entropy reveals that bipartite networks are highly complex and do not necessarily conform to the idea that complexity begets stability. Finally, I present the Julia package SpatialBoundaries.jl. This package allows the user to implement the spatial wombling algorithm for data arranged uniformly or randomly across space. Because the spatial wombling algorithm focuses on both the gradient as well as the direction of change for the given landscape it can be used both for detecting boundaries in the traditional sense as well as a more nuanced look at at the direction of changes. This approach could be a beneficial way with which to think about questions which relate to boundary detection for networks and how these relate to environmental boundaries

Evolutionary relationships of East African soda lake cichlid fish

This thesis examines the evolutionary relationships of the Alcolapia soda lake cichlid fishes of East Africa. The introduction presents background on the soda lakes in which the cichlids are found, the taxonomy and biology of the fishes, as well as the theoretical background to the study. Chapter two discusses the methods used in the thesis, addressing the benefits and limitations of each, as well as their suitability to the study in hand. Chapter three investigates the phylogenetics and phylogeography of soda lake cichlids sampled at several populations around the soda lakes and a single transplanted population outside of the focal lakes, employing a large genomic dataset generated through restriction site associated DNA (RAD) sequencing, and demonstrates low levels of interspecific genomic differentiation with high levels of ongoing gene flow. Chapter four uses the RAD dataset to test for signals of selection between Alcolapia species, employing genome-wide scans and outlier detection to characterise peaks of genomic divergence between species. Chapter five combines morphological (geometric morphometrics) and ecological (stable isotope, stomach contents) data with the RAD dataset from chapter three to consider biologically relevant diversification between Alcolapia species, testing for convergence and niche adaptation. Chapter six examines the ecomorphology of the soda lake fishes at an intraspecific level, testing for effects of geography and environment on morphological differentiation between populations. Finally, chapter seven draws together the conclusions inferred from the thesis, and discusses possible future directions for research in this system

Diversity and diversification of uropeltid snakes

Fossorial snakes are key to understanding snake origins and trends of fossoriality in early snake evolution. However, they are generally understudied due to their secretive lifestyle, making them less likely to be encountered without special effort. Given their phylogenetic position and fossorial habits, this PhD project aims to study the evolution of a major radiation of fossorial snakes – the family Uropeltidae. Currently there are eight recognised genera and ca. 56 species, distributed in the Western Ghats of India and Sri Lanka. They show morphological traits that are adaptations to fossoriality, which have never been studied in detail, or with quantitative approaches. Their heads are adapted for headfirst burrowing, hence being important structures to study adaptation to the physical environment. Moreover, snakes in this group are commonly known as shieldtails due to the unusual structures on their tails, whose diversity and function are poorly known. This project employs an integrative approach to generate a taxonomically comprehensive molecular phylogeny for uropeltids, and to study lineage and phenotypic diversity and diversification patterns. This work provides insights into spatial, temporal and morphological patterns of diversification in these organisms and understand the impact that fossoriality has on biotic diversification. In summary, this thesis advances the understanding of evolutionary relationships among uropeltids, uncovering unexpectedly high levels of uropeltid molecular diversity. Moreover, results estimated constant lineage accumulation rates in uropeltids, and a pattern of early burst of phenotypic evolution in tail tip traits. These results suggest that while this is not a case of adaptive radiation, tail tip morphology might have played an important ecological role early on in the diversification of the Uropeltidae