Evolutionary and Population Dynamics of Crustaceans in the Gulf of Mexico

Evolution occurs and can be conceptualized along a spectrum, bounded on one extreme by the relationships between deep lineages – such as phyla, classes, and orders – and on the other by the molecular dynamics of operational taxonomic units within a species, defined as population genetics. The purpose of this dissertation was to better understand the evolutionary and population dynamics of crustaceans within the Gulf of Mexico. In the second chapter of my dissertation, I provide a guide to best phylogenetic practice while reviewing infraordinal relationships within Decapoda, including the promise held by next-generation sequencing (NGS) approaches such as Anchored Hybrid Enrichment. Chapter III is a phylogenetic study of species relationships within the economically important shrimp genus, Farfantepenaeus, targeting three mitochondrial genes and uncovering an intriguing pattern of latitudinal speciation. As the first inclusive molecular phylogeny of the genus, we find support for the newly described species F. isabelae, but a lack of support for the species status of F. notialis. Additionally, our results suggest the existence of two distinct subspecies of F. brasiliensis. Chapter IV investigates the relative impacts of habitat heterogeneity and the presence of a possible glacial refugium in determining population dynamics of the Giant Deep-Sea Isopod, Bathynomus giganteus in the northern Gulf of Mexico. Through hybrid population genetics/genomics analyses and Bayesian testing of population models, we find strong evidence for habitat heterogeneity determining population dynamics for this charismatic deep-sea invertebrate. Chapter V further investigates the role of environment in determining and maintaining genetic diversity and population connectivity, specifically focused on establishing biological baselines with which we can diagnose health and resilience of the Gulf of Mexico. This was accomplished through a comparative NGS population genomics study of three species of mesopelagic crustaceans: Acanthephyra purpurea, Systellaspis debilis, and Robustosergia robusta. While diversity and connectivity differs in each species, the comparative results bespeak the importance of access to the Gulf Loop Current in determining and maintaining population dynamics. Overall, my work significantly contributes to our knowledge of Crustacea at the phylogenetic- and population genetic-level

Genetic and morphometric variation of Octopus vulgaris in the Benguela Current region

The Benguela Current is a cold eastern boundary current located on the south-western coast of the African continent. The establishment of its present day features approximately two million years ago has triggered allopatric events which have driven genetic and/or phenotypic differentiation in many of the warm-temperate organisms that previously had continuous distributions along the south and west coast of southern Africa. However, since many of these species have responded differently, despite similar isolation times, research in this region provides a unique opportunity to increase our understanding of evolutionary processes. The common octopus (Octopus vulgaris, Cuvier 1797) is a coastal, sedentary species, inhabiting coral reefs or rocky environments at depths of up to a 100m. It is considered to be one of the most extensively studied cephalopod species due to its worldwide distribution. However, very little research has been conducted on O. vulgaris in southern Africa. In order to gain a holistic understanding of the effects of the Benguela Current on population connectivity, genetic and phenotypic diversity, and evolutionary history of O. vulgaris, a comparative genetic and morphological study was conducted across the Benguela region. A total of 168 specimens of O. vulgaris were collected from four different regions across the Benguela system. A small tissue sample was preserved in ethanol for molecular analysis, and the specimen was frozen whole for morphometric analysis in the laboratory. Octopus vulgaris genetic population structure and evolutionary history was investigated using a 580bp fragment of the mitochondrial cytochrome b (cytb) gene for 76 individuals located within the Benguela region, yielding 10 different haplotypes. AMOVA and pairwise FST analyses revealed significant genetic differentiation suggesting a northern-southern Benguela divergence. Estimates of time since most recent common ancestor, based on biogeographical calibrators and coalescent analyses, indicated that isolation between the Angolan and South African population occurred between ~231 Ka and 1 Ma. Mismatch distribution analyses revealed a past population expansion within the South African O. vulgaris roughly 129.31 Ka, whilst Bayesian skyline plots were indicative of gradual demographic growth within the Angolan population in the last ~100 Ka. Observed O. vulgaris population structure and demographic history was likely the result of historical climate-induced change within the system. Reconstruction of phylogenetic relationships within the Octopus genus, using cytb and COI suggest that O. vulgaris is not a monophyletic group and a major systematic revision is required. Furthermore, unidentified individuals from South Africa were found to group with species from Indo-West Pacific Oceans and were therefore considered to have been translocated through ballast water from Asia. While the molecular analysis indicated a significant northern-southern Benguela structure results from the principle component analysis (PCA) and discriminate function analysis (DFA) were unable to distinguish between O. vulgaris from different sampling localities throughout the Benguela Current region based on soft-parts, hard-parts and meristic characters. The lack of phenotypic variation, despite significant genetic divergence, highlights the importance of multi-method approaches in gaining a holistic understanding of the taxonomy and biogeography of species

Novel Split-Based Approaches to Computing Phylogenetic Diversity and Planar Split Networks

EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Development and maintenance of genetic diversity in Scots pine, Pinus sylvestris (L.)

Forests are among the most important repositories of terrestrial biodiversity and provide a broad range of ecosystem services. During millennia, forests have changed, adapted and evolved under changing conditions. However, in the present century, forests are facing environmental changes at rates with no precedents. A major concern is the risk of declining forest genetic diversity, since genetic variation as the raw material underpinning adaptation is key in maintaining the resilience of forest ecosystems against environmental changes. Understanding the different processes responsible for developing and maintaining the genetic diversity of tree species is essential to better predict tree responses under new conditions. Therefore, this thesis aimed to determine how different forces interact to shape and maintain within and among population genetic diversity of Scots pine and what the implications are for conservation and management under forthcoming environmental conditions. From local to continental scales, we followed a multilevel approach, and found that (i) historic climate changes and geographical barriers have played an important role in shaping the extent and spatial distribution of current genetic diversity of Scots pine. Despite contemporary habitat reduction and fragmentation we found that (ii) high levels of neutral genetic diversity remain in the Scottish populations of Scots pine, with gene flow and specifically wind-driven gene flow dominating over genetic drift and preventing differentiation among the Scottish populations. However, (iii) considerable impacts in the spatial distribution of genetic variation have occurred as a consequence of intensive historical forest management practices. Furthermore, we found that (iv) substantial levels of adaptive genetic variation are present in the Scottish populations of Scots pine, likely a result of selective processes resulting from the different environments they live in, with highly heritable traits, although similar capacity for response through phenotypic plasticity to warming. Our results help to further disentangle the forces maintaining genetic diversity in one of most widespread conifers in the world, and improving predictions of likely range shifts and adaptation of the species in response to contemporary changes. We provide some recommendations to conservation and management practices

Understanding the shining Ramshorn snail, Segmentina Nitida: morphology, genetics and breeding

The Shining Ramshorn Snail, Segmentina nitida, is a rare freshwater snail found predominantly in drainage ditches along field margins and in marshland. It is experiencing marked declines in distribution in the United Kingdom (UK) and mainland Europe. The species was included in the IUCN Red Data Book for Invertebrates before a guideline change in 1994 and is included on the UK Biodiversity Action Plan (BAP) as a priority species for conservation. The BAP for S. nitida states that further research on the species required to inform reintroduction and translocation for its conservation. For this thesis, a modified sample evaluation method for Segmentina nitida was developed and evaluated. It increased sample assessment speed without significantly reducing accuracy in comparison to a traditional method of sample evaluation. Captive breeding of S. nitida was explored with the aim of developing simple breeding protocols that could provide stock for potential reintroduction of the species into historical locations. Breeding proved challenging due to fluctuations in water chemistry and subsequent high mortality rates. Geometric morphometric shape analyses were used to investigate variation in shell shape of the species across European populations from the UK, Germany, Poland and Sweden, and the Czech Republic. German and UK snails had similar shell morphologies, and Polish and Czech snails also clustered together morphologically, with the shape of Swedish snails being less distinct. Analysis of the population genetics of German, UK, Polish and Swedish populations using nuclear (ITS, microsatellites) and mitochondrial markers (COI) revealed two distinct lineages of S. nitida in Europe. One comprised of populations from Poland and Sweden (East), and one represented UK populations and a Swedish population (West) with the two lineages coexisting in Germany. These two lineages show no evidence of genetic admixture and can be delimited by both genetic markers and geometric morphometrics, indicating two evolutionarily distinct units, possibly equating to species. The genetic and shape differences between European populations has impacts the conservation of Segmentina nitida, especially in the UK, as previous descriptions of range may now be incorrect and the UK populations may be more significant globally than previously thought, if they are indeed S. nitida. Any future reintroduction plans in the UK and elsewhere would also need to take into account these genetic lineages, as they may result in the introduction of an invasive species or result in infertile offspring

Genetic diversity and evolution within the genus Bulinus and species-level interactions with the transmission of Schistosoma haematobium group parasites

Schistosomiasis is a Neglected Tropical Disease (NTD) prevalent across much of Africa, and also regions in South America, Asia, the Middle East and parts of Southern Europe. Caused by infections with dioecious parasitic flatworms of the Schistosoma genus, schistosomiasis results in an undue degree of suffering for humans and animals, particularly in Sub-Sharan Africa. Transmission occurs in freshwater containing specific intermediate host snails that act as vectors for the parasites; hosts becoming infected when the larval stages, released (shed) from the snails, burrow through the skin of the mammalian hosts that come into contact with the freshwater. Therefore, in humans this is a preventable water borne disease disproportionately affecting those that do not have access to safe water sources and good sanitation infrastructures. Mass drug administration (MDA) for the control of human schistosomiasis, which can occur in both intestinal and urogenital forms, is the recommended strategy by the World Health Organization (WHO), however, various factors contribute to the maintenance of schistosomiasis transmission in endemic areas of Africa. Potentially the biggest cause for persistence is the reservoir of infection that remains in freshwater intermediate host snails. Establishing the geographical distribution of intermediate host species in endemic regions and determining their associations with different schistosome species is paramount during schistosomiasis control programmes. Following years of neglect, a resurgence of interest in snail focussed surveillance and control is currently underway, with the WHO even recognising it as a critical action point in their 2020 road map for schistosomiasis control and elimination goals by 2030. However, rigorously tested and refined tools necessary for incorporating snails into schistosomiasis control programmes and the fundamental knowledge about the diversity of the snails and schistosomes underpinning such developments, are not available. Focusing on two endemic regions for urogenital schistosomiasis: the Niger River Valley, and the elimination setting of the Zanzibar Archipelago, this study provides new insights into the genetic diversity of Bulinus spp. and importantly, the associations they have with multiple S. haematobium group species in these regions. Furthermore, the first largescale approach for snail surveillance protocols are tested, showing the advantages that this approach will provide in certifying future elimination and in monitoring disease endemicity. Additionally, novel mitogenome data produced for Bulinus spp. from across Sub-Saharan Africa and the Indian Ocean islands are analysed, which sheds light on the evolutionary radiation of this important genus and the cryptic species diversity that has traditionally confounded taxonomy. The findings can be applied to implement new policies on snail surveillance in schistosomiasis control, whilst also providing a valuable resource for future research investigating the Bulinus genus

Sago Palm: Multiple Contributions to Food Security and Sustainable Livelihoods

Under-utilized food resource; Metroxylon sagu; Starch production; Sago palm forest; Sago suga

Sago Palm: Multiple Contributions to Food Security and Sustainable Livelihoods

Under-utilized food resource; Metroxylon sagu; Starch production; Sago palm forest; Sago suga