Building a Portuguese Coalition for Biodiversity Genomics

The diverse physiography of the Portuguese land and marine territory, spanning from continental Europe to the Atlantic archipelagos, has made it an important repository of biodiversity throughout the Pleistocene glacial cycles, leading to a remarkable diversity of species and ecosystems. This rich biodiversity is under threat from anthropogenic drivers, such as climate change, invasive species, land use changes, overexploitation or pathogen (re)emergence. The inventory, characterization and study of biodiversity at inter- and intra-specific levels using genomics is crucial to promote its preservation and recovery by informing biodiversity conservation policies, management measures and research. The participation of researchers from Portuguese institutions in the European Reference Genome Atlas (ERGA) initiative, and its pilot effort to generate reference genomes for European biodiversity, has reinforced the establishment of Biogenome Portugal. This nascent institutional network will connect the national community of researchers in genomics. Here, we describe the Portuguese contribution to ERGA’s pilot effort, which will generate high-quality reference genomes of six species from Portugal that are endemic, iconic and/or endangered, and include plants, insects and vertebrates (fish, birds and mammals) from mainland Portugal or the Azores islands. In addition, we outline the objectives of Biogenome Portugal, which aims to (i) promote scientific collaboration, (ii) contribute to advanced training, (iii) stimulate the participation of institutions and researchers based in Portugal in international biodiversity genomics initiatives, and (iv) contribute to the transfer of knowledge to stakeholders and engaging the public to preserve biodiversity. This initiative will strengthen biodiversity genomics research in Portugal and fuel the genomic inventory of Portuguese eukaryotic species. Such efforts will be critical to the conservation of the country’s rich biodiversity and will contribute to ERGA’s goal of generating reference genomes for European species.info:eu-repo/semantics/publishedVersio

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

ABSTRACT: A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ∼1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.info:eu-repo/semantics/publishedVersio

Determining the mechanisms driving the invasion success of the smallmouth bass (Micropterus dolomieu, Lacepède 1802)

Thesis (PhD)--Stellenbosch University, 2017.ENGLISH Abstract: Biological invasions represent a significant threat to the Earth’s biota, including freshwater ecosystems. Whilst various studies have been conducted on invasive species in the hopes of establishing a set of general guidelines to facilitate our understanding of the invasion pathway and the features (organismal or environmental) that may assist in a species’ invasion success, predictions and generalisations remain challenging and limited. While general guidelines and unified frameworks are essential in furthering our understanding of biological invasions, exploring the genetic and phenotypic variation in a species and the influence of extrinsic factors during adaptation to novel environments could provide insight into a species’ invasion success. By utilising an array of methods, spanning different disciplines, this dissertation evaluates the potential mechanisms driving a species’ invasive success using the smallmouth bass, Micropterus dolomieu, as model organism. First, I attempt to unravel the role of genetic diversity in a species’ invasive success, by assessing the genetic differentiation and diversity within M. dolomieu populations in the invaded South African (SA) range, and examine how the genetic diversity may change over time in both native (USA) and invasive ranges (Chapter 2). By conducting a three-way comparison on two mitochondrial (mtDNA) and nine microsatellite loci for a total of 572 M. dolomieu specimens, representing the contemporary invasive SA range, contemporary native USA range and the historic native USA range (dating back to the period of introduction into SA), I reveal the presence of elevated levels of genetic diversity for the invasive SA range. The levels of genetic diversity for both the contemporary native and invasive ranges are, however, substantially lower than those of the historic native range, suggesting that both contemporary populations experienced a recent genetic bottleneck followed by a rapid population expansion. As admixture, and more specifically introgressive hybridisation, may contribute to these elevated levels of genetic diversity observed within the invaded SA range, I subsequently test the hypothesis that hybridisation and introgression can occur between two invasive species in a novel invaded range (Chapter 3). Using two notorious freshwater invaders (M. dolomieu and M. salmoides), I assess the level of introgressive hybridisation between the two species, using two mtDNA and nine microsatellite loci. Despite large uncorrected pairwise distances being observed between the two species, unidirectional mitochondrial introgression was detected, suggesting that introgressive hybridisation may play a pivotal role in the successful establishment and spread of alien invasive species upon introduction. The remaining chapters focus on the role of morphological variation in response to environmental variation in the novel invaded range. First, I test the hypothesis that environmental variation drives morphological changes in phenotype (Chapter 4). Analyses of linear and geometric morphometrics, as well as environmental variables, show a strong correlation between body depth and flow regime, with streamlined fish inhabiting high-flow environments. In addition, the presence of variation in gape size among localities suggests a link between cranial morphology and prey composition associated with substrate type. These results support the idea that similar environments have convergent phenotypes and highlight the importance of phenotypic plasticity in facilitating the successful colonisation, establishment and spread of invasive species. However, as gene flow may erase phenotypic variation associated with plasticity, I continue by exploring the genetic basis to local adaptation (Chapter 5). By combining linear morphometrics and genotypic data, I demonstrate slight population structuring among sampled localities, corresponding to three distinct sections of the river (i.e., tributary, impoundment and mainstem). However, the presence of high levels of gene flow observed among populations suggesting that both local adaptation and phenotypic plasticity may play a key role. In conclusion, M. dolomieu appears to be a successful invader that fully exploits genetic and phenotypic variability to invade, persist and establish in an array of non-native environments.AFRIKAANSE OPSOMMING: Geen opsomming beskikbaar.Doctora

Phylogeography of the Cape girdled lizard, Cordylus cordylus : investigating biogeographic patterning in the Cape floristic region (CFR)

Thesis (MSc)--Stellenbosch University, 2013.ENGLISH ABSTRACT: In the present study I examined the phylogeography of the rupicolous Cape girdled lizard, Cordylus cordylus. Samples were collected across the species distribution range from 63 localities in the Eastern and Western Cape and Free State provinces of South Africa, yielding a total sample size of 207 specimens. Four DNA loci, two nuclear (PRLR, PTPN12) and two mitochondrial (16S rRNA, ND2), were sequenced. Bayesian inference, maximum likelihood and maximum parsimony methods were employed to test evolutionary relationships among populations, followed by population structure analyses, divergence time estimations and niche modelling. My results confirm the species monophyly and revealed the presence of two distinct clades. Clade 1 comprised specimens from the western and southern portions of the Western Cape coast, while clade 2 comprised specimens from the southern and eastern Cape coast and adjacent interior of the Eastern and Western Cape and Free State provinces. An area of sympatry between the two clades was observed in the Breede river valley. The divergence time estimates revealed an Early Pliocene (4.31 Ma), Late Miocene (6.01 Ma) divergence for each of the two clades retrieved. Phylogeographic data suggest that clade 1 is younger (lower haplotypic and nucleotide diversity), in comparison to clade 2. Furthermore, the niche modelling shows that C. cordylus occupies a wide range of unfavourable habitats. The absence of marked phylogeographic patterning within clades is very uncharacteristic for a rupicolous vertebrate species. The ecological pliability and generalist nature of C. cordylus presumably contributed to the observed phylogeographic pattern and have facilitated the absence of within clade differentiation. Moreover, I suggest that microclimatic variables, rather than geographic barriers influence the genetic structuring of C. cordylus

Data from: What doesn’t kill you might make you stronger: functional basis for variation in body armour

1. Predation has been proposed to be a selective agent in the evolution of morphological antipredator strategies in prey. Among vertebrates, one of the morphological traits that evolved multiple times is body armour, including carapaces, thickened keratinized scales and plates of dermal bone. 2. It has been generally assumed that body armour provides protection against a predatory attack; yet, few explicit tests of the hypothesis exist. Cordylidae, a relatively small family of southern African lizards, show considerable variation in the degree of body armour. Hence, this family provides an opportunity to test the hypothesis that body armour serves as protection against predators. 3. Experiments were conducted to test whether the bite forces of four species of mammalian predators were high enough to penetrate the skins of Karusasaurus polyzonus, Namazonurus peersi, Cordylus cordylus and Cordylus macropholis, as well as those of Ouroborus cataphractus individuals originating from three localities that differed in their predator diversity. Furthermore, histological techniques were used to test whether variation in skin toughness was associated with concomitant changes in the degree of epidermal (i.e. β-keratin) and dermal (i.e. osteoderm) armour. 4. The skin toughness values for four out of five cordylid lizards tested in this study were well below the bite forces of the mammalian predators. In contrast, the thick osteoderms in the dermis of O. cataphractus can withstand bites from several mongoose species. However, the significant variation in body armour that is present between the three populations of O. cataphractus does not seem to be related to predator diversity. 5. It is concluded that body armour can serve as protection against predation in O. cataphractus, but that alternative selection pressures, such as thermoregulation or predation by snakes, presumably underlie variation in defensive morphology in the other cordylid lizards

Skin Toughness

Skin toughness values (in N) for five species of cordylid lizards using the skulls of four species of (mongoose) predator

Data from: The ghost of introduction past: spatial and temporal variability in the genetic diversity of invasive smallmouth bass

Understanding the demographic history of introduced populations is essential for unravelling their invasive potential and adaptability to a novel environment. To this end, levels of genetic diversity within the native and invasive range of a species are often compared. Most studies, however, focus solely on contemporary samples, relying heavily on the premise that the historic population structure within the native range has been maintained over time. Here, we assess this assumption by conducting a three-way comparison of the genetic diversity of native (historic and contemporary) and invasive (contemporary) smallmouth bass (Micropterus dolomieu) populations. Analyses of a total of 572 M. dolomieu samples, representing the contemporary invasive South African range, contemporary and historical native USA range (dating back to the 1930s when these fish were first introduced into South Africa), revealed that the historical native range had higher genetic diversity levels when compared to both contemporary native and invasive ranges. These results suggest that both contemporary populations experienced a recent genetic bottleneck. Furthermore, the invasive range displayed significant population structure, whereas both historical and contemporary native USA populations revealed higher levels of admixture. Comparison of contemporary and historical samples showed both a historic introduction of M. dolomieu, as well as a more recent introduction, thereby demonstrating that undocumented introductions of this species have occurred. Although multiple introductions might have contributed to the high levels of genetic diversity in the invaded range, we discuss alternative factors that may have been responsible for the elevated levels of genetic diversity and highlight the importance of incorporating historic specimens into demographic analyses

Skin Morphology

Thickness of the osteoderm and beta-keratin layer (in mm) of dermal skin sectio