Landscape genomics of tropical high altitude plant species

Changes to species distributions involve demographic processes that occur over generations and affect allele frequencies within populations, leading to patterns of genetic restructuring. The specific genetic structuring patterns that will be observed as a consequence depend on explicit geographical features, such as topography and latitude. Over the first decades of phylogeography, the effect of climate history and geography on species genomes was examined at low resolution with DNA sequences and other traditional molecular markers. However, During the last five years it has become feasible to obtain genomic data for non-model organisms and large sample sizes. The present thesis spans the transition years between phylogeographic studies being restricted to low resolution molecular markers, and new methods facilitating the generation of genomic data for non-model species. As such, this thesis focuses on two main points. First, on the methodological aspects of utilising double digest RAD-seq (ddRAD) for individual-based population genetics and phylogeography of plant species. Second, on applying the obtained data to examine one of the classic. but as yet not fully explained, biodiversity patterns: the biodiversity excess within tropical mountains. The main contributions of this thesis at the methodological level are; (1) demonstrating the utility of DNA replicates for the estimation of genotyping error and optimisation of de novo assembly; (2) proposing a method for identifying paralogous loci resulting from recent gene duplications; and (3) showing that such logi provide a measure of population differentiation. Regarding the drivers of biodiversity excess within tropical mountains, I used landscape genomic analyses and ddRAD data to examine two plant species from the alpine grasslands of the Transmexican Volcanic Belt. As a main result, this thesis supports from a population-level perspective that tropical mountains; (1) allow for long-term in situ population persistence; and (2) promote population differentiation as a function of topographic isolation

Gene duplication, population genomics, and species-level differentiation within a tropical mountain shrub.

Gene duplication leads to paralogy, which complicates the de novo assembly of genotyping-by-sequencing (GBS) data. The issue of paralogous genes is exacerbated in plants, because they are particularly prone to gene duplication events. Paralogs are normally filtered from GBS data before undertaking population genomics or phylogenetic analyses. However, gene duplication plays an important role in the functional diversification of genes and it can also lead to the formation of postzygotic barriers. Using populations and closely related species of a tropical mountain shrub, we examine 1) the genomic differentiation produced by putative orthologs, and 2) the distribution of recent gene duplication among lineages and geography. We find high differentiation among populations from isolated mountain peaks and species-level differentiation within what is morphologically described as a single species. The inferred distribution of paralogs among populations is congruent with taxonomy and shows that GBS could be used to examine recent gene duplication as a source of genomic differentiation of nonmodel species

Long-term in situ persistence of biodiversity in tropical sky islands revealed by landscape genomics

Tropical mountains are areas of high species richness and endemism. Two historical phenomena may have contributed to this: (1) fragmentation and isolation of habitats may have promoted the genetic differentiation of populations and increased the possibility of allopatric divergence and speciation, and; (2) the mountain areas may have allowed long-term population persistence during global climate fluctuations. These two phenomena have been studied using either species occurrence data or estimating species divergence times. However, only few studies have used intraspecific genetic data to analyse the mechanisms by which endemism may emerge at the microevolutionary scale. Here, we use landscape analysis of genomic SNP data sampled from two high-elevation plant species from an archipelago of tropical sky-islands (the Transmexican Volcanic Belt) to test for population genetic differentiation, synchronous demographic changes and habitat persistence. We show that genetic differentiation can be explained by the degree of glacial habitat connectivity among mountains, and that mountains have facilitated the persistence of populations throughout glacial/interglacial cycles. Our results support the ongoing role of tropical mountains as cradles for biodiversity by uncovering cryptic differentiation and limits to gene flow

Monitoring of benthic eukaryotic communities in two tropical coastal lagoons through eDNA metabarcoding: a spatial and temporal approximation

Tropical coastal lagoons are important ecosystems that support high levels of biodiversity and provide several goods and services. Monitoring of benthic biodiversity and detection of harmful or invasive species is crucial, particularly in relation to seasonal and spatial variation of environmental conditions. In this study, eDNA metabarcoding was used in two tropical coastal lagoons, Chacahua (CH) and Corralero (C) (Southern Mexican Pacific), to describe the benthic biodiversity and its spatial–temporal dynamics. The distribution of benthic diversity within the lagoons showed a very particular pattern evidencing a transition from freshwater to seawater. Although the two lagoon systems are similar in terms of the species composition of metazoans and microeukaryotes, our findings indicate that they are different in taxa richness and structure, resulting in regional partitioning of the diversity with salinity as the driving factor of community composition in CH. Harmful, invasive, non-indigenous species, bioindicators and species of commercial importance were detected, demonstrating the reach of this technique for biodiversity monitoring along with the continued efforts of building species reference libraries

Genomic variation in recently collected maize landraces from Mexico

AbstractThe present dataset comprises 36,931 SNPs genotyped in 46 maize landraces native to Mexico as well as the teosinte subspecies Zea maiz ssp. parviglumis and ssp. mexicana. These landraces were collected directly from farmers mostly between 2006 and 2010. We accompany these data with a short description of the variation within each landrace, as well as maps, principal component analyses and neighbor joining trees showing the distribution of the genetic diversity relative to landrace, geographical features and maize biogeography. High levels of genetic variation were detected for the maize landraces (HE=0.234 to 0.318 (mean 0.311), while slightly lower levels were detected in Zea m. mexicana and Zea m. parviglumis (HE=0.262 and 0.234, respectively). The distribution of genetic variation was better explained by environmental variables given by the interaction of altitude and latitude than by landrace identity. This dataset is a follow up product of the Global Native Maize Project, an initiative to update the data on Mexican maize landraces and their wild relatives, and to generate information that is necessary for implementing the Mexican Biosafety Law

Genetic diversity and structure of two endangered mole salamander species of the Trans-Mexican Volcanic Belt

The most important factor leading to amphibian population declines and extinctions is habitat degradation and destruction. To help prevent further extinctions, studies are needed to make appropriate conservation decisions in small and fragmented populations. The goal of this study was to provide data from the population genetics of two micro-endemic mole salamanders from the Trans-Mexican Volcanic Belt. Nine microsatellite markers were used to study the population genetics of 152 individuals from two Ambystoma species. We sampled 38 individuals in two localities for A. altamirani and A. rivulare. We found medium to high levels of genetic diversity expressed as heterozygosity in the populations. However, all the populations presented few alleles per locus and genotypes. We found strong genetic structure between populations for each species. Effective population size was small but similar to that of the studies from other mole salamanders with restricted distributions or with recently fragmented habitats. Despite the medium to high levels of genetic diversity expressed as heterozygosity, we found few alleles, evidence of a genetic bottleneck and that the effective population size is small in all populations. Therefore, this study is important to propose better management plans and conservation efforts for these specie

Monitoring status and trends in genetic diversity for the Convention on Biological Diversity: An ongoing assessment of genetic indicators in nine countries

Recent scientific evidence shows that genetic diversity must be maintained, managed, and monitored to protect biodiversity and nature's contributions to people. Three genetic diversity indicators, two of which do not require DNA-based assessment, have been proposed for reporting to the Convention on Biological Diversity and other conservation and policy initiatives. These indicators allow an approximation of the status and trends of genetic diversity to inform policy, using existing demographic and geographic information. Application of these indicators has been initiated and here we describe ongoing efforts in calculating these indicators with examples. We specifically describe a project underway to apply these indicators in nine countries, provide example calculations, address concerns of policy makers and implementation challenges, and describe a roadmap for further development and deployment, incorporating feedback from the broader community. We also present guidance documents and data collection tools for calculating indicators. We demonstrate that Parties can successfully and cost-effectively report these genetic diversity indicators with existing biodiversity observation data, and, in doing so, better conserve the Earth's biodiversity

Genetic diversity Goals and Targets have improved, but remain insufficient for clear implementation of the post-2020 global biodiversity framework

Genetic diversity among and within populations of all species is necessary for people and nature to survive and thrive in a changing world. Over the past three years, commitments for conserving genetic diversity have become more ambitious and specific under the Convention on Biological Diversity’s (CBD) draft post-2020 global biodiversity framework (GBF). This Perspective article comments on how goals and targets of the GBF have evolved, the improvements that are still needed, lessons learned from this process, and connections between goals and targets and the actions and reporting that will be needed to maintain, protect, manage and monitor genetic diversity. It is possible and necessary that the GBF strives to maintain genetic diversity within and among populations of all species, to restore genetic connectivity, and to develop national genetic conservation strategies, and to report on these using proposed, feasible indicators

Introgressive hybridization in a Spiny-Tailed Iguana, Ctenosaura pectinata, and its implications for taxonomy and conservation

Introgression, the transmission of genetic material of one taxon into another through hybridization, can have various evolutionary outcomes. Previous studies have detected signs of introgression between western populations of the Mexican endemic and threatened spiny-tailed iguana, Ctenosaura pectinata. However, the extent of this phenomenon along the geographic distribution of the species is unknown. Here, we use multilocus data together with detailed geographic sampling to (1) define genotypic clusters within C. pectinata; (2) evaluate geographic concordance between maternally and biparentally inherited markers; (3) examine levels of introgression between genotypic clusters, and (4) suggest taxonomic modifications in light of this information. Applying clustering methods to genotypes of 341 individuals from 49 localities of C. pectinata and the closely related C. acanthura, we inferred the existence of five genotypic clusters. Contact zones between genotypic clusters with signatures of interbreeding were detected, showing different levels of geographic discordance with mtDNA lineages. In northern localities, mtDNA and microsatellites exhibit concordant distributions, supporting the resurrection of C. brachylopha. Similar concordance is observed along the distribution of C. acanthura, confirming its unique taxonomic identity. Genetic and geographic concordance is also observed for populations within southwestern Mexico, where the recognition of a new species awaits in depth taxonomic revision. In contrast, in western localities a striking pattern of discordance was detected where up to six mtDNA lineages co-occur with only two genotypic clusters. Given that the type specimen originated from this area, we suggest that individuals from western Mexico keep the name C. pectinata. Our results have profound implications for conservation, management, and forensics of Mexican iguanas

Long-term genetic consequences of mammal reintroductions into an Australian conservation reserve

Available online 05 January 2018Reintroduction programs aim to restore self-sustaining populations of threatened species to their historic range. However, demographic restoration may not reflect genetic restoration, which is necessary for the long-term persistence of populations. Four threatened Australian mammals, the greater stick-nest rat (Leporillus conditor), greater bilby (Macrotis lagotis), burrowing bettong (Bettongia lesueur) and western barred bandicoot (Perameles bougainville), were reintroduced at Arid Recovery Reserve in northern South Australia over the last 18 years. These reintroductions have been deemed successful based on population growth and persistence, however the genetic consequences of the reintroductions are not known. We generated large single nucleotide polymorphism (SNP) datasets for each species currently at Arid Recovery and compared them to samples collected from founders. We found that average genetic diversity in all populations at the Arid Recovery Reserve are close to, or exceeding, the levels measured in the founders. Increased genetic diversity in two species was achieved by admixing slightly diverged and inbred source populations. Our results suggest that genetic diversity in translocated populations can be improved or maintained over relatively long time frames, even in small conservation reserves, and highlight the power of admixture as a tool for conservation management.Lauren C. White, Katherine E. Moseby, Vicki A. Thomson, Stephen C. Donnellan, Jeremy J. Austi