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

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

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

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

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

Extinction risk of Mesoamerican crop wild relatives

Ensuring food security is one of the world's most critical issues as agricultural systems are already being impacted by global change. Crop wild relatives (CWR)—wild plants related to crops—possess genetic variability that can help adapt agriculture to a changing environment and sustainably increase crop yields to meet the food security challenge. Here we report the results of an extinction risk assessment of 224 wild relatives of some of the world's most important crops (i.e. chilli pepper, maize, common bean, avocado, cotton, potato, squash, vanilla and husk tomato) in Mesoamerica—an area of global significance as a centre of crop origin, domestication and of high CWR diversity. We show that 35% of the selected CWR taxa are threatened with extinction according to The International Union for Conservation of Nature (IUCN) Red List demonstrates that these valuable genetic resources are under high anthropogenic threat. The dominant threat processes are land use change for agriculture and farming, invasive and other problematic species (e.g. pests, genetically modified organisms) and use of biological resources, including overcollection and logging. The most significant drivers of extinction relate to smallholder agriculture—given its high incidence and ongoing shifts from traditional agriculture to modern practices (e.g. use of herbicides)—smallholder ranching and housing and urban development and introduced genetic material. There is an urgent need to increase knowledge and research around different aspects of CWR. Policies that support in situ and ex situ conservation of CWR and promote sustainable agriculture are pivotal to secure these resources for the benefit of current and future generations

Genetic diversity in space and time, an insurance vs climate change

Genetic diversity is the engine of evolution. Thanks to it species can adapt to different environmental conditions and we humans are able to domesticate wild species, modifying them to fit our needs. When climate changes, species either move with it, become extinct or adapt to the new conditions. The domesticated species upon which our food systems are based are also affected by environmental conditions, so adapting them to the current human induced climate change is of special concern. Mexico is a mega-diverse country where the domestication of important cultivates occurred, such as maize, beans and pumpkins. As a consequence, here there are crop wild relatives that have been evolving for million of years; and traditional crop varieties that have been grown in a wide range of environmental conditions for thousands of years, and that currently continue evolving. The genetic diversity enclosed within these crop wild relatives and traditional varieties is enormous, and likely holds the needed diversity to adapt our cultivate to climate change. Here, I will discuss the need to appreciate Mexican crops genetic diversity in terms of the evolutionary service it provides; and then I will discuss the outcomes and challenges of characterizing, modeling, conserving and using such genetic diversity at a national scale.Non UBCUnreviewedAuthor affiliation: CONABIOFacult

Metabarcoding of arthropod communities as biomonitoring tool for the conservation

Deforestation and fragmentation of forests contributes to dramatic loss of biodiversity and ecosystem services. As a strategy to combat this degradation, it has been proposed to recover deforested areas through forest plantations and to perform sustainable forestry as an alternative to illegal logging. For example, these strategies are part of the arguments used to change the type of natural protected area of the Nevado de Toluca Park, in Mexico. Although plantations and sustainable forestry ensure the persistence of the tree cover, these involve anthropogenic changes and disturbances, whose effects on fauna communities and biodiversity evolution are poorly known. To study these effects from an ecological perspective and to provide effective management recommendations data on species' distribution and abundance over large geographic and temporal scales is needed. Here, we perform arthropod biomonitoring of Nevado de Toluca forests lands subjected to conservation or different types of forestry, to examine changes at the biological community level. For this, we sampled around 3,000 pitfall traps during 15 days of the main rain season. These were subjected to metabarcoding (COI gene) sequencing for operational taxonomic units (OTUs) identification. We focus in the arthropods-community as bio-indicator, joining the community structure (diversity, abundance and richness) with the estimators of biological diversity (indices of diversity: abundance and species richness) to describe the behavior of arthropods-communities under different environmental and management conditions. Metabarcoding allowed to identify OTUs and describe communities with a resolution not feasible by traditional methods, due to the poor taxonomic knowledge of the area. When then analyses how components of Gamma diversity (regional pool of species = landscape), Alpha diversity (local pool) and Beta diversity (replacement/ turnover) between communities vary according to the different types of forest land conditions. We conclude arthropod metabarcoding is a reliable and informative biomonitoring tool that allowed to better understand the impact of forest management on arthropods communities.peerReviewe

Data from: Finding a needle in a haystack: distinguishing Mexican maize landraces using a small number of SNPs

In Mexico's territory, the center of origin and domestication of maize (Zea mays), there is a large phenotypic diversity of this crop. This diversity has been classified into “landraces.” Previous studies have reported that genomic variation in Mexican maize is better explained by environmental factors, particularly those related with altitude, than by landrace. Still, landraces are extensively used by agronomists, who recognize them as stable and discriminatory categories for the classification of samples. In order to investigate the genomic foundation of maize landraces, we analyzed genomic data (35,909 SNPs from Illumina MaizeSNP50 BeadChip) obtained from 50 samples representing five maize landraces (Comiteco, Conejo, Tehua, Zapalote Grande, and Zapalote Chico), and searched for markers suitable for landrace assignment. Landrace clusters could not be identified taking all the genomic information, but they become manifest taking only a subset of SNPs with high FST among landraces. Discriminant analysis of principal components was conducted to classify samples using SNP data. Two classification analyses were done, first classifying samples by landrace and then by altitude category. Through this classification method, we identified 20 landrace-informative SNPs and 14 altitude-informative SNPs, with only 6 SNPs in common for both analyses. These results show that Mexican maize phenotypic diversity can be classified in landraces using a small number of genomic markers, given the fact that landrace genomic diversity is influenced by environmental factors as well as artificial selection due to bio-cultural practices