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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. ispartof: CONSERVATION GENETICS vol:24 issue:2 pages:181-191 ispartof: location:Netherlands status: published

Neutral theory proposes that dispersal stochasticity is one of the main drivers of local diversity. Haplotypes-level genetic variation can now be efficiently sampled from across whole communities, thus making it possible to test neutral predictions from the genetic to species-level diversity, and higher. However, empirical data is still limited, with the few studies to date coming from temperate latitudes. Here, we focus on a tropical mountain within the Transmexican Volcanic Belt to evaluate spatially fine-scale patterns of arthropod community assembly to understand the role of dispersal limitation and landscape features as drivers of diversity. We sampled whole-communities of arthropods for eight orders at a spatial scale ranging from 50 m to 19 km, using whole community metabarcoding. We explored multiple hierarchical levels, from individual haplotypes to lineages at 0.5, 1.5, 3, 5, 7.5% similarity thresholds, to evaluate patterns of richness, turnover, and distance decay of similarity with isolation-by-distance and isolation-by resistance (costs to dispersal given by landscape features) approaches. Our results showed that distance and altitude influence distance decay of similarity at all hierarchical levels. This holds for arthropod groups of contrasting dispersal abilities, but with different strength depending on the spatial scale. Our results support a model where local-scale differentiation mediated by dispersal constraints, combined with long-term persistence of lineages, is an important driver of diversity within tropical sky islands., Nancy Gálvez-Reyes is a doctoral student from Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México (UNAM) and was supported by CONACYT (scholarship no. 401781). CONACYT also provided financial support with the project 178245 granted to D. Piñero. B. Emerson was supported by the Spanish Agencia Estatal de Investigación (CGL2017-85718-P), co-financed by FEDER. P. Arribas was supported by a postdoctoral grant by the Spanish Ministry of Economy and Competitiveness (MINECO, Spain) within the Juan de la Cierva Formación Program. C. Andújar was supported by the Spanish Ministry of Economy and Competitiveness (MINECO, Spain) (CGL2015-74178-JIN MINECO/FEDER, UE).

Societal Impact Statement Crop wild relatives (CWR) are plant taxa closely related to crops and are a source of high genetic diversity that can help adapt crops to the impacts of global change, particularly to meet increasing consumer demand in the face of the climate crisis. CWR provide vital ecosystem services and are increasingly important for food and nutrition security and sustainable and resilient agriculture. They therefore are of major biological, social, cultural and economic importance. Assessing the extinction risk of CWR is essential to prioritise in situ and ex situ conservation strategies in Mesoamerica to guarantee the long‐term survival and availability of these resources for present and future generations worldwide. Summary 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.

Mexico is the center of domestication and a center for diversity of maize. Area planted with maize is the country’s largest agricultural land use, mostly planted by smallholder family farmers known as campesinos. They generally plant native varieties, saving and sharing seed by and among themselves, enabling the evolutionary processes that sustain and generate crop genetic diversity to continue today. Campesinos have been viewed as largely subsistence farmers generating limited maize surpluses. Here, we show that subsistence production is insufficient for explaining the quantity of maize they produce and the extent of the area they plant across Mexico. Our hypothesis is that beyond supplying their own consumption needs, campesinos collectively produce maize to respond to the demand of non-maize producing local consumers. We quantify the extent of subsistence versus surplus production among campesinos, showing that they produce more maize than would be needed to feed themselves and generate substantial surpluses. We test statistically the association between the area campesinos plant with maize across the country with socioeconomic variables that link their production to the demand by other consumers, and examine the implications of the results for the supply and conservation of native maize in the country. Our results suggest that maize trading linking campesinos to other consumers may be important and widespread, contributing to create additional incentives beyond self-consumption to plant native varieties from saved seed. We conclude that there are important opportunities for maintaining maize evolution under domestication at large scale by strengthening local maize markets.

México es un centro de origen de la agricultura y domesticación de plantas. Como resultado, más de 130 cultivos son originarios de México y forman parte de un profundo entramado biocultural que permite realizar agricultura en un amplio rango de condiciones ambientales. Esta agrobiodiversidad emergió del proceso de la evolución bajo domesticación, el cual ocurrió de forma similar por miles de años, hasta el inicio de la revolución verde. A pesar de que la agricultura intensiva promovida por la revolución verde incrementó considerablemente los rendimientos y proveyó seguridad alimentaria para algunas regiones, ha tenido también consecuencias negativas al medio ambiente y a la salud humana, y además, en el caso de México, no satisface todas las necesidades de las condiciones productivas de los campesinos, considerando la heterogeneidad ambiental. Por lo tanto, es necesario buscar técnicas de producción alternativas, efectivas para cada contexto ambiental, socio-cultural y económico. Se propone una iniciativa con dos objetivos principales: 1) estudiar, conocer y conservar la diversidad genética de los cultivos nativos de México y sus parientes silvestres, y preservar el proceso de la evolución bajo domesticación que genera y mantiene dicha diversidad; y 2) utilizar esta diversidad para fortalecer la producción de alimentos y fibras de forma socialmente justa minimizando los impactos ambientales. Para cumplir estos objetivos, la iniciativa se enfoca en la fuente de variación disponible para la domesticación (diversidad genética y genómica funcional), el contexto en el que la domesticación actúa (mejoramiento y producción) y uno de sus mayores retos (cambio ambiental). La investigación en estos componentes debe enfocarse en conectar los aspectos teóricos del proceso evolutivo con aspectos prácticos de la conservación y producción. Se resumen los objetivos, retos principales y preguntas de investigación claves para cada componente, seguidos de una ruta crítica para la consolidación de esta iniciativa nacional y avances efectuados por la CONABIO.

The deforestation and degradation of natural habitats is the second largest contributor to carbon dioxide (CO2) emissions to the atmosphere. Temperate forests cover ∼16.5% of the Mexican landscape, and are a priority ecosystem for global conservation due to their high rate of endemism and species diversity. These forests also provide valuable ecosystem services, including the storage of organic carbon. Mexican temperate forests have lost more than half of their original cover, with ongoing forest degradation, resulting in CO2 emissions to the atmosphere. Most studies and carbon inventories only consider organic carbon stored in the aboveground biomass, and do not consider the organic carbon stored within soils of temperate forests. As a result, the emissions of CO2 due to deforestation are underestimated, and the value of temperate forests is underappreciated. To address this shortcoming, (1) we examine the extent and factors determining soil organic carbon stocks; (2) we estimate soil organic carbon stocks of Mexican temperate forests, the CO2 emissions caused by deforestation and avoided emissions from conservation and (3) we discuss the causes of loss of soil OC and management strategies to mitigate this loss. We propose that including the soil organic carbon stock-component is a priority for national projects targeting reducing emissions from deforestation. Also, urgent studies on the impacts of forest degradation in stocks of soil organic carbon are needed. Management strategies for conservation and rehabilitation of Mexican temperate forests must consider social and economic aspects of the local communities.

The Velazquez Woodpecker Melanerpes santacruzi is a highly polytypic species distributed from east-central Mexico to northern Nicaragua. The ample variation in body size, barring of the plumage, and the coloration of nasal tufts, neck, and belly have fueled debates about the taxonomy and evolutionary history of the species; however, the processes generating these patterns of variation and the underlying population dynamics throughout the species' distribution remain poorly understood. Here, we employed reduced representation genome sequencing (NextRAD) and Ecological Niche Modeling methods to test the distinctiveness of the Velazquez Woodpecker based on this new set of genomic data and analyze the correspondence of the genetic structure and ecological differentiation with phenotypic variation and geographic distribution. From phylogenetic and demographic analyses including the Golden-Fronted (M. aurifrons) and Red-bellied Woodpecker (M. carolinus), we obtained results congruent with previous molecular phylogenies. The clades of M. santacruzi and M. carolinus-M. aurifrons are reciprocally monophyletic, although the sister group relationship of M. aurifrons is ambiguous. Using genetic and ecological analyses, we found that the species is structured into three genetically and ecologically differentiated groups comprising the subspecies (1) M. s. santacruzi, (2) M. s. dubius and (3) M. s. grateloupensis-polygrammus-veraecrucis. These groups diverged recently, with two splits between 250,000 and 150,000 years ago, and show a significant genetic admixture among them, especially in their current contact zones. Ecological and demographic models suggest the existence of intermittent areas of sympatry and connectivity among populations of M. santacruzi since the Last Interglacial period. We also found evidence of bi-directional gene flow between the species M. aurifrons and the nearby populations of M. santacruzi (M. s. grateloupensis), along the Sierra Madre Oriental in northeastern Mexico. Gene flow seems to be uneven, with prevalence of movement in the direction from M. aurifrons to M. s. grateloupensis.

Biodiversity conservation calls for spatial explicit approaches to maximize the representation and persistence of genetic diversity given species’ idiosyncratic threats in mosaic landscapes, but conservation planning methodologies seldom account for this. Here, we introduce a novel approach that uses proxies of genetic diversity to identify conservation areas, applying systematic conservation planning tools to produce hierarchical prioritizations of the landscape. It accounts for: (i) evolutionary processes, including historical and environmental drivers of genetic diversity, and (ii) threat processes, considering taxa specific tolerance to human-modified habitats and their extinction risk status. We illustrate our approach with crop wild relatives (CWR) because their intra- and interspecific diversity is important for crop breeding and food security. Although we focus on Mesoamerican CWR within Mexico, our methodology offers new opportunities to effectively guide conservation and monitoring strategies to safeguard the evolutionary resilience of any taxa, including in regions of complex evolutionary histories and mosaic landscapes.

Studying and understanding the evolution of relictual natural populations is critical for developing conservation initiatives of endangered species, such as management in situ and assisted migration. Recently, genomic and bioinformatics tools have promised a wide avenue for developing more efficient programs. Genomic prediction (GP) models are one of such tools; although, in trees, only some successful examples exit. They have mostly been used to increase predictive ability in commercial traits and reduce breeding cycle length. Thus, it remains to be tested whether GP can be extended for the management and conservation of natural small and secluded populations. Here, we explored such a possibility in a pilot study to predict the performance of introduced saplings in a managed population of sacred fir (Abies religiosa; Pinaceae) in central Mexico. We genotyped over 200 naturally re-generated and introduced individuals with 2286 single nucleotide polymorphisms (SNP), derived from genotyping by sequencing, and used them to develop GP models for growth and physiological traits. After testing different training and validation datasets, and determining predictive ability of “across-groups” models with cross-validation techniques, acceptable predictive abilities (ry) were obtained for growth during the previous growing season, water potential, stem diameter, and aboveground biomass (0.36, 0.27, 0.26, and 0.24, respectively). The best models were always those built with natural saplings and used to predict the early performance of introduced individuals in the same environment, although fair predictabilities were also obtained when predicting performance between natural populations. Model fine-tuning resulted in reduced datasets of approximately 700 SNPs that helped optimizing phenotype predictability, particularly for water potential, for which ry was up to 0.28. These pilot-scale results are preliminary but encouraging and justify additional research efforts for implementing GP in small and secluded natural populations, particularly for endangered non-model species.

Aim: To (a) evaluate if colonization of newly emerged high-elevation habitats occurred from neighbouring highlands (allopatric divergence and niche conservatism) or from within the same mountain (peripatric or parapatric divergence and niche shift), and (b) test for the effect of past landscape configurations in geographically structuring biodiversity (a West-East structure spanning the central part of the Transmexican Volcanic Belt).Location: Transmexican Volcanic Belt, Mexico. Taxa: Coleoptera and Araneae. Methods: Coleoptera and Araneae communities were collected in a comparative sampling framework. Seven sky-islands were sampled within two high-elevation habitats separated by altitude. Samples were individually sequenced for a region of the mtDNA COI gene to delimit Operational Taxonomic Units (OTUs) and haplotypes within them. Richness was estimated at the community level, as well as genetic diversity within and among mountains and habitats. The West East structure was tested with a null model and an analysis of variance with permutations. Results: Few OTUs were shared between the Abies forests and alpine grasslands. High beta diversity was found across mountains. Beta diversity between the West – East grouping is higher than expected by chance. Main conclusions: Our results indicate that colonization from other mountains followed by allopatric divergence dominates as a source of OTU formation, and that despite some probable connectivity during glacial periods existed, ancient communities and genetic structures persist., We would like to thank CONACyT for the financial support granted through a master’s scholarship to AU and for the project Ciencia Básica (178245) granted to DP. BCE is supported by Spanish Agencia Estatal de Investigación (CGL2017-85718-P), co-financed by FEDER.

Mexico is the center of domestication and a center for diversity of maize. Area planted with maize is the country’s largest agricultural land use, mostly planted by smallholder family farmers known as campesinos. Due to the large area they plant with saved seed from native varieties in a wide variety of environments across the country, maize evolution under domestication continues today at a very large scale and under a multiplicity of selection pressures. Campesinos have been considered mainly subsistence farmers. Here we show that subsistence production is insufficient for explaining the scale of the area they plant with maize and on which its contemporary evolution under domestication depends. Our hypothesis is that beyond supplying their own consumption needs, campesinos across Mexico collectively produce maize to respond to the demand of non-maize producing local consumers. Here we quantify the extent of subsistence versus surplus production among campesinos, showing that subsistence production cannot explain the scale of their maize cultivation. Then, we test statistically the association between the scale of maize cultivation and socioeconomic variables that link campesino production to the demand by other consumers and examine the implications of the results for the supply and conservation of native maize in the country. Our results suggest that maize trading linking campesinos to other consumers may be important and widespread. We conclude that there are important opportunities for maintaining maize evolution under domestication at large scale by strengthening local maize markets.

Tropical mountains are areas of high species richness and endemism. Two historical phenomena may have contributed to this: (i) fragmentation and isolation of habitats may have promoted the genetic differentiation of populations and increased the possibility of allopatric divergence and speciation and (ii) 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 Trans-Mexican 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., Part of the analyses were carried out on the High Performance Computing Cluster supported by the Research and Specialist Computing Support service at UEA and at the City University of New York High Performance Computing Center, with support from the National Science Foundation (CNS‐0855217 and CNS‐0958379). This work was supported by Consejo Nacional de Ciencia y Tecnología (grant number CONACYT 213538 to AMY and CONACYT 178245 to DP), by Rosemary Grant Award for Graduate Student Research from the Society for the Study of Evolution granted to AMY, by grants from National Science Foundation (DEB‐1253710 to M.J.H.; DEB‐1343578 to Ana C. Carnaval, M.J.H., and Kyle C. McDonald); FAPESP (BIOTA, 2013/50297‐0 to A.C.C., M.J.H., and K.C.M.); and NASA through the Dimensions of Biodiversity Program.

Within-population phenotypic variation can be used as a proxy for adaptive potential and individual performance in forest plantations and natural populations. Such variation can be viewed as the sum of genetic factors and their interaction with environmental variation (e.g., soil characteristics), which lead identical genotypes to produce contrasting phenotypes in different environments, and introduced individuals to perform differently from local trees in plantations and test trials. Predicting this variation is of great interest to foresters working with commercially important species. Such is the case of sacred fir (Abies religiosa), a species that is an important source of wood and resin for communities living above 2500 m asl in central Mexico. We determined the contribution of both genetic and soil factors for predicting phenotypic performance of local naturally regenerated (NR) and introduced by reforestation (RF) seedlings in a sacred fir trial test performed by local communities in the Nevado de Toluca National Park. In spite of a low genetic differentiation between plant sources, NR seedlings outperformed RF plants in terms of height, diameter and water use. According to our models, a large part of these differences could be explained by the interaction of genetic, management and edaphic factors within the trial site, with local genotypes using more efficiently the available soil nitrogen than the introduced ones; thus indicating that planting could be changing plant microenvironment and have a measurable phenotypic effect. Association studies between genetic and edaphic variation further suggested that local adaptation might also be occurring at small within-population scales. All such traits, when correctly integrated, may result in fair genome-based phenotypic predictions for small secluded natural populations, which could be at the base of better reforestation practices, and conservation and assisted migration programs.

Crop wild relatives (CWR) are wild plants that are the ancestors of important crops for human well-being. CWR hold genetic diversity that can be vital for plant breeding programs and the sustainability of agriculture, particularly given global change. Conservation of CWR genetic diversity thus has become a global food security issue, and several countries are actively developing conservation strategies including the generation of a national checklist and inventory of CWR, the assessment of current threat status, the identification of knowledge and conservation, and the establishment of genetic reserves. In this context, Mexico, Guatemala, and El Salvador, in collaboration with experts abroad (University of Birmingham, UK, and IUCN), are working together in a project to contribute towards safeguarding Mesoamerican CWR (http://www.psmesoamerica.org/en/). One important step is to identify CWR conservation area networks framed within the systematic conservation planning approach. However, genetic diversity is generally not addressed during the planning process. As it is unfeasible to sample and perform genetic analyses of hundreds of species due to limited timeframes and conservation budgets, we propose a novel approach to overcome the lack of genetic data. We used two criteria to develop proxies for genetic diversity (PGD): environmental variability, as given by climate, soil and topographic spatially-defined variables; and historic differentiation, as shown by phylogeographic patterns found in other species of the same habitat and region. environmental variability, as given by climate, soil and topographic spatially-defined variables; and historic differentiation, as shown by phylogeographic patterns found in other species of the same habitat and region. We tested our approach by using genomic data from an empirical study of maize wild relatives distributed in Mexico. By combining species distribution models of 120 Mesoamerican CWR taxa and 102 PGD, we delimited areas of potential population differentiation. Furthermore, we considered each taxon's IUCN Red List category and habitat preference, assessed by experts during the project, to determine areas for CWR conservation in Mexico, using the Zonation conservation planning tool. Areas identified as important for CWR in situ conservation are located within sites of high cultural diversity and in areas where agriculture originated and traditional agriculture is ongoing. Also, our study design maximizes the representation of CWR throughout its distribution, thus highlighting the need for comprehensive analysis to encompass the genetic variability of taxa. The results of this work represent a first national and regional guide to promote CWR in situ conservation and sustainable management that contributes towards achievement of the CBD Global Strategy for Plant Conservation, Sustainable Development Goals and Aichi Targets.

Species delimitation is a major quest in biology and is essential for adequate management of the organismal diversity. A challenging example comprises the fish species of red snappers in the Western Atlantic. Red snappers have been traditionally recognized as two separate species based on morphology: Lutjanus campechanus (northern red snapper) and L. purpureus (southern red snapper). Recent genetic studies using mitochondrial markers, however, failed to delineate these nominal species, leading to the current lumping of the northern and southern populations into a single species ( L. campechanus ). This decision carries broad implications for conservation and management as red snappers have been commercially over-exploited across the Western Atlantic and are currently listed as vulnerable. To address this conflict, we examine genome-wide data collected throughout the range of the two species. Population genomics, phylogenetic and coalescent analyses favour the existence of two independent evolutionary lineages, a result that confirms the morphology-based delimitation scenario in agreement with conventional taxonomy. Despite finding evidence of introgression in geographically neighbouring populations in northern South America, our genomic analyses strongly support isolation and differentiation of these species, suggesting that the northern and southern red snappers should be treated as distinct taxonomic entities.

The environmental variables that define a species ecological niche should be associated with the evolutionary patterns present in the adaptations that resulted from living in these conditions. Thus, when comparing across species, we can expect to find an association between phylogenetically independent phenotypic characters and ecological niche evolution. Few studies have evaluated how organismal phenotypes might mirror patterns of niche evolution if these phenotypes reflect adaptations. Doing so could contribute on the understanding of the origin and maintenance of phenotypic diversity observed in nature. Here, we show the pattern of niche evolution of the pinyon pine lineage (Pinus subsection Cembroides); then, we suggest morphological adaptations possibly related to niche divergence, and finally, we test for correlation between ecological niche and morphology. We demonstrate that niche divergence is the general pattern within the clade and that it is positively correlated with adaptation.

In tropical sky-islands, cold-affinity populations tend to become isolated at highlands during the interglacial periods, and to expand into the lowlands where they become more connected during the glacial periods. Although this has been widely studied in trees, it is poorly understood how fungal symbionts can differentiate among mountains (allopatrically), or within a single mountain (parapatrically) due to climate fluctuations. Here, we conducted population genomic analyses on the ectomycorrhizal fungus Laccaria trichodermophora in three tropical sky-islands using Genotyping by Sequencing (GBS) at low DNA concentrations. There were no significant differences between altitudes within a single mountain, but we observed significant genetic differentiation among populations from different mountains, supporting the allopatric differentiation hypothesis. Our results indicate that L. trichodermophora populations are under a sky-island population dynamics that started during the Pleistocene climate fluctuations.

Restriction site‐associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for nonmodel organisms, potentially revolutionizing the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (i) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci; and (ii) quantify error rates for loci, alleles and single‐nucleotide polymorphisms. As an empirical example, we use a double‐digest RAD data set of a nonmodel plant species, Berberis alpina, collected from high‐altitude mountains in Mexico., This work has been supported by a CONACYT doctorate scholarship to AMY (213538), by a CONACYT Grant to DP (178245), by a SSE Rosemary Grant Student Research Award to AMY and by an SNSF Grant (PP00P3_144870) to N. Alvarez.

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 F ST 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.

Understanding how speciation relates to ecological divergence has long fascinated biologists. It is assumed that ecological divergence is essential to sympatric speciation, as a mechanism to avoid competition and eventually lead to reproductive isolation, while divergence in allopatry is not necessarily associated with niche differentiation. The impact of the spatial context of divergence on the evolutionary rates of abiotic dimensions of the ecological niche has rarely been explored for an entire clade. Here, we compare the magnitude of climatic niche shifts between sympatric versus allopatric divergence of lineages in butterflies. By combining next-generation sequencing, parametric biogeography and ecological niche analyses applied to a genus-wide phylogeny of Palaearctic Pyrgus butterflies, we compare evolutionary rates along eight climatic dimensions across sister lineages that diverged in large-scale sympatry versus allopatry. In order to examine the possible effects of the spatial scale at which sympatry is defined, we considered three sets of biogeographic assignments, ranging from narrow to broad definition. Our findings suggest higher rates of niche evolution along all climatic dimensions for sister lineages that diverge in sympatry, when using a narrow delineation of biogeographic areas. This result contrasts with significantly lower rates of climatic niche evolution found in cases of allopatric speciation, despite the biogeographic regions defined here being characterized by significantly different climates. Higher rates in allopatry are retrieved when biogeographic areas are too widely defined—in such a case allopatric events may be recorded as sympatric. Our results reveal the macro-evolutionary significance of abiotic niche differentiation involved in speciation processes within biogeographic regions, and illustrate the importance of the spatial scale chosen to define areas when applying parametric biogeographic analyses.

Juniperus blancoi is a rare subtropical conifer with a wide yet restricted distribution and three recognized varieties. In this study, its ecological and genetic exchangeability are tested based on morphological descriptions, habitat differences, size measures, growth form, population genetics estimates and phylogeography, using the trnC-trnD plastid DNA region. Populations show differences in their habitat and morphological characteristics. Phylogeographic structure indicates a complex evolutionary history of expansion, fragmentation, and isolation processes. This resulted in high haplotype diversity (h = 0.863) and differentiation values (Dest = 0.866 and Dest > 0.5 in most pairwise comparisons) and a clear geographic structure with well defined groups. As a consequence, although the species has only 8 known populations, it must be divided into at least five distinct conservation units. Thus protecting a rare species could imply the conservation of a complex evolutionary history of non-exchangeable populations.

Maize evolution under domestication is a process that continues today. Case studies suggest that Mexican smallholder family farmers, known ascampesinos, contribute importantly to this, but their significance has not been explicitly quantified and analysed as a whole. Here, we examine the evolutionary and food security implications of the scale and scope under whichcampesinosproduce maize. We gathered official municipal-level data on maize production under rainfed conditions and identifiedcampesinoagriculture as occurring in municipalities with average yields of less than or equal to 3 t ha−1. Environmental conditions vary widely in those municipalities and are associated with a great diversity of maize races, representing 85.3% of native maize samples collected in the country. We estimate that in those municipalities, around 1.38 × 1011genetically different individual plants are subjected to evolution under domestication each season. This implies that 5.24 × 108mother plants contribute to the next generation with their standing genetic diversity and rare alleles. Such a large breeding population size also increases the total number of adaptive mutations that may appear and be selected for. We also estimate thatcampesinoagriculture could potentially feed around 54.7 million people in Mexico. These analyses provide insights about the contributions of smallholder agriculture around the world.

[Aim] To synthesize data on the physical and phylogeographical history of the Mexican highlands, with a focus on the Trans‐Mexican Volcanic Belt (TMVB), and (2) to propose approaches and analyses needed for examining the interaction of climate and volcanism., [Location] Mexico., [Methods] We performed a literature and data survey of the climatic, geological and phylogeographical history of the Mexican highlands. We then assessed how the expected effects of topographic isolation, co‐occurring palaeoclimatic fluctuations and volcanism can be tested against the distribution of genetic diversity of high‐elevation taxa., [Results] The Mexican highlands present a complex biogeographical, climatic and geological history. Montane taxa have been exposed to a sky‐island dynamic through climate fluctuations, allowing for long‐term in situ population persistence, while also promoting recent divergence and speciation events. Volcanic activity transformed part of the Mexican highlands during the Pleistocene, mainly in the TMVB, leading to co‐occurring climate and topographical changes. The TMVB highlands provide a suitable template to examine how low‐latitude mountains can facilitate both the long‐term persistence of biodiversity as well as allopatric and parapatric speciation driven by climatic and geological events., [Main conclusions] Climate fluctuations, together with recent volcanism, have driven the diversification and local persistence of biodiversity within the Mexican highlands. The climate–volcanism interaction is challenging to study; however, this can be overcome by coupling genomic data with landscape analyses that integrate the geological and climatic history of the region., This work was supported by Consejo Nacional de Ciencia y Tecnología doctorate scholarship to A.M.Y. (CONACYT 213538) and by CONACYT grant 178245.

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., This work was supported by Consejo Nacional de Ciencia y Tecnología (grant number CONACYT 213538 to A.M.Y. and CONACYT 178245 to D.P.), by Rosemary Grant Award for Graduate Student Research from the Society for the Study of Evolution to A.M.Y. and by a Swiss National Science Foundation (grant number PP00P3_144870 to Na.A. and PZ00P3_148224 to Ni.A.).

Western North America and Mexico contain a large number of conifer species. This diversity could be the product of orographic and climate changes of the late Tertiary and Quaternary. In this study, we focus on the evolutionary history of Juniperus blancoi, in order to determine the impact of climate change and environmental heterogeneity on population differentiation. We estimated the population structure, phylogenetic relationships and historical demography of J. blancoi populations using nuclear genes. We correlated genetic structure with ecological differentiation, divergence times and changes in population size. Populations of J. blancoi are differentiated into three lineages that correspond to low-, mid- and high-altitude populations. The three groups diversified in the late Miocene, early Pliocene, with only a few events of gene flow since then. Two lineages in the north exhibited a pattern of population growth during the Pleistocene that could be linked to climate changes. Populations of J. blancoi experienced significant ecological differentiation and early divergence events, which correspond to periods of global cooling and mountain uplift during the Miocene. This suggests that mountain ranges in tropical and subtropical latitudes play an important role in the speciation and persistence of conifer taxa in diversity hotspots, by providing diverse environmental conditions.

The 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. Keywords: Maize, Teosinte, Maize SNP50K BeadChip, Mexican landraces, Proyecto Global de Maíces Nativos