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Aim: (1) 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.

Conservation success depends on translating theory into practical guidance and tools that are relevant and useful for non‐scientists. While the complexity of population genetics has challenged the usage of straightforward metrics for conservation, several practical guidelines have been advanced, such as those regarding effective population size (Ne). Allendorf et al. highlight limitations of Ne as a metric for practical use. Specifically, they demonstrate that while Ne is sufficient for predicting heterozygosity, it is not predictive of the number of alleles, another key variable in conservation genetics. This has important implications for Ne‐based metrics, such as the Ne 500 indicator recently adopted in the Convention on Biological Diversity's Kunming–Montreal Global Biodiversity Framework. As developers and advocates of the Ne 500 indicator, we agree with this assessment, and acknowledge that Ne does not comprehensively predict changes in allelic variation. In this article we briefly summarize several major points in Allendorf et al. and provide practical suggestions to better account for allelic variation during indicator assessments. These suggestions include reporting major declines in Nc as part of genetic assessments, clearly articulating the intention and caveats of the Ne 500 indicator, integrating simulations into genetic assessments, and assessing the number of genetically distinct populations. We conclude that the Ne 500 indicator remains a valuable metric uniquely capable of capturing critical aspects of a species' genetic status while remaining accessible and interpretable to policymakers and other non‐geneticists. By acknowledging the limitations of focusing solely on Ne and providing options for more thorough and nuanced understandings of genetic diversity, we hope to guide future usage of the Ne 500 indicator and help bridge the gap between conservation genetics theory and practice.

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.

Local adaptation is a fundamental process that allows populations to thrive in their native environment, often increasing genetic differentiation with neighboring stands. However, detecting the molecular basis and selective factors responsible for local adaptation remains a challenge, particularly in sessile, non‐model species with long life cycles, such as forest trees. Local adaptation in trees is not only modeled by climatic factors, but also by soil variation. Such variation depends on dynamic geological and ecological processes that generate a highly heterogeneous selective mosaic that may differentially condition tree adaptation both at the range‐wide and local scales. This could be particularly manifest in species inhabiting mountain ranges that were formed by diverse geological events, like sacred fir (Abies religiosa), a conifer endemic to the mountains of central Mexico. Here, we used landscape genomics approaches to investigate how chemical edaphic variation influences the genetic structure of this species at the range‐wide and local scales. After controlling for neutral genetic structure, we performed genotype‐environment associations and identified 49 and 23 candidate SNPs at the range‐wide and local scales, respectively, with little overlap between scales. We then developed polygenic models with such candidates, which accounted for ~20% of the range‐wide variation in soil Ca2+ concentration, electric conductivity (EC), and pH, and for the local variation in soil EC and organic carbon content (OC). Spatial Principal Component Analyses further highlighted the role of geography and population isolation in explaining this genetic‐soil co‐variation. Our findings reveal that local adaptation in trees is the result of an intricate interaction between soil chemical properties and the local population's genetic makeup, and that the selective factors driving such adaptation greatly vary and are not necessarily predictable across spatial scales. These results highlight the need to consider edaphic variation in forest genetic studies (including common garden experiments) and in conservation, management and assisted migration programs.

Several Mesoamerican crops constitute wild‐to‐domesticated complexes generated by multiple initial domestication events, and continuous gene flow among crop populations and between these populations and their wild relatives. It has been suggested that the domestication of cotton (Gossypium hirsutum) started in the northwest of the Yucatán Peninsula, from where it spread to other regions inside and outside of Mexico. We tested this hypothesis by assembling chloroplast genomes of 23 wild, landraces, and breeding lines (transgene‐introgressed and conventional). The phylogenetic analysis showed that the evolutionary history of cotton in Mexico involves multiple events of introgression and genetic divergence. From this, we conclude that Mexican landraces arose from multiple wild populations. Our results also revealed that their structural and functional chloroplast organizations had been preserved. However, genetic diversity decreases as a consequence of domestication, mainly in transgene‐introgressed (TI) individuals (π = 0.00020, 0.00001, 0.00016, 0, and 0, of wild, TI‐wild, landraces, TI‐landraces, and breeding lines, respectively). We identified homologous regions that differentiate wild from domesticated plants and indicate a relationship among the samples. A decrease in genetic diversity associated with transgene introgression in cotton was identified for the first time, and our outcomes are therefore relevant to both biosecurity and agrobiodiversity conservation. Domestication of cotton landraces in Mexico. Changes in chloroplast genetic diversity related to cotton domestication and management.

Societal Impact Statement Agricultural sustainability depends on the adaptation of crops to their local environment. Smallholder farmers who save seed provide an essential “evosystem” service by growing locally adapted seed varieties that can recruit biodiversity to enhance their growth and defense. While professional plant breeding has diverted evolutionary processes away from local adaptation, smallholder farmers, particularly those in centers of origin for crops, benefit society by selecting and propagating diverse crop varieties that allow local adaptation processes to perpetuate. Given that smallholders support society through the generation of evosystem services, changes in policy and practice are needed to support the livelihoods of smallholder farmers in ways that mitigate risk and recognize their important contributions to agricultural sustainability. To enhance the reach of this work, a Spanish language version of the paper is available in the Supporting Information (see Translation_ES). [Correction added on 18 June 2024, after first online publication: The preceding sentence has been added in this version.] Summary Long‐term food security and agricultural sustainability depend on protecting the eco‐evolutionary processes that select for local adaptation in crops. Since seed systems structure how people acquire seed, institutional and social changes influence evolutionary processes within agroecosystems. Since World War II, the rise of professional breeding has bifurcated seed systems into traditional and formal systems, which has negatively affected agrobiodiversity, crop evolution, and agricultural sustainability. In traditional seed systems, farmers often save seed from plants that best provide desired qualities, selecting landrace crop varieties to adapt to local environmental conditions. In formal or centralized seed systems, farmers buy seeds bred primarily for maximizing yield under ideal conditions. When farmers source seeds externally, evolutionary processes underlying local adaptation are disrupted. Here, we argue that traditional seed systems provide important evosystem services, or the evolutionary processes resulting from the maintenance and use of genetic diversity that benefit society. We present a framework on how seed systems influence the evolutionary processes that enable local adaptation, which is necessary for sustainable agriculture. We discuss how changes in human values underlying traditional and formal seed systems can alter evolutionary processes that underlie local adaptation. We conclude that developing policies that support people in managing ecological and evolutionary processes within seed systems is needed to address current and future challenges of global food security and agricultural sustainability. La sostenibilidad agrícola depende de la adaptación de los cultivos a sus ambientes locales. Las y los campesinos proveen un servicio “evosistémico” esencial al cultivar variedades de semillas localmente adaptadas, que a su vez reclutan una biodiversidad promotora de su crecimiento y defensa. Mientras que el fitomejoramiento a nivel profesional ha desviado en estos procesos evolutivos de la adaptación local, los campesinos, particularmente aquellos en centros de origen de cultivos, benefician a la sociedad seleccionando variedades de cultivos más diversas. Dado que los campesinos benefician a la sociedad a través de la generación de servicios evosistémicos, se necesitan cambios en la política y a la práctica para sustentarlos de manera que se mitiguen los riesgos y se reconozcan sus importantes contribuciones a la sostenibilidad agrícola. Agricultural sustainability depends on the adaptation of crops to their local environment. Smallholder farmers who save seed provide an essential “evosystem” service by growing locally adapted seed varieties that can recruit biodiversity to enhance their growth and defense. While professional plant breeding has diverted evolutionary processes away from local adaptation, smallholder farmers, particularly those in centers of origin for crops, benefit society by selecting and propagating diverse crop varieties that allow local adaptation processes to perpetuate. Given that smallholders support society through the generation of evosystem services, changes in policy and practice are needed to support the livelihoods of smallholder farmers in ways that mitigate risk and recognize their important contributions to agricultural sustainability.

Urbanization modifies ecosystem conditions and evolutionary processes. This includes air pollution, mostly as tropospheric ozone (O3), which contributes to the decline of urban and peri‐urban forests. A notable case are fir (Abies religiosa) forests in the peripheral mountains southwest of Mexico City, which have been severely affected by O3 pollution since the 1970s. Interestingly, some young individuals exhibiting minimal O3—related damage have been observed within a zone of significant O3 exposure. Using this setting as a natural experiment, we compared asymptomatic and symptomatic individuals of similar age (≤15 years old; n = 10) using histologic, metabolomic, and transcriptomic approaches. Plants were sampled during days of high (170 ppb) and moderate (87 ppb) O3 concentration. Given that there have been reforestation efforts in the region, with plants from different source populations, we first confirmed that all analyzed individuals clustered within the local genetic group when compared to a species‐wide panel (Admixture analysis with ~1.5K SNPs). We observed thicker epidermis and more collapsed cells in the palisade parenchyma of needles from symptomatic individuals than from their asymptomatic counterparts, with differences increasing with needle age. Furthermore, symptomatic individuals exhibited lower concentrations of various terpenes (ß‐pinene, ß‐caryophylene oxide, α‐caryophylene, and ß‐α‐cubebene) than asymptomatic trees, as evidenced through GC–MS. Finally, transcriptomic analyses revealed differential expression for 13 genes related to carbohydrate metabolism, plant defense, and gene regulation. Our results indicate a rapid and contrasting phenotypic response among trees, likely influenced by standing genetic variation and/or plastic mechanisms. They open the door to future evolutionary studies for understanding how O3 tolerance develops in urban environments, and how this knowledge could contribute to forest restoration. RESUMEN La urbanización altera tanto las condiciones del ecosistema como los procesos evolutivos, siendo la contaminación del aire, principalmente el ozono troposférico (O3), un factor que contribuye al declive de los bosques urbanos y periurbanos. Un ejemplo destacado son los bosques de oyamel (Abies religiosa) en las montañas periféricas al suroeste de la Ciudad de México, que han sufrido graves afectaciones por la contaminación de O3 desde la década de 1970. Resulta curioso observar que algunos individuos jóvenes presentan un daño mínimo relacionado con el O3 dentro de zonas con una exposición significativa a este contaminante. Aprovechando este entorno como un experimento natural, hemos comparado individuos asintomáticos y sintomáticos de edad similar (≤15 años; n = 10) mediante enfoques histológicos, metabolómicos y transcriptómicos. Las muestras de plantas se recolectaron durante días con concentraciones altas (170 ppb) y moderadas (87 ppb) de O3. Dado que se han llevado a cabo esfuerzos de reforestación en la región con plantas de diferentes poblaciones, primero confirmamos que todos los individuos analizados se organizaron dentro del grupo genético local en comparación con un amplio panel poblacional de esta misma especie (Análisis de Admixture con ~1.5 K SNPs). Observamos una epidermis más gruesa y más células colapsadas en el parénquima en empalizada de las agujas de los individuos sintomáticos que de sus contrapartes asintomáticas, y estas diferencias aumentaban con la edad de la aguja. Además, los individuos sintomáticos exhibieron concentraciones más bajas de varios terpenos (ß‐pineno, óxido de ß‐cariofileno, α‐cariofileno y ß‐α‐cubebeno) que los árboles asintomáticos, según se evidenció mediante GC–MS. Por último, los análisis transcriptómicos revelaron una expresión diferencial para trece genes relacionados con el metabolismo de carbohidratos, la defensa de plantas y la regulación génica. Nuestros resultados indican una respuesta fenotípica rápida y contrastante entre los árboles, probablemente influenciada por la variación genética presente y/o mecanismos plásticos. Estos hallazgos abren la puerta a futuros estudios evolutivos para comprender cómo se desarrolla la tolerancia al O3 en entornos urbanos y cómo este conocimiento podría contribuir a la restauración forestal. Urbanization alters ecosystems and evolutionary processes. Processes like air pollution by tropospheric ozone contribute to the decline of urban and peri‐urban ecosystems, such as Abies religiosa forests in the peripheral mountains southwest of Mexico City. Despite ozone exposure, some young individuals present minimal damage, suggesting contrasting phenotypic responses that may be influenced by genetic variations and/or plastic mechanisms, opening new perspectives for evolutionary studies on ozone tolerance and forest restoration.

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.

Conservation success depends on translating theory into practical guidance and tools that are relevant and useful for non‐scientists. While the complexity of population genetics has challenged the usage of straightforward metrics for conservation, several practical guidelines have been advanced, such as those regarding effective population size ( N e ). Allendorf et al. highlight limitations of N e as a metric for practical use. Specifically, they demonstrate that while N e is sufficient for predicting heterozygosity, it is not predictive of the number of alleles, another key variable in conservation genetics. This has important implications for N e ‐based metrics, such as the N e 500 indicator recently adopted in the Convention on Biological Diversity's Kunming–Montreal Global Biodiversity Framework. As developers and advocates of the N e 500 indicator, we agree with this assessment, and acknowledge that N e does not comprehensively predict changes in allelic variation. In this article we briefly summarize several major points in Allendorf et al. and provide practical suggestions to better account for allelic variation during indicator assessments. These suggestions include reporting major declines in N c as part of genetic assessments, clearly articulating the intention and caveats of the N e 500 indicator, integrating simulations into genetic assessments, and assessing the number of genetically distinct populations. We conclude that the N e 500 indicator remains a valuable metric uniquely capable of capturing critical aspects of a species' genetic status while remaining accessible and interpretable to policymakers and other non‐geneticists. By acknowledging the limitations of focusing solely on N e and providing options for more thorough and nuanced understandings of genetic diversity, we hope to guide future usage of the N e 500 indicator and help bridge the gap between conservation genetics theory and practice.

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.