Anastasia Klimova

Background and Aims: Crop wild relatives (CWR) are an important source for crop improvement, but they are often threatened by overharvesting and habitat fragmentation. This is the case for Agave angustifolia, one of the most important CWRs of cultivated agave species in the tequila and mezcal industries. Despite its cultural and economic importance, no range-wide genomic assessments exist for this species. Methods: We analyzed double-digest genotyping-by-sequencing (GBS) data from 215 wild individuals from 67 populations spanning the entire Mexican distribution range of A. angustifolia. We combined newly generated data (97 individuals) with previously published sequences (118 individuals). We combined genomic data with species distribution models for past and future climatic scenarios, performed environmental association and genomic offset analyses, and tested spatial versus environmental drivers of differentiation. Key Results: In terms of climate and genomic offset, we found that although some populations—especially coastal ones—are expected to experience a considerable challenge adapting to changing environments, the species as a whole is likely to benefit from the warmer, drier conditions predicted by climate change projections. We identified specific wild populations that harbour climate-adapted alleles and are best positioned for persistence and crop improvement. While contemporary populations showed moderate-to-high genomic diversity, recent demographic impacts from wild harvest and local cultivation may not yet be detectable due to the species’ long generation time and vegetative propagation. Genome-wide divergence among A. angustifolia populations was driven by Pleistocene climate oscillations and isolation-by-environment. Conclusions: Our study highlights both resilience and risk across the range of A. angustifolia, providing a comprehensive genetic framework for conserving its adaptive potential in the face of environmental change.

The study consisted of two feeding strategies (treatments) in duplicate (6 Ha ponds) at a commercial farm. Basic water variables, nitrogenous compounds, productive response, and bacterial diversity in the shrimp gut (16S rRNA gene sequencing) were monitored during a 163-day production period. Some water quality variables showed differences between the two feeding strategies (NO3-N, TSS, and chlorophyll a). Shrimp reared with automated feeding (CA) had a significantly higher final weight (35.87 ± 0.09 g/ind.) compared to those on traditional feeding (SA) (30.20 ± 1.06 g/ind.); weekly growth, productivity (kg/Ha), and total biomass harvested per pond were also higher (P < 0.05). During the study, 19 phyla, 30 classes, and 124 bacterial genera were recorded. The phylum Pseudomonadota had the greatest abundance, accounting for 65.1% in CA and 50.3% in SA. Fusobacteriota was the second most abundant, 16.8%, in CA and 7.1% in SA. The contribution of the remaining phyla ranged from 0.6 % to 4.7%. The Mann-Whitney U test showed no differences in the relative abundance of the Phyla, but did show differences at the class level, between the two feeding strategies. Alpha diversity was not different between treatments; however, Beta diversity revealed that automated and traditional feeding generated distinct microbial profiles. It is concluded that automated feeding influenced water quality, productive response, and modulated microbial colonization of the gut in shrimp reared in commercial ponds.

The Ficus carica L., is an important crop due to its adaptability to soils, climates and its high commercial value. Ficus carica represents a strategic crop for the Baja California peninsula, Mexico. There are few studies on the structure of taxonomic profiles in relation to the ecological niches of the soil, roots, and rhizosphere in Ficus carica. This study aimed to characterize the bacterial microbiome of the soil, rhizosphere and root associated with F. carica in an arid region of the Baja California peninsula, Mexico. Soil, rhizosphere, and root (endophytic microbiome) samples were collected from the F. carica agroecosystem in San Juan de los Planes, B.C.S, Mexico, and subsequently subjected to 16S rRNA metabarcoding analysis. Abundance plots were generated using microViz package. Alpha and beta diversity were estimated, and groups were compared using Kruskal-Wallis and Wilcoxon post-hoc tests (p<0.05). In the rhizosphere (M) and roots (R) most prevalent phyla (frequency ≥ 0.5) were Proteobacteria (M 35 % and R 10 %), Bacteroidota (M 25 % and R 35 %) and Patescibacteria (M 20 % and R 35 %); while Firmicutes (Soil 53 % and M 10 %) stood out in the soil (S), where it had its greatest abundance. The roots showed a higher abundance of Microscillaceae, LWQ8, and YM_S32_TM7-50-20. The rhizosphere recorded an abundance of Microscillaceae, YM_S32_TM7-50-20, and Saccharimonadaceae, whereas Bacillaceae predominated in the soil. These findings could boost sustainable strategies, such as the formulation of bioinoculants in arid regions.

Background and Aims: Genetic information is essential for understanding evolutionary processes across different temporal scales, particularly those occurring over contemporary or recent generations influenced by management, and for guiding conservation actions. These components are now explicitly incorporated into the Kunming–Montreal Global Biodiversity Framework (GBF), which emphasizes metrics such as the effective population size as key indicators for monitoring and management. However, the genetic context of partly clonal and economically important systems remains insufficiently explored. Agave karwinskii, a mezcal-producing species with a restricted distribution in southern Mexico, which occurs along a gradient of management intensity dominated by clonal propagation, provides an excellent model for informing conservation strategies in these understudied systems. Methods: We generated genomic data using restriction site-associated DNA sequencing and conducted population-level analyses, integrating the biological and management context of the species to understand its genetic patterns and delineate conservation units. We also evaluated GBF-relevant indicators to assess genetic diversity and support management planning. Key Results: Agave karwinskii exhibited high genetic diversity (Hs = 0.25) and moderate population differentiation (FST = 0.19), shaped by geographical, ecological and, particularly, management factors. We identified 173 single nucleotide polymorphisms as candidate loci potentially associated with local adaptation to environmental variation, including 15 robust single nucleotide polymorphisms consistently detected by four complementary approaches and associated with defence responses, adaptation to environmental stressors, growth and metabolic regulation. Two evolutionarily significant units and seven management units were delineated. The effective population size declined sharply in clonal and semi-cultivated systems, with most units falling below the GBF threshold (Ne > 500), despite large census sizes. Traditional mixed management helps to maintain diversity by promoting gene flow and reducing inbreeding, acting as a form of in situ conservation. Conclusions: This study provides a population genetic framework for understanding evolutionary processes influenced by management and guiding conservation strategies in A. karwinskii, offering insights applicable to other perennial, partly clonal and semi-domesticated plant species.

Identification of the spatial distribution of genetic variation is a central goal of evolutionary biology that can elucidate the mechanisms of evolution and speciation, shed light on the processes that affect geographical ranges, and locate populations of conservation concern. Genomic studies of species exhibiting high morphological variability adapted to heterogeneous landscapes may be particularly informative. Agave cerulata Trel. is one of the most abundant Agave species, represented by three subspecies and one variety, distributed along the latitudinal and climatic gradients of the Baja California Peninsula. By analysing over 50 000 single nucleotide polymorphisms from 39 populations sampled across the species’ distribution, we determined how selection and drift have shaped the genomic structure and diversity of A. cerulata. Moreover, we tested for concordance between genetic structure and morphological subspecies and answered long-standing questions regarding the subspecies/variety status of A. cerulata. Our data support the presence of two major regional genomic clusters, with the spatial distribution of genomic diversity driven by Holocene range expansion. Furthermore, the patterns of fine-scale genetic differentiation differed between the two regional clusters. In northern Baja California, neutral factors, such as isolation by distance and gene flow, have contributed to high admixture and low population divergence. In the southern group, differentiation was stronger and was associated with climate, particularly temperature extremes and precipitation seasonality. Finally, our data revealed a more complex pattern of population structuring than that suggested by morphological subspecies designations, with mixed support for the currently recognized taxonomic boundaries on the Baja California Peninsula.

Plant domestication in Mesoamerica gave the world crops of global significance, such as maize, beans, squashes, cocoa, and cotton. Additionally, it has introduced species of regional economic importance, which still display intermediate levels of domestication, including Agave, Opuntia, columnar cacti, Amaranthus, and various ornamental species. Agaves, in particular, hold immense cultural and economic significance in Mexico and play a crucial ecological role in wild plant communities. However, current agricultural practices have negatively impacted both wild populations of agave through overexploitation and habitat destruction, as well as cultivated plants by reducing available landraces and promoting the use of homogeneous plant material. Using genomic data (RADseq) and over 50,000 SNPs, we aimed to assess how local social and political decisions may have influenced genomic diversity and differentiation in intensively managed, clonally propagated Agave angustifolia (Espadín) in the state of Oaxaca, the cultivated A. angustifolia used to produce mezcal known as Bacanora in the state of Sonora, and their wild counterparts from both regions. We found evidence suggesting that Espadín recently arose through farmer selection of a clonal lineage with desirable mezcal production attributes (i.e., hybrid vigor), apparently from an unsampled cultivated variety, a cross between genetically distinct wild populations, or by hybridization between wild and cultivated plants. Espadín samples were represented by closely related heterozygous genotypes, with considerable genetic differentiation from wild plants. On the other hand, the genomic composition of cultivated Bacanora agave appears to have been influenced by a recently lifted ban (in 1992) on its cultivation and distillation, which, along with the relatively lower popularity of this beverage, allowed cultivated Bacanora agave to maintain the genetic diversity found in wild populations of the region. We found that social and political decisions may have important impacts on crop genomic diversity and differentiation.

Premise: Research on neutral and adaptive processes that lead to the divergence of species and populations is a crucial component in evolutionary and conservation genetics. Agave sobria is an endemic group of subspecies scattered on canyons along a latitudinal gradient and distinct environments of the Baja California Peninsula, Mexico. Agave sobria represents a unique opportunity to study the process of genetic differentiation in a highly heterogeneous environment. Methods: Using genotyping‐by‐sequencing, we genotyped 8453 single‐nucleotide polymorphisms (SNPs) in all A. sobria subspecies, including 19 A. sobria and three closely related A. cerulata ssp. subcerulata populations. We assessed neutral genetic structure and diversity at both the interspecific and intraspecific levels, evaluated the amount and direction of gene flow, and identified putatively adaptive SNPs. Results: We found low support for the currently recognized subspecies. We detected neutral (i.e., isolation by distance) and adaptive divergence linked to eco‐geographic characteristics of the habitat. High genetic connectivity indicated that gene flow between central and northern populations may have homogenizing effects preventing population differentiation. For the southernmost A. sobria ssp. frailensis , temperature and geographic isolation appear to be the main drivers of adaptive differentiation, with outlier SNPs located in coding regions involved in response to abiotic stress and immunology. Conclusions: In A. sobria , environmental isolation and geographic gradients affect the genetic structure, creating opportunities for local adaptation. Our results emphasize the importance of including neutral and adaptive perspectives, the combination of which allows a better understanding of the complexity of the processes that lead to population differentiation.

Plant domestication in Mesoamerica gave the world crops of global significance, such as maize, beans, squashes, cocoa, and cotton. Additionally, it has introduced species of regional economic importance, which still display intermediate levels of domestication, including Agave, Opuntia, columnar cacti, Amaranthus, and various ornamental species. Agaves, in particular, hold immense cultural and economic significance in Mexico and play a crucial ecological role in wild plant communities. However, current agricultural practices have negatively impacted both wild populations of agave through overexploitation and habitat destruction, as well as cultivated plants by reducing available landraces and promoting the use of homogeneous plant material. Using genomic data (RADseq) and over 50,000 SNPs, we aimed to assess how local social and political decisions may have influenced genomic diversity and differentiation in intensively managed, clonally propagated Agave angustifolia (Espadín) in the state of Oaxaca, as well as in the cultivated A. angustifolia used to produce mezcal known as Bacanora in the state of Sonora and their wild counterparts from both regions. We found evidence suggesting that Espadín recently aroused through farmer selection of a clonal lineage with desirable mezcal production attributes (i.e., hybrid vigor), apparently from a cross between genetically distinct wild populations or by hybridization between wild and cultivated varieties. Espadín samples were represented by closely related heterozygous genotypes, with considerable genetic differentiation from wild plants. On the other hand, the genomic composition of cultivated Bacanora agave apparently was influenced by a recently lifted ban (in 1992) on its cultivation and distillation, which, along with the relatively lower popularity of this beverage, allowed cultivated Bacanora agave to maintain the genetic diversity found in wild populations of the regions. We found that social and political decisions may have important impacts on crop genomic diversity and differentiation.

Background and Aims: Understanding spatial patterns of neutral and adaptive genetic variation and linking them to future climate change have become crucial in assessing the genetic vulnerability of species and developing conservation strategies. Using a combination of genomic approaches, this study aimed to explain the demographic history of Washingtonia palms, predict the adaptive potential in Washingtonia palm populations on the Baja California Peninsula (BCP) and southern California, and determine the geographical areas where climate change will have the most drastic effects. Methods: We used over 5000 single nucleotide polymorphisms from 155 individuals across 18 populations spanning the entire distribution range of Washingtonia palms on the BCP and southern California. We examined past and current genetic diversity distribution patterns and identified outliers using genetic differentiation and genotype–environment association methods. Genetic vulnerability was predicted, and species distribution modelling was utilized for the geographical regions that will be at risk under future climate scenarios. Key Results: Demographic modelling supported a bottleneck related to the Wisconsin glaciation, which was stronger and longer in northern Washingtonia populations. Genomic diversity presented a strong relationship to geography and provided evidence for range expansions from several refugia. Gradient Forest Analysis revealed that the genetic variation was shaped primarily by variables related to latitude and temperature during the coldest quarter, indicating adaptation to local thermal environments. We found limited adaptive potential and high levels of genetic vulnerability in lowland southern and central populations. Accordingly, species distribution modelling found that the southern distribution range will be affected by climate change, particularly under a high-emissions scenario. Conclusions: Our findings include a history of population bottleneck related to postglacial range expansion, population divergence with limited gene flow, and probable future changes in distribution under changing conditions. Under long-term climate change, southern and central lowland populations of Washingtonia will experience harsher climate conditions and strong genomic offset.

Agaves are an outstanding arid‐adapted group of species that provide a unique chance to study the influence of multiple potential factors (i.e., geological and ecological) on plant population structure and diversification in the heterogeneous environment of the Baja California Peninsula. However, relatively little is known about the phylogeography of the endemic agave species of this region. Herein, we used over 10,000 single‐nucleotide polymorphisms (SNPs) and spatial data from the Agave aurea species complex (i.e., A. aurea ssp. aurea, A. aurea ssp. promontorii, and A. aurea var. capensis) to resolve genetic relationships within this complex and uncover fine‐scale population structure, diversity patterns, and their potential underlying drivers. Analyses resolved low genetic structure within this complex, suggesting that A. aurea is more likely to represent several closely related populations than separate species or varieties/subspecies. We found that geographical and historical ecological characteristics—including precipitation, latitude, and past climatic fluctuations—have played an important role in the spatial distribution of diversity and structure in A. aurea. Finally, species distribution modeling results suggested that climate change will become critical in the extinction risk of A. aurea, with the northernmost population being particularly vulnerable. The low population genetic structure found in A. aurea is consistent with agave's life history, and it is probably related to continuity of distribution, relatively low habitat fragmentation, and dispersion by pollinators. Together, these findings have important implications for management and conservation programs in agave, such as creating and evaluating protected areas and translocating and augmentation of particular populations.