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The Notomicrus traili species group (Coleoptera: Noteridae) is a lineage of aquatic beetles distributed throughout South America and extends into Mexico and the West Indies. Previous research has revealed a species complex within this group, with multiple distinct clades sharing overlapping distributions and lineages attributed to N. traili and the closely related Notomicrus gracilipes recovered as polyphyletic. Here, we perform targeted capture of ultraconserved elements (UCEs) to examine relationships and patterns of evolution within the N. traili group. First, we use short‐read whole‐genome sequencing of four noterid genera to design a noterid‐specific UCE probe set (Noteridae 3.4Kv1) targeting over 3400 unique loci. Using this probe set, we capture UCE data from population‐level sampling of 44 traili group specimens from across the Neotropics, with an emphasis on the Guiana Shield where distributions of several putative N. traili group populations overlap. We subject the resulting data matrix to various trimming and data completeness treatments and reconstruct the phylogeny with both concatenated maximum likelihood and coalescent congruent methods. We recover robust phylogenetic estimates that identify several phylogenetically distinct clades within the traili group that share overlapping distributions. To test for the genetic distinctiveness of populations, we extract single nucleotide polymorphism (SNP) data from UCE alignments using a chimeric reference method to map UCE‐enriched reads and examine patterns of genetic clustering using principal component analyses (PCAs) and STRUCTURE. Population genetic results are highly concordant with recovered phylogenetic structure, revealing a high degree of co‐ancestry shared within identified clades, contrasting with limited ancestry sharing between clades. We recover a pattern consistent with repeated diversification and dispersal of the traili group in the Neotropics, highlighting the efficacy of a tailored UCE approach for facilitating shallow‐scale phylogenetic reconstructions and population genetic analyses, which can reveal novel aspects of coleopteran phylogeography. [ABSTRACT FROM AUTHOR]

Corynorhinus mexicanus is an insectivorous bat endemic to Mexico that inhabits the high and humid regions of the Sierra Madre Oriental (SMO), the Trans-Mexican Volcanic Belt (TMVB), and the Sierra Madre Occidental (SMOC). A previous study suggested that C. mexicanus could be a cryptic species complex due to the genetic divergence observed between specimens from the TMVB and SMOC. The present study implemented phylogenetic, population genetics, and morphological analyses to evaluate the hypothesis that C. mexicanus is a species complex. The phylogenetic analysis indicated that C. mexicanus is a polyphyletic species composed of three indirectly related lineages. The estimated divergence times for the lineages suggest that they first originated during the Pliocene, while the second and third shared a common ancestor with C. townsendii 1.55 million years ago, and diverged 600,000 years ago during the Middle Pleistocene. The population genetics analysis reveals the SMO lineage of C. mexicanus is an isolated genetic group and highly diverged from the rest of lineages (SMOC and TMVB). The morphological analyses showed variation in the skull and mandible associated with the lineages and sex of the specimens, highlighting a difference in mandible shape between the specimens of the SMO and the rest of C. mexicanus. The results of this study suggest the presence of an undescribed species of the genus Corynorhinus. [ABSTRACT FROM AUTHOR]

Coastal wetlands worldwide are experiencing high rates of loss and degradation that may lead to a reduction in diversity in faunal populations. Since salt marsh habitats are subject to a multitude of stressors, evaluations of the genetic diversity, connectivity, and potential resilience of faunal communities within salt marsh habitats are relevant. This study characterizes mitochondrial DNA (mtDNA) diversity for three common faunal residents of salt marshes along the northern Gulf of Mexico. Gulf Killifish (Fundulus grandis) samples were characterized for 1077 bp of the concatenated nucleotide sequence corresponding to the Control Region and Nitrogen Dehydrogenase, Subunits 2 and 5. Daggerblade grass shrimp (Palaemon pugio) samples were characterized using 466 bp of 16sRNA sequence, and phloem-feeding planthoppers (Prokelisia marginata) were characterized using 372 bp of Cytochrome c Oxidase Subunit I (COI) sequence. For F. grandis, our data revealed high levels of haplotypic diversity, evidence of isolation by distance (IBD), and regional population structuring associated with the distribution of two distinct phylogroups and distinct historical demography signatures. P. pugio and P. marginata displayed low levels of haplotypic diversity and evidence of population structure, but both appear to contain only snapshots of the total potential diversity for these species in the Gulf of Mexico. Greater resolution of the patterns of historical demography of Gulf Killifish may be obtained in future studies by including localities from Florida and Mexico. For both P. pugio and planthoppers, future studies would benefit from the characterization of genetic markers with a higher degree of polymorphism. We conclude that despite these three species inhabiting the same habitats along the same stretch of coast, each is subject to a different combination of evolutionary forces, and this study was able to reconstruct differences in how the genetic variation in each of these species emerged, and how it is maintained. [ABSTRACT FROM AUTHOR]

Little is known of the migratory ecology and population genetics of the lyside sulphur butterfly Kricogonia lyside (Godart) (Pieridae: Coliadinae). Mass migrations involving huge numbers of these butterflies have long been known to occur in the southern USA, Mexico and Greater Antilles, but these reports have been based mainly on chance encounters. A review of the limited literature on migrations of K. lyside in North America is presented here, together with results from field observations of a recent mass migration in north-western Mexico. Overall, these data confirm that migrations of K. lyside are often unidirectional, but can change direction over relatively short time periods, and are most probably 'triggered' by substantial rainfall following a prolonged dry period. Several important questions on these enigmatic migrations, however, including, but not limited to, location of source populations, ultimate destinations, numbers of individuals involved and purpose, remain to be answered. Analysis of mitochondrial DNA barcodes revealed that genetic diversity of the cytochrome c oxidase subunit I (COI) gene is much higher in K. lyside than that seen in the long-distance migrating nymphalid butterflies, the monarch (Danaus plexippus) and painted lady (Vanessa cardui), and that a large historical population expansion occurred during the mid-Pleistocene. [ABSTRACT FROM AUTHOR]

Abies hidalgensis is an endemic species from the state of Hidalgo, Mexico, that has been registered only in nine fragmented relict populations that have a total of 1 000 individuals among them. Intensive forest management takes place in five of the populations under specific programs focused on Pinus spp. Still, it is necessary to know the impact of these activities on the genetic diversity of the threatened species, if restoration and conservation strategies are to be proposed. The aim of this work was to estimate the effect of forest management on the genetic structure of A. hidalgensis using seven nuclear molecular markers developed for A. guatemalensis (Ab07, Ab08, Ab09, Ab12, Ab15, Ab20, Ab23). The species was sampled growing under two different conditions; (i) areas under forest management and (ii) conserved areas. Two indexes of genetic diversity were evaluated, observed and expected heterozygosity. The genetic structure was determined by an analysis of molecular variance and a Bayesian assignment model. A bottleneck analysis was also carried out. The populations were found to have a common genetic base (differentiation coefficient FST = 0.056, number of migrants per generation Nm = 43), which suggests recent fragmentation of the distribution, which in turn increases the bottleneck effect in managed areas (Wilcoxon probability Wp = 0.007 and 0.016). This explains the apparently high heterozygous level (He = 0.69) and low inbreeding. Our results are important as they may be used to design strategies for management and conservation of A. hidalgensis. [ABSTRACT FROM AUTHOR]

(1) Background: Chagas disease is the main neglected tropical disease in America. It is estimated that around 6 million people are currently infected with the parasite in Latin America, and 25 million live in endemic areas with active transmission. The disease causes an estimated economic loss of USD 24 billion dollars annually, with a loss of 75,200 working years per year of life; it is responsible for around ~12,000 deaths annually. Although Mexico is an endemic country that recorded 10,186 new cases of Chagas disease during the period of 1990–2017, few studies have evaluated the genetic diversity of genes that could be involved in the prophylaxis and/or diagnosis of the parasite. One of the possible candidates proposed as a vaccine target is the 24 kDa trypomastigote excretory–secretory protein, Tc24, whose protection is linked to the stimulation of T. cruzi-specific CD8+ immune responses. (2) Methods: The aim of the present study was to evaluate the fine-scale genetic diversity and structure of Tc24 in T. cruzi isolates from Mexico, and to compare them with other populations reported in the Americas with the aim to reconsider the potential role of Tc24 as a key candidate for the prophylaxis and improvement of the diagnosis of Chagas disease in Mexico. (3) Results: Of the 25 Mexican isolates analysed, 48% (12) were recovered from humans and 24% (6) recovered from Triatoma barberi and Triatoma dimidiata. Phylogenetic inferences revealed a polytomy in the T. cruzi clade with two defined subgroups, one formed by all sequences of the DTU I and the other formed by DTU II–VI; both subgroups had high branch support. Genetic population analysis detected a single (monomorphic) haplotype of TcI throughout the entire distribution across both Mexico and South America. This information was supported by Nei's pairwise distances, where the sequences of TcI showed no genetic differences. (4) Conclusions: Given that both previous studies and the findings of the present work confirmed that TcI is the only genotype detected from human isolates obtained from various states of Mexico, and that there is no significant genetic variability in any of them, it is possible to propose the development of in silico strategies for the production of antigens that optimise the diagnosis of Chagas disease, such as quantitative ELISA methods that use this region of Tc24. [ABSTRACT FROM AUTHOR]

Promoting neglected and underutilized crop species is a possible solution to deal with the complex challenges of global food security. Chayote is a Neglected and Underutilized Cucurbit Species (NUCuS), which is recognized as a fruit vegetable in Latin America and is widely grown in Asia and Africa. However, basic biological knowledge about the crop is insufficient in scientific sources, especially outside of its center of origin. In this study, limited observations on reproductive characters were conducted, differentiating accessions from Mexico, Japan, and Myanmar. Cytological evaluation among Mexican and Japanese accessions showed that the relative nuclear DNA content is 1.55 ± 0.05 pg, the estimated genome size is 1511 at 2C/Mbp, and the observed mitotic chromosomal number is 2n = 28. The genetic diversity of 21 chayote accessions was also examined using six microsatellite markers. A global low genetic heterozygosity (Ho = 0.286 and He = 0.408) and three genetic groups were detected. The results established the basis to provide insights into chayote arrival history in Asia by looking at the crop's reproductive morphology, cytology, and genetic diversity status outside its origin center. This could help in developing sustainable utilization and conservation programs for chayote. [ABSTRACT FROM AUTHOR]

In this study, we examined whether the genetic diversity of Didelphis marsupialis is structured or their populations maintain high gene flow as expected in common species. Forty-eight Tomahawk traps were set for four consecutive nights in The Highlands and the Central Depression, State of Chiapas, Mexico. Eight microsatellites were amplified to examine genetic diversity. Genetic structure was evaluated in terms of the null allele-corrected pairwise global Fst estimates, according to the ENA and INA methods. An Analysis of Molecular Variance and a Bayesian analysis were carried out classifying the opossums by region and population. We found a moderate genetic diversity (He = 0.57–0.62) and an intermediate genetic differentiation between population (Fst = 0.11, P = 0.009). Genetic distances showed a closer relationship between individuals from populations that had a similar disturbance level. The Bayesian analysis showed a marked structure both between regions and between populations. Our results show in the common opossum moderate levels of gene flow, limited possibly by the habitat fragmentation due to anthropogenic disturbance. Further genetics studies and conservation efforts on this marsupial are recommended. Our findings are relevant for the conservation of common marsupial species in Mexico. [ABSTRACT FROM AUTHOR]

Juglans pyriformis Liebm. (Juglandaceae) is a threatened and endemic tree that grows in the cloud forest of Mexico. Natural populations of this species have been reduced due to, among others, changes in land use, overexploitation, and logging, with probable effects on its genetic diversity and structure. To determine the levels of variation and genetic structure of two populations with different silvicultural regimes, six inter-simple sequence repeat (ISSR) primers were used to amplify DNA from 35 individuals from a high-logging population and 32 from a low-logging population. The results show a higher polymorphism in the low-logging population (81.5%) compared to the high-logging population (77.4%). The genetic differentiation coefficient (PhiPT) values (0.109), genetic distance (0.134) and STRUCTURE analysis (Fst = 0.2271, P = 0.04) show significant genetic differentiation between populations. Rare, private, and monomorphic bands were detected in both populations. These results confirm the trend of reduced genetic variation due to logging. [ABSTRACT FROM AUTHOR]

Complex speciation, involving rapid divergence and multiple bouts of post-divergence gene flow, can obfuscate phylogenetic relationships and species limits. In North America, cases of complex speciation are common, due at least in part to the cyclical Pleistocene glacial history of the continent. Scrub-Jays in the genus Aphelocoma provide a useful case study in complex speciation because their range throughout North America is structured by phylogeographic barriers with multiple cases of secondary contact between divergent lineages. Here, we show that a comprehensive approach to genomic reconstruction of evolutionary history, i.e. synthesizing results from species delimitation, species tree reconstruction, demographic model testing, and tests for gene flow, is capable of clarifying evolutionary history despite complex speciation. We find concordant evidence across all statistical approaches for the distinctiveness of an endemic southern Mexico lineage (A. w. sumichrasti), culminating in support for the species status of this lineage under any commonly applied species concept. We also find novel genomic evidence for the species status of a Texas endemic lineage A. w. texana , for which equivocal species delimitation results were clarified by demographic modeling and spatially explicit models of gene flow. Finally, we find that complex signatures of both ancient and modern gene flow between the non-sister California Scrub-Jay (Aphelocoma californica) and Woodhouse's Scrub-Jay (Aphelocoma woodhouseii) result in discordant gene trees throughout the species' genomes despite clear support for their overall isolation and species status. In sum, we find that a multi-faceted approach to genomic analysis can increase our understanding of complex speciation histories, even in well-studied groups. Given the emerging recognition that complex speciation is relatively commonplace, the comprehensive framework that we demonstrate for interrogation of species limits and evolutionary history using genomic data can provide a necessary roadmap for disentangling the impacts of gene flow and incomplete lineage sorting (ILS) to better understand the systematics of other groups with similarly complex evolutionary histories. [Gene flow; genomics; introgression; phylogenomics; population genetics; species delimitation; species trees; systematics.] [ABSTRACT FROM AUTHOR]

The evolution of new variants of plant pathogens is one of the biggest challenges to controlling and managing plant diseases. Of the forces driving these evolutionary processes, global migration events are particularly important for widely distributed diseases such as potato late blight, caused by the oomycete Phytophthora infestans . However, little is known about its migration routes outside North America and Europe. This work used genotypic data from population studies to elucidate the migration history originating the Colombian P. infestans population. For this purpose, a dataset of 1,706 P. infestans genotypes was recollected, representing North and South America, Europe, and Asia. Descriptive analysis and historical records from North America and Europe were used to propose three global migration hypotheses, differing on the origin of the disease (Mexico or Peru) and the hypothesis that it returned to South America from Europe. These scenarios were tested using approximate Bayesian computation. According to this analysis, the most probable scenario (posterior probability = 0.631) was the one proposing a Peruvian origin for P. infestans , an initial migration toward Colombia and Mexico, and a later event from Mexico to the United States and then to Europe and Asia, with no return to northern South America. In Colombia, the scenario considering a single migration from Peru and posterior migrations within Colombia was the most probable, with a posterior probability of 0.640. The obtained results support the hypothesis of a Peruvian origin for P. infestans followed by rare colonization events worldwide., Competing Interests: The author(s) declare no conflict of interest.

Aim: Understanding speciation mechanisms requires disentangling processes that promote and erode population‐level divergence. Three hypotheses are raised that contemporary population structure is mainly shaped by refugial isolation, gene flow or both. Testing these hypotheses requires range‐wide phylogeography and integrative analyses across scales. Here we aimed to (1) re‐estimate the previously unresolved nuclear divergence within a widespread bat; (2) test the above three phylogeographical hypotheses and (3) inform conservation management under climatic change. Location: North America including the Caribbean. Taxon: The big brown bat (Eptesicus fuscus). Methods: We collected range‐wide samples and genome‐wide markers using restriction site‐associated DNA sequencing. Population structure was analysed by clustering methods and spatial estimations. Nuclear phylogeographical divergence was estimated using tree methods (concatenation and coalescence) and network analyses (TreeMix). Phylogeographical hypotheses were tested by comparing alternative evolutionary scenarios using demographic modelling. Species distribution modelling was used to help identify Pleistocene refugia and predict future range shifts under climatic change. Results: We identified three populations in the Caribbean, eastern and western North America. The western population further split into three phylogeographical clades: Pacific, southwestern North America and Mexico. Discordance among mitochondrial and nuclear topologies reflected strong impacts of gene flow without sex bias. Demographic modelling supported scenarios of historical isolation followed by secondary gene flow and estimated Holocene divergence times. Species distribution was essentially continuous during glaciation with possible regional isolation, and northward range shifts were predicted under future climatic change. Main Conclusions: Contemporary population divergence of big brown bats was shaped by both historical isolation and secondary gene flow, supporting the third phylogeographical hypothesis. While climatic change likely triggered initial divergence, ongoing gene flow has largely impacted the dynamic within‐species evolution and generated population divergence without speciation. [ABSTRACT FROM AUTHOR]

Populations are locally adapted when they exhibit higher fitness than foreign populations in their native habitat. Maize landrace adaptations to highland and lowland conditions are of interest to researchers and breeders. To determine the prevalence and strength of local adaptation in maize landraces, we performed a reciprocal transplant experiment across an elevational gradient in Mexico. We grew 120 landraces, grouped into four populations (Mexican Highland, Mexican Lowland, South American Highland, South American Lowland), in Mexican highland and lowland common gardens and collected phenotypes relevant to fitness and known highland‐adaptive traits such as anthocyanin pigmentation and macrohair density. 67k DArTseq markers were generated from field specimens to allow comparisons between phenotypic patterns and population genetic structure. We found phenotypic patterns consistent with local adaptation, though these patterns differ between the Mexican and South American populations. Quantitative trait differentiation (QST) was greater than neutral allele frequency differentiation (FST) for many traits, signaling directional selection between pairs of populations. All populations exhibited higher fitness metric values when grown at their native elevation, and Mexican landraces had higher fitness than South American landraces when grown in these Mexican sites. As environmental distance between landraces' native collection sites and common garden sites increased, fitness values dropped, suggesting landraces are adapted to environmental conditions at their natal sites. Correlations between fitness and anthocyanin pigmentation and macrohair traits were stronger in the highland site than the lowland site, supporting their status as highland‐adaptive. These results give substance to the long‐held presumption of local adaptation of New World maize landraces to elevation and other environmental variables across North and South America. [ABSTRACT FROM AUTHOR]

We studied the rupicolous and dioecious species of Bakerantha (Bromeliaceae) that grow as narrow endemics in central-eastern Mexico. We aimed to describe the spatio-temporal framework in which Bakerantha and its species originated using a phylogeographic and population genetics approach. We carried out population genetics analyses on 29 populations of the five Bakerantha spp. using plastid and nuclear DNA sequences. The data were used to analyse their diversity, genetic structure and demography, to carry out molecular dating and to reconstruction their ancestral area. Our analyses revealed that speciation in Bakerantha began in the Late Pliocene, associated with vicariance resulting from the rise of the Trans-Mexican Volcanic Belt, a barrier that isolated the Bakerantha spp. to its north and south, and subsequent dispersal events in the Sierra Madre Oriental. Genetic data suggest that the species have achieved a high degree of genetic differentiation and variation, but most of them lack intraspecific structure, even though species have remained stable over the time due their life history traits. [ABSTRACT FROM AUTHOR]

Simple Summary: Species decline has accelerated in recent decades, with rare species often being the first to go extinct, mainly due to low population sizes. This study worked with Pachyphytum cesium (Crassulaceae), an endemic species from central Mexico threatened by human activities and climate change. To increase our knowledge of the species, we analyze the diversity and genetic structure of all known populations of P. caesium to change their current genetic status and propose conservation strategies. The results indicate that this species presents low to moderate levels of genetic diversity and incipiently structured populations due to low genetic flow. We found that genetic parameters are essential to the conservation strategies and status vulnerability reclassification. Based on our results, we propose reclassifying the conservation status of the species in danger of extinction; hence a series of conservation strategies are provided to prevent its disappearance. Genetic studies in rare species are important to determine their patterns of genetic diversity among populations and implement conservation plans aimed to reduce extinction risks. Pachyphytum caesium is an endemic species with extremely small populations in central Mexico. This work analyzes the diversity and genetic structure of Pachyphytum cesium (Crassulaceae) to change the conservation status and propose conservation strategies. Twelve dominant ISSR markers were used to describe the genetic diversity of all known populations. Additionally, we carried out two simulations to explore how the loss of individuals or the local populations extinction affect the genetics parameters of the species. The average results indicated moderate levels of genetic diversity (number of alleles = 89.7 ± 3.9, expected heterozygosity = 0.212 ± 0.0, and percentage of polymorphic loci = 56.1 ± 3.9), parameters that decreased significantly when simulations were performed in P. caesium. Additionally, a genetic structure of the populations was found with low gene flow (Nm = 0.92). Genetic parameters are negatively affected by the loss of individuals and the local extinction of populations. Based on our results, we propose to reclassify the conservation status of the species in danger of extinction, hence a series of conservation strategies are provided to prevent its disappearance. [ABSTRACT FROM AUTHOR]

Aligning the ecological and social dimensions of the connections present between users that harvest a shared natural resource is a necessary step toward sustainable management. However, contrasting estimates of connectivity across disciplines is a challenging task and few empirical studies have focused on population dynamics within fish species with a complex life history. We used a collaborative approach merging citizen science, population genetics, oceanographic modeling, and interviews to collect empirical connectivity data of individual fish, fishing sites, and fishers. We integrated the data within a multilevel social-ecological network framework describing the interactions between two communities of small-scale fishers (Bahia Kino and Puerto Libertad, Sonora, Mexico) targeting leopard grouper (Mycteroperca rosacea). We identified two types of social-ecological links, including the use of specific fishing sites by individual fishers and the harvest of individual fish by individual fishers. Despite their fishing zones not overlapping, the ecological links between two communities located ~150 km apart were consistent and reciprocal where fishing grounds from each community acted as a source of fish to the other during the larval or juvenile/adult stages, respectively. As a result, fishers from the two communities frequently captured fish that were second-degree relatives. In contrast, the probability of social ties among fishers changed significantly depending on the type of connection and was considerably low for leadership and kinship although some communication was present. Our study highlighted how local actions (e.g., recovery from marine reserves or overfishing) are likely to impact the neighboring community as much as locally. The geographic scale and strength of key ecological process supporting fish stocks through the fish life cycle seem to be larger than those of social connections among fishers. Fishers and managers could benefit from a broader regional perspective that strengthens connections between communities about shared goals and activities. We examine some insights learned on the constraints of connectivity given different attributes of each ecological and social component and methodological challenges identified. We also discuss ways to improve collaborative management between the two communities. [ABSTRACT FROM AUTHOR]

Dispersal is a fundamental process in the functioning of animal societies as it regulates the degree to which closely related individuals are spatially concentrated. A species' dispersal pattern can be complex as it emerges from individuals' decisions shaped by the cost–benefit tradeoffs associated with either remaining in the natal group or dispersing. Given the potential complexity, combining long‐term demographic information with molecular data can provide important insights into dispersal patterns of a species. Based on a 15‐year study that integrates multiyear demographic data on six groups with longitudinal and cross‐sectional genetic sampling of 20 groups (N = 169 individuals, N = 21 polymorphic microsatellite loci), we describe the various dispersal strategies of male and female black howler monkeys (Alouatta pigra) inhabiting Palenque National Park, Mexico. Genetically confirmed dispersal events (N = 21 of 59 males; N = 6 of 65 females) together with spatial autocorrelation analyses revealed that the dispersal pattern of black howlers is bisexual with strong sex‐biases in both dispersal rate (males disperse more often than females) and dispersal distance (females disperse farther than males). Observational and genetic data confirm that both males and females can successfully immigrate into established groups, as well as form new groups with other dispersing individuals. Additionally, both males and females may disperse singly, as well as in pairs, and both may also disperse secondarily. Overall, our findings suggest multiple dispersal trajectories for black howler males and females, and longer multiyear studies are needed to unravel which demographic, ecological and social factors underlie individuals' decisions about whether to disperse and which dispersal options to take. [ABSTRACT FROM AUTHOR]

Coastal dunes are unique habitats, threatened by human activities. In biogeographical terms, coastal dunes are habitat islands, being discrete and distinct patches of similar habitat among themselves, separated from each other by a different type of habitat. Furthermore, coastal dunes harbor endemic species, adapted to living solely in the habitats found on specific dune systems. For example, the honeypot ant Myrmecocystus baja is endemic and restricted to coastal dunes of Mexico's Baja California Pacific coast. This ecological and biogeographical scenario led to the questions whether their geographical isolation is reflected in their genetic diversity and structuring, and how their demographic history is related with the formation of the dune system habitats. To answer these questions, population genetic, isolation-with-migration, and phylogeographical analyses were carried out, based on mitochondrial and five nuclear intronic markers. Minimal gene flow was detected only between two of the dune systems sampled; otherwise, the M. baja populations were found to be isolated and genetically structured, and their divergence generally pre-dated the modern-day dune systems. It is therefore highly likely that these ants were already present in paleodunes and that each of the populations was established from founder populations as the dunes formed. These findings highlight the importance of coastal dunes for species such as the honeypot ant from Baja California, in promoting genetic differentiation., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Recent climatic conditions are affecting biodiversity, particularly those species highly isolated and at their distribution limits such as trout (Oncorhynchus sp.) inhabiting the Northern Sierra Madre Occidental (NSMO) in Mexico, which is a current conservation concern due to their fragmented distribution and anthropogenic threads. Here, we compiled previously published data from 24 microsatellite loci from multiple localities of trout throughout the NSMO to construct geographic genetic structuring hypotheses. Our results confirm two genetically distinct subgroups within the NSMO corresponding to the northern populations from Río Yaqui-Río Bavispe and Río Casas Grandes, and the southern population from Río Yaqui-Río Sirupa and Río Conchos. In addition, we found a strong genetic differentiation between most of the locations sampled. We assembled species distribution models (SDM) to estimate the current distribution of trout. The SDM show that suitable environmental conditions may exist between northern and southern populations but are highly fragmented. In addition, association analyzes between FST and environmental factors show that the minimum temperature of the coldest month, the precipitation of wettest month, and the compound topographic index were responsible for the genetic structure. These results along with the limited mobility of the species, support limited connectivity as a possible explanation for current north and south arrangement of diversity. This study provides deep insights into the ecology and divergence processes within Northern Sierra Madre Occidental trout, and for the urgent development of effective conservation strategies for each of those lineages. [ABSTRACT FROM AUTHOR]

The boll weevil, Anthonomus grandis Boheman (Coleoptera: Curculionidae), is an important pest of commercial cotton across the Americas. In the United States, eradication of this species is complicated by re‐infestations of areas where eradication has been previously successful and by the existence of morphologically similar variants that can confound identification efforts. To date, no study has applied a high‐throughput sequencing approach to better understand the population genetic structure of the boll weevil. Furthermore, only a single study has investigated genetic relationships between populations in North and South America. We used double digest restriction site‐associated DNA sequencing (ddRADseq) to resolve the population genomic structure of the boll weevil in the southern United States, northern Mexico, and Argentina. Additionally, we assembled the first complete mitochondrial genome for this species and generated a preliminary whole genome assembly, both of which were used to improve the identification of informative loci. Downstream analyses revealed two main lineages—one consisting of populations found geographically west of the Sierra Madre Occidental mountain range and the second consisting of populations found to the east—were revealed, and both were sub‐structured. Population geographic structure was consistent with the isolation by distance model, indicating that geogrpahic distance is likely a primary mechanism driving divergence in this species. Boll weevil populations from Argentina were found to be more closely related to the eastern lineage, suggesting a recent colonization of South America by the eastern lineage, but additional sampling across Mexico, Central America and South America is needed to further clarify their origin. Finally, we uncovered an instance of population turnover or replacement, highlighting the temporal instability of population structure. [ABSTRACT FROM AUTHOR]

In the Alvarado Lagoon System (ALS) in south-central Veracruz on Mexico's gulf coast, the blue land crab, Cardisoma guanhumi, a semi-terrestrial crustacean species, represents an important fishery resource, but one that is subject to overexploitation and habitat destruction. Identifying genetic diversity and the genetic unit are required to establish efficient conservation strategies. The present study's goal was to assess the genetic structure and degree of genetic diversity of C. guanhumi populations along the ALS. A fragment of the D-loop region of the mtDNA (750 bp) and a partial sequence of the COI gene (580 pb) was sequenced for 120 specimens collected at four sites in the ALS. Genetic diversity indices were estimated for each marker. The study sites' gene flow was estimated, as was the effective population size and the mutational rate for each locality. A haplotype network was built to estimate the gene genealogies of the populations. A Tajima's neutrality test, Fu tests, and mismatch analysis were performed to detect demographic expansion. Results show that this C. guanhumi population has high genetic diversity with a large gene flow among the localities studied and expanded during the recent evolutionary past. All haplotypes from both markers are novel for the species, according to the NCBI GenBank. The high genetic diversity and genetic connectivity among sites suggests that the size of blue crab populations in the ALS has not been drastically affected by past exploitation. Finally, management strategies are proposed to protect the species. [ABSTRACT FROM AUTHOR]

Chromoblastomycosis is a chronic severely mutilating disease caused by fungi of the order Chaetothyriales. Classically, Phialophora verrucosa has been listed among these etiologic agents. This species is known to occur in the environment and has been found to cause other infections like phaeohyphomycosis, while reported cases of chromoblastomycosis are scant. Phialophora is phylogenetically diverse, and thus retrospective confirmation of etiology is necessary. We studied ten proven cases of chromoblastomycosis from Mexico and further analyzed the population genetics and genomics of the Phialophora species to understand their pathogenicity and predilection. The clinical strains were molecularly identified as Phialophora americana (n = 4), Phialophora chinensis (n = 4), and Phialophora macrospora (n = 2). No genetic distinction between clinical and environmental strains was possible. Further analysis of strains from diverse origins are needed to address eventual differences in virulence and niche predilection between the species. [ABSTRACT FROM AUTHOR]

With more than 200 species, the genus Agave is one of the most interesting and complex groups of plants in the world, considering for instance its great diversity and adaptations. The adaptations include the production of a single, massive inflorescence (the largest among plants) where after growing for many years, sometimes more than 30, the rosette dies shortly afterward, and the remarkable coevolution with their main pollinators, nectarivorous bats, in particular of the genus Leptonycteris. The physiological adaptations of Agave species include a photosynthetic metabolism that allows efficient use of water and a large degree of succulence, helping to store water and resources for their massive flowering event. Ecologically, the agaves are keystone species on which numerous animal species depend for their subsistence due to the large amounts of pollen and nectar they produce, that support many pollinators, including bats, perching birds, hummingbirds, moths, and bees. Moreover, in many regions of Mexico and in the southwestern United States, agaves are dominant species. We describe the contributions of H. S. Gentry to the understanding of agaves and review recent advances on the study of the ecology and evolution of the genus. We analyze the present and inferred past distribution patterns of different species in the genus, describing differences in their climatic niche and adaptations to dry conditions. We interpret these patterns using molecular clock data and phylogenetic analyses and information of their coevolving pollinators and from phylogeographic, morphological, and ecological studies and discuss the prospects for their future conservation and management. [ABSTRACT FROM AUTHOR]

Anthropogenic perturbations introduce novel selective pressures to natural environments, impacting the genomic variability of organisms and thus altering the evolutionary trajectory of populations. Water overexploitation for agricultural purposes and defective policies in Cuatro Cienegas, Coahuila, Mexico, have strongly impacted its water reservoir, pushing entire hydrological systems to the brink of extinction along with their native populations. Here, we studied the effects of continuous water overexploitation on an environmental aquatic lineage of Pseudomonas otitidis over a 13-year period which encompasses three desiccation events. By comparing the genomes of a population sample from 2003 (original state) and 2015 (perturbed state), we analyzed the demographic history and evolutionary response to perturbation of this lineage. Through coalescent simulations, we obtained a demographic model of contraction-expansion-contraction which points to the occurrence of an evolutionary rescue event. Loss of genomic and nucleotide variation alongside an increment in mean and variance of Tajima's D , characteristic of sudden population expansions, support this observation. In addition, a significant increase in recombination rate (R/θ) was observed, pointing to horizontal gene transfer playing a role in population recovery. Furthermore, the gain of phosphorylation, DNA recombination, small-molecule metabolism and transport and loss of biosynthetic and regulatory genes suggest a functional shift in response to the environmental perturbation. Despite subsequent sampling events in the studied site, no pseudomonad was found until the lagoon completely dried in 2017. We speculate about the causes of P. otitidis final decline or possible extinction. Overall our results are evidence of adaptive responses at the genomic level of bacterial populations in a heavily exploited aquifer. [ABSTRACT FROM AUTHOR]

The humanitarian crisis on the US-Mexico border is a long-standing and evolving crisis in which nearly 8,000 deaths have been reported in the last two decades. These deaths are largely distributed across the Arizona-Mexico and Texas-Mexico border regions, where demographic trends for immigrants attempting to cross into the United States have shifted dramatically. The demographic change and volume of immigrants seeking shelter in the United States present new challenges for the forensic practitioners entrusted with the identification of individuals who lose their lives during the final segment of their journey. Within this border context, this study investigated how genetic variation inferred from forensically significant microsatellites can provide valuable information on regions of origin for unidentified remains at the group level. To explore how to mobilize these genetic data to inform identification strategies, the authors conducted a comparative genetic analysis of identified and unidentified immigrant cases from the Arizona- and Texas-Mexico contexts, as well as 27 other Latin American groups. Allele frequencies were utilized to calculate F ST, and relationships were visually depicted in a multidimensional scaling plot. A Spearman correlation coefficient analysis assessed the strength and significance of population relationships, and an agglomerative clustering analysis assessed population clusters. Results indicate that Arizona-Mexico immigrants have the strongest relationship (>80%) with groups from El Salvador, Guatemala, Mexico, and an indigenous group from southern Mexico. Texas-Mexico immigrants have the strongest relationships (>80%) with groups from Belize, Colombia, Costa Rica, El Salvador, Guatemala, Honduras, and Nicaragua. These findings agree with, and are discussed in comparison with, previously reported demographic trends, population genetics research, and population history analyses. The authors emphasize the utility and necessity of coupling genetic variation research with a nuanced anthropological perspective for identification processes in the US-Mexico border context. [ABSTRACT FROM AUTHOR]

Premise: Past climate fluctuations during the Holocene and Pleistocene shaped the distribution of several plant species in temperate areas over the world. Wild maize, commonly known as teosinte, is a good system to evaluate the effects of historical climate fluctuations on genetic diversity due to its wide distribution in Mexico with contrasting environmental conditions. We explored the influence of contemporary factors and historical environmental shifts on genetic diversity, including present and three historical periods using neutral markers. Methods: We used 22 nuclear microsatellite loci to examine the genetic diversity of 14 populations of Zea mays subsp. parviglumis and 15 populations of Zea mays subsp. mexicana (527 individuals total). We implemented genetic structure analyses to evaluate genetic differentiation between and within subspecies. We applied coalescent‐based demographic analysis and species distribution modeling to evaluate the effects of historical environmental shifts. Results: We found 355 alleles in total for the two subspecies and variable levels of diversity in each (Z. mays subsp. parviglumis expected heterozygosity HE = 0.3646–0.7699; Z. mays subsp. mexicana HE = 0.5885–0.7671). We detected significant genetic structure among populations (DEST = 0.4332) with significant heterozygote deficiency (FIS = 0.1796), and variable selfing rates (sg2 = 0.0–0.3090). The Bayesian assignment analysis differentiated four genetic groups. Demographic and species distribution modeling analysis suggested that environmental shifts were influential in the amount of genetic diversity. Conclusions: Our analyses suggest that the current genetic diversity in teosinte is shaped by factors such as local adaptation and genetic isolation, along with historical environmental fluctuations. [ABSTRACT FROM AUTHOR]

Population structure across a species distribution primarily reflects historical, ecological, and evolutionary processes. However, large‐scale contemporaneous changes in land use have the potential to create changes in habitat quality and thereby cause changes in gene flow, population structure, and distributions. As such, land‐use changes in one portion of a species range may explain declines in other portions of their range. For example, many burrowing owl populations have declined or become extirpated near the northern edge of the species' breeding distribution during the second half of the 20th century. In the same period, large extensions of thornscrub were converted to irrigated agriculture in northwestern Mexico. These irrigated areas may now support the highest densities of burrowing owls in North America. We tested the hypothesis that burrowing owls that colonized this recently created owl habitat in northwestern Mexico originated from declining migratory populations from the northern portion of the species' range (migration‐driven breeding dispersal whereby long‐distance migrants from Canada and the United States became year‐round residents in the newly created irrigated agriculture areas in Mexico). We used 10 novel microsatellite markers to genotype 1,560 owls from 36 study locations in Canada, Mexico, and the United States. We found that burrowing owl populations are practically panmictic throughout the entire North American breeding range. However, an analysis of molecular variance provided some evidence that burrowing owl populations in northwestern Mexico and Canada together are more genetically differentiated from the rest of the populations in the breeding range, lending some support to our migration‐driven breeding dispersal hypothesis. We found evidence of subtle genetic differentiation associated with irrigated agricultural areas in southern Sonora and Sinaloa in northwestern Mexico. Our results suggest that land use can produce location‐specific population dynamics leading to subtle genetic structure even in the absence of dispersal barriers. [ABSTRACT FROM AUTHOR]

We studied HLA class I (HLA-A , -B) and class II (HLA-DRB1 , -DQB1) allele groups and alleles by PCR-SSP based typing in a total of 15,318 mixed ancestry Mexicans from all the states of the country divided into 78 sample sets, providing information regarding allelic and haplotypic frequencies and their linkage disequilibrium, as well as admixture estimates and genetic substructure. We identified the presence of 4268 unique HLA extended haplotypes across Mexico and find that the ten most frequent (HF > 1%) HLA haplotypes with significant linkage disequilibrium (Δ'≥0.1) in Mexico (accounting for 20% of the haplotypic diversity of the country) are of primarily Native American ancestry (A*02~B*39~DRB1*04~DQB1*03:02, A*02~B*35~DRB1*08~DQB1*04, A*68~B*39~DRB1*04~DQB1*03:02, A*02~B*35~DRB1*04~DQB1*03:02, A*24~B*39~DRB1*14~DQB1*03:01, A*24~B*35~DRB1*04~DQB1*03:02, A*24~B*39~DRB1*04~DQB1*03:02, A*02~B*40:02~DRB1*04~DQB1*03:02, A*68~B*35~DRB1*04~DQB1*03:02, A*02~B*15:01~DRB1*04~DQB1*03:02). Admixture estimates obtained by a maximum likelihood method using HLA-A / -B / -DRB1 as genetic estimators revealed that the main genetic components in Mexico as a whole are Native American (ranging from 37.8% in the northern part of the country to 81.5% in the southeastern region) and European (ranging from 11.5% in the southeast to 62.6% in northern Mexico). African admixture ranged from 0.0 to 12.7% not following any specific pattern. We were able to detect three major immunogenetic clusters correlating with genetic diversity and differential admixture within Mexico: North, Central and Southeast, which is in accordance with previous reports using genome-wide data. Our findings provide insights into the population immunogenetic substructure of the whole country and add to the knowledge of mixed ancestry Latin American population genetics, important for disease association studies, detection of demographic signatures on population variation and improved allocation of public health resources. [ABSTRACT FROM AUTHOR]

We studied HLA class I (HLA-A , -B) and class II (HLA-DRB1 , -DQB1) alleles by PCR-SSP based typing in 498 Mexicans from the state of Michoacán living in the city of Morelia (N = 150) and rural communities (N = 348), to obtain information regarding allelic and haplotypic frequencies. We find that the ten most frequent haplotypes found in the state of Michoacán include 12 Native American and two European haplotypes. Admixture estimates revealed that the main genetic components in the state of Michoacán are Native American (48.79 ± 1.44%) and European (43.10 ± 0.86%), while African genetic component is less apparent (8.11 ± 0.85%). Our findings add to the growing knowledge on the population genetics of Western Mexico and provide new HLA data on populations from Michoacán. [ABSTRACT FROM AUTHOR]

Pontoscolex corethrurus (Müller, 1857) is an invasive tropical earthworm, globally distributed. It reproduces through parthenogenesis, which theoretically results in low genetic diversity. The analysis of the population structure of P. corethrurus using molecular markers may significantly contribute to understanding the ecology and reproductive system of this earthworm species. This work assessed the genetic diversity and population structure of P. corethrurus with 34 polymorphic inter simple sequence repeat markers, covering four populations in tropical and temperate pastures from Veracruz State. Nuclear markers distinguished two genetic clusters, probably corresponding to two distinct genetic lineages. The number of clones detected in the AC population was lower than expected for a parthenogenetic species. Also, the apparent lack of differences in population structures related to the geographic region among the populations studied may indicate that human-mediated transference is prevalent in these areas. Still, most individuals apparently belong to lineage A, and only a few individuals seem to belong to the lineage B. Thus, the admixture signatures found among the four populations of P. corethrurus may have facilitated a successful invasion by directly increasing fitness. In summary, addressing the genetic variation of P. corethrurus with ISSR markers was a suitable approach, as it evidenced the genetic diversity and relationships in the populations evaluated. [ABSTRACT FROM AUTHOR]

The Tehuacán-Cuicatlán Valley, located at the southeast of the state of Puebla and the northeast of the state of Oaxaca in Central Mexico, south of the Trans-Mexican Volcanic Belt (TMVB), is of particular interest for understanding the evolutionary dynamics of arid and semi-arid environments, being one of the main reservoirs of biological diversity for the arid zones of North America, including the highest diversity of Agavaceae worldwide and high levels of endemism. Studying in detail the phylogeography, environmental history and population genetics of representative species will hopefully shed light on the evolutionary and ecological dynamics that generated the tremendous biodiversity and endemism of this important region in Mexico. We sequenced three non-coding regions of chloroplast genome of Agave kerchovei , a representative species of the Tehuacán Valley, generating 2,188 bp from 128 individuals sampled from eight populations throughout the species range. We used this data set to (i) characterize the levels of genetic diversity and genetic structure in A. kerchovei ; (ii) predict the distribution of A. kerchovei for the present day, and to reconstruct the past geographical history of the species by constructing ecological niche models (ENM); and (iii) compare the levels of diversity in this species with those estimated for the widely distributed Agave lechuguilla. Agave kerchovei has high levels of total chloroplast genetic variation (Hd = 0.718), especially considering that it is a species with a very restricted distribution. However, intrapopulation diversity is low (zero in some populations), and genetic structure is high (F ST = 0.928, G ST = 0.824), which can be expected for endemic species with isolated populations. Our data suggest that Pleistocene glacial cycles have played an important role in the distribution of A. kerchovei , where the climatic variability of the region – likely associated with its topographic complexity – had a significant effect on the levels of genetic diversity and population dynamics, while the potential distribution of the species seems to be stable since the middle Holocene (6 kya). We conclude that in A. kerchovei there is a core group of populations in the Tehuacán Valley, and peripheric populations that appear to be evolving independently and thus the species is fundamentally an endemic species from the Tehuacán Valley while the populations outside the Valley appear to be in the process of incipient speciation. [ABSTRACT FROM AUTHOR]

Forestry systems in Mexico are examples of traditional management of land and biodiversity that integrates the use, conservation and restoration of forest elements. Current in situ management practices of Agave maximiliana in western Mexico include the tolerance of many forest elements, reintroduction of young Agave plants and germination of seeds. More intense forms of management include monocultures, which are agroindustrialized systems developed in more recent times and characterized by the establishment of high densities of A. maximiliana plants in deforested areas and abandoned agricultural lands. We compared monocultures, forestry systems and wild populations (i.e., non/slightly-exploited forests) in order to evaluate whether these practices have had an effect on intraspecific morphological and genetic variation and divergence. We also tested whether divergence has a positive relationship with environmental and geographic distance. We analyzed 16 phenotypic traits in 17 populations of A. maximiliana , and 14 populations were further examined by amplifying 9 SSR loci. We employed multivariate methods and analyses of variance in phenotypic and genetic traits to test whether clusters and the percentage of variation contained in the managed and wild categories can be identified. Tests of isolation by environment (IBE) and distance (IBD) were performed to detect the magnitude of divergence explained by climatic and geographic variables. We found that forestry systems are effective as reservoirs of morphological and genetic diversity, since they maintain levels similar to those of wild populations. Moreover, the monocultures showed similar levels, reflecting their recent emergence. While the species showed high morphological diversity (IMD = 0.638, SE ± 0.07), it had low to intermediate genetic diversity (A = 2.37, H E = 0.418). Similar morphological and genetic divergences were found among populations, but these were not correlated with each other in population pairs. Non-significant morphological differentiation was found among categories. Only IBE was significant in the genetic structure (β = 0.32, p = 0.007), while neither IBE nor IBD was detected in the morphological differentiation. We discuss the implications of these results in the context of the weaknesses and strengths of A. maximiliana in the face of the socio-ecological changes predicted for the study area in the short term. [ABSTRACT FROM AUTHOR]

Determining the effects of disturbance on genetic variation of plant populations is an important step in establishing conservation strategies for the survival of natural populations. Disturbance reduces effective population size, leading to lower variation through genetic drift. However, a plant species' life cycle will influence the magnitude and speed of the response to disturbance. In this report, genetic structure and variability are evaluated for Ceratozamia fuscoviridis , a critically endangered, endemic, long-lived cycad from Mexico, at four sites with different levels of disturbance. Genetic analysis was performed using intersimple sequence repeat (ISSR) and simple sequence repeat (SSR) markers. Populations 1 and 3 were classified as conserved (disturbance index [DI] = 3.11 ± 1.117) and populations 2 and 4 as disturbed ( D I = 6.37 ± 1.414). Levels of genetic diversity according to ISSR markers ranged from 0.169 to 0.279 for expected heterozygosity (H E), and the informative index (I) ranged from 0.266 to 0.425. In general, the genetic diversity measure with ISSRs was greater in the conserved sites than in the disturbed ones. For the SSRs, H E ranged from 0.711 to 0.793, while I ranged from 1.391 to 1.621. Genetic structure shown with these markers does not correspond with geographic distance but does correspond with the conservation state of the populations. We found that there is a negative effect of perturbation on the genetic diversity of C. fuscoviridis. The loss of diversity can lead to various processes such as inbreeding and genetic drift that, in the long term, can culminate in local extinctions. We propose that studies should aim to evaluate the genetic diversity of juveniles, as it is possible that disturbances result in changes in the biology of the species that lead to divergences in the genetic diversity of adults and earlier stages. [ABSTRACT FROM AUTHOR]

Context: The majority of remaining tropical forests exist as fragments embedded in a matrix of agricultural production. Understanding the effects of these agricultural landscapes on species dispersal is crucial in the development of successful conservation planning. Objective: The objective of this study was to examine the influence of five landscape features within a coffee agroecosystem (i.e., slope, elevation, streams, riparian effect, and tree cover) on Heteromys desmarestianus goldmani gene flow. We expected that landscape variables linked to more intense agricultural management (e.g., low tree cover, riparian effect) would reduce gene flow in H. d. goldmani. Methods: This study was conducted in a 4 km × 2 km area within the coffee growing region of Soconusco in Chiapas, Mexico. We used 12 microsatellite markers to calculate individual-based estimates of gene flow as a measure of dispersal. We used resistance surface modelling, using ResistanceGA (Peterman in Methods Ecol Evol 9:1638–1647, 2018) to identify if any of the landscape features analyzed explained the patterns of gene flow. Results: Our results showed patterns of population structure and weak isolation-by-distance, as found previously for H. d. goldmani by Otero Jiménez et al. (Conserv Genet 19:495–499, 2018). Slope and tree cover were the two landscape features that could best explain gene flow patterns. More specifically, intermediate slopes and tree cover represent the lowest resistance to gene flow for H. d. goldmani and, thus, have a role in promoting gene flow in this species. Conclusion: This study highlights the potential of integrating molecular and landscape data to explore population connectivity of elusive species, such as terrestrial small mammals. Our study adds to the growing body of literature in landscape genetics by demonstrating that a rodent species shows population structure at a small scale resulting from landscape factors linked to agricultural management. [ABSTRACT FROM AUTHOR]

Endangered Sonoran (Antilocapra americana sonoriensis) and Peninsular (A. a. peninsularis) pronghorn persist largely because of captive breeding and reintroduction efforts. Recovery team managers want to re‐establish pronghorn in their native range, but there is currently uncertainty regarding the subspecies status of extinct pronghorn populations that historically inhabited southern California, USA, and northern Baja California, Mexico. To address this uncertainty, we genotyped museum specimens and conducted phylogenetic and population genetic analyses of historical data in the context of 3 contemporary pronghorn populations. The historical northern Baja California pronghorn share the most ancestry with contemporary Peninsular pronghorn, whereas pronghorn in southern California share more ancestry with contemporary American (A. a. americana) pronghorn. For reintroductions into northern Baja California, the Peninsular subspecies is more appropriate based on museum genetic data. For reintroductions into Southern California, ecological and genetic factors are both important, as the subspecies most genetically related to historical populations (American) may not be well‐adapted to the hot, low‐elevation deserts of the reintroduction area. © 2019 The Wildlife Society. Extinct pronghorn populations in northern Baja California, Mexico, share ancestry with the contemporary Peninsular subspecies, justifying the release of captive bred endangered Peninsular pronghorn at sites in this area. Ancestry of extinct populations in southern California, USA, is less certain; therefore, ecological data and conservation goals should be prioritized in determining which subspecies to release into this area. [ABSTRACT FROM AUTHOR]

Population genetic structure can aide in developing conservation and management strategies by characterizing populations on local and regional scales. The Elegant Tern (Thalasseus elegans) has a restricted breeding range, with a majority of its nesting population historically found on Isla Rasa, Gulf of California, Mexico. Since the late 1950s, increased frequency of low marine productivity due to warm oceanographic anomalies, such as El Niño events, have caused northward expansion of Elegant Tern breeding colonies into southern California, USA. To test the hypothesis that high gene flow occurs between Gulf of California and southern California Elegant Tern breeding colonies, restriction-site associated DNA sequencing was used to analyze 5,510 single nucleotide polymorphisms from 69 Elegant Terns sampled across four known breeding sites: Isla Rasa, Mexico (n = 30), San Diego National Wildlife Refuge, USA (n = 17), Bolsa Chica Ecological Reserve, USA (n = 11), and Port of Los Angeles, USA (n = 11). Analyses revealed little population subdivision, with non-significant genetic differentiation (FST) among sites and no geographic association of individuals, but there was subtle clustering of individuals by breeding site. These results suggest a strong degree of gene flow among the Gulf of California and southern California nesting colonies and indicate that Elegant Terns have a fluid breeding distribution and move readily among nesting sites. [ABSTRACT FROM AUTHOR]

Incomplete or geographically biased sampling poses significant problems for research in phylogeography, population genetics, phylogenetics, and species delimitation. Despite the power of using genome-wide genetic markers in systematics and related fields, approaches such as the multispecies coalescent remain unable to easily account for unsampled lineages. The Empidonax difficilis / Empidonax occidentalis complex of small tyrannid flycatchers (Aves: Tyrannidae) is a classic example of widely distributed species with limited phenotypic geographic variation that was broken into two largely cryptic (or "sibling") lineages following extensive study. Though the group is well-characterized north of the US Mexico border, the evolutionary distinctiveness and phylogenetic relationships of southern populations remain obscure. In this article, we use dense genomic and geographic sampling across the majority of the range of the E. difficilis/E. occidentalis complex to assess whether current taxonomy and species limits reflect underlying evolutionary patterns, or whether they are an artifact of historically biased or incomplete sampling. We find that additional samples from Mexico render the widely recognized species-level lineage E. occidentalis paraphyletic, though it retains support in the best-fit species delimitation model from clustering analyses. We further identify a highly divergent unrecognized lineage in a previously unsampled portion of the group's range, which a cline analysis suggests is more reproductively isolated than the currently recognized species E. difficilis and E. occidentalis. Our phylogeny supports a southern origin of these taxa. Our results highlight the pervasive impacts of biased geographic sampling, even in well-studied vertebrate groups like birds, and illustrate what is a common problem when attempting to define species in the face of recent divergence and reticulate evolution. [ABSTRACT FROM AUTHOR]

Since their introduction to Mexico goats have undergone a long process of adaptation and selection, resulting in highly rustic local animals. However, importation of improved breeds has led to the extinction of some regional breeds. For example, the Criolla Negra goat breed is known for its rusticity and high milk quality, but is in decline. A genetic characterization was done of a Criolla Negra population. Hair samples were collected in three goat herds located in different municipalities of the state of Querétaro, Mexico: Cadereyta de Montes (n= 7); El Marqués (n= 11); and San Juan del Río (n= 27). Thirty microsatellites were used to quantify the number of alleles per marker (NA), median number of alleles (MNA), number of effective alleles (NEA), observed heterozygosis (Ho), expected heterozygosis (He), polymorphic data content (PDC), the fixation index (FIS) and Hardy Weinberg equilibrium (HWE). The Criolla Negra population was compared to thirteen breeds forming part of the BioGoat project. Genetic diversity was found to be high in this population. A total of 243 alleles were identified with an MNA of 8.1 alleles per marker. The markers were informative (PDC= 0.06) for polymorphism. The He (0.71) and Ho (0.62) values indicate a slight imbalance in the population. Reynolds genetic distance results showed the Criolla Negra breed to be genetically furthest from the Anglonubia breed and nearest the Murciano-Granadina breed. The studied Criolla Negra goat population exhibits a breed structure well differentiated from the other breeds in the analysis. [ABSTRACT FROM AUTHOR]

Summary: Pseudomonas aeruginosa is a widely distributed environmental bacterium but is also an opportunistic pathogen that represents an important health hazard due to its high intrinsic antibiotic resistance and its production of virulence factors. The genetic structure of P. aeruginosa populations using whole genome sequences shows the existence of three clades, one of which (PA7 clade) has a higher genetic diversity. These three clades include clinical and environmental isolates that are very diverse in terms of geographical origins and isolation date. Here, we report the characterization of two distinct clonal P. aeruginosa groups that form a part of the PA14 clade (clade 2) sampled from the Churince system in Cuatro Ciénegas Basin (CCB). One of the clonal groups that we report here was isolated in 2011 (group 2A) and was displaced by the other clonal group (2B) in 2015. Both Churince groups are unable to produce pyoverdine but can produce other virulence‐associated traits. The existence of these unique P. aeruginosa clonal groups in the Churince system is of ecological and evolutionary significance since the microbiota of this site is generally very distinct from other lineages, and this is the first time that a population of P. aeruginosa has been found in CCB. [ABSTRACT FROM AUTHOR]

Investigating how crop domestication and early farming mediated crop attributes, distributions, and interactions with antagonists may shed light on today's agricultural pest problems. Crop domestication generally involved artificial selection for traits desirable to early farmers, for example, increased productivity or yield, and enhanced qualities, though invariably it altered the interactions between crops and insects, and expanded the geographical ranges of crops. Thus, some studies suggest that with crop domestication and spread, insect populations on wild crop ancestors gave rise to pestiferous insect populations on crops. Here, we addressed whether the emergence of corn leafhopper (Dalbulus maidis) as an agricultural pest may be associated with domestication and early spread of maize (Zea mays mays). We used AFLP markers and mitochondrial COI sequences to assess population genetic structuring and haplotype relationships among corn leafhopper samples from maize and its wild relative Zea diploperennis from multiple locations in Mexico and Argentina. We uncovered seven corn leafhopper haplotypes contained within two haplogroups, one haplogroup containing haplotypes associated with maize and the other containing haplotypes associated with Z. diploperennis in a mountainous habitat. Within the first haplogroup, one haplotype was predominant across Mexican locations, and another across Argentinean locations; both were considered pestiferous. We suggested that the divergence times of the maize‐associated haplogroup and of the "pestiferous" haplotypes are correlated with the chronology of maize spread following its domestication. Overall, our results support a hypothesis positing that maize domestication favored corn leafhopper genotypes preadapted for exploiting maize so that they became pestiferous, and that with the geographical expansion of maize farming, corn leafhopper colonized Z. diploperennis, a host exclusive to secluded habitats that serves as a refuge for archaic corn leafhopper genotypic diversity. Broadly, our results help explain the extents to which crop domestication and early spread may have mediated the emergence of today's agricultural pests. [ABSTRACT FROM AUTHOR]

Introduction: Defoliation and light competition are ubiquitous stressors that can strongly limit plant performance. Tolerance to defoliation is often associated with compensatory growth, which could be positively or negatively related to plant growth. Genetic variation in growth, tolerance and compensation, in turn, plays an important role in the evolutionary adaptation of plants to changing disturbance regimes but this issue has been poorly investigated for long-lived woody species. We quantified genetic variation in plant growth and growth parameters, tolerance to defoliation and compensation for a population of the understorey palm Chamaedorea elegans. In addition, we evaluated genetic correlations between growth and tolerance/compensation. Methods: We performed a greenhouse experiment with 711 seedlings from 43 families with twelve or more individuals of C. elegans. Seeds were collected in southeast Mexico within a 0.7 ha natural forest area. A two-third defoliation treatment (repeated every two months) was applied to half of the individuals to simulate leaf loss. Compensatory responses in specific leaf area, biomass allocation to leaves and growth per unit leaf area were quantified using iterative growth models. Results: We found that growth rate was highly heritable and that plants compensated strongly for leaf loss. However, genetic variation in tolerance, compensation, and the individual compensatory responses was low. We found strong correlations between family mean growth rates in control and defoliation treatments. We did not find indications for growth-tolerance/compensation trade-offs: genetic correlation between tolerance/compensation and growth rate were not significant. Implications: The high genetic variation in growth rate, but low genetic variation in tolerance and compensation observed here suggest high ability to adapt to changes in environment that require different growth rates, but a low potential for evolutionary adaptation to changes in damage or herbivory. The strong correlations between family mean growth rates in control and defoliation treatments suggest that performance differences among families are also maintained under stress of disturbance. [ABSTRACT FROM AUTHOR]

Nymphoides species are cosmopolitan aquatics with floating leaves and frequent in freshwater wetlands. Nymphoides fallax is restricted to highlands of Mexico and Guatemala. We tested the transferability of 10 microsatellite loci previously developed for N. peltata in 18 populations of N. fallax. Seven polymorphic loci were successfully amplified. Allele sizes were automatically obtained using 2100 Bioanalyzer Expert software. Genotypes were determined using the allele dosage method. Chromosome counts confirmed that N. fallax is a tetraploid. Alleles per locus ranged from 5 to 17; the observed and expected heterozygosities per population ranged from 0.51 to 0.66 and from 0.72 to 0.81, respectively. We observed higher genetic diversity within populations (92%) than among populations (8%). Our results show that cross-amplification is a valid technique for studying Nymphoides. No clones were found, indicating that N. fallax relies heavily on sexual reproduction. Our work may stimulate further population genetic studies of the genus Nymphoides that could be useful for conservation programs, as well as to promote additional research on landscape genetics and reproductive mechanisms in aquatic plants. [ABSTRACT FROM AUTHOR]

In Mexico, the American horseshoe crab, Limulus polyphemus, is regarded as in danger of extinction, with a distribution range limited to the Yucatan Peninsula. Population genetics knowledge of this species in Mexico is incipient. We conducted a base-line genetic survey of eight localities on the northern coast of the Yucatan Peninsula to assess patterns of genetic structure, genetic variation, and gene flow among these localities. We analyzed DNA samples from 190 L. polyphemus specimens using 14 nuclear-encoded microsatellites and a region of the mitochondrial Cytochrome Oxidase I (COI) gene. Total allelic richness was 5.432, similar to previous figures for populations at the northern and southern extremes of the species' global distribution. Observed heterozygosities (Ho) were 0.540–0.590, while expected heterozygosities (He) were 0.479–0.532, and there was no evidence of population bottlenecks. We found 129 mtDNA haplotypes (121 of which were found in single individuals) and 275 polymorphic sites, and the mean haplotype diversity among sites was high (0.852 ± 0.027 SD). AMOVAs based on both microsatellite and mtDNA data revealed that L. polyphemus from the northern Yucatan Peninsula show low genetic structure (Fst < 0.05, p > 0.05) and high gene flow (Nm = 10.967) favored by the absence of geographic barriers between coastal lagoons, suggesting that they constitute a single population. This was further confirmed by discriminant analyses of principal components using microsatellite data. This information is useful in establishing coordinated conservation efforts among federal and state protected areas. [Display omitted] • We analyzed DNA of 190 Limulus polyphemus specimens using 14 microsatellites and a region of the COI gene. • Population genetics analyses revealed that L. polyphemus from the northern Yucatan Peninsula show low genetic structure (Fst < 0.05, p > 0.05). • Horseshoe crabs inhabiting the northern coast of the Yucatan Peninsula constitute a single population. • Based on our results, the studied population should be considered a single management unit. [ABSTRACT FROM AUTHOR]

We studied HLA class I (HLA-A , -B) and class II (HLA-DRB1 , -DQB1) alleles by PCR-SSP based typing in 144 Mexicans from the state of Guerrero to obtain information regarding allelic and haplotypic frequencies. We find that the ten most frequent haplotypes in the state of Guerrero include eight Native American and two European haplotypes. Admixture estimates revealed that the main genetic components in the state of Guerrero are Native American (61.36 ± 2.69% by ML; 54.17% of Native American haplotypes) and European (35.01 ± 4.59% by ML; 32.29% of European haplotypes), and a relatively low African genetic component (3.63 ± 2.38% by ML; 5.90% of African haplotypes). [ABSTRACT FROM AUTHOR]

Copyright of Revista Ciencias de la Salud is the property of Colegio Mayor de Nuestra Senora del Rosario and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Background: Genotyping and georeferencing in tuberculosis (TB) have been used to characterize the distribution of the disease and occurrence of transmission within specific groups and communities. Objective: The objective of this study was to test the hypothesis that diabetes mellitus (DM) and pulmonary TB may occur in spatial and molecular aggregations. Material and methods: Retrospective cohort study of patients with pulmonary TB. The study area included 12 municipalities in the Sanitary Jurisdiction of Orizaba, Veracruz, México. Patients with acid-fast bacilli in sputum smears and/or Mycobacterium tuberculosis in sputum cultures were recruited from 1995 to 2010. Clinical (standardized questionnaire, physical examination, chest X-ray, blood glucose test and HIV test), microbiological, epidemiological, and molecular evaluations were carried out. Patients were considered “genotype-clustered” if two or more isolates from different patients were identified within 12 months of each other and had six or more IS6110 bands in an identical pattern, or < 6 bands with identical IS6110 RFLP patterns and spoligotype with the same spacer oligonucleotides. Residential and health care centers addresses were georeferenced. We used a Jeep hand GPS. The coordinates were transferred from the GPS files to ArcGIS using ArcMap 9.3. We evaluated global spatial aggregation of patients in IS6110-RFLP/ spoligotype clusters using global Moran´s I. Since global distribution was not random, we evaluated “hotspots” using Getis-Ord Gi* statistic. Using bivariate and multivariate analysis we analyzed sociodemographic, behavioral, clinic and bacteriological conditions associated with “hotspots”. We used STATA® v13.1 for all statistical analysis. Results: From 1995 to 2010, 1,370 patients >20 years were diagnosed with pulmonary TB; 33% had DM. The proportion of isolates that were genotyped was 80.7% (n = 1105), of which 31% (n = 342) were grouped in 91 genotype clusters with 2 to 23 patients each; 65.9% of total clusters were small (2 members) involving 35.08% of patients. Twenty three (22.7) percent of cases were classified as recent transmission. Moran`s I indicated that distribution of patients in IS6110-RFLP/spoligotype clusters was not random (Moran`s I = 0.035468, Z value = 7.0, p = 0.00). Local spatial analysis showed statistically significant spatial aggregation of patients in IS6110-RFLP/spoligotype clusters identifying “hotspots” and “coldspots”. GI* statistic showed that the hotspot for spatial clustering was located in Camerino Z. Mendoza municipality; 14.6% (50/342) of patients in genotype clusters were located in a hotspot; of these, 60% (30/50) lived with DM. Using logistic regression the statistically significant variables associated with hotspots were: DM [adjusted Odds Ratio (aOR) 7.04, 95% Confidence interval (CI) 3.03–16.38] and attending the health center in Camerino Z. Mendoza (aOR18.04, 95% CI 7.35–44.28). Conclusions: The combination of molecular and epidemiological information with geospatial data allowed us to identify the concurrence of molecular clustering and spatial aggregation of patients with DM and TB. This information may be highly useful for TB control programs. [ABSTRACT FROM AUTHOR]

Copyright of Revista Mexicana de Biodiversidad is the property of Universidad Nacional Autonoma de Mexico, Instituto de Biologia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Understanding the genetic structure of Native American populations is important to clarify their diversity, demographic history, and to identify genetic factors relevant for biomedical traits. Here, we show a demographic history reconstruction from 12 Native American whole genomes belonging to six distinct ethnic groups representing the three main described genetic clusters of Mexico (Northern, Southern, and Maya). Effective population size estimates of all Native American groups remained below 2,000 individuals for up to 10,000 years ago. The proportion of missense variants predicted as damaging is higher for undescribed (~30%) than for previously reported variants (~15%). Several variants previously associated with biological traits are highly frequent in the Native American genomes. These findings suggest that the demographic and adaptive processes that occurred in these groups shaped their genetic architecture and could have implications in biological processes of the Native Americans and Mestizos of today. [ABSTRACT FROM AUTHOR]

Background: Mycale cecilia is an abundant Eastern Tropical Pacific sponge living in a wide variety of habitats, including coral reefs where it may directly interact with corals. It is also known to possess secondary metabolites of pharmacological value. These aspects highlight the importance of having a better understanding of its biology, and genetic and population diversity., Methods and Results: In the present study, we isolated and characterized twelve novel microsatellite loci by Illumina MiSeq sequencing. The loci were tested in 30 specimens collected from two coral reef localities (La Paz, Baja California Sur and Isabel Island, Nayarit) from the Mexican Pacific using M13(-21) labeling. All loci were polymorphic, with two to nine alleles per locus. Expected heterozygosities varied from 0.616 to 0.901. Eleven loci were tested and successfully amplified in M. microsigmatosa from the Gulf of Mexico., Conclusion: Here we report the first microsatellite loci developed for a sponge species from the Eastern Pacific coast. These molecular markers will be used for population genetic studies of M. cecilia, and potentially in other congeneric species; particularly in vulnerable marine areas that require protection, such as coral reefs., (© 2023. The Author(s).)

Blastocystis sp. is a widespread microorganism that colonizes the intestinal tract of several animals, including human beings, while its pathogenic role in humans is still under debate. The objective of the present study was to describe the frequency of Blastocystis sp. subtypes (STs) and their genetic variation within and among samples recovered from scholars inhabiting two rural villages with tropical climates and compare this information with previously documented data from arid and temperate zones in Mexico. Blastocystis sp. positive samples and ST identification were achieved by coprological analysis screening and Polymerase Chain Reaction-sequencing, respectively. Classical population genetics indexes (nucleotide diversity (π), haplotype polymorphism (θ), gene flow (Nm), genetic differentiation (ST), and Tajima's D) were calculated by comparing the sequences here obtained (n = 42) and those from previous studies from the arid (n = 80) and temperate (n = 61) climates from Mexico. Although Blastocystis sp. was the parasite most frequently found between 33% and 26% in both communities, only STs 1–3 were found. Haplotype network inference of Blastocystis sp. STs showed different haplotype profiles among STs vs. climate zones, although no specific haplotypes were identified for any particular climatic zone. Population genetics indexes showed different values within STs and climate zones (π and θ values ranged from 0.004 to 0.147; Nm > 4 and ST from 0.006 to 0.12). Our results show that Blastocystis sp. subtypes exhibit a different genetic variability profile according to the climate zone, suggesting a balancing process between the genetic variability within the Blastocystis sp. subtype and the number of haplotypes identified in each climate. • Blastocystis sp. subtypes (STs) 1–3 in rural communities of south-southeastern Mexico are reported for the first time. • Each Blastocystis sp. ST showed a different genetic variability depending on the climate zone. • A balancing process in the genetic variability within subtypes and their haplotypes in each climate zone may occur. [ABSTRACT FROM AUTHOR]