Whole-organism community DNA (wocDNA) metabarcoding has become a necessary and powerful tool to study mixed communities from bulk samples by detecting short DNA sequences. This review integrates the use of arthropods as ecological indicators through wocDNA metabarcoding, covering key methodological aspects from sampling design to bioinformatics, and highlighting ASV-based (Amplicon Sequence Variants) pipelines for incorporating haplotype-level variation. The success of wocDNA metabarcoding relies on proper sampling methods, good laboratory practices, cleaning of bulk samples, selecting suitable arthropod sizes, efficient DNA extractions, accurate library quantification, appropriate genetic markers for accurate taxonomic identification, and effective sequence filtering. Incorporating haplotype data into monitoring unveils intraspecific variation that could complement species-level diversity, thus enhancing conventional analyses. Choosing abundance- or incidence-based approaches is key for selecting appropriate statistical methods. WocDNA metabarcoding provides biodiversity estimates for entire communities and allows researchers to derive insights that can inform the formulation or refinement of hypotheses. These refined hypotheses, based on the obtained biodiversity estimates, can then guide ecosystem conservation.

The Mexican fruit fly, Anastrepha ludens is an important pest that causes widespread damage to a number of fruit crops in Mexico. The Sterile Insect Technique (SIT) is commonly used for its control. However, the existence of natural barriers can give rise to a population structure in neutral loci and possibly behavioral or adaptive traits that interfere with SIT. For this reason, it is important to understand the genetic diversity and structure of A. ludens populations and to better understand the evolutionary ecology and population processes in view of possible expansions and possible host shifts due to climate change. We genotyped nine nuclear DNA (nDNA) microsatellite loci among fruit fly populations collected from five biogeographic areas within Mexico, Mexican Plateau, the Northeastern Coastal Plain, the Pacific Coast, the Gulf Coast of Mexico, the Soconusco and a laboratory strain. The nuclear genetic diversity was moderate (from He = 0.34 to He = 0.39) within the wild mexfly population. We found that populations were clustered in three genetic groups (K=3). The diversity and genetic structure of A. ludens are produced by environmental and geological conditions as well as local conditions like anthropogenic perturbation which would produce population expansion and the existence of possible predators that would affect the population density. Gene flow showed recent migration among populations. The laboratory strain showed less diversity than the wild samples. Large values of current and ancestral population size suggest high resistance to climatic changes, probably due to biological attributes, such as its polyphagous, multivoltine and high dispersal characteristics. In particular ecosystem fragmentation and perturbation as well as the existence of new plant hosts all of which would probably increase the abundance of flies.

1. Tropical ectotherm species tend to have narrower physiological limits than species from temperate areas. As a consequence, tropical species are considered highly vulnerable to climate change since minor temperature increases can push them beyond their physiological thermal tolerance. Differences in physiological tolerances can also be seen at finer evolutionary scales, such as among populations of ectotherm species along elevation gradients, highlighting the physiological sensitivity of such organisms. 2. Here we analyze the influence of elevation and bioclimatic domains, defined by temperature and precipitation, on thermal sensitivities of a terrestrial direct-developing frog (Craugastor loki) in a tropical gradient. We address the following questions: i) Does preferred temperature vary with elevation and among bioclimatic domains? ii) Do thermal tolerance limits, i.e. critical thermal maximum and critical thermal minimum vary with elevation and bioclimatic domains?, and iii) Are populations from high elevations more vulnerable to climate warming?  3. We found that along an elevation gradient body temperature decreases as environmental temperature increases. The preferred temperature tends to moderately increase with elevation within the sampled bioclimatic domains. Our results indicate that the ideal thermal landscape for this species is located at mid-elevations, where the thermal accuracy (db) and thermal quality of the environment (de) are suitable. The critical thermal maximum is variable across elevations and among the bioclimatic domains, decreasing as elevation increases. Conversely, the critical thermal minimum is not as variable as the critical thermal maximum.  4. Populations from the lowlands may be more vulnerable to future increases in temperature. We highlight that the critical thermal maximum is related to high temperatures exhibited across the elevation gradient and within in each bioclimatic domain, therefore, it is a response to high environmental temperatures.

Neutral theory proposes that dispersal stochasticity is one of the main drivers of local diversity. Haplotypes-level genetic variation can now be efficiently sampled from across whole communities, thus making it possible to test neutral predictions from the genetic to species-level diversity, and higher. However, empirical data is still limited, with the few studies to date coming from temperate latitudes. Here, we focus on a tropical mountain within the Transmexican Volcanic Belt to evaluate spatially fine-scale patterns of arthropod community assembly to understand the role of dispersal limitation and landscape features as drivers of diversity. We sampled whole-communities of arthropods for eight orders at a spatial scale ranging from 50 m to 19 km, using whole community metabarcoding. We explored multiple hierarchical levels, from individual haplotypes to lineages at 0.5, 1.5, 3, 5, 7.5% similarity thresholds, to evaluate patterns of richness, turnover, and distance decay of similarity with isolation-by-distance and isolation-by-resistance (costs to dispersal given by landscape features) approaches. Our results showed that distance and altitude influence distance decay of similarity at all hierarchical levels. This holds for arthropod groups of contrasting dispersal abilities, but with different strength depending on the spatial scale. Our results support a model where local-scale differentiation mediated by dispersal constraints, combined with long-term persistence of lineages, is an important driver of diversity within tropical sky islands.

Eradication of herbivores, due to human disturbances, produces a demographic outburst of highly competitive prey species, which in turn reduces plant species diversity. This happens at Los Tuxtlas tropical rainforest, Mexico, where a population outburst of the understory palm Astrocaryum mexicanum is ostensibly excluding tree species, but how this is occurring is still unknown. We used a neighborhood approach to explore the effects of palm shading and palm crowding on the survival and growth (RGR) of saplings of six common tree species. Sixteen to 32 saplings (1.5-2.5 m height) per species were used as focal individuals of circular neighborhoods (4 m radius), which included palms ≥ 1cm stem length potentially competing for light or soil resources. Shading was estimated using hemispherical photographs. Overall, survivorship was high combining all species (93.8%/yr). In most species shading produced a displacement of the crown, which increased with specific leaf area of species. In three species shading had a negative effect on RGR without any effect of crowding, the contrary occurred in two species, and in one species no effects were found. No effects due to trees (DBH ≥ 1cm) crowding were detected. The shading effect increased with species leaf dry matter content (LDMC), while the effect of crowding declined with LDMC and increased with sapling total leaf area. We argue that the species-dependent palm shading/crowding effects were related to the shade tolerance of sapling species. In the long-term such species-specific responses could have consequences for forest structure and composition, as saplings develop to mature stages.

The widespread use of genomic tools has allowed for a deeper understanding of the genetics and the evolutionary dynamics of domestication. Recent studies have suggested that multiple domestications and introgression are more common than previously thought. However, the ability to correctly infer the domestication process depends on having an adequate representation of wild relatives. Cultivated maize (Zea mays spp. mays) is one of the most important crops in the world, with a long and a relatively well documented history of domestication. The current consensus points towards a single domestication event from teosinte Zea mays spp. parviglumis from the Balsas Basin in Southwest central Mexico. However, the underlying diversity of teosintes from lowlands Z. mays spp. parviglumis and highlands Zea mays spp. mexicana) was not taken into account in early studies. We used 32,739 SNPs obtained from 29 teosinte populations and 43 maize landraces to explore the relationship between wild and cultivated members of Zea. We then inferred levels of gene flow among teosinte populations and maize, the degree of population structure of Zea mays subspecies, and potential domestication location of maize. We confirmed a strong geographic structure within Z. mays spp. parviglumis and documented multiple gene flow events with other members of the genus, including an event between Z. mays spp. mexicana and maize. Our results suggest that the likely ancestor of maize may have been domesticated not in the Balsas Basin as previously thought, but in Jalisco or in the Pacific coast, and that different populations of the teosinte subspecies have contributed to modern maize’s gene pool. Our results points towards a long period of domestication marked by gene flow with wild relatives, making domestication a long and ongoing process.

The runner bean is a legume species from Mesoamerica closely related to common bean (Phaseolus vulgaris). It is a perennial species, but it is usually cultivated in small-scale agriculture as an annual crop for its dry seeds and edible immature pods. Unlike the common bean, P. coccineus has received little attention from a genetic standpoint. In this work we aim to (1) provide information about the domestication history and domestication events of P. coccineus; (2) examine the distribution and level of genetic diversity in wild and cultivated Mexican populations of this species; and, (3) identify candidate loci to natural and artificial selection. For this, we generated genotyping by sequencing data (42,548 SNPs) from 242 individuals of P. coccineus and the domesticated forms of the closely related species P. vulgaris (20) and P. dumosus (35). Eight genetic clusters were detected, of which half corresponds to wild populations and the rest to domesticated plants. The cultivated populations conform a monophyletic clade, suggesting that only one domestication event occurred in Mexico, and that it took place around populations of the Trans-Mexican Volcanic Belt. No difference between wild and domesticated levels of genetic diversity was detected and effective population sizes are relatively high, supporting a weak genetic bottleneck during domestication. Most populations presented an excess of heterozygotes, probably due to inbreeding depression. One population of P. coccineus subsp. striatus had the greatest excess and seems to be genetically isolated despite being geographically close to other wild populations. Contrasting with previous studies, we did not find evidence of recent gene flow between wild and cultivated populations. Based on outlier detection methods, we identified 24 domestication-related SNPs, 13 related to cultivar diversification and eight under natural selection. Few of these SNPs fell within annotated loci, but the annotated domestication-related SNPs are highly expressed in flowers and pods. Our results contribute to the understanding of the domestication history of P. coccineus, and highlight how the genetic signatures of domestication can be substantially different between closely related species.

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

Tropical mountains are areas of high species richness and endemism. Two historical phenomena may have contributed to this: (1) fragmentation and isolation of habitats may have promoted the genetic differentiation of populations and increased the possibility of allopatric divergence and speciation, and; (2) the mountain areas may have allowed long-term population persistence during global climate fluctuations. These two phenomena have been studied using either species occurrence data or estimating species divergence times. However, only few studies have used intraspecific genetic data to analyse the mechanisms by which endemism may emerge at the microevolutionary scale. Here, we use landscape analysis of genomic SNP data sampled from two high-elevation plant species from an archipelago of tropical sky-islands (the Transmexican Volcanic Belt) to test for population genetic differentiation, synchronous demographic changes and habitat persistence. We show that genetic differentiation can be explained by the degree of glacial habitat connectivity among mountains, and that mountains have facilitated the persistence of populations throughout glacial/interglacial cycles. Our results support the ongoing role of tropical mountains as cradles for biodiversity by uncovering cryptic differentiation and limits to gene flow.

The present dataset comprises 36,931 SNPs genotyped in 46 maize landraces native to Mexico as well as the teosinte subspecies Zea maiz ssp. Parviglumis and ssp. Mexicana. These landraces were collected directly from farmers mostly between 2006 and 2010. We accompany these data with a short description of the variation within each landrace, as well as maps, principal component analyses and neighbor joining trees showing the distribution of the genetic diversity relative to landrace, geographical features and maize biogeography. High levels of genetic variation were detected for the maize landraces (HE = 0.234 to 0.318 (mean 0.311), while slightly lower levels were detected in Zea m. mexicana and Zea m. parviglumis (HE = 0.262 and 0.234, respectively). The distribution of genetic variation was better explained by environmental variables given by the interaction of altitude and latitude than by landrace identity. This dataset is a following up product of the Global Native Maize Project, an initiative to update the data on Mexican maize landraces and their wild relatives, and to generate information that is necessary for implementing the Mexican Biosafety Law.