Aim To evaluate the genetic diversity and phylogeographical structure of Boa constrictor imperator, in order to identify the key historical events responsible for its current distribution and diversity. Location The Neotropical region of Mexico and mainland Central America. Methods We used data from the mitochondrial cytochrome b gene, nuclear ornithine decarboxylase intron and microsatellites to perform spatial genetic analyses, and coalescence methods to infer phylogeographical structure, divergence times and historical demography. Results Cytochrome b results revealed two main reciprocally monophyletic lineages, one along the Mexican Pacific coast and another along the Gulf of Mexico, Yucatán Peninsula and Central America, diverging c. 5.2 Ma. Both lineages are subdivided into haplogroups and show steady historical growth and a more recent population expansion. High genetic diversity was observed for both cytochrome b (h = 0.944) and microsatellites (HNei = 0.810–0.900). Main conclusions We demonstrate deep phylogeographical structure with two reciprocally monophyletic lineages and five genetic clusters in Mexico and Central America. Our results suggest that several geographical barriers (including the Trans‐Mexican Volcanic Belt and the Motagua–Polochic–Jocotán faults) and ecological features generated this structure. We report genetic diversity values for the boa at a regional scale and suggest that the two lineages may be considered distinct species.

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.

Interspecific hybridization can lead to adaptation and speciation, especially in the context of recent radiations. The emblematic Crocodylus (true crocodiles) is the most broadly distributed, ecologically diverse, and species-rich crocodylian genus. Nonetheless, their within-species evolutionary processes are poorly resolved mainly due to their potential for hybridization. Notably, the evolutionary outcomes when hybridization is ancient and involves long-lived species, like crocodiles, remain largely unexplored. Here, we evaluate the genomic admixture between the American (Crocodylus acutus) and the Morelet's (Crocodylus moreletii) species, and demonstrate that this hybridization system challenges the definition of species boundaries and poses a triple conservation conundrum: what has been recognized as C. acutus is actually two distinct species, therefore its taxonomic reassessment is needed; we identified two evolutionary distinct hybrids lineages, which are genetically discernible from the parental species; the remaining C. moreletii populations evidence its likely extinction as a species and/or evolution via hybridization. Hence, the crocodiles' distinct species and hybrids lineages warrant recognition and need urgent conservation efforts.