Multiple introgression events during the diversification history of the edible Mexican grasshopper genus Sphenarium (Orthoptera: Pyrgomorphidae).

Speciation with gene flow often leads to ambiguous phylogenetic reconstructions, reticulate patterns of relatedness and conflicting nuclear versus mitochondrial (mt) lineages. Here we employed a fragment of the COI mtDNA gene and nuclear genome-wide data (3RAD) to assess the diversification history of Sphenarium, an orthopteran genus of great economic importance in Mexico that is presumed to have experienced hybridisation events in some of its species. We carried out separate phylogenetic analyses to evaluate the existence of mito-nuclear discordance in the species relationships, and also assessed the genomic diversity and population genomic structure and investigated the existence of interspecific introgression and species limits of the taxa involved based on the nuclear dataset. The species delineation analyses discriminated all the currently recognised species, but also supported the existence of four undescribed species. The mt and nuclear topologies had four discordant species relationships that can be explained by mt introgression, where the mt haplotypes of S. purpurascens appear to have replaced those of S. purpurascens A and B, S. variabile and S. zapotecum. Moreover, our analyses supported the existence of nuclear introgression events between four species pairs that are distributed in the Sierra Madre del Sur province in southeast Mexico, with three of them occurring in the Tehuantepec Isthmus region. Our study highlights the relevance of genomic data to address the relative importance of allopatric isolation versus gene flow in speciation.

Genome and cuticular hydrocarbon-based species delimitation shed light on potential drivers of speciation in a Neotropical ant species complex.

Geographic separation that leads to the evolution of reproductive isolation between populations generally is considered the most common form of speciation. However, speciation may also occur in the absence of geographic barriers due to phenotypic and genotypic factors such as chemical cue divergence, mating signal divergence, and mitonuclear conflict. Here, we performed an integrative study based on two genome-wide techniques (3RAD and ultraconserved elements) coupled with cuticular hydrocarbon (CHC) and mitochondrial (mt) DNA sequence data, to assess the species limits within the Ectatomma ruidum species complex, a widespread and conspicuous group of Neotropical ants for which heteroplasmy (i.e., presence of multiple mtDNA variants in an individual) has been recently discovered in some populations from southeast Mexico. Our analyses indicate the existence of at least five distinct species in this complex: two widely distributed across the Neotropics, and three that are restricted to southeast Mexico and that apparently have high levels of heteroplasmy. We found that species boundaries in the complex did not coincide with geographic barriers. We therefore consider possible roles of alternative drivers that may have promoted the observed patterns of speciation, including mitonuclear incompatibility, CHC differentiation, and colony structure. Our study highlights the importance of simultaneously assessing different sources of evidence to disentangle the species limits of taxa with complicated evolutionary histories.

Phylogenomics of the Mesoamerican alligator-lizard genera Abronia and Mesaspis (Anguidae: Gerrhonotinae) reveals multiple independent clades of arboreal and terrestrial species.

Abronia and Mesaspis are two of the five anguid lizard genera in the subfamily Gerrhonotinae. Their members are restricted to Mesoamerica, and most have allopatric distributions. Species of Abronia are primarily arboreal and occur in cloud and seasonally dry pine-oak forests, whereas those of Mesaspis are terrestrial and inhabit mesic microhabitats of montane forests. Recent molecular studies suggest that although these genera together form a monophyletic group, neither genus is monophyletic. Here we performed a phylogenetic study of Abronia and Mesaspis based on the most comprehensive taxonomic sampling of these genera to date and double digest restriction site-associated (ddRADseq) data. Our reconstructed phylogeny differed considerably from all previously published topologies, consistently recovering multiple independent clades of arboreal and terrestrial species and Abronia and Mesaspis as non-monophyletic. Geography, rather than current taxonomy, provides the best explanation of their phylogenetic relationships. Our analyses consistently recovered two main clades, distributed on the highlands of Middle America east and west of the Isthmus of Tehuantepec, respectively, and each composed of subclades of Abronia and Mesaspis. In the former main clade, members of the subgenus Auriculabronia formed the sister taxon to the Mesaspis moreletii complex, whereas the main clade west of the Isthmus was composed of two clades with a subclade of Abronia and another of Mesaspis each (one clade on the Atlantic versant of the main mountain ranges of eastern Mexico and another one on the Sierra Madre del Sur exclusive of its Atlantic versant) and a third clade with species of the subgenera Abronia and Scopaeabronia. We discuss the taxonomic implications of our results for the classification of the examined taxa and list the morphological characters that diagnose the recovered clades. This study highlights the utility of ddRADseq data to reconstruct the evolutionary history of supraspecific vertebrate taxa.

Extensive mitochondrial heteroplasmy in the neotropical ants of the Ectatomma ruidum complex (Formicidae: Ectatomminae).

We assembled mitogenomes from 21 ant workers assigned to four morphospecies (E. ruidum spp. 1-4) and putative hybrids of the Ectatomma ruidum complex (E. ruidum spp. 2x3), and to E. tuberculatum using NGS data. Mitogenomes from specimens of E. ruidum spp. 3, 4 and 2 × 3 had a high proportion of polymorphic sites. We investigated whether polymorphisms in mitogenomes are due to nuclear mt paralogues (numts) or due to the presence of more than one mitogenome within an individual (heteroplasmy). We did not find loss of function signals in polymorphic protein-coding genes, and observed strong evidence for purifying selection in two haplotype-phased genes, which indicate the presence of two functional mitochondrial genomes coexisting within individuals instead of numts. Heteroplasmy due to hybrid paternal leakage is not supported by phylogenetic analyses. Our results reveal the presence of a fast-evolving secondary mitochondrial lineage of uncertain origin in the E. ruidum complex.

Phylogenomics and species delimitation in the knob-scaled lizards of the genus Xenosaurus (Squamata: Xenosauridae) using ddRADseq data reveal a substantial underestimation of diversity.

Middle American knob-scaled lizards of the genus Xenosaurus are a unique radiation of viviparous species that are generally characterized by a flattened body shape and a crevice-dwelling ecology. Only eight species of Xenosaurus, one of them with five subspecies (X. grandis), have been formally described. However, species limits within Xenosaurus have never been examined using molecular data, and no complete phylogeny of the genus has been published. Here, we used ddRADseq data from all of the described and potentially undescribed taxa of Xenosaurus to investigate species limits, and to obtain a phylogenetic hypothesis for the genus. We analyzed the data using a variety of phylogenetic models, and were able to reconstruct a well-resolved and generally well-supported phylogeny for this group. We found Xenosaurus to be composed of four major, allopatric clades concordant with geography. The first and second clades that branch off the tree are distributed on the Atlantic slopes of the Sierra Madre Oriental and are composed of X. mendozai, X. platyceps, and X. newmanorum, and X. tzacualtipantecus and an undescribed species from Puebla, respectively. The third clade is distributed from the Atlantic slopes of the Mexican Transvolcanic Belt in west-central Veracruz south to the Pacific slopes of the Sierra Madre del Sur in Guerrero and Oaxaca, and is composed of X. g. grandis, X. rectocollaris, X. phalaroanthereon, X. g. agrenon, X. penai, and four undescribed species from Oaxaca. The last clade is composed of the four taxa that are geographically closest to the Isthmus of Tehuantepec (X. g. arboreus, X. g. rackhami, X. g. sanmartinensis, and an undescribed species from Oaxaca). We also utilized a variety of molecular species delimitation approaches, including analyses with GMYC, PTP, BPP, and BFD∗, which suggested that species diversity in Xenosaurus is at least 30% higher than currently estimated.