Mitonuclear discordance is a frequently encountered pattern in phylogeographic studies and occurs when mitochondrial and nuclear DNA display conflicting signals. Discordance among these genetic markers can be caused by several factors including confounded taxonomies, gene flow, and incomplete lineage sorting. In this study, we present a strong case of mitonuclear discordance in a species complex of toads (Bufonidae: Incilius coccifer complex) found in the Chortís Block of Central America. To determine the cause of mitonuclear discordance in this complex, we used spatially explicit genetic data to test species limits and relationships, characterize demographic history, and quantify gene flow. We found extensive mitonuclear discordance among the three recognized species within this group, especially in populations within the Chortís Highlands of Honduras. Our data reveal nuclear introgression within the Chortís Highlands populations that was most probably driven by cyclical range expansions due to climatic fluctuations. Though we determined introgression occurred within the nuclear genome, our data suggest that it is not the key factor in driving mitonuclear discordance in the entire species complex. Rather, due to a lack of discernible geographic pattern between mitochondrial and nuclear DNA, as well as a relatively recent divergence time of this complex, we concluded that mitonuclear discordance has been caused by incomplete lineage sorting. Our study provides a framework to test sources of mitonuclear discordance and highlights the importance of using multiple marker types to test species boundaries in cryptic species.

Single-locus molecular barcoding is a useful method for identifying overlooked and undescribed biodiversity, providing the groundwork for further systematic study and taxonomic investigation. A variety of methods for delimiting species from barcoding libraries have been developed and applied, allowing for rapid estimates of species diversity in a broad range of taxa. However, tree-based and distance-based analyses can infer different group assignments, potentially over- or underestimating the number of putative species groups. Here, we explore diversity of mainland species of anole lizards from the Chortís Block biogeographical province of northern Central America using a DNA barcoding approach, generating and analyzing cytochrome oxidase subunit I (COI) sequences for over 400 samples assignable to 33 of 38 (86.8%) native and one introduced mainland species. We subsequently tested the effects different models of nucleotide substitution, different species-delimitation algorithms, and reducing our dataset had on species delimitation estimates. We performed of two distance-based (ABGD, RESL) and three tree-based (bPTP, mPTP, GMYC) analyses on both the full dataset and a dataset consisting only of unique halotypes. From 34 nominal taxa, analyses of the full dataset recovered between 34 and 64 operational taxonomic units (OTUs), while analyses of the reduced dataset inferred between 36 and 59. Reassigning individuals to either mPTP-inferred or ABGD clustered (7.2% threshold) groups improved the detection of a barcoding gap across three different models of nucleotide substitution, removing overlap between intra- and interspecific distances. Our results highlight the underestimated diversity of mainland Chortís Block anoles, but the lack of congruence between analyses demonstrates the importance of considering multiple analytical methods when dealing with single-locus datasets. We recommend future studies consider the effects of different models of nucleotide substitution on proposed barcoding gaps, as well as the effect reducing a dataset to unique haplotypes may have on proposed diversity estimates.

Geophis Wagler is the fourth largest genus of colubrid snakes in the Western Hemisphere, with 46 species currently recognized. Since the last major treatment of this genus, there have been 12 new species described, three taxa elevated to the species level, and two taxa previously recognized at the species level synonymized with other taxa. We present a checklist for the genus Geophis, summarizing information on taxonomic history, type material and locality, distribution, and species group assignment for 46 species. We also provide an identification key for the 46 species, followed by a brief analysis of distributional patterns and conservation status.

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Approaches that integrate multiple independent, yet complimentary, lines of evidence have been effectively utilized to identify and evaluate species diversity. Integrative approaches are especially useful in taxa that exhibit cryptic diversity and are highly morphologically conserved, as well as organisms whose distributions may be sympatric or parapatric. The Incilius coccifer complex in Honduras is comprised of three putative taxa: I. coccifer, I. ibarrai and I. porteri. The taxonomy of the I. coccifer complex has been a source of debate among specialists, with some recognizing three species, while others choose to recognize one widespread taxon. To assess species boundaries and evaluate the taxonomic structure for the I. coccifer complex, we utilized a combination of comprehensive field sampling, molecular phylogenetics and macroecological modelling. Using 58 samples representing all three putative taxa, we generated sequence data from the mitochondrial loci 16S and COI in order to assess genetic diversity and phylogenetic relationships, and tested putative species boundaries using General Mixed Yule‐Coalescent models. To evaluate macroecological differences in the distribution of putative taxa, we utilized maximum entropy modelling and identified areas of suitable and non‐suitable habitat, as well as identifying potential areas of overlap between species habitats. We recovered three clades that broadly correspond to the three named taxa that, while being monophyletic, are separated by relatively small genetic distances. Species distribution models revealed that I. coccifer is macroecologically different than the other two taxa, but that I. ibarrai and I. porteri are highly similar. We uncovered cases of sympatry between pairs of species in at least three localities in Honduras, suggesting the potential for hybridization in these closely related lineages.

2012). Cryptic diversity in disjunct populations of Middle American Montane Pitvipers: a systematic reassessment of Cerrophidion godmani. -Zoologica Scripta, 41, 455-470. The discovery and taxonomic recognition of cryptic species has become increasingly frequent with the application of molecular phylogenetic analyses, particularly for species with broad geographic distributions. In this study we focus on the venomous pitviper species Cerrophidion godmani that is widely distributed throughout the highlands of Central America. We provide evidence based on both molecular phylogenetic analyses and morphological data that C. godmani represents three deeply divergent lineages and is possibly non-monophyletic. These three lineages are relatively conserved in their morphology and tend to be highly variable among individuals, but we do find sufficient morphological characters to diagnose them as evolutionarily distinct. We apply these data, together with known geographic distributions of populations, to infer boundaries of these three divergent evolutionary lineages. Based on the body of evidence, we formally name and describe two new species of Cerrophidion and redescribe C. godmani sensu stricto.

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A new species of palm-pitviper of the genus Bothriechis is described from Refugio de Vida Silvestre Texíguat in northern Honduras. The new species differs from congeners by having 19 dorsal scale rows at midbody, a bright green dorsal coloration in adults, the prelacunal scale fused to the second supralabial, and in representing a northern lineage that is sister to Bothriechis lateralis, which is distributed in Costa Rica and western Panama and is isolated from the new taxon by the Nicaraguan Depression. This represents the 15th endemic species occurring in Refugio de Vida Silvestre Texíguat, one of the richest herpetofaunal sites in Honduras, itself being the country with the highest degree of herpetofaunal endemism in Central America. We name this new species in honor of a Honduran conservationist slain in fighting against illegal logging, highlighting the sacrifices of rural activists in battling these issues and the critical importance of conservation in these areas.