Genomic‐scale datasets, sophisticated analytical techniques, and conceptual advances have disproportionately failed to resolve species boundaries in some groups relative to others. To understand the processes that underlie taxonomic intractability, we dissect the speciation history of an Australian lizard clade that arguably represents a “worst‐case” scenario for species delimitation within vertebrates: the Ctenotus inornatus...

The effects of genetic introgression on species boundaries and how they affect species’ integrity and persistence over evolutionary time have received increased attention. The increasing availability of genomic data has revealed contrasting patterns of gene flow across genomic regions, which impose challenges to inferences of evolutionary relationships and of patterns of genetic admixture across lineages. By characterizing pat...

A period of isolation in allopatry typically precedes local adaptation and subsequent divergence among lineages. Alternatively, locally adapted phenotypes may arise and persist in the face of gene flow, resulting in strong correlations between ecologically‐relevant phenotypic variation and corresponding environmental gradients. Quantifying genetic, ecological, and phenotypic divergence in such lineages can provide insights int...

In this issue of Molecular Ecology , Yamasaki et al. (2020) use genetic data from extensive sampling of Rhinogobius goby fish across the Ryukyu Archipelago in Japan to demonstrate the parallel speciation of a freshwater form from an ancestral amphidromous form. They then show that ecosystem size strongly predicts the probability of speciation between the two forms across islands. In doing so, this study connects population‐lev...

Aim To investigate (a) historical biogeographical connections and species interchange among rain forest habitats and (b) the role of riverine barriers on population divergence and speciation in the Neotropical region. Location Amazonia and Atlantic Forest in South America. Taxon Bothrops jararacussu species group (Serpentes: Viperidae). Methods We inferred phylogenetic relationships within Bothrops with an emphasis on the jara...

Scientists have long been trying to understand why the Neotropical region holds the highest diversity of birds on Earth. Recently, there has been increased interest in morphological variation between and within species, and in how climate, topography, and anthropogenic pressures may explain and affect phenotypic variation. Because morphological data are not always available for many species at the local or regional scale, we a...

Aim To examine historical connections between rain forest habitats in the Neotropics based on the evolutionary history of the arboreal pit viper Bothrops bilineatus . Location Amazonia and Atlantic Forest in South America. Methods We inferred phylogenetic relationships within Bothrops and phylogeographic relationships within B. bilineatus using both concatenated and species tree approaches under a Bayesian framework based on f...

The Cercosaurini tribe stands out from other Gymnophthalmidae lizards for including several species with morphological adaptations to aquatic lifestyle (“Crocodile‐Like Morphology” – CLM ). Recent molecular phylogenies of Cercosaurini demonstrated the paraphyly of CLM species, implicitly suggesting that adaptations to the aquatic life evolved more than once. However, CLM species have remained poorly sampled, and a number of un...

Shifts in the geographic distribution of habitats over time can promote dispersal and vicariance, thereby influencing large‐scale biogeographic patterns and ecological processes. An example is that of transient corridors of suitable habitat across disjunct but ecologically similar regions, which have been associated with climate change over time. Such connections likely played a role in the assembly of tropical communities, es...