Clinal genomic analysis reveals strong reproductive isolation across a steep habitat transition in stickleback fish

Genomic Architecture Underlying the Striking Colour Variation in the Presence of Gene Flow for the Guinan Toad-Headed Lizard

How divergence occurs between closely related organisms in the absence of geographic barriers to gene flow stands as one of the long-standing questions in evolutionary biology. Previous studies suggested that the interplay between selection, gene flow and recombination strongly affected the process of divergence with gene flow. However, the extent to which these forces interact to drive divergence remains largely ambiguous. Guinan toad-headed lizards (Phrynocephalus guinanensis) in the Mugetan Desert exhibit striking colour differences from lizards outside the desert and provide an excellent model to address this question. Through extensive sampling and whole genome sequencing, we obtained genotypes for 191 samples from 14 populations inside and outside the desert. Despite the colour differences, continuous and asymmetric gene flow was detected across the desert border. More importantly, 273 highly diverged regions (HDRs) were identified between them, accounting only for 0.47% of the genome but widely distributed across 20 (out of the total 24) chromosomes. Strong signatures of selection were identified in HDRs, and local recombination rates were repressed. Furthermore, five HDRs exhibited significantly higher divergence, which contained key genes associated with crucial functions in animal coloration, including pteridine and melanocyte pigmentation. Genes related to retinal cells and steroid hormones were identified in other HDRs, which might have also contributed to the formation of colour variation in the presence of gene flow. This study provided novel insights into the understanding of the evolutionary mechanisms of genetic divergence in the presence of gene flow.

The Role of Hybridization in Species Formation and Persistence

Hybridization, or interbreeding between different taxa, was traditionally considered to be rare and to have a largely detrimental impact on biodiversity, sometimes leading to the breakdown of reproductive isolation and even to the reversal of speciation. However, modern genomic and analytical methods have shown that hybridization is common in some of the most diverse clades across the tree of life, sometimes leading to rapid increase of phenotypic variability, to introgression of adaptive alleles, to the formation of hybrid species, and even to entire species radiations. In this review, we identify consensus among diverse research programs to show how the field has progressed. Hybridization is a multifaceted evolutionary process that can strongly influence species formation and facilitate adaptation and persistence of species in a rapidly changing world. Progress on testing this hypothesis will require cooperation among different subdisciplines.

How does communication evolve? Insights from geographic variation in facial signaling in Polistes paper wasps

Communication systems require coordination between senders and receivers; therefore, understanding how novel signals arise is challenging. Intraspecific geographic variation in signaling provides an opportunity to investigate the factors that shape signal evolution. Facial signals in Polistes paper wasps provide an interesting case study for the causes and consequences of geographic variation in signaling systems. Two species of paper wasps, Polistes dominula and Polistes fuscatus, have been well studied for their facial patterns that signal quality and individual identity, respectively. Remarkably, whether or not facial patterns are used as signals at all appears to vary geographically in both species. The relative evidence for the roles of phenotypic plasticity versus genetic differentiation is discussed. Future research directions that leverage geographic variation in Polistes hold promise to substantially contribute to understanding the links between signals and behavior, as well as the evolution of cognition.

Bray-Curtis (AFD) differentiation in molecular ecology: Forecasting, an adjustment ( A A), and comparative performance in selection detection

Geographic genetic differentiation measures are used for purposes such as assessing genetic diversity and connectivity, and searching for signals of selection. Confirmation by unrelated measures can minimize false positives. A popular differentiation measure, Bray-Curtis, has been used increasingly in molecular ecology, renamed AFD (hereafter called BCAFD). Critically, BCAFD is expected to be partially independent of the commonly used Hill "Q-profile" measures. BCAFD needs scrutiny for potential biases, by examining limits on its value, and comparing simulations against expectations. BCAFD has two dependencies on within-population (alpha) variation, undesirable for a between-population (beta) measure. The first dependency is derived from similarity toG ST andF ST . The second dependency is that BCAFD cannot be larger than the highest allele proportion in either location (alpha variation), which can be overcome by data-filtering or by a modified statistic A A or "Adjusted AFD". The first dependency does not forestall applications such as assessing connectivity or selection, if we know the measure's null behavior under selective neutrality with specified conditions-which is shown in this article for A A, for equilibrium, and nonequilibrium, for the commonly used data type of single-nucleotide-polymorphisms (SNPs) in two locations. Thus, A A can be used in tandem with mathematically contrasting differentiation measures, with the aim of reducing false inferences. For detecting adaptive loci, the relative performance of A A and other measures was evaluated, showing that it is best to use two mathematically different measures simultaneously, and that A A is in one of the best such pairwise criteria. For any application, using A A, rather than BCAFD, avoids the counterintuitive limitation by maximum allele proportion within localities.