Diversification and asymmetrical gene flow across time and space: lineage sorting and hybridization in polytypic barking frogs

Abstract

Young species complexes that are widespread across ecologically disparate regions offer important insights into the process of speciation because of their relevance to how local adaptation and gene flow influence diversification. We used mitochondrial DNA and up to 28 152 genomewide single nucleotide polymorphisms from polytypic barking frogs (Craugastor augusti complex) to infer phylogenetic relationships and test for the signature of introgressive hybridization among diverging lineages. Our phylogenetic reconstructions suggest (i) a rapid Pliocene-Pleistocene radiation that produced at least nine distinct lineages and (ii) that geographic features of the arid Central Mexican Plateau contributed to two independent northward expansions. Despite clear lineage differentiation (many private alleles and high between-lineage FST scores), D-statistic tests, which differentiate introgression from ancestral polymorphism, allowed us to identify two putative instances of reticulate gene flow. Partitioned D-statistics provided evidence that these events occurred in the same direction between clades but at different points in time. After correcting for geographic distance, we found that lineages involved in hybrid gene flow interactions had higher levels of genetic variation than independently evolving lineages. These findings suggest that the nature of hybrid compatibility can be conserved overlong periods of evolutionary time and that hybridization between diverging lineages may contribute to standing levels of genetic variation.

Amphibian molecular ecology and how it has informed conservation

“…This is currently untenable for most amphibians because of their large genome sizes and the lack of suitable assembled amphibian reference genomes. Several intermediate technologies are being used in amphibians to obtain information for hundreds or thousands of distinct loci across the genome, including restriction-site-associated DNA (RAD) sequencing (Baird et al 2008;Streicher et al 2014) and target-capture sequencing (Mamanova et al 2010;Hedtke et al 2013). RAD sequencing generates data for anonymous sites in the genome that flank restriction enzyme recognition sites, and as such generally does not fall within protein-coding regions.…”

“…High-throughput sequencing has become more accessible and allows for studies that investigate orders of magnitude more individuals and loci than was previously possible for the same cost and effort. Genomic approaches and resources for amphibians are beginning to become available, including RAD-tag sequencing (Streicher et al 2014) and transcriptome-based exon capture arrays (Hedtke et al 2013;McCartney-Melstad et al 2015), with additional full-genome assemblies likely coming soon. New analytical methods are also being designed to take advantage of the large amounts of data these genomic studies produce to provide deeper insights into important questions in molecular ecology (Alexander et al 2009;Fumagalli et al 2014;Korneliussen et al 2014).…”

Inferring responses to climate dynamics from historical demography in neotropical forest lizards

“…Methods that build upon coalescent theory to account for historical heterogeneity across taxa under a single statistical framework (21,22) provide increased power to test concerted demographic responses at the level of ecological assemblages. These highly flexible approaches have profited from novel bench and analytical methods that build on genomic or reduced genome data, resulting in improved estimates of demographic parameters and histories (23)(24)(25). Although still rare, studies that combine coalescent-based demographic simulations and broader genomic sampling across taxa are unquestionably deepening our understanding of how tropical diversity came to be distributed (17).…”

Inferring speciation history in the Andes with reduced‐representation sequence data: an example in the bay‐backed antpittas (Aves; Grallariidae; Grallaria hypoleuca s. l.)

“…However, the numbers of ABBA/BABA sites reported here are comparable to other recent studies of nonmodel organisms (Eaton & Ree ; Streicher et al . ).…”