Genetic analyses reveal cryptic introgression in secretive marsh bird populations

Unraveling the genomic landscape of Campylorhynchus wrens along western Ecuador's precipitation gradient: Insights into hybridization, isolation by distance, and isolation by the environment

Environmental gradients have the potential to influence genetic differentiation among populations ultimately leading to allopatric speciation. However, environmental gradients can also facilitate hybridization between closely related taxa. We investigated a putative hybrid zone in western Ecuador, involving two polytypic wren species (Aves: Troglodytidae), Campylorhynchus zonatus and C. fasciatus. Our study addressed two primary questions: (1) Is there evidence of population structure and genetic admixture between these taxa in western Ecuador? and (2) What are the relative contributions of isolation by distance and isolation by the environment to the observed genetic differentiation along the environmental gradient in this region? We analyzed 4409 single-nucleotide polymorphisms (SNPs) from 112 blood samples sequenced using ddRadSeq and a de novo assembly. The optimum number of genetic clusters ranged from 2 to 4, aligning with geographic origins, known phylogenetics, and physical or ecological constraints. We observed notable transitions in admixture proportions along the environmental gradient in western Ecuador between C. z. brevirostris and the northern and southern genetic clusters of C. f. pallescens. Genetic differentiation between the two C. f. pallescens populations could be attributed to an unreported potential physical barrier in central western Ecuador, where the proximity of the Andes to the coastline restricts lowland habitats, limiting dispersal and gene flow, especially among dry-habitat specialists. The observed admixture in C. f. pallescens suggests that this subspecies may be a hybrid between C. z. brevirostris and C. fasciatus, with varying degrees of admixture in western Ecuador and northwestern Peru. We found evidence of isolation by distance, while isolation by the environment was less pronounced but still significant for annual mean precipitation and precipitation seasonality. This study enhances our understanding of avian population genomics in tropical regions.

Estimating hybridization rates in the wild: Easier said than done?

Hybridization has important effects on the evolutionary trajectories of natural populations but estimates of this process in the wild and at the individual-level are lacking. Justyn et al. attempted to fill this gap using the citizen science database eBird but there are limitations to this approach. Here, we outline and directly test these limitations using literature searches, case studies, and a comparison between eBird and Birds of North America (BNA), a database that documents hybridization using the scientific literature. We use a hybrid zone between Lazuli and Indigo buntings to highlight the importance of considering geographic range when estimating rates of hybridization and two literature searches to show the importance of considering cryptic hybrids (those that cannot be identified using phenotypic traits) when quantifying these rates. We also use BNA and a case study of hybrid White-faced and Glossy Ibises to show that citizen scientists are underreporting hybrids compared with experts. Justyn et al. highlighted an important gap in the literature, but their results likely represent the lower limit of hybridization between birds and a more nuanced interpretation of their results (e.g., considering extrinsic postzygotic selection) is needed.

Development of a Panel of Genotyping-in-Thousands by Sequencing in Capsicum

Genotyping by sequencing (GBS) enables genotyping of multiple loci at low cost. However, the single nucleotide polymorphisms (SNPs) revealed by GBS tend to be randomly distributed between individuals, limiting their direct comparisons without applying the various filter options to obtain a comparable dataset of SNPs. Here, we developed a panel of a multiplex targeted sequencing method, genotyping-in-thousands by sequencing (GT-seq), to genotype SNPs in Capsicum spp. Previously developed Fluidigm^® SNP markers were converted to GT-seq markers and combined with new GT-seq markers developed using SNP information obtained through GBS. We then optimized multiplex PCR conditions: we obtained the highest genotyping rate when the first PCR consisted of 25 cycles. In addition, we determined that 101 primer pairs performed best when amplifying target sequences of 79 bp. We minimized interference of multiplex PCR by primer dimer formation using the PrimerPooler program. Using our GT-seq pipeline on Illumina Miseq and Nextseq platforms, we genotyped up to 1,500 (Miseq) and 1,300 (Nextseq) samples for the optimum panel size of 100 loci. To allow the genotyping of Capsicum species, we designed 332 informative GT-seq markers from Fluidigm SNP markers and GBS-derived SNPs. This study illustrates the first application of GT-seq in crop plants. The GT-seq marker set developed here will be a useful tool for molecular breeding of peppers in the future.

Hybridization between two recently diverged Neotropical passerines: The Pearly-bellied Seedeater Sporophila pileata, and the Copper Seedeater S. bouvreuil (Aves, Passeriformes, Thraupidae)

The small Neotropical finches called capuchinos are outstanding because they have experienced one of the most recent and explosive avian radiations ever documented for birds. Despite very low morphological and niche divergence among species, many of them are reproductively isolated when in sympatry due to strong sexual selection in plumage traits. However, a specific pair of mostly parapatric species, the Pearly-bellied, Sporophila pileata, and the Copper Seedeaters, S. bouvreuil, has confounded taxonomists because individuals with intermediate color patterns can be found. By analyzing diagnostic COI mtDNA sequences and adult male plumage we provide evidence for hybridization. Paternity tests using microsatellites also indicated that representatives with intermediate plumage pattern can be fertile. Our findings are consistent with the classification of S. bouvreuil and S. pileata as distinct taxa, but we demonstrate that the sexual selection mechanisms involved in the isolation of other reproductively sympatric capuchinos are not applicable to this pair of species, likely because of reduced barriers to mate recognition.