Gene Duplication, Population Genomics, and Species-Level Differentiation within a Tropical Mountain Shrub

Abstract

Gene duplication leads to paralogy, which complicates the de novo assembly of genotyping-by-sequencing (GBS) data. The issue of paralogous genes is exacerbated in plants, because they are particularly prone to gene duplication events. Paralogs are normally filtered from GBS data before undertaking population genomics or phylogenetic analyses. However, gene duplication plays an important role in the functional diversification of genes and it can also lead to the formation of postzygotic barriers. Using populations and closely related species of a tropical mountain shrub, we examine 1) the genomic differentiation produced by putative orthologs, and 2) the distribution of recent gene duplication among lineages and geography. We find high differentiation among populations from isolated mountain peaks and species-level differentiation within what is morphologically described as a single species. The inferred distribution of paralogs among populations is congruent with taxonomy and shows that GBS could be used to examine recent gene duplication as a source of genomic differentiation of nonmodel species.

Genetic evidence for species cohesion, substructure and hybrids in spruce

“…To consider the consequences of potential unresolved paralogy in our reference assembly, we recalculated the genetic covariance matrix based on 692 loci that conformed more closely to the binomial expectation for heterozygous individuals (0.1 < locus mean binomial [read counts | p = 0.5] <0.9), and found a high correlation ( r = 0.93) between covariance matrices, and a very similar PCA based on the 692 loci. Additionally, we considered the frequency of heterozygotes (as called in the vcf ) at each SNP and locality and identified those SNPs at which all individuals at a location were heterozygotes (cf., Mastretta‐Yanes et al, ; McKinney, Waples, Seeb, & Seeb, ), and for which the exclusive heterozygosity was found at four or more sampling localities (similar results for different numbers of localities). These criteria were satisfied by 271 SNPs, of which 209 (77%) were also excluded by the binomial criterion above.…”

Comparative phylogeography of trans‐Andean freshwater fishes based on genome‐wide nuclear and mitochondrial markers

“…Note that the temporal divergence of our target fish orders (Gymnotiformes, Characiformes and Siluriformes) is well over 100 my old (Arcila et al, ; Betancur‐R et al., ). There is also a potential for paralogous locus assembly (Mastretta‐Yanes et al, ; Verdu et al, ), a problem that is exacerbated in fishes due to multiple rounds of whole genome duplications (Hughes et al, ). By contrast, data missingness is not likely to pose a large effect on our analyses of sequence capture data given that we successfully assembled ~92% of the ~one thousand target loci across both populations and species.…”

Biodiversity in the Mexican highlands and the interaction of geology, geography and climate within the Trans‐Mexican Volcanic Belt

“…Such data would be useful to examine the climate–volcanism interaction because they can provide thousands of variable loci, thus allowing for more fine‐scale population history analyses. Genomic data can also better facilitate the exploration of the processes underlying speciation in novel ways, including the effect of secondary contact (Leaché et al ., ) and the potential role of gene duplication on population differentiation (Mastretta‐Yanes et al ., ).…”