Furman BLS et al. (2017), Limited genomic consequences of hybridization b...

XB-ART-53638

Sci Rep 2017 Apr 24;71:1091. doi: 10.1038/s41598-017-01104-9.

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Limited genomic consequences of hybridization between two African clawed frogs, Xenopus gilli and X. laevis (Anura: Pipidae).

Furman BLS , Cauret CMS , Colby GA , Measey GJ , Evans BJ .

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The Cape platanna, Xenopus gilli, an endangered frog, hybridizes with the African clawed frog, X. laevis, in South Africa. Estimates of the extent of gene flow between these species range from pervasive to rare. Efforts have been made in the last 30 years to minimize hybridization between these two species in the west population of X. gilli, but not the east populations. To further explore the impact of hybridization and the efforts to minimize it, we examined molecular variation in one mitochondrial and 13 nuclear genes in genetic samples collected recently (2013) and also over two decades ago (1994). Despite the presence of F 1 hybrids, none of the genomic regions we surveyed had evidence of gene flow between these species, indicating a lack of extensive introgression. Additionally we found no significant effect of sampling time on genetic diversity of populations of each species. Thus, we speculate that F 1 hybrids have low fitness and are not backcrossing with the parental species to an appreciable degree. Within X. gilli, evidence for gene flow was recovered between eastern and western populations, a finding that has implications for conservation management of this species and its threatened habitat.

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Species referenced: Xenopus
Genes referenced: prmt6

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	Figure 1. Sampling locations. For each species, numbers indicate the sum of number of individuals from each locality sampled in 1994 and 2013. An inset indicates the study area in southern Africa and altitude in meters is indicate on the scale. The map was made using the R package Marmap81 using topographic data from the National Oceanic and Atmospheric Administration, USA.
	Figure 2. Evolutionary models considered for X. gilli sequence data from east and west populations included (a) population division without subsequent gene flow, (b) separation followed by ongoing gene flow, and (c) separation followed by secondary contact after a period of no gene flow. Model parameters include the population polymorphism parameter θ, which is assumed to be constant in the ancestral and both descendant populations, the time of speciation T, the amount of migration m, and the time of secondary contact τ.
	Figure 3. Representative gene trees that collectively provide no evidence of genetic exchange between X. gilli and X. laevis. The phylogeny on the left illustrates divergence between 16S rDNA mitochondrial sequences in the east and west populations of X. gilli, and with one shared sequence (indicated with an arrow) that occurred on both sides of False Bay. The nuclear phylogenies in the center and right provide examples of no shared alleles and shared alleles between the east and west X. gilli populations, respectively. Gene name acronyms are described in the Materials and Methods section. These and other phylogenies are depicted with sample labels in Fig. S1.
	Figure 4. (a) Structure analyses for 10 loci, which had sequence data for all populations. (b) Likelihood for each value of K.
	Figure 5. Genetic diversity statistics including rarefied estimates of allelic diversity (top panels) and nucleotide diversity (π) weighted by length of sequence; bottom panels). For allelic diversity, the analysis considered the same 10 loci as were analyzed by the STRUCTURE analysis (see Materials and Methods). Allelic diversity for X. laevis did not include PRMT6 locus because this locus only had four alleles for the west 1994 population.

References [+] :

Altschul, Basic local alignment search tool. 1990, Pubmed