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Microsatellites have been a workhorse of evolutionary genetic studies for decades and are still commonly in use for estimating signatures of genetic diversity at the population and species level across a multitude of taxa. Yet, the very high mutation rate of these loci is a double-edged sword, conferring great sensitivity at shallow levels of analysis (e.g. paternity analysis) but yielding considerable uncertainty for deeper evolutionary comparisons. For the present study, we used reduced representation genome-wide data (restriction site-associated DNA sequencing (RADseq)) to test for patterns of interspecific hybridization previously characterized using microsatellite data in a contact zone between two closely related mouse lemur species in Madagascar (Microcebus murinusandMicrocebus griseorufus). We revisit this system by examining populations in, near, and far from the contact zone, including many of the same individuals that had previously been identified as hybrids with microsatellite data. Surprisingly, we find no evidence for admixed nuclear ancestry. Instead, re-analyses of microsatellite data and simulations suggest that previously inferred hybrids were false positives and that the program NewHybridscan be particularly sensitive to erroneously inferring hybrid ancestry. Combined with results from coalescent-based analyses and evidence for local syntopic co-occurrence, we conclude that the two mouse lemur species are in fact completely reproductively isolated, thus providing a new understanding of the evolutionary rate whereby reproductive isolation can be achieved in a primate.
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Model‐based genotype and ancestry estimation for potential hybrids with mixed‐ploidy
Abstract Non‐random mating among individuals can lead to spatial clustering of genetically similar individuals and population stratification. This deviation from panmixia is commonly observed in natural populations. Consequently, individuals can have parentage in single populations or involving hybridization between differentiated populations. Accounting for this mixture and structure is important when mapping the genetics of traits and learning about the formative evolutionary processes that shape genetic variation among individuals and populations. Stratified genetic relatedness among individuals is commonly quantified using estimates of ancestry that are derived from a statistical model. Development of these models for polyploid and mixed‐ploidy individuals and populations has lagged behind those for diploids. Here, we extend and test a hierarchical Bayesian model, calledentropy, which can use low‐depth sequence data to estimate genotype and ancestry parameters in autopolyploid and mixed‐ploidy individuals (including sex chromosomes and autosomes within individuals). Our analysis of simulated data illustrated the trade‐off between sequencing depth and genome coverage and found lower error associated with low‐depth sequencing across a larger fraction of the genome than with high‐depth sequencing across a smaller fraction of the genome. The model has high accuracy and sensitivity as verified with simulated data and through analysis of admixture among populations of diploid and tetraploidArabidopsis arenosa.
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- Award ID(s):
- 1638602
- PAR ID:
- 10451001
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- Molecular Ecology Resources
- Volume:
- 21
- Issue:
- 5
- ISSN:
- 1755-098X
- Page Range / eLocation ID:
- p. 1434-1451
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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