Population structure, inbreeding and stripe pattern abnormalities in plains zebras

One of the most iconic wild equids, the plains zebra occupies a broad
region of sub-Saharan Africa and exhibits a wide range of phenotypic
diversity in stripe patterns that have been used to classify multiple
sub-species. After decades of relative stability, albeit with a loss of at
least one recognized subspecies, the total population of plains zebras has
undergone an approximate 25% decline since 2002. Individuals with abnormal
stripe patterns have been recognized in recent years but the extent to
which their appearance is related to demography and/or genetics is
unclear. Investigating population genetic health and genetic structure are
essential for developing effective strategies for plains zebra
conservation. We collected DNA from 140 plains zebra, including 7 with
abnormal stripe patterns, from 9 locations across the range of plains
zebra, and analyzed data from restriction site-associated and whole genome
sequencing (RAD-seq, WGS) libraries to better understand the relationships
between population structure, genetic diversity, inbreeding, and abnormal
phenotypes. We find that genetic structure does not coincide with
described subspecific variation, but does distinguish geographic regions
in which anthropogenic habitat fragmentation is associated with reduced
gene flow and increased evidence of inbreeding, especially in certain
parts of East Africa. Further, zebras with abnormal striping exhibited
increased levels of inbreeding relative to normally striped individuals
from the same populations. Our results point to a genetic cause of stripe
pattern abnormalities, and dramatic evidence of the consequences of
habitat fragmentation.