Population structure, inbreeding and stripe pattern abnormalities in plains zebras

@article{Larison2020PopulationSI,
  title={Population structure, inbreeding and stripe pattern abnormalities in plains zebras},
  author={Brenda Larison and Christopher B. Kaelin and Ryan J. Harrigan and Corneliu Henegar and Daniel I Rubenstein and Pauline L. Kamath and Ortwin H. K. Aschenborn and Thomas B. Smith and Gregory S. Barsh},
  journal={Molecular Ecology},
  year={2020},
  volume={30},
  pages={379 - 390}
}
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 subspecies. 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… 
7 Citations
Epigenetic models developed for plains zebras predict age in domestic horses and endangered equids
TLDR
An interaction between chronological age and inbreeding is associated with age acceleration estimated by the EPM, suggesting a cumulative effect of inbreeding on biological aging throughout life.
Epigenetic models predict age and aging in plains zebras and other equids
TLDR
Using blood and biopsy samples from known age plains zebras, epigenetic clocks (ECs) to predict chronological age, and epigenetic pacemaker models to predict biological age are developed and described, finding moderate support for a slight acceleration of aging with increased inbreeding.
Melanism in a wild sifaka population: Darker where cold and fragmented
TLDR
Three hypotheses that may explain pelage color and pattern variation within a population of wild primates, diademed sifakas, exhibiting striking diversity in coloration are explored: isolation by distance, an environmental gradient, or unique local adaptation.
Host Genetic Diversity and Infectious Diseases. Focus on Wild Boar, Red Deer and Tuberculosis
TLDR
A disconnection between studies treating genetic diversity and those dealing with infectious diseases is found and despite the existing disconnection, the knowledge gathered in each discipline can be applied to the other.
Commonly used Hardy-Weinberg equilibrium filtering schemes impact population structure inferences using RADseq data
TLDR
This work shows that the removal of loci exhibiting departures from HWE after pooling across samples significantly reduces the degree of inferred population structure within a dataset, and provides recommendations for best practice regarding the implementation of HWE filtering for RADseq datasets.
Title: Commonly used Hardy-Weinberg equilibrium filtering schemes impact 1 population structure inferences using RADseq data
TLDR
This work shows that the removal of loci exhibiting departures from Hardy-Weinberg equilibrium after pooling across samples significantly reduces the degree of inferred population structure within a dataset (despite this approach being widely used).
The seven ways eukaryotes produce repeated colour motifs on external tissues
TLDR
A novel classification consisting of seven families of primary mechanisms: Turing(-like), cellular automaton, multi-induction, physical cracking, random, neuromuscular and printing is proposed and six pattern modifiers are reported, acting synergistically with these primary mechanisms to enhance the spectrum of repeated colour patterns.

References

SHOWING 1-10 OF 68 REFERENCES
A southern African origin and cryptic structure in the highly mobile plains zebra
TLDR
Genome-wide data from all plains zebra subspecies reveal a population genetic structure at odds with morphology-based subspecies delineation, modern and ancient variation, and a probable southern African origin of all extant populations.
Extensive population genetic structure in the giraffe
TLDR
There are at least six genealogically distinct lineages of giraffe in Africa, with little evidence of interbreeding between them, and such extreme genetic subdivision within a large vertebrate with high dispersal capabilities is unprecedented and exceeds that of any other large African mammal.
Contrasting historical and recent gene flow among African buffalo herds in the Caprivi Strip of Namibia.
TLDR
Historically, African buffalo moved freely throughout the Caprivi Strip, whereas recent gene flow has been more restricted, supporting efforts to maintain the connectivity of buffalo herds across this region and demonstrating the utility of contrasting genetic inferences from different time scales.
Comparative phylogeography of African savannah ungulates 1
TLDR
Data from across taxa reveal distinct regional lineages, which reflect the survival and divergence of populations in isolated savannah refugia during the climatic oscillations of the Pleistocene, and suggest a stable, long‐standing savannah refuge in the south.
A newly discovered wildlife migration in Namibia and Botswana is the longest in Africa
Abstract Migrations of most animal taxa are declining as a result of anthropogenic pressures and land-use transformation. Here, we document and characterize a previously unknown multi-country
Regional Differences in Seasonal Timing of Rainfall Discriminate between Genetically Distinct East African Giraffe Taxa
TLDR
The results suggest that selection associated with regional timing of events in the annual climatic cycle may help maintain genetic and phenotypic divergence in giraffes, and suggest that synchronization of reproduction with seasonal rainfall cycles that are geographically distinct may contribute to reproductive isolation.
Mid‐Holocene decline in African buffalos inferred from Bayesian coalescent‐based analyses of microsatellites and mitochondrial DNA
TLDR
It is proposed that the mid‐Holocene aridification of East Africa caused a major decline in the effective population size of the buffalo, a species reliant on moist savannah habitat for its existence.
Concordance on zebra stripes: a comment on Larison et al. (2015)
TLDR
In the second multifactorial analysis of striping in zebras, Larison et al. investigated the environmental factors that explain geographical variation in striping within a single species and found that greater intensities of intraspecific striping were associated with warmer temperatures and high precipitation.
Genomic Runs of Homozygosity Record Population History and Consanguinity
TLDR
Genome-wide analysis of long and shorter ROH allows categorisation of the mainly indigenous populations sampled here into four major groups in which the majority of the population are inferred to have: recent parental relatedness (south and west Asians), shared parental ancestry arising hundreds to thousands of years ago through long term isolation and restricted effective population size (Ne), but little recent inbreeding (Oceanians), and the occasional cryptically inbred individual.
Are subspecies useful in evolutionary and conservation biology?
  • A. Phillimore, I. Owens
  • Biology, Environmental Science
    Proceedings of the Royal Society B: Biological Sciences
  • 2006
TLDR
It is shown that 36% of avian subspecies are, in fact, phylogenetically distinct, and the overall level of congruence between taxonomic subspecies and molecular phylogenetic data is greater than previously thought.
...
...