A southern African origin and cryptic structure in the highly mobile plains zebra

@article{Pedersen2017ASA,
  title={A southern African origin and cryptic structure in the highly mobile plains zebra},
  author={Casper-Emil T Pedersen and Anders Albrechtsen and Paul D. Etter and Eric A. Johnson and Ludovic Orlando and Loun{\`e}s Chikhi and Hans R. Siegismund and Rasmus Heller},
  journal={Nature Ecology \& Evolution},
  year={2017},
  volume={2},
  pages={491-498}
}
The plains zebra (Equus quagga) is an ecologically important species of the African savannah. It is also one of the most numerous and widely distributed ungulates, and six subspecies have been described based on morphological variation. However, the within-species evolutionary processes have been difficult to resolve due to its high mobility and a lack of consensus regarding the population structure. We obtained genome-wide DNA polymorphism data from more than 167,000 loci for 59 plains zebras… 
Population structure, inbreeding and stripe pattern abnormalities in plains zebras
TLDR
It is found that genetic structure did not coincide with described subspecific variation, but did 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.
Cryptic patterns of speciation in cryptic primates: microendemic mouse lemurs and the multispecies coalescent
TLDR
It is found that incorporating gene flow into the MSC can greatly affect divergence time estimates, and it is concluded that a previously identified mitochondrial lineage warrants full species status, and is named M. jonahi.
Complex processes of cryptic speciation in mouse lemurs from a micro-endemism hotspot in Madagascar
TLDR
This study focuses on a conservation hotspot in northeastern Madagascar where at least five species of mouse lemur occur, some of them in sympatry, and describes one of them, M. jonahi, as new to science and is accompanied by a complete genome.
Human origins in a southern African palaeo-wetland and first migrations
TLDR
A southern African origin of anatomically modern humans with sustained homeland occupation before the first migrations of people that appear to have been driven by regional climate changes is proposed.
Vicariance followed by secondary gene flow in a young gazelle species complex
TLDR
Genomic data obtained by restriction site‐associated (RAD) sequencing of 106 gazelle individuals are used to shed light on the evolutionary processes underlying Grant's gazelles divergence, to characterize their genetic structure and to assess the presence of gene flow between the main lineages in the species complex.
Recent range expansion in Australian hummock grasses (Triodia) inferred using genotyping-by-sequencing
TLDR
Investigation of populations of the widespread AAZ grass Triodia basedowii finds evidence for range expansion in an arid-adapted plant is consistent with similar patterns in AAZ animals and likely reflects a general response to the opening of new habitat during aridification.
Cryptic Patterns of Speciation in Cryptic Primates: Microendemic Mouse Lemurs and the Multispecies Coalescent.
TLDR
Divergence time estimates reported here are based on the MSC calibrated with pedigree-based mutation rates and are considerably more recent than previously published fossil-calibrated relaxed-clock estimates and suggest rapid evolution of reproductive isolation in the focal lineages, and in the mouse lemur clade generally.
The evolution of Bolbites onitoides (Coleoptera: Scarabaeidae: Phanaeini): its phylogenetic significance, geographical polychromatism and the subspecies problem
TLDR
It is concluded that B. onitoides should continue to be treated as a single monotypic species and an evolutionary scenario where the role of the iridescence in sexual selection, as hypothesized in a previous work, may be an exaptation, not an adaptation, among the horned Phanaeina.
Demography and adaptation promoting evolutionary transitions in a mammalian genus that diversified during the Pleistocene.
TLDR
Comparative genomics is used to assess expectations for the origin and diversification of a mammalian genus during a period of extreme environmental change and finds progressive reductions in effective population size (Ne), despite very large census sizes in modern C. capreolus populations.
Genomic methods reveal independent demographic histories despite strong morphological conservatism in fish species
TLDR
The results show that strong morphologic conservatism in marine environments can lead to species that are difficult to distinguish morphologically but that are characterized by an independent evolutionary history, and thus that deserve species-specific management strategies.
...
...

References

SHOWING 1-10 OF 66 REFERENCES
High variation and very low differentiation in wide ranging plains zebra (Equus quagga): insights from mtDNA and microsatellites
TLDR
The zebra showed the lowest overall differentiation recorded in any African ungulate studied so far, and the only other species showing a similar absence of genetic structuring is the African buffalo, but this taxon lacks the high levels of morphological variation present in the plains zebra.
Regional genetic structuring and evolutionary history of the impala Aepyceros melampus.
TLDR
It is suggested that the presence of such previously unknown regional structuring within the subspecies reflects a pattern of colonization from a formerly large panmictic population in southern Africa toward east Africa, supported by a progressive decline in population diversity indices towardEast Africa and a significant increase in the quantity theta/(1 - theta).
Phylogeography of three closely related African bovids (tribe Alcelaphini).
TLDR
A scenario where these antelopes, previously with wide pan-African distributions, became extinct except in a few refugia is suggested, where the hartebeest, and probably also the topi, survived inRefugia north of the equator, in the east and the west, respectively, as well as one in the south.
Pan-African Genetic Structure in the African Buffalo (Syncerus caffer): Investigating Intraspecific Divergence
TLDR
The African buffalo most likely expanded and diverged in the late to middle Pleistocene from an ancestral population located around the current-day Central African Republic, adapting morphologically to colonize new habitats, hence developing the variety of ecophenotypes observed today.
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 rapid loss of stripes: the evolutionary history of the extinct quagga
TLDR
It is shown that the quagga displayed little genetic diversity and very recently diverged from the plains zebra, probably during the penultimate glacial maximum, which emphasizes the importance of Pleistocene climate changes for phylogeographic patterns in African as well as Holarctic fauna.
Revising the recent evolutionary history of equids using ancient DNA
TLDR
Phylogenetic analyses support a major revision of the recent evolutionary history of equids and reveal two new species, a South American hippidion and a descendant of a basal lineage potentially related to Middle Pleistocene equids.
A survey of equid mitochondrial DNA: Implications for the evolution, genetic diversity and conservation of Equus
TLDR
The phylogenetic analysis of the mitochondrial DNA sequences of the control region and 12S rRNA gene provides further evidence that the deepest node in the phylogeny of the extant species is a divergence between twolineages, with the later speciation events of the zebras and asses occurring either as one or more rapid radiations, or withextensive secondary contact after speciation.
Hybridization between subspecies of waterbuck (Kobus ellipsiprymnus) in zones of overlap with limited introgression
TLDR
A high degree of genetic differentiation was found between subspecies, although this was most evident from the microsatellite data, and hybridization was suggested in the phenotypically and geographically intermediate Nairobi NP population in Kenya.
Mitochondrial Phylogenomics of Modern and Ancient Equids
TLDR
Bayesian and Maximum Likelihood phylogenetic inference confirms that zebras are monophyletic within the genus Equus, and the Plains and Grevy’sZebras form a well-supported monophyletsic group, and additional mitochondrial genome sequence data is required before revisiting the exact timing of the lineage radiation leading up to modern equids.
...
...