Genetic diversity and demographic history of the largest remaining migratory population of brindled wildebeest (Connochaetes taurinus taurinus) in southern Africa

Abstract

The blue wildebeest (Connochaetes taurinus) is a keystone species in the savannahs of southern Africa, where it maintains shortgrass plains and serves as an important prey source for large carnivores. Despite being the second-largest migratory wildebeest population, the brindled wildebeest (C. t. taurinus) of the Greater Liuwa Ecosystem (GLE) of western Zambia have remained largely unstudied, until recently. While studies have increased understanding of recent demography, migration, and population limiting factors, the level of genetic diversity, patterns of gene flow, and long-term demographic history of brindled wildebeest in the GLE remains unknown. Most genetic studies of wildebeest have focused on small, heavily-managed populations, rather than large, migratory populations of high conservation significance. We used restriction-site associated DNA sequencing (RAD-seq) to assess genetic diversity, population structure, and demographic history of brindled wildebeest in the GLE. Using SNPs from 1,730 loci genotyped across 75 individuals, we found moderate levels of genetic diversity in GLE brindled wildebeest (He = 0.210), very low levels of inbreeding (FIS = 0.033), and an effective population size of about one tenth the estimated population size. No genetic population structure was evident within the GLE. Analyses of the site frequency spectrum found signatures of expansion during the Middle Pleistocene followed by population decline in the Late Pleistocene and early Holocene, a pattern previously observed in other African ungulates. These results will supplement field studies in developing effective conservation plans for wildebeest as they face continued and increasing threats of habitat loss, poaching, and other human impacts across their remaining range.

Fig 1. Location of study area.

(a) Image of a brindled wildebeest (Connochaetes taurinus taurinus; photograph by S. Szarmach). (b) Sampling map depicting where wildebeest tissues were collected (white dots) in the Greater Liuwa Ecosystem (“GLE”). Borders are shown for Liuwa Plain National Park and the surrounding Upper West Zambezi Game Management Area. (c) Location of sampling area (yellow star) within Zambia and broader region. Basemap: NASA Earth Observatory Blue Marble satellite image (obtained through NASA Worldview).

Fig 2. Schematic of the five demographic scenarios modeled in the coalescent simulator fastsimcoal2.

For each model, parameters describing effective population size (N) and select times before present (T) were estimated.

Fig 3. Brindled wildebeest show no signs of population subdivision within the Greater Liuwa Ecosystem.

Principal component analysis (PCA) of GLE brindled wildebeest (n =  75) based on 1,730 SNPs.

Fig 4. Expected and observed heterozygosity for 1,730 SNPs genotyped in Greater Liuwa Ecosystem brindled wildebeest (n =  75).

Boxplots show median and interquartile range.

Fig 5. Stairway plot representing inferred changes in effective population size (N_e) over time for the Greater Liuwa Ecosystem brindled wildebeest population.

The red line shows the median estimated effective population size, the dark grey lines encompass the 75% CI, and the light gray lines contain the 95% CI, determined from 200 bootstrapped site frequency spectrums.