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opencc-zeroDec 2011View details →

Data from: Comparative landscape genetic analyses show a Belgian motorway to be a gene flow barrier for red deer (Cervus elaphus), but not wild boars (Sus scrofa)

While motorways are often assumed to influence the movement behaviour of large mammals, there are surprisingly few studies that show an influence of these linear structures on the genetic make-up of wild ungulate populations. Here, we analyse the spatial genetic structure of red deer (Cervus elaphus) and wild boars (Sus scrofa) along a stretch of motorway in the Walloon part of Belgium. Altogether 876 red deer were genotyped at 13 microsatellite loci, and 325 wild boars at 14 loci. In the case of the red deer, different genetic clustering tools identified two genetic subpopulations whose borders matched the motorway well. Conversely, no genetic structure was identified in the case of the wild boar. Analysis of isolation-by-distance patterns of pairs of individuals on the same side and on different sides of the motorway also suggested that the road was a barrier to red deer, but not to wild boar movement. While telemetry studies seem to confirm that red deer are more affected by motorways then wild boar, the red deer sample size was also much larger than that of the wild boars. We therefore repeated the analysis of genetic structure in the red deer with randomly sub-sampled datasets of decreasing size. The power to detect the genetic structure using clustering methods decreased with decreasing sample size.

opencc-zeroDec 2016View details →

Data from: Speciation over the edge: gene flow among non-human primate species across a formidable biogeographic barrier

Many genera of terrestrial vertebrates diversified exclusively on one or the other side of Wallace's Line, which lies between Borneo and Sulawesi islands in Southeast Asia, and demarcates one of the sharpest biogeographic transition zones in the world. Macaque monkeys are unusual among vertebrate genera in that they are distributed on both sides of Wallace's Line, raising the question of whether dispersal across this barrier was an evolutionary one-off or a more protracted exchange—and if the latter, what were the genomic consequences. To explore the nature of speciation over the edge of this biogeographic divide, we used genomic data to test for evidence of gene flow between macaque species across Wallace's Line after macaques colonized Sulawesi. We recovered evidence of post-colonization gene flow, most prominently on the X chromosome. These results are consistent with the proposal that gene flow is a pervasive component of speciation—even when barriers to gene flow seem almost insurmountable.

Figure 2 in The Zagros Mountains acting as a natural barrier to gene flow in the Middle East: more evidence from the evolutionary history of spiny-tailed lizards (Uromasticinae: Saara)

Figure 2. The phylogenetic tree of the Uromasticinae subfamily, including the genera Saara and Uromastyx, based two mtDNA (Cytb and 16S) and one nDNA (ACM4) genes. The trees showed the same topologies for both ML and BI trees, and therefore, only the BI tree is presented. The ML bootstrap values and BI posterior probabilities are next to the nodes, respectively.

Figure 5 in The Zagros Mountains acting as a natural barrier to gene flow in the Middle East: more evidence from the evolutionary history of spiny-tailed lizards (Uromasticinae: Saara)

Figure 5. The biogeographic analysis of Saara with S-DIVA (A) and BBM (B) based on Cytb. For these analyses, three regions were considered: (A: blue nodes) the Mesopotamian plain [or western part of Zagros Mountains (WZM); distribution of S. loricata], (B: green nodes) the central Iranian Plateau [or eastern part of Zagros Mountains (EZM); distribution of S. asmussi] and (C: pink nodes) India/Pakistan (IP); distribution of S. hardwickii. The dark blue and dark green circles around nodes show dispersal and vicariance events, respectively.

Figure 1 in The Zagros Mountains acting as a natural barrier to gene flow in the Middle East: more evidence from the evolutionary history of spiny-tailed lizards (Uromasticinae: Saara)

Figure 1. Geographical distribution range of the genus Saara. The grey circles represent distribution points (the points were obtained from valid references e.g. GBIF, reptile database, etc.) and black circles refer to locations of samples that were used in the genetic analyses. Distribution ranges of S. loricata, S. asmussi and S. hardwickii are illustrated with blue, green and pink cross-hatches, respectively.

Figure 3 in The Zagros Mountains acting as a natural barrier to gene flow in the Middle East: more evidence from the evolutionary history of spiny-tailed lizards (Uromasticinae: Saara)

Figure 3. Parsimony haplotype networks of Saara loricata and S. asmussi based on two mtDNA (Cytb and 16S) genes. The haplogroups (A) and (B) refer to S. loricata with Cytb and 16S, respectively. The haplogroups (C) and (D) refer to S. asmussi with Cytb and 16S, respectively.

opencc-zeroJun 2023View details →

Data and R script for: Barriers to chimpanzee gene flow at the south‐east edge of their distribution

Populations on the edge of a species' distribution may represent an important source of adaptive diversity, yet these populations tend to be more fragmented and are more likely to be geographically isolated. Lack of genetic exchanges between such populations, due to barriers to animal movement, can not only compromise adaptive potential but also lead to the fixation of deleterious alleles. The south‐eastern edge of chimpanzee distribution is particularly fragmented, and conflicting hypotheses have been proposed about population connectivity and viability. To address this uncertainty, we generated both mitochondrial and MiSeq‐based microsatellite genotypes for 290 individuals ranging across western Tanzania. While shared mitochondrial haplotypes confirmed historical gene flow, our microsatellite analyses revealed two distinct clusters, suggesting two populations currently isolated from one another. However, we found evidence of high levels of gene flow maintained within each of these clusters, one of which covers an 18,000 km2 ecosystem. Landscape genetic analyses confirmed the presence of barriers to gene flow with rivers and bare habitats highly restricting chimpanzee movement. Our study demonstrates how advances in sequencing technologies, combined with the development of landscape genetics approaches, can resolve ambiguities in the genetic history of critical populations and better inform conservation efforts of endangered species.