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Genetic structure of fragmented southern populations of African Cape buffalo (Syncerus caffer caffer).

Smitz N, Cornélis D, Chardonnet P, Caron A, de Garine-Wichatitsky M, Jori F, Mouton A, Latinne A, Pigneur LM, Melletti M, Kanapeckas KL, Marescaux J, Pereira CL, Michaux J - BMC Evol. Biol. (2014)

Bottom Line: African wildlife experienced a reduction in population size and geographical distribution over the last millennium, particularly since the 19th century as a result of human demographic expansion, wildlife overexploitation, habitat degradation and cattle-borne diseases.We showed that the current genetic structure of southern African Cape buffalo populations results from both ancient and recent processes.The more recent S cluster genetic drift probably results of processes that occurred over the last centuries (habitat fragmentation, diseases).

View Article: PubMed Central - PubMed

ABSTRACT

Background: African wildlife experienced a reduction in population size and geographical distribution over the last millennium, particularly since the 19th century as a result of human demographic expansion, wildlife overexploitation, habitat degradation and cattle-borne diseases. In many areas, ungulate populations are now largely confined within a network of loosely connected protected areas. These metapopulations face gene flow restriction and run the risk of genetic diversity erosion. In this context, we assessed the "genetic health" of free ranging southern African Cape buffalo populations (S.c. caffer) and investigated the origins of their current genetic structure. The analyses were based on 264 samples from 6 southern African countries that were genotyped for 14 autosomal and 3 Y-chromosomal microsatellites.

Results: The analyses differentiated three significant genetic clusters, hereafter referred to as Northern (N), Central (C) and Southern (S) clusters. The results suggest that splitting of the N and C clusters occurred around 6000 to 8400 years ago. Both N and C clusters displayed high genetic diversity (mean allelic richness (A r ) of 7.217, average genetic diversity over loci of 0.594, mean private alleles (P a ) of 11), low differentiation, and an absence of an inbreeding depression signal (mean F IS = 0.037). The third (S) cluster, a tiny population enclosed within a small isolated protected area, likely originated from a more recent isolation and experienced genetic drift (F IS = 0.062, mean A r = 6.160, P a = 2). This study also highlighted the impact of translocations between clusters on the genetic structure of several African buffalo populations. Lower differentiation estimates were observed between C and N sampling localities that experienced translocation over the last century.

Conclusions: We showed that the current genetic structure of southern African Cape buffalo populations results from both ancient and recent processes. The splitting time of N and C clusters suggests that the current pattern results from human-induced factors and/or from the aridification process that occurred during the Holocene period. The more recent S cluster genetic drift probably results of processes that occurred over the last centuries (habitat fragmentation, diseases). Management practices of African buffalo populations should consider the micro-evolutionary changes highlighted in the present study.

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Plot of the factorial correspondence analysis (FCA). A.: Global FCA including the three clusters. Red: Southern cluster, Green: Central Cluster, Blue: Northern Cluster. B.: FCA on the Northern cluster. Turquoise: Marromeu samples, Dark blue: other populations included in the Northern cluster.
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Fig6: Plot of the factorial correspondence analysis (FCA). A.: Global FCA including the three clusters. Red: Southern cluster, Green: Central Cluster, Blue: Northern Cluster. B.: FCA on the Northern cluster. Turquoise: Marromeu samples, Dark blue: other populations included in the Northern cluster.

Mentions: Finally, the three clusters identified by STRUCTURE 2.3 appeared to be relatively well defined, with the Southern cluster being more clearly separated from the two others based on visual assessment of the FCA plot (Figure 6A.). Furthermore, within the Northern cluster, a very smooth separation appeared between the Marromeu SL compared to all other SLs included in this cluster (Figure 6B).Figure 6


Genetic structure of fragmented southern populations of African Cape buffalo (Syncerus caffer caffer).

Smitz N, Cornélis D, Chardonnet P, Caron A, de Garine-Wichatitsky M, Jori F, Mouton A, Latinne A, Pigneur LM, Melletti M, Kanapeckas KL, Marescaux J, Pereira CL, Michaux J - BMC Evol. Biol. (2014)

Plot of the factorial correspondence analysis (FCA). A.: Global FCA including the three clusters. Red: Southern cluster, Green: Central Cluster, Blue: Northern Cluster. B.: FCA on the Northern cluster. Turquoise: Marromeu samples, Dark blue: other populations included in the Northern cluster.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4232705&req=5

Fig6: Plot of the factorial correspondence analysis (FCA). A.: Global FCA including the three clusters. Red: Southern cluster, Green: Central Cluster, Blue: Northern Cluster. B.: FCA on the Northern cluster. Turquoise: Marromeu samples, Dark blue: other populations included in the Northern cluster.
Mentions: Finally, the three clusters identified by STRUCTURE 2.3 appeared to be relatively well defined, with the Southern cluster being more clearly separated from the two others based on visual assessment of the FCA plot (Figure 6A.). Furthermore, within the Northern cluster, a very smooth separation appeared between the Marromeu SL compared to all other SLs included in this cluster (Figure 6B).Figure 6

Bottom Line: African wildlife experienced a reduction in population size and geographical distribution over the last millennium, particularly since the 19th century as a result of human demographic expansion, wildlife overexploitation, habitat degradation and cattle-borne diseases.We showed that the current genetic structure of southern African Cape buffalo populations results from both ancient and recent processes.The more recent S cluster genetic drift probably results of processes that occurred over the last centuries (habitat fragmentation, diseases).

View Article: PubMed Central - PubMed

ABSTRACT

Background: African wildlife experienced a reduction in population size and geographical distribution over the last millennium, particularly since the 19th century as a result of human demographic expansion, wildlife overexploitation, habitat degradation and cattle-borne diseases. In many areas, ungulate populations are now largely confined within a network of loosely connected protected areas. These metapopulations face gene flow restriction and run the risk of genetic diversity erosion. In this context, we assessed the "genetic health" of free ranging southern African Cape buffalo populations (S.c. caffer) and investigated the origins of their current genetic structure. The analyses were based on 264 samples from 6 southern African countries that were genotyped for 14 autosomal and 3 Y-chromosomal microsatellites.

Results: The analyses differentiated three significant genetic clusters, hereafter referred to as Northern (N), Central (C) and Southern (S) clusters. The results suggest that splitting of the N and C clusters occurred around 6000 to 8400 years ago. Both N and C clusters displayed high genetic diversity (mean allelic richness (A r ) of 7.217, average genetic diversity over loci of 0.594, mean private alleles (P a ) of 11), low differentiation, and an absence of an inbreeding depression signal (mean F IS = 0.037). The third (S) cluster, a tiny population enclosed within a small isolated protected area, likely originated from a more recent isolation and experienced genetic drift (F IS = 0.062, mean A r = 6.160, P a = 2). This study also highlighted the impact of translocations between clusters on the genetic structure of several African buffalo populations. Lower differentiation estimates were observed between C and N sampling localities that experienced translocation over the last century.

Conclusions: We showed that the current genetic structure of southern African Cape buffalo populations results from both ancient and recent processes. The splitting time of N and C clusters suggests that the current pattern results from human-induced factors and/or from the aridification process that occurred during the Holocene period. The more recent S cluster genetic drift probably results of processes that occurred over the last centuries (habitat fragmentation, diseases). Management practices of African buffalo populations should consider the micro-evolutionary changes highlighted in the present study.

Show MeSH
Related in: MedlinePlus