Lions in West-Africa

[chui_]

(09-01-2019, 10:13 PM)BorneanTiger Wrote: The Atlas leopard (formerly Panthera pardus panthera) got lumped with other mainland African leopards, as well as the Zanzibar leopard (formerly Panthera pardus adersi, which is possibly extant) into a single African subspecies, Panthera pardus pardus, in the same way that the Barbary lion (Panthera leo leo) got lumped with the Asiatic lion (formerly Panthera leo persica), West African lion (formerly Panthera leo senegalensis), and (northern) Central African lion (formerly Panthera leo azandica / kamptzi / senegalensis) into a single Northern subspecies (Panthera leo leo), but that doesn't mean that there are no genetic differences between these lions. On the contrary, even if Western and (northern) Central African lions are more closely related to the Asiatic and Barbary lions than to Southern and South-Eastern Africans, they still have genetic differences, partly as shown in this thread: 

Those studies on the phylogentics of lions are more recent and appear to be more comprehensive than the studies which concluded there was no subdivision among African leopards (from 1996 and 2001). The point I was trying to make is that the lack of recognition as a distinct subspecies for the Barbary leopard in the last 2 decades meant there was little to no effort to preserve this population. In contrast, other highly endangered leopard populations like the Amur and Arabian leopards have received much more attention because they have mostly been recognized as distinct subspecies.

The most recent study on the phylogenitics of African leopards using a more comprehensive sample suggests that there is indeed significant subdivision among African leopards – comparable to or exceeding that which exists between recognized Asian subspecies. The authors also noted that further diversity may be expected with samples from North Africa and North/East Africa.  

"Historical mitochondrial diversity in African leopards (Panthera pardus) revealed by archival museum specimens." 2017 by Anco et al.

Abstract 

Once found throughout Africa and Eurasia, the leopard (Panthera pardus) was recently uplisted from Near Threatened to Vulnerable by the International Union for the Conservation of Nature (IUCN). Historically, more than 50% of the leopard's global range occurred in continental Africa, yet sampling from this part of the species' distribution is only sparsely represented in prior studies examining patterns of genetic variation at the continental or global level. Broad sampling to determine baseline patterns of genetic variation throughout the leopard's historical distribution is important, as these measures are currently used by the IUCN to direct conservation priorities and management plans. By including data from 182 historical museum specimens, faecal samples from ongoing field surveys, and published sequences representing sub-Saharan Africa, we identify previously unrecognized genetic diversity in African leopards. Our mtDNA data indicates high levels of divergence among regional populations and strongly differentiated lineages in West Africa on par with recent studies of other large vertebrates. We provide a reference benchmark of genetic diversity in African leopards against which future monitoring can be compared. These findings emphasize the utility of historical museum collections in understanding the processes that shape present biodiversity. Additionally, we suggest future research to clarify African leopard taxonomy and to differentiate between delineated units requiring monitoring or conservation action.

Other relevant excerpts from this paper.

"Leopards exhibited population structuring at large geographic scales (West, Central-East/Central-Southern, and Southern Africa), suggesting strong evidence against panmixia in this species. AMOVA and pairwise FST analyses support differentiation in the ND-5 locus spanning five major haplogroups: West Africa, Coastal West-Central Africa, Central- East-Africa, Central-Southern Africa, and Southern Africa. Distinction between CEA and CSA as two independent regional populations is supported by pairwise FST analyses (Figure 4). Although still high, FST[CEA-CSA]¼0.40, was the lowest among all African leopard population comparisons. CSA showed higher levels of differentiation from WA and CWCA leopard populations, than the latter two did to CEA, indicating that CSA leopards are reproducing in isolation from neighbouring populations (Figure 4). Furthermore, CSA exhibited the highest levels of differentiation when compared with the two selected Asiatic subspecies: FST[CSA-nimr]¼0.98 and FST[CSA-saxicolor]¼0.97 (Figure 4)."

"The African leopard harbours a greater degree of genetic diversity than previously indicated and is partitioned in a pattern providing strong support for significant genetic subdivision. Our pairwise FST analyses using mtDNA revealed leopard populations throughout sub-Saharan Africa retain highly divergent copies of the ND-5 locus on levels approaching, and in some instances exceeding, FST values observed between Asiatic populations (Arabian and Persian leopards) presently recognized by the IUCN as separate subspecies (Figure 4). AMOVA revealed population structuring indicating a lack of gene flow between larger geographic regions (West Africa, Central-East/Central-Southern Africa, and Southern Africa) and among all the populations within regions. Two populations, CEA and CSA showed decreased pairwise differences relative to other populations, which could be an artifact of decreased sampling. Lastly, the star-like phylogeny, widespread distribution, and connectedness of the H10 haplotype points to a likely origin of diversity for the ancestral haplotype of this locus in Central and East Africa. We caution this work may not fully express the degree of genetic diversity present in African leopards, especially given sampling deficiencies in North Africa, parts of West Africa, and in Northeastern Africa.

This study has raised important questions regarding the taxonomic status of leopards in Africa. First, these findings support a distinction between African populations and Arabian and Persian leopard populations. We found additional strong support for an East-West split in African leopards, which may correspond to previously hypothesized taxonomic groupings (Figure 1, Table 1) and is congruent with numerous recent phylogeographic analyses of widespread African taxa (Moodley & Bruford 2007; Lorenzen et al. 2012; Dobigny et al. 2013; Smitz et al. 2013; Bertola et al. 2016; Fennessy et al. 2016). More sampling is needed to accurately delineate geographic features acting as potential barriers to gene flow (e.g. Sanaga River in Central Cameroon), while a suture zone has been identified between CWCA and CEA populations (Figures 2 and 3). In addition, we have identified previously unrecognized levels of genetic diversity in historical collections of African leopards not represented in contemporary leopard populations. While only based on mtDNA, the reconstruction of a haplotype network using novel samples of African leopards has reopened a >15-year-old conversation regarding African leopard diversity and taxonomy. We acknowledge that our results are limited by the use of mtDNA, and consequently single locus data. We therefore, strongly recommend multilocus sampling to investigate whether African leopards exhibit evidence of discordance between mitochondrial and nuclear markers (Toews & Brelsford 2012). These findings will provide the foundation for our ongoing analysis of temporal changes in phylogeographic patterns using sequence capture from historical collections, which will contribute to management and planning strategies to conserve remaining genetic diversity in the African leopard." Reply