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Map of Zambia showing the five main areas sampled: LV (Luangwa Valley); CO (Corridor); ZA (Lower Zambezi); KF (Kafue); and SI (Sioma Ngwezi). Eastern region consists of LV, CO and ZA. Western region consists of KF and SI. More detailed location information for each sample is available in S1 Table.
Source publication
Analysis of DNA sequence diversity at the 12S to 16S mitochondrial genes of 165 African lions (Panthera leo) from five main areas in Zambia has uncovered haplotypes which link Southern Africa with East Africa. Phylogenetic analysis suggests Zambia may serve as a bridge connecting the lion populations in southern Africa to eastern Africa, supporting...
Citations
... STRU CTU RE results from the SNP panel data from lions across their natural range identify four clusters: West & Central Africa, India (the two clades of the northern subspecies, P. leo leo), East Africa, Southern Africa (the two clades of the southern subspecies, P. leo melanochaita) (Fig. 2C). Main regions of admixture are Ethiopia and Zambia, as is visible in the STRU CTU RE plots (Fig. 2C), and was also found using microsatellite data [18,20] and mtDNA [37]. It is well known that STRU CTU RE is sensitive to groups of closely related individuals, such as siblings, family groups, or in our case, an inbred population [38,39] and that identification of ancestral populations may be an over-interpretation of the data, depending on demographic histories [40]. ...
Background
Previous phylogeographic studies of the lion (Panthera leo) have improved our insight into the distribution of genetic variation, as well as a revised taxonomy which now recognizes a northern (Panthera leo leo) and a southern (Panthera leo melanochaita) subspecies. However, existing whole range phylogeographic studies on lions either consist of very limited numbers of samples, or are focused on mitochondrial DNA and/or a limited set of microsatellites. The geographic extent of genetic lineages and their phylogenetic relationships remain uncertain, clouded by massive sampling gaps, sex-biased dispersal and incomplete lineage sorting.
Results
In this study we present results of low depth whole genome sequencing and subsequent variant calling in ten lions sampled throughout the geographic range, resulting in the discovery of >150,000 Single Nucleotide Polymorphisms (SNPs). Phylogenetic analyses revealed the same basal split between northern and southern populations, as well as four population clusters on a more local scale. Further, we designed a SNP panel, including 125 autosomal and 14 mitochondrial SNPs, which was tested on >200 lions from across their range. Results allow us to assign individuals to one of these four major clades (West & Central Africa, India, East Africa, or Southern Africa) and delineate these clades in more detail.
Conclusions
The results presented here, particularly the validated SNP panel, have important applications, not only for studying populations on a local geographic scale, but also for tracing samples of unknown origin for forensic purposes, and for guiding conservation management of ex situ populations. Thus, these genomic resources not only contribute to our understanding of the evolutionary history of the lion, but may also play a crucial role in conservation efforts aimed at protecting the species in its full diversity.
... As a rough guideline for acceptable translocation distance from a genetics perspective, we propose to use a distance which can reasonably be covered by natural, possibly multigenerational, dispersal. Natural dispersal of lions depends on a range of factors, including geography, landscape use, prey density and climate; males especially being capable dispersers, covering up to 200 km (Curry et al., 2015;Elliot et al., 2014;Packer and Pusey, 1987;Tumenta et al., 2013;Tuqa et al., 2014;Van Hooft et al., 2018). A stepping stone mode of dispersal over multiple generations therefore allows them to cover great distances. ...
... Although we focus our assessment on continent-wide patterns of diversity, population structure can also be determined on a more local scale. Few countries have had a country-wide or regional assessment of lion population structure so far, but if this information is available, e.g. for Tanzania (Smitz et al., 2018) or Zambia (Curry et al., 2015), we urge managers to include this information to make informed management decisions. ...
Conservation translocations have become an important management tool, particularly for large wildlife species such as the lion (Panthera leo). When planning translocations, the genetic background of populations needs to be taken into account; failure to do so risks disrupting existing patterns of genetic variation, ultimately leading to genetic homogenization, and thereby reducing resilience and adaptability of the species. We urge wildlife managers to include knowledge of the genetic background of source/target populations, as well as species‐wide patterns, in any management intervention. We present a hierarchical decision‐making tool in which we list 132 lion populations/Lion Conservation Units, and provide information on genetic assignment, uncertainty, and suitability for translocation for each source/target combination. By including four levels of suitability, from ‘first choice’ to ‘no option’, we provide managers with a range of options. To illustrate the extent of international trade of lions, and the potential disruption of natural patterns of intra‐specific diversity, we mined the CITES Trade Database for estimated trade quantities of live individuals imported into lion range states during the past 4 decades. We identified 1056 recorded individuals with a potential risk of interbreeding with wild lions, 772 being captive‐sourced. Scoring each of the records with our decision‐making tool illustrates that only 7% of the translocated individuals were ‘first choice’ and 73% were 'no option'. We acknowledge that other, non‐genetic factors are important in the decision‐making process, hence a pragmatic approach is needed. A framework in which source/target populations are scored based on suitability is not only relevant to lion, but also to other species of wildlife that are frequently translocated. We hope that the presented overview supports managers to include genetics in future management decisions, and contributes towards conservation of the lion in its full diversity.
... Although nuclear diversity has decreased significantly, mtDNA diversity has remained constant over time (Table 1). Mitochondrial DNA is matrilineally inherited, and localized studies show there is little or no female-mediated gene flow between subpopulations across Africa (Tende et al. 2014a;Curry et al. 2015;. Female lions primarily remain with their natal pride while males disperse (Pusey et al. 1987;Spong and Creel 2001 (Stander 2006;Ngwenya et al. 2013;Gatta 2016) and can span different habitats (Bauer et al. 2003;Lehmann et al. 2008;Loveridge et al. 2009). ...
Direct comparisons between historical and contemporary populations allow for detecting changes in genetic diversity through time and assessment of the impact of habitat fragmentation. Here, we determined the genetic architecture of both historical and modern lions to document changes in genetic diversity over the last century. We surveyed microsatellite and mitochondrial genome variation from 143 high-quality museum specimens of known provenance, allowing us to directly compare this information with data from several recently published nuclear and mitochondrial studies. Our results provide evidence for male-mediated gene flow and recent isolation of local subpopulations, likely due to habitat fragmentation. Nuclear markers showed a significant decrease in genetic diversity from the historical (HE=0.833) to the modern (HE=0.796) populations, while mitochondrial genetic diversity was maintained (Hd=0.98 for both). While the historical population appears to have been panmictic based on nDNA data, hierarchical structure analysis identified four tiers of genetic structure in modern populations and was able to detect most sampling locations. Mitogenome analyses identified 4 clusters: Southern, Mixed, Eastern, and Western; and were consistent between modern and historically sampled haplotypes. Within the last century, habitat fragmentation caused lion subpopulations to become more geographically isolated as human expansion changed the African landscape. This resulted in an increase in fine-scale nuclear genetic structure and loss of genetic diversity as lion subpopulations became more differentiated, while mitochondrial structure and diversity were maintained over time.
... Although nuclear diversity has decreased significantly, mtDNA diversity has remained constant over time (table 1). mtDNA is matrilineally inherited, and localized studies show that there is little or no femalemediated gene flow between subpopulations across Africa (Tende et al. 2014a;Curry et al. 2015. Female lions primarily remain with their natal pride, whereas males disperse (Pusey et al. 1987;Spong and Creel 2001). ...
Direct comparisons between historical and contemporary populations allow for detecting changes in genetic diversity through time and assessment of the impact of habitat fragmentation. Here, we determined the genetic architecture of both historical and modern lions to document changes in genetic diversity over the last century. We surveyed microsatellite and mitochondrial genome variation from 143 high-quality museum specimens of known provenance, allowing us to directly compare this information with data from several recently published nuclear and mitochondrial studies. Our results provide evidence for male-mediated gene flow and recent isolation of local subpopulations, likely due to habitat fragmentation. Nuclear markers showed a significant decrease in genetic diversity from the historical (HE=0.833) to the modern (HE=0.796) populations, while mitochondrial genetic diversity was maintained (Hd = 0.98 for both). While the historical population appears to have been panmictic based on nDNA data, hierarchical structure analysis identified four tiers of genetic structure in modern populations and was able to detect most sampling locations. Mitogenome analyses identified 4 clusters: Southern, Mixed, Eastern, and Western; and were consistent between modern and historically sampled haplotypes. Within the last century, habitat fragmentation caused lion subpopulations to become more geographically isolated as human expansion changed the African landscape. This resulted in an increase in fine-scale nuclear genetic structure and loss of genetic diversity as lion subpopulations became more differentiated, while mitochondrial structure and diversity were maintained over time.
... Although nuclear diversity has decreased significantly, mtDNA diversity has remained constant over time (Table 1). Mitochondrial DNA is matrilineally inherited, and localized studies show there is little or no female-mediated gene flow between subpopulations across Africa (32,46,47). Female lions primarily remain with their natal pride while males disperse (48,49). ...
The Scramble for Africa in the late 1800s marked the beginning of increased human population growth in Africa. Here, we determined the genetic architecture of both historical and modern lions to identify changes in genetic diversity that occurred during this period of landscape and anthropogenic change. We surveyed microsatellite and mitochondrial genetic variation from 143 high-quality museum specimens of known provenance and combined them with data from recently published nuclear and mitochondrial studies. Analysis of variation at 9 microsatellites and 280 polymorphic mitogenome SNPs indicate the presence of male-mediated gene flow and recent isolation of local subpopulations, likely due to habitat fragmentation. Nuclear markers showed a significant decrease in genetic diversity from the historical (HE=0.833) to the modern (HE=0.796) populations, while mitochondrial genetic diversity was maintained (Hd=0.98 for both). While the historical population appears to have been panmictic based on nDNA data, hierarchical structure analysis identified four tiers of fine structure in modern populations, able to detect most sampling locations. Mitochondrial analyses identified 4 clusters: Southern, Mixed, Eastern, and Western; and were consistent between modern and historically sampled haplotypes. Within the last century, habitat fragmentation caused lion subpopulations to become more isolated as human expansion changed the African landscape. This resulted in an increase in fine-scale nuclear genetic structure and loss of genetic diversity as subpopulations became more differentiated, while mitochondrial structure and diversity was maintained over time.
... Of the 12 samples eliminated, ten were duplicate individuals and two were not lions. The 409 samples analyzed consist of 324 males, 83 females, and 2 unknown (S1 Appendix), including all individuals previously studied in Curry et al. [12]. DNA was extracted using standard protocols and procedures used in the DNA Technologies Core Laboratory at Texas A&M University in College Station, TX (http://vetmed.tamu. ...
... edu/dnacore). PCR amplification was done using the KAPA Biosystems KAPA2G Robust HotStart PCR Kit with protocols described in Curry et al. [12] for mtDNA and Curry & Derr [14] for microsatellites. Cycling profiles for mtDNA and microsatellite amplification can be found in S2 Appendix. ...
... Diversity calculations and phylogenetic analyses were carried out as in Curry et al. [12] so a direct comparison could be made with the larger sample size. The data was analyzed using Arlequin v3.5 [18] as a full Zambian population and separated into eastern and western subpopulations. ...
The Luangwa Valley in eastern Zambia is a transverse offshoot of the Great Rift Valley system. This region appears to have an isolating effect as evidenced by suspected endemic subspecies, such as the Cookson’s wildebeest and Thornicroft’s giraffe. Recent mitochondrial DNA studies demonstrated that African lions in Zambia consist of two highly diverse eastern and western sub-populations. Herein, we report nuclear and mitochondrial DNA results from 409 lions that support this population substructure across Zambia but proposes only partial isolation of the Luangwa Valley with more movement between the populations than previously thought. Population assignment analysis identifies two populations with little evidence of admixture assigning lions to either the eastern or western sub-populations. A high occurrence of private alleles and clear evidence for a Wahlund effect further justify the presence of a highly structured population. But, while mitochondrial DNA analysis still shows little to no matrilineal gene flow (FST = 0.53) between sub-populations, microsatellite analysis suggests there is gene flow (FST = 0.04) with low but significant isolation-by-distance and an average of 6 migrants per generation. Evidence of isolation-by-distance is also found in factorial correspondence analysis with the Lower Zambezi National Park and eastern corridor clusters overlapping isolated clusters of the Luangwa Valley and western sub-population. From this evidence, the Luangwa Valley appears separated from the western sub-population with some dispersal through the southern regions of the eastern sub-population. Both the eastern and western sub-populations have high heterozygosity (0.68 and 0.69, respectively) and genetic diversity (0.47 and 0.50, respectively) values, indicative of genetically healthy populations.
... Three lion samples (Sample ID: 2011-000254, 2011000387 and 2011000446) were used to design the new STR primers. These samples have proven to have good amplification success and were used as positive controls in another study (Curry, White & Derr, 2015). PCR amplification was done using domestic cat primers (Menotti-Raymond et al., 1999) for the candidate microsatellites with the KAPA Biosystems Table 1. ...
... We tested the efficiency of the Leo STRs by fragment analysis of DNA from 30 lions (Table 3). DNA samples with SampleID: 2011000*** were chosen from an existing study (Curry et al., 2015). Samples with a range of mitochondrial (mtDNA) haplotypes were chosen to capture the widest range of diversity. ...
... Smears were marked as being 'fragmented' (*F*), with lower molecular weight smears (<1000 bp) additionally marked as 'degraded' (D**). Samples that had previous difficulty with amplification (Curry et al., 2015), likely due to some fragmentation, were marked as 'previously problematic' (P**). ...
Cross-species amplification using domestic cat microsatellite primers is the primary method used for nuclear genetic research in lions (Panthera leo). Genetic differences introduced over 10.8 million years of divergence between the two species make these markers problematic when using low quality and low quantity DNA, a common issue in wildlife genetic research. To increase amplification success of microsatellites in the lion, miniSTRs (<150 bp) with primers designed to be closer to the target region and specific to the lion were developed. Lion specific STRs were successfully designed for 14 of 17 commonly used microsatellites, 10 of 14 being miniSTRs, all with 100% amplification success when tested on 30 lion samples with DNA of varying quality and quantity.
... The African lion (Panthera leo) is listed as "Vulnerable" by the International Union for Conservation of Nature (IUCN), with a 43% population decline between 1993 and 2014 [1,19], and majority of lion populations exising in protected areas [20]. Several studies exist on various aspects of lion conservation in different African countries [21][22][23][24][25]. In Ethiopia, lions are generally considered important socially and culturally [26], however substantial gaps remain in our knowledge of Ethiopian lions. ...
Human-lion conflict is one of the leading threats to lion populations and while livestock loss is a source of conflict, the degree to which livestock depredation is tolerated by people varies between regions and across cultures. Knowledge of local attitudes towards lions and identification of drivers of human-lion conflict can help formulate mitigation measures aimed at promoting coexistence of humans with lions. We assessed locals’ attitudes towards lions in and around Gambella National Park and compared the findings with published data from Kafa Biosphere Reserve, both in western Ethiopia. We used household interviews to quantify livestock loss. We found that depredation was relatively low and that disease and theft were the top factors of livestock loss. Remarkably, however, tolerance of lions was lower around Gambella National Park than in Kafa Biosphere Reserve. Multivariate analysis revealed that education level, number of livestock per household, livestock loss due to depredation, and livestock loss due to theft were strong predictors of locals’ attitude towards lion population growth and conservation. We show that the amount of livestock depredation alone is not sufficient to understand human-lion conflicts and we highlight the importance of accounting for cultural differences in lion conservation. The low cultural value of lions in the Gambella region corroborate the findings of our study. In combination with growing human population and land-use change pressures, low cultural value poses serious challenges to long-term lion conservation in the Gambella region. We recommend using Arnstein’s ladder of participation in conservation education programs to move towards proactive involvement of locals in conservation.
... The contemporary lion collection consists of modern African lion DNA samples and appropriate data available from previous studies (Antunes et al 2008;Bertola et (Curry et al 2015). This sub-study uncovered genetic variation within the African lion population which had never previously been seen. ...
Sumatran Tigers Panthera tigris sumatrae inhabit 12 tiger conservation landscapes that stretch across Sumatra Island. Conservation efforts for these species require robust, information-based research, including a genetic approach. This study analyzed the haplotype diversity of P. t. sumatrae based on the mitochondrial CO1 (Cytochrome Oxidase Subunit 1) gene. Specifically, a nucleotide guanine at position 121 was found, distinguishing P. t. sumatrae from other tiger subspecies. Among the 17 sequences of P. t. sumatrae, two haplotypes were detected: 13 individuals were in haplotype 1 (Hap_1), and four individuals were in haplotype 2 (Hap_2). Hap_1 individuals predominantly originated from Riau and North Sumatra, while Hap_2 individuals were primarily from West Sumatra. Haplotype diversity (Hd) (0.382±0.113) and nucleotide diversity (pi) (0.00038±0.00011) confirmed the low genetic diversity. Five seized samples exhibited Hap_2, suggesting they might have originated from Riau and North Sumatra. However, this result cannot be described as current due to the significant changes in P. t. sumatrae habitat. Further genetic studies, such as whole-genome analysis, are needed to detect the origin and variation of P. t. sumatrae across all landscapes.
