The African Lion: A Long History of Interdisciplinary Research

Packer, Craig

doi:10.3389/fevo.2019.00259

Cited by 13 publications

(8 citation statements)

References 56 publications

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“…This study should aid in conservation efforts for the lion and enable studies across many facets of evolutionary biology, such as improving our knowledge of possible hybridization across the genus Panthera, or the basis of their phenotypic diversity. Undeniably, lion research has a historic legacy of collaboration across fields [65] and this genome will aid in future endeavors to prevent further loss of one of the world's most iconic species. Most importantly, it will enable low-cost resequencing efforts to be completed, in addition to a wide range of other genetic studies, in order to further the conservation efforts of the lion.…”

Section: Discussionmentioning

confidence: 99%

Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long-read data

et al. 2020

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Background: The lion (Panthera leo) is one of the most popular and iconic feline species on the planet, yet in spite of its popularity, the last century has seen massive declines for lion populations worldwide. Genomic resources for endangered species represent an important way forward for the field of conservation, enabling high-resolution studies of demography, disease, and population dynamics. Here, we present a chromosome-level assembly from a captive African lion from the Exotic Feline Rescue Center (Center Point, IN) as a resource for current and subsequent genetic work of the sole social species of the Panthera clade. Results: Our assembly is composed of 10x Genomics Chromium data, Dovetail Hi-C, and Oxford Nanopore longread data. Synteny is highly conserved between the lion, other Panthera genomes, and the domestic cat. We find variability in the length of runs of homozygosity across lion genomes, indicating contrasting histories of recent and possibly intense inbreeding and bottleneck events. Demographic analyses reveal similar ancient histories across all individuals during the Pleistocene except the Asiatic lion, which shows a more rapid decline in population size. We show a substantial influence on the reference genome choice in the inference of demographic history and heterozygosity. Conclusions:We demonstrate that the choice of reference genome is important when comparing heterozygosity estimates across species and those inferred from different references should not be compared to each other. In addition, estimates of heterozygosity or the amount or length of runs of homozygosity should not be taken as reflective of a species, as these can differ substantially among individuals. This high-quality genome will greatly aid in the continuing research and conservation efforts for the lion, which is rapidly moving towards becoming a species in danger of extinction.

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Section: Discussionmentioning

confidence: 99%

Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long-read data

et al. 2020

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“…This study will allow a surge forward in conservation efforts for the lion and enable studies across many facets of evolutionary biology, such as the highly conserved, yet phenotypic diversity of the genus Panthera. Undeniably, lion research has a historic legacy of collaboration across fields [77] and this genome will aid in future endeavors to prevent further loss of one of the world's most iconic species. Most importantly, it will enable low-cost resequencing efforts to be completed, in addition to a wide range of other genetic studies, in order to further the conservation efforts of the lion.…”

Section: Discussionmentioning

confidence: 99%

Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long read data

Armstrong

Taylor

Miller

et al. 2019

Preprint

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The lion (Panthera leo) is one of the most popular and iconic feline species on the planet, yet in spite of its popularity, the last century has seen massive declines for lion populations worldwide. Genomic resources for endangered species represent an important way forward for the field of conservation, enabling high-resolution studies of demography, disease, and population dynamics. Here, we present a chromosome-level assembly for the captive African lion from the Exotic Feline Rescue Center as a resource for current and subsequent genetic work of the sole social species of the Panthera clade. Our assembly is composed of 10x Genomics Chromium data, Dovetail Hi-C, and Oxford Nanopore long-read data. Synteny is highly conserved between the lion, other Panthera genomes, and the domestic cat. We find variability in the length and levels of homozygosity across the genomes of the lion sequenced here and other previous published resequence data, indicating contrasting histories of recent and ancient small population sizes and/or inbreeding. Demographic analyses reveal similar histories across all individuals except the Asiatic lion, which shows a more rapid decline in population size. This high-quality genome will greatly aid in the continuing research and conservation efforts for the lion. using the domestic cat or tiger as a reference [18]. Felid karyotypes are thought to be highly conserved [19,20], but studies have shown a reference mapping bias for estimation of statistics such as heterozygosity [21] and accurate allele calling [22], both of which are important for assessing population history.The causes of the decline in lions are multifactorial. Lions have been hunted by humans for thousands of years, possibly first as a direct competitor and threat to our survival [23], for initiation rituals and rites of passage (e.g. [24][25][26]), to reduce predation of domesticated animals, and more recently for sport [27][28][29][30]. The recent rise of illegal trade in lion parts and illicit breeding practices has escalated over the past ten years, bringing hunting practices and international laws into the spotlight. In addition, several documentaries have exposed the lion breeding industry within South Africa, which uses fenced lions for 'petting', canned hunting experiences, and ultimately as skeletons for export, likely destined for Asian medicines [31]. Accurate and rapid genotyping could aid law enforcement to reveal whether the origins of trafficked goods are from wild or captive populations.Moreover, rapid population decline has put lions at the forefront of the conservation debate over translocations and how best to manage populations. Many efforts to restore previous populations have focused on translocation lions within and between various South African lion populations (e.g. [32,33]. Information about local population adaptation, deleterious alleles, and potential inbreeding is lacking, which further complicates managed relocations. While increasing genetic diversity remains a widely accepted conservation goal...

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“…We deployed 210 camera traps in a 1,125‐km 2 grid within the central part of Serengeti National Park. The camera trap grid lies within the Serengeti Lion Project’s long‐term (~50 yr) monitoring area (Packer et al 2005, Packer 2019) and covers an intersection of open plains and woodland savannah (Fig. 1).…”

Section: Methodsmentioning

confidence: 99%

“…Last, the Serengeti is one of the most well‐studied ecosystems with decades of prior research (Sinclair and Norton‐Griffiths 1979, Sinclair and Arcese 1995, Sinclair et al 2008, 2015). Multiple years of camera trap data on the ungulate community (Swanson et al 2015) along with long‐term predator monitoring (Packer et al 2005, Packer 2019) and remotely sensed observations of resource availability offer an unprecedented opportunity to examine the drivers of mixed‐species groups over space and time.…”

Section: Introductionmentioning

confidence: 99%

Mixed‐species groups of Serengeti grazers: a test of the stress gradient hypothesis

Beaudrot

Palmer

Anderson

et al. 2020

Ecology

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Understanding the role of species interactions within communities is a central focus of ecology. A key challenge is to understand variation in species interactions along environmental gradients. The stress gradient hypothesis posits that positive interactions increase and competitive interactions decrease with increasing consumer pressure or environmental stress. This hypothesis has received extensive attention in plant community ecology, but only a handful of tests in animals. Furthermore, few empirical studies have examined multiple co‐occurring stressors. Here we test predictions of the stress gradient hypothesis using the occurrence of mixed‐species groups in six common grazing ungulate species within the Serengeti‐Mara ecosystem. We use mixed‐species groups as a proxy for potential positive interactions because they may enhance protection from predators or increase access to high‐quality forage. Alternatively, competition for resources may limit the formation of mixed‐species groups. Using more than 115,000 camera trap observations collected over 5 yr, we found that mixed‐species groups were more likely to occur in risky areas (i.e., areas closer to lion vantage points and in woodland habitat where lions hunt preferentially) and during time periods when resource levels were high. These results are consistent with the interpretation that stress from high predation risk may contribute to the formation of mixed‐species groups, but that competition for resources may prevent their formation when food availability is low. Our results are consistent with support for the stress gradient hypothesis in animals along a consumer pressure gradient while identifying the potential influence of a co‐occurring stressor, thus providing a link between research in plant community ecology on the stress gradient hypothesis, and research in animal ecology on trade‐offs between foraging and risk in landscapes of fear.

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The African Lion: A Long History of Interdisciplinary Research

Cited by 13 publications

References 56 publications

Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long-read data

Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long-read data

Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long read data

Mixed‐species groups of Serengeti grazers: a test of the stress gradient hypothesis

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