Genomic analysis supports Cape Lion population connectivity prior to colonial eradication and extinction.

Cape lions (Panthera leo melanochaitus) formerly ranged throughout the grassland plains of the "Cape Flats" in what is today known as the Western Cape Province, South Africa. Cape lions were likely eradicated because of overhunting and habitat loss after European colonization. European naturalists originally described Cape lions as "black-maned lions" and claimed that they were phenotypically distinct. However, other depictions and historical descriptions of lions from the Cape report mixed or light coloration and without black or extensively developed manes. These findings suggest that, rather than forming a distinct population, Cape lions may have had phenotypic and genotypic variation similar to other African lions. Here we investigate Cape lion genome characteristics, population dynamics, and genetic distinctiveness prior to their extinction. We generated genomic data from 2 historic Cape lions to compare to 118 existing high-coverage mitogenomes, and low-coverage nuclear genomes of 53 lions from 13 African countries. We show that, before their eradication, lions from the Cape Flats had diverse mitogenomes and nuclear genomes that clustered with lions from both southern and eastern Africa. Cape lions had high genome-wide heterozygosity and low inbreeding coefficients, indicating that populations in the Cape Flats went extinct so rapidly that genomic effects associated with long-term small population size and isolation were not detectable. Our findings do not support the characterization of Cape lions as phylogeographically distinct, as originally put forth by some European naturalists, and illustrates how alternative knowledge systems, for example, Indigenous perspectives, could potentially further inform interpretations of species histories.

Getting to the Meat of It: The Effects of a Captive Diet upon the Skull Morphology of the Lion and Tiger.

Zoo animals are crucial for conserving and potentially re-introducing species to the wild, yet it is known that the morphology of captive animals differs from that of wild animals. It is important to know how and why zoo and wild animal morphology differs to better care for captive animals and enhance their survival in reintroductions, and to understand how plasticity may influence morphology, which is supposedly indicative of evolutionary relationships. Using museum collections, we took 56 morphological measurements of skulls and mandibles from 617 captive and wild lions and tigers, reflecting each species' recent historical range. Linear morphometrics were used to identify differences in size and shape. Skull size does not differ between captive and wild lions and tigers, but skull and mandible shape does. Differences occur in regions associated with biting, indicating that diet has influenced forces acting upon the skull and mandible. The diets of captive big cats used in this study predominantly consisted of whole or partial carcasses, which closely resemble the mechanical properties of wild diets. Thus, we speculate that the additional impacts of killing, manipulating and consuming large prey in the wild have driven differentiation between captive and wild big cats.

Ancient DNA reveals genetic admixture in China during tiger evolution.

The tiger (Panthera tigris) is a charismatic megafauna species that originated and diversified in Asia and probably experienced population contraction and expansion during the Pleistocene, resulting in low genetic diversity of modern tigers. However, little is known about patterns of genomic diversity in ancient populations. Here we generated whole-genome sequences from ancient or historical (100-10,000 yr old) specimens collected across mainland Asia, including a 10,600-yr-old Russian Far East specimen (RUSA21, 8× coverage) plus six ancient mitogenomes, 14 South China tigers (0.1-12×) and three Caspian tigers (4-8×). Admixture analysis showed that RUSA21 clustered within modern Northeast Asian phylogroups and partially derived from an extinct Late Pleistocene lineage. While some of the 8,000-10,000-yr-old Russian Far East mitogenomes are basal to all tigers, one 2,000-yr-old specimen resembles present Amur tigers. Phylogenomic analyses suggested that the Caspian tiger probably dispersed from an ancestral Northeast Asian population and experienced gene flow from southern Bengal tigers. Lastly, genome-wide monophyly supported the South China tiger as a distinct subspecies, albeit with mitochondrial paraphyly, hence resolving its longstanding taxonomic controversy. The distribution of mitochondrial haplogroups corroborated by biogeographical modelling suggested that Southwest China was a Late Pleistocene refugium for a relic basal lineage. As suitable habitat returned, admixture between divergent lineages of South China tigers took place in Eastern China, promoting the evolution of other northern subspecies. Altogether, our analysis of ancient genomes sheds light on the evolutionary history of tigers and supports the existence of nine modern subspecies.

Phenotypic plasticity determines differences between the skulls of tigers from mainland Asia.

Tiger subspecific taxonomy is controversial because of morphological and genetic variation found between now fragmented populations, yet the extent to which phenotypic plasticity or genetic variation affects phenotypes of putative tiger subspecies has not been explicitly addressed. In order to assess the role of phenotypic plasticity in determining skull variation, we compared skull morphology among continental tigers from zoos and the wild. In turn, we examine continental tiger skulls from across their wild range, to evaluate how the different environmental conditions experienced by individuals in the wild can influence morphological variation. Fifty-seven measurements from 172 specimens were used to analyse size and shape differences among wild and captive continental tiger skulls. Captive specimens have broader skulls, and shorter rostral depths and mandible heights than wild specimens. In addition, sagittal crest size is larger in wild Amur tigers compared with those from captivity, and it is larger in wild Amur tigers compared with other wild continental tigers. The degree of phenotypic plasticity shown by the sagittal crest, skull width and rostral height suggests that the distinctive shape of Amur tiger skulls compared with that of other continental tigers is mostly a phenotypically plastic response to differences in their environments.

Current trends suggest most Asian countries are unlikely to meet future biodiversity targets on protected areas.

Aichi Target 11 committed governments to protect ≥17% of their terrestrial environments by 2020, yet it was rarely achieved, raising questions about the post-2020 Global Biodiversity Framework goal to protect 30% by 2030. Asia is a challenging continent for such targets, combining high biodiversity with dense human populations. Here, we evaluated achievements in Asia against Aichi Target 11. We found that Asia was the most underperforming continent globally, with just 13.2% of terrestrial protected area (PA) coverage, averaging 14.1 ± SE 1.8% per country in 2020. 73.1% of terrestrial ecoregions had <17% representation and only 7% of PAs even had an assessment of management effectiveness. We found that a higher agricultural land in 2015 was associated with lower PA coverage today. Asian countries also showed a remarkably slow average annual pace of 0.4 ± SE 0.1% increase of PA extent. These combined lines of evidence suggest that the ambitious 2030 targets are unlikely to be achieved in Asia unless the PA coverage to increase 2.4-5.9 times faster. We provided three recommendations to support Asian countries to meet their post-2020 biodiversity targets: complete reporting and the wider adoption "other effective area-based conservation measures"; restoring disturbed landscapes; and bolstering transboundary PAs.

Sex differences in the winter activity of desert hedgehogs (Paraechinus aethiopicus) in a resource-rich habitat in Qatar.

Hedgehogs' wide distribution and breadth of habitat use means they are a good model taxon for investigating behavioural responses to winter conditions, such as low temperatures and resource availability. We investigated the over-winter behaviour of desert hedgehogs (Paraechinus aethiopicus) in Qatar by radio-tracking 20 individuals and monitoring the body mass of 31 hedgehogs. Females spent more nights (38.63% of nights tracked) inactive than males (12.6%) and had lower monthly activity levels. The mean temperature on nights where hedgehogs were inactive was 14.9 °C compared with 17.0 °C when hedgehogs were active. By December, females lost a higher percentage of their November body mass than did males, but by February males had lost a higher percentage than females. We conclude that these sex differences in behaviour are a result of differing reproductive strategies with males becoming more active early in spring to search for mates, whereas female hedgehogs conserve energy for producing and raising young and avoid harassment by males. The winter activity of males may be facilitated by the resource-rich environment created by humans at this study site, and basking behaviour. This study highlights intraspecific and interspecific variation in behavioural strategies/tactics in response to winter conditions.

Lions and brown bears colonized North America in multiple synchronous waves of dispersal across the Bering Land Bridge.

The Bering Land Bridge connecting North America and Eurasia was periodically exposed and inundated by oscillating sea levels during the Pleistocene glacial cycles. This land connection allowed the intermittent dispersal of animals, including humans, between Western Beringia (far northeast Asia) and Eastern Beringia (northwest North America), changing the faunal community composition of both continents. The Pleistocene glacial cycles also had profound impacts on temperature, precipitation and vegetation, impacting faunal community structure and demography. While these palaeoenvironmental impacts have been studied in many large herbivores from Beringia (e.g., bison, mammoths, horses), the Pleistocene population dynamics of the diverse guild of carnivorans present in the region are less well understood, due to their lower abundances. In this study, we analyse mitochondrial genome data from ancient brown bears (Ursus arctos; n = 103) and lions (Panthera spp.; n = 39), two megafaunal carnivorans that dispersed into North America during the Pleistocene. Our results reveal striking synchronicity in the population dynamics of Beringian lions and brown bears, with multiple waves of dispersal across the Bering Land Bridge coinciding with glacial periods of low sea levels, as well as synchronous local extinctions in Eastern Beringia during Marine Isotope Stage 3. The evolutionary histories of these two taxa underline the crucial biogeographical role of the Bering Land Bridge in the distribution, turnover and maintenance of megafaunal populations in North America.

Genomic evidence for the Chinese mountain cat as a wildcat conspecific (Felis silvestris bieti) and its introgression to domestic cats.

The Qinghai-Tibet Plateau endemic Chinese mountain cat has a controversial taxonomic status, whether it is a true species or a wildcat (Felis silvestris) subspecies and whether it has contributed to cat (F. s. catus) domestication in East Asia. Here, we sampled F. silvestris lineages across China and sequenced 51 nuclear genomes, 55 mitogenomes, and multilocus regions from 270 modern or museum specimens. Genome-wide analyses classified the Chinese mountain cat as a wildcat conspecific F. s. bieti, which was not involved in cat domestication of China, thus supporting a single domestication origin arising from the African wildcat (F. s. lybica). A complex hybridization scenario including ancient introgression from the Asiatic wildcat (F. s. ornata) to F. s. bieti, and contemporary gene flow between F. s. bieti and sympatric domestic cats that are likely recent Plateau arrivals, raises the prospect of disrupted wildcat genetic integrity, an issue with profound conservation implications.

A genomic exploration of the early evolution of extant cats and their sabre-toothed relatives.

Background: The evolutionary relationships of Felidae during their Early-Middle Miocene radiation is contentious. Although the early common ancestors have been subsumed under the grade-group Pseudaelurus, this group is thought to be paraphyletic, including the early ancestors of both modern cats and extinct sabretooths. Methods: Here, we sequenced a draft nuclear genome of Smilodon populator, dated to 13,182 ± 90 cal BP, making this the oldest palaeogenome from South America to date, a region known to be problematic for ancient DNA preservation. We analysed this genome, together with genomes from other extinct and extant cats to investigate their phylogenetic relationships. Results: We confirm a deep divergence (~20.65 Ma) within sabre-toothed cats. Through the analysis of both simulated and empirical data, we show a lack of gene flow between Smilodon and contemporary Felidae. Conclusions: Given that some species traditionally assigned to Pseudaelurus originated in the Early Miocene ~20 Ma, this indicates that some species of Pseudaelurus may be younger than the lineages they purportedly gave rise to, further supporting the hypothesis that Pseudaelurus was paraphyletic.

Extended survival of Pleistocene Siberian wolves into the early 20th century on the island of Honshu.

The Japanese or Honshu wolf was one the most distinct gray wolf subspecies due to its small stature and endemicity to the islands of Honshu, Shikoku, and Kyushu. Long revered as a guardian of farmers and travellers, it was persecuted from the 17th century following a rabies epidemic, which led to its extinction in the early 20th century. To better understand its evolutionary history, we sequenced the nuclear genome of a 19th century Honshu wolf specimen to an average depth of coverage of 3.7✕. We find Honshu wolves were closely related to a lineage of Siberian wolves that were previously believed to have gone extinct in the Late Pleistocene, thereby extending the survival of this ancient lineage until the early 20th century. We also detected significant gene flow between Japanese dogs and the Honshu wolf, corroborating previous reports on Honshu wolf dog interbreeding.

The occurrence and distribution of bats in Qatar.

The distributions of bat species in Qatar have not previously been recorded. We conducted the first nation-wide survey of bats in Qatar. Based on sonogram analysis, we identified Asellia tridens, Otonycteris hemprichii, and Pipistrellus kuhlii. The most commonly recorded species was Asellia tridens, the only species recorded in the northern half of the country. Contrary to our prediction, the likelihood of recording bats was not higher in the northern half of the country where there are many irrigated farms. The distributions of the bat species may result from differences in human land use and disturbance, and from the distance to the main body of the Arabian Peninsula. A key habitat feature for Asellia tridens and Otonycteris hemprichii may be the presence of roosting sites in less disturbed sinkholes/caves, which are therefore crucial for bat conservation.

Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens.

Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1-4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of which were key characteristics for predation on Pleistocene megafauna [5]. Previous mitochondrial DNA phylogenies suggested that it was a highly divergent sister lineage to all extant cat species [6-8]. However, mitochondrial phylogenies can be misled by hybridization [9], incomplete lineage sorting (ILS), or sex-biased dispersal patterns [10], which might be especially relevant for Homotherium since widespread mito-nuclear discrepancies have been uncovered in modern cats [10]. To examine the evolutionary history of Homotherium, we generated a ∼7x nuclear genome and a ∼38x exome from H. latidens using shotgun and target-capture sequencing approaches. Phylogenetic analyses reveal Homotherium as highly divergent (∼22.5 Ma) from living cat species, with no detectable signs of gene flow. Comparative genomic analyses found signatures of positive selection in several genes, including those involved in vision, cognitive function, and energy consumption, putatively consistent with diurnal activity, well-developed social behavior, and cursorial hunting [5]. Finally, we uncover relatively high levels of genetic diversity, suggesting that Homotherium may have been more abundant than the limited fossil record suggests [3, 4, 11-14]. Our findings complement and extend previous inferences from both the fossil record and initial molecular studies, enhancing our understanding of the evolution and ecology of this remarkable lineage.

Characteristics and Demography of a Free-Ranging Ethiopian Hedgehog, Paraechinus aethiopicus, Population in Qatar.

Information on population characteristics of Paraechinusis is valuable for ensuring long term survival of populations, however, studies are currently lacking. Here we investigate the population dynamics of Ethiopian hedgehogs based on a capture-mark-recapture study in Qatar by fitting Jolly-Seber and Cormack-Jolly-Seber models. Over the 19 months of the study, we estimate a mean population of 60 hedgehogs, giving a density of 7 hedgehogs per km2 in our 8.5 km2 search area. The monthly abundance of hedgehogs decreased over the study and although survival was constant over the study period, with a mean monthly rate of 75%, there was a decline in the number of new entrants over time. We also studied these parameters over one year, excluding winter, and found that monthly estimates of juvenile and subadult survival decreased over time. We surmise that survival of juveniles may be a factor in the decrease in abundance and there may be implications for the persistence of this population, with anthropogenic influenced resources playing an important role. We caught between 91.3% and 100% of the estimated population at this site, indicating that our capture methodology was efficient. We conclude that the methodology used here is transferrable to other hedgehog species.

The evolutionary history of extinct and living lions.

Lions are one of the world's most iconic megafauna, yet little is known about their temporal and spatial demographic history and population differentiation. We analyzed a genomic dataset of 20 specimens: two ca. 30,000-y-old cave lions (Panthera leo spelaea), 12 historic lions (Panthera leo leo/Panthera leo melanochaita) that lived between the 15th and 20th centuries outside the current geographic distribution of lions, and 6 present-day lions from Africa and India. We found that cave and modern lions shared an ancestor ca. 500,000 y ago and that the 2 lineages likely did not hybridize following their divergence. Within modern lions, we found 2 main lineages that diverged ca. 70,000 y ago, with clear evidence of subsequent gene flow. Our data also reveal a nearly complete absence of genetic diversity within Indian lions, probably due to well-documented extremely low effective population sizes in the recent past. Our results contribute toward the understanding of the evolutionary history of lions and complement conservation efforts to protect the diversity of this vulnerable species.

Post K-Pg diversification of the mammalian order Eulipotyphla as suggested by phylogenomic analyses of ultra-conserved elements.

The origin of the mammalian order Eulipotyphla has been debated intensively with arguments around whether they began diversifying before or after the Cretaceous-Palaeogene (K-Pg) boundary at 66 Ma. Here, we used an in-solution nucleotide capture method and next generation DNA sequencing to determine the sequence of hundreds of ultra-conserved elements (UCEs), and conducted phylogenomic and molecular dating analyses for the four extant eulipotyphlan lineages-Erinaceidae, Solenodontidae, Soricidae, and Talpidae. Concatenated maximum-likelihood analyses with single or partitioned models and a coalescent species-tree analysis showed that divergences among the four major eulipotyphlan lineages occurred within a short period of evolutionary time, but did not resolve the interrelationships among them. Alternative suboptimal phylogenetic hypotheses received consistently the same amount of support from different UCE loci, and were not significantly different from the maximum likelihood tree topology, suggesting the prevalence of stochastic lineage sorting. Molecular dating analyses that incorporated among-lineage evolutionary rate differences supported a scenario where the four eulipotyphlan families diversified between 57.8 and 63.2 Ma. Given short branch lengths with low support values, traces of rampant genome-wide stochastic lineage sorting, and post K-Pg diversification, we concluded that the crown eulipotyphlan lineages arose through a rapid diversification after the K-Pg boundary when novel niches were created by the mass extinction of species.

A comparison of the Ranging behaviour and habitat use of the Ethiopian hedgehog (Paraechinus aethiopicus) in Qatar with hedgehog taxa from temperate environments.

We investigated seasonal changes in the ecology and behaviour of the Ethiopian hedgehog (Paraechinus aethiopicus) in Qatar, particularly in respect to differences in behaviour between hedgehogs living in arid environments and hedgehogs in temperate mesic environments. These comparisons will allow us to explore behavioural adaptations to different environments across hedgehog taxa. We radio-tracked 30 hedgehogs in Qatar over two years, and measured home range size, habitat preference, travel speed, activity and body mass. Whilst we found no difference in body mass between males and females, male home range size was over twice as large as that for females. Unlike hedgehogs in Europe, males maintained large home ranges during the non-breeding season. This behaviour may be sustained by the low cost of maintaining a large home range; males travelled less far per hour during the non-breeding season. Habitat use was non-random; arid areas with human influence, including rubbish dumping sites, was the most selected habitat type compared with its availability. Dense scrub and/or trees was the most selected habitat for nesting. This study gives us greater understanding as to how hedgehog taxa are adapted to their environment and therefore how they may be conserved, for example, the recent increase of "lower" level human activities, including irrigated farms and food waste, in harsh arid environments may have influenced the space use by Ethiopian hedgehogs.

No longer locally extinct? Tracing the origins of a lion (Panthera leo) living in Gabon.

Lions (Panthera leo) are of particular conservation concern due to evidence of recent, widespread population declines in what has hitherto been seen as a common species, robust to anthropogenic disturbance. Here we use non-invasive methods to recover complete mitochondrial genomes from single hair samples collected in the field in order to explore the identity of the Gabonese Plateaux Batéké lion. Comparison of the mitogenomes against a comprehensive dataset of African lion sequences that includes relevant geographically proximate lion populations from both contemporary and ancient sources, enabled us to identify the Plateaux Batéké lion as a close maternal relative to now extirpated populations found in Gabon and nearby Congo during the twentieth century, and to extant populations of Southern Africa. Our study demonstrates the relevance of ancient DNA methods to field conservation work, and the ability of trace field samples to provide copious genetic information about free-ranging animals.

Hedgehogs on the move: Testing the effects of land use change on home range size and movement patterns of free-ranging Ethiopian hedgehogs.

Degradation and alteration of natural environments because of agriculture and other land uses have major consequences on vertebrate populations, particularly on spatial organization and movement patterns. We used GPS tracking to study the effect of land use and sex on the home range size and movement of a typical model species, the Ethiopian hedgehogs. We used free-ranging hedgehogs from two areas with different land use practices: 24 from an area dominated by irrigated farms (12 ♂♂, 12 ♀♀) and 22 from a natural desert environment within a biosphere reserve (12 ♂♂, 10 ♀♀). Animals were significantly heavier in the resource-rich irrigated farms area (417.71 ±12.77SE g) in comparison to the natural desert area (376.37±12.71SE g). Both habitat and sex significantly influenced the home range size of hedgehogs. Home ranges were larger in the reserve than in the farms area. Total home ranges averaged 103 ha (±17 SE) for males and 42 ha (±11SE) for females in the farms area, but were much larger in the reserve averaging 230 ha (±33 SE) for males and 150 ha (±29 SE) for females. The home ranges of individuals of both sexes overlapped. Although females were heavier than males, body weight had no effect on home range size. The results suggest that resources provided in the farms (e.g. food, water, and shelters) influenced animal density and space use. Females aggregated around high-resource areas (either farms or rawdhats), whereas males roamed over greater distances, likely in search of mating opportunities to maximize reproductive success. Most individual home ranges overlapped with many other individuals of either sex, suggesting a non-territorial, promiscuous mating. Patterns of space use and habitat utilization are key factors in shaping aspects of reproductive biology and mating system. To minimize the impacts of agriculture on local wildlife, we recommend that biodiversity-friendly agro-environmental schemes be introduced in the Middle East where the transformation from dry lands to 'islands of fertility' is often extreme.

Molecular phylogenetic analysis of nuclear genes suggests a Cenozoic over-water dispersal origin for the Cuban solenodon.

The Cuban solenodon (Solenodon cubanus) is one of the most enigmatic mammals and is an extremely rare species with a distribution limited to a small part of the island of Cuba. Despite its rarity, in 2012 seven individuals of S. cubanus were captured and sampled successfully for DNA analysis, providing new insights into the evolutionary origin of this species and into the origins of the Caribbean fauna, which remain controversial. We conducted molecular phylogenetic analyses of five nuclear genes (Apob, Atp7a, Bdnf, Brca1 and Rag1; total, 4,602 bp) from 35 species of the mammalian order Eulipotyphla. Based on Bayesian relaxed molecular clock analyses, the family Solenodontidae diverged from other eulipotyphlan in the Paleocene, after the bolide impact on the Yucatan Peninsula, and S. cubanus diverged from the Hispaniolan solenodon (S. paradoxus) in the Early Pliocene. The strikingly recent divergence time estimates suggest that S. cubanus and its ancestral lineage originated via over-water dispersal rather than vicariance events, as had previously been hypothesised.

Assessing uncertainty in sighting records: an example of the Barbary lion.

As species become rare and approach extinction, purported sightings can be controversial, especially when scarce management resources are at stake. We consider the probability that each individual sighting of a series is valid. Obtaining these probabilities requires a strict framework to ensure that they are as accurately representative as possible. We used a process, which has proven to provide accurate estimates from a group of experts, to obtain probabilities for the validation of 32 sightings of the Barbary lion. We consider the scenario where experts are simply asked whether a sighting was valid, as well as asking them to score the sighting based on distinguishablity, observer competence, and verifiability. We find that asking experts to provide scores for these three aspects resulted in each sighting being considered more individually, meaning that this new questioning method provides very different estimated probabilities that a sighting is valid, which greatly affects the outcome from an extinction model. We consider linear opinion pooling and logarithm opinion pooling to combine the three scores, and also to combine opinions on each sighting. We find the two methods produce similar outcomes, allowing the user to focus on chosen features of each method, such as satisfying the marginalisation property or being externally Bayesian.