Assessing current genetic status of the Hainan gibbon using historical and demographic baselines: implications for conservation management of species of extreme rarity

Evidence-based conservation planning is crucial for informing management decisions for species of extreme rarity, but collection of robust data on genetic status or other parameters can be extremely challenging for such species. The Hainan gibbon, possibly the world's rarest mammal, consists of a single population of c.25 individuals restricted to one protected area on Hainan Island, China, and has persisted for over 30 years at exceptionally low population size. Analysis of genotypes at 11 microsatellite loci from faecal samples for 36% of the current global population and tissue samples from 62% of existing historical museum specimens demonstrates limited current genetic diversity (Na=2.27, Ar=2.24, He =0.43); diversity has declined since the 19th century and even further within the last 30 years, representing declines of c.30% from historical levels (Na=3.36, Ar=3.29, He =0.63). Significant differentiation is seen between current and historical samples (FST =0.156, P=0.0315), and the current population exhibits extremely small Ne (current Ne =2.16). There is evidence for both a recent population bottleneck and an earlier bottleneck, with population size already reasonably low by the late 19th century (historical Ne =1162.96). Individuals in the current population are related at the level of half- to full-siblings between social groups, and full-siblings or parent-offspring within a social group, suggesting that inbreeding is likely to increase in the future. The species' current reduced genetic diversity must be considered during conservation planning, particularly for expectations of likely population recovery, indicating that intensive, carefully planned management is essential

Using dogs to find cats: detection dogs as a survey method for wide-ranging cheetah

Rapid global large carnivore declines make evaluations of remaining populations critical. Yet landscape-scale evaluations of presence, abundance and distribution are difficult, as many species are wide-ranging, occur only at low densities and are elusive. Insufficient information-gathering tools for many large carnivore species compounds these challenges. Specially trained detection dogs have demonstrated effectiveness for carnivore surveys, but are untested on extremely sparse, wide-ranging species, such as cheetah Acinonyx jubatus. In this study, we conducted the first rigorous cheetah survey using detection dogs in a key transboundary area in the remote Liuwa–Mussuma Transfrontier Conservation Area (TFCA) in Western Zambia. We proposed to (1) evaluate the effectiveness of detection dog versus spoor surveys in detecting cheetah presence; (2) extract and analyze DNA from scat samples to estimate minimum population size and genetic effective population size; (3) determine the extent of cheetah occurrence in the unprotected transboundary corridor. Two detection dog teams surveyed 2432 km2 containing 74 randomly located transects in the transfrontier area. Twenty-seven cheetah scats were detected and confirmed by genetic analysis, while no cheetah spoor was detected, clearly demonstrating the superiority of detection dogs in detecting cheetah presence. Combining scat samples with opportunistically collected samples, we estimated 17–19 cheetahs, an effective population size of 8–14 and a density of 5.9–6.6 per 1000 km2. Cheetah utilized key transfrontier areas outside of the national park; however, because utilization appears low, improved connectivity and protection for these areas are critical. Approximately one third of Africa's estimated cheetah resides in protected areas, with 87% in transboundary areas. Our study demonstrates the efficacy of detection dog survey methods in providing information on cheetah across large landscapes. It will have particular value in areas where other survey means may be impossible, such as TFCAs, where size, remoteness and lack of accessibility often make traditional survey methods difficult or cost prohibitive

The effect of the last glacial age on speciation and population genetic structure of the endangered Ethiopian wolf (Canis simensis).

During the last glacial age, Afro-alpine habitats were widespread across the highlands of Ethiopia. A wolf-like canid ancestor is thought to have colonized this expanding habitat and given rise to a new species that was remarkably well adapted to the high altitude environment: the Ethiopian wolf Canis simensis. Here, we address the timing of genetic divergence and examine population genetic history and structure by investigating the distribution of mitochondrial DNA (mtDNA) sequence variation. The pattern of mtDNA variation and geographical distribution indicate an initial population expansion, probably immediately after divergence from the wolf-like ancestor, around 100,000 years ago. The partition of mtDNA haplotypes that followed was most likely the result of habitat reduction and fragmentation at the onset of deglaciation approximately 15,000 years ago. Phylogenetic and geographical associations suggest that the most likely genetic partitioning corresponds to three mountain areas, Arsi/Bale, Wollo/Shoa and Simien/Mt. Guna. Although there is a degree of clustering of haplotypes from both sides of the Rift Valley, the lack of reciprocal monophyly does not support the taxonomic classification of two subspecies. This study highlights the importance of populations north of the Rift Valley for the maintenance of genetic variability within the species and has consequent implications for conservation

A century of decline: loss of genetic diversity in a southern African lion-conservation stronghold

Aim: There is a dearth of evidence that determines the genetic diversity of populations contained within present-day protected areas compared with their historical state prior to large-scale species declines, making inferences about a species’ conservation genetic status difficult to assess. The aim of this paper was to demonstrate the use of historical specimens to assess the change in genetic diversity over a defined spatial area. Location: Like many other species, African lion populations (Panthera leo) are undergoing dramatic contractions in range and declines in numbers, motivating the identification of a number of lion-conservation strongholds across East and southern Africa. We focus on one such stronghold, the Kavango–Zambezi transfrontier conservation area (KAZA) of Botswana, Namibia, Zambia and Zimbabwe. Methods: We compare genetic diversity between historical museum specimens, collected during the late 19th and early 20th century, with samples from the modern extant population. We use 16 microsatellite markers and sequence 337 base pairs of the hypervariable control region (HVR1) of the mitochondrial genome. We use bootstrap resampling to allow for comparisons between the historical and modern data. Results: We show that the genetic diversity of the modern population was reduced by 12%–17%, with a reduction in allelic diversity of approximately 15%, compared to historical populations, in addition to having lost a number of mitochondrial haplotypes. We also identify a number of “ghost alleles” in the historical samples which are no longer present in the extant population. Main Conclusions: We argue a rapid decline in allelic richness after 1895 suggests the erosion of genetic diversity coincides with the rise of a European colonial presence and the outbreak of rinderpest in the region. Our results support the need to improved connectivity between protected areas in order to prevent further loss of genetic diversity in the region

A century of decline: Loss of genetic diversity in a southern African lion‐conservation stronghold

Aim: There is a dearth of evidence that determines the genetic diversity of populations contained within present-day protected areas compared with their historical state prior to large-scale species declines, making inferences about a species’ conservation genetic status difficult to assess. The aim of this paper was to demonstrate the use of historical specimens to assess the change in genetic diversity over a defined spatial area. Location: Like many other species, African lion populations (Panthera leo) are undergoing dramatic contractions in range and declines in numbers, motivating the identification of a number of lion-conservation strongholds across East and southern Africa. We focus on one such stronghold, the Kavango–Zambezi transfrontier conservation area (KAZA) of Botswana, Namibia, Zambia and Zimbabwe. Methods: We compare genetic diversity between historical museum specimens, collected during the late 19th and early 20th century, with samples from the modern extant population. We use 16 microsatellite markers and sequence 337 base pairs of the hypervariable control region (HVR1) of the mitochondrial genome. We use bootstrap resampling to allow for comparisons between the historical and modern data. Results: We show that the genetic diversity of the modern population was reduced by 12%–17%, with a reduction in allelic diversity of approximately 15%, compared to historical populations, in addition to having lost a number of mitochondrial haplotypes. We also identify a number of “ghost alleles” in the historical samples which are no longer present in the extant population. Main Conclusions: We argue a rapid decline in allelic richness after 1895 suggests the erosion of genetic diversity coincides with the rise of a European colonial presence and the outbreak of rinderpest in the region. Our results support the need to improved connectivity between protected areas in order to prevent further loss of genetic diversity in the region

Genetic diversity and population structure in the endangered giant otter, Pteronura brasiliensis

We assessed levels of genetic diversity and investigated patterns of population structure in three remnant populations of the endangered giant otter, Pteronura brasiliensis, using microsatellite loci. All populations displayed moderate to low levels of heterozygosity and allelic richness (H O 0.56–0.57, A R 4.00–5.15) and effective population sizes were low (N E 10.8–54) although only the Iténez population exhibited the signature of a genetic bottleneck. Population structure analyses revealed a pattern in which the populations of the Upper Amazon, Orinoco and Essequibo drainages comprised partially differentiated segments of a northern South American metapopulation, whereas the population of the Iténez appeared isolated. The observed patterns are congruent with previous mitochondrial DNA analysis which suggested the Iténez and northern South American groups constitute two evolutionary significant units. The results presented here should be considered in planning future policies aiming to manage the recovery of the giant otter across its range

Genetic diversity and introgression in the Scottish Wildcat

This paper describes a genetic analysis of wild-living cats in Scotland. Samples from 230 wild-living Scottish cats (including 13 museum skins) and 74 house cats from England and Scotland were surveyed for nine microsatellite loci. Pelage characteristics of the wild-living cats were recorded, and the cats were then grouped into five separate categories depending on the degree to which they conformed to the characteristics attributed to Felis silvestris Schreber, 1775. Allele frequency differences between the morphological groups are greater than those among the three house cat samples. Analysis of genetic distances suggests that more of the differences between individuals can be explained by pelage than geographical proximity, and that pelage and geographical location are not confounded. Ordination of the genetic distances suggests two main groups of wild-living cats, with intermediates, and one group is genetically very similar to the house cats, while the other group contains all cats taxonomically identified as wildcat based on morphology. A genetic mixture analysis gives similar results to the ordination, but also suggests that the genotypes of a substantial number of cats in the wildcat group are drawn from a gene pool with genotypes in approximately equilibrium proportions. We argue that this is evidence that these cats do not have very recent domestic ancestry. However, from the morphological data it is highly likely that this gene pool also contains a contribution from earlier introgression of domestic cat genes