Genetic consequences of population expansions and contractions in the common hippopotamus (Hippopotamus amphibius) since the Late Pleistocene

Genetic diversity and demographic history of the largest remaining migratory population of brindled wildebeest (Connochaetes taurinus taurinus) in southern Africa

The blue wildebeest (Connochaetes taurinus) is a keystone species in the savannahs of southern Africa, where it maintains shortgrass plains and serves as an important prey source for large carnivores. Despite being the second-largest migratory wildebeest population, the brindled wildebeest (C. t. taurinus) of the Greater Liuwa Ecosystem (GLE) of western Zambia have remained largely unstudied, until recently. While studies have increased understanding of recent demography, migration, and population limiting factors, the level of genetic diversity, patterns of gene flow, and long-term demographic history of brindled wildebeest in the GLE remains unknown. Most genetic studies of wildebeest have focused on small, heavily-managed populations, rather than large, migratory populations of high conservation significance. We used restriction-site associated DNA sequencing (RAD-seq) to assess genetic diversity, population structure, and demographic history of brindled wildebeest in the GLE. Using SNPs from 1,730 loci genotyped across 75 individuals, we found moderate levels of genetic diversity in GLE brindled wildebeest (He =  0.210), very low levels of inbreeding (FIS =  0.033), and an effective population size of about one tenth the estimated population size. No genetic population structure was evident within the GLE. Analyses of the site frequency spectrum found signatures of expansion during the Middle Pleistocene followed by population decline in the Late Pleistocene and early Holocene, a pattern previously observed in other African ungulates. These results will supplement field studies in developing effective conservation plans for wildebeest as they face continued and increasing threats of habitat loss, poaching, and other human impacts across their remaining range.

Inferring genetic structure when there is little: population genetics versus genomics of the threatened bat Miniopterus schreibersii across Europe

Despite their paramount importance in molecular ecology and conservation, genetic diversity and structure remain challenging to quantify with traditional genotyping methods. Next-generation sequencing holds great promises, but this has not been properly tested in highly mobile species. In this article, we compared microsatellite and RAD-sequencing (RAD-seq) analyses to investigate population structure in the declining bent-winged bat (Miniopterus schreibersii) across Europe. Both markers retrieved general patterns of weak range-wide differentiation, little sex-biased dispersal, and strong isolation by distance that associated with significant genetic structure between the three Mediterranean Peninsulas, which could have acted as glacial refugia. Microsatellites proved uninformative in individual-based analyses, but the resolution offered by genomic SNPs illuminated on regional substructures within several countries, with colonies sharing migrators of distinct ancestry without admixture. This finding is consistent with a marked philopatry and spatial partitioning between mating and rearing grounds in the species, which was suspected from marked-recaptured data. Our study advocates that genomic data are necessary to properly unveil the genetic footprints left by biogeographic processes and social organization in long-distant flyers, which are otherwise rapidly blurred by their high levels of gene flow.

A synthesis of human conflict with an African megaherbivore; the common hippopotamus

The common hippopotamus is an extant African megaherbivore that is relatively understudied by scientists and underfunded by conservation organisations. Conflict with people, however, is a major concern given the danger that hippos pose to human life. Moreover, very little is known about human–hippo conflict (HHC), and experimental fieldwork on mitigation methods has hardly been conducted. Here we conduct an exhaustive review of the primary and grey literature outlining how the conflict between people and hippos arises, the impacts of conflict on both human communities and hippo populations, and all known intervention measures. Our review highlights the effectiveness of barriers around crops, riparian buffer zones (that exclude cattle and crop planting), and payments for environmental services as tools to mitigate HHC. This study also highlights the knowledge gaps in HHC research, particularly the spatial scale of HHC, the lack of field experimental research on deterrents, and a paucity of knowledge on outcomes of projected climate change and HHC.

American mastodon mitochondrial genomes suggest multiple dispersal events in response to Pleistocene climate oscillations

Pleistocene glacial-interglacial cycles are correlated with dramatic temperature oscillations. Examining how species responded to these natural fluctuations can provide valuable insights into the impacts of present-day anthropogenic climate change. Here we present a phylogeographic study of the extinct American mastodon (Mammut americanum), based on 35 complete mitochondrial genomes. These data reveal the presence of multiple lineages within this species, including two distinct clades from eastern Beringia. Our molecular date estimates suggest that these clades arose at different times, supporting a pattern of repeated northern expansion and local extirpation in response to glacial cycling. Consistent with this hypothesis, we also note lower levels of genetic diversity among northern mastodons than in endemic clades south of the continental ice sheets. The results of our study highlight the complex relationships between population dispersals and climate change, and can provide testable hypotheses for extant species expected to experience substantial biogeographic impacts from rising temperatures.

Pleistocene population dynamics can inform the consequences of current climate change. This phylogeography of 35 complete American mastodon mitochondrial genomes suggests distinct lineages in this species repeatedly expanded northwards and then went locally extinct in response to glacial cycles.

Demographic expansion of an African opportunistic carnivore during the Neolithic revolution

The diffusion of Neolithic technology together with the Holocene Climatic Optimum fostered the spread of human settlements and pastoral activities in North Africa, resulting in profound and enduring consequences for the dynamics of species, communities and landscapes. Here, we investigate the demographic history of the African wolf (Canis lupaster), a recently recognized canid species, to understand if demographic trends of this generalist and opportunistic carnivore reflect the increase in food availability that emerged after the arrival of the Neolithic economy in North Africa. We screened nuclear and mitochondrial DNA in samples collected throughout Algeria and Tunisia, and implemented coalescent approaches to estimate the variation of effective population sizes from present to ancestral time. We have found consistent evidence supporting the hypothesis that the African wolf population experienced a meaningful expansion concurring with a period of rapid population expansion of domesticates linked to the advent of agricultural practices.

Phylogeography of a cryptic speciation continuum in Eurasian spadefoot toads (Pelobates)

Cryptic phylogeographic diversifications provide unique models to examine the role of phylogenetic divergence on the evolution of reproductive isolation, without extrinsic factors such as ecological and behavioural differentiation. Yet, to date very few comparative studies have been attempted within such radiations. Here, we characterize a new speciation continuum in a group of widespread Eurasian amphibians, the Pelobates spadefoot toads, by conducting multilocus (restriction site associated DNA sequencing and mitochondrial DNA) phylogenetic, phylogeographic and hybrid zone analyses. Within the P. syriacus complex, we discovered species-level cryptic divergences (>5 million years ago [My]) between populations distributed in the Near-East (hereafter P. syriacus sensu stricto [s.s.]) and southeastern Europe (hereafter P. balcanicus), each featuring deep intraspecific lineages. Altogether, we could scale hybridizability to divergence time along six different stages, spanning from sympatry without gene flow (P. fuscus and P. balcanicus, >10 My), parapatry with highly restricted hybridization (P. balcanicus and P. syriacus s.s., >5 My), narrow hybrid zones (~15 km) consistent with partial reproductive isolation (P. fuscus and P. vespertinus, ~3 My), to extensive admixture between Pleistocene and refugial lineages (≤2 My). This full spectrum empirically supports a gradual build up of reproductive barriers through time, reversible up until a threshold that we estimate at ~3 My. Hence, cryptic phylogeographic lineages may fade away or become reproductively isolated species simply depending on the time they persist in allopatry, and without definite ecomorphological divergence.

Did Late Pleistocene climate change result in parallel genetic structure and demographic bottlenecks in sympatric Central African crocodiles, Mecistops and Osteolaemus?

The mid-Holocene has had profound demographic impacts on wildlife on the African continent, although there is little known about the impacts on species from Central Africa. Understanding the impacts of climate change on codistributed species can enhance our understanding of ecosystem dynamics and for formulating restoration objectives. We took a multigenome comparative approach to examine the phylogeographic structure of two poorly known Central African crocodile species-Mecistops sp. aff. cataphractus and Osteolaemus tetraspis. In addition, we conducted coalescent-based demographic reconstructions to test the hypothesis that population decline was driven by climate change since the Last Glacial Maximum, vs. more recent anthropogenic pressures. Using a hierarchical Bayesian model to reconstruct demographic history, we show that both species had dramatic declines (>97%) in effective population size in the 'period following the Last Glacial Maximum 1,500-18,000 YBP. Identification of genetic structuring showed both species have similar regional structure corresponding to major geological features (i.e., hydrologic basin) and that small observed differences between them are best explained by the differences in their ecology and the likely impact that climate change had on their habitat needs. Our results support our hypothesis that climatic effects, presumably on forest and wetland habitat, had a congruent negative impact on both species.

Achieving optimal welfare for the Nile hippopotamus (Hippopotamus amphibius) in North American zoos and aquariums

Compared to other megafauna managed in zoos and aquariums, the current state of welfare for the Nile hippopotamus (Hippopotamus amphibius) is poorly understood. Complex behavior and physiological characteristics make hippos a difficult species to manage. Thus, hippos in managed care are currently at risk for a decreased state of welfare. In an effort to assess and improve conditions for this species, a survey was administered to North American institutions housing Nile hippos. This assessment utilized a multiple-choice format and consisted of questions relating to group structure, behavior, and exhibit design, allowing for the creation of cross-institutional, welfare-based analysis. Responses were gathered from 85.29% of the institutions to which the survey was distributed. Despite recommendations for maintaining groups of at least five individuals (Forthman, 1998), only 34.25% of hippos in North America were housed in groups of three or more. The survey also highlighted that 39.29% of institutions secure their hippos in holding areas overnight, despite their highly active nocturnal propensities. A better understanding of hippo behavior and environmental preferences can be used to inform wellness-oriented management practices to achieve a state of "optimal welfare".

Molecular cytogenetics of tragelaphine and alcelaphine interspecies hybrids: hybridization, introgression and speciation in some African antelope

Hybridization can occur naturally among diverging lineages as part of the evolutionary process leading to complete reproductive isolation, or it can result from range shifts and habitat alteration through global warming and/or other anthropogenic influences. Here we report a molecular cytogenetic investigation of hybridization between taxonomically distinct species of the Alcelaphini (Alcelaphus buselaphus 2n = 40 × Damaliscus lunatus 2n = 36) and the Tragelaphini (Tragelaphus strepsiceros 2n = 31/32 × Tragelaphus angasii 2n = 55/56). Cross-species fluorescence in situ hybridization provides unequivocal evidence of the scale of karyotypic difference distinguishing parental species. The findings suggest that although hybrid meiosis of the former cross would necessitate the formation of a chain of seven, a ring of four and one trivalent, the progeny follow Haldane's rule showing F₁ male sterility and female fertility. The tragelaphine F₁ hybrid, a male, was similarly sterile and, given the 11 trivalents and chain of five anticipated in its meiosis, not unexpectedly so. We discuss these findings within the context of the broader evolutionary significance of hybridization in African antelope, and reflect on what these hold for our views of antelope species and their conservation.

Evolutionary melting pots: a biodiversity hotspot shaped by ring diversifications around the Black Sea in the Eastern tree frog (Hyla orientalis)

Hotspots of intraspecific genetic diversity, which are of primary importance for the conservation of species, have been associated with glacial refugia, that is areas where species survived the Quaternary climatic oscillations. However, the proximate mechanisms generating these hotspots remain an open issue. Hotspots may reflect the long-term persistence of large refugial populations; alternatively, they may result from allopatric differentiation between small and isolated populations, that later admixed. Here, we test these two scenarios in a widely distributed species of tree frog, Hyla orientalis, which inhabits Asia Minor and southeastern Europe. We apply a fine-scale phylogeographic survey, combining fast-evolving mitochondrial and nuclear markers, with a dense sampling throughout the range, as well as ecological niche modelling, to understand what shaped the genetic variation of this species. We documented an important diversity centre around the Black Sea, composed of multiple allopatric and/or parapatric diversifications, likely driven by a combination of Pleistocene climatic fluctuations and complex regional topography. Remarkably, this diversification forms a ring around the Black Sea, from the Caucasus through Anatolia and eastern Europe, with terminal forms coming into contact and partially admixing in Crimea. Our results support the view that glacial refugia generate rather than host genetic diversity and can also function as evolutionary melting pots of biodiversity. Moreover, we report a new case of ring diversification, triggered by a large, yet cohesive dispersal barrier, a very rare situation in nature. Finally, we emphasize the Black Sea region as an important centre of intraspecific diversity in the Palearctic with implications for conservation.