Aardwolf population diversity and phylogenetic positioning inferred using complete mitochondrial genomes

The aardwolf (Proteles cristata) is a unique, insectivorous species of the family Hyaenidae. It occupies a disjunct range in eastern and southern Africa and is possibly a remaining member of a historical dog-like hyaena clade. Although both local and global population status and trends are largely unknown, aardwolves are not uncommon in arid grasslands and the IUCN conservation status of Least Concern appears to be justified.However, they are one of the least studied of the four hyaena species,and we have scarce information about the genetic structure of aardwolf populations. Here, we present the first complete aardwolf mitochondrial genomes and provide novel information about aardwolf evolutionary origins and genetic structure within a single population. Through the investigation of complete mitochondrial genomes from five individuals from a single population within South Africa, we find the mitochondrial diversity of this population to be neither particularly high nor low compared to a number of other mammalian species. Moreover, we also provide additional evidence towards the basal position of the aardwolf within Hyaenidae with a divergence time of 13.0 Ma (95% CI 10.1–16.4 Ma) from all other extant hyaena species.The European Research Council, the National Research Foundation (NRF, South Africa), and the Spanish Ministry of Economy and Competitiveness (MINECO).http://www.sawma.co.zaam2020Mammal Research InstituteZoology and Entomolog

Ancient human genomes and environmental DNA from the cement attaching 2,000 year-old head lice nits

Over the past few decades there has been an increased demand for genome analysis of ancient human remains. Destructive sampling is increasingly difficult for ethical reasons, and previous methods of breaking the skull to access the petrous bone are often forbidden for curatorial reasons, together with teeth which may be missing or too precious to sample. However, most ancient humans carried head lice, and their eggs abound in historical hair specimens. Here we show that host DNA is protected by the cement that glues head lice eggs (nits) to the hair of ancient Argentinian mummies, 1,500–2,000 years old. The cement also preserves ancient environmental DNA of the skin, including the earliest recorded case of Merkel Cell Polyomavirus. We also show that human DNA obtained from nit cement can equal human genome assessment from tooth DNA, can increase assessment from petrous bone by two-fold, and by four-fold DNA over bloodmeal of adult lice a millennium younger. Genome-wide analyses from nit cement DNA also enables identification of the population genetic affinities of ancient humans. In metric studies of the sheaths, the length of the cement tube negatively correlated with the age of the specimens, while hair linear distance between nit and scalp informed about environmental conditions at the time before death. Ectoparasitic lice sheaths on hair, feathers, skins, or mummified remains can offer an alternative, non-destructive source of high-quality ancient DNA from a variety of host taxa and reveal details of their historical environment

Historic sampling of a vanishing beast: Population structure and diversity in the Black Rhinoceros

The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north–south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity

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 similar to 38x exome from H. latidens using shotgun and target-capture sequencing approaches. Phylogenetic analyses reveal Homotherium as highly divergent (similar to 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

Genomic insights into the evolutionary relationships and demographic history of kiwi.

Kiwi are a unique and emblematic group of birds endemic to New Zealand. Deep-time evolutionary relationships among the five extant kiwi species have been difficult to resolve, in part due to the absence of pre-Quaternary fossils to inform speciation events. Here, we utilise single representative nuclear genomes of all five extant kiwi species (great spotted kiwi, little spotted kiwi, Okarito brown kiwi, North Island brown kiwi, and southern brown kiwi) and investigate their evolutionary histories with phylogenomic, genetic diversity, and deep-time (past million years) demographic analyses. We uncover relatively low levels of gene-tree phylogenetic discordance across the genomes, suggesting clear distinction between species. However, we also find indications of post-divergence gene flow, concordant with recent reports of interspecific hybrids. The four species for which unbiased levels of genetic diversity could be calculated, due to the availability of reference assemblies (all species except the southern brown kiwi), show relatively low levels of genetic diversity, which we suggest reflects a combination of older environmental as well as more recent anthropogenic influence. In addition, we suggest hypotheses regarding the impact of known past environmental events, such as volcanic eruptions and glacial periods, on the similarities and differences observed in the demographic histories of the five kiwi species over the past million years

Phylogeography of the European brook lamprey (Lampetra planeri) and the European river lamprey (Lampetra fluviatilis) species pair based on mitochondrial data

De Cahsan B, Nagel R, Schedina I-M, et al. Phylogeography of the European brook lamprey (Lampetra planeri) and the European river lamprey (Lampetra fluviatilis) species pair based on mitochondrial data. JOURNAL OF FISH BIOLOGY. 2020;96(4):905-912.The European river lamprey Lampetra fluviatilis and the European brook lamprey Lampetra planeri (Block 1784) are classified as a paired species, characterized by notably different life histories but morphological similarities. Previous work has further shown limited genetic differentiation between these two species at the mitochondrial DNA level. Here, we expand on this previous work, which focused on lamprey species from the Iberian Peninsula in the south and mainland Europe in the north, by sequencing three mitochondrial marker regions of Lampetra individuals from five river systems in Ireland and five in southern Italy. Our results corroborate the previously identified pattern of genetic diversity for the species pair. We also show significant genetic differentiation between Irish and mainland European lamprey populations, suggesting another ichthyogeographic district distinct from those previously defined. Finally, our results stress the importance of southern Italian L. planeri populations, which maintain several private alleles and notable genetic diversity

Southern introgression increases adaptive immune gene variability in northern range margin populations of Fire-bellied toad

Northern range margin populations of the European fire‐bellied toad (Bombina bombina) have rapidly declined during recent decades. Extensive agricultural land use has fragmented the landscape, leading to habitat disruption and loss, as well as eutrophication of ponds. In Northern Germany (Schleswig‐Holstein) and Southern Sweden (Skåne), this population decline resulted in decreased gene flow from surrounding populations, low genetic diversity, and a putative reduction in adaptive potential, leaving populations vulnerable to future environmental and climatic changes. Previous studies using mitochondrial control region and nuclear transcriptome‐wide SNP data detected introgressive hybridization in multiple northern B. bombina populations after unreported release of toads from Austria. Here, we determine the impact of this introgression by comparing the body conditions (proxy for fitness) of introgressed and nonintrogressed populations and the genetic consequences in two candidate genes for putative local adaptation (the MHC II gene as part of the adaptive immune system and the stress response gene HSP70 kDa). We detected regional differences in body condition and observed significantly elevated levels of within individual MHC allele counts in introgressed Swedish populations, associated with a tendency toward higher body weight, relative to regional nonintrogressed populations. These differences were not observed among introgressed and nonintrogressed German populations. Genetic diversity in both MHC and HSP was generally lower in northern than Austrian populations. Our study sheds light on the potential benefits of translocations of more distantly related conspecifics as a means to increase adaptive genetic variability and fitness of genetically depauperate range margin populations without distortion of local adaptation