The genome of recently admixed individuals or hybrids has characteristic genetic patterns that can be used to learn about their recent admixture history. One of these are patterns of interancestry ...heterozygosity, which can be inferred from SNP data from either called genotypes or genotype likelihoods, without the need for information on genomic location. This makes them applicable to a wide range of data that are often used in evolutionary and conservation genomic studies, such as low‐depth sequencing mapped to scaffolds and reduced representation sequencing. Here we implement maximum likelihood estimation of interancestry heterozygosity patterns using two complementary models. We furthermore develop apoh (Admixture Pedigrees of Hybrids), a software that uses estimates of paired ancestry proportions to detect recently admixed individuals or hybrids, and to suggest possible admixture pedigrees. It furthermore calculates several hybrid indices that make it easier to identify and rank possible admixture pedigrees that could give rise to the estimated patterns. We implemented apoh both as a command line tool and as a Graphical User Interface that allows the user to automatically and interactively explore, rank and visualize compatible recent admixture pedigrees, and calculate the different summary indices. We validate the performance of the method using admixed family trios from the 1000 Genomes Project. In addition, we show its applicability on identifying recent hybrids from RAD‐seq data of Grant's gazelle (Nanger granti and Nanger petersii) and whole genome low‐depth data of waterbuck (Kobus ellipsiprymnus) which shows complex admixture of up to four populations.
Processes leading to range contractions and population declines of Arctic megafauna during the late Pleistocene and early Holocene are uncertain, with intense debate on the roles of human hunting, ...climatic change, and their synergy. Obstacles to a resolution have included an overreliance on correlative rather than process‐explicit approaches for inferring drivers of distributional and demographic change. Here, we disentangle the ecological mechanisms and threats that were integral in the decline and extinction of the muskox (Ovibos moschatus) in Eurasia and in its expansion in North America using process‐explicit macroecological models. The approach integrates modern and fossil occurrence records, ancient DNA, spatiotemporal reconstructions of past climatic change, species‐specific population ecology, and the growth and spread of anatomically modern humans. We show that accurately reconstructing inferences of past demographic changes for muskox over the last 21,000 years require high dispersal abilities, large maximum densities, and a small Allee effect. Analyses of validated process‐explicit projections indicate that climatic change was the primary driver of muskox distribution shifts and demographic changes across its previously extensive (circumpolar) range, with populations responding negatively to rapid warming events. Regional analyses show that the range collapse and extinction of the muskox in Europe (~13,000 years ago) was likely caused by humans operating in synergy with climatic warming. In Canada and Greenland, climatic change and human activities probably combined to drive recent population sizes. The impact of past climatic change on the range and extinction dynamics of muskox during the Pleistocene–Holocene transition signals a vulnerability of this species to future increased warming. By better establishing the ecological processes that shaped the distribution of the muskox through space and time, we show that process‐explicit macroecological models have important applications for the future conservation and management of this iconic species in a warming Arctic.
We reconstructed 21,000 years of climate‐ and human‐driven range dynamics of muskox by integrating modern occurrence records, fossil records, paleoclimate reconstructions, ancient DNA sequences, human expansion models and spatially explicit process‐explicit macroecological models. Models that could reconcile inferences of demographic change from fossils were used to determine the likely chains of causality responsible for the contemporary distribution of muskox. We show that climatic change was a primary driver of the structure and dynamics of the distribution of muskox, with human activities, and their interactions with climatic changes, being important in some regions.
Being able to assign sex to individuals and identify autosomal and sex‐linked scaffolds are essential in most population genomic analyses. Non‐model organisms often have genome assemblies at ...scaffold‐level and lack characterization of sex‐linked scaffolds. Previous methods to identify sex and sex‐linked scaffolds have relied on synteny between the non‐model organism and a closely related species or prior knowledge about the sex of the samples to identify sex‐linked scaffolds. In the latter case, the difference in depth of coverage between the autosomes and the sex chromosomes are used. Here, we present “sex assignment through coverage” (SATC), a method to assign sex to samples and identify sex‐linked scaffolds from next generation sequencing (NGS) data. The method works for species with a homogametic/heterogametic sex determination system and only requires a scaffold‐level reference assembly and sampling of both sexes with whole genome sequencing (WGS) data. We use the sequencing depth distribution across scaffolds to jointly identify: (i) male and female individuals, and (ii) sex‐linked scaffolds. This is achieved through projecting the scaffold depths into a low‐dimensional space using principal component analysis (PCA) and subsequent Gaussian mixture clustering. We demonstrate the applicability of our method using data from five mammal species and a bird species complex. The method is freely available at https://github.com/popgenDK/SATC as R code and a graphical user interface (GUI).
see also the Perspective by Iulia Darolti and Judith E. Mank.
Large carnivores are generally sensitive to ecosystem changes because their specialized diet and position at the top of the trophic pyramid is associated with small population sizes. Accordingly, low ...genetic diversity at the whole-genome level has been reported for all big cat species, including the widely distributed leopard. However, all previous whole-genome analyses of leopards are based on the Far Eastern Amur leopards that live at the extremity of the species’ distribution and therefore are not necessarily representative of the whole species. We sequenced 53 whole genomes of African leopards. Strikingly, we found that the genomic diversity in the African leopard is 2- to 5-fold higher than in other big cats, including the Amur leopard, likely because of an exceptionally high effective population size maintained by the African leopard throughout the Pleistocene. Furthermore, we detected ongoing gene flow and very low population differentiation within African leopards compared with those of other big cats. We corroborated this by showing a complete absence of an otherwise ubiquitous equatorial forest barrier to gene flow. This sets the leopard apart from most other widely distributed large African mammals, including lions. These results revise our understanding of trophic sensitivity and highlight the remarkable resilience of the African leopard, likely because of its extraordinary habitat versatility and broad dietary niche.
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•African and Amur leopards have markedly different demographic trajectories•Among big cats, African leopards have the highest genetic diversity•Gene flow on a continent-wide scale maintains low genetic differentiation•Broad dietary and habitat niche likely explain the extraordinary genetic makeup
Pečnerová et al. analyze whole-genome data from 53 African leopards and identify genetic features that set the African leopard apart from the Amur leopards, as well as the other big cats. This includes long-term high effective population size and exceptionally high levels of genetic diversity and connectivity.
The muskox and reindeer are the only ruminants that have evolved to survive in harsh Arctic environments. However, the genetic basis of this Arctic adaptation remains largely unclear. Here, we ...compared a de novo assembled muskox genome with reindeer and other ruminant genomes to identify convergent amino acid substitutions, rapidly evolving genes and positively selected genes among the two Arctic ruminants. We found these candidate genes were mainly involved in brown adipose tissue (BAT) thermogenesis and circadian rhythm. Furthermore, by integrating transcriptomic data from goat adipose tissues (white and brown), we demonstrated that muskox and reindeer may have evolved modulating mitochondrion, lipid metabolism and angiogenesis pathways to enhance BAT thermogenesis. In addition, results from co-immunoprecipitation experiments prove that convergent amino acid substitution of the angiogenesis-related gene hypoxia-inducible factor 2alpha (
), resulting in weakening of its interaction with prolyl hydroxylase domain-containing protein 2 (PHD2), may increase angiogenesis of BAT. Altogether, our work provides new insights into the molecular mechanisms involved in Arctic adaptation.
Grant's gazelles have recently been proposed to be a species complex comprising three highly divergent mtDNA lineages (Nanger granti, N. notata and N. petersii). The three lineages have ...nonoverlapping distributions in East Africa, but without any obvious geographical divisions, making them an interesting model for studying the early‐stage evolutionary dynamics of allopatric speciation in detail. Here, we use genomic data obtained by restriction site‐associated (RAD) sequencing of 106 gazelle individuals to shed light on the evolutionary processes underlying Grant's gazelle divergence, to characterize their genetic structure and to assess the presence of gene flow between the main lineages in the species complex. We date the species divergence to 134,000 years ago, which is recent in evolutionary terms. We find population subdivision within N. granti, which coincides with the previously suggested two subspecies, N. g. granti and N. g. robertsii. Moreover, these two lineages seem to have hybridized in Masai Mara. Perhaps more surprisingly given their extreme genetic differentiation, N. granti and N. petersii also show signs of prolonged admixture in Mkomazi, which we identified as a hybrid population most likely founded by allopatric lineages coming into secondary contact. Despite the admixed composition of this population, elevated X chromosomal differentiation suggests that selection may be shaping the outcome of hybridization in this population. Our results therefore provide detailed insights into the processes of allopatric speciation and secondary contact in a recently radiated species complex.
The muskox (Ovibos moschatus) is the largest terrestrial herbivore in the Arctic and plays a vital role in the tundra ecosystem 1–4. Its range, abundance, and genetic diversity have declined ...dramatically over the past 30,000 years 5. Two subspecies are recognized, but little is known about the genetic structure and how this relates to the species history. One unresolved question is how and when the species dispersed into its present range, notably the present strongholds in the Canadian archipelago and Greenland. We used genotyping by sequencing (GBS) data from 116 muskox individuals and genotype likelihood-based methods to infer the genetic diversity and distribution of genetic variation in the species. We identified a basal split separating the two recognized subspecies, in agreement with isolation of the muskox into several refugia in the Nearctic around 21,000 years ago 6, near the last glacial maximum (LGM). In addition, we found evidence of strong, successive founder effects inflicting a progressive loss of genetic diversity as the muskox colonized the insular High Arctic from an unknown Nearctic origin. These have resulted in exceptionally low genetic diversity in the Greenlandic populations, as well as extremely high genetic differentiation among regional populations. Our results highlight the need for further investigations of genetic erosion in Nearctic terrestrial mammals, of which several show similar colonization histories in the High Artic.
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•Successive founder effects caused progressive loss of genetic diversity in the muskox•Evidence of strong population structure in the muskox•Extremely low genetic diversity in the Greenlandic muskox populations•Arctic mammals show striking similarities in their genetic history
Hansen et al. analyze genetic variation in the muskox, the largest herbivore in the Arctic. The muskox has experienced drastic declines in population size, leading to lower genetic diversity levels than most herbivores. The low genetic diversity and strong genetic structure holds implications for the future conservation efforts for the species.
The reindeer is an Arctic species that exhibits distinctive biological characteristics, for which the underlying genetic basis remains largely unknown. We compared the genomes of reindeer against ...those of other ruminants and nonruminant mammals to reveal the genetic basis of light arrhythmicity, high vitamin D metabolic efficiency, the antler growth trait of females, and docility. We validate that two reindeer vitamin D metabolic genes (
and
) show signs of positive selection and exhibit higher catalytic activity than those of other ruminants. A mutation upstream of the reindeer
gene endows an extra functional binding motif of the androgen receptor and thereby may result in female antlers. Furthermore, a mutation (proline-1172→threonine) in reindeer PER2 results in loss of binding ability with CRY1, which may explain circadian arrhythmicity in reindeer.
The worldwide sheep population comprises more than 1000 breeds. Together, these exhibit a considerable morphological diversity, which has not been extensively investigated at the molecular level. ...Here, we analyze whole-genome sequencing individuals of 1,098 domestic sheep from 154 breeds, and 69 wild sheep from seven Ovis species. On average, we detected 6.8%, 1.0% and 0.2% introgressed sequence in domestic sheep originating from Iranian mouflon, urial and argali, respectively, with rare introgressions from other wild species. Interestingly, several introgressed haplotypes contributed to the morphological differentiations across sheep breeds, such as a RXFP2 haplotype from Iranian mouflon conferring the spiral horn trait, a MSRB3 haplotype from argali strongly associated with ear morphology, and a VPS13B haplotype probably originating from urial and mouflon possibly associated with facial traits. Our results reveal that introgression events from wild Ovis species contributed to the high rate of morphological differentiation in sheep breeds, but also to individual variation within breeds. We propose that long divergent haplotypes are a ubiquitous source of phenotypic variation that allows adaptation to a variable environment, and that these remain intact in the receiving population probably due to reduced recombination.
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