Museomics Dissects the Genetic Basis for Adaptive Seasonal Coloration in the Least Weasel

Dissecting the link between genetic variation and adaptive phenotypes provides outstanding opportunities to understand fundamental evolutionary processes. Here, we use a museomics approach to investigate the genetic basis and evolution of winter coat coloration morphs in least weasels (Mustela nivalis), a repeated adaptation for camouflage in mammals with seasonal pelage color moults across regions with varying winter snow. Whole-genome sequence data were obtained from biological collections and mapped onto a newly assembled reference genome for the species. Sampling represented two replicate transition zones between nivalis and vulgaris coloration morphs in Europe, which typically develop white or brown winter coats, respectively. Population analyses showed that the morph distribution across transition zones is not a by-product of historical structure. Association scans linked a 200-kb genomic region to coloration morph, which was validated by genotyping museum specimens from intermorph experimental crosses. Genotyping the wild populations narrowed down the association to pigmentation gene MC1R and pinpointed a candidate amino acid change cosegregating with coloration morph. This polymorphism replaces an ancestral leucine residue by lysine at the start of the first extracellular loop of the protein in the vulgaris morph. A selective sweep signature overlapped the association region in vulgaris, suggesting that past adaptation favored winter-brown morphs and can anchor future adaptive responses to decreasing winter snow. Using biological collections as valuable resources to study natural adaptations, our study showed a new evolutionary route generating winter color variation in mammals and that seasonal camouflage can be modulated by changes at single key genes

Ancient reindeer mitogenomes reveal island-hopping colonisation of the Arctic archipelagos

Climate warming at the end of the last glacial period had profound effects on the distribution of cold-adapted species. As their range shifted towards northern latitudes, they were able to colonise previously glaciated areas, including remote Arctic islands. However, there is still uncertainty about the routes and timing of colonisation. At the end of the last ice age, reindeer/caribou (Rangifer tarandus) expanded to the Holarctic region and colonised the archipelagos of Svalbard and Franz Josef Land. Earlier studies have proposed two possible colonisation routes, either from the Eurasian mainland or from Canada via Greenland. Here, we used 174 ancient, historical and modern mitogenomes to reconstruct the phylogeny of reindeer across its whole range and to infer the colonisation route of the Arctic islands. Our data shows a close affinity among Svalbard, Franz Josef Land and Novaya Zemlya reindeer. We also found tentative evidence for positive selection in the mitochondrial gene ND4, which is possibly associated with increased heat production. Our results thus support a colonisation of the Eurasian Arctic archipelagos from the Eurasian mainland and provide some insights into the evolutionary history and adaptation of the species to its High Arctic habitat

Resolution of the type material of the Asian elephant, Elephas maximus Linnaeus, 1758 (Proboscidea, Elephantidae)

The understanding of Earth’s biodiversity depends critically on the accurate identification and nomenclature of species. Many species were described centuries ago, and in a surprising number of cases their nomenclature or type material remain unclear or inconsistent. A prime example is provided by Elephas maximus, one of the most iconic and well-known mammalian species, described and named by Linnaeus (1758) and today designating the Asian elephant. We used morphological, ancient DNA (aDNA), and high-throughput ancient proteomic analyses to demonstrate that a widely discussed syntype specimen of E. maximus, a complete foetus preserved in ethanol, is actually an African elephant, genus Loxodonta. We further discovered that an additional E. maximus syntype, mentioned in a description by John Ray (1693) cited by Linnaeus, has been preserved as an almost complete skeleton at the Natural History Museum of the University of Florence. Having confirmed its identity as an Asian elephant through both morphological and ancient DNA analyses, we designate this specimen as the lectotype of E. maximus

Genomic insights into the conservation status of the world’s last remaining Sumatran rhinoceros populations

Highly endangered species like the Sumatran rhinoceros are at risk from inbreeding. Five historical and 16 modern genomes from across the species range show mutational load, but little evidence for local adaptation, suggesting that future inbreeding depression could be mitigated by assisted gene flow among populations. Small populations are often exposed to high inbreeding and mutational load that can increase the risk of extinction. The Sumatran rhinoceros was widespread in Southeast Asia, but is now restricted to small and isolated populations on Sumatra and Borneo, and most likely extinct on the Malay Peninsula. Here, we analyse 5 historical and 16 modern genomes from these populations to investigate the genomic consequences of the recent decline, such as increased inbreeding and mutational load. We find that the Malay Peninsula population experienced increased inbreeding shortly before extirpation, which possibly was accompanied by purging. The populations on Sumatra and Borneo instead show low inbreeding, but high mutational load. The currently small population sizes may thus in the near future lead to inbreeding depression. Moreover, we find little evidence for differences in local adaptation among populations, suggesting that future inbreeding depression could potentially be mitigated by assisted gene flow among populations

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

ABSTRACT: A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ∼1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.info:eu-repo/semantics/publishedVersio

From the Past to the Present: Wolf Phylogeography and Demographic History Based on the Mitochondrial Control Region

The global distribution of the grey wolf (Canis lupus) is a complex assembly consisting of a large number of populations and described subspecies. How these lineages are related to one another is still not fully resolved, largely due to the fact that large geographical regions remain poorly sampled both at the core and periphery of the species’ range. Analyses of ancient wolves have also suffered from uneven sampling, but have shown indications of a major turnover at some point during the Pleistocene-Holocene boundary in northern North America. Here we analyze variation in the mitochondrial control region in 122 contemporary wolves from some of the less studied populations, as well as six samples from the previously unstudied Greenland subspecies (Canis l. orion) and two Late Pleistocene samples from Siberia. Together with the publicly available control region sequences of both modern and ancient wolves, this study examines genetic diversity on a wide geographical and temporal scale that includes both Eurasia and North America. We identify 13 new haplotypes, of which the majority is found in northern and eastern Asia. The results show that the Greenland samples are all represented by one haplotype, previously identified in North American wolves, among which this population seems to trace its maternal lineage. The phylogeny and network analyses show a wide spatial distribution of several lineages, but also some clusters with more distinct geographical affiliation. In North America, we find support for an end-Pleistocene population bottleneck through coalescent simulations under an approximate Bayesian framework in contrast to previous studies that suggested an extinction-replacement event. However, we find no support for a similar bottleneck in Eurasia. Overall, this global analysis helps to clarify our understanding of the complex history for wolves in Eurasia and North America

Evolution, ecology and conservation-revisiting three decades of Arctic fox population genetic research

Three decades have passed since the Arctic fox (Vulpes lagopus) was first put into a population genetic perspective. With the aim of addressing how microevolution operates on different biological levels, we here review genetic processes in the Arctic fox at the level of species, populations and individuals. Historical and present dispersal patterns, especially in the presence of sea ice, are the most powerful factors that create a highly homogeneous genetic structure across the circumpolar distribution, with low detectable divergence between the coastal and lemming ecotypes. With dispersal less pronounced or absent, other processes emerge; populations that are currently isolated, for example, because of the lack of sea ice, are genetically divergent. Moreover, small populations generally display signatures of genetic drift, inbreeding, inbreeding depression and, under specific situations, hybridization with domestic fox breeds. Mating system and social organization in the Arctic fox appear to be determined by the ecological context, with complex mating patterns and social groups being more common under resource-rich conditions. In isolated populations, complex social groups and inbreeding avoidance have been documented. We emphasize the value of genetic data to decipher many previously unknown aspects of Arctic fox biology, while these data also raise numerous questions that remain unanswered. Pronounced intra-specific ecological variation makes the Arctic fox an ideal study organism for population genetic processes and the emergence of functional genomics will generate an even deeper understanding of evolution, ecology and conservation issues for several species

4000-year-old reindeer mitogenomes from the Volga-Kama region reveal continuity among the forest reindeer in northeastern part of European Russia

Abstract There are three main ecotypes of reindeer in Eurasia: tundra reindeer, boreal forest reindeer and High Arctic reindeer. Of these, especially the forest reindeer has suff ered due to human over hunting and habitat fragmentation. Forest reindeer was still found in the Volga-Kama region at the beginning of the 20th century, but has since disappeared from the region. In order to investigate the genetic relationships of these histori-cal, southernly distributed forest reindeer populations, the authors obtained mitogenome sequences from six individuals from Pestretsy II, an archaeological site located in Tatarstan and dated to around 4000 calibrated years before the present (cal BP). The sequences reported in this study represent the fi rst published ancient reindeer mitogenomes. The authors observed genetic continuity between the historical reindeer from Tatarstan and present day wild populations from the taiga zone of northeastern part of European Russia. Interestingly, four out of the six studied individuals belong to mitochondrial control region haplogroup II, which today is a major haplogroup among the semi-domestic reindeer in Fennoscandia. Even though the haplotypes observed in Pestretsy II site are not closely related to the major haplotypes observed among the Fennoscandian semi-domestic reindeer, the results suggest that this haplogroup may have its origin east of Fennoscandia. It is also interesting to note that the size of the reindeers from the Pestretsy II site was one of the largest observed in the Holocene.Аннотация В Евразии существует три основных экотипа северного оленя: тундровый северный олень, таежный северный олень и высокоарктический северный олень. Из них лесные северные олени особенно пострадали из-за чрезмерной охоты человека и фрагментации среды обитания. Лесной северный олень еще встречался в Волго-Камском регионе в начале XX века, но с тех пор исчез из данного региона. Чтобы исследовать генетические связи этих исторических, южно-распределенных популяций лесных северных оленей, авторы получили последовательности митогенома от шести особей из Пестречинской II стоянки, археологического памятника, расположенного в Татарстане и датируемого около 4000 калиброванных лет назад (кал. л.н.). Последовательности митохондриального ДНК, описанные в этом исследовании, представляют собой первые опубликованные древние митогеномы северного оленя. Авторы выявили генетическую преемственность между историческим северным оленем из Татарстана и современными дикими популяциями из таежной зоны северо-восточной части европейской части России. Интересно, что четыре из шести исследованных особей принадлежат к гаплогруппе II, она сегодня является основной гаплогруппой среди полудомашних оленей в Фенноскандии. Несмотря на то, что гаплотипы, наблюдаемые у северных оленей из Пестречинской II стоянки, не тесно связаны с основными гаплотипами, наблюдаемыми среди полудомашних северных оленей Фенноскандии, результаты показывают, что эта гаплогруппа может иметь свое происхождение к востоку от Фенноскандии. Интересно также отметить, что размеры северных оленей из Пестречинской II стоянки были одними из самых крупных наблюдавшихся в голоцене

Reindeer from Sámi offering sites document the replacement of wild reindeer genetic lineages by domestic ones in Northern Finland starting from 1400 to 1600 AD

Abstract Reindeer herding emerged among the indigenous Sámi of Northern Fennoscandia between ca. 800 and 1500 CE. While the details of the reindeer domestication process are still actively debated, it has been hypothesized that the transition to reindeer herding affected Sámi ritual practice, especially animal offerings given at various sacred sites. To explore this hypothesis, we analyzed DNA from reindeer bone samples dating to ca. 1200–1700 CE from Sámi offering sites located in present-day Northern Finland as well as from samples originating from ancient dwelling site in Southern Finland and Kola Peninsula, Russia. The results show that haplotypes related to wild Finnish forest reindeer (Rangifer tarandus fennicus) began to be replaced by haplotypes common in modern domesticated reindeer in the faunal assemblages from offering sites starting between 1400 and 1600 CE. The results suggest that, although the role of reindeer herding in the economy of the Sámi communities varied greatly, the transition to reindeer herding may have affected ritual practices, testifying to a shared way of reciprocating with the land and animals

Uamericanus_haploidised_fasta

Haploidised fasta sequence generated by mapping Illumina short reads to the reference genome assembly of the giant panda, then randomly selecting a single high quality nucleotide from the read stack for each position of the reference genome. See the original publication for full details. The raw sequencing data is also available from the European Nucleotide Archive. Note that this file will contain abundant errors in comparison to a consensus base call from high coverage data