Temporal genomic data hold great potential for studying evolutionary processes, including speciation. However, sampling across speciation events would in many cases require genomic time series that stretch well into the Early Pleistocene (>1 million years). Although theoretical models suggest that DNA should survive on this timescale 1 , the oldest genomic data recovered so far is from a 560-780 ka old horse specimen 2 . Here we report the recovery of genome-wide data from three Early and Middle Pleistocene mammoth specimens, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these gave rise to the woolly mammoth, whereas the other represents a previously unrecognised lineage that was ancestral to the first mammoths to colonise North America. Our analyses reveal that the North American Columbian mammoth traces its ancestry to a Middle Pleistocene hybridisation between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were present already a million years ago. These findings highlight the potential of deep time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.

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While present-day taxa are valuable proxies for understanding the biology of extinct species, it is also crucial to examine physical remains in order to obtain a more comprehensive view of their behavior, social structure, and life histories [1, 2]. For example, information on demographic parameters such as age distribution and sex ratios in fossil assemblages can be used to accurately infer socioecological patterns (e.g., [3]). Here we use genomic data to determine the sex of 98 woolly mammoth (Mammuthus primigenius) specimens in order to infer social and behavioral patterns in the last 60,000 years of the species' existence. We report a significant excess of males among the identified samples (69% versus 31%; p < 0.0002). We argue that this male bias among mammoth remains is best explained by males more often being caught in natural traps that favor preservation. We hypothesize that this is a consequence of social structure in proboscideans, which is characterized by matriarchal hierarchy and sex segregation. Without the experience associated with living in a matriarchal family group, or a bachelor group with an experienced bull, young or solitary males may have been more prone to die in natural traps where good preservation is more likely.

Tropical forests of Central and South America represent hotspots of biological diversity. Tree squirrels of the tribe Sciurini are an excellent model system for the study of tropical biodiversity as these squirrels disperse exceptional distances, and after colonizing the tropics of the Central and South America, they have diversified rapidly. Here, we compare signals from DNA sequences with morphological signals using pictures of skulls and computational simulations. Phylogenetic analyses reveal step-wise geographic divergence across the Northern Hemisphere. In Central and South America, tree squirrels form two separate clades, which split from a common ancestor. Simulations of ancestral distributions show western Amazonia as the epicenter of speciation in South America. This finding suggests that wet tropical forests on the foothills of Andes possibly served as refugia of squirrel diversification during Pleistocene climatic oscillations. Comparison of phylogeny and morphology reveals one major discrepancy: Microsciurus species are a single clade morphologically but are polyphyletic genetically. Modeling of morphology-diet relationships shows that the only group of species with a direct link between skull shape and diet are the bark-gleaning insectivorous species of Microsciurus. This finding suggests that the current designation of Microsciurus as a genus is based on convergent ecologically driven changes in morphology.

Although genetic diversity has been recognized as a key component of biodiversity since the first Convention on Biological Diversity (CBD) in 1993, it has rarely been included in conservation policies and regulations. Even less appreciated is the role that ancient and historical DNA (aDNA and hDNA, respectively) could play in unlocking the temporal dimension of genetic diversity, allowing key conservation issues to be resolved, including setting baselines for intraspecies genetic diversity, estimating changes in effective population size (N e) , and identifying the genealogical continuity of populations. Here, we discuss how genetic information from ancient and historical specimens can play a central role in preserving biodiversity and highlight specific conservation policies that could incorporate such data to help countries meet their CBD obligations. Genetic biodiversityThree levels of biodiversity constitute the variation of life on our planet: diversity of ecosystems, species diversity (number and distribution of species), and genetic diversity (amount and distribution of genetic variation within species or populations). The need to monitor biodiversity at all three levels has been globally recognized in international policy since 1993 when the Convention on Biological Diversity i (CBD) came into effect. Today, we face dramatic biodiversity loss due to the combined effects of habitat damage, fragmentation and alteration, climate change, and other global change stressors. Most frequently, this loss is calculated in terms of the number of species, but relatively little is known about loss of diversity within species and populations at the genome level (but see [1]). Genetic diversity within species and populations is necessary for long-term survival as it allows resilience and adaptation not only for individuals, but also for populations, species, and entire ecosystems [2]. This diversity is particularly relevant in the Anthropocene, characterized by significant, rapid, and global changes to habitats and environmental conditions. Despite the importance of genetic diversity in biodiversity protection and management, it has rarely been included in policies and regulations [3]. But, with the ongoing development of the CBD post-2020 Global Biodiversity Framework (expected to be concluded in May 2022), there is an opportunity to address this significant blind spot by adopting genetic diversity targets and indicators.

The onset of the Holocene was associated with a global temperature increase, which led to a rise in sea levels and isolation of the last surviving population of woolly mammoths on Wrangel Island. Understanding what happened with the population's genetic diversity at the time of the isolation and during the ensuing 6000 years can help clarify the effects of bottlenecks and subsequent limited population sizes in species approaching extinction. Previous genetic studies have highlighted questions about how the Holocene Wrangel population was established and how the isolation event affected genetic diversity. Here, we generated high‐quality mitogenomes from 21 radiocarbon‐dated woolly mammoths to compare the ancestral large and genetically diverse Late Pleistocene Siberian population and the small Holocene Wrangel population. Our results indicate that mitogenome diversity was reduced to one single haplotype at the time of the isolation, and thus that the Holocene Wrangel Island population was established by a single maternal lineage. Moreover, we show that the ensuing small effective population size coincided with fixation of a nonsynonymous mutation, and a comparative analysis of mutation rates suggests that the evolutionary rate was accelerated in the Holocene population. These results suggest that isolation on Wrangel Island led to an increase in the frequency of deleterious genetic variation, and thus are consistent with the hypothesis that strong genetic drift in small populations leads to purifying selection being less effective in removing deleterious mutations.

Pečnerová, P. & Martínková, N. (2012). Evolutionary history of tree squirrels (Rodentia, Sciurini) based on multilocus phylogeny reconstruction. -Zoologica Scripta, 41, 211-219. Tree squirrels of the tribe Sciurini represent a group with unresolved phylogenetic relationships in gene trees. We used partial sequences of mitochondrial genes for 12S rRNA, 16S rRNA, cytochrome b and d-loop, and nuclear irbp, c-myc exon 2 and 3 and rag1 genes to reconstruct phylogenetic relationships within the tribe, maximizing the number of analysed species. Bayesian inference analysis of the concatenated sequences revealed common trends that were similar to those retrieved with supertree reconstruction. We confirmed congruence between phylogeny and zoogeography. The first group that diverged from a common ancestor was genus Tamiasciurus, followed by Palaearctic Sciurus and Indomalayan Rheithrosciurus macrotis. Nearctic and Neotropical Sciurus species formed a monophyletic group that included Microsciurus and Syntheosciurus. Neotropical Sciurini were monophyletic with a putative exception of Syntheosciurus brochus that was included in a polychotomy with Nearctic Sciurus in supertree analyses. Our data indicate that Sciurini tree squirrels originated in the northern hemisphere and ancestors of contemporary taxa attained their current distribution through overland colonization from the nearest continent rather than through trans-Pacific dispersal.

Background After over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data. Results Here we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses. Conclusions We propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.