Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics

Ancient DNA (aDNA) has played a major role in our understanding of the past. Important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understanding of processes such as past demography, introgression, domestication, adaptation and speciation. However, to date and with the notable exception of microbiomes and sediments, most aDNA studies have focused on single taxa or taxonomic groups, making the study of changes at the community level challenging. This is rather surprising because current sequencing and analytical approaches allow us to obtain and analyse aDNA from multiple source materials. When combined, these data can enable the simultaneous study of multiple taxa through space and time, and could thus provide a more comprehensive understanding of ecosystem-wide changes. It is therefore timely to develop an integrative approach to aDNA studies by combining data from multiple taxa and substrates. In this review, we discuss the various applications, associated challenges and future prospects of such an approach

Dense sampling of bird diversity increases power of comparative genomics (vol 587, pg 252, 2020)

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Ancient and Modern Genomes Unravel the Evolutionary History of the Rhinoceros Family

Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (∼16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines. © 2021 The Authors.The authors acknowledge support from the Science for Life Laboratory, the Garvan Institute of Medical Research, the Knut and Alice Wallenberg Foundation, and the National Genomics Infrastructure funded by the Swedish Research Council and Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure. We thank the Natural History Museum at the University of Oslo for providing the Javan rhinoceros sample. We thank the Museum of the Institute of Plant and Animal Ecology (UB RAS, Ekaterinburg) for providing the sample of Siberian unicorn. M.T.P.G. was supported by European Research Council (ERC) Consolidator grant 681396 (Extinction Genomics). E.D.L. was supported by Independent Research Fund Denmark grant 8021-00218B . A.C. was supported by an Australian Research Council Laureate Fellowship ( FL140100260 ). T.M.B. is supported by funding from the ERC under the European Union’s Horizon 2020 research and innovation program (grant agreement 864203 ), grant BFU2017-86471-P ( MINECO /FEDER, UE), “Unidad de Excelencia María de Maeztu” funded by the AEI ( CEX2018-000792-M ), Howard Hughes International Early Career, and Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya ( GRC 2017 SGR 880 ). L.D. was supported by the Swedish Research Council ( 2017-04647 ) and Formas ( 2018-01640 ). We thank Dmitry Bogdanov and Roger Hall for giving us permission to use their rhinoceros artwork

Contemporary effective population size and predicted maintenance of genetic diversity in the endangered kea (<i>Nestor notabilis</i>)

<p>Population size and the potential for maintenance of genetic diversity are critical information for the monitoring of species of conservation concern. However, direct estimates of population size are not always feasible, making indirect genetic approaches a valuable alternative. We estimated contemporary effective population size (<i>N</i>_e) in the endangered kea (<i>Nestor notabilis</i>) using three different methods. We then inferred the census size (<i>N</i>_C) using published <i>N</i>_e/<i>N</i>_C ratios and modelled the future maintenance of genetic diversity assuming a number of demographic parameters. Short-term <i>N</i>_e was small with a range-wide <i>N</i>_e < 250–700, while <i>N</i>_C was within the range of the current estimate (c. 1000–5000). Forward simulations showed low probability of retaining 90% of rare alleles without immigration. However, the probability of maintaining genetic diversity was high with immigration, juvenile survival of ≥ 30%, and an initial sex ratio of c. 0.5–0.6. Despite the low <i>N</i>_e in kea, predator control and/or artificial immigration might be sufficient to maintain the present genetic diversity.</p

Diaspore traits discriminate good from weak colonisers on high elevation summits

The richness of plant species in Swiss alpine-nival summits increased during the climate warming of the 20th century. Thirty-seven summits (2797-3418 m a.s.l.) with both old (~1900-1920) and recent (~2000) plant inventories were used to test whether biological species traits can explain the observed rates of summit colonisation. Species were classified into two groups: good colonisers (colonising five or more summits) and weak colonisers (fewer than five new summits). We compared species traits related to growth, reproduction and dispersal between these two groups and between the good colonisers and a group of high alpine grassland species. The observed colonisation pattern was subsequently compared to a simulated random colonisation pattern. The distribution of new species on the summits was not random, and 16 species exhibited a colonisation rate higher than expected by chance. Taraxacum alpinum aggr. and Cardamine resedifolia were the best colonisers. Results showed that diaspore traits enhancing long-distance dispersal were more frequent among good colonisers than among weak colonisers. Good colonisers were mostly characterised by pappi or narrow wings on their diaspores. Both groups were able to grow on soils more bare and rocky than species from the alpine grasslands. All other biological traits that we considered were similar among the three alpine species groups. These results are important for improving predictive models of species distribution under climate chang

Low spatial genetic differentiation associated with rapid recolonization in the New Zealand fur seal arctocephalus forsteri

Population declines resulting from anthropogenic activities are of major consequence for the long-term survival of species because the resulting loss of genetic diversity can lead to extinction via the effects of inbreeding depression, fixation of deleterious mutations, and loss of adaptive potential. Otariid pinnipeds have been exploited commercially to near extinction with some species showing higher demographic resilience and recolonization potential than others. The New Zealand fur seal (NZFS) was heavily impacted by commercial sealing between the late 18th and early 19th centuries, but has recolonized its former range in southern Australia. The species has also recolonized its former range in New Zealand, yet little is known about the pattern of recolonization. Here, we first used 11 microsatellite markers (n = 383) to investigate the contemporary population structure and dispersal patterns in the NZFS (Arctocephalus forsteri). Secondly, we model postsealing recolonization with 1 additional mtDNA cytochrome b (n = 261) marker. Our data identified 3 genetic clusters: an Australian, a subantarctic, and a New Zealand one, with a weak and probably transient subdivision within the latter cluster. Demographic history scenarios supported a recolonization of the New Zealand coastline from remote west coast colonies, which is consistent with contemporary gene flow and with the species' high resilience. The present data suggest the management of distinct genetic units in the North and South of New Zealand along a genetic gradient. Assignment of individuals to their colony of origin was limited (32%) with the present data indicating the current microsatellite markers are unlikely sufficient to assign fisheries bycatch of NZFSs to colonies.Nicolas Dussex, Bruce C. Robertson, Alexander T. Salis, Aleksandr Kalinin, Hugh Best, Neil J. Gemmel

Genomic and fitness consequences of inbreeding in an endangered carnivore

Reduced fitness through genetic drift and inbreeding is a major threat to small and isolated populations. Although previous studies have generally used genetically verified pedigrees to document effects of inbreeding and gene flow, these often fail to capture the whole inbreeding history of the species. By assembling a draft arctic fox (Vulpes lagopus) genome and re-sequencing complete genomes of 23 additional foxes born before and after a well-documented immigration event in Scandinavia, we here look into the genomic consequences of inbreeding and genetic rescue. We found a difference in genome-wide diversity, with 18% higher heterozygosity and 81% lower FROH in immigrant F1 compared to native individuals. However, more distant descendants of immigrants (F2, F3) did not show the same pattern. We also found that foxes with lower inbreeding had higher probability to survive their first year of life. Our results demonstrate the important link between genetic variation and fitness as well as the transient nature of genetic rescue. Moreover, our results have implications in conservation biology as they demonstrate that inbreeding depression can effectively be detected in the wild by a genomic approach

A genome-wide investigation of adaptive signatures in protein-coding genes related to tool behaviour in New Caledonian and Hawaiian crows.

Very few animals habitually manufacture and use tools. It has been suggested that advanced tool behaviour co-evolves with a suite of behavioural, morphological and life history traits. In fact, there are indications for such an adaptive complex in tool-using crows (genus Corvus species). Here, we sequenced the genomes of two habitually tool-using and ten non-tool-using crow species to search for genomic signatures associated with a tool-using lifestyle. Using comparative genomic and population genetic approaches, we screened for signals of selection in protein-coding genes in the tool-using New Caledonian and Hawaiian crows. While we detected signals of recent selection in New Caledonian crows near genes associated with bill morphology, our data indicate that genetic changes in these two lineages are surprisingly subtle, with little evidence at present for convergence. We explore the biological explanations for these findings, such as the relative roles of gene regulation and protein-coding changes, as well as the possibility that statistical power to detect selection in recently diverged lineages may have been insufficient. Our study contributes to a growing body of literature aiming to decipher the genetic basis of recently evolved complex behaviour

Consequences of past climate change and recent human persecution on mitogenomic diversity in the arctic fox

Ancient DNA provides a powerful means to investigate the timing, rate and extent of population declines caused by extrinsic factors, such as past climate change and human activities. One species probably affected by both these factors is the arctic fox, which had a large distribution during the last glaciation that subsequently contracted at the start of the Holocene. More recently, the arctic fox population in Scandinavia went through a demographic bottleneck owing to human persecution. To investigate the consequences of these processes, we generated mitogenome sequences from a temporal dataset comprising Pleistocene, historical and modern arctic fox samples. We found no evidence that Pleistocene populations in mid-latitude Europe or Russia contributed to the present-day gene pool of the Scandinavian population, suggesting that postglacial climate warming led to local population extinctions. Furthermore, during the twentieth-century bottleneck in Scandinavia, at least half of the mitogenome haplotypes were lost, consistent with a 20-fold reduction in female effective population size. In conclusion, these results suggest that the arctic fox in mainland Western Europe has lost genetic diversity as a result of both past climate change and human persecution. Consequently, it might be particularly vulnerable to the future Challenges posed by climate change. This article is part of a discussion meeting issue ‘The past is a Foreign country: how much can the fossil record actually inform conservation?’publishedVersio