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Sökning: WFRF:(Diez del Molino David)

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  • Lord, Edana, et al. (författare)
  • Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros
  • 2020
  • Ingår i: Current Biology. - : CELL PRESS. - 0960-9822 .- 1879-0445. ; 30:19
  • Tidskriftsartikel (refereegranskat)abstract
    • Ancient DNA has significantly improved our understanding of the evolution and population history of extinct megafauna. However, few studies have used complete ancient genomes to examine species responses to climate change prior to extinction. The woolly rhinoceros (Coelodonta antiquitatis) was a cold-adapted megaherbivore widely distributed across northern Eurasia during the Late Pleistocene and became extinct approximately 14 thousand years before present (ka BP). While humans and climate change have been proposed as potential causes of extinction [1-3], knowledge is limited on how the woolly rhinoceros was impacted by human arrival and climatic fluctuations [2]. Here, we use one complete nuclear genome and 14 mitogenomes to investigate the demographic history of woolly rhinoceros leading up to its extinction. Unlike other northern megafauna, the effective population size of woolly rhinoceros likely increased at 29.7 ka BP and subsequently remained stable until close to the species’ extinction. Analysis of the nuclear genome from a similar to 18.5-ka-old specimen did not indicate any increased inbreeding or reduced genetic diversity, suggesting that the population size remained steady for more than 13 ka following the arrival of humans [4]. The population contraction leading to extinction of the woolly rhinoceros may have thus been sudden and mostly driven by rapid warming in the Bolling-Allerod interstadial. Furthermore, we identify woolly rhinoceros-specific adaptations to arctic climate, similar to those of the woolly mammoth. This study highlights how species respond differently to climatic fluctuations and further illustrates the potential of palaeogenomics to study the evolutionary history of extinct species.
  • Dussex, Nicolas, et al. (författare)
  • Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics
  • 2021
  • Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : ROYAL SOC. - 0962-8452 .- 1471-2954. ; 288:1957
  • Forskningsöversikt (refereegranskat)abstract
    • 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.
  • Feuerborn, Tatiana R., et al. (författare)
  • Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets
  • 2020
  • Ingår i: BMC Genomics. - 1471-2164 .- 1471-2164. ; 21:1
  • Tidskriftsartikel (refereegranskat)abstract
    • 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.
  • Pečnerová, Patrícia, et al. (författare)
  • Changes in variation at the MHC class II DQA locus during the final demise of the woolly mammoth
  • 2016
  • Ingår i: Scientific Reports. - 2045-2322. ; 6
  • Tidskriftsartikel (refereegranskat)abstract
    • According to the nearly-neutral theory of evolution, the relative strengths of selection and drift shift in favour of drift at small population sizes. Numerous studies have analysed the effect of bottlenecks and small population sizes on genetic diversity in the MHC, which plays a central role in pathogen recognition and immune defense and is thus considered a model example for the study of adaptive evolution. However, to understand changes in genetic diversity at loci under selection, it is necessary to compare the genetic diversity of a population before and after the bottleneck. In this study, we analyse three fragments of the MHC DQA gene in woolly mammoth samples radiocarbon dated to before and after a well-documented bottleneck that took place about ten thousand years ago. Our results indicate a decrease in observed heterozygosity and number of alleles, suggesting that genetic drift had an impact on the variation on MHC. Based on coalescent simulations, we found no evidence of balancing selection maintaining MHC diversity during the Holocene. However, strong trans-species polymorphism among mammoths and elephants points to historical effects of balancing selection on the woolly mammoth lineage.
  • Pečnerová, Patrícia, et al. (författare)
  • Genome-Based Sexing Provides Clues about Behavior and Social Structure in the Woolly Mammoth
  • 2017
  • Ingår i: Current Biology. - 0960-9822 .- 1879-0445. ; 27:22, s. 3505-3510.e3
  • Tidskriftsartikel (refereegranskat)abstract
    • 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. Wehypothesize 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.
  • van der Valk, Tom, et al. (författare)
  • Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas
  • 2019
  • Ingår i: Current Biology. - 0960-9822 .- 1879-0445. ; 29:1, s. 165-170.e6
  • Tidskriftsartikel (refereegranskat)abstract
    • Many endangered species have experienced severe population declines within the last centuries [1, 2]. However, despite concerns about negative fitness effects resulting from increased genetic drift and inbreeding, there is a lack of empirical data on genomic changes in conjunction with such declines [3-7]. Here, we use whole genomes recovered from century-old historical museum specimens to quantify the genomic consequences of small population size in the critically endangered Grauer's and endangered mountain gorillas. We find a reduction of genetic diversity and increase in inbreeding and genetic load in the Grauer's gorilla, which experienced severe population declines in recent decades. In contrast, the small but relatively stable mountain gorilla population has experienced little genomic change during the last century. These results suggest that species histories as well as the rate of demographic change may influence how population declines affect genome diversity.
  • Dehasque, Marianne, et al. (författare)
  • Combining Bayesian age models and genetics to investigate population dynamics and extinction of the last mammoths in northern Siberia
  • 2021
  • Ingår i: Quaternary Science Reviews. - 0277-3791 .- 1873-457X. ; 259
  • Tidskriftsartikel (refereegranskat)abstract
    • To understand the causes and implications of an extinction event, detailed information is necessary. However, this can be challenging when working with poorly resolved paleontological data sets. One approach to increase the data resolution is by combining different methods. In this study, we used both radiocarbon and genetic data to reconstruct the population history and extinction dynamics of the woolly mammoth in northern Siberia. We generated 88 new radiocarbon dates and combined these with previously published dates from 626 specimens to construct Bayesian age models. These models show that mammoths disappeared on the eastern Siberian mainland before the onset of the Younger Dryas (12.9–11.7 ky cal BP). Mammoths did however persist in the northernmost parts of central and western Siberia until the early Holocene. Further genetic results of 131 high quality mitogenomes, including 22 new mitogenomes generated in this study, support the hypothesis that mammoths from, or closely related to, a central and/or west- Siberian population recolonized Wrangel Island over the now submerged northern Siberian plains. As mammoths became trapped on the island due to rising sea levels, they lived another ca. 6000 years on Wrangel Island before eventually going extinct ca. 4000 years ago.
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