Search

Your search keyword '"Díez-Del-Molino, David"' showing total 234 results
Start Over Author "Díez-Del-Molino, David"
234 results on '"Díez-Del-Molino, David"'

2. Temporal dynamics of woolly mammoth genome erosion prior to extinction

Author

Dehasque, Marianne, Morales, Hernán E., Díez-del-Molino, David, Pečnerová, Patrícia, Chacón-Duque, J. Camilo, Kanellidou, Foteini, Muller, Héloïse, Plotnikov, Valerii, Protopopov, Albert, Tikhonov, Alexei, Nikolskiy, Pavel, Danilov, Gleb K., Giannì, Maddalena, van der Sluis, Laura, Higham, Tom, Heintzman, Peter D., Oskolkov, Nikolay, Gilbert, M. Thomas P., Götherström, Anders, van der Valk, Tom, Vartanyan, Sergey, and Dalén, Love

Published
2024
Full Text
View/download PDF

3. Population genomics of the critically endangered kākāpō

Author

Dussex, Nicolas, van der Valk, Tom, Morales, Hernán E, Wheat, Christopher W, Díez-del-Molino, David, von Seth, Johanna, Foster, Yasmin, Kutschera, Verena E, Guschanski, Katerina, Rhie, Arang, Phillippy, Adam M, Korlach, Jonas, Howe, Kerstin, Chow, William, Pelan, Sarah, Damas, Joanna D Mendes, Lewin, Harris A, Hastie, Alex R, Formenti, Giulio, Fedrigo, Olivier, Guhlin, Joseph, Harrop, Thomas WR, Le Lec, Marissa F, Dearden, Peter K, Haggerty, Leanne, Martin, Fergal J, Kodali, Vamsi, Thibaud-Nissen, Françoise, Iorns, David, Knapp, Michael, Gemmell, Neil J, Robertson, Fiona, Moorhouse, Ron, Digby, Andrew, Eason, Daryl, Vercoe, Deidre, Howard, Jason, Jarvis, Erich D, Robertson, Bruce C, and Dalén, Love

Subjects
Human Genome, Genetics, Life on Land, bottleneck, conservation, inbreeding, kākāpō, mutational load, purging
Abstract

The kākāpō is a flightless parrot endemic to New Zealand. Once common in the archipelago, only 201 individuals remain today, most of them descending from an isolated island population. We report the first genome-wide analyses of the species, including a high-quality genome assembly for kākāpō, one of the first chromosome-level reference genomes sequenced by the Vertebrate Genomes Project (VGP). We also sequenced and analyzed 35 modern genomes from the sole surviving island population and 14 genomes from the extinct mainland population. While theory suggests that such a small population is likely to have accumulated deleterious mutations through genetic drift, our analyses on the impact of the long-term small population size in kākāpō indicate that present-day island kākāpō have a reduced number of harmful mutations compared to mainland individuals. We hypothesize that this reduced mutational load is due to the island population having been subjected to a combination of genetic drift and purging of deleterious mutations, through increased inbreeding and purifying selection, since its isolation from the mainland ∼10,000 years ago. Our results provide evidence that small populations can survive even when isolated for hundreds of generations. This work provides key insights into kākāpō breeding and recovery and more generally into the application of genetic tools in conservation efforts for endangered species.

Published
2021

4. Million-year-old DNA sheds light on the genomic history of mammoths

Author

van der Valk, Tom, Pečnerová, Patrícia, Díez-del-Molino, David, Bergström, Anders, Oppenheimer, Jonas, Hartmann, Stefanie, Xenikoudakis, Georgios, Thomas, Jessica A, Dehasque, Marianne, Sağlıcan, Ekin, Fidan, Fatma Rabia, Barnes, Ian, Liu, Shanlin, Somel, Mehmet, Heintzman, Peter D, Nikolskiy, Pavel, Shapiro, Beth, Skoglund, Pontus, Hofreiter, Michael, Lister, Adrian M, Götherström, Anders, and Dalén, Love

Subjects
Genetics, Human Genome, Biotechnology, Acclimatization, Alleles, Animals, Bayes Theorem, DNA, Ancient, Elephants, Europe, Evolution, Molecular, Female, Fossils, Genetic Variation, Genome, Mitochondrial, Genomics, Mammoths, Markov Chains, Molar, North America, Phylogeny, Radiometric Dating, Siberia, Time Factors, General Science & Technology
Abstract

Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale1, the oldest genomic data recovered so far are from a horse specimen dated to 780-560 thousand years ago2. Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, 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 lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization 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 already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.

Published
2021

5. Genomics of adaptive evolution in the woolly mammoth

Author

Díez-del-Molino, David, Dehasque, Marianne, Chacón-Duque, J. Camilo, Pečnerová, Patrícia, Tikhonov, Alexei, Protopopov, Albert, Plotnikov, Valeri, Kanellidou, Foteini, Nikolskiy, Pavel, Mortensen, Peter, Danilov, Gleb K., Vartanyan, Sergey, Gilbert, M. Thomas P., Lister, Adrian M., Heintzman, Peter D., van der Valk, Tom, and Dalén, Love

Published
2023
Full Text
View/download PDF

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

Author

Dussex, Nicolas, Bergfeldt, Nora, de Anca Prado, Violeta, Dehasque, Marianne, Díez-del-Molino, David, Ersmark, Erik, Kanellidou, Foteini, Larsson, Petter, Lemež, Špela, Lord, Edana, Mármol-Sánchez, Emilio, Meleg, Ioana N., Måsviken, Johannes, Naidoo, Thijessen, Studerus, Jovanka, Vicente, Mário, von Seth, Johanna, Götherström, Anders, Dalén, Love, and Heintzman, Peter D.

Published
2021

8. Ancient and historical DNA in conservation policy

Author

Jensen, Evelyn L., Díez-del-Molino, David, Gilbert, M. Thomas P., Bertola, Laura D., Borges, Filipa, Cubric-Curik, Vlatka, de Navascués, Miguel, Frandsen, Peter, Heuertz, Myriam, Hvilsom, Christina, Jiménez-Mena, Belén, Miettinen, Antti, Moest, Markus, Pečnerová, Patrícia, Barnes, Ian, and Vernesi, Cristiano

Published
2022
Full Text
View/download PDF

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

Author

von Seth, Johanna, Dussex, Nicolas, Díez-del-Molino, David, van der Valk, Tom, Kutschera, Verena E., Kierczak, Marcin, Steiner, Cynthia C., Liu, Shanlin, Gilbert, M. Thomas P., Sinding, Mikkel-Holger S., Prost, Stefan, Guschanski, Katerina, Nathan, Senthilvel K. S. S., Brace, Selina, Chan, Yvonne L., Wheat, Christopher W., Skoglund, Pontus, Ryder, Oliver A., Goossens, Benoit, Götherström, Anders, and Dalén, Love

Published
2021
Full Text
View/download PDF

16. Moose genomes reveal past glacial demography and the origin of modern lineages

Author

Dussex, Nicolas, Alberti, Federica, Heino, Matti T., Olsen, Remi-Andre, van der Valk, Tom, Ryman, Nils, Laikre, Linda, Ahlgren, Hans, Askeyev, Igor V., Askeyev, Oleg V., Shaymuratova, Dilyara N., Askeyev, Arthur O., Döppes, Doris, Friedrich, Ronny, Lindauer, Susanne, Rosendahl, Wilfried, Aspi, Jouni, Hofreiter, Michael, Lidén, Kerstin, Dalén, Love, and Díez-del-Molino, David

Published
2020
Full Text
View/download PDF

19. Early Neolithic genomes from the eastern Fertile Crescent

Author

Broushaki, Farnaz, Thomas, Mark G., Link, Vivian, López, Saioa, van Dorp, Lucy, Kirsanow, Karola, Hofmanová, Zuzana, Diekmann, Yoan, Cassidy, Lara M., Díez-del-Molino, David, Kousathanas, Athanasios, Sell, Christian, Robson, Harry K., Martiniano, Rui, Blöcher, Jens, Scheu, Amelie, Kreutzer, Susanne, Bollongino, Ruth, Bobo, Dean, Davoudi, Hossein, Munoz, Olivia, Currat, Mathias, Abdi, Kamyar, Biglari, Fereidoun, Craig, Oliver E., Bradley, Daniel G., Shennan, Stephen, Veeramah, Krishna R., Mashkour, Marjan, Wegmann, Daniel, Hellenthal, Garrett, and Burger, Joachim

Published
2016

20. Early farmers from across Europe directly descended from Neolithic Aegeans

Author

Hofmanová, Zuzana, Kreutzer, Susanne, Hellenthal, Garrett, Sell, Christian, Diekmann, Yoan, Díez-del-Molino, David, van Dorp, Lucy, López, Saioa, Kousathanas, Athanasios, Link, Vivian, Kirsanow, Karola, Cassidy, Lara M., Martiniano, Rui, Strobel, Melanie, Scheu, Amelie, Kotsakis, Kostas, Halstead, Paul, Triantaphyllou, Sevi, Kyparissi-Apostolika, Nina, Urem-Kotsou, Dushka, Ziota, Christina, Adaktylou, Fotini, Gopalan, Shyamalika, Bobo, Dean M., Winkelbach, Laura, Blöcher, Jens, Unterländer, Martina, Leuenberger, Christoph, Çilingiroğlu, Çiler, Horejs, Barbara, Gerritsen, Fokke, Shennan, Stephen J., Bradley, Daniel G., Currat, Mathias, Veeramah, Krishna R., Wegmann, Daniel, Thomas, Mark G., Papageorgopoulou, Christina, and Burger, Joachim

Published
2016

21. New indicators for monitoring genetic diversity applied to alpine brown trout populations using whole genome sequence data.

Author

Kurland, Sara, Saha, Atal, Keehnen, Naomi, de la Paz Celorio‐Mancera, Maria, Díez‐del‐Molino, David, Ryman, Nils, and Laikre, Linda

Subjects
WHOLE genome sequencing, ARCTIC char, GENETIC variation, BROWN trout, GENETIC load, INBREEDING, HOMOZYGOSITY
Abstract

International policy recently adopted commitments to maintain genetic diversity in wild populations to secure their adaptive potential, including metrics to monitor temporal trends in genetic diversity – so‐called indicators. A national programme for assessing trends in genetic diversity was recently initiated in Sweden. Relating to this effort, we systematically assess contemporary genome‐wide temporal trends (40 years) in wild populations using the newly adopted indicators and whole genome sequencing (WGS). We use pooled and individual WGS data from brown trout (Salmo trutta) in eight alpine lakes in protected areas. Observed temporal trends in diversity metrics (nucleotide diversity, Watterson's ϴ and heterozygosity) lie within proposed acceptable threshold values for six of the lakes, but with consistently low values in lakes above the tree line and declines observed in these northern‐most lakes. Local effective population size is low in all lakes, highlighting the importance of continued protection of interconnected systems to allow genetic connectivity for long‐term viability of these populations. Inbreeding (FROH) spans 10%–30% and is mostly represented by ancient (<1 Mb) runs of homozygosity, with observations of little change in mutational load. We also investigate adaptive dynamics over evolutionarily short time frames (a few generations); identifying putative parallel selection across all lakes within a gene pertaining to skin pigmentation as well as candidates of selection unique to specific lakes and lake systems involved in reproduction and immunity. We demonstrate the utility of WGS for systematic monitoring of natural populations, a priority concern if genetic diversity is to be protected. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

24. Additional file 1 of GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species

Author

Kutschera, Verena E., Kierczak, Marcin, van der Valk, Tom, von Seth, Johanna, Dussex, Nicolas, Lord, Edana, Dehasque, Marianne, Stanton, David W. G., Khoonsari, Payam Emami, Nystedt, Björn, Dalén, Love, and Díez-del-Molino, David

Abstract

Additional file 1. Supplementary Information, which contains Extended methods notes 1–2, Tables S1-S3 and Figures S1–S4

Published
2022
Full Text
View/download PDF

25. Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets

Author

Swedish Research Council, European Commission, Stockholm University, Feuerborn, Tatiana R. [0000-0003-1610-3402], Palkopoulou, Eleftheria [0000-0001-7382-7509], van der Valk, Tom [0000-0001-6582-3452], von Seth, Johanna [0000-0002-1324-7489], Munters, Arielle R. [0000-0003-1512-6565], Pečnerová, Patrícia [0000-0001-9350-1987], Dehasque, Marianne [0000-0002-4640-8306], Ureña, Irene [0000-0001-9724-9977], Ersmark, Erik [0000-0003-4186-7498], Krzewińska, Maja [0000-0002-6702-8724], Rodríguez-Varela, Ricardo [0000-0002-4173-8648], Götherström, Anders [0000-0001-8579-1304], Dalén, Love [0000-0001-6307-8188], Díez-Del-Molino, David [0000-0002-9701-5940], Feuerborn, Tatiana R., Palkopoulou, Eleftheria, van der Valk, Tom, von Seth, Johanna, Munters, Arielle R., Pečnerová, Patrícia, Dehasque, Marianne, Ureña, Irene, Ersmark, Erik, Lagerholm, Vendela Kempe, Krzewińska, Maja, Rodríguez-Varela, Ricardo, Götherström, Anders, Dalén, Love, Díez-Del-Molino, David, Swedish Research Council, European Commission, Stockholm University, Feuerborn, Tatiana R. [0000-0003-1610-3402], Palkopoulou, Eleftheria [0000-0001-7382-7509], van der Valk, Tom [0000-0001-6582-3452], von Seth, Johanna [0000-0002-1324-7489], Munters, Arielle R. [0000-0003-1512-6565], Pečnerová, Patrícia [0000-0001-9350-1987], Dehasque, Marianne [0000-0002-4640-8306], Ureña, Irene [0000-0001-9724-9977], Ersmark, Erik [0000-0003-4186-7498], Krzewińska, Maja [0000-0002-6702-8724], Rodríguez-Varela, Ricardo [0000-0002-4173-8648], Götherström, Anders [0000-0001-8579-1304], Dalén, Love [0000-0001-6307-8188], Díez-Del-Molino, David [0000-0002-9701-5940], Feuerborn, Tatiana R., Palkopoulou, Eleftheria, van der Valk, Tom, von Seth, Johanna, Munters, Arielle R., Pečnerová, Patrícia, Dehasque, Marianne, Ureña, Irene, Ersmark, Erik, Lagerholm, Vendela Kempe, Krzewińska, Maja, Rodríguez-Varela, Ricardo, Götherström, Anders, Dalén, Love, and Díez-Del-Molino, David

Abstract

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.

Published
2020

26. GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species

Author

Kutschera, Verena E., primary, Kierczak, Marcin, additional, van der Valk, Tom, additional, von Seth, Johanna, additional, Dussex, Nicolas, additional, Lord, Edana, additional, Dehasque, Marianne, additional, Stanton, David W. G., additional, Khoonsari, Payam Emami, additional, Nystedt, Björn, additional, Dalén, Love, additional, and Díez-del-Molino, David, additional

Published
2022
Full Text
View/download PDF

27. Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros

Author

Lord, Edana, Dussex, Nicolas, Kierczak, Marcin, Díez-del-Molino, David, Ryder, Oliver A., Stanton, David W.G., Gilbert, M. Thomas P., Sánchez-Barreiro, Fátima, Zhang, Guojie, Sinding, Mikkel-Holger S., Lorenzen, Eline D., Willerslev, Eske, Protopopov, Albert, Shidlovskiy, Fedor, Fedorov, Sergey, Bocherens, Hervé, Nathan, Senthilvel K.S.S., Goossens, Benoit, van der Plicht, Johannes, Chan, Yvonne L., Prost, Stefan, Potapova, Olga, Kirillova, Irina, Lister, Adrian M., Heintzman, Peter D., Kapp, Joshua D., Shapiro, Beth, Vartanyan, Sergey, Götherström, Anders, and Dalén, Love

Published
2020
Full Text
View/download PDF

28. Combining Bayesian age models and genetics to investigate population dynamics and extinction of the last mammoths in northern Siberia

Author

Dehasque, Marianne, Pečnerová, Patrícia, Muller, Héloïse, Tikhonov, Alexei, Nikolskiy, Pavel, Tsigankova, Valeriya, Danilov, Gleb K., Díez-del-Molino, David, Vartanyan, Sergey, Dalén, Love, Lister, Adrian M., Dehasque, Marianne, Pečnerová, Patrícia, Muller, Héloïse, Tikhonov, Alexei, Nikolskiy, Pavel, Tsigankova, Valeriya, Danilov, Gleb K., Díez-del-Molino, David, Vartanyan, Sergey, Dalén, Love, and Lister, Adrian M.

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.

Published
2021
Full Text
View/download PDF

29. Combining Bayesian age models and genetics to investigate population dynamics and extinction of the last mammoths in northern Siberia

Author

Dehasque, Marianne, primary, Pečnerová, Patrícia, additional, Muller, Héloïse, additional, Tikhonov, Alexei, additional, Nikolskiy, Pavel, additional, Tsigankova, Valeriya I., additional, Danilov, Gleb K., additional, Díez-del-Molino, David, additional, Vartanyan, Sergey, additional, Dalén, Love, additional, and Lister, Adrian M., additional

Published
2021
Full Text
View/download PDF

30. The Arrival of Siberian Ancestry Connecting the Eastern Baltic to Uralic Speakers further East

Author

Saag, Lehti, Laneman, Margot, Varul, Liivi, Malve, Martin, Valk, Heiki, Razzak, Maria A., Shirobokov, Ivan G., Khartanovich, Valeri I., Mikhaylova, Elena R., Kushniarevich, Alena, Scheib, Christiana Lyn, Solnik, Anu, Reisberg, Tuuli, Parik, Jüri, Saag, Lauri, Metspalu, Ene, Rootsi, Siiri, Montinaro, Francesco, Remm, Maido, Mägi, Reedik, D’Atanasio, Eugenia, Crema, Enrico Ryunosuke, Díez-del-Molino, David, Thomas, Mark G., Kriiska, Aivar, Kivisild, Toomas, Villems, Richard, Lang, Valter, Metspalu, Mait, and Tambets, Kristiina

Published
2019
Full Text
View/download PDF

32. Inference of natural selection from ancient DNA

Author

Dehasque, Marianne, primary, Ávila-Arcos, María C., additional, Díez-del-Molino, David, additional, Fumagalli, Matteo, additional, Guschanski, Katerina, additional, Lorenzen, Eline D., additional, Malaspinas, Anna-Sapfo, additional, Marques-Bonet, Tomas, additional, Martin, Michael D., additional, Murray, Gemma G. R., additional, Papadopulos, Alexander S. T., additional, Therkildsen, Nina Overgaard, additional, Wegmann, Daniel, additional, Dalén, Love, additional, and Foote, Andrew D., additional

Published
2020
Full Text
View/download PDF

33. Additional file 2 of Moose genomes reveal past glacial demography and the origin of modern lineages

Author

Dussex, Nicolas, Alberti, Federica, Heino, Matti T., Remi-Andre Olsen, Valk, Tom Van Der, Ryman, Nils, Laikre, Linda, Ahlgren, Hans, Askeyev, Igor V., Askeyev, Oleg V., Shaymuratova, Dilyara N., Askeyev, Arthur O., Döppes, Doris, Friedrich, Ronny, Lindauer, Susanne, Rosendahl, Wilfried, Aspi, Jouni, Hofreiter, Michael, Lidén, Kerstin, Dalén, Love, and Díez-Del-Molino, David

Abstract

Additional file 2: Figure S1. Identification of scaffolds linked to chromosome X using sequencing coverage and scaffold length. Green dots correspond to scaffolds assigned as linked to chromosome X. The red lines indicate the median coverage for all scaffolds. The blue lines represent half the median coverage which corresponds to the coverage of scaffolds linked to chromosome X. Figure S2. Past demography for moose (Alces alces) using PSMC. Thin lines represent 100 bootstrap runs. The x-axis corresponds to time before present in years on a log scale, assuming an estimated substitution rate of 0.7 × 10− 8 substitutions/site/generation [30] and a generation time of 7 years [31]. The y-axis corresponds to the effective population size Ne. Figure S3. Past demography for moose (Alces alces) using a Bayesian Skyline Plot (BSP). Demographic reconstruction was inferred in BEAST using 14 European 16,693 bp mitogenomes. Timing of events was estimated assuming a mean rate of 9 × 10− 9 substitutions/site/year based on Zurano et al. [93] and a standard deviation of 0.01. The x axis is in calendar years before present and y axis represents changes in effective population size (shown as the product of Nef and generation time T). The black line corresponds to the median estimate and the blue lines show the 95% highest posterior density intervals. Figure S4. Distribution of runs of homozygosity (ROH) in moose (Alces alces). ROH ≥500 kb are shown.

Published
2020
Full Text
View/download PDF

35. Inference of natural selection from ancient DNA

Author

Dehasque, Marianne, Ávila‐Arcos, María C., Díez‐del‐Molino, David, Fumagalli, Matteo, Guschanski, Katerina, Lorenzen, Eline D., Malaspinas, Anna‐Sapfo, Marques‐Bonet, Tomas, Martin, Michael D., Murray, Gemma G. R., Papadopulos, Alexander S. T., Therkildsen, Nina Overgaard, Wegmann, Daniel, Dalén, Love, Foote, Andrew D., Dehasque, Marianne, Ávila‐Arcos, María C., Díez‐del‐Molino, David, Fumagalli, Matteo, Guschanski, Katerina, Lorenzen, Eline D., Malaspinas, Anna‐Sapfo, Marques‐Bonet, Tomas, Martin, Michael D., Murray, Gemma G. R., Papadopulos, Alexander S. T., Therkildsen, Nina Overgaard, Wegmann, Daniel, Dalén, Love, and Foote, Andrew D.

Abstract

Evolutionary processes, including selection, can be indirectly inferred based on patterns of genomic variation among contemporary populations or species. However, this often requires unrealistic assumptions of ancestral demography and selective regimes. Sequencing ancient DNA from temporally spaced samples can inform about past selection processes, as time series data allow direct quantification of population parameters collected before, during, and after genetic changes driven by selection. In this Comment and Opinion, we advocate for the inclusion of temporal sampling and the generation of paleogenomic datasets in evolutionary biology, and highlight some of the recent advances that have yet to be broadly applied by evolutionary biologists. In doing so, we consider the expected signatures of balancing, purifying, and positive selection in time series data, and detail how this can advance our understanding of the chronology and tempo of genomic change driven by selection. However, we also recognize the limitations of such data, which can suffer from postmortem damage, fragmentation, low coverage, and typically low sample size. We therefore highlight the many assumptions and considerations associated with analyzing paleogenomic data and the assumptions associated with analytical methods.

Published
2020

36. Competitive mapping allows to identify and exclude human DNA contamination in ancient faunal genomic datasets

Author

Feuerborn, Tatiana R., primary, Palkopoulou, Elle, additional, van der Valk, Tom, additional, von Seth, Johanna, additional, Munters, Arielle R., additional, Pečnerová, Patrícia, additional, Dehasque, Marianne, additional, Ureña, Irene, additional, Ersmark, Erik, additional, Lagerholm, Vendela Kempe, additional, Krzewinska, Maja, additional, Rodríguez-Varela, Ricardo, additional, Götherström, Anders, additional, Dalén, Love, additional, and Díez-del-Molino, David, additional

Published
2020
Full Text
View/download PDF

38. Historical genomes reveal the genomic consequences of recent population decline in Eastern Gorillas

Author

European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Fundación la Caixa, Generalitat de Catalunya, Agencia Estatal de Investigación (España), Valk, Tom van der., Díez-del-Molino, David, Marqués-Bonet, Tomàs, Guschanski, Katerina, Dalén, Love, European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Fundación la Caixa, Generalitat de Catalunya, Agencia Estatal de Investigación (España), Valk, Tom van der., Díez-del-Molino, David, Marqués-Bonet, Tomàs, Guschanski, Katerina, and Dalén, Love

Abstract

Van der Valk et al. investigate the genomic consequences of recent population decline using 100-year-old museum specimens. They find a reduction in genetic diversity, increase in inbreeding, and increase in deleterious mutations in the critically endangered Grauer's gorillas.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.

Published
2019

39. A western route of prehistoric human migration from Africa into the Iberian Peninsula

Author

González Fortes, Gloria, Tassi, Franco, Trucchi, Emiliano, Henneberger, Kirstin, Paijmans, Johanna L. A., Díez del Molino, David, Schroeder, Hannes, Susca, Roberta Rosa, Barroso-Ruíz, Cecilio, Bermúdez, Francisco J., Barroso-Medina, C., Bettencourt, Ana M. S., Sampaio, Hugo Aluai, Grandal-d'Anglade, Aurora, Salas, Antonio, Lombera Hermida, Arturo de, Fábregas Valcarce, Ramón, Vaquero, Manuel, Alonso, Susana, Lozano, Marina, Rodríguez, Xosé Pedro, Fernández-Rodríguez, Carlos, Manica, Andrea, Hofreiter, Michael, Barbujani, Guido, González Fortes, Gloria, Tassi, Franco, Trucchi, Emiliano, Henneberger, Kirstin, Paijmans, Johanna L. A., Díez del Molino, David, Schroeder, Hannes, Susca, Roberta Rosa, Barroso-Ruíz, Cecilio, Bermúdez, Francisco J., Barroso-Medina, C., Bettencourt, Ana M. S., Sampaio, Hugo Aluai, Grandal-d'Anglade, Aurora, Salas, Antonio, Lombera Hermida, Arturo de, Fábregas Valcarce, Ramón, Vaquero, Manuel, Alonso, Susana, Lozano, Marina, Rodríguez, Xosé Pedro, Fernández-Rodríguez, Carlos, Manica, Andrea, Hofreiter, Michael, and Barbujani, Guido

Abstract

[Abstract] Being at the western fringe of Europe, Iberia had a peculiar prehistory and a complex pattern of Neolithization. A few studies, all based on modern populations, reported the presence of DNA of likely African origin in this region, generally concluding it was the result of recent gene flow, probably during the Islamic period. Here, we provide evidence of much older gene flow from Africa to Iberia by sequencing whole genomes from four human remains from northern Portugal and southern Spain dated around 4000 years BP (from the Middle Neolithic to the Bronze Age). We found one of them to carry an unequivocal sub-Saharan mitogenome of most probably West or West-Central African origin, to our knowledge never reported before in prehistoric remains outside Africa. Our analyses of ancient nuclear genomes show small but significant levels of sub-Saharan African affinity in several ancient Iberian samples, which indicates that what we detected was not an occasional individual phenomenon, but an admixture event recognizable at the population level. We interpret this result as evidence of an early migration process from Africa into the Iberian Peninsula through a western route, possibly across the Strait of Gibraltar.

Published
2019

41. Mitogenome evolution in the last surviving woolly mammoth population reveals neutral and functional consequences of small population size

Author

Pečnerová, Patrícia, primary, Palkopoulou, Eleftheria, additional, Wheat, Christopher W., additional, Skoglund, Pontus, additional, Vartanyan, Sergey, additional, Tikhonov, Alexei, additional, Nikolskiy, Pavel, additional, van der Plicht, Johannes, additional, Díez-del-Molino, David, additional, and Dalén, Love, additional

Published
2017
Full Text
View/download PDF

42. Mitogenome evolution in the last surviving woolly mammoth population reveals neutral and functional consequences of small population size

Author

Pečnerová, Patrícia, Palkopoulou, Eleftheria, Wheat, Christopher W., Skoglund, Pontus, Vartanyan, Sergey, Tikhonov, Alexei, Nikolskiy, Pavel, van der Plicht, Johannes, Díez-del-Molino, David, Dalén, Love, Pečnerová, Patrícia, Palkopoulou, Eleftheria, Wheat, Christopher W., Skoglund, Pontus, Vartanyan, Sergey, Tikhonov, Alexei, Nikolskiy, Pavel, van der Plicht, Johannes, Díez-del-Molino, David, and Dalén, Love

Published
2017
Full Text
View/download PDF

43. Genetic diversity and population structure of the non-native Eastern mosquitofish (Gambusia holbrooki) in Mediterranean streams

Author

Díez del Molino, David, García Marín, José Luis, and Universitat de Girona. Departament de Biologia

Subjects
Tesis i dissertacions acadèmiques, Biología de las poblaciones, Ríos mediterráneos, Mosquitofish, Mediterranean rivers, 574 - Ecologia general i biodiversitat, Introduced organisms, Population biology, Diversidad genética, Genetic diversity, Animals invasors, Diversitat genètica, Animales invasores, 504 - Ciències del medi ambient, Gambusia holbrooki, Biologia de poblacions, Gambezi, Rius Mediterranis, Gambúsies
Abstract

Mosquitofish is a small, voracious, highly fecund freshwater fish species originated from northeaster America, that was introduced worldwide to control mosquito populations. In this thesis we have studied the genetics of the invasion of Mediterranean streams by the mosquitofish (Gambusia holbrooki) to discover some of the aspects that drive their successfully invasive life history. Comparison of introduced populations with the American sources of invasion indicated that there was no loss of genetic diversity due to the invasion process. Local genetic diversity levels and overall population structure were maintained among generations in introduced populations. We observed adaptive response to pollutants in the Flix reservoir, Ebro River, but that human perturbations do not prevent mosquitofish dispersal along rivers. Finally, unregulated human-assisted translocations probably increase the opportunities for colonization of new environments, and therefore need to be controlled., La gambúsia és un peix molt voraç i fecund originari de les masses d’aigua dolça del nord-est d’Amèrica, que va a ser introduïda en tot el món pel control biològic de les poblacions de mosquit. En aquesta tesis se analitzen els processos genètics relacionats amb l’èxit invasor de la gambúsia (Gambusia holbrooki) en les conques mediterrànies. Les poblacions de gambusia introduïdes catalanes mantenen els nivells de diversitat genètica presents a les poblacions Americànes que van ser les fonts dels invasors de Europa. En aquestas poblacions introduïdes, els nivells locals i patrons hidrogràfics de diversitat genètica es mantenen entre generacions. Hi a una resposta selectiva als contaminants en les poblacions de gamusia a l’embassament de Flix, riu Ebro, però aquestes pertorbacions humanes no limiten la dispersió de la gambúsia. Finalment, les translocacions d’exemplars per l’home augmenten les oportunitats de colonitzar nous ambients i per això han de ser controlats.

Published
2015

44. Changes in variation at the MHC class II DQA locus during the final demise of the woolly mammoth.

Author

Pečnerová, Patrícia, Díez-Del-Molino, David, Vartanyan, Sergey, Dalén, Love, Pečnerová, Patrícia, Díez-Del-Molino, David, Vartanyan, Sergey, and Dalén, Love

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.

Published
2016
Full Text
View/download PDF

47. Early farmers from across Europe directly descended from Neolithic Aegeans

Author

Hofmanová, Zuzana, primary, Kreutzer, Susanne, additional, Hellenthal, Garrett, additional, Sell, Christian, additional, Diekmann, Yoan, additional, Díez del Molino, David, additional, van Dorp, Lucy, additional, López, Saioa, additional, Kousathanas, Athanasios, additional, Link, Vivian, additional, Kirsanow, Karola, additional, Cassidy, Lara M, additional, Martiniano, Rui, additional, Strobel, Melanie, additional, Scheu, Amelie, additional, Kotsakis, Kostas, additional, Halstead, Paul, additional, Triantaphyllou, Sevi, additional, Kyparissi-Apostolika, Nina, additional, Urem-Kotsou, Dushanka-Christina, additional, Ziota, Christina, additional, Adaktylou, Fotini, additional, Gopalan, Shyamalika, additional, Bobo, Dean M, additional, Winkelbach, Laura, additional, Blöcher, Jens, additional, Unterländer, Martina, additional, Leuenberger, Christoph, additional, Çilingiroğlu, Çiler, additional, Horejs, Barbara, additional, Gerritsen, Fokke, additional, Shennan, Stephen, additional, Bradley, Daniel G, additional, Currat, Mathias, additional, Veeramah, Krishna, additional, Wegmann, Daniel, additional, Thomas, Mark G, additional, Papageorgopoulou, Christina, additional, and Burger, Joachim, additional

Published
2015
Full Text
View/download PDF

49. Gene Flow and Maintenance of Genetic Diversity in Invasive Mosquitofish (Gambusia holbrooki).

Author

Díez-del-Molino, David, Carmona-Catot, Gerard, Araguas, Rosa-Maria, Vidal, Oriol, Sanz, Nuria, García-Berthou, Emili, and García-Marín, Jose-Luis

Subjects
*GENE flow, *EASTERN mosquitofish, *FISH genetics, *INTRODUCED species, *FISH populations, *HYDROGRAPHY, *FISH habitats, *FISHES
Abstract

Genetic analyses contribute to studies of biological invasions by mapping the origin and dispersal patterns of invasive species occupying new territories. Using microsatellite loci, we assessed the genetic diversity and spatial population structure of mosquitofish (Gambusia holbrooki) that had invaded Spanish watersheds, along with the American locations close to the suspected potential source populations. Mosquitofish populations from the Spanish streams that were studied had similar levels of genetic diversity to the American samples; therefore, these populations did not appear to have undergone substantial losses of genetic diversity during the invasion process. Population structure analyses indicated that the Spanish populations fell into four main clusters, which were primarily associated with hydrography. Dispersal patterns indicated that local populations were highly connected upstream and downstream through active dispersal, with an average of 21.5% fish from other locations in each population. After initially introducing fish to one location in a given basin, such dispersal potential might contribute to the spread and colonization of suitable habitats throughout the entire river basin. The two-dimension isolation-by-distance pattern here obtained, indicated that the human-mediated translocation of mosquitofish among the three study basins is a regular occurrence. Overall, both phenomena, high natural dispersal and human translocation, favor gene flow among river basins and the retention of high genetic diversity, which might help retain the invasive potential of mosquitofish populations. [ABSTRACT FROM AUTHOR]

Published
2013
Full Text
View/download PDF

50. Gene Flow and Maintenance of Genetic Diversity in Invasive Mosquitofish (Gambusia holbrooki).

Author

Díez-del-Molino, David, Carmona-Catot, Gerard, Araguas, Rosa-Maria, Vidal, Oriol, Sanz, Nuria, García-Berthou, Emili, and García-Marín, Jose-Luis

Subjects
GENE flow, EASTERN mosquitofish, FISH genetics, INTRODUCED species, FISH populations, HYDROGRAPHY, FISH habitats, FISHES
Abstract

Genetic analyses contribute to studies of biological invasions by mapping the origin and dispersal patterns of invasive species occupying new territories. Using microsatellite loci, we assessed the genetic diversity and spatial population structure of mosquitofish (Gambusia holbrooki) that had invaded Spanish watersheds, along with the American locations close to the suspected potential source populations. Mosquitofish populations from the Spanish streams that were studied had similar levels of genetic diversity to the American samples; therefore, these populations did not appear to have undergone substantial losses of genetic diversity during the invasion process. Population structure analyses indicated that the Spanish populations fell into four main clusters, which were primarily associated with hydrography. Dispersal patterns indicated that local populations were highly connected upstream and downstream through active dispersal, with an average of 21.5% fish from other locations in each population. After initially introducing fish to one location in a given basin, such dispersal potential might contribute to the spread and colonization of suitable habitats throughout the entire river basin. The two-dimension isolation-by-distance pattern here obtained, indicated that the human-mediated translocation of mosquitofish among the three study basins is a regular occurrence. Overall, both phenomena, high natural dispersal and human translocation, favor gene flow among river basins and the retention of high genetic diversity, which might help retain the invasive potential of mosquitofish populations. [ABSTRACT FROM AUTHOR]

Published
2013
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results