MEET THE TEAM
Dr. Andrew Foote
Andrew Foote is an evolutionary ecologist with an interest in adaptation and speciation. After completing his PhD at Aberdeen University, he undertook independent research fellowships based at the Copenhagen University, Uppsala University and most recently the University of Bern. Using a multi-disciplinary approach that combines ancient DNA, genomics and behavioural studies Andrew has investigated adaptation and speciation in the killer whale, which has radiated into different forms and ecotypes. His current research is focused on applying palaeogenomics approaches to model systems for understanding the evolutionary processes and underlying mechanisms of adaptation and speciation.
Foote AD, Morin PA (2016) Genome-wide SNP data suggests complex ancestry of sympatric North Pacific killer whale ecotypes. Heredity 117, 316-325
Foote AD et al. (2016) Genome culture coevolution promotes rapid divergence of killer whale ecotypes. Nature Communications 7:11693
Foote AD, et al. (2015) Convergent evolution of the genomes of marine mammals. Nature Genetics 47, 272-275
Foote AD, Newton J, Ávila-Arcos MC, et al. (2013) Tracking niche variation over millennial timescales in sympatric killer whale lineages. Proceedings of the Royal Society, B 280: 20131481
Foote AD, Kaschner K, Schultze S, et al. (2013) Ancient DNA reveals that bowhead whale lineages survived Late Pleistocene climate change and habitat shifts. Nature Communications 4:1677
Asst. Prof. Anna-Sapfo Malaspinas
University of Lausanne
Department of Computational Biology
Anna is a computational biologist specialised in population genetics. The main aim of her research group - currently located at the University of Bern - is to characterize evolutionary processes (genetic drift, natural selection, migration and mutation) while relying on genomics data from both modern and ancient samples. The Malaspinas group develop analytical and computational methods to analyze and interpret time sampled data and apply those methods to novel ancient DNA datasets via collaborative projects. This work should allow to quantify and time adaptive and migration events - notably related to the human colonization of the world - while generating unique datasets.
Malaspinas A-S et al. (2016) A genomic history of Aboriginal Australia. Nature 538, 207–214
Malaspinas A-S (2016) Methods to characterize selective sweeps using time serial samples: an ancient DNA perspective. Molecular Ecology 25, 24–41
Moreno-Mayar JV, Rasmussen S, Seguin-Orlando A, Rasmussen M, Liang M, Flam ST, Lie BA, Gilfillan GD, Nielsen R, Thorsby E, Willerslev E*, Malaspinas A-S* (2014) Genome-wide Ancestry Patterns in Rapanui Suggest Pre-European Admixture with Native Americans. Current Biology 24, 2518–2525.
Malaspinas A-S et al. (2014) Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil. Current Biology 24, R1035–R1037
Malaspinas A-S, Malaspinas O, Evans SN, Slatkin M (2012) Estimating allele age and selection coefficient from time-serial data. Genetics 192, 599–607
Associate Prof. Eline Lorenzen
Natural History Museum of Denmark
The University of Copenhagen
Øster Voldgade 5-7
Eline Lorenzen is a molecular and palaeoecologist, and studies the ecology and evolution of genetic and phenotypic diversity through time, primarily in large mammals. After completing her PhD at University of Copenhagen, she undertook independently funded post doctoral fellowships at the Centre for GeoGenetics, a Centre of Excellence at University of Copenhagen, and at University of California, Berkeley. Eline is permanent faculty in the Natural History Museum of Denmark, where she is also Curator of Mammalogy. Her interdisciplinary research combines population genomics of past and present populations with insights from macroecology, archaeology, the palaeosciences and climate change research to identify and understand the evolutionary forces that have shaped past and present patterns of biological diversity. In addition, her group uses the analysis of geometric morphometrics and stable isotopes to understand patterns of phenotypic diversity within species and populations through time, linking morphological and genetic patterns.
Liu S*, Lorenzen ED*, Fumagalli M*, Li B*, et al. (2014) Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears. Cell 157: 785–794
Willerslev E*, Davison J*, Moora M*, Zobel M*, Coissac E*, Edwards ME*, Lorenzen ED*, Madsen MV*, Gussarova G*, Haile J*, et al. (2014) Fifty thousand years of arctic vegetation and megafauna diet. Nature 506: 47–51
Lorenzen ED, Heller R, Siegismund HR (2012) Invited review: Comparative phylogeography of African savannah ungulates. Molecular Ecology 21: 3656–3670
Lorenzen ED*, Nogués-Bravo D*, Orlando L*, Weinstock J*, Binladen J*, Marske KA*, et al. (2011) Species-specific responses of Late Quaternary megafauna to climate and humans. Nature 479, 359-64
Prof. Love Dalén
Dept. of Bioinformatics and Genetics
Swedish Museum Natural History
Love Dalén is an evolutionary geneticist whose research interests are focused on using palaeogenetics to investigate evolutionary consequences of past environmental and anthropogenic change. His current research ranges from projects that aim to investigate the impact of Pleistocene climate change on animal micro-evolution, to projects that explore the genetic consequences of small population size in animals that have gone through human-induced population declines in the last century. Dalén has a PhD in Zoology from Stockholm University, where he worked in population genetics of the arctic fox. After his PhD, he took up a postdoctoral position in Madrid and, following this, a Marie-Curie Fellowship at Royal Holloway University of London. Since 2009, he has held a permanent research position at the Swedish Museum of Natural History, where he now works as a Professor in evolutionary genetics and is head of the department’s research section. His research group comprises several postdocs and PhD students, working on a broad range of
palaeogenomic projects, for example on woolly mammoth, lemmings, arctic foxes and Sumatran rhinos.
Palkopoulou E, Baca M, /…/ Dalén L. 2016. Synchronous genetic turnovers across Western Eurasia in Late Pleistocene collared lemmings. Global Change Biology, 22: 1710–1721.
Skoglund P, Ersmark E, Palkopoulou E, Dalén L. (2015) Ancient wolf genome reveals an early divergence of domestic dog ancestors and admixture into high-latitude breeds. Current Biology, 25: 1515–1519.
Palkopoulou E, Mallick S, Skoglund P, Enk J, Rohland N, Li H, Omrak A, Vartanyan S, Poinar H, Götherström A, Reich D, Dalén L. (2015) Complete genomes reveal signatures of demographic and genetic declines in the woolly mammoth. Current Biology, 25, 1395–1400.
Xenikoudakis G, Ersmark E, Tison JL, Waits L, Kindberg J, Swenson JE, Dalén L. (2015) Consequences of a demographic bottleneck on genetic structure and variation in the Scandinavian brown bear. Molecular Ecology, 24: 3441–3454.
Dalén L, Orlando L, Shapiro B, Brandström-Durling M, Quam R, Gilbert MTP, Fernández-Lomana JCD, Willerslev E, Arsuaga JL, Götherström A. (2012) Partial genetic turnover in neandertals: continuity in the east and population replacement in the west. Molecular Biology and Evolution, 29: 1893-1897.
Asst. Prof. María C. Ávila-Arcos
International Laboratory for
Human Genome Research
National Autonomous University of Mexico
María is a human genomics scientist deeply interested in population genetics and paleogenomics. During her PhD she took part in the first initiatives worldwide to use Next Generation Sequencing on ancient DNA. This included work investigating the efficacy of protocols such as DNA enrichment through capture enrichment. As a postdoctoral fellow at Stanford University under the advice of Dr. Carlos Bustamante, she studied genomic data from ancient and modern human populations to address contentious issues regarding the initial peopling of the Americas as well the identification of ethno-geographic origins within Africa of 17th-century remains of African-born enslaved individuals. Since October 2015, she has lead her own research group on population and evolutionary genomics at UNAM, Mexico. Informed by her previous experience, María’s current research turns around the analysis of genetic data from human populations, past and present, to learn about the processes that generate the genetic makeup of groups of humans through time. The ongoing projects in the Ávila-Arcos group involve the characterization of genomes of Mexican Indigenous and Afro-Mexican populations.
Ávila-Arcos MC et al. (2015) Comparative performance of two whole genome capture methodologies on ancient DNA Illumina libraries. Methods in Ecology and Evolution 1, 725–734
Ávila-Arcos MC et al. (2011) Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA. Scientific Reports 1: 74
Ávila-Arcos MC et al. (2013) One hundred twenty years of koala retrovirus evolution determined from museum skins. Molecular Biology and Evolution 30, 299-304
Der Sarkissian C, Allentoft ME, Ávila-Arcos MC, Barnett R, Campos PF, Cappellini E, Ermini L, Fernández R, da Fonseca R, Ginolhac A, Hansen AJ (2015) Ancient genomics. Philosophical Transactions of the Royal Society B 19:20130387
Schroeder H, Ávila-Arcos MC, Malaspinas AS, Poznik GD, Sandoval-Velasco M, Carpenter ML, Moreno-Mayar JV, Sikora M, Johnson PL, Allentoft ME, Samaniego JA (2015) Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean. Proceedings of the National Academy of Sciences 112, 3669-3673
Dr. Marie Louis
Scottish Oceans Institute
University of St Andrews
St Andrews, KY16 8LB
Marie Louis is a molecular ecologist whose research interests are adaptation and evolutionary history. She completed her PhD at the Centre d’Etudes Biologiques de Chizé, University of La Rochelle, France on the social, ecological and genetic structure of bottlenose dolphins in the North-East Atlantic. She used a multi-disciplinary approach including population genetics, ecology, behaviour and morphometrics to understand the drivers of population structure of the species in Europe. She is currently on an independent post-doctoral fellowship funded by the Fyssen and Total Foundations at the University of St Andrews and leading an international collaboration involving the University of Bangor, Centre for
GeoGenetics (University of Copenhagen), University of Groningen and NOAA to study the role of ecological
specialisations in driving the evolution of populations, and their ability to adapt to novel environments. For this project, she is combining population genomics and paleogenomics approaches and using the bottlenose dolphin as a case-study species. She is particularly interested in using time-series dataset to better understand evolutionary history and the mechanisms of local adaptation.
Louis M, Fontaine M, Spitz J, Schlund E, Dabin W, Deaville R, Caurant F, Cherel Y, Guinet C, Simon-Bouhet B (2014) Ecological opportunities and specializations shaped genetic divergence in a highly mobile marine top predator. Proceedings of the Royal Society Biological Sciences 281: 20141558.
Louis M, Viricel A, Lucas T, Peltier H, Alfonsi E, Berrow S, Brownlow A, Covelo P, Dabin W, Deaville R, de Stephanis R, Gally F, Gauffier P, Penrose R, Silva MA, Guinet C, Simon-Bouhet B (2014) Habitat-driven population structure of bottlenose dolphins, Tursiops truncatus, in the North-East Atlantic. Molecular Ecology 23, 857–874.
Cammen K, Andrews K, Carroll E, Foote AD, Humble E, Khudyakov J, Louis M, McGowen M, Olsen M, Van Cise A (2016) Genomics methods take the plunge: advances in high-throughput sequencing of marine mammals. Journal of Heredity 107, 481-495.
Morin PA, Louis M, Hill AD, Simon-Bouhet B, Lang AR, Foote AD In Press. SNP discovery from single and multiplex genome assemblies of non-model organisms. Methods for Molecular Biology (Book Chapter).
Dr. Matteo Fumagalli
Department of Life Sciences
Silwood Park campus
Imperial College London
Ascot, SL5 7PY
Matteo Fumagalli is a computational biologist with research interests in bioinformatics and evolutionary genomics. He completed his PhD in Bioengineering from the Polytechnic University of Milan, Italy, and then obtained postdoctoral fellowships to undertake research activity at the University of California in Berkeley (EMBO fellow) and University College London (HFSPO fellow). He is currently a Research Fellow at Imperial College London with a proleptic appointment as Lecturer in Quantitative Ecology and Evolution. Matteo is interested in developing and implementing computational tools to analyse large-scale genomic data for population genetics purposes. His main research area is to understand the biological mechanisms of species adaptation to environments, including pathogens, diet and cold climate.
Fumagalli M*, Moltke I*, Grarup N, Racimo F et al. (2015) Greenlandic Inuit show genetic signatures of diet and climate adaptation. Science 349, 1343-1347
Fumagalli M, Sironi M (2014) Human genome variability, natural selection and infectious diseases. Current opinion in immunology 30,9-16
Fumagalli M*, Vieira FG*, Linderoth T, Nielsen R (2014) ngsTools: methods for population genetics analyses from next-generation sequencing data. Bioinformatics 30:1486-1487
Liu S*, Lorenzen ED*, Fumagalli M*, Li B*, Harris K, et al. (2014) Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears. Cell 157:785-794
Fumagalli M, Sironi M, Pozzoli U, Ferrer-Admetlla A, Pattini L, Nielsen R (2011) Signatures of environmental genetic adaptation pinpoint pathogens as the main selective pressure through human evolution. PloS Genetics 7:e1002355
Associate Prof. Michael D. Martin
Department of Natural History
NTNU University Museum
Norwegian University of Science and Technology (NTNU)
Michael Martin is an evolutionary geneticist whose research focuses on reconstructing and interpreting the evolutionary histories of plants, animals, and their pathogens through the analysis of complex genomic data. Martin completed postdoctoral training at the Centre for GeoGenetics (University of Copenhagen) and the Centre for Theoretical Evolutionary Genomics (University of California Berkeley) before obtaining his current tenure-track position (Onsager Fellowship in molecular biodiversity) at the NTNU University Museum. Martin is particularly attracted to cases in which ancient nucleic acids enable an understanding of present-day distributions of biodiversity. As a young faculty member at a museum of natural history and archaeology, Martin is charged with the development of new analytic methods to increase applications of genomic analysis to degraded genetic material in large natural history collections.
Martin MD, Olsen MT, Samaniego JA, et al. (2016) The population genomic basis of geographic differentiation in North American common ragweed (Ambrosia artemisiifolia L.). Ecology and Evolution 6: 3760-3771.
Martin MD, Vieira FG, Ho SYW, et al. (2016) Genomic characterization of a South American Phytophthora hybrid mandates reassessment of the geographic origins of Phytophthora infestans. Molecular Biology and Evolution 33:478-491.
Martin MD, Ho SYW, Wales N, et al. (2014) Persistence of the mitochondrial lineage of the Irish potato famine pathogen in the New World. Molecular Biology and Evolution 31:1414-1420.
Martin MD, Zimmer EA, Olsen MT, et al. (2014) Herbarium specimens reveal a phylogeographic shift in common ragweed during native range disturbance. Molecular Ecology 23:1701-1716.
Martin MD, Cappellini E, Samaniego JA, et al. (2013) Reconstructing genome evolution in historic samples of the Irish potato famine pathogen. Nature Communications 4: doi: 10.1038/ncomms3172.
Asst. Prof. Nina Overgaard
Department of Natural Resources
208 Fernow Hall
Nina Overgaard Therkildsen is a molecular ecologist with a particular interest in using population genomics to inform sustainable fisheries management and marine conservation. Her research integrates analysis of both modern and historical samples to examine how contemporary environmental change and human impacts shape demographic, ecological, and microevolutionary processes over decadal time scales. She is particularly interested in how human activities cause rapid evolution in many wild populations and in the roles that ongoing genetic adaptation and geographic distribution shifts will play for species persistence in our rapidly changing world. She earned her PhD at the Technical University of Denmark and completed postdoctoral training at Stanford University before establishing her research group as an Assistant Professor at Cornell University.
Therkildsen, NO and Palumbi SR (2017) Practical low-coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species. Molecular Ecology Resources 17, 194-208
Kelley JL, Brown AP, Therkildsen, NO, Foote AD (2016) The life aquatic: advances in marine vertebrate genomics. Nature Reviews Genetics 17, 523-534
Bonanomi S, Therkildsen NO, Retzel A, Hedeholm RB, Pedersen MV, Meldrup D, Pampoulie C, Hemmer-Hansen J, Grønkjær P, Nielsen EE (2016) Historical DNA documents long distance natal homing in marine fish. Molecular Ecology 25, 2727–2734
Therkildsen NO, Hemmer-Hansen J, Hedeholm RB, Wisz M, Pampoulie C, Meldrup D, Bonanomi S, Retzel A, Olsen MA, Nielsen, EE (2013) Spatiotemporal SNP analysis reveals pronounced biocomplexity at the northern range margin of Atlantic cod Gadus morhua. Evolutionary Applications 6, 690-705
Therkildsen NO, Hemmer-Hansen J, Als TD, Swain DP, Morgan J, Trippel E, Meldrup D, Nielsen EE (2013) Microevolution in time and space: SNP analysis of historical DNA reveals dynamic signatures of selection in Atlantic cod. Molecular Ecology 22, 2424-2440
Prof. Ole Seehausen, Ole
Institute of Ecology & Evolution
University of Bern
Department Fish Ecology & Evolution
Center for Ecology, Evolution and Biogeochemistry
Ole Seehausen is an evolutionary biologist whose research program contributes to a better understanding of the ecological and evolutionary processes that facilitate or constrain the origins of biological diversity and the role of evolutionary processes in extinction. By combining fieldwork in the large lakes of tropical Africa and lakes around the European Alps with population genomic and phylogenomic analyses, phenotypic analyses and experiments, he has for many years tried to clarify how changes in the environment interact with organism traits and genomic variables in the processes of evolutionary diversification and extinction. His main contributions have been about the diverse and environment-dependent roles of interspecific hybridization and the interaction between natural and sexual selection in rapid adaptive radiations, and about how environmental change triggers implosive loss of species diversity through evolutionary processes that can be considered the reversal of speciation. A few years ago he began working on fossils and fossil-derived aDNA of cichlid fish extracted from sediment cores taken in Lake Victoria and other African lakes.
Meier JI, Marques DA, Mwaiko S, Wagner CE, Excoffier L, Seehausen O. (2017) Ancient hybridization fuels rapid cichlid fish adaptive radiations. Nature Communications 8:14363 | DOI: 10.1038/ncomms14363
Mc Gee MD, Borstein SR, Neches RY, Buescher HH, Seehausen O, Wainwright PC. (2015) A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids. Science 350, 1077-1079.
Brawand D, Wagner CE, Li YI, …(68 co-authors)…Lindblad-Toh K*, Seehausen O*, Di Palma F*. (2014). The genomic substrate for adaptive radiation: genomes of five African cichlid fish. Nature 513, 375-381
Vonlanthen P, Bittner D, Hudson AG, Young KA, Müller R, Lundsgaard-Hansen B, Roy D, Di Piazza S, Largiader CR, Seehausen O. (2012). Eutrophication causes speciation reversal in whitefish adaptive radiations. Nature 482, 357-362
Wagner, CE, Harmon, L, Seehausen O. (2012). Ecological opportunity and sexual selection together predict adaptive radiation. Nature 487, 366-369
Prof. M. Thomas P. Gilbert
Section for Evolutionary Genomics
Natural History Museum of Denmark
The University of Copenhagen
Øster Voldgade 5-7
Tom Gilbert is a molecular biologist whose research focuses on the development, adaptation and implementation of laboratory methods of relevance to the archaeology, anthropology, ecology and evolutionary biology communities. With a D.Phil in ancient DNA from the University of Oxford, he subsequently was a postdoctoral fellow at the University of Arizona, before moving to Copenhagen as a Marie Curie Fellow. He subsequently became permanent faculty in the Natural History Museum of Denmark, where he is head of the Evolutionary Genomics section. Although his group’s research is very broad, a hallmark is the integration of ancient, historic and modern genomic (and even transcriptomic and proteomic) data, many of which have focused on documenting evolutionary changes in action through systems that include wild and domestic animals and plants, as well as pathogens and even microbial communities. He currently also holds an ERC Consolidator grant that is exploring the genomic consequences of severe population bottlenecks and recoveries, with a particular focus of eventual application in conservation biology.
Ramos-Madrigal J, Smith BD, Moreno-Mayar JV, Gopalakrishnan S, Ross-Ibarra J, Gilbert MTP, Wales N (2016) Genome sequence of a 5,310-year-old maize cob provides insights into the early stages of maize domestication. Current Biology 26:1-7
Alberdi A, Aizpurua O, Bohmann K, Zepeda-Mendoza ML, Gilbert MTP (2016) Do vertebrate gut metagenomes confer rapid ecological adaptation? Trends in Ecology and Evolution 31:689-699
Martin MD, Vieira FG, Ho SYW, Wales N, Schubert M, Seguin-Orlando A, Ristaino JB, Gilbert MTP (2016) Genomic characterization of a South American Phytophthora hybrid mandates reassessment of the geographic origins of Phytophthora infestans. Molecular Biology and Evolution 33:478-491
Schroeder H, Ávila-Arcos MC, Malaspinas A-S, Poznik GD, Sandoval Velasco M, Carpenter ML, Moreno Mayar J-V, Sikora M, Johnson PLF, Allentoft ME, Samaniego JA, Haviser JB, Dee M, Stafford Jr. TW, Salas A, Orlando L, Willerslev E, Bustamante CD, Gilbert MTP (2015) Genome-wide ancestry of 17th century enslaved Africans from the Caribbean. Proc Natl Acad Sci USA 112: 3669–3673
da Fonseca RR, Smith BD, Wales N, Cappellini E, Skoglund P, Fumagalli M, Samaniego JA, Carøe C, Ávila-Arcos MC, Korneliussen TS, Vieira FG, Jakobsson M, Arriaza B, Willerslev E, Nielsen R, Hufford MB, Albrechtsen A, Ross-Ibarra J, Gilbert MTP (2015) The origin and evolution of maize in the American Southwest. Nature Plants 14003 doi: 10.1038/NPLANTS.2014.3
ICREA Prof. Tomas Marques-Bonet
Director Institut Evolutionary Biology (CSIC-UPF)
DR. Aiguader 88
Dr. Marques-Bonet is the Principal Investigator of the group "Comparative Genomics" as a part of the Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra) and also head of the comparative genomics group at CNAG-CRG (Centro Nacional de Analisis Genomico). He is an EMBO Young Investigator and was awarded with projects from the European Research Council among other funding agencies. His group is now focused on characterizing human specific genomics features, including comparative epigenetics and gene regulation, or the study of the demographic histories in humans and great apes. With a total of more than 90 peer-reviewed publications, he has published as a corresponding author in journals such as Science, Nature, Genome Research, Plos Genetics, NAR or Genome Biology.
deManuel et al. (2016) Chimpanzee diversity reveals ancestral admixture with bonobos. Science
Irene Hernando-Herraez et al. (2015) A genome-wide comparative study of the DNA methylation landscape in great apes. Nucleic Acid Research
Xue, Prado-Martinez (2015) Population sequencing of Mountain gorillas reveal the genomic impact of long-term population decline and inbreeding. Science
Javier Prado-Martinez et al. (2013) Great ape genetic diversity and population history. Nature
Hernando-Herraez et al. (2013) Dynamics of DNA Methylation in Recent Human and Great Apes Evolution. PLOS Genetics
Dr. Jennifer A. Jackson
British Antarctic Survey
Jennifer Jackson is a molecular ecologist whose research spans evolutionary phylogenetics, population genetics, population dynamics and mark recapture modelling. She trained in evolutionary genetics at the University of Oxford, followed by postdoctoral fellowships on the population genetics of whales at the University of Auckland and Oregon State University. As director of Marine Research Limited, she conducted a global review of humpback whales and has been a research scientist at the British Antarctic Survey since her return to the UK. She has a leading role in cetacean assessments as the chair of the International Whaling Commission’s ‘Southern Hemisphere’ sub-committee and as a member of the IUCN’s cetacean specialist group. She is particularly interested in the use of genetics to improve the understanding of species population dynamics, structure, abundance, exploitation impacts and resilience over management-relevant timescales.
Jackson JA, EL Carroll, TD Smith, AN Zerbini, NJ Patenaude, C Scott Baker (2016) An integrated approach to historical population assessment of the great whales: case of the New Zealand southern right whale. Royal Society Open Science 150669
Jackson JA, DJ Steel, P Beerli, BC Congdon, C Olavarría, M S Leslie, C Pomilla, H Rosenbaum, CS Baker (2014) Global diversity and oceanic divergence of humpback whales. Proceedings of the Royal Society Series B: Biological Sciences 281 (1786) 20133222
Jackson JA, L Laikre, CS Baker, KC Kendall et al. (2012) Guidelines for collecting and maintaining archives for genetic monitoring. Conservation Genetics Resources 4, 527-536
Jackson JA, N Patenaude, E Carroll, CS Baker (2008) How few whales were there after whaling? Inference from contemporary mtDNA diversity. Molecular Ecology 17, 236-251
Prof. Daniel Wegmann
University of Fribourg
Department of Biology
Chemin du Musée 10
Daniel Wegmann is a computational biologist at the University of Fribourg, Switzerland. He obtained his PhD from the University of Bern, Switzerland, and got postdoctoral training both at the University of California Los Angeles, USA, as well as at the Ecole Polytéchnique Fédérale de Lausanne, Switzerland. Daniel is primarily interested in elucidating and quantifying the evolutionary and ecological processes that have shaped the biological diversity we observe today. To achieve this, his group designs and evaluates new statistical and computational approaches to infer evolutionary histories from genetic data, preferably through model-based inference, for which the group develops dedicated machine learning algorithms. A lot of the recent work focused on novel methods to infer evolutionary processes (mutation rates, genetic drift and selection) and population genetic quantities (e.g. genetic diversity or genotypes) from low-depth data, and in particular ancient DNA data. For instance, the group recently developed methods to analyse ancient DNA while statistically accounting for the characteristic damage present in such data.
Kousathanas A, Leuenberger C, Link V, Sell C, Burger J & Wegmann D (2017). Inferring heterozygosity from ancient and low coverage genomes. Genetics 205: 317-332.
Broushaki F, Thomas MG, Link V, … (26 co-authors) …, Wegmann D*, Hellenthal G* & Burger J* (2016). Early neolithic genomes from the eastern Fertile Crescent. Science 353: 499-503.
Hofmanová Z, Kreutzer S, Hellenthal G, … (32 co-authors) …, Wegmann D, Thomas MG, Papageorgopoulou C & Burger J (2016). Early farmers from across Europe directly descended from Neolithic Aegeans. PNAS 113: 6886-6891.
Ferrer-Admetlla A, Leuenberger C, Jensen JD & Wegmann D (2016). An approximate Markov model for the Wright-Fisher diffusion and its application to time-series data. Genetics 203(2):831-846.
Wegmann D, Kessner D, Veeramah KR, Mathias RA, Nicolae DL, Yanek LR, Sun YV, Torgerson DG, Rafaels N, Mosley T, Becker LC, Ruczinski I, Beaty TH, Kardia SLR, Meyers DA, Barnes KC, Becker DM, Freimer N and Novembre J (2011). Recombination rates in admixed individuals identified by ancestry-based inference. Nature Genetics 43:9 847-853
Asst. Prof. Katerina Guschanski
Evolutionary Biology Centre
Department of Ecology and Genetics/Animal Ecology
SE-752 36 Uppsala
Katerina Guschanski is an evolutionary geneticist who studies how genetic diversity and the interaction of organisms with their environment change through time and space and how climatic and anthropogenic factors contribute to this change. To tackle these broad questions, she is working at the intersection of ecology, molecular biology, large-scale comparative and functional genomics, and bioinformatics. Current research projects range from quantifying the effects of human-driven population decline on genetic diversity and evolutionary potential of great apes, speciation in primates, and the evolution of host-associated microbiomes through time, over demographic transitions, and in response to drastic environmental change. Katerina did her PhD at the Max Planck Institute of Evolutionary Anthropology studying the molecular ecology of mountain gorillas. She then took up a postdoctoral researcher position at Imperial College London and later an EMBO and HFSP funded postdoc at the University of Lausanne. Since 2015, Katerina is a group leader at Uppsala University.
van der Valk T, Sandoval-Castellanos E, Caillaud D, Ngobobo U, Binyinyi E, Nishuli R, Stoinski T, Gilissen E, Sonet G,
Semal P, Kalthoff DC, Dalén L, Guschanski K. 2018. Significant loss of mitochondrial diversity within the last century due to extinction of peripheral populations in eastern gorillas. Scientific Reports 8 (1): 6551
Hooper R, Brealey J, van der Valk T, Alberdi A, Durban JW, Fearnbach H, Robertson KM, Baird RW, Hanson MB, Wade P, Gilbert T, Phillip Morin A, Wolf JBW, Foote AD*, Guschanski K*. 2018. Characterising the microbiome from host shotgun sequencing data: bacterial and diatom community dynamics derived from killer whale skin. Molecular Ecology 2018;00:1–19. https://doi.org/10.1111/ mec.14860
Guschanski K, Warnefors M, Kaessmann H. 2017. The evolution of duplicate gene expression in mammalian organs. Genome Research 27: 1461-1474.
Guschanski K, Krause J, Sawyer S, Bailey S, Finstermeier K, Valente LM, Sabin R, Gilissen E, Sonet G, Nagy ZT, Lenglet G, Mayer F, Savolainen V. 2013. Next-generation museomics disentangles one of the largest primate
radiations. Systematic Biology 62: 539-554.
Dr. David Díez del Molino
Swedish Museum Natural History
Department of Bioinformatics and Genetics
Archaeological Research Laboratory
Department of Archaeology and Classical Studies
SE-106 91 Stockholm
David Díez-del-Molino is an evolutionary biologist interested in the study of animal and human populations using methods at the intersect of the population genetics and computational genomics fields. David has a PhD in population genetics from the University of Girona, where he studied the genetic basis of biological invasions. After that he took a postdoctoral position as Marie-Curie Fellow at University College London. Since 2016 he is a postdoctoral researcher at the Swedish Museum of Natural History and since 2018 he is also based at the Archaeological Research Laboratory, at the University of Stockholm. His current research is focused in three main areas: using genomic tools to shed light on the origin and history of human populations by using modern and ancient DNA; using extinct megafaunal, historical, and modern-day endangered species to study near-extinction population dynamics; and harnessing the temporal resolution provided by ancient DNA to solve questions related to species conservation and adaptation to rapid environmental changes.
Díez-del-Molino D, Sánchez-Barreiro F, Barnes I, Gilbert MTP, Dalén L. 2018. Quantifying Temporal Genomic Erosion in Endangered Species. Trends in ecology & evolution, 33(3):176-185.
Pečnerová P, Díez-del-Molino D, Dussex N, Feuerborn T, von Seth J, van der Plicht J, Nikolskiy P, Tikhonov A, Vartanyan S, Dalén L. 2017. Genome-Based Sexing Provides Clues about Behavior and Social Structure in the Woolly Mammoth. Current Biology. 27(22):3505-10.
Broushaki F, Thomas MG, Link V, López S, van Dorp L, Kirsanow K, Hofmanová Z, Diekmann Y, Cassidy LM, Díez-del-Molino D,.... Burger J. 2016. Early Neolithic genomes from the eastern Fertile Crescent. Science. aaf7943.
Hofmanová Z, Kreutzer S, Hellenthal G, Sell C, Diekmann Y, Díez-del-Molino D,.... Burger J. Early farmers from across Europe directly descended from Neolithic Aegeans. 2016. PNAS. 113(25):6886-91.
Vera M, Díez‐del‐Molino D, García‐Marín JL. 2016 Genomic survey provides insights into the evolutionary changes that occurred during European expansion of the invasive mosquitofish (Gambusia holbrooki). Molecular Ecology. 25(5):1089-105.
Dr. Gemma Murray
Department of Veterinary Medicine
Gemma Murray is an evolutionary biologist, with research interests in evolutionary genomics and population genetics. She completed her PhD at the University of Cambridge, where she developed methods of analysing bacterial genome sequences to understand the evolutionary dynamics of bacterial pathogens and how they adapt to new species. She undertook postdoctoral research at the University of California, Santa Cruz, where she studied the genomes of extinct and endangered animals, and used population genetic models to infer the historic size of populations, and the impact of selective pressures on their genome evolution. She is currently a Research Associate in the Department of Veterinary Medicine at the University of Cambridge, and a Research Fellow at Newnham College, where she is investigating the selective pressures and population genetic factors involved in the transition from commensalism to pathogenesis in bacteria.
Murray GGR, Soares AER, Novak BJ, Schaefer NK, Cahill JA, Baker AJ, Demboski J, Doll A, Da Fonseca RR, Fulton TL, Gilbert MTP, Heintzman PD, Letts B, McIntosh G, O’Connell BL, Peck M, Pipes M-L, Rice ES, Santos KM, Sohrweide AG, Vohr SH, Corbett-Detig RB, Green RE & Shapiro B (2017). Natural selection shaped the rise and fall of passenger pigeon genomic diversity. Science. 358 (6375). DOI: 10.1126/science.aao0960.
Murray GGR, Weinert LA, Rhule EL, Welch JJ. (2016) The Phylogeny of Rickettsia Using Different Evolutionary Signatures: How Tree-Like is Bacterial Evolution? Systematic Biology 65:2, 265-279. DOI: 10.1093/sysbio/syv084.
Murray GGR, Wang F, Harrison EM, Paterson GK, Mather AE, Harris SR, Holmes MA, Rambaut A & Welch JJ (2016). The effect of genetic structure on molecular dating and tests for temporal signal. Methods in Ecology and Evolution. 7 (1). DOI: 10.1111/2041-210X.12466.
Murray GGR, Woolhouse MEJ, Tapio M, Mbole-Kariuki MN, Sonstegard TS, Thumbi SM, Jennings AE, Conradie van Wyk I, Chase-Topping M, Kiara H, Toye P, Coetzer K, Bronsvoort BM deC & Hanotte O. 2013. Genetic susceptibility to infectious disease in East African Shorthorn Zebu: a genome-wide analysis of the effect of heterozygosity and exotic introgression. BMC Evolutionary Biology 13 (246). DOI: 10.1186/1471-2148-13-246.