Professors - Postdocs PhD students - Administrative staff

Billede af Tom Gilbert

Tom Gilbert

Professor and Head of EvoGenomics

I am Professor of Palaeogenomics at the museum, and head of the Evolutionary Genomics research section. My research interests are broad, spanning evolutionary and conservation biology, to anthropology, and bioarchaeology, with study systems ranging from human and plant pathogens, to biotechnology-related microbes, plants and animals. I am particularly driven by the development and implementation of new techniques (e.g. population-, phylo- and meta-genomics), and the application of cross-disciplinary approaches as a means to improve on our understanding of questions within such fields. Key current activities include co-coordinating the B10k project (http://b10k.genomics.cn/), that aims to sequence the majority of avian genomes, coordinating the EUROTAST training network (www.eurotast.eu) that helped improve our understanding of the transatlantic slave trade, as well as sitting on the executive committee of MICROWINE (www.microwine.eu), a 15 PhD network exploring the role of microbes in the future of the wine industry.


Billede af Matthew Collins Matthew Collins

Professor

I am a Niels Bohr Professor of Palaeoproteomics at the University of Copenhagen and Professor of Archaeology at the University of York. I am the founder of BioArCh, a joint initiative between the Departments of Biology, Chemistry and Archaeology to further the use of biomolecular methods to tackle archaeological problems.
Matthews research focuses on the persistence of proteins in ancient samples, using modelling to explore the racemization of amino acids and thermal history to predict the survival of DNA and other molecules. In particular he is interested in developing technological solutions of direct practical application in the humanities.
Using a combination of approaches (including immunology and protein mass spectrometry) his research detects and interprets protein remnants in archaeological and fossil remains. This includes using peptide fingerprinting to identify animal species in bones, manuscripts and other tissues, using protein mass spectroscopy to explore proteomes in ancient tissues, and to recovery dietary signals, and protein degradation as a tool to estimate the age of samples.

Eline Lorenzen

Associate Professor and Curator of mammals

I am Associate Professor and Curator of Mammals at the Museum. My work is highly interdisciplinary and encompasses several areas, including continental-scale biogeography, past demographic inference using ancient DNA, and population genomic analysis of modern populations.

I am a molecular ecologist, and am broadly interested in how climate change, environmental shifts and human impacts have shaped the biodiversity, abundance and evolution of past and present of megafauna (large mammal) species and communities. I have worked in Africa, Northern Eurasia and North America on projects relating to terrestrial and marine organisms. 


Enrico Cappellini

Associate Professor

I investigate ancient proteins by mass spectrometry-based sequencing. He is part of the Palaeoproteomics research group as an associate professor. He is interested in analysis of very ancient proteins (> 1 Ma) and proteins from cultural heritage material.


Hannes Schroeder

Assistant Professor

I am a molecular anthropologist and my research interests center primarily around the uses of genomic data in answering questions relating to the human past. I have conducted fieldwork around globe, including Europe, South America, Africa and the Caribbean. Between 2011 and 2015, I was one of the principal coordinators of the EUROTAST Marie Curie ITN (www.eurotast.eu) and as of 2016 I am leading the CITIGEN project (www.citigen.org), a collaborative research project that looks at the societal uses of genomic data. Since 2013, I have also been involved in the ERC Synergy project NEXUS1492 (www.nexus1492.eu) and as of 2016 I am also part of the ArchSci2020 Marie Curie ITN (www.archsci2020.com). Follow me on Twitter.


Kristine Bohmann

Assistant Professor

I work with environmental DNA and its use in diet and biodiversity studies with particular focus on DNA metabarcoding and methodological improvements. I am currently affiliated with University of East Anglia on a postdoc scholarship from the Danish Council of Independent Research on a project investigating how changes in climate and land use affect insect communities. In this project I assess insect biodiversity through molecular analyses of a collection of insectivorous bat guano spanning 45 years. Furthermore, I work on different projects based on a variety of other environmental samples such as stomach contents from birds and leeches, blood meals from vampire bats and faeces from solenodons, leopards and other animals. Currently, I co-supervise PhD Student Martin Nielsen on a project on molecular assessment of insect diversity, PhD Student Christina Lynggaard on a leech microbiome project and MSc student Kristian Greisen on a project on water quality assessment through molecular identification of indicator species.


Morten Limborg

Assistant Professor

My research interests are within the fields of population genetics, genomics and evolution. I use salmonids to study processes of local adaptation and ecological speciation in the wild. Salmonid fishes have fascinated scientists for centuries due to their iconic and diverse set of habitats and eco-morphs. In addition, the salmonid lineage underwent two whole-genome duplication events that provided an enormous DNA template to support adaptive radiation and speciation. These assets make salmonids excellent model species for studying fundamental issues relating to adaptation and speciation in the wild. Knowledge about the mechanisms and conditions required for species to evolve by adapting to new surroundings is of paramount importance for predicting future responses to climatically (or anthropogenically) induced environmental change. It is my goal that my research will contribute towards a better understanding of the genomic mechanisms leading to adaptive divergence and speciation in the wild, as well as under which conditions creation of new species or eco-morphs can be expected. Read more about my research here.


Morten Tange Olsen

Assistant Professor

I am Assistant Professor and Curator of Marine Mammals at the Natural History Museum of Denmark.

My research interest lies in understanding the patterns and processes governing wildlife abundance and distribution with a particular focus on the ecology and evolution of marine mammals, but also including pathogens, birds, fish, insects and plants. 

I teach and manage the course "Marine Mammal Biology and Research" offered at the University of Copenhagen, and have fully or partially supervised more than 40 PhD, MSc or BSc students. Finally, I am the chairman of the Danish Marine Mammal Society and member of several international and national expert groups on the conservation and management of pinnipeds (e.g. HELCOM and NAMMCO).


Shyam Gopalakrishnan

Assistant Professor

I am currently a Post. doc. in Tom Gilbert's lab, funded through a Carlsberg Foundation grant. My current research is focused on studying the relationship between dogs and wolves of the world, with emphasis on the domestication dynamics of dogs. I am particularly interested in estimating the date and location of dog domestication, and adaptation of dogs to environmental challenges through adaptive gene flow from sympatric wolves. More broadly, I am interested in applying statistical methods to population and evolutionary genomics questions, including in areas such as selection, adaptation and demographic history.


Postdocs


Ainara Sistiaga Gutiérrez

Postdoc

Ainara Sistiaga is a new Marie Curie Postdoc in the Matthew Collins group. She comes from Canary Islands, Spain where she completed her BA and PhD in the application of lipid analysis to the study of diet in human evolution. As part of the Marie Curie fellowship she will be spending the first 2 years in MIT (USA) and the third year in Evogenomics developing new markers of specific gut bacterial action applying lipidomic and proteomic tools. In the frame of the fellowship she will be exploring the correlation between lipidomes, proteomes and genomes in modern and mummified microbiome substrates and well as exploring the diagenesis of faecal material.


Alberto Taurozzi

Postdoc

I am a Molecular Cell Biologist by training, I obtained my PhD in Biology at the University of York (England) in 2016 where I conducted research of prostate cancer. I am currently funded by PROTEIOS under the supervision of Matthew Collins and Enrico Cappellini. My role within the group is novel method development, with major research aims including: estimating age at death biochemically and biomarker discovery to detect and characterise disease in ancient samples.


Angie Chen

Postdoc

My name is Yan-Jun (Angie) Chen and a postdoc in the Computational Biodiscovery group with Thomas Sicheritz-Pontén. I am originally from Taiwan where I had a bachelor degree in Life Science and master in Ecology and Evolutionary Biology. My PhD was in the Department of Plant and Environmental Sciences at KU about plant-microbe interaction using RNAi technique to silence a transcription factor. My previous postdoc project was studying aggressiveness in wheat-yellow rust interaction using large genomic and transcriptomic data analysis. I am interested in working on the intersection between molecular biology and bioinformatics, leveraging a computational and analytical skill set to answer and propose complex biological questions. I am currently working on 1) MetaPig project to modulate the pig gut microbiome for increasing feed efficiency and gut health and 2) FoodTranscriptomics project to decipher the microbial activity in food fermenting cultures.


Antton Alberdi

Postdoc

I am an ecologist from the Basque Country with research interests in ecological adaptation, evolutionary biology and biogeography. I am currently leading a challenging project supervised by Tom Gilbert that aims to reconstruct the postglacial spatio-temporal dynamics of European cave-dwelling bats, their diet and their gut microbiomes, to understand their adaptation to the changing environment. For that task, aided by a collaborator network of >15 researchers and speleologists, I am exploring caves all over the continent seeking large bat guano accumulations to get vertical core samples and analyze the DNA remains of different strata using ancient and environmental DNA techniques. 


Ashot Margaryan

Postdoc

I am a biochemist and geneticist from Armenia and since late 2013 I specialised in ancient human genomics. For the past four year I've been working on my PhD project called "Population Genomics of Vikings" at the Centre for GeoGenetics, Natural History Museum of Denmark. As part of this project I collected and whole-genome analysed hundreds of ancient (Viking) human remains to reconstruct the genetic history of the Vikings 1000 years ago. I've joined Tom Gilbert's group as a postdoc since September 2017 as part of the DNAmark project. I am doing the bioinformatics part of DNAmark and focusing my efforts on the assembly of organelle genomes from various extant species from Denmark.


Frido Welker

Postdoc

I am a postdoc in the ancient protein group (Matthew/Enrico) at the SNM, funded by a VILLUM Fonden grant awarded to Enrico Cappellini. My research interests lie on the interface of human evolution and ancient protein analysis. I obtained my PhD at the MPI-EVA where I developed and applied novel methods in the field of ancient protein research (palaeoproteomics) to describe and phylogenetically characterize novel hominin fossils based on ancient protein sequences alone. I have a particular interest in using ancient protein sequences for phylogenetic reconstructions. At the SNM, my research will focus on extending our ability to retrieve and utilize ancient protein sequences from hominin specimens, with a particular focus on hominin evolution. Concurrently, I remain affiliated with the MPI-EVA and will supervise a PhD student there who works on the interface of zooarchaeology and palaeoproteomics.


Gabriele Scorrano

Postdoc

I am a molecular anthropologist specialized in the ancient human DNA and proteins analysis. I obtained my PhD in Ecology and Evolutionary Biology in the University of Rome Tor Vergata and since late 2012 I worked as post-doc at the Center of Molecular Anthropology for Ancient DNA study, University of Rome Tor Vergata. I've jointed Enrico Cappellini's group as a Marie Curie post-doc since November 2017. The project aims at reconstructing the ancestry and oral disease of Palaeolithic, Neolithic and Bronze Age anatomically modern humans from Central-Southern Italy, using genome-wide profiling and mass spectrometry-based proteomic analysis of skeletal remains and mineralised dental plaque (archaeological dental calculus).


Jazmin Ramos Madrigal

Postdoc

My main interests are evolutionary biology and biodiversity. In particular, I have always been amazed by plant species. Their enormous diversity, genome flexibility and richness in biochemical processes, make them a unique subject of study from an evolutionary perspective. 

I am currently working in understanding the early stages of maize domestication (Zea mays) using ancient DNA. I am interested in identifying the possible maize dispersal routes from its center of domestication in Mexico into the rest of the Americas, as well as the natural and artificial processes that shaped its genome through time, to become the delicious crop we know today.


José Alfredo Samaniego Castruita

Postdoc

I am doing a shared Postdoc at Eline Lorenzen's group and Tom Gilbert's group. I have a background in Genomic Sciences and bioinformatics. The projects I have worked on involve the use of bioinformatic analyses with NGS data (whole genome sequencing and capture data) in ancient an modern plants, animals, viruses; metagenomics; population genetics; phylogenetic analyses; pipeline development; among others. My current research focuses on phylogenomics and population structure of polar bears and narwhals. I am also interested in the assembly of organellar genomes with high amount of numts or nupts (odins) using NGS data (Odintifier).



Kimmo Sirén

Postdoc

I’m Kimmo Sirén and I joined the Computational Biodiscovery group of Thomas Sicheritz-Pontén as a postdoc. I am working in MetaCheese project. I have a PhD from the Institute of Viticulture & Oenology in DLR Rheinpfalz in Germany where I investigated how microbial communities impact the chemical and sensory composition of Riesling wines in the Microwine project. Such approaches can be extended to any fermented food studies in general. Besides wine and winemaking, I like using machine learning and other statistical tools to analyse multidisciplinary data such as metabolomic and metagenomic data. I have a MSc in Viticulture and Oenology from France/Germany, and a BSc in Mathematics from Uni Helsinki.

Marcela Sandoval Velasco

Postdoc

I have always been fascinated by knowing, understanding and using the information encoded in one of life's most essential components - DNA, and I'm particularly interested in applying new methodological and technological improvements, such as HTS, to the study of evolutionary processes and the history of populations. Originally from Mexico, I joined Tom Gilbert's group as a PhD fellow funded by the EUROTAST project (http://eurotast.eu/). My PhD research was focused on exploring, comparing, and applying new methodological developments related to DNA extractions, sequencing library preparations, and DNA enrichment methods, for the generation of genome-wide data from ancient and historical poorly-preserved samples. After handing in my PhD in July, I have been working as a Postdoc as part of the NEWPLAN Project studying carrot color evolution and the identification of specific alleles giving rise to the black color. 


Marie Louis

Postdoc

I am a post-doc in Eline Lorenzen’s group. I am interested in understanding the mechanisms underlying the evolution of natural populations, and the role of past climate variations and behaviour in shaping genetic divergence. I am also keen on applying genetic tools to address conservation questions such as the delineation of management units. As part of my post-doc, I will be working on population genomics of modern narwhals using samples from their whole high Arctic distribution. I will be looking at population structure and how past climate variations have impacted the demographic history of the species.



Marie-Eve Monchamp

Postdoc

I am an aquatic ecologist broadly interested in the evolution and genetic diversity of natural communities impacted by environmental change. Originally from Montreal, Canada, I obtained my PhD in Environmental systems science at the Swiss Federal Institute of Technology in Zurich, where I studied the diversity and phylogenetic structure of planktonic communities in lakes impacted by human activities using DNA-based methods applied to sediment cores. I am currently a postdoc in Tom Gilbert's group where I am involved in a collaborative project (Denmark – Switzerland) reconstructing the past 20,000 years of evolution and ecosystem dynamics in Lake Victoria from sediment cores, fossils and ancient DNA. 


Michael Westbury

Postdoc

I am currently a Postdoc in the Lorenzen group. My research interests involve working with nuclear genomic data from both ancient and modern specimens and putting this into an evolutionary context. While working at the Lorenzen group I will be both producing and analysing nuclear genomic data from a variety of marine mammalian species of the arctic. Through the use of both contemporary and ancient specimens I plan to investigate how the population dynamics of these species have changed over time and the influences previous climatic fluctuations may have had on the demographic history of these species.


Miyako Kodama

Postdoc

I joined Tom Gilbert's lab as a postdoctoral researcher in 2016. I am originally from Fukuoka, Japan and I have received my doctoral degree from the University of Washington in Seattle in 2015. I am broadly interested in understanding how commercially important traits are affected by the underlying genetics, epigenomics and transcriptomics, as well as their associated microbiome in plant and animal species. I am currently investigating how host genome and gut microbiome interact and affect size and growth in farmed Atlantic salmon.  


Ostaizka Aizpurua

Postdoc

I am a biologist that has focused her research on the dietary and sensorial ecology of piscivorous bats so far. In my postdoctoral project, under the supervision of Tom Gilbert, I have added a new angle to the study of fishing bats by analyzing the role of gut microorganisms in the adaptation process of insectivorous bats to piscivory. Using the European long-fingered bat as a central species, I am comparing its microbiome profiles to other phylogenetically and ecologically related bats, as well as studying the variations of the gut microbiomes and the digestion efficiencies when completely insectivorous populations include fish into their diet. 



Sen Li

Postdoc

I am Sen Li from China, my job at the section is the bioinformatics manager of the new EU project -- HoloFood. A short evo-history of my background: I did my undergraduate in Automation Engineering in China, then moved to Sweden, my master's degree was in Engineering Physics from Chalmers Tech. Uni. After that I finished my PhD in Evolutionary Genetics from Uppsala University in 2012. I was working at CMEC@KU as a bioinformatics/computing manager since 2013 and had a short staying at BRIC@KU before moving to the Section for Evolutionary Genomics.



Åshild Vågene

Postdoc

I am an archaeogeneticist with a background in archaeology, palaeopathology and genetics. My research interests are the study of ancient bacterial and viral pathogens, pathogen evolution, zoonoses and the emergence and origins of infectious diseases. I obtained my PhD at the end 2018 from the MPI-SHH and the University of Tübingen in Germany. During my doctoral research I studied the genomic evolution of ancient pathogens recovered from pre- and post-contact archaeological human remains from across the New World. Specifically, I studied the causative bacterial agents of tuberculosis and enteric (paratyphoid) fever. I joined Tom Gilbert’s group as a postdoc in February 2019, where I will continue to investigate the evolutionary histories of ancient pathogens using genome-wide data generated from archaeological tissues.

PhD Students


Abigail Lowe

PhD Student

I am a PhD student in Matthew Collins' group. I am currently based between the University of York and the Natural History Museum in London. I have a background in computer science and bioinformatics, so my project will aim to fuse traditional palaeoproteomics methods with computational models in order to answer questions within evolution and natural history. I just began at the museum in October 2016, so my exact research question is still to be decided



Adam Koziol

PhD Student

My research interests mainly fall within evolutionary biology and adaptation that I hope to further expand during my time here. My project will involve the study of the hologenome which is the connection between the host genome and the associated genomes of microbiota known as the metagenome. In this project we hope to unveil the hologenomic mechanisms underpinning adaptation to a range of environmental conditions. Previously my research focus involved the application of environmental DNA metabarcoding to assess eukaryotic community compositions in marine environments which I studied in Perth, Western Australia.


Anna Fotakis

PhD Student

My interests fall into understanding our past by using the latest biomolecular techniques. In particular I am interest in changes and adaptations of our microbiomes, through time and how the interplay has fallen between our environment, past human population movement, health and disease.

To achieve this I work in combining both shotgun ancient proteomics and shotgun metagenomics on archaeological samples. Tom Gilbert and Enrico Cappellini supervise my project.


Amanda Bolt Botnen

PhD Student

I am a biologist with a keen interest in evolution. My PhD research uses environmental DNA (eDNA), such as faecal material, from domesticated animals to understand the gut microorganism community from both a temporal and a health aspect. The primary focus is on the change of the gut microbiome since domestication and its role in the process of domestication. The research also aims to study changes in the microbiome before and after industrialisation and the increased use of antibiotics in agriculture.


Anne Marie Eriksen

PhD Student

I have a background as a Conservator of Natural History and joined Tom Gilbert’s group in 2015 when I started my PhD research, which is a collaboration with the National Museum of Denmark. I am investigating microbial degradation of archaeological bones, with a special focus on bones found at submerged Mesolithic settlements. My aim is to develop the understanding of the quality, and in particular degradation, of DNA in archaeological bone material. Microbes play a major role in bone degradation, in the current study we are investigating the structure of their community, and how the local environment around the bone influences their diversity and function throughout the burial period.



Bharath Nair

PhD Student

I am a TALENT doctoral fellow in the Palaeoproteomics research group supervised by Prof. Matthew Collins and co-supervised by Prof. Carsten Wiuf (Dept. of Mathematics). I did my Integrated M.Sc. in Chemistry at National Institute of Technology Rourkela, India.

My research interests include biochemistry, data analysis, mass spectrometry, and proteomics. My PhD project 'ModProD' aims at exploring in finescale detail the survival of a model protein, and attempt to map as many as possible of the breakdown products using a combination of analytical methods and mathematical analysis. By combining experimental, analytical, and data processing methods, this project would hopefully give us a better understanding of ancient protein decay.



Camilla Scharff-Olsen

Research Assistant

I’m a biologist with specialisation in Ecology and an interest in population structure, conservation and biodiversity. I did my Master’s at the University of Copenhagen and finished in the summer of 2018. My Master thesis was about population structure and putative ecotypes in Arctic ringed seals.
I’m currently working as a research assistant in Tom Gilbert’s group on a large project investigating wolf genomic to discover the evolutionary history and population structures of the wolf thus including ancient, historic and modern samples.


Christina Islas Lynggaard

PhD Student

I am a biologist with a special interest in parasitology. I joined Tom Gilbert's group in 2017 as a PhD student. My project aims to characterize the gut microbiome of leeches from different families, habitats and feeding habits. By generating a metagenomic dataset of the bacterial symbiont of leeches I aim to explore the role of gut microbiome in food digestion. It will also involve taking environmental DNA (eDNA) samples for a better understanding of the variables that can affect the bacterial diversity in the gut content of these parasites.


Eden Richards

PhD student

My previous academic training and working career has been as a geoarchaeologist. I am now working towards a double PhD position shared between Copenhagen and York under the MC ArchSci2020 scheme. I am primarily supervised by Hannes Schroeder (Cph) and Kirsty Penkman (York) but also working with Matthew Collins (Cph/York). I am currently exploring ZooMS technology to see if it can be used as a method for determination of gender. I will be exploring this using proteins in dental enamel with a specific focus on archaeological fauna. The project is in very early stages of development so research questions are yet to be further defined. Before coming to Copenhagen I worked as a commercial geoarchaeologist for ARCA at The University of Winchester. I have experience in the field of archaeology as well as in a laboratory environment. I am moving into more detailed protein chemistry at KU and I am looking forward to the challenges this is going to bring.


Fabiana di Gianvincenzo

PhD Student

I am a PhD student in Enrico Cappellini’s group and I come from Italy. In June 2017, I earned my degree in Chemistry in University of Pisa, where my studies where focused on the analysis of artwork materials for the safeguard of Cultural Heritage. As part of the TEMPERA European Training Network, I will now be studying proteinaceous binders in ancient works of art.


Fátima Sánchez Barreiro

PhD Student

I am a PhD student in Tom Gilbert’s group since the beginning of 2017, and my research is framed within the Extinction Genomics project. The goal of my part of the project is to assess the population status and genomic diversity of the two species of African rhinoceros, the black rhino (Diceros bicornis) and the white rhino (Ceratotherium simum). These two species have undergone severe population declines in the recent past, and while conservation efforts to preserve their populations aren’t scarce, the species-specific genomic consequences of these population crashes are not fully understood yet. To unravel this question I am making use of museum rhino specimens, ancient DNA genomic techniques, and high throughput sequencing.


George Pacheco

PhD Student

Evolutionary Biologist initially trained in the northeast of Brazil with a profound interest in the genomic architecture of the mind. Since early 2013, I have been in the section, where I defended my MSc thesis working on the population genomics of feral pigeons. Presently, I am PhD Fellow part of the Science without Borders Programme and my doctoral utmost goal is to gather sufficient evidence to claim that the Rock Dove complex has potential to be considered as an amenable model organism for investigations in genomics and evo‐devo. In order to achieve that, I have been working with several genomic approaches such as GBS, capture and ancient sequencing.


Jonas Niemann

PhD Student

I am a Bioinformatician currently conducting a project on extinct genomes at the universities of Copenhagen and York. The PhD is supervised by Tom Gilbert and Matthew Collins, and funded by the Marie Curie scheme ArchSci2020 (www.archsci2020.eu/). While my main project focuses on the process of extinction and the possibility of de-extinction of several species, I have developed a particular interest in algorithm development and the upcoming field of metagenomics. Before starting my PhD I have completed my undergrad studies in Bioinformatics at Wageningen University in the Netherlands, where I wrote my thesis on the improvement of QTL analysis methods."



Joshua Evans

PhD student

I am a PhD student in Tom Gilbert's group, visiting from the School of Geography and the Environment at Oxford. My current research focusses on novel food fermentation practices at a leading restaurant and an experimental distillery in Copenhagen, and how their teams combining Japanese techniques, particularly kōji and miso, with Nordic raw materials might be changing the ecology and evolution of the microbes involved compared to their traditional counterparts. In general I am interested in integrating social and natural science methods to investigate how humans and non-human companions change each other in food systems past and present. I have a Master's in History and Philosophy of Science from Cambridge and a Bachelor's in the Humanities from Yale, so I am not really a scientist but I like to work together.



Kamille Krause

Research Assistant

I am a research assistant in the Computational Biodiscovery group of Thomas Sicheritz on the “Dynamics of Antimicrobial Resistance in the Urban Water Cycle in Europe” or DARWIN project for short in collaboration with DTU Environment. I am working on building a bioinformatic data governance platform for storage, management and exploitation of metagenomic data sets from the DARWIN project. I have a MSc in Biotechnology from DTU, and have previously worked with a wide variety of projects and types of data ranging from the metagenomic and genomic analyses of marine copepod genetics and ecology, through testing cross-reactivity of commercial snake antivenoms using high-density peptide microarray analyses, to now including the handling of metagenomic datasets of European water samples


Lara Puetz

PhD Student

My research interests have mainly focused on marine conservation biology and oceanography, and more recently, the use of molecular tools in understanding evolutionary and ecological processes. Past work has ranged from conservation genetics of deep sea hydrothermal vent tubeworms to acoustically monitoring sperm whale distributions within and around marine protected areas.

I recently joined the Gilbert group where I will be studying both the adaptive role of the gut metagenome, and its relationship with the host genome in East African cichlid fish. Cichlids in the East African Lakes are one of the major systems that have been used to study sympatric speciation in vertebrates, with extensive data available on their morphology, systematics and behaviour.  I propose to complement this dataset through metagenomic characterisation of the microbial community within the cichlid gut from a range of phenotypes, including hybrids. Analysis of this data will shed for the first time, insights into not only the metagenomic basis of the speciation in general, but also more specific insights into the limits of metagenomic plasticity and its relationship with the host genome. 


Liam Lanigan

Research Assistant

With a background in bioarchaeology and palaeopathology, my interests are answering questions related to oral health and infectious disease in past populations with proteomics. During my time at the Natural History Museum of Denmark, I have been exploring the metaproteomics of dental calculus and what it can tell us about oral disease in medieval Danes. I am currently working on a number of projects, including using proteins from teeth to determine sex and age in archaeological human remains. I hope to turn this current research into a PhD under Prof. Matthew Collins.


Maiken Hemme Bro-Jørgensen

PhD Student

I am a double PhD student at Evolutionary Genomics at University of Copenhagen and the Archaeological Research Laboratory at Stockholm University as part of the Marie Curie ArchSci2020 network under the supervision of Morten Tange Olsen (KU), Kerstin Lidén (SU) and Aikaterini Glykou (SU). 

My research aims to investigate the population genomic history of different seal species in the Baltic Sea, assessing genetic, life history and demographic processes associated with climatic changes and intense human hunting pressure by analysing ancient DNA from archaeological seal bone material from the Atlantic to the Subatlantic Period. My main focus is on grey seals and the now extinct Baltic harp seal population. 

I was trained as a biologist at University of Copenhagen and undertook my MSc research in Tom Gilbert's group working on ancient DNA from drinking horns.


Marta Ciucani

PhD Student

I’m a biologist with a special interest in biodiversity and evolution. I earned my Master’s Degree at the University of Bologna in 2016 and I joined Tom Gilbert’s group in 2017 as an intern student working on Pleistocene Italian Wolf samples.

Currently, I am a PhD fellow in Pleistocene Wolf Evolution at the Natural History Museum of Denmark with Tom Gilbert and co-supervised by Matthew Collins.

My research aims to study ancient canid biodiversity using palaeogenomic and palaeoproteomic tools to recover evolutionary informative nucleotide and peptide data from subfossil samples from across the wolves’ Eurasian range in general, but Italy in particular. The primary goal of this project is to improve the information available upon which hypotheses as to the origin, spread, and evolution of this group of canids can be built. 


Martin Nielsen

PhD Student

I am a general biologist with a key interest in conservation and biodiversity. I use molecular biology tools, and especially the concept of metabarcoding, to investigate the diet of various bats and birds, and do molecular diversity assessments of bulk insect samples. Through my master, I investigated molecular methods to assess diversity in large and complex arthropod samples, and assessed means for method optimization and simplification. My PhD is mainly focused on arthropod diversity. Using molecular tools, I seek to investigate how arthropod diversity change in time or space, or between different habitats, which eventually could prove a vital instrument for general diversity assessments. Besides this, I am a hobby nature photographer, sports fisher, family farther and run two websites (www.descna.com and www.apieceofnature.eu).


Meaghan Mackie

Research Assistant

I am a research assistant with the Palaeoproteomics group. My research interests are heavily influenced from my archaeological background, which I apply to study ancient proteins. I am particularly interested in human disease and health, but have also worked with zooarchaeological and artistic materials. For my MSc, I extracted proteins from Roman ancient dental calculus (mineralized plaque), examining the results for insight into the health and life of the individuals sampled and also the preservation ability of calculus. My current position deals with laboratory and mass spectrometry work, and I am gaining more interest and experience in data analysis to understand the raw information I generate, especially in regard to post-translational modifications (PTMs) on peptide sequences to determine age and damage.



Meng Zhao

Research Assistant

I work in GeoGenetics Center, assisting Assist. Prof. Mikkel Winther Pedersen on Lake Victoria Sediment DNA Metabarcoding project. I mainly work with DNA extraction, metabarcoding PCRs and generating barcode database. I completed my bachelor degree in Biology/Microbiology at New England College (NH, USA), my main study was based on measuring catalase gene express in a bacterium under the oxidative stress environment by using qRT-PCR. Positive Danish living attitude and advanced educational technology attracted me to proceed my master degree in Pharmaceutical Science at the University of Copenhagen. My main research area was in drug delivery and I completed my thesis project on investigating metal-based anticancer drug delivery system (August 2017). 

Mikkel Skovrind

PhD Student

I am a PhD student in Eline Lorenzen’s group working on the circumpolar distributed arctic beluga whale (Delphinapterus leucas). I focus on the population structure and the phylogenomic relation to closely related species. The main focus of my PhD is on generating whole-genome sequences from multiple animals across the entire distribution, but I will also be working with morphometrics, microbiomes and genetic analyses of their diet. I have a general interest in how the differentiated environment/behavior of animals is related to their genomic diversification; which was also the subjects of my previous work that focused on stenohaline anadromous fishes. This means anything that has to do with evolution and marine animals catch my attention. 


Morgan McCarthy

PhD Student

I am a PhD fellow from the Marie Skłodowska-Curie TALENT Doctoral Programme under the supervision of Morten Tange Olsen (UCPH) and Phillip Morin (SWFSC). I’m a marine biologist and for my PhD, I am focusing on how genomics can be used to study an offshore, deep-diving family of cetaceans known as beaked whales. I will investigate connectivity of populations around Hawaii, Mexico and Southern California. I will also assemble complete mitochondrial and whole genomes for a new species of beaked whale to revise its position in beaked whale phylogeny. I have a BA in Earth and Planetary Sciences from Johns Hopkins University in Baltimore, Maryland, where in collaboration with the University of Bremen, I compared the reproduction and feeding strategies of two globally invasive crab species. Afterwards, I began a joint Erasmus Mundus MSc in Tropical Biodiversity and Ecosystems at the University of Brussels, University of Florence and University of Queensland, using mitochondrial and nuclear DNA markers to study a suspected dugong population decline in Queensland, Australia. After my masters, I worked with beaked whale genomes at NOAA’s Marine Mammal Genetics Program at the Southwest Fisheries Science Center in San Diego, California.



Nataly Canales

PhD Student

I am Nataly from Peru. Since I was a toddler I was amazed by the biodiversity in my home country, which motivated me to study Genetics, then I did my master's degree in Bioinformatics in China. My research background is quite diverse ranging vipers, bacteria and crops. Now, for this new stage, I'm thrilled to unravel the evolutionary history of Cinchona bark from modern and ancient samples. This project has a special meaning for me since Cinchona is originally from my region and has played a big role for almost 400 years for our civilization.


Physilia Chua

PhD Student

I am a conservationist with a background in biology and ecology. I obtained my Master’s Degree in Environmental Sciences from the University of Freiburg in Germany. As part of the Plant.ID Marie Curie network, I will be working with environmental DNA to elucidate the diet of capercaillies (wood grouse) in the Alps and Norway through the use of shotgun sequencing techniques.


Sarah Mak

PhD Student

I am Sarah from Hong Kong with a background in ecology. Currently, I am a PhD fellow in Tom Gilbert’s group, co-supervised by Anders Hansen from Centre for GeoGenetics. My main research focuses on optimizing the microbial DNA profiling from heavily inhibited liquids (e.g. wine and water samples) using target capture methodologies. The project is a part of MICROWINE project (http://microwine.eu/). I also have interests in method comparisons, environmental DNA (eDNA) and coral biology.



Stephen Garrett

PhD Student

I am a botanist and plant taxonomist focused on understanding the mechanics and drivers of plant evolution and biological diversity across the globe. My research interests include plant genetics, plant morphology, taxonomy, patterns of plant evolution, biogeography, data analysis and modelling techniques for pushing the frontiers of biodiversity description and conservation, and uncovering unknown plant stories. My PhD research involves unravelling the complex taxonomy and species delimitation of the hemi-parasitic Euphrasia genus; using the Danish Euphrasia species as a case study for tackling genus-wide taxonomic difficulty due to extensive hybridisation and polyploidy.



Tuuli Kasso

PhD Student

As a COFUND TALENT PhD Fellow, my project Divine Animals explores the biomolecular archives of beeswax (ArcHives) and parchment (Beasts2Craft) for medieval husbandry, craft and trade. My supervisors are Prof. Matthew Collins and Prof. Matthew Driscoll (The Arnamagnæan Institute), and my PhD aims to investigate Nordic archival materials, mainly the Fragmenta Membranea at the National Library of Finland. I have an interdisciplinary background with degrees on conservation, art history, archaeology and archaeological sciences, and now as a learning scientist I aim to combine my knowledge on cultural history with the state-of-the-art methods at EvoGenomics for my PhD.


Theis Trolle Jensen

PhD Student

I am a Bioarchaeologist currently doing a MC double PhD between York and Copenhagen through the ArchSci2020 initiative. I am being supervised by Matthew Collins, Enrico Cappellini and Mikkel Sørensen.

I am studying Early Mesolithic bone tools by Zooarchaeology by Mass Spectrometry for species identification. I am particularly interested in bone points, which were used as projectiles during hunting.

Bone preservation from the Early Mesolithic in Southern Scandinavia is in general poor, which has resulted in a hiatus regarding species availability during the first thousand years. Because the bone points were often rammed down into the deeper sediments, it may be, that they constitute one of the richest sources of bone from this period, and may thus help to understand both species composition but also how people used the available species just after the last Ice Age.


Vanessa Iurif

PhD Student

I am enrolled in a PhD program in Bioenergy in Brazil and I will join Tom Gilbert’s group in order to develop part of my research.

My PhD project aims to identify biological factors that contribute to the decrease in ethanol productivity at a fermentation industry in Brazil. Considering that ethanol production occurs in a non-aseptic environment and the presence of contaminants microorganisms affects ethanol productivity, metagenomic analyses will be important for identify microbial groups and understand their dynamics on fermentation tanks.


Xenia Weber

PhD Student

For my PhD I am working on walrus genomes obtained from archaeological and contemporary samples under the supervision of Morten Tange Olsen and Peter Jordan (University of Groningen). The project is under the MC ArchSci2020 scheme and aims to investigate the effect of human-environmental factors on gene flow, adaptive traits and genetic diversity in walruses. I also plan to investigate how walrus artefacts were sourced, traded and used by various North European cultures including the Thules and Vikings. Before coming to Copenhagen I studied at the Australian National University, Canberra, where I completed research into speciation within kelp and gained a background in plant science, systematics and evolutionary biology. Recently I have developed a particular interest in using ancient DNA approaches to reveal the ancestral genomes of contemporary plants and animals, and hence understand fundamental evolutionary processes that have led to the biodiversity we see today.


Administrative Staff


Cecilie Toudal Pedersen

Section administrator, Special Consultant

Responsible for the administration at EvoGenomics, including hiring, budgets, accounting and reporting to external funding bodies. Moreover, I'm the project manager for the ArchSci2020 EU ITN project.

Previous to SNM I worked as a communication officer at Research and Innovation at KU central administration and before that I worked at the Danish Ministry of Foreign Affairs.

I have a master’s degree in Public Administration and International Development Studies.


Christina Lehmkuhl Noer

Project Coordinator

I am the project coordinator of the DNAmark project - creating a Danish DNA reference database. I am mainly working with coordination/planning, research management and communication/outreach of DNAmark. I will keep track of all the plant, animal and fungi samples from collection/taxonomic identification to the lab and finally into the reference database/website. I have a PhD in animal behaviour and conservation from KU and Copenhagen Zoo. Previously to this job I have worked as a project manager at the outreach department at the Natural History Museum of Denmark.



Line Pedersen

Student Assistant

I am in the middle of my bachelor's degree in biochemistry at the University of Copenhagen. I am working as Matthew Collin’s personal assistant where I am supporting him with the daily responses to e-mails and booking meetings.  It also includes dealing with Rejsud, expenses and travels. 


Fotografi af Sigrid Egevang Jensen

Sigrid Egevang Jensen

Student Assistant

While doing my bachelor's degree in Biochemistry at University of Copenhagen, I support the administration of the Evolutionary Genomics section. This includes dealing with RejsUd, expenses and travels, updating the homepage and helping guests and new students.