Master theses

Misled by the mitochondrial genome – A phylogenetic study in Topaza hummingbirds by Tobias Andermann (then Hofmann), 2015


Available master projects

Here you can find a selection of available master projects to choose from. In addition, you can contact and institution or research group of interest on the list and see what they have to offer!

Uppsala University, Sweden

Fabien Burki’s research group

We aim to integrate the poorly studied protists (aka microbial eukaryotes) in global evolutionary models, using a combination of culture-independent genomic methods, analyses of environmental DNA, and phylogenetics. The main research themes in my lab are:

  • Reconstructing the eukaryotic tree of life
  • Taxonomically and phylogenetically resolving the eukaryotic environmental diversity
  • Origin and spread of photosynthesis in eukaryotes
  • The evolution of parasitism in marine invertebrates
  • Method development in single-cell genomics using microfluidics
We are constantly looking for motivated students, do not hesitate to contact me if you are interested in working on these questions.
Website for more info:

Stockholm University, Sweden

Phylogeny of a group of Acoela (marine worms)


A large portion of biodiversity is still unknown, and this is especially true for marine habitats and microscopic organisms. In this project you will study the phylogeny of a group of microscopic marine worms that belong to the group Acoela. You will collect material from marine habitats, sequence DNA and perform a phylogenetic analysis of the group. The aim is to produce a phylogenetic hypothesis that can explain the evolution of morphological features in these animals and serve as a basis for their classification.

Contact/supervisor: Ulf Jondelius

New species of Acoela


In this project you will analyse the phylogenetic relationships within a group (genus) of Acoela using molecular data and describe and name new species based on studies of their morphology and on analyses of DNA sequences. The material has already been collected, prepared for histological study and partially sequenced. You will do some additional sequencing, perform phylogenetic analyses and morphological studies. The aim is to produce complete descriptions of the new species that will be published in a scientific journal.

Contact/supervisor: Ulf Jondelius

Radiations in tropical Trichoptera

(Insects, Trichoptera)

One of the research projects in entomology aims at explaining the phylogenetic relationships and biogeography among the ultra high diversity of caddisflies (Trichoptera) on New Caledonia. New Caledonia is a small island in the Pacific Ocean and serves as a nearly isolated experimental laboratory for studying species radiations, and studies under the project covers working out phylogenetic hypotheses based on molecular data, and analyzing the biogeographic pattern of the group by using on modern modern analytical tools. The morphology of the insects will be examined by using light and compound microscopes. Scanning electron microscopy is used when needed. A part of the study will also include describing species new to science, and publishing results in a scientific journal.

Contact/supervisor: Kjell-Arne Johansson

Swedish Museum of Natural History

Phone: +46 (0)8 5195 4088
Personal website

Beetle systematics

(Insects, Coleoptera)

One fifth of all described species on earth are beetles, why beetle research is important and aquatic beetles are in focus for some of the research at the Swedish Museum of Natural History. We can offer master thesis subjects in the following categories: 1) Taxonomic, e.g. DNA Barcoding, description of new species, sorting out difficult species complexes/sister species 2) Phylogenetic, e.g. reconstructing phylogenetic hypotheses of evolutionary relatedness among species, genera or families and using the trees to propose natural classifications and test if previously suggested groupings are monophyletic 3) Evolutionary, here it is often about using phylogenetic trees/hypotheses to answer questions like how old is a group (dating), when did some colonization events or habitat switches occur and how many where they, how fast was the speciation in a group, or how did some characters evolve or co-evolve. Practically, master thesis projects in all three categories usually involves, but in different amounts, molecular lab work to collect DNA data, microscope studies of morphology, computer-analyses, e.g. various phylogenetic analyses of DNA data. They can also include collection in the field. We work a lot with the fauna of Madagascar but also the Swedish/European fauna and globally.

Contact/supervisor: Johannes Bergsten

Swedish Museum of Natural History

Phone: +46 (0)8 5195 4192
Personal website

Morphology and systematics in brittle stars (Ophiuroidea)

(Echinodermata, Ophiuroidea)

This project studies the phylogeny and taxonomy of brittle stars with mainly morphological methods by means of SEM. Projects on different levels can be offered, e.g. studies of skeletal structures (e.g. arm plates, jaws, dental plates) to understand homologies, comparative studies of ontogeny in a phylogenetic context, as well as alpha taxonomic studies including description of new species. Training includes taxonomic methods and principles, identification of brittle stars, skills in SEM preparation and operating the instrument, and interpretation of images. The MSc project also includes digital image processing, database usage and design, and writing a scientific paper.

Contact/supervisor: Sabine Stohr

Swedish Museum of Natural History

Phone: +46 (0)8 5195 5105
Personal website

Morphology and systematics in Nematods


Nematodes are very diverse, abundant and ubiquitous, and play important role in ecosystem functioning and human life. This project focuses on the global diversity and evolution of free-living nematodes, and their interactions with other organisms (origin of parasitism). The putative MSc project can focus on: 1) a survey of the nematode fauna of Sweden or of New Caledonia, (2) a taxonomic study including the description of new species from around the world, or (3) metabarcoding analysis of nematode communities. It will include training in general sampling techniques, field work in Sweden, microscopy, identification, phylogenetic analysis, preparation of scientific publications.

Contact/supervisor: Oleksandr Holovachov

Swedish Museum of Natural History

Phone: +46 (0)8 5195 4273
Personal website


(Vertebrata, Actinopterygii)

The Ichthyology team is specialized in studies of freshwater fishes from Sweden, Latin America, Asia, and to some extent also Asia. The most focal taxonomic groups are cichlids (Cichlidae) and cyprinids (Cyprinidae), which are the two most species-rich vertebrate families, presenting a large number of systematic problems at different levels. We are particularly interested in theoretical aspects on species, historical biogeographical analyses, and the use of GIS and FishBase for large scale analyses of biological parameters in a phylogenetic perspective. We supervise morphological/molecular genetic projects that also include a wider biological outlook (e.g., mimicry, growth allometries, ontogeny, dispersal biology), and preferably analyses at the level of species or genus. Certain years we may offer participation in field work. Hot topics at the moment include cichlids from Lake Tanganyika, dwarf cichlids from South America, cyprinid fishes from Myanmar, and the phylogeny of the Cyprinidae. The degree project must be conducted within the framework of an ongoing research project.

Contact/supervisor: Sven Kulander

Swedish Museum of Natural History

Phone: +46 (0)8 5195 4116
Personal website

Cenozoic Miocene Mammals from Central Europe

(Vertebrata, Mammalia)

One research project at the Swedish Museum of Natural History deals with fossil mammals from Central Europe. The studies are focussed on the evolution, systematics, and biogeography of small mammals (insectivores, bats and rodents) during the Miocene thermal optimum about 18 million years ago. Morphologic, morphometric, and microstructure analyses are used to investigate specimens on genus and species level. Investigation includes light microscopy and scanning electron microscope, for both analysis and documentation.

Contact/supervisor: Thomas Mors

Swedish Museum of Natural History

Phone: +46 (0)8 5195 5107
Personal website

Projects concerning the ecological adaptations (ecomorphology) of carnivores

(Vertebrata, Mammalia)

Research concerning the evolution of carnivores at the Swedish Museum of Natural History is based on an extensive database of morphometric data on the functional attributes of a large number of species (85% of living terrestrial carnivores). This database can be analysed in conjunction with another database, with climate and environment data on more than 200 sites from all continents. These data can be analysed in many ways (geographically, phylogenetically, ecologically, etc.) to provide a basis for understanding the ecological and evolutionary role of carnivores. The projects are expected to provide experience in the use of a number of statistical methods, interpreting results according to scientific principles, and in some cases may lead to development of new analytic methods.

Contact/supervisor: Lars Werdelin

Swedish Museum of Natural History

Phone: +46 (0)8 5195 4202
Personal website

Animal-plant interaction in the Cretaceous of Scania

(Bivalvia and mangrove)

During the late Cretaceous (ca 80-65 Ma), the northeastern part of Skne (southern Sweden) was covered by a shallow sea. The Swedish Museum of Natural History holds extensive collections of fossil shells from this environment, including large numbers of oyster shells representing different species living in a range of different environments. The collection includes oysters living on the roots of mangrove trees, as well as species preferring other substrates. As the substrate leaves a mark on the oyster shell it is possible to analyze what environmental preferences different species had and to reconstruct the fossil ecosystem, including animal-plant interactions. The project will start with an inventory of fossil oysters in the collections of the Swedish Museum of Natural History, potentially in combination with fieldwork in Skne. The following analysis on substrate preferences of individual species will focus on species from the mangrove environment to outline the interaction of oysters and mangrove and between different species of oysters. Is it possible identify the type of mangrove the oysters were living on? The work will provide experience in fossil preparation, latex molding to study negative marks, photography and statistical analysis of data, as well as potentially experience in palaeontological fieldwork.

Contact/supervisor: Christian Skovsted

Swedish Museum of Natural History

Phone: +46 (0)8 5195 5133
Personal website

Palaeoecology in the oldest coral reefs on Earth

(Cnidaria and Porifera)

During the early Cambrian (ca 543-515 Ma), environments comparable to modern coral reefs evolved for the first time. The Cambrian reefs were primarily constructed by sponges and algae, but were also home to a large number of other invertebrate animals that are sometimes preserved as fossils. Some of the best preserved early Cambrian reefs are found along the coast of southern Labrador in Canada. The Labrador reefs preserve a number of different micro-environments and the purpose of the proposed project is to study differences in the fauna between these environments to be able to understand the life environments and ecological demands of individual organisms. The project will include preparation of collected material in acetic acid, identification of acid-resistant fossils using electron microscopy (SEM) and comparisons of faunas along a transect between two reef bodies.

Contact/supervisor: Christian Skovsted

Swedish Museum of Natural History

Phone: +46 (0)8 5195 5133
Personal website

Ancient DNA and population genetics

(Vertebrata, Mammalia)

Genetic analysis is an excellent tool to investigate different population processes such as divergence, gene flow among regions, local adaptation and population demography, and how these processes might be affected by different environmental factors. At the ancient DNA and population genetics research group at the Swedish Museum of Natural History, we use genetic analysis on both modern samples and prehistoric fossils up to 100,000 years old to study these population processes. We can offer MSc projects on two main themes: ancient DNA and contemporary genetics. Ancient DNA research is aimed at retrieving genetic data from historical specimens. This can involve anything from 100-year-old samples stored in a museum, to analyses on Ice Age species such as mammoth and cave lion. Examples of questions that could be addressed include the taxonomy of extinct species and extinction/recolonisation dynamics of populations through time. Using DNA analysis on contemporary samples, it is possible to address a wide variety of questions. At present, we are working both on assessing population genetic structure in different mammals as well as using DNA technology for diet analysis. We are happy to discuss any type of MSc project within either of the two themes discussed above. Further information about the research group is available at

Contact/supervisor: Love Dalen

Swedish Museum of Natural History

Phone: +46 (0)8 5195 4281
Personal website

Museomics and avian evolution

(Vertebrata, Passeriformes)

The research group for avian systematics at the Swedish Museum of Natural History use genomic data to study the evolution of birds. Our research is mainly focused on passerine birds in the Indo-Pacific region and the questions we address span from phylogenetics and biogeography to hybridization and population genetics.  We welcome one or several students to participate in this work.  In a typical project the student will map genomic data from museum samples against a de novo reference genome and then use the aligned data set to address specific evolutionary questions.

Contact/supervisor – Martin Irestedt

Swedish Museum of Natural History

Phone: +46 (0)8 5195 4059
Personal website

Lund University, Sweden

Patterns of morphometric variation and infra-specific taxonomy of a highly polymorphic Nordic vascular plant species

(Composits, Asteraceae)

In the Nordic countries, the infra-specific taxonomy and variation of polymorphic but common and widespread plant species have not received much attention in recent years. As a consequence, there are several species or groups of species within which two or more infraspecific taxa are currently recognized in standard floras but for which the infraspecific taxonomy has never been thoroughly investigated. The aim of this group of projects is to select one such species or group of species, measure a set of variable characters and map their distribution throughout the Nordic countries based on herbarium specimens in the public herbaria, use various multivariate statistical methods to analyse to what extent the variation in different morphological characters correlate, and, ultimately, try to find out which (if any) combinations of characters that may be used for defining and circumscribing geographical or ecological races that may deserve to be recognized taxonomically. Depending on the species chosen, the study area may also be extended to regions outside of the Nordic countries. Pilot studies with molecular markers may optionally be added to these projects with the aim of assessing to what extent the morphometric variation correlates with the pattern of molecular variation, but without prior knowledge of a suitable molecular marker system for these particular plant species the odds for finding a marker system that may reveal suitable levels and patterns of variation may be rather high. Taxonomically complex or interesting species that would need to studied in this way include, but is not restricted to, Platanthera bifolia, Allium schoenoprasum, Bromus hordeaceus, Caltha palustris, Ranunculus polyanthemos, Ranunculus subborealis, Thalictrum minus, Thalictrum simplex, Anthylllis vulneraria, Lathyrus japonicus, Vicia sepium, Polygala vulgaris, Geum rivale, Potentilla argentea, Viola canina, Rumex acetosa, Veronica maritima/spicata, Pedicularis palustris, Campanula rotundifolia, Achillea millefolium, Carlina vulgaris, Cirsium arvense, Erigeron uniflorus, Gnaphalium uiginosum, Gnaphalium norvegicum/sylvaticum, Leucanthemum irkutianum/vulgare, Solidago virgaurea, Sonchus arvensis, Tripeurospermum maritimum and Valeriana sambucifolia. Yet another option would be to study the circumscription of the morphologically defined sections of the genus Hieracium.

Contact/supervisor – Torbjörn Tyler

Department of Biology, Botanical collections, Lund University

Phone: +46 (0)46 222 4234
Personal website

University of Gothenburg, Sweden

Molecular systematics of Clitellata

(Annelida, segmented worms)

The overall aim of our research is to establish a classification of Clitellata (or Oligochaeta) that is congruent with a well-supported set of hypotheses of the clitellate Tree of life, including its deep as well as terminal nodes. The big picture deals with the phylogenetic position of Clitellata within the Annelida and the basal evolutionary history of the clitellate families and other higher taxa, such as Crassiclitellata (the earthworms). At the other end of the spectrum are the delimitation and identification of separately evolving metapopulation lineages (=species), primarily using a combination of rapidly evolving mitochondrial and nuclear genes. A number of widely distributed morphospecies of Clitellata, showing preliminary evidence of cryptic speciation are studied, and the amount of genetic within and between lineages will be analyzed. Morphological variation and ecological differences are also be evaluated when possible or necessary (as in the case of asexual species). We can offer a number of Masters projects (30, 45 or 60 credit points) dealing with taxonomy and phylogeny of selected groups of terrestrial, freshwater or marine clitellates.

Contact/supervisor – Christer Ersus, Professor emeritus

Department of Biological and Environmental Sciences University of Gothenburg

Phone: +46 (0)31 786 3645
Personal website

Evolution of hummingbird pollination in tetraploid Silene spp.

(North American Silene spp.; Caryophyllaceae)

We have in previous studies found that the large variation in e.g., ecology, morphology, and pollination exhibited by North American Silene species probably all stems back to a single polyploidization event in the Quarternary. However, reconstruction of the the species phylogeny was comprimised by the polyploidy. We now have developed a model to cope with this, and in this project you will specifically trace the origins of hummingbird pollination syndrome in the group. For calibration of the timescale, we will try to use fossil DNA sampled from permafrost. You will collaborate various aspects with scientists from USA, Germany, Scotland, and Norway. To be conducted with the Botany building research group.

Contact/supervisor – Bengt Oxelman

Department of Biological and Environmental Sciences University of GothenburgPhone: +46 (0)31 786 2678
Personal website

Species delimitation in wild Dahlias

(Dahlia coccinea & allies; Asteraceae)

The genus Dahlia comprises about 35 species in Central and South America, with a centre of diversity in Mexico. Over 10,000 cultivars are known today and widely cultivated worldwide. The tubers of some species are used as starch source and consumed locally. Despite a tremendous variation in the cultivated forms, they are all believed to have originated from the crossing between 2 wild species, including Dahlia coccinea. This project aims at using NGS data to i) testing whether D. coccinea constitutes a monophyletic clade (is a good species); ii) assessing whether naturally occurring colour variants are phylogenetically clustered (form natural groups); and iii) estimating the environmental requirements of the species and assessing whether it will expand or contract under future climate change. Sampling of living specimens will be done from living collections at the Botanical gardens in Gothenburg, Copenhagen and Hamburg. To be conducted with the Botany building research group.

Contact/supervisor – Alexandre Antonelli

Department of Biological and Environmental Sciences University of Gothenburg

Phone: +46 (0)70 398 9570
Personal website

What is Gentianella baltica (Murb.) Börner?

(Gentianella balticaG. campestris; Gentianaceae)

Gentianella baltica is a red-listed plant occurring at some locations on the Swedish westcoast. It is very similar to G. campestris, and differs mainly by being annual and flowering late in the season,instead overwintering as a rosette. You will test the genetic distictiveness using next-generation sequence data from several populations, and also from other closely related taxa. You will collect G. baltica in the field during September-October, and also use herbarium material. To be conducted with the Botany building research group.

Contact/supervisor – Bengt Oxelman

Department of Biological and Environmental Sciences University of GothenburgPhone: +46 (0)31 786 2678
Personal website

Why are some plants woody but not others?

Evolution, biogeography, macroecology

Woody plants (trees and shrubs) cover 30 percent of the planet’s land area and offer crucial ecosystem services. It is unclear, however, why some plants are woody and others herbaceous. As a first step to solve this evolutionary puzzle, our close collaborator, Dr. Frederic Lens (Naturalis Biodiversity Center, The Netherlands) has created a database of nearly 7000 derived woody species that have evolved from herbaceous relatives.

This novel database shows that many of these woody species occur in continental regions with a marked drought period, suggesting that drought may have triggered wood formation in hundreds of independent lineages. In addition to the drought link, a number of broad-scale questions can be tackled, such as (1) When did derived woodiness evolve and is it linked with shifts in net diversification rates (radiations or evolutionary dead-ends)?, and (2) Is derived woodiness adaptive to islands, potentially related to island gigantism?

For this Masters project, we seek a motivated, independent student with a bio-informatics background and familiar with spatial analyses and the program R. The work may involve travels to The Netherlands (Leiden) and Germany covered by the department.

Contact: Alexandre Antonelli,; Frederic Lens,

Patterns in the accumulation of genetic data

Diversity, evolution, spatial patterns

Very few organism groups have genetic data for all or even for a large fraction of the species and analyses of diversity patterns therefore have to make assumptions about the placement of the missing species. For computational convenience and due to lack of knowledge it is generally assumed that they are placed randomly in the phylogeny even though there are good reasons to expect this to be wrong. In this project we wish to analyze the pattern of accumulation of genetic data among species to better understand what determines what species have and does not have genetic data in order to enable researchers to better include the missing species into evolutionary or ecological analyses

For this master project familiarity with spatial analyses, with the program R and with basic bioinformatics or phylogenetics is desired but not required.

Contact: Søren Faurby,

Co-extinction of scavengers and prey

Birds, mammals, diversity, spatial patterns

Highest species richness of scavenging brids is currenty found in east Africa, just at the same area where most of the large mammals occur. Scavenging birds, however, also have seen a massive extinction in the Late-Pleistocne/Early-Holocene and in particular they used to be hihgly diverse in North and South America, feeding on the likewise diverse mammalian megafauna community that used to live there. The goal of this project is to estimate historic ranges of the extinct scavenging birds and compare these with previously estimated ranges for their mammalian prey. After this we will analyse the correlation between the historical diversities of scavenging birds and prey and compare with the contemporary pattern for both. Many scavenging birds are highly endangered and the resulting knowledge may both improve the understanding of co-extinction patterns as well as hopefully inform ongoing conservation efforts to avoid future extinctions.

This project will be conducted in collaboration with and co-supervised by post-doc Ferran Sayol.

For this master project familiarity with spatial analyses and with the program R is desired but not required.

Contact: Søren Faurby,

Mismatch between pollinators and plants

Extinction, islands, birds, pollination, plant-animal interactions

Oceanic islands have seen very large extinction rates, with as much as 90% of all extinct birds being island dwellers. As a function of this, many other species may potentially suffer in the future, as in the case of red flowered plants, which generally are exclusively bird pollinated. The goal of this project is to identify the fraction of plant species on various oceanic islands being red (and therefore likely bird pollinated) and compare these ratios with the recent diversity of pollinating birds as well as estimates of historic diversities of birds on islands, which are being estimated by post-doc Ferran Sayol. We will thereby be able to identify islands with a deficit of current pollinators, which therefore may be of particular conservation concern.

This project will be conducted in close collaboration with island biologist Manual Steinbauer (

For this master project familiarity with spatial analyses and with the program R is desired but not required.

Contact: Søren Faurby,

Human alternation of the species-area relationship

Extinction, invasive species, islands, ecological rules, birds

As discussed above, there has been substantial extinctions of birds on islands, but at the same time a large number of non-native species has also been introduced to many islands. This project will analyze the combined effect of these two opposing factors and focus on the species-area relationship, which is one of the fundamental patterns of island biogeography. More specifically, the goal is to compare the relationship between island area and the number of bird species using three different datasets. 1) Current pattern including non-native species, 2) Current pattern only including native species and 3) Estimated pattern including current and extinct native birds.

This project will be conducted in collaboration with and co-supervised by post-doc Ferran Sayol and in in collaboration with bird macro-ecologist Tim Blackburn (

For this master project familiarity with spatial analyses and with the program R is desired but not required.

Contact: Søren Faurby,

Global distribution of palm spinescence and mega-herbivores

Palms, animal-plant interactions, macroecology

To quantify the global distribution of spinescence in palms (e.g. broad-scale patterns of species richness of palms that have spines) and how this is related to the current and historical distribution of mega-herbivores. Many palms are armed, often fiercely, with spines (as in Aiphanes minima, pictured here). These likely evolved as a response to mega-herbivores as defense structures. Here, we will ask, where are global hotpots of spinescence in palms? Is the distribution of spinescence related to the distribution of extant and extinct mammalian mega-herbivores?

For this master project in plant evolution, familiarity with spatial analyses and with the program R is desired but not required.

Contact: Christine Bacon,

Developing models for rainforest evolution

Evolution, tropical forest, diversity patterns

Palms have been recorded in the fossil history of tropical rainforests since they first emerged (see Wing et al. 2009, depicted below). Along with other mega-thermal angiosperms, those that are frost-intolerant and have physiological requirements that largely constrain them to tropical environments, they have been proposed as models for rainforest evolution.In this project we explicitly test the idea of palms being models for tropical rainforest presence or absence at a global-scale. Using data from transects, we test whether their distribution matches current tropical biomes at various geographical scales.

For this master project in evolution/conservation, familiarity with spatial analyses and with the program R is desired but not required.

Contact: Christine Bacon,

Evolution of tropical ants in changing geography and climate

Evolution, biogeography, Indo-Pacific

Ever wondered why the tropics are so blooming in life? This is your opportunity to contribute in research trying to figure out what may explain the diversity of species we observe today!

The project focuses on two ant groups having remarkable differences in life histories: the genus Anonychomyrma is enrolled in mutualisms with plants and prefers moist environments; ants in the genus Iridomyrmex are aggressive scavengers and prefers drier environments. The aim of the study is to estimate the ants’ responses (timing and direction of dispersal) to geographical, climate, and sea-level change over the past 20 million years, and to find out whether those responses happened as a result of different adaptations (evolved mutualisms, nesting in dry habitats).

The successful applicant will get access to a unique DNA-sequence dataset of ants collected in remote places (Melanesia) over more than 10 years (2002-2015).

For this master project in evolution/biogeography, familiarity with phylogenetic analyses and with the program R is desired but not required.

Contact: Pavel Matos,

University of Copenhagen, Denmark

No projects available at the moment.

University of Oslo, Norway

No projects available at the moment.

Norwegian University of Science and Technology, Norway

No projects available at the moment.