Biosystematics and evolutionary genomics

NTNU University Museum's research areas:

Biosystematics and evolutionary genomics

Biosystematics is the study of biological diversity, through the description of diversity and understanding of processes leading to evolutionary development.

The research focuses on deriving the history of all living beings on earth, through naming species, deriving relationships and understanding how species formation takes place.

Projects

Projects

DarwinPlants: DarwinPlants seeks to understand the genetic basis of the rapid evolution of diversity in a unique and threatened group of plants from the Galápagos Islands. Studies of the forms and distribution patterns of species on the world's oceanic island chains have provided scientists with major insights into the process of evolution. Among these chains is the Galápagos archipelago, where Charles Darwin collected the specimens and observations that would eventually lead to the formation of his theory of evolutionary change through natural selection. Daisy trees (genus Scalesia) are one special group of plants found only on the Galápagos islands. Within a relatively small time period (four million years), the plants evolved from a single ancestor into 15 different species with drastic variation in size and shape, as well as diversity of life habits and strategies. For this reason, these plants have been called 'the Darwin?s finches of the plant world'. The main objective of our project is to determine the genetic mechanisms that have allowed such a rapid and dramatic diversification in this group. Our team will use several advanced approaches to determine these mechanisms, including next-generation sequencing of the entire genome (DNA) and transcriptome (RNA) contained in hundreds of individual plants. We use this data to apply phylogenetic and population genetic methods to achieve our secondary objective, to reconstruct the evolutionary history of all of the Scalesia species.

Contact person: Michael D. Martin

Web page: darwin-plants.com

Project period: 2019-2023

Team: Michael D. Martin, José Cerca, Vanessa Bieker, Patricia Jaramillo, Lene Rostgaard Nielsen, Loren Rieseberg, Neelima R. Sinha, Rasmus Nielsen, Tom Gilbert, Gitte Petersen, Ole Seberg, Bent Petersen, Michael D. Nowak, Gonzalo Rivas-Torres, Mario Fernández-Mazuecos, Pablo Vargas

Understanding how—and how fast—organisms can respond to environmental change is key for predicting their resilience in facing global climate change. This is especially true in the Arctic, which is experiencing the most pronounced warming. Svalbard, an isolated, High-Arctic archipelago and the fastest warming site on Earth, is home to an endemic subspecies of wild reindeer that is uniquely adapted to its extreme Arctic home. Following colonization of Svalbard millennia ago, the population evolved several adaptations to this harsh and highly stochastic environment, including thick fur, a small body, a highly specialized diet, and altered metabolism. ColdRein seeks to directly assess how these isolated animals were able to adapt to a harsh and highly stochastic environment. To accomplish this, we will apply powerful evolutionary simulations and implement cutting-edge approaches to analyze hundreds of whole-genome sequences from modern reindeer populations from polar regions, including Svalbard. We will use this information to investigate how long-term changes in population size and dispersal reflect changes in the environment, such as gain or loss of sea ice corridors. Then, using genome sequences derived from ancient reindeer bones and antlers collected from the archipelago, we’ll look directly back in time through the history of Svalbard reindeer evolution, identifying the genetic changes that enabled the reindeer’s rapid evolution, and tracking these changes in time and space.

Contact person: Michael D. Martin

Project period: 2021-2025

Team: Michael D. Martin, Love Dalén, John Speakman, Brage Hansen, Eline Lorenzen, Knut Røed, Elzbieta Krol, Leif Egil Loe, Katerina Guschanski

BiGTREE is a HKdir-funded training network between Norway, Peru and Colombia. This network aims to provide training in cutting-edge genomics and bioinformation in the field of biodiversity genomics. Through this comprehensive scheme, Norwegian and Latin American students and staff will benefit from collaboration, increased knowledge, impacts, visibility, and reach of their research. Through mutual mobility and cooperation, our ultimate goal is to contribute towards the conservation of biodiversity and prediction of the impacts of climatic change. A major role of BiGTREE is to provide mobility scholarships to MSc students from Peru and Colombia to travel and stay in Norway for up to 3 months. Additionally, we provide funding for Norwegian students to travel and stay in either Peru or Colombia as part of their MSc project work.

Contact person: Michael D. Martin

Web site: bigtree-training.org

Team: Michael D. Martin, José Cerca, Sarah Martin, Jaime G. Morin Lagos, Dimitar Dimitrov, Nataliya Budaeva, Hugo de Boer, Inger Skrede, Letty Salinas, César Arana, Jorge Ramirez, Rina Ramirez, Diana Silva, Jimmy Cabra-Garcia, Yherson Franchesco Molina-Henao, Andrea Niño, Camilo Andres Salazar Clavijo, Adriana Corrales, Geimy Carolina Pardo Díaz, María del Rosario Castañeda, María Camila Pizano

Biodiversity estimates and red-list assessments will be flawed if undiscovered taxonomic diversity remains undetected. This project aims to reveal intraspecific genetic lineages (cryptic species) in red-listed species of lichens and vascular plants by combining genomic analyses (phytogeography and species delimitation) with distribution modelling. Both observation-only and specimen-based data will be used, including relevant old archived collections.

Contact person: Associate Professor Mika Bendiksby

Collaborators: Michael D. Martin, James Speed and Vibekke Vange (NTNU University Museum), Einar Timdal and Rune Halvorsen (Natural History Museum, University of Oslo) og Håkon Holien (NORD University).

Duration: 2017-ongoing

Funding: The Norwegian Biodiversity Information Centre (Norwegian Taxonomy Initiative) and the NTNU University Museum.

The principal purpose of the present study has been to elucidate evolutionary relationships within subfamily Lamioideae using various molecular tools. Objectives: (1) identify major phylogenetic groups within subfamily Lamioideae, reveal their interrelationships, and to update their classification accordingly; (2) infer the biogeographic history of subfamily Lamioideae and subgroups, and relate it to climatic and geological events of the past; and, (3) investigate allopolyploid speciation.

Contact person: Associate Professor Mika Bendiksby

Collaborators: Yasaman Salmaki (Univ. of Teheran), Olof Ryding (Natural History Museum of Denmark), Bryan Drew (Univ. of Nebraska)

Duration: 2002-ongoing

Funding: The Norwegian Research Council (project no: 154145), Natural History Museum (University of Oslo), and NTNU University Museum.

Extended project page.

Sea slugs, or nudibranchs, had not been studied at all in Norway the past 60 years, until our project was initialised in 1997. We are studying diversity of species and their distribution in Norwegian waters, in total about 100 species are known. Several taxonomic problems warrant species delimitation and description. We use DNA barcoding to map and study the nudibranch fauna, its diversity and distribution.

  • Contact person: Torkild Bakken (project leader)
  • Collaborators: Jussi Evertsen (Guri Kunna High School), Bernard Picton (National Museum of Northern Ireland), Alexander Martynov (Zoological Museum, University of Moscow).
  • Project period: 1997 – ongoing.

Polychaete worms are among the most abundant organisms in the seabed sediments. In Norwegian waters, about 700 species are known, and many unknown. The main aim of the project is to provide new knowledge of polychaetes from coastal areas to the deep sea. Taxonomic challenges of species and species groups are investigated in terms of species delimitation and description, with careful morphological assessments and DNA barcoding as main tools. Patterns of species distribution is of particular interest.

  • Contact person: Torkild Bakken (project leader)
  • Collaborators: Jon Anders Kongsrud (University Museum of Bergen, University of Bergen), Eivind Oug (NIVA).
  • Project period: 2009 – ongoing.
  • Financial support: The project have received support from the Norwegian Taxonomy Initiative, and Norwegian Deepwater Programme. 

Project site

Some genera of tribe Tanytarsini are very species rich, while others are rare and species poor. Some genera are geographically restricted while others are practically cosmopolitan. Some show special adaptations to the environment they live in while others are generalists.

In this project we wish to explore the evolutionary (phylogenetic) relationships among genera in Tanytarsini to:

  • Find the most likely evolutionary history of the tribe
  • See if geographical distribution and environmental adaptations can be explained by the phylogeny

 

Contact person: Professor Torbjørn Ekrem, researcher Elisabeth Stur

Collaborators: Erik Boström, NTNU Vitenskapsmuseet; Wojciech Giłka, Universitetet i Gdansk; Endre Willassen, Universitetsmuseet i Bergen

Project period: Ongoing

Funding: NTNU

In this project we apply recently developed spatial phylogenetics methods to explore spatial biodiversity within the entire vascular flora of Norway, which contains about 2880 plant species. For this, we use genetic sequence data both publicly available and derived from herbarium collections to analyse spatial patterns of vascular plant diversity, centres of endemism and phytogeographic regions that developed in response to recent cycles of glaciation.

Contact person: Michael Martin

Project period: 2016-2018.

This study is conducted in collaboration with Prof. Brent Mishler at University of California, Berkeley (California, USA).

Funding: NTNU University Museum.

Species of the chironomid genus Cricotopus are known from all geographical regions and have immature stages in running and standing water. Several species are difficult to separate on morphology and many are assumed to be unknown to science. Additionally, hybridization is thought to occur between some species. In collaboration with colleagues from USA and Japan we investigate the species boundaries of the sylvestris-group and use molecular and morphological data to analyze the species diversity.

Contact person: Researcher Elisabeth Stur

Collaborators: Prof. Torbjørn Ekrem (NTNU University Museum), Prof. Susan Gresens (Towson University, Maryland), Researcher Natsuko Kondo (NIES, Tsukuba).

Status: ongoing

Funded by NTNU, Towson University, NIES

Photo: Corynoneura male from Jonsvatn (Trondheim). Photo: Aina Mærk AspaasSpecies of the genus Corynoneura are among the smallest chironomids we know of. Most species are only 1-2 mm long. In this project, we revise existing species, examine types and describe species new to science. Genetic data and morphology are used in an integrative approach to analyze species boundaries and DNA barcodes are used to associate different life stages. The project utilizes material and data generated through previous projects funded by the Norwegian Taxonomy Initiative and NorBOL.

Contact: Researcher Elisabeth Stur

Project period: 2015-2020

Collaborators: Dr. Sofia Wiedenbrug (München), Prof. Torbjørn Ekrem

Funding: NTNU, private.

Domestication has had a tremendous effect on crop species—altering phenotypes, decreasing effective population sizes, and reducing genetic diversity. In addition to transforming the species under selection, it is increasingly understood that domestication also impacts crop pathogens. Ustilago maydis, the fungus that causes corn smut disease, has a paradoxical history as a scourge to farmers and a delicacy in Mexican cuisine. Surprisingly, genetic data suggest living U. maydis individuals—including those infecting the wild teosinte progenitor—descend from a common ancestor dating to the domestication of maize. To investigate whether recent maize breeding or propagation of the fungus for food may obscure the pathogen’s evolutionary history, we are sequencing genomes from historic corn smut collected at theUniversity of California Berkeley’s Jepson Herbarium and the U.S. National Fungus Collections. These historical samples are processed in the NTNU University Museum’s specialized Clean Lab. In addition, modern U. maydis accessions are being used to generate a genomic reference panel to provide context for the historic specimens.
Contact person: Associate professor Michael Martin

Collaborators: Assistant professor Benjamin Blackman (UC Berkeley), Dr. Nathan Wales (University of Toulouse)

Period: 2017-2018

Funding: Peder Sather Center for Advanced Study

Phytophthora infestans is a fungus-like organism that causes late blight disease of potatoes and which, after introduction to Europe in the 1840s, caused the Irish potato famine. Its ability to overcome the defenses of its potato host via rapid genome evolution makes P. infestans a persistent threat to global potato crops. Currently this threat can be definitely controlled only through repeated applications of fungicides. This project applies population genomic approaches to a diverse isolates collected from Mexico, the putative center of origin of P. infestans. We use bioinformatic tools to assess the diversity of infection-related genes in order to characterize future threats to global potato production. We are also examining global genetic structure in order to reconstruct this pathogen’s pathways of migration, as well as its evolutionary history on different New World hosts.

Contact person: Associate professor Michael Martin
Collaborators: Professor Niklaus Grunwald (Oregon State University), Assistant Professor Erica Goss (University of Florida), Dhirendra Niroula (NTNU)

Period: Ongoing

Funding: NTNU

The ragweeds (Asteraceae, genus Ambrosia) are a group of about 40 species of plants adapted to wind-pollination and largely native to North America. The center of diversity of this genus appears to be in the Sonoran Desert region of North America, although some species are widespread throughout North America, and others occur mostly in South America. Some species are desert plants, and many are also weedy pioneers. The most successful and widespread Ambrosia weed is the globally distributed invasive species Ambrosia artemisiifolia (common ragweed), which belongs to a highly specialized complex whose members range across North America. The evolutionary relationships between ragweed species are confused, especially in collections from the Caribbean, S. America, Europe, and West Africa. We are using low-depth genomic sequencing and de novo assembly tools to generate a whole chloroplast genome sequence for every member of the genus Ambrosia in an attempt to resolve the evolutionary relationships in this taxonomically difficult genus. Special focus will be given to A. maritima, which has a curious distribution in southern Europe, Israel, and possibly Africa, and may be the only ragweed species naturalized in the Old World.

Contact person: Associate professor Michael Martin
Collaborators: Professor Gerhard Karrer (University of Natural Resources and Life Science, Austria), Dr. Péter Poczai (University of Helsinki)

Period: Ongoing

Funding: NTNU

Studying invasive plants offers opportunities to answer fundamental evolutionary questions about whether parallel adaptation to similar introduced environments affects the same genomic regions. Ambrosia artemisiifolia (common ragweed) is an annual weed that is native to North America. In Europe, it became invasive upon introduction during the late 19th century and is today established on all continents except Antarctica. Its highly allergic pollen is the main cause of hay fever, and the plant presents a major cost to public health in many areas. We combine genomic data from historic herbarium sheets with modern data from both the native (North America) and introduced (Europe) ranges to infer temporal changes in the population structure.

Contact person: Associate professor Michael Martin
Collaborators: Assistant professor Kay Hodgins (University of Melbourne), Professor Tom Gilbert (University of Copenhagen), François Bretagnolle (University of Burgundy)

Period: 2016-2020

Funding: NTNU

The Galápagos archipelago is a hotspot of biodiversity and an invaluable microcosm for studying the processes of evolution. The islands are home to the endemic plant genus Scalesia, whose remarkable connection to Asteraceae (the daisy/sunflower family) was first recorded by Charles Darwin. All are descendants of a daisy-like ancestor from the west coast of South America that arrived to the newly forming volcanic islands less than 4 million years ago. Then occurred a rapid radiation into 17 species with herbaceous qualities and astounding morphological diversity that ranges from woody rainforest canopy species to small shrubs that grow directly from bare lava rock. Known as the botanical equivalent of Darwin’s finches, the plants are famously specialized even amongst the organic riches of the Galápagos, and many of these threatened species are important members of the islands’ endemic vegetation. But as their a rapid radiation left these species highly invariant at nuclear genetic markers, biogeographic relationships with the genus are still completely unknown. We are using diverse genomic approaches to explore the evolution and diversification of this fascinating group.

Contact person: Associate professor Michael Martin
Collaborators: Professor Tom Gilbert (University of Copenhagen), Professor Ole Seberg (University of Copenhagen), Assistant professor Gitte Pedersen (University of Stockholm)

Period: Ongoing

Funding: NTNU

Mapping uncharted diversity: a first comprehensive survey of lichenicolous fungi in Norway.

 

Contact person: Associate Professor Mika Bendiksby

Duration: 2020-2023

The project MULTIWHALE will study the complex question of how multiple stressors (anthropogenic pollutants, disturbance/whale watching activities and fluctuating prey resources) affect biological responses such as gene expression, endocrine, physiological, and behavioural responses at the individual and population level in Norwegian killer whales in the context of ecological differences within the population.

We combine field and modelling studies to understand the long term and short-term effects of multiple stressors, and if the effects are equal within the population. Some individuals eat seals in addition to fish, which may make them more susceptible to the effects of anthropogenic stressors.

The MULTIWHALE results are important for understanding of the cumulative response in killer whale health and status, conservation of killer whales in Norwegian waters, the management of their harvestable prey types (seals and fish), and for sustainable whale watching.

Contact person: Associate professor Andrew Foote

Web side: Multiwhale at UiO

Duration: 2021-2025

Norway is generally considered to host a large diversity of rotifer species, having perhaps 500 of the global 2000 species, based on gross best estimates. The majority is found in shallow freshwater locations. Thus, considering the current known species number is around 310 species in fresh water (347 in total across all nature types), this group holds a large potential for containing new species for Norway.

In addition to rotifers, we also expect that coastal fishless ponds may be a hotspot for groups of invertebrates within other taxa that are currently classified as red listed and may additionally host new species. Furthermore, by completing a barcode library for rotifers, these traditionally taxonomic demanding organisms will have a significantly decreased work load required for future distribution mapping.

Collaboration: 

  • Markus Majaneva, Norwegian Institute for Nature Research
  • Diego Fontaneto, Water Research Institute of Italy
  • Erling Brekke, Rådgivende Biologer A/S

Contact person: Glenn Dunshea

The main goal of this project is to discover new species to Norway and science. We will search for species currently known from the Alps and Arctic regions.

There will be a focus on species groups with high potential for discovering new species to science. In addition, the project aims at increasing the knowledge of the autecology and distribution of bryophytes in Norwegian mountains. This knowledge will be used to improve the Nature in Norway nature-type system (NiN) through generalized species lists.

Thirdly we aim at collecting fresh material of as many bryophyte taxa as possible for barcoding. Barcoding of Norwegian specimens will be an important contribution and a supplement to the ongoing barcoding of the Norwegian bryophyte flora.

The project is organized with six field meetings where national and international bryophyte experts meet up with master students and members from Moseklubben (Norwegian Bryological Society) to survey selected areas and exchange knowledge. 

Collaboration:

  • Hans H. Blom, NIBIO
  • Rune Halvorsen NHM, UiO
  • Torbjørn Høitomt and John Gunnar Bryjulvsrud, Biofokus
  • Magni O. Kyrkjeeide, NINA
  • Kristin Wangen, Miljøfaglig Utredning
  • Leif Appelgren, Ecofact
     

Info about project: Centre for Biodiversity Dynamics (CBD)

Contact person: Torbjørn Ekrem

Past projects biosystematics