Munch Lab

Waiting for good mutations

We know intuitively that individuals from small isolated populations are often more related with each than individuals in large populations are. Whereas closely related individuals have a shared relative in the recent past, distantly related individuals will have to look back many many generations to find such a common ancestor. This leaves more time for genomic mutations to produce differences between the two individuals, and this is why individuals from large populations show more differences between their genomes than individuals from a small one do.

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Current research

Our goal is to understand how mutation, selection and recombination together shape genetic variation, the evolution of genomes and the formation of new species. We develop and apply population genetic method on full genomes to address these questions in both living and ancestral species.

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Research overview

The technological advances in genomic sequencing now make it possible to characterise the genetic variation of any living species. However, the interpretation of these vast amounts of data requires a deep understanding of the evolutionary mechanisms that produce the observed variation as well as computationally efficient methods for their analysis. By combining development of new genetic theory and efficient implementation of computations, my research program focuses on the fundamental mechanisms that produce genetic variation. I strongly believe that groundbreaking research in this field requires a highly collaborative approach and I happily maintain a international network of research partners.

Recent progress

2014-12-12-Cover-AvianTogether with a large group of researchers I recently published an analysis of 48 bird genomes. Along with other works from this consortium, published as a special issue by Science, the analysis of these full size genomes provides a highly resolved phylogenetic tree describing the rapid diversification of birds that followed the decline of the dinosaurs. The analysis also shows that many groups of birds exhibit high levels of incomplete lineage sorting, with the result that their phylogenetic relationships often change along the genomes.
September_CoverThe seven publications in 2014 also includes a paper in Genome Research showcasing new population genetic insights that let me measure the rate of genetic recombination in species ancestral to those living today. In a commissioned review, which made the front page of BioEssays, I elaborate on these ideas and describe how this new approach makes it is possible to gain new important insight into how the genome controls recombination and how recombination in turn influences genome evolution. My current work follows this line new line of research.

Current research

My overarching interest is in developing and applying population genetic methods on genome scale data sets to understand the forces that govern the evolution of genomes and the emergence of new species. I am currently working  on methods for inference of recombination patterns in ancestral populations that applies coalescent hidden Markov models to full genome data. I have published a recombination map of the human-chimpanzee ancestor that allowed me to study the changes recombination patterns that occurred in humans and chimpanzees since these species separated. I am currently working on extending this approach to all the species ancestral to the great apes and I expect that this analysis will expose how recombination patterns evolve and how recombination drives non-adaptive evolution of genomes.

Selected publications

A fine-scale recombination map of the human–chimpanzee ancestor reveals faster change in humans than in chimpanzees and a strong impact of GC-biased gene conversion
Munch K, Mailund T, Dutheil JY, Schierup MH
Genome Research (2014) 24: 467-47

Unraveling recombination rate evolution using ancestral recombination maps (Comissioned review)
Munch K, Schierup MH, Mailund T
BioEssays (2014) 36:9 892–900

The bonobo genome compared with the chimpanzee and human genomes
Prüfer K, Munch K, Hellmann I, Akagi K, Miller JR, Walenz B, Koren S, Sutton G, Kodira C, Winer T, Knight JR, Mullikin JC, Meader SJ, Ponting CP, Lunter G, Higashino S, Hobolth A, Dutheil J, Karakoc E, Alkan C, Sajjadian S, Catacchio CR, Ventura M, Marques-Bonet T, Eichler EE, Andre C, Atencia R, Mugisha L, Patterson P, Siebauer M, Good JM, Fischer A, Ptak SE, Lachmann M, Symer D, Mailund T, Schierup MH, Andres AM, Kelso J, Paabo S
Nature (2012) 486 527-31

Great ape genetic diversity mapped

The genomes of the great apes have been sequenced with the Gorilla and Bonobo genomes completing the picture last year. This gave us valuable new information about the patterns of genetic differences between humans and the other great apes and a detailed picture of the ancestral relationship of this group of species.

Grafic Bickerstaff I, Clee PS, Drass J, Gadsby E, Idoaga A, Sudmant P
Grafic Bickerstaff I, Clee PS, Drass J, Gadsby E, Idoaga A, Sudmant P

Until now, however, we have lacked a comparable account of the differences of individuals within each species. As part of an international collaboration we publish today in Nature a deep survey of the genetic diversity of the species and subspecies of great apes. This shows that several of the apes including the Orangutan have genetic diversities that dwarf that of humans: where two humans show one difference for each thousand positions in the genome the orangutan sports two.The larger genetic diversity of apes allows us to peak further into the evolutionary past of these species to better understand the mechanisms shaping genomes as species evolve. The close relationship of humans and the other great apes means that a better knowledge of these processes will also over time contribute a better understanding of human evolution. Among other results analysis of the 78 genomes sequenced in this study has produced a first full picture of great ape evolution integrating within-species history with the more ancient history of how these species arose from common ancestors.

Knowledge of the patterns of diversity is also crucial in distinguishing the different subspecies of Chimpanzees, Gorillas and Orangutans and will aid zoos in planning of breeding programs to keep separate the different subspecies in captivity and thereby conserving their individual characteristics.