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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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.

Bonobo genome shows that bonobos and chimpanzees resemble us in separate ways

Most people think that the chimpanzee alone is our closest relative, but in fact there is a second ape, the bonobo, that we are just as related to. Humans split from the other apes 5-6 million years ago and only 1-2 million years ago the ancestor to bonobos and chimpanzees split into these two species. This likely happened when the Congo river formed, separating the two species – chimpanzees and bonobos do not swim. bonobos live south of the river in the Democratic Republic of Congo.

Although darker and more slender than chimpanzees they are similar in appearance, but they Ulindidiffer strikingly from chimpanzees in social and sexual behavior. In chimpanzees the male is the dominant sex, hierarchy and conflict resolution is based on aggression. In bonobos females are dominant, hierarchy is based on mother’s status and conflicts are resolved through sex. These strikingly different behavioral characteristics have made scientists dub the bonobo “the hippie ape” and “the make love not war ape”. Our collaborators at the Max Planck Institute for Evolutionary Anthropology in Leipzig tell us that if they throw a toy into a chimpanzee cage the chimpanzees with fight over it leaving the winner to play with it alone. If it is thrown into a bonobo cage everyone will have sex and then share the toy. Several of the social and sexual traits that are only found in one of these apes are also found in humans. The frequent non-conceptive sexual behavior is thus shared with humans but not with chimpanzees, lethal aggression is found in chimpanzees and humans but not in bonobos humans and bonobos are very playful whereas chimpanzees are less so, and chimpanzees and humans apply cooperative hunting whereas bonobos do not.

Today the bonobo genome is published in Nature revealing a detailed account of our relation to bonobos and chimpanzees. The genomic DNA was obtained from the female bonobo Ulindi from Leipzig zoo while she was anesthetized anyway by the dentist. The Bioinformatics Research Centre has participated in the bonobo genome consortium and I have led an effort contributing a bioinformatic analysis of the bonobo genome, the results of which define the topic of the paper published today. The bioinformatical approach we apply is unique because it combines the analysis of genetics within species with the genetics between species, combining these two traditionally separated fields into one model.

Comparing the bonobo genome to the already known genomes of humans and chimpanzees we have shown that for some parts of the genome (about 3%) it is not bonobos and chimpanzees that are most similar but humans and bonobos or humans and chimpanzees. This patchwork of genetic relatedness results because the three species are so closely related that they may share genes inherited from the common ancestor of all three species. 25% of our protein coding genes has parts that are more similar to bonobo or chimpanzee than these are to each other. Future research may reveal if any of these genes are responsible for traits we only share with one of these apes. A candidate could be the TAAR8 gene that has a variant only shared between humans and bonobos. The gene codes for a protein receptor that is known to help mice smell amines in urine and may provide social cues in bonobos.

Gorilla genome reveals our ancestry as genetic patchwork

The chimpanzee is our closest cousin in the tree of life. Humans and chimpanzees split into separate species about 5-6 million years ago. The gorilla is more remotely related to both humans and chimpanzees separating about 8 million years ago. Today the Gorilla genome is published in Nature revealing surprising properties of our own genetic history. As expected most of our genes are most similar to the ones of the chimpanzee, but it turns out that about many of our genes are more like gorilla genes than chimpanzee genes. The genetic material on chromosomes is mixed in sexual reproduction making each gene free follow its own path through evolution. Because human, chimpanzee and chimpanzee are quite equally related this results in mix of genes different kinds of relatedness. For most genes humans-and chimpanzees are most related, but 15% of chimpanzee genes are more related to the gorilla than to our genes and 15% of our genes are gorillas are more related to gorillas than to chimpanzees.

kamilahWe have elucidated this genetic patchwork that reflects the evolutionary history of humans, chimpanzees and gorillas. Analyzing these patterns has allowed us to firmly establish how important natural selection is to evolution of these species. They find that the genetic variation is smaller genes compared to the genome average because that natural selection removes mutations that disrupt gene function. The bioinformatical approach we apply is unique because it combines the analysis of genetics within species with the genetics between species, combining these two traditionally separated fields into one model. Our analyses also illuminate the process by which western and eastern gorillas split into separate sub-species. Although we commonly think of such speciations as happing at a distinct point in time, this does not always reflect reality. This study shows that the separation into western and eastern gorillas happened over an extended period of time.

No magic bullet explains Ice Age megafauna extinctions

mammothWas it humans or climate change that caused the extinctions of the iconic Ice Age mammals (megafauna) such as the woolly rhinoceros and woolly mammoth? For decades, scientists have been debating the reasons behind these enigmatic Ice Age mass extinctions, which caused the loss of a third of the large mammal species in Eurasia and two thirds of the species in North America. In an extensive, inter-disciplinary research collaboration, involving over 40 academic institutions around the world, we have tried to tackle the contentious question in the biggest study of its kind. As so often in science the answers turn out to be far more complicated than imagined. The study, published online today in Nature reveals that neither climate nor humans alone can account for the Ice Age mass extinctions. Using ancient megafauna DNA, climate data and the archaeological record, the findings indicate dramatically different responses of Ice Age species to climate change and humans. For example, the study shows that humans played no part in the extinction of the woolly rhino or the musk ox i Eurasia and that their demise can be entirely explained by climate change. On the other hand, humans aren’t off the hook when it comes to the extinction of the wild horse and the bison in Siberia. Our ancestors share responsibility for the megafauna extinctions with climate change. While the reindeer remain relatively unaffected by any of these factors, the causes of the extinction of the mammoths is still a mystery. Despite the unparalleled amount of data analysed in this study, we find no clear pattern distinguishing species that went extinct from species that survived, suggesting that it will be extremely challenging for experts to predict how existing mammals will
respond to future global climate change.