Phylogenetics

In addition to genome-wide data, we also work with datasets sampling one or a small number of genetic loci. These datasets can be used to reconstruct gene trees to infer relationships among populations, as well as divergence times and changes in populations size. In these projects, we often make use of mitochondrial genome sequences from ancient samples, but we have also worked with multilocus datasets from extant animals and populations.

Sabre tooth cats

In a recent project working with Prof Michi Hofreiter’s Group in Potsdam, we used hybridisation capture to obtain partial mitochondrial genome sequences of extinct sabre-toothed cats (see Paijmans et al. 2017). This allowed us to reconstruct their evolutionary relationship to modern felids, as well as their divergence times.

We recovered genetic data from this mandible of a Late Pleistocene European sabre-toothed cat that was recovered from the North Seq (left). This allowed us to calculate a time calibrated phylogeny of extinct sabre-toothed cats (Homotherium and Smilodon) and their living relatives. See Paijmans et al. 2017.

Cave bear homing behaviour

Another project using mitochondrial genome sequences investigated cave bears from northern Spain (see Fortes et al. 2016). This project ran in collaboration with Gloria Fortes and Aurora Grandal-d’Anglade at the University of Coruna and Prof. Michi Hofreiter’s Group in Potsdam. Using a combination of radiocarbon and molecular dating, we showed that cave bears occupied five Spanish caves simultaneously and in close geographic proximity during the Late Pleistocene. Their mitochondrial haplotypes, however, segregate almost perfectly into their respective caves. Cave bear mothers would give birth to their cubs inside caves, and this genetic pattern indicates that the Spanish cave bears were returning to their birth caves for hibernation – the first record of this type of homing behaviour in cave bears.

The map shows five caves in northern Spain which were occupied simultaneously by cave bears. Their mitochondrial haplotypes segregate almost perfectly into these cave s(network bottom left), providing evidence of homing behaviour. See Fortes et al. 2016.

African vipers

A study published this year investigated the phylogeny and biogeography of the African viper genus Bitis. This group includes iconic snakes such as the puff adders and Gaboon vipers. Run in conjunction with Wolfgang Wüster at Bangor, and Krystal Tolley at the South African National Biodiversity Institute in Cape Town, this study provided the most comprehensively sampled multilocus phylogeny of the genus to date. Molecular dating also showed that open and arid habitat Bitis lineages diversified long before these habitats came to dominate African ecosystems, unlike open habitat mammals, whose diversification seems to have occurred synchronously with the open habitat expansion (see Barlow et al. 2019).

Mitochondrial phylogeny of Bitis highlighting the four major subgenera. See Barlow et al. 2018.
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