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. 2024 Feb 12;14(1):3015.
doi: 10.1038/s41598-023-48112-6.

Ancient and modern DNA track temporal and spatial population dynamics in the European fallow deer since the Eemian interglacial

K H Baker  1 , H W I Gray  1 , A M Lister  2 , N Spassov  3 , A J Welch  1 , K Trantalidou  4 , B De Cupere  5 , E Bonillas  1 , M De Jong  1 , C Çakırlar  6 , N Sykes  7 , A R Hoelzel  8
Affiliations

Ancient and modern DNA track temporal and spatial population dynamics in the European fallow deer since the Eemian interglacial

K H Baker et al. Sci Rep. .

Abstract

Anthropogenic factors have impacted the diversity and evolutionary trajectory of various species. This can be through factors such as pressure on population size or range, habitat fragmentation, or extensive manipulation and translocation. Here we use time-calibrated data to better understand the pattern and processes of evolution in the heavily manipulated European fallow deer (Dama dama). During the Pleistocene, fallow deer had a broad distribution across Europe and were found as far north as Britain during the Eemian interglacial. The last glacial period saw fallow deer retreat to southern refugia and they did not disperse north afterwards. Their recolonisation was mediated by people and, from northern Europe and the British Isles, fallow deer were transported around the world. We use ancient and modern mitochondrial DNA (mtDNA) and mitogenomic data from Eemian Britain to assess the pattern of change in distribution and lineage structure across Europe over time. We find founder effects and mixed lineages in the northern populations, and stability over time for populations in southern Europe. The Eemian sample was most similar to a lineage currently in Italy, suggesting an early establishment of the relevant refuge. We consider the implications for the integration of anthropogenic and natural processes towards a better understanding of the evolution of fallow deer in Europe.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Map figure showing the distribution of sample sites by location and age in the European region. Translocated samples from Sweden, Barbuda and Canada are not shown. Darker grey shading is the approximate modern distribution (after https://www.iucnredlist.org/species/42188/10656554).
Figure 2
Figure 2
Bayesian inferred phylogenies for ancient-only and modern-only D. dama mtDNA control region haplotypes, generated using MrBayes. The trees illustrate a similar topology that persists over time. Posterior probability support values are presented at nodes. Colours refer to collection localities and time periods. Scale bar = substitutions per site.
Figure 3
Figure 3
Time-calibrated tree using an ancient-only D. dama mtDNA control region dataset. Generated in BEAST utilising the strict-clock and exponential growth demographic model. Bars correspond to 95% highest posterior density (HPD) of divergence estimates at each node. Colour bars at terminal nodes correspond to localities and time periods given in Fig. 2. Posterior probability support values are given at respective nodes. The ‘//’ symbol denotes a shortening of branch length for the outgroup. The values given at the root node are the divergence time estimate (Ka) followed by the 95% HPD in parentheses. The oldest haplotypes (from the Neolithic) are indicated with a red dot. Red and yellow colours show well-supported lineages.
Figure 4
Figure 4
Time-calibrated tree using the ancient-and-modern D. dama mtDNA control region dataset. Generated in BEAST utilising the strict-clock and exponential growth demographic model. Bars correspond to 95% highest posterior density (HPD) of divergence estimates. Posterior probability support values are given at respective nodes. The ‘//’ symbol denotes a shortening of branch length for the outgroup. The values given at the root node are the divergence time estimate (Ka) followed by the 95% HPD in parentheses. The oldest haplotypes (from the Neolithic) are indicated with a red dot. Red and yellow colours show well-supported lineages.
Figure 5
Figure 5
Time-calibrated tree using the mitogenome D. dama mtDNA dataset, including the haplotype from the Eemian. Generated in BEAST utilising the uncorrelated lognormal relaxed clock and the logistic growth demographic model. Bars at nodes correspond to 95% highest posterior density (HPD) of divergence estimates (Ma). Posterior probability support values are given at respective nodes. Only posterior probabilities less than one are shown. The ‘//’ symbol denotes a shortening of branch length for the outgroup. The values given at the two deepest nodes, representing divergences with Cervus elephus (root) and Megaloceros giganteus outgroups, are the divergence time estimates (Ma) followed by the 95% HPD in parentheses. Red and yellow colours show well-supported lineages.
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