Purifying Selection, Density Blocking and Unnoticed Mitochondrial DNA Diversity in the Red Deer, Cervus elaphus

Abstract

The trajectories of postglacial range expansions, the occurrence of lineage patches and the formation and maintenance of secondary contact between lineages may mostly reflect neutral demographic processes, including density blocking, that may leave long-lasting genetic signatures. However, a few studies have recently shown that climate may also play a role. We used red deer, a large, mobile herbivore that is assumed to be sensitive to climate change, to test hypotheses of possible selection on the mitochondrial DNA cytochrome b gene (mtDNA cytb) and competitive and/or density-blocking (using mtDNA control region). We searched for a possible link between the phylogeographic structure and abiotic climatic variables. Finally, we tested for isolation by distance and isolation by environment and assessed the impact of human-mediated translocations on the genetic structure of red deer. Our analysis of 30 red deer populations in Poland using the mtDNA control region (N = 357) and cytochrome b (N = 50) markers not only confirmed the presence of the Western and South-Eastern lineages of the species but also indicated the presence of a previously unnoticed, rare relic haplotype that grouped together C. e. italicus from Italy (the Mesola deer). No significant signs of positive selection were detected for the mtDNA cytb gene in the studied red deer. However, a significant signal for purifying selection was found in our study that may explain the narrowness of the contact zone because gene flow between the Western and South-Eastern lineages should drive relatively strong mito-nuclear incompatibilities. MtDNA control region differentiation among red deer populations in Poland correlated with different abiotic climatic variables. Strikingly, the southernmost ice sheet limits during the Elsterian was the most important factor, and it explained the largest amount of variation. However, neither isolation by distance (IBD) nor isolation by environment (IBE) were recorded, and a very limited impact of human translocations was evident. The above-mentioned results suggest that in contemporary red deer populations in Poland, the phylogeographic pattern is well preserved, and long-term processes (density and/or competitive blocking) still play a major role.

Phylogeography of the Tyrrhenian red deer (Cervus elaphus corsicanus) resolved using ancient DNA of radiocarbon-dated subfossils

“…3 ). The most recent study including Mesola red deer 56 found them to be highly divergent (as in the present study) and to be closely related to a rare haplotype found in the Polish Carpathians. This “Mesola lineage”, as the authors dubbed it, is in all likelihood identical to our haplogroup D and would thus include the Mesola deer, at least some maternal lineages in Eastern Europe and possibly C .…”

“…e . maral , the Mesola lineage 56 would turn out to be identical to what in the first large-scale phylogeographic study of red deer was called the Middle-Eastern lineage 4 or haplogroup D (present study).…”

Subspecies dynamics in space and time: A study of the red deer complex using ancient and modern DNA and morphology

“…These findings are corroborated in the network(Figure 3): the maral haplotypes from Turkey and the Caucasus are highly genetically diverse, falling far from the main Western/Central European cluster, but group with the Italian samples from the southern Apennines and Mesola. The latter were recently suggested as a separate subspecies, C. e. italicus, byZachos, Mattioli, Ferretti, and Lorenzini (2014), and their mitochondrial relationship to marals has been supported based on fossil and molecular evidence(Borowski et al, 2016;Croitor & Cojocaru, 2016). C. e. maral distantly connects Western Asian and European deer to the Central Asian subspecies (C. h. yarkandensis, bactrianus and hanglu) and to East Asian wapitoids(Figure 3).5 Central Asian elaphoids, C. h. bactrianus, yarkandensis and hanglu, together form a monophyletic clade, with bactrianus Rom.…”

Genetic diversity, genetic structure and diet of ancient and contemporary red deer (Cervus elaphus L.) from north-eastern France

“…La Petite-Pierre). Based on 331 bp of d-loop AVd4 showed 100% similarity to red deer sequences from Poland (HQ534304, HQ534309, HQ534310, KX496902, KX496903, KX496905, KX496915) [ 69 , 70 ], and the Czech Republic (KM410131) [ 71 ].…”