1. Introgression among maternal lineages inferred from complete mitogenomes and molecular dating helps resolve phylogeography of European roe deerElena Bužan, Stefan Cidilko, Luka Duniš, Tilen Komel, Boštjan Pokorny, A. J. M. Hewison, Anna Korzekwa, 2026, original scientific article Abstract: Background The European roe deer (Capreolus capreolus) is one of the most widespread ungulates in Europe, with a phylogeographic structure mainly shaped by Pleistocene glacial cycles and secondary contacts with the Siberian roe deer (C. pygargus). Methods We sequenced 52 complete mitogenomes of C. capreolus from Slovenia, Poland and France, and combined them with 24 publicly available sequences of C. capreolus and C. pygargus, yielding an alignment of 76 genomes representing 59 haplotypes (42 from C. capreolus and 17 from C. pygargus). Phylogeographic structure was assessed using a median-joining network, and divergence times were estimated using a time-calibrated Bayesian phylogeny based on mitochondrial coding regions, incorporating published ancient C. pygargus mitogenomes. We additionally screened mitochondrial protein-coding genes for selection. Results The haplotype network recovered the three major European roe deer clades (Eastern, Central, and Western) and detected Central-clade haplotypes in France. Two Polish haplotypes (Cp9 and Cp10), detected in C. capreolus, clustered within the C. pygargus mitochondrial lineage, supporting mitochondrial introgression. Time-calibrated phylogenies placed introgressed haplotypes within established C. pygargus lineages. Selection analyses provided limited evidence for episodic positive selection restricted to a small number of codons. Conclusions Whole mitogenomes improve resolution of roe deer phylogeography and reveal introgressed maternal lineages, while time-calibrated phylogenies and selection tests add evolutionary context for interpreting mtDNA diversity in genus Capreolus.
Keywords: mitogenome, introgression, Bayesian molecular dating, Roe deer, phylogeography
Published in RUP: 15.07.2026; Views: 511; Downloads: 14
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2. Bridging mountains and seas : genomic and plastid data evidence for two migration routes of Drypis spinosa across the Adriatic–Ionian regionPeter Glasnović, Ivan Radosavljević, Sara Laura Šarančić, Damjan Mitić, Boštjan Surina, 2026, original scientific article Abstract: Aim Amphi–Adriatic–Ionian plant taxa, distributed on both the Balkan and Apennine peninsulas, exemplify one of the many diversity patterns characteristic of the Mediterranean biodiversity hotspot. To better understand these patterns, we examined the genetic and morphological variability, as well as the present day and Last Glacial Maximum (LGM) potential distribution of a scree-dwelling plant endemic to the study region. Location Amphi–Adriatic–Ionian region within the Mediterranean basin. Taxon Drypis spinosa L. (Caryophyllaceae). Methods Population genomics and phylogeographic patterns were investigated by analysing single–nucleotide polymorphisms (SNPs) and plastid DNA markers. Morphometric techniques were additionally used to assess taxonomic relationships. Environmental niche modelling (ENM) was applied to evaluate potential occurrences under present-day and LGM conditions. Results Genetic data revealed concordant patterns of genetic diversity, indicating that the mountainous areas of the western Balkans harbour the highest genetic variability in D. spinosa. Historical connections were detected among populations from the Kvarner area, the central and southern Apennines, and the Scardo–Pindic Mountains. Neither molecular nor morphological analyses supported the historically proposed lower-rank taxonomic distinctions. ENM suggests a substantial increase in favourable conditions during the LGM compared to the present day. Main Conclusions Our findings indicate two primary links between the Balkan Peninsula and the Apennines: one spanning the northern and central Adriatic Sea, involving populations from the Kvarner area and the central Dinaric Alps, and another connecting the Scardo–Pindic Mountains across the Ionian Sea. This reveals a biogeographical pattern not previously documented in plants with an Amphi–Adriatic–Ionian distribution.
Keywords: Amphi–Adriatic–Ionian distribution, environmental niche modelling, genomics, Mediterranean, morphometrics, phylogeography, plastid DNA
Published in RUP: 25.05.2026; Views: 618; Downloads: 14
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3. Population genomics and the environmental drivers of population structure in a cosmopolitan marine predator, Tursiops truncatusDaniel M. Moore, André E. Moura, Ada Natoli, Elena Papale, Mónica A. Silva, Tilen Genov, Stefania Gaspari, Giuseppa Buscaino, Per Berggren, A. Rus Hoelzel, 2025, original scientific article Abstract: The marine environment comprises vast regions without physical barriers to movement, making the understanding of population isolation and the evolution of diversity challenging. This is especially the case for highly mobile marine species. Here we investigate populations of the common bottlenose dolphin (Tursiops truncatus) across the Mediterranean Sea and adjacent North Atlantic using high-resolution genomic markers (RADseq) and stable isotope analyses to better understand the evolution of population structure in this system. High-resolution genomic data and broad geographic sampling revealed patterns of structure not previously identified, and integration with stable isotope data suggests that prey choice varies across this region. Unexpected patterns included genetic and isotopic similarity between the North Atlantic and the region around Sicily (but not including the medially located Gulf of Cádiz and surrounding regions). The regional habitat within and beyond the Mediterranean Sea is structured with ocean frontal systems including thermal and halocline transitions, several of which show alignment with genetic transitions within our data. Our data help to distinguish among possible drivers of population differentiation for a marine predator that has the potential for long-distance dispersion. 1 Introduction
Keywords: genomics, phylogeography, population structure, stable isotopes, Tursiops truncatus
Published in RUP: 27.12.2025; Views: 1054; Downloads: 7
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4. Drivers of population structure of the bottlenose dolphin (Tursiops truncatus) in the Eastern Mediterranean SeaStefania Gaspari, A. P. Scheinin, Draško Holcer, Caterina Maria Fortuna, Chiara Natali, Tilen Genov, Alexandros Frantzis, Guido Chelazzi, André E. Moura, 2015, original scientific article Keywords: bottlenose dolphin, Tursiops truncatus, population structure, phylogeography, Mediterranean Sea, gene flow
Published in RUP: 15.10.2015; Views: 6080; Downloads: 130
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5. Patterns of plastid DNA differentiation in Erythronium (Liliaceae) are consistent with allopatric lineage divergence in Europe across longitude and latitudeLázsló Bartha, Gábor Sramkó, Polina A. Volkova, Boštjan Surina, Alexander L. Ivanov, Horia Banciu, 2015, original scientific article Keywords: Karpati, kriptični refugiji, disperzija, kontinentalno-oceanski gradient, Carpathian Basin, cryptic northern refugia, long distance dispersal, ocenic-continental gradient, phylogeography, temperate species
Published in RUP: 15.10.2015; Views: 5603; Downloads: 223
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7. Multiple pleistocene refugia and post-glacial colonization in the European chub (Squalius cephalus) revealed by combined use of nuclear and mitochondrial markersMária Seifertová, Josef Bryja, Martina Vyskočilová, Natália Martínková, Andrea Šimková, 2012, original scientific article Abstract: To analyse patterns of nuclear and mitochondrial genetic variation in the European chub, Squalius cephalus (Linnaeus, 1758), in order to understand the evolutionary history of this species and to test biogeographical hypotheses for the existence of co-distributed European freshwater fish species
Keywords: freshwater fish, European chub, Squalius cephalus, glacial refugia, Cytochrome b, microsatellites, phylogeography, population structure, Europe
Published in RUP: 15.10.2013; Views: 6910; Downloads: 413
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8. Quaternary range dynamics of ecologically divergent species (Edraianthus serpyllifolius and E. tenuifolius, Campanulaceae) within the Balkan refugiumBoštjan Surina, Peter Schönswetter, Gerald M. Schneeweiss, 2011, original scientific article Abstract: We investigated Quaternary range dynamics of two closely related but ecologically divergent species (cold-tolerant Edraianthus serpyllifolius and thermophilic Edraianthus tenuifolius) with overlapping distribution ranges endemic to the western Balkan Peninsula, an important yet understudied Pleistocene refugium. Our aims were: to test predictions of the 'refugia-within refugia' model of strong genetic subdivisions due to population isolation in separate refugia; to explore whether two ecologically divergent species reacted differently to Pleistocene climatic fluctuations; and to test predictions of the displacement refugia model of stronger differentiation among populations in the thermophilic E. tenuifolius compared with the cold-tolerant E. serpyllifolius
Keywords: Campanulaceae, Edraianthus, phylogeography, plant migartion, Dinaric Alps, dispersal barriers, refugium, Pleistocene
Published in RUP: 15.10.2013; Views: 7148; Downloads: 445
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