Phylogeny of the Formicoxenus genus-group (Hymenoptera: Formicidae) reveals isolated lineages of Leptothorax acervorum in the Iberian Peninsula predating the Last Glacial Maximum

The Formicoxenus genus-group comprises six genera within the tribe Crematogastrini. The group is well known for repeated evolution of social parasitism among closely related taxa and cold-adapted species with large distribution ranges in the Nearctic and Palearctic regions. Previous analyses based on nuclear markers (ultraconserved elements, UCEs) and mitochondrial genes suggest close relationship between Formicoxenus Mayr, 1855, Leptothorax Mayr, 1855 and Harpagoxenus Forel, 1893. However, scant sampling has limited phylogenetic assessment of these genera. Also, previous phylogeographic analyses of L. acervorum (Fabricius, 1793) have been limited to its West-Palearctic range of distribution, which has provided a narrow view on recolonization, population structure and existing refugia of the species. Here, we inferred the phylogenenetic history of genera within the Formicoxenus genus-group and reconstructed the phylogeography of L. acervorum with more extensive sampling. We employed four datasets consisting of whole genomes and sequences of the COI. The topologies of previous nuclear and our inferences based on mitochondrial genomes were overall congruent. Further, Formicoxenus may not be monophyletic. We found several monophyletic lineages that do not correspond to the current species described within Leptothorax, especially in the Nearctic region. We identified a monophyletic L. acervorum lineage that comprises both Nearctic and Palearctic locations. The most recent expansion within L. acervorum probably occurred within the last 0.5 Ma with isolated populations predating the Last Glacial Maximum (LGM), which are localized in at least two refugial areas (Pyrenean and Northern plateau) in the Iberian Peninsula. The patterns recovered suggest a shared glacial refugium in the Iberian Peninsula with cold-adapted trees that currently share high-altitude environments in this region.

Hybridization and introgression are prevalent in Southern European Erysimum (Brassicaceae) species

Background and Aims: Hybridization is a common and important force in plant evolution. One of its outcomes is introgression - the transfer of small genomic regions from one taxon to another by hybridization and repeated backcrossing. This process is believed to be common in glacial refugia, where range expansions and contractions can lead to cycles of sympatry and isolation, creating conditions for extensive hybridization and introgression. Polyploidization is another genome-wide process with a major influence on plant evolution. Both hybridization and polyploidization can have complex effects on plant evolution. However, these effects are often difficult to understand in recently evolved species complexes. Methods: We combined flow cytometry, transcriptomic and genomic analyses, and pollen-tube growth assays to investigate the consequences of polyploidization, hybridization, and introgression on the recent evolution of several Erysimum (Brassicaceae) species from the South of the Iberian Peninsula, a well-known glacial refugium. This species complex differentiated in the last 2Myr, and its evolution has been hypothesized to be determined mainly by polyploidization, interspecific hybridization, and introgression. Key Results: Our results support a scenario of widespread hybridization involving both extant and ghost taxa. Several taxa studied here, most notably those with purple corollas, are polyploids, likely of allopolyploid origin. Moreover, hybridization in this group might be an ongoing phenomenon, as prezygotic barriers appeared weak in many cases. Conclusions: The evolution of Erysimum spp. has been determined by hybridization to a large extent. The adaptive value of such genomic exchanges remains unclear, but our results indicate the importance of hybridization for plant diversification across evolutionary scales.

Mitogenome Phylogeny Including Data from Additional Subspecies Provides New Insights into the Historical Biogeography of the Eurasian lynx Lynx lynx

Previous molecular studies of the wide-ranging Eurasian lynx Lynx lynx focused mainly on its northern Palearctic populations, with the consequence that the reconstruction of this species’ evolutionary history did not include genetic variation present in its southern Palearctic distribution. We sampled a previously not considered Asian subspecies (L. l. dinniki), added published data from another Asian subspecies (L. l. isabellinus), and reassessed the Eurasian lynx mtDNA phylogeny along with previously published data from northern Palearctic populations. Our mitogenome-based analyses revealed the existence of three major clades (A: Central Asia, B: SE Europe/SW Asia, C: Europe and Northern Asia) and at least five lineages, with diversification in Lynx lynx commencing at least 28kyr earlier than hitherto estimated. The subspecies L. l. isabellinus harbors the most basal matriline, consistent with the origin of Lynx lynx in this subspecies’ current range. L. l. dinniki harbors the second most basal matriline, which is related to, and may be the source of, the mtDNA diversity of the critically endangered Balkan lynx L. l. balcanicus. Our results suggest that the Anatolian peninsula was a glacial refugium for Eurasian lynx, with previously unconsidered implications for the colonization of Europe by this species.

Phylogeography of Prunus armeniaca L. revealed by chloroplast DNA and nuclear ribosomal sequences

To clarify the phytogeography of Prunus armeniaca L., two chloroplast DNA fragments (trnL-trnF and ycf1) and the nuclear ribosomal DNA internal transcribed spacer (ITS) were employed to assess genetic variation across 12 P. armeniaca populations. The results of cpDNA and ITS sequence data analysis showed a high the level of genetic diversity (cpDNA: HT = 0.499; ITS: HT = 0.876) and a low level of genetic differentiation (cpDNA: FST = 0.1628; ITS: FST = 0.0297) in P. armeniaca. Analysis of molecular variance (AMOVA) revealed that most of the genetic variation in P. armeniaca occurred among individuals within populations. The value of interpopulation differentiation (NST) was significantly higher than the number of substitution types (GST), indicating genealogical structure in P. armeniaca. P. armeniaca shared genotypes with related species and may be associated with them through continuous and extensive gene flow. The haplotypes/genotypes of cultivated apricot populations in Xinjiang, North China, and foreign apricot populations were mixed with large numbers of haplotypes/genotypes of wild apricot populations from the Ili River Valley. The wild apricot populations in the Ili River Valley contained the ancestral haplotypes/genotypes with the highest genetic diversity and were located in an area considered a potential glacial refugium for P. armeniaca. Since population expansion occurred 16.53 kyr ago, the area has provided a suitable climate for the population and protected the genetic diversity of P. armeniaca.

Phylogeography of Aphanius fasciatus (Osteichthyes: Aphaniidae) in the Mediterranean Sea, with a focus on its conservation in Cyprus

Aphanius fasciatus is a small fish occurring in Mediterranean brackish environments. In Cyprus it is known from three localities separated by long stretches of coast. The genetic diversity of these populations was evaluated using fragments of two mitochondrial genes. A comparison with the other available data showed that Cyprus populations represent a distinct lineage. The other lineages are concentrated in a relatively small area between the Strait of Sicily and the Western Ionian Sea, while all other areas include a subset of these lineages, suggesting that the aforementioned area might have acted as a glacial refugium. Landlocked North-African populations diverge from all other populations, suggesting that they might have originated in the Late Pleistocene, during transgression events of the Mediterranean Sea in North-African inland water bodies. The genetic diversity of A. fasciatus varied across different Cyprus populations, with a pattern mirroring the degree of environmental degradation, which likely affected population genetic variability through demographic reductions. The three Cyprus populations showed genetic uniqueness, suggesting the need of population-based management practices; the low genetic diversity of two populations, and the number of threats affecting them, suggest that the species should be considered endangered at national level and deserves protection measures.

Fine-Scale Spatial Patterns of the Genetic Diversity of European Beech (Fagus sylvatica L.) around a Mountainous Glacial Refugium in the SW Balkans

Beech (Fagus sylvatica L.) is one of the most important forest trees in Europe and its current broad expanse over the continent is believed to be the outcome of the Holocene postglacial expansion of lineages originating from different glacial refugia. Studies using gene markers, pollen profiles and fossils suggest the main locations of glacial refugia in Southern Europe. In this study, we conduct a fine-scale genetic study on the beech populations surrounding the Almopia basin, an area that is said to have hosted one of the main European glacial refugia for several plant and animal species during the Pleistocene Epoch. We test the hypothesis of the existence of a local refugium in the study area for beech to understand the spatial genetic pattern of the putative refugial beech populations in the area and to investigate possible genetic connections between the local beech populations and the European expansion of the species. The genetic diversity of 100 sampled trees in 20 plots representing the expansion of beech in the area was studied using chloroplast and nuclear DNA microsatellites (cpSSR and nSSR, respectively). All three cpSSR regions were polymorphic, resulting in eight haplotypes, separated spatially in two distinct groups (one on the western and the other on the eastern part of the Almopia basin) that correspond to two different postglacial beech lineages. Furthermore, the cpSSR sequences of the eastern lineage are genetically identical to those of beech populations extending over central and northern Europe. The nSSR markers were highly polymorphic, and the trees studied were separated into two genetic groups that coincided with the cpSSR ones in locations where the topography is more pronounced. These results indicated that the Almopia region was indeed a major refugium for beech that possibly produced two main postglacial lineages for Europe, one of which is connected with the majority of beech populations growing on the continent. These southern refugial populations are important diversity centers that need to be the subject of special management and conservation.

Post-glacial expansion dynamics, not refugial isolation, shaped the genetic structure of a migratory bird, the Yellow Warbler (Setophaga petechia)

During the glacial periods of the Pleistocene, swathes of the Northern Hemisphere were covered by ice sheets, tundra and permafrost leaving large areas uninhabitable for temperate and boreal species. The glacial refugia paradigm proposes that, during glaciations, species living in the Northern Hemisphere were forced southwards, forming isolated, insular populations that persisted in disjunct regions known as refugia. According to this hypothesis, as ice sheets retreated, species recolonised the continent from these glacial refugia, and the mixing of these lineages is responsible for modern patterns of genetic diversity. However, an alternative hypothesis is that complex genetic patterns could also arise simply from heterogenous post-glacial expansion dynamics, without separate refugia. Both mitochondrial and genomic data from the North American Yellow warbler (Setophaga petechia) shows the presence of an eastern and western clade, a pattern often ascribed to the presence of two refugia. Using a climate-informed spatial genetic modelling (CISGeM) framework, we were able to reconstruct past population sizes, range expansions, and likely recolonisation dynamics of this species, generating spatially and temporally explicit demographic reconstructions. The model captures the empirical genetic structure despite including only a single, large glacial refugium. The contemporary population structure observed in the data was generated during the expansion dynamics after the glaciation and is due to unbalanced rates of northward advance to the east and west linked to the melting of the icesheets. Thus, modern population structure in this species is consistent with expansion dynamics, and refugial isolation is not required to explain it, highlighting the importance of explicitly testing drivers of geographic structure.

Mollusc successions reveal northward postglacial shifts of Alpine species ranges (Bohemian Massif, Czech Republic)

The Alps are an important hotspot of species diversity and endemism, as well as a presumed glacial refugium of several species’ groups including land snails. The recent ranges of Alpine endemics are well known, but their fluctuations during the postglacial period mirroring local climate changes are understudied. By analysing five Late Glacial and Holocene mollusc successions from two areas in the southernmost part of the Bohemian Massif (Czech Republic) situated about 100 km north of the Alps, we reveal details of these fluctuations. The Alpine endemic rocky dweller Chilostoma achates had reached the southern part of the Bohemian Massif already in the Late Glacial and disappeared in the Mid-Holocene canopy forest optimum. On the contrary, the northern boundaries of Alpine canopy forest epigeic snails extended further north than today at the turn of the Middle and Late-Holocene, pointing to a more favourable forest microclimate. The earliest known occurrences of several temperate canopy forest central European species, especially Causa holosericea and Discus perspectivus, imply the role of different areas in the Alps as their glacial refugia.