The Convention on Biological Diversity (CBD) aims at the conservation of all three levels of biodiversity, that is, ecosystems, species and genes. Genetic diversity represents evolutionary potential and is important for ecosystem functioning. Unfortunately, genetic diversity in natural populations is hardly considered in conservation strategies because it is difficult to measure and has been hypothesised to co-vary with species richness. This means that species richness is taken as a surrogate of genetic diversity in conservation planning, though their relationship has not been properly evaluated. We tested whether the genetic and species levels of biodiversity co-vary, using a large-scale and multi-species approach. We chose the high-mountain flora of the Alps and the Carpathians as study systems and demonstrate that species richness and genetic diversity are not correlated. Species richness thus cannot act as a surrogate for genetic diversity. Our results have important consequences for implementing the CBD when designing conservation strategies.
The Carpathians belong to the main elements of the European Alpine System and have an important biogeographical location between the Balkan ranges in the South, the Alps in the West and the Scandinavian range in the North. However, until recently this area was rarely included in detailed phylogeographical studies that could bring insights into its biogeographical history, links with other mountain ranges and contemporary genetic structure of populations. Here, available phylogeographical studies on high‐mountain plants that include data concerning the Carpathians are reviewed in order to (1) discuss regional phylogeographical structure and divergence of the Carpathian populations from those in other European mountain ranges, and (2) outline further perspectives of the Carpathian phylogeography. Analysis of available studies revealed the complexity of the biogeographical history of high‐mountain plants. The studies show a deep phylogeographical structure in the Carpathians, mostly concurring with classical biogeographical boundaries, and suggesting a long‐term isolation and restricted gene flow between the main Carpathian regions. For some species, though, recent dispersal events among isolated mountain ranges were detected. Such contrasting patterns were found at a larger geographical scale as well (e. g., between the Carpathians and the Alps). Several examples suggest the importance of the Carpathians in migration of arctic‐alpine plants from the East and towards the North. In most reviewed studies, however, the Carpathians are only marginally represented and detailed intraspecific studies based on dense population coverage in all disjunct areas of species' ranges are clearly needed to obtain reliable information and confirm the preliminary phylogeographical patterns emerging from the overview presented here.
A survey of amplified fragment length polymorphism (AFLP) and chloroplast DNA (cpDNA) variation was conducted to elucidate the phylogeography of Campanula alpina, a key species of silicicolous alpine grasslands in the Carpathians with a disjunct distribution in the Eastern European Alps. The Carpathians experienced a different glacial history from the Alps: local glaciers were present only in the highest massifs, while alpine habitats extended over larger areas related to their present distribution in this region. We asked: (i) whether in the Carpathians a high-mountain plant exhibits a complex phylogeographical structure or rather signatures of recent migrations, and (ii) whether the disjunct part of the species' distribution in the Alps resulted from a recent colonization from the Carpathians or from a restricted expansion from separate Eastern Alpine refugia. Our study revealed a clear phylogeographical pattern in AFLPs supported by congruent groups of distinct cpDNA haplotypes. Highest genetic differentiation was observed between the Alps and the Carpathians, indicating a long-term isolation between populations from these two mountain ranges. Further genetic division within the Carpathians suggests that current species' distribution is composed of several groups which have been isolated from each other for a long period. One genetic break separates Western from Southeastern Carpathian material, which is in line with a classical biogeographical boundary. A further, strongly supported genetic group was identified at the southwestern edge of the Carpathian arch. In the Eastern Alps, genetic traces of glacial survival in separate refugial areas in the calcareous northern part and the siliceous central part were found.
In the recent years, many protocols aimed at reproducibly sequencing reduced--genome subsets in non--model organisms have been published. Among them, RAD--sequencing is one of the most widely used. It relies on digesting DNA with specific restriction enzymes and performing size selection on the resulting fragments. Despite its utility, this method is of a limited use with degraded DNA samples, such as those isolated from museum specimens, as these are either less likely to harbor fragments long enough to comprise two restriction sites making possible ligation of the technical sequences required or performing size selection of the resulting fragments. In addition, RAD--sequencing also reveals a suboptimal technique when applied to an evolutionary scale larger than the intra--specific level, as polymophisms in the restriction sites cause loci dropout. Here, we address both of these limitations by a novel method called hybridization RAD (hyRAD). In this method, biotinylated RAD fragments, covering a random fraction of the genome, are used as baits for capturing homologous fragments from samples processed through a classical genomic shotgun sequencing protocol. This simple and cost-effective approach allows sequencing orthologous sequences even from highly degraded DNA samples, opening new avenues of research in the field of museum genomics. Not relying on the restriction site presence, it improves among--sample loci coverage, and can be applied to broader phylogenetic scales. In a trial study, hyRAD allowed us to obtain a large set of orthologous loci from fresh and museum samples from a non--model butterfly species, with over 10.000 single nucleotide polymorphisms present in all eight analyzed specimens, including 58 years old museum samples.
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