Danijela Popović

Genomics and the challenging translation into conservation practice

The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice as scaling up to genome-wide data can improve traditional conservation genetic inferences and provide qualitatively novel insights. However, the generation of genomic data and subsequent analyses and interpretations remain challenging and largely confined to academic research in ecology and evolution. This generates a gap between basic research and applicable solutions for conservation managers faced with multifaceted problems. Before the real-world conservation potential of genomic research can be realized, we suggest that current infrastructures need to be modified, methods must mature, analytical pipelines need to be developed, and successful case studies must be disseminated to practitioners.

Microsatellite multiplex assay for the analysis of Atlantic sturgeon populations

We have developed a multiplex assay covering 16 microsatellite loci, amplified in four polymerase chain reaction (PCR) assays, and loaded on the ABI DNA Analyzer in two separate panels. The assay was tested on 603 individuals originating from wild populations and hatchery stocks of Atlantic sturgeon. The assay was also tested on 12 individuals of European sturgeon and appeared to be almost equally useful. The multiplex assay designed in this study can be successfully applied in studies requiring high genetic resolution, such as relatedness analysis, selective breeding programs, and stock identification of Atlantic sturgeon.

Human-mediated dispersal of cats in the Neolithic Central Europe

Archeological and genetic evidence suggest that all domestic cats derived from the Near Eastern wildcat (Felis silvestris lybica) and were first domesticated in the Near East around 10,000 years ago. The spread of the domesticated form in Europe occurred much later, primarily mediated by Greek and Phoenician traders and afterward by Romans who introduced cats to Western and Central Europe around 2000 years ago. We investigated mtDNA of Holocene Felis remains and provide evidence of an unexpectedly early presence of cats bearing the Near Eastern wildcat mtDNA haplotypes in Central Europe, being ahead of Roman period by over 2000 years. The appearance of the Near Eastern wildcats in Central Europe coincides with the peak of Neolithic settlement density, moreover most of those cats belonged to the same mtDNA lineages as those domesticated in the Near East. Thus, although we cannot fully exclude that the Near Eastern wildcats appeared in Central Europe as a result of introgression with European wildcat, our findings support the hypothesis that the Near Eastern wildcats spread across Europe together with the first farmers, perhaps as commensal animals. We also found that cats dated to the Neolithic period belonged to different mtDNA lineages than those brought to Central Europe in Roman times, this supports the hypothesis that the gene pool of contemporary European domestic cats might have been established from two different source populations that contributed in different periods.

Microsatellite Mutation Rate in Atlantic Sturgeon (Acipenser oxyrinchus)

Understanding mutation rates can greatly extend the utility of population and conservation genetic analyses. Herein, we present an estimate of genome-wide microsatellite mutation rate in Atlantic sturgeon (Acipenser oxyrinchus) based on parent-offspring transmission patterns. We screened 307 individuals for parentage and mutation-rate analysis applying 43 variable markers. Out of 13228 allele transfers, 11 mutations were detected, producing a mutation rate of 8.3 × 10-4 per locus per generation (95% confidence interval: 1.48 × 10-3, 4.15 × 10-4). Single-step mutations predominated and there were trends toward mutations in loci with greater polymorphism and allele length. Two of the detected mutations were most probably cluster mutations, being identified in 12 and 28 sibs, respectively. Finally, we observed evidences of polyploidy based on the sporadic presence of 3 or 4 alleles per locus in the genotyped individuals, supporting previous reports of incomplete diploidization in Atlantic sturgeon.

Impact of climatic changes in the Late Pleistocene on migrations and extinction of mammals in Europe: four case studies

Climate changes that occurred during the Late Pleistocene have profound effects on the distribution of many plant and animal species and influenced the formation of contemporary faunas and floras of Europe. The course and mechanisms of responses of species to the past climate changes are now being intensively studied by the use of direct radiocarbon dating and genetic analyses of fossil remains. Here, we review the advances in understanding these processes by the example of four mammal species: woolly mammoth (Mammuthus primigenius), cave bear (Ursus spelaeus s. l.), saiga antelope (Saiga tatarica) and collared lemmings (Dicrostonyx ssp.). The cases discussed here as well as others show that the migrations, range shifts and local extinctions were the main responses to climate changes and that the dynamics of these climate driven processes were much more profound than it was previously thought. Each species reacted by its individual manner, which depended on its biology and adaptation abilities to the changing environment and climate conditions. The most severe changes in European ecosystems that affected the largest number of species took place around 33–31 ka BP, during the Last Glacial Maximum 22–19 ka BP and the Late Glacial warming 15–13 ka BP.

Introgression of peled (Coregonus peled) into European whitefish (C. lavaretus) in Poland

Abstract Human-induced hybridization between previously allopatric species deserves special attention from conservationists. The European whitefish (Coregonus lavaretus), native fish species in Poland, hybridizes with another coregonid fish—peled (Coregonus peled) due to artificial fertilization in the hatcheries. The latter species is native to Siberian waters and was introduced into Poland in 1966. The offspring of these two species are fertile, and interspecific hybrids have been shown to be present in certain Polish lakes. In this study, we estimate the level of peled introgression into the whitefish gene pool and verify the presence of pure whitefish populations in the four Polish lakes. Genetic analysis of 12 microsatellite loci and ITS 1 (internal transcribed spacer 1) fragment sequences revealed limited introgression. Bayesian admixture analysis showed that only one lake harbored an admixed population. All six admixed individuals possessed European whitefish mtDNA haplotypes. This study is the first comprehensive investigation of whitefish genetic diversity in Poland and revealed very limited introgression of peled. Obtained results showed that pure whitefish populations are still present in Poland and represent appropriate source for supportive breeding programs.

Complete mitochondrial genome sequences of Atlantic sturgeon, Acipenser oxyrinchus oxyrinchus, Gulf sturgeon, A. o. desotoi and European sturgeon A. sturio (Acipenseriformes: Acipenseridae) obtained through next generation sequencing

Abstract Complete mitochondrial genome sequences of European sturgeon and two subspecies of the North American, Atlantic and Gulf sturgeons were determined using MiSeq Illumina technology. All three genomes show typical vertebrate organization. They possess 22 tRNA genes, 13 protein-coding genes, 2 rRNA (ribosomal RNA) genes and a non-coding control region. Excluding ND6, all protein-coding genes are on the heavy strand. The whole mitogenome sequences have been deposited in GenBank under accession numbers KP997216–KP997218.

Restitution of vimba (Vimba vimba, Cyprinidae) in Poland: genetic variability of existing and restored populations

Until 1960s, vimba was found abundantly in Polish rivers and was an important species for the fishing industry. Overfishing, water pollution and dam constructions brought most of the vimba populations close to extinction. We analyzed the genetic variability of several remnant vimba populations in the Vistula and Oder river basins. The 305-bp fragment encompassing the 5′-end of the mtDNA control region was sequenced in a total of 202 wild specimens derived from six populations. Six different haplotypes were distinguished. The population of Barycz River was found to be the most polymorphic and was chosen as a source of breeding material for the vimba restitution program. In the years 2000–2008 fishes from this river were caught, spawned in captivity and released to the same river. The number of fishes returning to the Barycz River spawning grounds was monitored in the following years. In 2008, it was almost 70 times higher than the number of fishes recorded in 2003, when the lowest population size was observed. The haplotype and nucleotide diversities of the restored population were similar to those of the original population.