Efekt klimatických změn na genetickou strukturu populací a jejich úloha při adaptivních radiacích

Jižní Oceán a jeho enormně chladný a křehký kontinet Antarktida si doposud prošly řadou zásadních klimatických změn. Antarktida byla tradičně nazírána jako pustá krajina a mnoho se také nevědělo o druhové diverzitě organizmů nebo fylogeografii. Tato práce si klade za cíl osvětlit a upřesnit zásadní hypotézy týkající se zmíněných biologických vlastností živočišných společenstev jak v šelfových vodách, tak i v suchozemském prostředí Antarktidy. Pomocí multilokusové analýzy bylo zjišťováno, jak souvisí životní styl - bentický nebo pelagický, se zřetelem na délku pelagického larválního stádia notothenioidních ryb, s konektivitou mezi jejich populacemi. Životní styl, spolu s oceánografickými faktory, je vhodným vodítkem k odhadu genového toku mezi populacemi. Je však životní styl faktorem ovlivňujícím populační dynamiku v dobách glaciace? Tuto otázku jsme aplikovali jak u fylogeneticky blízce příbuzných skupin ryb Notothenioidea nebo ježovek Echinoidea, tak také u fylogeneticky nepříbuzných druhů shelfových a hlubokomořských antarktických Invertebrata, dostupných v NCBI databázi. Ukazuje se, že populace bentických druhů prošly recentnější expanzí, než populace hlubokomořských nebo pelagických orgnismů. Studium evoluce mořského života jsme vyvážili studiem evoluce terestrických ekosystémů. Zde jsme se...The Southern Ocean and its enormously cold, remote and yet the wildest continent, the Antarctic, have experienced numerous rapid climatic changes. It used to be viewed as a barren wasteland with limited knowledge of species diversity or phylogeography. Recently, all aforementioned premises are being increasingly questioned, and this thesis aims to shed light on them. Firstly, multi-locus genetic markers were used to evaluate if it is the lifestyle, benthic or pelagic, including the duration of the pelagic larval period that determines the population connectivity of particular notothenioid species. It was the adult's fish lifestyle along with the oceanographic factors that are responsible for the gene flow between localities. Secondly, is lifestyle a factor determining the extent to which Pleistocene growing grounded ice sheet affected species past population dynamics? The attention was paid to Notothenioidea fish, then to Echinoidea sea urchins, and lastly to NCBI database available antarctic marine shelf and deep-sea fauna. Our findings suggest that the last glacial maximum affected more profoundly the population size of benthic shelf species. At the same time, those living in the water column or inhabiting deep slopes had more ancient population size changes. The Antarctic terrestrial evolution...Department of ZoologyKatedra zoologieFaculty of SciencePřírodovědecká fakult

Genome fractionation and loss of heterozygosity in hybrids and polyploids: Mechanisms, consequences for selection, and link to gene function

Hybridization and genome duplication have played crucial roles in the evolution of many animal and plant taxa. The subgenomes of parental species undergo considerable changes in hybrids and polyploids, which often selectively eliminate segments of one subgenome. However, the mechanisms underlying these changes are not well understood, particularly when the hybridization is linked with asexual reproduction that opens up unexpected evolutionary pathways. To elucidate this problem, we compared published cytogenetic and RNAseq data with exome sequences of asexual diploid and polyploid hybrids between three fish species; Cobitis elongatoides, C taenia, and C tanaitica. Clonal genomes remained generally static at chromosome-scale levels but their heterozygosity gradually deteriorated at the level of individual genes owing to allelic deletions and conversions. Interestingly, the impact of both processes varies among animals and genomic regions depending on ploidy level and the properties of affected genes. Namely, polyploids were more tolerant to deletions than diploid asexuals where conversions prevailed, and genomic restructuring events accumulated preferentially in genes characterized by high transcription levels and GC-content, strong purifying selection and specific functions like interacting with intracellular membranes. Although hybrids were phenotypically more similar to C taenia, we found that they preferentially retained C elongatoides alleles. This demonstrates that favored subgenome is not necessarily the transcriptionally dominant one. This study demonstrated that subgenomes in asexual hybrids and polyploids evolve under a complex interplay of selection and several molecular mechanisms whose efficiency depends on the organism's ploidy level, as well as functional properties and parental ancestry of the genomic region.Web of Science38125274525

Cryophilic Tardigrada have disjunct and bipolar distribution and establish long-term stable, low-density demes

Glaciers are inhabited by various cryophilic organisms ranging from single celled to multicellular, like Tardigrada (water bears). Owing to their scattered distribution, glaciers represent extremely fragmented habitats, and it remains unclear how their inhabitants survive and disperse among such isolated patches. This study investigates the biogeography of the tardigrade genus Cryoconicus, whose distribution, population stability, and interregional connectivity are examined by screening the collections from ~ 60 glaciers worldwide and by a phylogeographic analysis. We found that two Cryoconicus species occur at low densities on two Arctic glaciers in Svalbard, far from their previously reported Antarctic and Central Asian ranges. Screening of worldwide databases and DNA metabarcoding indicated that these species are absent or rare in the intermediate areas, suggesting large disjunctions in their ranges. In particular, the genetic data and multiyear resampling showed that Cryoconicus kaczmareki established a stable population on the Ebba Glacier (Svalbard), which has been isolated from its Asian core range since before the last glacial maximum. Our findings suggest that glacial invertebrates may possess wide yet largely disjunctive ranges. Interpolar- or intercontinental-scale movements of cryophilic meiofauna may occur, but migration connectivity is not sufficient to mitigate the differentiation of the local population. Revealed biogeographic patterns further demonstrate that inhabitants of extreme environments may establish isolated and highly fragmented populations that persist long term, even if at very low densities

The effect of climatic changes on genetic build-up of populations and their role in promoting adaptive radiations

The Southern Ocean and its enormously cold, remote and yet the wildest continent, the Antarctic, have experienced numerous rapid climatic changes. It used to be viewed as a barren wasteland with limited knowledge of species diversity or phylogeography. Recently, all aforementioned premises are being increasingly questioned, and this thesis aims to shed light on them. Firstly, multi-locus genetic markers were used to evaluate if it is the lifestyle, benthic or pelagic, including the duration of the pelagic larval period that determines the population connectivity of particular notothenioid species. It was the adult's fish lifestyle along with the oceanographic factors that are responsible for the gene flow between localities. Secondly, is lifestyle a factor determining the extent to which Pleistocene growing grounded ice sheet affected species past population dynamics? The attention was paid to Notothenioidea fish, then to Echinoidea sea urchins, and lastly to NCBI database available antarctic marine shelf and deep-sea fauna. Our findings suggest that the last glacial maximum affected more profoundly the population size of benthic shelf species. At the same time, those living in the water column or inhabiting deep slopes had more ancient population size changes. The Antarctic terrestrial evolution..

A revision of the trichostrongylid nematode Cooperia Ransom, 1907, from deer game: recent integrative research confirms the existence of the ancient host-specific species Cooperia ventricosa (Rudolphi, 1809)

The trichostrongylid roundworms of the genus Cooperia, which are important in veterinary medicine, currently comprise 19 valid species that parasitize the small intestine of both free-living and domestic ruminants. Only four Cooperia spp. have been reported in Europe, namely C. oncophora, C. punctata, C. curticei and C. pectinata. In 2018–2022, 25 red deer (Cervus elaphus) and 30 sika deer (Cervus nippon) of both sexes and various ages from several remote locations in the Czech Republic were parasitologically examined. Intestinal nematodes of the genus Cooperia were found only in two northern regions. Using the globally recognized key book on trichostrongylid nematodes, they were preliminarily identified as C. pectinata. However, a molecular analysis of cox2 and ITS rDNA gene sequences revealed that Cooperia sp. parasitizing Czech deer is a separate taxon that is more closely related to C. oncophora than to C. pectinata. A subsequent morphological analysis and literature survey confirmed the independence of deer Cooperia sp., which is similar but not identical to bovid C. pectinata. Previous long-term correct identifications of bovid C. pectinata and misidentifications of deer Cooperia species were caused by a fundamental error in the key book mentioned above. Interestingly, the ancient trichostrongylid nematode Strongylus ventricosus from the type host red deer (Cervus elaphus) shot near Greifswald (Germany) was described by Rudolphi in 1809. Rudolphi's type material (one male and four females) was deposited in the Museum für Naturkunde (Berlin). Later, the ancient species S. ventricosus was taken as a synonym for various Cooperia spp. Our current re-examination of the type male indicated that there is a relatively good agreement with our new material from Czech deer regarding the most important characteristics of S. ventricosus (i.e., the shape and size of the male spicules); however, Rudolphi's type material is in rather poor condition. The suggested resurrection of the deer Cooperia sp. in this study as Cooperia ventricosa (Rudolphi, 1809) requires verification by collecting and analyzing new nematode material from the type locality near Greifswald