population structure
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Natural selection is usually studied between mutants that differ in reproductive rate, but are subject to the same population structure. Here we explore how natural selection acts on mutants that have the same reproductive rate, but different population structures. In our framework, population structure is given by a graph that specifies where offspring can disperse. The invading mutant disperses offspring on a different graph than the resident wild-type. We find that more densely connected dispersal graphs tend to increase the invader's fixation probability, but the exact relationship between structure and fixation probability is subtle. We present three main results. First, we prove that if both invader and resident are on complete dispersal graphs, then removing a single edge in the invader's dispersal graph reduces its fixation probability. Second, we show that for certain island models higher invader's connectivity increases its fixation probability, but the magnitude of the effect depends on the exact layout of the connections. Third, we show that for lattices the effect of different connectivity is comparable to that of different fitness: for large population size, the invader's fixation probability is either constant or exponentially small, depending on whether it is more or less connected than the resident.
Changes in the age structure of the population of Czechoslovakia that have occurred or are likely to occur between 1961 and 2000 are examined. A general trend toward an older population is noted.
- Klíčová slova
- Age Distribution--changes *, Age Factors, Czechoslovakia, Demographic Aging *, Demographic Factors, Developed Countries, Eastern Europe, Estimation Technics, Europe, Population, Population Characteristics, Population Dynamics, Population Projection *, Research Methodology,
- MeSH
- demografie MeSH
- populace MeSH
- populační charakteristiky MeSH
- populační dynamika * MeSH
- předpověď * MeSH
- statistika jako téma MeSH
- věkové faktory MeSH
- věkové rozložení * MeSH
- vyspělé země MeSH
- výzkum MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Československo MeSH
- Evropa MeSH
- východní Evropa MeSH
African pangolins are hunted for their meat and for use in local traditional medicine, as well as for their scales, which are trafficked internationally, especially to growing Asian markets. Pangolin's population genetic structure can be used to trace the geographic origins of trafficked scales, but substantial sampling gaps across pangolins' ranges hinder these efforts. In this study, we documented population structure and dynamics in the two species of African pangolin, the white-bellied pangolin (Phataginus tricuspis) and the giant pangolin (Smutsia gigantea) in the underexplored Republic of Congo. Using the mitochondrial control region and two nuclear markers (beta-fibrinogen and titin), we identified high genetic diversity in both species. We document a distinct mitochondrial lineage of the white-bellied pangolin, which was most likely shaped by river barriers together with dynamics of forest refugia related to the climatic shifts during the Pleistocene. We detected population growth in the white-bellied pangolin coinciding with a dry period during the Pleistocene, suggesting some ability for this typically forest-dwelling species to persist under diverse environmental conditions. Using landscape genetics, we found all but one of the pangolins we sampled at bush meat markets originated locally. A single individual appeared to have been imported to Congo from Cameroon. These findings significantly contribute to our understanding of pangolin population biology and local trade dynamics. In addition, our data from a previously unstudied part of pangolins' ranges will help us to better understand international wildlife trafficking patterns and to target conservation and protection strategies for these highly vulnerable species.
- Klíčová slova
- Congo Basin, Conservation genetics, Genetic diversity, Pangolins, Phylogeography, Population structure, Wildlife trade,
- MeSH
- fylogeneze MeSH
- genetická variace * MeSH
- luskouni * genetika MeSH
- mitochondriální DNA genetika MeSH
- populační dynamika MeSH
- populační genetika MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Kongo MeSH
- Názvy látek
- mitochondriální DNA MeSH
In a recent interdisciplinary study, Das et al. have attempted to trace the homeland of Ashkenazi Jews and of their historical language, Yiddish (Das et al. 2016 Localizing Ashkenazic Jews to Primeval Villages in the Ancient Iranian Lands of Ashkenaz. Genome Biol Evol. 8:1132-1149). Das et al. applied the geographic population structure (GPS) method to autosomal genotyping data and inferred geographic coordinates of populations supposedly ancestral to Ashkenazi Jews, placing them in Eastern Turkey. They argued that this unexpected genetic result goes against the widely accepted notion of Ashkenazi origin in the Levant, and speculated that Yiddish was originally a Slavic language strongly influenced by Iranian and Turkic languages, and later remodeled completely under Germanic influence. In our view, there are major conceptual problems with both the genetic and linguistic parts of the work. We argue that GPS is a provenancing tool suited to inferring the geographic region where a modern and recently unadmixed genome is most likely to arise, but is hardly suitable for admixed populations and for tracing ancestry up to 1,000 years before present, as its authors have previously claimed. Moreover, all methods of historical linguistics concur that Yiddish is a Germanic language, with no reliable evidence for Slavic, Iranian, or Turkic substrata.
- Klíčová slova
- Ashkenazi Jews, Yiddish, geographic population structure, population genetics, relexification.,
- MeSH
- genom lidský MeSH
- lidé MeSH
- migrace lidstva * MeSH
- molekulární evoluce * MeSH
- populace genetika MeSH
- populační genetika metody normy MeSH
- rodokmen MeSH
- Židé genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
Annual killifishes of the genus Nothobranchius are widespread across East Africa, with a particularly high biodiversity in lowland Tanzania. While they are typically found in ephemeral pools, the pools vary greatly in size, connectivity and inundation patterns. It was previously suggested that main river channels formed significant barriers to Nothobranchius dispersal. Here, we study the distribution of genetic lineages in an equatorial part of their range where main river channels that may act as barriers occur and closely related lineages frequently coexist in secondary contact zones. We used single-nucleotide polymorphism (SNP) dataset from double-digest restriction site-associated DNA (ddRAD) sequencing to investigate how genetic diversity is structured in Nothobranchius species from the coastal lowlands of Tanzania. Our analyses resolved some uncertain phylogenetic relationships within the N. melanospilus and N. guentheri species groups and placed N. flammicomantis outside the Coastal clade. Rather than a shared intraspecific genetic diversity pattern across four coexisting and widely distributed species, we found highly diverse patterns of intra-specific genetic structure among N. eggersi, N. janpapi, N. melanospilus and N. ocellatus. Populations of Nothobranchius species from the humid coastal lowlands of Tanzania are therefore structured, but not constrained by barriers formed by river channels or by basins - in contrast to Nothobranchius species from the dry part of their distribution. Some of the genetic relationships determined call for a re-evaluation of taxonomic delimitations.
- Klíčová slova
- Diversification, Freshwater fish, Gene flow, Phylogenomics, Population structure, Temporary pools,
- MeSH
- Cyprinodontidae MeSH
- fylogeneze * MeSH
- genetická variace MeSH
- jednonukleotidový polymorfismus MeSH
- metagenomika MeSH
- populační genetika * MeSH
- sekvenční analýza DNA MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Tanzanie MeSH
In order to disentangle the contribution of host and parasite biology to host specificity, we compared the structure and population dynamics of the Gyrodactylus (von Nordmann, 1832) flatworm community living on sympatric three-spined Gasterosteus aculeatus L. and nine-spined Pungitius pungitius (L.) stickleback. Between April 2002 and March 2003, a small lowland creek was sampled monthly. Species identity of about 75% of the worms per host was determined with a genetic nuclear marker (ITS1). Each stickleback species hosted a characteristic gill- and fin-parasitic Gyrodactylus: G. arcuatus Bychowsky, 1933 and G. gasterostei Gläser, 1974 respectively infecting the three-spined stickleback, with G. rarus Wegener, 1910 and G. pungitii Malmberg, 1964 infecting the nine-spined stickleback. Host size and seasonal dynamics were strong determinants of parasite abundance. A strong interaction between host and parasite species determined infection levels and affected three levels of parasite organisation: community structure, population structure and topographical specialisation. Community and population structure were shaped by asymmetric cross-infections, resulting in a net transmission of the Gyro-dactylus species typical of the nine-spined stickleback towards the three-spined stickleback. Host density was not a major determinant of parasite exchange. Aggregation and topographical specialisation of the Gyrodactylus species of the three-spined stickleback were more pronounced than that of the nine-spined stickleback.
- MeSH
- časové faktory MeSH
- druhová specificita MeSH
- ekosystém MeSH
- infekce červy třídy Trematoda parazitologie veterinární MeSH
- nemoci ryb parazitologie MeSH
- pohlavní dimorfismus MeSH
- populační dynamika MeSH
- roční období MeSH
- Smegmamorpha klasifikace genetika parazitologie MeSH
- Trematoda klasifikace parazitologie MeSH
- velikost těla MeSH
- zvířata MeSH
- Check Tag
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The aoudad (Ammotragus lervia Pallas 1777) is an ungulate species, native to the mountain ranges of North Africa. In the second half of the twentieth century, it was successfully introduced in some European countries, mainly for hunting purposes, i.e. in Croatia, the Czech Republic, Italy, and Spain. We used neutral genetic markers, the mitochondrial DNA control region sequence and microsatellite loci, to characterize and compare genetic diversity and spatial pattern of genetic structure on different timeframes among all European aoudad populations. Four distinct control region haplotypes found in European aoudad populations indicate that the aoudad has been introduced in Europe from multiple genetic sources, with the population in the Sierra Espuña as the only population in which more than one haplotype was detected. The number of detected microsatellite alleles within all populations (< 3.61) and mean proportion of shared alleles within all analysed populations (< 0.55) indicates relatively low genetic variability, as expected for new populations funded by a small number of individuals. In STRUCTURE results with K = 2-4, Croatian and Czech populations cluster in the same genetic cluster, indicating joined origin. Among three populations from Spain, Almeria population shows as genetically distinct from others in results, while other Spanish populations diverge at K = 4. Maintenance of genetic diversity should be included in the management of populations to sustain their viability, specially for small Czech population with high proportion of shared alleles (0.85) and Croatian population that had the smallest estimated effective population size (Ne = 5.4).
- MeSH
- alely MeSH
- genetická variace genetika MeSH
- haplotypy genetika MeSH
- mikrosatelitní repetice genetika MeSH
- mitochondriální DNA genetika MeSH
- populační genetika * MeSH
- přežvýkavci klasifikace genetika MeSH
- savci genetika MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Česká republika MeSH
- Evropa MeSH
- Španělsko MeSH
- Názvy látek
- mitochondriální DNA MeSH
BACKGROUND AND AIMS: Historical changes in environmental conditions and colonization-extinction dynamics have a direct impact on the genetic structure of plant populations. However, understanding how past environmental conditions influenced the evolution of species with high gene flow is challenging when signals for genetic isolation and adaptation are swamped by gene flow. We investigated the spatial distribution and genetic structure of the widespread terrestrial orchid Epipactis helleborine to identify glacial refugia, characterize postglacial population dynamics and assess its adaptive potential. METHODS: Ecological niche modelling was used to locate possible glacial refugia and postglacial recolonization opportunities of E. helleborine. A large single-nucleotide polymorphism (SNP) dataset obtained through genotyping by sequencing was used to define population genetic diversity and structure and to identify sources of postglacial gene flow. Outlier analyses were used to elucidate how adaptation to the local environment contributed to population divergence. KEY RESULTS: The distribution of climatically suitable areas was restricted during the Last Glacial Maximum to the Mediterranean, south-western Europe and small areas in the Alps and Carpathians. Within-population genetic diversity was high in E. helleborine (mean expected heterozygosity, 0.373 ± 0.006; observed heterozygosity, 0.571 ± 0.012; allelic richness, 1.387 ± 0.007). Italy and central Europe are likely to have acted as important genetic sources during postglacial recolonization. Adaptive SNPs were associated with temperature, elevation and precipitation. CONCLUSIONS: Forests in the Mediterranean and Carpathians are likely to have acted as glacial refugia for Epipactis helleborine. Postglacial migration northwards and to higher elevations resulted in the dispersal and diversification of E. helleborine in central Europe and Italy, and to geographical isolation and divergent adaptation in Greek and Italian populations. Distinguishing adaptive from neutral genetic diversity allowed us to conclude that E. helleborine has a high adaptive potential to climate change and demonstrates that signals of adaptation and historical isolation can be identified even in species with high gene flow.
- Klíčová slova
- Epipactis helleborine, environment association analysis, environmental niche modelling, genotype–environment associations, genotyping by sequencing, landscape genomics, local adaptation, natural selection,
- MeSH
- ekosystém * MeSH
- genetická variace * MeSH
- genetické struktury MeSH
- populační genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Evropa MeSH
Monogenean parasites with a broad host range and direct life cycle provide insight into population genetic structure and dispersal processes. Dactylogyrus vistulae infects over 50 cyprinoid fish species across the western Palearctic, making it an ideal model for assessing host and geographic influences on parasite population structure. Herein, we utilized 20 microsatellite loci and mitochondrial COI sequences to analyze the genetic variability and structure of D. vistulae populations, with a deeper focus on Czech river systems. Low allelic variance was observed across most populations, except in the Aoos River, Greece, where high genetic diversity suggests either a large population size or an ancestral refugium. Moderate variance was detected in the Middle East, though some Anatolian populations exhibited reduced diversity, likely due to recent colonization. Czech populations showed weak genetic structuring despite occupying distinct river basins, likely due to fish translocations. Mitochondrial COI analysis revealed up to 18.5% haplotype divergence, with the highest diversity in the Padano-Venetian, Caspian Sea, and Dalmatian districts. Dalmatian haplotypes formed a distinct haplogroup, though genetic similarities between Padano-Venetian and Dalmatian populations suggest historical connections or fish host introductions. These results support a south-to-north D. vistulae dispersal through the Balkans, associated with cyprinoid fish migration. This study highlights the roles of host dispersal, environmental factors, and human influence in shaping fish parasite population structure, emphasizing the need for further genomic and ecological research.
- Klíčová slova
- Biogeography, Fish parasites, Microsatellites, Mitochondrial markers, Monogenea, Population genetics,
- MeSH
- Cyprinidae * parazitologie MeSH
- fylogeneze MeSH
- genetická variace * MeSH
- haplotypy MeSH
- infekce červy třídy Trematoda * veterinární parazitologie epidemiologie MeSH
- mikrosatelitní repetice MeSH
- nemoci ryb * parazitologie epidemiologie MeSH
- ploštěnci * genetika klasifikace izolace a purifikace MeSH
- populační genetika MeSH
- respirační komplex IV genetika MeSH
- žábry * parazitologie MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Česká republika MeSH
- Názvy látek
- respirační komplex IV MeSH
Although dairy goat production, characterized by traditional production on small farms, is an important source of income in the Czech Republic and Slovakia, locally adapted breeds have not been fully consolidated over the last 100 yr due to large fluctuations in population size and inconsistent breeding programs that allowed for different crossbreeding strategies. Our main objective in this study was therefore to assess the conservation status of 4 Czech (Alpine Goat, White Shorthair, Brown Shorthair, and Czech Landrace) and 1 Slovak (Slovak White Shorthair) local goat breeds, to analyze their population structure and admixture, and to estimate their relatedness to several neighboring breeds. Our analyses included 142 goats belonging to 5 local breeds genotyped with the Illumina 50K BeadChip, and 618 previously genotyped animals representing 15 goat breeds from Austria and Switzerland (all analyses based on 46,862 autosomal SNPs and 760 animals). In general, the conservation status of the Czech and Slovak local goat breeds was satisfactory, with the exception of the Brown Shorthair goat, as the analyzed parameters (heterozygosity, haplotype richness, runs of homozygosity-based inbreeding, and effective population size) were mostly above the median of 20 breeds. However, for all 5 Czech and Slovakian breeds, an examination of historical effective population size indicated a substantial decline about 8 to 22 generations ago. In addition, our study revealed that the Czech and Slovakian breeds are not fully consolidated; for instance, White Shorthair and Brown Shorthair were not clearly distinguishable. Considerable admixture, especially in Czech Landrace (effective number of parental clusters = 4.2), and low but numerous migration rates from other Austrian and Swiss breeds were found. These results provide valuable insights for future breeding programs and genetic diversity management of local Czech and Slovak goat breeds.
- Klíčová slova
- conservation status, diversity, genomics, goats, population structure,
- MeSH
- chov * MeSH
- genomika MeSH
- genotyp MeSH
- jednonukleotidový polymorfismus MeSH
- kozy * genetika MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Česká republika MeSH
- Slovenská republika MeSH
