Browsing by Subject "GENETIC-STRUCTURE"

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  • Acanski, Jelena; Vujic, Ante; Djan, Mihajla; Obreht Vidakovic, Dragana; Ståhls, Gunilla; Radenkovic, Snezana (2016)
    Several recent studies have detected and described complexes of cryptic and sibling species in the genus Merodon (Diptera, Syrphidae). One representative of these complexes is the Merodon avidus complex that contains four sibling species, which have proven difficult to distinguish using traditional morphological characters. In the present study, we use two geometric morphometric approaches, as well as molecular characters of the 5' -end of the mtDNA COI gene, to delimit sibling taxa. Analyses based on these data were used to strengthen species boundaries within the complex, and to validate the status of a previously-recognized cryptic taxon from Lesvos Island (Greece), here described as Merodon megavidus Vujic & Radenkovic sp. nov. Geometric morphometric results of both wing and surstylus shape confirm the present classification for three sibling species-M. avidus (Rossi, 1790), M. moenium Wiedemann in Meigen, 1822 and M. ibericus Vujic, 2015-and, importantly, clearly discriminate the newly-described taxon Merodon megavidus sp. nov. In addition to our geometric morphometric results, supporting characters were obtained from molecular analyses of mtDNA COI sequences, which clearly differentiated M. megavidus sp. nov. from the other members of the M. avidus complex. Molecular analyses revealed that the earliest divergence of M. ibericus occurred around 800 ky BP, while the most recent separation happened between M. avidus and M. moenium around 87 ky BP.
  • Ronnas, Cecilia; Werth, Silke; Ovaskainen, Otso; Varkonyi, Gergely; Scheidegger, Christoph; Snall, Tord (2017)
    Accurate estimates of gamete and offspring dispersal range are required for the understanding and prediction of spatial population dynamics and species persistence. Little is known about gamete dispersal in fungi, especially in lichen-forming ascomycetes. Here, we estimate the dispersal functions of clonal propagules, gametes and ascospores of the epiphytic lichen Lobaria pulmonaria. We use hierarchical Bayesian parentage analysis, which integrates genetic and ecological information from multiannual colonization and dispersal source data collected in a large, oldgrowth forest landscape. The effective dispersal range of gametes is several hundred metres to kilometres from potential paternal individuals. By contrast, clonal propagules disperse only tens of metres, and ascospores disperse over several thousand metres. Our study reveals the dispersal distances of individual reproductive units; clonal propagules, gametes and ascospores, which is of great importance for a thorough understanding of the spatial dynamics of ascomycetes. Sexual reproduction occurs between distant individuals. However, whereas gametes and ascospores disperse over long distances, the overall rate of colonization of trees is low. Hence, establishment is the limiting factor for the colonization of new host trees by the lichen in old- growth landscapes.
  • Huang, Yue; Zou, Jie; Kang, Zongjing; Zhang, Xiaoping; Penttinen, Petri; Zhang, Xiaoping; Li, Xiaolin (2021)
    We inoculated Tuber aestivum and Tuber sinoaestivum on Carya illinoinensis to explore the effects of inoculation on host plant growth, enzyme activities, the physicochemical properties of rhizosphere soil, the denitrifying bacterial community in the rhizosphere, and the distribution of mating type genes in the rhizosphere. We found that the Tuber spp. inoculation increased the height of the host plant and that the stem circumference of the host was greater two months after inoculation. Six months after inoculation, the peroxidase activity of the seedlings inoculated with T. sinoaestivum was higher than that of the control. At four and six months after inoculation, the superoxidase dismutase activities of the seedlings inoculated with T. aestivum were higher than those of the seedlings inoculated with T. sinoaestivum. Six months after inoculation, nitrate nitrogen content was lowest in the control and highest in the T. sinoaestivum treatment. Among the nirS-type denitrifying bacteria community, the relative abundances of Proteobacteria were high. T. aestivum and T. sinoaestivum inoculation did not affect the diversity of denitrifying bacteria. The mating type genes MAT1-1-1 and MAT1-2-1 were detected in the rhizosphere of C. illinoinensis inoculated with T. sinoaestivum and T. aestivum, and MAT1-1-1 dominated over MAT1-21. (c) 2021 British Mycological Society. Published by Elsevier Ltd. All rights reserved.
  • Yang, Bin; Cui, Leilei; Perez-Enciso, Miguel; Traspov, Aleksei; Crooijmans, Richard P. M. A.; Zinovieva, Natalia; Schook, Lawrence B.; Archibald, Alan; Gatphayak, Kesinee; Knorr, Christophe; Triantafyllidis, Alex; Alexandri, Panoraia; Semiadi, Gono; Hanotte, Olivier; Dias, Deodalia; Dovc, Peter; Uimari, Pekka; Iacolina, Laura; Scandura, Massimo; Groenen, Martien A. M.; Huang, Lusheng; Megens, Hendrik-Jan (2017)
    Background: Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection. Results: A deep phylogeographic division reflects the dichotomy between early domestication centers. In the core Eastern and Western domestication regions, Chinese pigs show differentiation between breeds due to geographic isolation, whereas this is less pronounced in European pigs. The inferred European origin of pigs in the Americas, Africa, and Australia reflects European expansion during the sixteenth to nineteenth centuries. Human-mediated introgression, which is due, in particular, to importing Chinese pigs into the UK during the eighteenth and nineteenth centuries, played an important role in the formation of modern pig breeds. Inbreeding levels vary markedly between populations, from almost no runs of homozygosity (ROH) in a number of Asian wild boar populations, to up to 20% of the genome covered by ROH in a number of Southern European breeds. Commercial populations show moderate ROH statistics. For domesticated pigs and wild boars in Asia and Europe, we identified highly differentiated loci that include candidate genes related to muscle and body development, central nervous system, reproduction, and energy balance, which are putatively under artificial selection. Conclusions: Key events related to domestication, dispersal, and mixing of pigs from different regions are reflected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the past decades started selecting Western breeds to improve local Chinese pigs. Furthermore, signatures of ongoing and past selection, acting at different times and on different genetic backgrounds, enhance our insight in the mechanism of domestication and selection. The global diversity statistics presented here highlight concerns for maintaining agro-diversity, but also provide a necessary framework for directing genetic conservation.
  • Murphy, Robert; Palm, Martin; Mustonen, Ville; Warringer, Jonas; Farewell, Anne; Parts, Leopold; Moradigaravand, Danesh (2021)
    Escherichia coli is a common bacterial species in the gastrointestinal tracts of warm-blooded animals and humans. Pathogenicity and antimicrobial resistance in E. coli may emerge via host switching from animal reservoirs. Despite its potential clinical importance, knowledge of the population structure of commensal E. coli within wild hosts and the epidemiological links between E. coli in nonhuman hosts and E. coli in humans is still scarce. In this study, we analyzed the whole-genome sequencing data of a collection of 119 commensal E. coli strains recovered from the guts of 55 mammal and bird species in Mexico and Venezuela in the 1990s. We observed low concordance between the population structures of E. coli isolates colonizing wild animals and the phylogeny, taxonomy, and ecological and physiological attributes of the host species, with distantly related E. coli strains often colonizing the same or similar host species and distantly related host species often hosting closely related E. coli strains. We found no evidence for recent transmission of E. coli genomes from wild animals to either domesticated animals or humans. However, multiple livestockand human-related virulence factor genes were present in E. coli of wild animals, including virulence factors characteristic of Shiga toxin-producing E. coli (STEC) and atypical enteropathogenic E. coli (aEPEC), where several isolates from wild hosts harbored the locus of enterocyte effacement (LEE) pathogenicity island. Moreover, E. coli isolates from wild animal hosts often harbored known antibiotic resistance determinants, including those against ciprofloxacin, aminoglycosides, tetracyclines, and beta-lactams, with some determinants present in multiple, distantly related E. coli lineages colonizing very different host animals. We conclude that genome pools of E. coli colonizing the guts of wild animals and humans share virulence and antibiotic resistance genes, underscoring the idea that wild animals could serve as reservoirs for E. coli pathogenicity in human and livestock infections. IMPORTANCE Escherichia coli is a clinically important bacterial species implicated in humanand livestock-associated infections worldwide. The bacterium is known to reside in the guts of humans, livestock, and wild animals. Although wild animals are recognized as potential reservoirs for pathogenic E. coli strains, the knowledge of the population structure of E. coli in wild hosts is still scarce. In this study, we used fine resolution of whole-genome sequencing to provide novel insights into the evolution of E. coli genomes from a small yet diverse collection of strains recovered within a broad range of wild animal species (including mammals and birds), the coevolution of E. coli strains with their hosts, and the genetics of pathogenicity of E. coli strains in wild hosts in Mexico. Our results provide evidence for the clinical importance of wild animals as reservoirs for pathogenic strains and highlight the need to include nonhuman hosts in the surveillance programs for E. coli infections.
  • Tabatabaei, Seyedeh Narjes; Abdoli, Asghar; Ahmadzadeh, Faraham; Primmer, Craig R.; Swatdipong, Akarapong; Segherloo, Iraj Hashemzadeh (2020)
    A total of 120 Caspian Sea trout specimens from five streams and Lar Lake of the Lar National Park plus 27 Caspian Sea trout specimens (out-group) from the Babolrud River drainage in the Caspian Sea Basin (Iran) were analyzed using 12 microsatellite loci to assess population genetic structure and to estimate the contribution of each population to the lake-run stock. In addition to the Babolrud River population that was significantly differentiated (P <0.001) from that in Lar National Park, the Dalichay population was significantly differentiated from other populations (P <0.001). The Dalichay and Absefid populations showed no contribution to the lake-run trout stock, while the others that did not show population genetic structure showed a 100% contribution to the lake-run trout stock. The different contributions to the lake-run trout stock estimated here may be related to the habitat qualifies that make the habitats suitable for natural Caspian Sea trout production or to different migratory behaviors between resident and lake-run trout. The results show that more stringent protection of the stream habitats for the contributing populations should be considered in order to sustain recreational fishing in the lake.
  • Plis, Kamila; Niedzialkowska, Magdalena; Borowik, Tomasz; Lang, Johannes; Heddergott, Mike; Tiainen, Juha; Bunevich, Aleksey; Sprem, Nikica; Paule, Ladislav; Danilkin, Aleksey; Kholodova, Marina; Zvychaynaya, Elena; Kashinina, Nadezhda; Pokorny, Bostjan; Flajsman, Katarina; Paulauskas, Algimantas; Djan, Mihajla; Ristic, Zoran; Novak, Lubos; Kusza, Szilvia; Miller, Christine; Tsaparis, Dimitris; Stoyanov, Stoyan; Shkvyria, Maryna; Suchentrunk, Franz; Kutal, Miroslav; Lavadinovic, Vukan; Snjegota, Dragana; Krapal, Ana-Maria; Danila, Gabriel; Veeroja, Rauno; Dulko, Elzbieta; Jedrzejewska, Bogumila (2022)
    To provide the most comprehensive picture of species phylogeny and phylogeography of European roe deer (Capreolus capreolus), we analyzed mtDNA control region (610 bp) of 1469 samples of roe deer from Central and Eastern Europe and included into the analyses additional 1541 mtDNA sequences from GenBank from other regions of the continent. We detected two mtDNA lineages of the species: European and Siberian (an introgression of C. pygargus mtDNA into C. capreolus). The Siberian lineage was most frequent in the eastern part of the continent and declined toward Central Europe. The European lineage contained three clades (Central, Eastern, and Western) composed of several haplogroups, many of which were separated in space. The Western clade appeared to have a discontinuous range from Portugal to Russia. Most of the haplogroups in the Central and the Eastern clades were under expansion during the Weichselian glacial period before the Last Glacial Maximum (LGM), while the expansion time of the Western clade overlapped with the Eemian interglacial. The high genetic diversity of extant roe deer is the result of their survival during the LGM probably in a large, contiguous range spanning from the Iberian Peninsula to the Caucasus Mts and in two northern refugia.
  • Zueva, Ksenia J.; Lumme, Jaakko; Veselov, Alexey E.; Primmer, Craig R.; Pritchard, Victoria L. (2021)
    Our ability to examine genetic variation across entire genomes has enabled many studies searching for the genetic basis of local adaptation. These studies have identified numerous loci as candidates for differential local selection; however, relatively few have examined the overlap among candidate loci identified from independent studies of the same species in different geographic areas or evolutionary lineages. We used an allelotyping approach with a 220K SNP array to characterize the population genetic structure of Atlantic salmon in north-eastern Europe and ask whether the same genomic segments emerged as outliers among populations in different geographic regions. Genome-wide data recapitulated the phylogeographic structure previously inferred from mtDNA and microsatellite markers. Independent analyses of three genetically and geographically distinct groups of populations repeatedly inferred the same 17 haploblocks to contain loci under differential local selection. The most strongly supported of these replicated haploblocks had known strong associations with life-history variation or immune response in Atlantic salmon. Our results are consistent with these genomic segments harbouring large-effect loci which have a major role in Atlantic salmon diversification and are ideal targets for validation studies.
  • Jerney, Jacqueline; Rengefors, Karin; Nagai, Satoshi; Krock, Bernd; Sjöqvist, Conny; Suikkanen, Sanna; Kremp, Anke (2022)
    Genetic diversity is the basis for evolutionary adaptation and selection under changing environmental conditions. Phytoplankton populations are genotypically diverse, can become genetically differentiated within small spatiotemporal scales and many species form resting stages. Resting stage accumulations in sediments (seed banks) are expected to serve as reservoirs for genetic information, but so far their role in maintaining phytoplankton diversity and in evolution has remained unclear. In this study we used the toxic dinoflagellate Alexandrium ostenfeldii (Dinophyceae) as a model organism to investigate if (i) the benthic seed bank is more diverse than the pelagic population and (ii) the pelagic population is seasonally differentiated. Resting stages (benthic) and plankton (pelagic) samples were collected at a coastal bloom site in the Baltic Sea, followed by cell isolation and genotyping using microsatellite markers (MS) and restriction site associated DNA sequencing (RAD). High clonal diversity (98%-100%) combined with intermediate to low gene diversity (0.58-0.03, depending on the marker) was found. Surprisingly, the benthic and pelagic fractions of the population were equally diverse, and the pelagic fraction was temporally homogeneous, despite seasonal fluctuation of environmental selection pressures. The results of this study suggest that continuous benthic-pelagic coupling, combined with frequent sexual reproduction, as indicated by persistent linkage equilibrium, prevent the dominance of single clonal lineages in a dynamic environment. Both processes harmonize the pelagic with the benthic population and thus prevent seasonal population differentiation. At the same time, frequent sexual reproduction and benthic-pelagic coupling maintain high clonal diversity in both habitats.
  • Wessman, Jaana; Schönauer, Stefan; Miettunen, Jouko; Turunen, Hannu; Parviainen, Pekka; Seppänen, Jouni K.; Congdon, Eliza; Service, Susan; Koiranen, Markku; Ekelund, Jesper; Laitinen, Jaana; Taanila, Anja; Tammelin, Tuija; Hintsanen, Mirka; Pulkki-Raback, Laura; Keltikangas-Jarvinen, Liisa; Viikari, Jorma; Raitakari, Olli T.; Joukamaa, Matti; Jarvelin, Marjo-Riitta; Freimer, Nelson; Palotie, Leena; Veijola, Juha; Mannila, Heikki; Paunio, Tiina (2012)
  • Strelkov, Petr; Katolikova, Marina; Vainola, Risto (2017)
    In a temporal comparison over 18 years, we documented changes in the position and structure of the North European blue mussel hybrid zone in the resund strait, between Mytilus edulis of the marine Kattegat and Mytilus trossulus of the brackish Baltic Sea. In 1987 the midpoint of the 140-km wide multilocus allozyme cline in shallow-water populations was estimated to be located halfway along the strait. In 2005, it was shifted 25 km towards the Baltic end of the Oresund, and was located near the fixed link (bridge) that was built across the strait meanwhile in the 1990s. The cline also appeared to have become narrower and the extent of hybridity among individuals decreased. Factors that theoretically can control the position and shape of a clinal hybrid zone involve environmental gradients between habitats that differentially favor the two hybridizing taxa, or barriers to geographical dispersal of the organism. We consider two alternative hypotheses to explain the movement of the mussel hybrid zone. (1) Environmental change related to climate warming: the more stenothermal M. trossulus was pushed out from the resund towards the cool Baltic by elevated temperatures. (2) Change of dispersal dynamics: the construction of the fixed link locally affected mussel dispersion which attracted the zone. We raise the question whether similar changes have taken place also in the other euryhaline taxa where genetic clines between Baltic vs. Kattegat populations occur.
  • Van Steenberge, Maarten W.; Vanhove, Maarten P. M.; Manda, Auguste Chocha; Larmuseau, Maarten H. D.; Swart, Belinda L.; Khang'Mate, Faustin; Arndt, Allan; Hellemans, Bart; Van Houdt, Jeroen; Micha, Jean-Claude; Koblmueller, Stephan; Roodt-Wilding, Rouvay; Volckaert, Filip A. M. (2020)
    Aim The formation history of Africa's current river basins remains largely unknown. In order to date changes in landscape and climate, we studied the biogeography of the African freshwater fish with the largest natural distribution. We also validated biogeographical units. Location Continental Africa. Taxon Clarias gariepinus sl. Methods We investigated mitochondrial cytb sequences of 443 individuals from 97 localities, using a haplotype network and a genetic landscape analysis. We inferred a dated phylogeny using maximum likelihood and Bayesian inference approaches and reconstructed ancestral areas with S-DEC and S-DIVA models. Microsatellite genotyping complemented the mitochondrial approach in the Congo basin, where the latter revealed complex patterns. Results Limited differentiation is found in northern and south-western Africa, and sharp genetic differentiation in the continent's east and centre. Populations with affinities to neighbouring basins occur at the edges of the Congo province. High diversity exists in the south of the Congo basin. The Zambezi province is partitioned into eastern, central and western sectors. In the east, specimens were related to those from the Congo. In the west, they were similar to Southern representatives. Phylogenetic inference placed the origin of C. gariepinus in the East Coast, with intraspecific diversification starting around the Great Lakes. These events occurred ca. 4.8-1.65 and 2.3-0.8 MYA respectively. Main conclusions Clades of C. gariepinus sl. show a clear geographical signature. The origin of C. gariepinus in the East Coast and diversification around the Great Lakes coincided with the periods of increased aridity. Low genetic differentiation in northern and southern Africa may result from connectivity during recent periods of higher rainfall. In contrast to other widespread African freshwater fish, colonization rather than extinction seemed to mediate distribution patterns. This can be explained by a high ecological tolerance. We highlight the species' suitability to study landscape and climate evolution at various scales.