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Brejon Lamartinière E, Tremble K, Dentinger BTM, Dasmahapatra KK, Hoffman JI. Runs of homozygosity reveal contrasting histories of inbreeding across global lineages of the edible porcini mushroom, Boletus edulis. Mol Ecol 2024:e17470. [PMID: 39034770 DOI: 10.1111/mec.17470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 06/26/2024] [Accepted: 07/03/2024] [Indexed: 07/23/2024]
Abstract
Inbreeding, the mating of individuals that are related through common ancestry, is of central importance in evolutionary and conservation biology due to its impacts on individual fitness and population dynamics. However, while advanced genomic approaches have revolutionised the study of inbreeding in animals, genomic studies of inbreeding are rare in plants and lacking in fungi. We investigated global patterns of inbreeding in the prized edible porcini mushroom Boletus edulis using 225 whole genomes from seven lineages distributed across the northern hemisphere. Genomic inbreeding was quantified using runs of homozygosity (ROHs). We found appreciable variation both among and within lineages, with some individuals having over 20% of their genomes in ROHs. Much of this variation could be explained by a combination of elevation and latitude, and to a lesser extent by predicted habitat suitability during the last glacial maximum. In line with this, the majority of ROHs were short, reflecting ancient common ancestry dating back approximately 200-1700 generations ago, while longer ROHs indicative of recent common ancestry (less than approximately 50 generations ago) were infrequent. Our study reveals the inbreeding legacy of major climatic events in a widely distributed forest mutualist, aligning with prevailing theories and empirical studies of the impacts of historical glaciation events on the dominant forest tree species of the northern hemisphere.
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Affiliation(s)
- Etienne Brejon Lamartinière
- Department of Evolutionary Population Genetics, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Department of Animal Behaviour, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Keaton Tremble
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Bryn T M Dentinger
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
- Natural History Museum of Utah, Salt Lake City, Utah, USA
| | | | - Joseph I Hoffman
- Department of Evolutionary Population Genetics, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Department of Animal Behaviour, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Bielefeld, Münster, Germany
- British Antarctic Survey, Cambridge, UK
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2
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Capblancq T, Sękiewicz K, Dering M. Forest genomics in the Caucasus through the lens of its dominant tree species - Fagus orientalis. Mol Ecol 2024:e17475. [PMID: 39021282 DOI: 10.1111/mec.17475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/29/2024] [Accepted: 06/14/2024] [Indexed: 07/20/2024]
Abstract
The last glacial period is known to have greatly influenced the demographic history of temperate forest trees, with important range contractions and post-glacial expansions that led to the formation of multiple genetic lineages and secondary contact zones in the Northern Hemisphere. These dynamics have been extensively studied for European and North American species but are still poorly understood in other temperate regions of rich biodiversity such as the Caucasus. Our study helps filling that gap by deciphering the genomic landscapes of F. orientalis across the South Caucasus. The use of genome-wide data confirmed a past demographic history strongly influenced by the Last Glacial Maximum, revealing two disjunct glacial refugia in the Colchis and Hyrcanian regions. The resulting patterns of genetic diversity, load and differentiation are not always concordant across the region, with genetic load pinpointing the location of the glacial refugia more efficiently than genetic diversity alone. The Hyrcanian forests show depleted genetic diversity and substantial isolation, even if long-distance gene flow is still present with the main centre of diversity in the Greater Caucasus. Finally, we characterize a strong heterogeneity of genetic diversity and differentiation along the species chromosomes, with noticeably a first chromosome showing low diversity and weak differentiation.
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Affiliation(s)
- Thibaut Capblancq
- Université Grenoble-Alpes, Université Savoie Mont Blanc, CNRS, Laboratoire d'Écologie Alpine, Grenoble, France
| | | | - Monika Dering
- Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland
- Department of Silviculture, Faculty of Forestry and Wood Technology, Poznań University of Life Sciences, Poznań, Poland
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3
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Hošek J, Pokorný P, Storch D, Kvaček J, Havig J, Novák J, Hájková P, Jamrichová E, Brengman L, Radoměřský T, Křížek M, Magna T, Rapprich V, Laufek F, Hamilton T, Pack A, Di Rocco T, Horáček I. Hot spring oases in the periglacial desert as the Last Glacial Maximum refugia for temperate trees in Central Europe. SCIENCE ADVANCES 2024; 10:eado6611. [PMID: 38820152 PMCID: PMC11141633 DOI: 10.1126/sciadv.ado6611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 04/30/2024] [Indexed: 06/02/2024]
Abstract
Northern glacial refugia are a hotly debated concept. The idea that many temperate organisms survived the Last Glacial Maximum (LGM; ~26.5 to 19 thousand years) in several sites across central and northern Europe stems from phylogeographic analyses, yet direct fossil evidence has thus far been missing. Here, we present the first unequivocal proof that thermophilous trees such as oak (Quercus), linden (Tilia), and common ash (Fraxinus excelsior) survived the LGM in Central Europe. The persistence of the refugium was promoted by a steady influx of hydrothermal waters that locally maintained a humid and warm microclimate. We reconstructed the geological and palaeohydrological factors responsible for the emergence of hot springs during the LGM and argue that refugia of this type, allowing the long-term survival and rapid post-LGM dispersal of temperate elements, were not exceptional in the European periglacial zone.
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Affiliation(s)
- Jan Hošek
- Czech Geological Survey, Klárov 3, Prague 1, Czech Republic
- Center for Theoretical Study, Charles University and the Czech Academy of Sciences, Jilská 1, Prague 1, Czech Republic
| | - Petr Pokorný
- Center for Theoretical Study, Charles University and the Czech Academy of Sciences, Jilská 1, Prague 1, Czech Republic
| | - David Storch
- Center for Theoretical Study, Charles University and the Czech Academy of Sciences, Jilská 1, Prague 1, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2, Czech Republic
| | - Jiří Kvaček
- Department of Palaeontology, National Museum Prague, Václavské nám. 68, Prague, Czech Republic
| | - Jeff Havig
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jan Novák
- Department of Botany, Faculty of Science, Charles University, Benátská 2, Prague 2, Czech Republic
| | - Petra Hájková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, Czech Republic
- Department of Paleoecology, Institute of Botany, The Czech Academy of Sciences, Lidická 25/27, Brno, Czech Republic
| | - Eva Jamrichová
- Department of Paleoecology, Institute of Botany, The Czech Academy of Sciences, Lidická 25/27, Brno, Czech Republic
| | - Latisha Brengman
- Earth and Environmental Sciences Department, University of Minnesota Duluth, Duluth, MN 55812, USA
| | - Tomáš Radoměřský
- Czech Geological Survey, Klárov 3, Prague 1, Czech Republic
- Institute of Geology and Palaeontology, Faculty of Science, Charles University, Albertov 6, 128 43 Prague 2, Czech Republic
| | - Marek Křížek
- Department of Physical Geography and Geoecology, Faculty of Science, Charles University, Albertov 6, Prague 2, Czech Republic
| | - Tomáš Magna
- Czech Geological Survey, Klárov 3, Prague 1, Czech Republic
| | | | | | - Trinity Hamilton
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Andreas Pack
- Universität Göttingen, Geowissenschaftliches Zentrum, Goldschmidtstraße 1, Göttingen, Germany
| | - Tommaso Di Rocco
- Universität Göttingen, Geowissenschaftliches Zentrum, Goldschmidtstraße 1, Göttingen, Germany
| | - Ivan Horáček
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 2, Czech Republic
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4
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Mitka J, Wróblewska A, Boroń P, Kucharzyk S, Stachurska-Swakoń A. Perhaps there were northern refugia in LGM? The phylogeographic structure of the thermophilic tree Carpinus betulus in the Carpathian region. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167214. [PMID: 37730049 DOI: 10.1016/j.scitotenv.2023.167214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/15/2023] [Accepted: 09/17/2023] [Indexed: 09/22/2023]
Abstract
Carpinus betulus L., the hornbeam, is a component of lowland and highland forests in Europe. By examining the postglacial migratory history of thermophilic tree species, the study aimed to unravel their putative glacial microrefugia in the Carpathian region. The present study points to the two distinct genetic AFLP groups of C. betulus in the Carpathian region that represent different genetic lineages based on Bayesian analysis. They differed in Nei's gene diversity index h, and the analysis of molecular variance AMOVA showed a percentage variation of the populations between the groups of 13.74 %. Principal coordinate analysis (PCoA) of 368 AFLP tree samples confirmed the presence of two genetic groups. Ninety-five populations underwent principal component analysis (PCA) to show the main correlations between genetic diversity indices and bioclimatic/climate variables (WorldClim and Carpatclim). The generalized logistic model (GLM) showed the significance of Nei's genetic index h in delimiting genetic groups. The results of population-genetic and multivariate analyses determined that the two genetic groups nowadays are spatially diffused and do not show a clear geographic pattern, pointing to a genetic melting pot. We found ecological links between genetic diversity and bioclimatic characteristics, especially the precipitation in the coldest quarter - Bio19. The refugial Maxent model indicates a significant contribution of the Bio7 variable (both linked with a continental type of climate) to the occurrence of the species during the LGM in Europe. We suggest the relict character of hornbeam populations in a specific climatic-terrain niche in the northern part of the Carpathian Basin.
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Affiliation(s)
- Józef Mitka
- Jagiellonian University in Kraków, Faculty of Biology, ul. Gronostajowa 3, 30-387 Kraków, Poland.
| | - Ada Wróblewska
- University of Bialystok, Faculty of Biology, ul. K. Ciołkowskiego 1J, 15-245 Białystok, Poland
| | - Piotr Boroń
- University of Agriculture in Kraków, Department of Forest Ecosystems Protection, 29 Listopada 46, 31-425 Kraków, Poland
| | - Stanisław Kucharzyk
- Bieszczady National Park, Ecological Education Unit, Bełska 7, 38-700 Ustrzyki Dolne, Poland
| | - Alina Stachurska-Swakoń
- Jagiellonian University in Kraków, Faculty of Biology, ul. Gronostajowa 3, 30-387 Kraków, Poland
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5
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Molnár ÁP, Demeter L, Biró M, Chytrý M, Bartha S, Gantuya B, Molnár Z. Is there a massive glacial-Holocene flora continuity in Central Europe? Biol Rev Camb Philos Soc 2023; 98:2307-2319. [PMID: 37646107 DOI: 10.1111/brv.13007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 09/01/2023]
Abstract
The prevailing paradigm about the Quaternary ecological and evolutionary history of Central European ecosystems is that they were repeatedly impoverished by regional extinctions of most species during the glacial periods, followed by massive recolonizations from southern and eastern refugia during interglacial periods. Recent literature partially contradicts this view and provides evidence to re-evaluate this Postglacial Recolonization Hypothesis and develop an alternative one. We examined the long-term history of the flora of the Carpathian (Pannonian) Basin by synthesising recent advances in ecological, phylogeographical, palaeoecological and palaeoclimatological research, and analysing the cold tolerance of the native flora of a test area (Hungary, the central part of the Carpathian Basin). We found that (1) many species have likely occurred there continuously since before the Last Glacial Maximum (LGM); (2) most of the present-day native flora (1404 species, about 80%) can occur in climates as cold as or colder than the LGM (mean annual temperature ≤+3.5°C); and (3) grasslands and forests can be species-rich under an LGM-like cold climate. These arguments support an alternative hypothesis, which we call the Flora Continuity Hypothesis. It states that long-term continuity of much of the flora in the Carpathian Basin is more plausible than regional extinctions during the LGM followed by massive postglacial recolonizations. The long-term continuity of the region's flora may have fundamental implications not only for understanding local biogeography and ecology (e.g. the temporal scale of processes), but also for conservation strategies focusing on protecting ancient species-rich ecosystems and local gene pools.
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Affiliation(s)
- Ábel Péter Molnár
- Hungarian University of Agriculture and Life Sciences, Institute for Wildlife Management and Nature Conservation, Páter Károly u. 1., Gödöllő, 2100, Hungary
- Doctoral School of Biological Sciences, Hungarian University of Agriculture and Life Sciences, Páter Károly u. 1., Gödöllő, 2100, Hungary
| | - László Demeter
- Centre for Ecological Research, Institute of Ecology and Botany, Alkotmány u. 2-4., Vácrátót, 2163, Hungary
| | - Marianna Biró
- Centre for Ecological Research, Institute of Ecology and Botany, Alkotmány u. 2-4., Vácrátót, 2163, Hungary
| | - Milan Chytrý
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
| | - Sándor Bartha
- Centre for Ecological Research, Institute of Ecology and Botany, Alkotmány u. 2-4., Vácrátót, 2163, Hungary
| | - Batdelger Gantuya
- Botanic Garden and Research Institute, Mongolian Academy of Sciences, 13th Street, Peace Avenue 54a, Bayanzurkh district, Ulaanbaatar, 13330, Mongolia
- Doctoral School of Biology, Eötvös Lorand University, Budapest, Pázmány P. stny. 1/C., Budapest, 1117, Hungary
| | - Zsolt Molnár
- Centre for Ecological Research, Institute of Ecology and Botany, Alkotmány u. 2-4., Vácrátót, 2163, Hungary
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6
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Urbaniak J, Kwiatkowski P. The molecular population structure of Swertia perennis (Gentianaceae) in Central Europe. Sci Rep 2023; 13:17059. [PMID: 37816773 PMCID: PMC10564900 DOI: 10.1038/s41598-023-43731-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/27/2023] [Indexed: 10/12/2023] Open
Abstract
Phylogeographic analysis of Swertia perennis, a typical European subalpine springtime species, revealed the existence of at least five major phylogenetic lineages. A large phylogeographic separation exists among these geographical regions, which confirms the existence of glacial refugia in the Pyrenees, but also in the Eastern and Central Alps. The results obtained from the analyzes indicate the existence of three major differences between the populations of the Alps and the Pyrenees, but also between the populations of the Alps and those of other geographical regions (Carpathians, southern Czech Republic, Sudetes and northern Poland). The studied populations from the Black Forest and from north-eastern and southern Poland are a relic of the former wider distribution of these (periglacial) genetic groups within Swertia perennis. Our results also confirm the existence of biogeographical links between the Carpathians and the Hercynian Range and the Alps. Certainly, there was an exchange of genes between populations located in the eastern Alps, the Carpathians and the Hercynian ranges (Czech Republic, Jeseníky, Sudetes, Ore Mountains). This confirms previous results of comparative studies on the genetic diversity of populations of other vascular plant species.
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Affiliation(s)
- Jacek Urbaniak
- Department of Botany and Plant Ecology, Wrocław University of Environmental and Life Sciences, Wrocław, Poland.
| | - Paweł Kwiatkowski
- Institute of Biology, Biotechnology, and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
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7
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Brusentsov II, Gordeev MI, Yurchenko AA, Karagodin DA, Moskaev AV, Hodge JM, Burlak VA, Artemov GN, Sibataev AK, Becker N, Sharakhov IV, Baricheva EM, Sharakhova MV. Patterns of genetic differentiation imply distinct phylogeographic history of the mosquito species Anopheles messeae and Anopheles daciae in Eurasia. Mol Ecol 2023; 32:5609-5625. [PMID: 37702976 DOI: 10.1111/mec.17127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 08/17/2023] [Accepted: 08/24/2023] [Indexed: 09/14/2023]
Abstract
Detailed knowledge of phylogeography is important for control of mosquito species involved in the transmission of human infectious diseases. Anopheles messeae is a geographically widespread and genetically diverse dominant vector of malaria in Eurasia. A closely related species, An. daciae, was originally distinguished from An. messeae based on five nucleotide substitutions in its ribosomal DNA (rDNA). However, the patterns of phylogeographic history of these species in Eurasia remain poorly understood. Here, using internal transcribed spacer 2 (ITS2) of rDNA and karyotyping for the species identification we determined the composition of five Anopheles species in 28 locations in Eurasia. Based on the frequencies of 11 polymorphic chromosomal inversions used as genetic markers, a large-scale population genetics analysis was performed of 1932 mosquitoes identified as An. messeae, An. daciae and their hybrids. The largest genetic differences between the species were detected in the X sex chromosome suggesting a potential involvement of this chromosome in speciation. The frequencies of autosomal inversions in the same locations differed by 13%-45% between the species demonstrating a restricted gene flow between the species. Overall, An. messeae was identified as a diverse species with a more complex population structure than An. daciae. The clinal gradients in frequencies of chromosomal inversions were determined in both species implicating their possible involvement in climate adaptations. The frequencies of hybrids were low ~1% in northern Europe but high up to 50% in south-eastern populations. Thus, our study revealed critical differences in patterns of phylogeographic history between An. messeae and An. daciae in Eurasia. This knowledge will help to predict the potential of the malaria transmission in the northern territories of the continent.
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Affiliation(s)
- Ilya I Brusentsov
- Department of Entomology, Virginia Polytechnic Institute and State University and Fralin Life Sciences Institute, Blacksburg, Virginia, USA
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
| | | | - Andrey A Yurchenko
- Department of Entomology, Virginia Polytechnic Institute and State University and Fralin Life Sciences Institute, Blacksburg, Virginia, USA
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Dimitriy A Karagodin
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
| | | | - James M Hodge
- Department of Entomology, Virginia Polytechnic Institute and State University and Fralin Life Sciences Institute, Blacksburg, Virginia, USA
| | - Vladimir A Burlak
- Laboratory of Ecology, Genetics, and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Gleb N Artemov
- Laboratory of Ecology, Genetics, and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Anuarbek K Sibataev
- Department of General Biology and Genomics, L.N. Gumilyov Eurasian National University, Nur-Sultan, Kazakhstan
- Department of Agricultural Biology, Tomsk State University, Tomsk, Russia
| | - Norbert Becker
- Center for Organismal Studies, University of Heidelberg, Heidelberg, Germany
- German Mosquito Control Association, Speyer, Germany
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic Institute and State University and Fralin Life Sciences Institute, Blacksburg, Virginia, USA
- Laboratory of Ecology, Genetics, and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Elina M Baricheva
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Maria V Sharakhova
- Department of Entomology, Virginia Polytechnic Institute and State University and Fralin Life Sciences Institute, Blacksburg, Virginia, USA
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
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8
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Urbaniak J, Kwiatkowski P. The Role of the Hercynian Mountains of Central Europe in Shaping Plant Migration Patterns in the Pleistocene-A Review. PLANTS (BASEL, SWITZERLAND) 2023; 12:3317. [PMID: 37765481 PMCID: PMC10537488 DOI: 10.3390/plants12183317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 08/31/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023]
Abstract
The climatic changes that took place in Europe during the Quaternary period influenced plant habitats as well as their species and vegetation composition. In this article, biogeographical studies on Hercynian mountain plants that include data for the Alps, Carpathians, and European lowlands are reviewed in order to discuss the phylogeographical structure and divergence of the Hercynian populations from those in other European mountain ranges, Scandinavia, and lowlands. The analyzed studies show specific phylogeographical relations between the Hercynian mountains, Alps, Scandinavia, Carpathians, and European lowlands. The results also indicate that the genetic patterns of plant populations in the Hercynian Mountains may differ significantly in terms of origin. The main migration routes of species to the Hercynian ranges began in the Alps or Carpathians. Some species, such as Rubus chamaemorus L., Salix lapponum L., and Salix herbacea L., are glacial relics that may have arrived and settled in the Hercynian Mountains during the Ice Age and that survived in isolated habitats. The Hercynian Mountains are composed of various smaller mountain ranges and are a crossroads of migration routes from different parts of Europe; thus, intensive hybridization has occurred between the plant populations therein, which is indicated by the presence of several divergent genetic lines.
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Affiliation(s)
- Jacek Urbaniak
- Department of Botany and Plant Ecology, Wrocław University of Environmental and Life Sciences, 50-363 Wrocław, Poland
| | - Paweł Kwiatkowski
- Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-032 Katowice, Poland;
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9
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Herczeg D, Palomar G, Zieliński P, van Riemsdijk I, Babik W, Dankovics R, Halpern B, Cvijanović M, Vörös J. Genomic analysis reveals complex population structure within the smooth newt, Lissotriton vulgaris, in Central Europe. Ecol Evol 2023; 13:e10478. [PMID: 37664508 PMCID: PMC10469019 DOI: 10.1002/ece3.10478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 08/01/2023] [Accepted: 08/08/2023] [Indexed: 09/05/2023] Open
Abstract
Species with wide-range distributions usually display high genetic variation. This variation can be partly explained by historical lineages that were temporally isolated from each other and are back into secondary reproductive contact, and partly by local adaptations. The smooth newt (Lissotriton vulgaris) is one of the most widely distributed amphibians species across Eurasia and forms a species complex with a partially overlapping distribution and morphology. In the present study, we explored the population genomic structure of smooth newt lineages in the Carpathian Basin (CB) relying on single-nucleotide polymorphisms. Our dataset included new and previously published data to study the secondary contact zone between lineages in the CB and also tested for the barrier effect of rivers to gene flow between these lineages. We confirmed the presence of the South L. v. vulgaris Lineage distributed in Transdanubia and we provided new distribution records of L. v. ampelensis inhabiting the eastern territories of the CB. High genetic diversity of smooth newts was observed, especially in the North Hungarian Mountains and at the interfluves of the main rivers in the South with four distinct lineages of L. v. vulgaris and one lineage of L. v. ampelensis showing a low level of admixture with the spatially closest L. v. vulgaris lineage. Moreover, admixture detected at the interfluve of the main rivers (i.e. Danube and Tisza) suggested a secondary contact zone in the area. Finally, we found that the river Danube has a very weak effect on population divergence, while the river Tisza is a geographical barrier limiting gene flow between smooth newt lineages. As the range boundaries of L. v. vulgaris and L. v. ampelensis in the CB coincide with the river Tisza, our study underpins the influence of rivers in lineage diversification.
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Affiliation(s)
- Dávid Herczeg
- ELKH‐ELTE‐MTM Integrative Ecology Research GroupBudapestHungary
- Department of Systematic Zoology and Ecology, Institute of BiologyELTE Eötvös Loránd UniversityBudapestHungary
| | - Gemma Palomar
- Department of Genetics, Physiology, and Microbiology, Faculty of Biological SciencesComplutense University of MadridMadridSpain
- Institute of Environmental SciencesFaculty of Biology, Jagiellonian UniversityKrakówPoland
| | - Piotr Zieliński
- Institute of Environmental SciencesFaculty of Biology, Jagiellonian UniversityKrakówPoland
| | | | - Wiesław Babik
- Institute of Environmental SciencesFaculty of Biology, Jagiellonian UniversityKrakówPoland
| | | | - Bálint Halpern
- ELKH‐ELTE‐MTM Integrative Ecology Research GroupBudapestHungary
- Department of Systematic Zoology and Ecology, Institute of BiologyELTE Eötvös Loránd UniversityBudapestHungary
- MME Birdlife HungaryBudapestHungary
| | - Milena Cvijanović
- Institute for Biological Research “Siniša Stanković”, National Institute of the Republic of SerbiaUniversity of BelgradeBelgradeSerbia
| | - Judit Vörös
- Department of ZoologyHungarian Natural History MuseumBudapestHungary
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10
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Fu J, Wen L. Impacts of Quaternary glaciation, geological history and geography on animal species history in continental East Asia: A phylogeographic review. Mol Ecol 2023; 32:4497-4514. [PMID: 37332105 DOI: 10.1111/mec.17053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 06/20/2023]
Abstract
Continental East Asia has a mild Pleistocene climate and a complex recent geological history. Phylogeographic studies of animals over the last 30 years have produced several distinctive patterns. Glaciation refugia are numerous and are not restricted to any particular regions. Most of them are localized and species-specific, although several large refugia, for example the mountains of SW China, are shared by multiple species and have refugia-within-refugia. Furthermore, postglaciation range expansion events vary greatly in time, scale and direction. Large-scale south-to-north post-LGM expansions are few and mostly occurred in the northern regions. Additionally, several unique geographic features, including the three-step terrain of China and the northern arid belt, have significant impacts on many species histories. Overall, the impacts of Pleistocene glaciations, particularly the LGM, on species history vary drastically from nondetectable to significant. The impacts are the least for species from the southwestern region and are most dominant for species from the north. Geological events play a more significant role in shaping species history than Pleistocene climatic changes. Phylogeographic patterns among animals species are highly consistent with those of plants. Future phylogeographic endeavour in East Asia should be hypothesis-driven and seek processes that underlie common patterns. The wide use of genomic data allow accurate estimates of historical population processes and exploration of older history beyond the Pleistocene.
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Affiliation(s)
- Jinzhong Fu
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Longying Wen
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
- Key Laboratory of Sichuan Institute for Protecting Endangered Birds in the Southwest Mountains, College of Life Sciences, Leshan Normal University, Leshan, China
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11
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Phylogeography of Ramalina farinacea (Lichenized Fungi, Ascomycota) in the Mediterranean Basin, Europe, and Macaronesia. DIVERSITY 2023. [DOI: 10.3390/d15030310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Ramalina farinacea is an epiphytic lichen-forming fungus with a broad geographic distribution, especially in the Northern Hemisphere. In the eighties of the last century, it was hypothesized that R. farinacea had originated in the Macaronesian–Mediterranean region, with the Canary Islands as its probable southernmost limit, and thereafter it would have increased its distribution area. In order to explore the phylogeography of this emblematic lichen, we analyzed 120 thalli of R. farinacea collected in 38 localities distributed in temperate and boreal Europe, the Western Mediterranean Basin, and several Macaronesian archipelagos in the Atlantic Ocean. Data from two nuclear markers (nrITS and uid70) of the mycobiont were obtained to calculate genetic diversity indices to infer the phylogenies and haplotype networks and to investigate population structure. In addition, dating analysis was conducted to provide a valuable hypothesis of the timing of the origin and diversification of R. farinacea and its close allies. Our results highlight that phylogenetic species circumscription in the “Ramalina farinacea group” is complex and suggests that incomplete lineage sorting is at the base of conflicting phylogenetic signals. The existence of a high number of haplotypes restricted to the Macaronesian region, together with the diversification of R. farinacea in the Pleistocene, suggests that this species and its closest relatives originated during relatively recent geological times and then expanded its range to higher latitudes. However, our data cannot rule out whether the species originated from the Macaronesian archipelagos exclusively or also from the Mediterranean Basin. In conclusion, the present work provides a valuable biogeographical hypothesis for disentangling the evolution of this epiphytic lichen in space and time.
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12
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Gerschwitz‐Eidt MA, Dillenberger MS, Kadereit JW. Phylogeny of Saxifraga section Saxifraga subsection Arachnoideae (Saxifragaceae) and the origin of low elevation shade-dwelling species. Ecol Evol 2023; 13:e9728. [PMID: 36636428 PMCID: PMC9829489 DOI: 10.1002/ece3.9728] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 12/23/2022] [Indexed: 01/11/2023] Open
Abstract
Saxifraga section Saxifraga subsection Arachnoideae is a lineage of 12 species distributed mainly in the European Alps. It is unusual in terms of ecological diversification by containing both high elevation species from exposed alpine habitats and low elevation species from shady habitats such as overhanging rocks and cave entrances. Our aims are to explore which of these habitat types is ancestral, and to identify the possible drivers of this remarkable ecological diversification. Using a Hybseq DNA-sequencing approach and a complete species sample we reconstructed and dated the phylogeny of subsection Arachnoideae. Using Landolt indicator values, this phylogenetic tree was used for the reconstruction of the evolution of temperature, light and soil pH requirements in this lineage. Diversification of subsection Arachnoideae started in the late Pliocene and continued through the Pleistocene. Both diversification among and within clades was largely allopatric, and species from shady habitats with low light requirements are distributed in well-known refugia. We hypothesize that low light requirements evolved when species persisting in cold-stage refugia were forced into marginal habitats by more competitive warm-stage vegetation. While we do not claim that such competition resulted in speciation, it very likely resulted in adaptive evolution.
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Affiliation(s)
- Michael A. Gerschwitz‐Eidt
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg‐UniversitätMainzGermany
| | - Markus S. Dillenberger
- Institut für Biologie, AG Systematische Botanik und Pflanzengeographie, Freie Universität BerlinBerlinGermany
| | - Joachim W. Kadereit
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg‐UniversitätMainzGermany,Present address:
Systematik, Biodiversität und Evolution der PflanzenLudwig‐Maximilians‐Universität MünchenMunichGermany
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13
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Ilić T, Kuzmanović N, Vukojičić S, Lakušić D. Phytogeographic Characteristics of Montane Coniferous Forests of the Central Balkan Peninsula (SE Europe). PLANTS (BASEL, SWITZERLAND) 2022; 11:3194. [PMID: 36501234 PMCID: PMC9741231 DOI: 10.3390/plants11233194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/12/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
We investigated taxonomic and endemic richness, patterns of spatial distribution, cenotic and spatial diversification, and chorological and life form spectra of montane coniferous forests in the central part of the Balkan Peninsula. We collected information on 1435 taxa (1351 at the level of species and 84 subspecies) with 65,289 species-occurrence data, published in 1930 original plots with a total area of about 215 ha in the analysis. All statistical analyses (univariate and multivariate) were performed on binary matrices prepared for different levels of analysis. Our main results showed that the montane coniferous forests of the central Balkan Peninsula represent very species-rich vegetation. At the same time, the high proportion of endemics indicated that the montane coniferous forests of the central Balkan Peninsula differ significantly from Central European and boreal forests of a similar type. Furthermore, we found that there were regional differences in the species composition of the coniferous forests of the Balkan Peninsula, and that the primary centers of floristic richness are located in the area of the central and continental Dinarides. This latter finding suggested that the true centers of the richness of European coniferous forests are located south of the Limestone Alps-Western Dinarides-Carpathian Foothills line in Romania, which used to be considered the center of the richness of the coniferous forests in Europe.
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14
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The velocity of postglacial migration of fire-adapted boreal tree species in eastern North America. Proc Natl Acad Sci U S A 2022; 119:e2210496119. [PMID: 36252032 PMCID: PMC9618057 DOI: 10.1073/pnas.2210496119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Earth's climate has been warming rapidly since the beginning of the industrial era, forcing terrestrial organisms to adapt. Migration constitutes one of the most effective processes for surviving and thriving, although the speed at which tree species migrate as a function of climate change is unknown. One way to predict latitudinal movement of trees under the climate of the twenty-first century is to examine past migration since the Last Glacial Maximum. In this study, radiocarbon-dated macrofossils were used to calculate the velocity of past migration of jack pine (Pinus banksiana) and black spruce (Picea mariana), two important fire-adapted conifers of the North American boreal forest. Jack pine migrated at a mean rate of 19 km per century (km-cent) from unglaciated sites in the central and southeastern United States to the northern limit of the species in subarctic Canada. However, the velocity increased between unglaciated and early deglaciated sites in southern Quebec and slowed from early to mid-Holocene in central and eastern Quebec. Migration was at its lowest speed in late-Holocene times, when it stopped about 3,000 y ago. Compared with jack pine, black spruce migrated at a faster mean rate of 25 km-cent from the ice border at the last interstadial (Bølling/Allerød) to the species tree limit. The modern range of both species was nearly occupied about 6,000 y ago. The factors modulating the changing velocity of jack pine migration were closely associated with the warm-dry climate of the late Pleistocene-Holocene transition and the more humid climate of the mid- and late-Holocene.
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15
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Padullés Cubino J. Environmental drivers of taxonomic and functional turnover of tree assemblages in Europe. OIKOS 2022. [DOI: 10.1111/oik.09579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Josep Padullés Cubino
- Dept of Botany and Zoology, Faculty of Science, Masaryk Univ. Brno Czech Republic
- Centre for Ecological Research and Forestry Applications (CREAF) Cerdanyola del Vallès Spain
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16
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Phylogeographic structure of common sage (Salvia officinalis L.) reveals microrefugia throughout the Balkans and colonizations of the Apennines. Sci Rep 2022; 12:15726. [PMID: 36130954 PMCID: PMC9492721 DOI: 10.1038/s41598-022-20055-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/08/2022] [Indexed: 11/24/2022] Open
Abstract
Studying the population-genetic and phylogeographic structures of a representative species of a particular geographical region can not only provide us with information regarding its evolutionary history, but also improve our understanding of the evolutionary processes underlying the patterns of species diversity in that area. By analysing eight highly polymorphic microsatellite loci and two chloroplast DNA regions, we have investigated the influence of Pleistocene climate fluctuations on the evolutionary history of Salvia officinalis L. (common sage). The populations with the highest genetic diversity were located in the central parts of the Balkan distribution range. A large group of closely related haplotypes was distributed throughout the Balkans and the central Apennines, while the private lineage occupied the southern Apennines. In addition, two highly differentiated lineages were scattered only over the Balkans. The results suggest that a single refugium of the studied species from the last glacial period was located in the central part of the range in the Balkans. Numerous microrefugia, probably spanning several glaciation cycles, were scattered across the Balkans, while colonisation of the Apennines from the Balkans occurred at least on two occasions.
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17
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Molfini M, Mancini E, Bologna MA. Phylogeny of European
Pyrochroa
(Coleoptera, Pyrochroidae) reveals cryptic taxa and different glacial histories. ZOOL SCR 2022. [DOI: 10.1111/zsc.12569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marco Molfini
- Department of Science Roma Tre University Rome Italy
| | - Emiliano Mancini
- Department of Biology and Biotechnology “Charles Darwin” Sapienza University Rome Italy
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18
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Kitamura K, Matsui T, Kobayashi M, Namikawa K. A comprehensive overview of studies related to the ecology and genetics of
Fagus crenata
Blume (Siebold's beech, Japanese beech) at the species' northernmost range limit. Ecol Res 2022. [DOI: 10.1111/1440-1703.12356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Keiko Kitamura
- Hokkaido Research Center Forestry and Forest Products Research Institute, Forest Research and Management Organization Sapporo Hokkaido Japan
| | - Tetsuya Matsui
- Center for Biodiversity and Climate Change Forestry and Forest Products Research Institute, Forest Research and Management Organization Ibaraki Japan
- Faculty of Life and Environmental Sciences University of Tsukuba Tsukuba Japan
| | | | - Kanji Namikawa
- Biological Laboratory Sapporo Campus, Hokkaido University of Education Sapporo Hokkaido Japan
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19
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Plis K, Niedziałkowska M, Borowik T, Lang J, Heddergott M, Tiainen J, Bunevich A, Šprem N, Paule L, Danilkin A, Kholodova M, Zvychaynaya E, Kashinina N, Pokorny B, Flajšman K, Paulauskas A, Djan M, Ristić Z, Novák L, Kusza S, Miller C, Tsaparis D, Stoyanov S, Shkvyria M, Suchentrunk F, Kutal M, Lavadinović V, Šnjegota D, Krapal A, Dănilă G, Veeroja R, Dulko E, Jędrzejewska B. Pan‐European phylogeography of the European roe deer (
Capreolus capreolus
). Ecol Evol 2022; 12:e8931. [PMID: 35600675 PMCID: PMC9120558 DOI: 10.1002/ece3.8931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 04/13/2022] [Accepted: 04/25/2022] [Indexed: 11/18/2022] Open
Abstract
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.
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Affiliation(s)
- Kamila Plis
- Mammal Research Institute Polish Academy of Sciences Białowieża Poland
| | | | - Tomasz Borowik
- Mammal Research Institute Polish Academy of Sciences Białowieża Poland
| | - Johannes Lang
- Working Group for Wildlife Research at Clinic for Birds, Reptiles, Amphibians and Fish Justus‐Liebig‐University Giessen Gießen Germany
| | - Mike Heddergott
- Department of Zoology Musée National d’Histoire Naturelle Luxembourg City Luxembourg
| | - Juha Tiainen
- Lammi Biological Station University of Helsinki Lammi Finland
- Natural Resources Institute Finland (Luke) Helsinki Finland
| | - Aleksey Bunevich
- State National Park Belovezhskaya Pushcha Kamenyuki Republic of Belarus
| | - Nikica Šprem
- Department of Fisheries, Apiculture, Wildlife Management and Special Zoology Faculty of Agriculture University of Zagreb Zagreb Croatia
| | - Ladislav Paule
- Department of Phytology Technical University in Zvolen Zvolen Slovak Republic
| | - Aleksey Danilkin
- A.N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow Russia
| | - Marina Kholodova
- A.N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow Russia
| | - Elena Zvychaynaya
- A.N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow Russia
| | - Nadezhda Kashinina
- A.N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow Russia
| | - Boštjan Pokorny
- Faculty of Environmental Protection Velenje Slovenia
- Department of Forest Ecology Slovenian Forestry Institute Ljubljana Slovenia
| | - Katarina Flajšman
- Department of Forest Ecology Slovenian Forestry Institute Ljubljana Slovenia
| | | | - Mihajla Djan
- Department of Biology and Ecology Faculty of Sciences University of Novi Sad Novi Sad Republic of Serbia
| | - Zoran Ristić
- Department of Geography, Tourism and Hotel Management Faculty of Sciences University of Novi Sad Novi Sad Serbia
| | - Luboš Novák
- Department of Forest Protection and Wildlife Management Mendel University in Brno Brno Czech Republic
| | - Szilvia Kusza
- Centre for Agricultural Genomics and Biotechnology Faculty of Agricultural and Food Sciences and Environmental Management University of Debrecen Debrecen Hungary
| | | | - Dimitris Tsaparis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC) Hellenic Centre for Marine Research Heraklion, Crete Greece
| | - Stoyan Stoyanov
- Wildlife Management Department University of Forestry Sofia Bulgaria
| | | | - Franz Suchentrunk
- Research Institute of Wildlife Ecology University of Veterinary Medicine Vienna Vienna Austria
| | - Miroslav Kutal
- Department of Forest Ecology Faculty of Forestry and Wood Technology Mendel University in Brno Brno Czech Republic
| | | | - Dragana Šnjegota
- Faculty of Natural Sciences and Mathematics University of Banja Luka Banja Luka Bosnia and Herzegovina
| | - Ana‐Maria Krapal
- "Grigore Antipa" National Museum of Natural History Bucharest Romania
| | - Gabriel Dănilă
- Faculty of Forestry Stefan cel Mare University of Suceava Suceava Romania
| | - Rauno Veeroja
- Department of Wildlife Monitoring Estonian Environment Agency Tallin Estonia
| | - Elżbieta Dulko
- Department of Anesthesiology University of Virginia Health System Charlottesville Virginia USA
- Faculty of Biology University of Warsaw Warszawa Poland
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20
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Kirschner P, Perez MF, Záveská E, Sanmartín I, Marquer L, Schlick-Steiner BC, Alvarez N, Steiner FM, Schönswetter P. Congruent evolutionary responses of European steppe biota to late Quaternary climate change. Nat Commun 2022; 13:1921. [PMID: 35396388 PMCID: PMC8993823 DOI: 10.1038/s41467-022-29267-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 03/08/2022] [Indexed: 11/09/2022] Open
Abstract
Quaternary climatic oscillations had a large impact on European biogeography. Alternation of cold and warm stages caused recurrent glaciations, massive vegetation shifts, and large-scale range alterations in many species. The Eurasian steppe biome and its grasslands are a noteworthy example; they underwent climate-driven, large-scale contractions during warm stages and expansions during cold stages. Here, we evaluate the impact of these range alterations on the late Quaternary demography of several phylogenetically distant plant and insect species, typical of the Eurasian steppes. We compare three explicit demographic hypotheses by applying an approach combining convolutional neural networks with approximate Bayesian computation. We identified congruent demographic responses of cold stage expansion and warm stage contraction across all species, but also species-specific effects. The demographic history of the Eurasian steppe biota reflects major paleoecological turning points in the late Quaternary and emphasizes the role of climate as a driving force underlying patterns of genetic variance on the biome level.
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Affiliation(s)
- Philipp Kirschner
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020, Innsbruck, Austria. .,Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria.
| | - Manolo F Perez
- Real Jardín Botánico, CSIC, Plaza de Murillo 2, 28014, Madrid, Spain.,Departamento de Genetica e Evolucao, Universidade Federal de Sao Carlos, Rodovia Washington Luis, km 235, 13565905, Sao Carlos, Brazil
| | - Eliška Záveská
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020, Innsbruck, Austria.,Institute of Botany of the Czech Academy of Sciences, Zámek 1, 25243, Průhonice, Czech Republic
| | - Isabel Sanmartín
- Real Jardín Botánico, CSIC, Plaza de Murillo 2, 28014, Madrid, Spain
| | - Laurent Marquer
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020, Innsbruck, Austria
| | | | - Nadir Alvarez
- Geneva Natural History Museum of Geneva, Route de Malagnou 1, 1208, Genève, Switzerland.,Department of Genetics and Evolution, University of Geneva, Boulevard D'Yvoy 4, 1205, Genève, Switzerland
| | | | - Florian M Steiner
- Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria
| | - Peter Schönswetter
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020, Innsbruck, Austria.
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21
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Rešetnik I, Záveská E, Grgurev M, Bogdanović S, Bartolić P, Frajman B. Stability in the South, Turbulence Toward the North: Evolutionary History of Aurinia saxatilis (Brassicaceae) Revealed by Phylogenomic and Climatic Modelling Data. FRONTIERS IN PLANT SCIENCE 2022; 13:822331. [PMID: 35360300 PMCID: PMC8964184 DOI: 10.3389/fpls.2022.822331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
The Balkan Peninsula played an important role in the evolution of many Mediterranean plants and served as a major source for post-Pleistocene colonisation of central and northern Europe. Its complex geo-climatic history and environmental heterogeneity significantly influenced spatiotemporal diversification and resulted in intricate phylogeographic patterns. To explore the evolutionary dynamics and phylogeographic patterns within the widespread eastern Mediterranean and central European species Aurinia saxatilis, we used a combination of phylogenomic (restriction-site associated DNA sequencing, RADseq) and phylogenetic (sequences of the plastid marker ndhF) data as well as species distribution models generated for the present and the Last Glacial Maximum (LGM). The inferred phylogenies retrieved three main geographically distinct lineages. The southern lineage is restricted to the eastern Mediterranean, where it is distributed throughout the Aegean area, the southern Balkan Peninsula, and the southern Apennine Peninsula, and corresponds to the species main distribution area during the LGM. The eastern lineage extends from the eastern Balkan Peninsula over the Carpathians to central Europe, while the central lineage occupies the central Balkan Peninsula. Molecular dating places the divergence among all the three lineages to the early to middle Pleistocene, indicating their long-term independent evolutionary trajectories. Our data revealed an early divergence and stable in situ persistence of the southernmost, eastern Mediterranean lineage, whereas the mainland, south-east European lineages experienced more complex and turbulent evolutionary dynamics triggered by Pleistocene climatic oscillations. Our data also support the existence of multiple glacial refugia in southeast Europe and highlight the central Balkan Peninsula not only as a cradle of lineage diversifications but also as a source of lineage dispersal. Finally, the extant genetic variation within A. saxatilis is congruent with the taxonomic separation of peripatric A. saxatilis subsp. saxatilis and A. saxatilis subsp. orientalis, whereas the taxonomic status of A. saxatilis subsp. megalocarpa remains doubtful.
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Affiliation(s)
- Ivana Rešetnik
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Eliška Záveská
- Institute of Botany, Czech Academy of Sciences, Prague, Czechia
| | - Marin Grgurev
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Sandro Bogdanović
- Department of Agricultural Botany, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Zagreb, Croatia
| | - Paolo Bartolić
- Department of Botany, Charles University, Prague, Czechia
| | - Božo Frajman
- Department of Botany, University of Innsbruck, Innsbruck, Austria
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22
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Reconstructing Neanderthal diet: The case for carbohydrates. J Hum Evol 2021; 162:103105. [PMID: 34923240 DOI: 10.1016/j.jhevol.2021.103105] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 12/22/2022]
Abstract
Evidence for plants rarely survives on Paleolithic sites, while animal bones and biomolecular analyses suggest animal produce was important to hominin populations, leading to the perspective that Neanderthals had a very-high-protein diet. But although individual and short-term survival is possible on a relatively low-carbohydrate diet, populations are unlikely to have thrived and reproduced without plants and the carbohydrates they provide. Today, nutritional guidelines recommend that around half the diet should be carbohydrate, while low intake is considered to compromise physical performance and successful reproduction. This is likely to have been the same for Paleolithic populations, highlighting an anomaly in that the basic physiological recommendations do not match the extensive archaeological evidence. Neanderthals had large, energy-expensive brains and led physically active lifestyles, suggesting that for optimal health they would have required high amounts of carbohydrates. To address this anomaly, we begin by outlining the essential role of carbohydrates in the human reproduction cycle and the brain and the effects on physical performance. We then evaluate the evidence for resource availability and the archaeological evidence for Neanderthal diet and investigate three ways that the anomaly between the archaeological evidence and the hypothetical dietary requirements might be explained. First, Neanderthals may have had an as yet unidentified genetic adaptation to an alternative physiological method to spare blood glucose and glycogen reserves for essential purposes. Second, they may have existed on a less-than-optimum diet and survived rather than thrived. Third, the methods used in dietary reconstruction could mask a complex combination of dietary plant and animal proportions. We end by proposing that analyses of Paleolithic diet and subsistence strategies need to be grounded in the minimum recommendations throughout the life course and that this provides a context for interpretation of the archaeological evidence from the behavioral and environmental perspectives.
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23
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Urbaniak J, Kwiatkowski P, Pawlikowski P. Genetic diversity of Salixlapponum populations in Central Europe. PHYTOKEYS 2021; 184:83-101. [PMID: 34785973 PMCID: PMC8589822 DOI: 10.3897/phytokeys.184.71641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Salixlapponum is a cold-tolerant relict species in Europe that occurs in several sites, probably reflecting previous migration routes of S.lapponum during the Pleistocene. However, only a few data are available on the genetic structures of populations of S.lapponum. In this study, we use PCR-ISSR markers to investigate genetic variation in 19 European populations of S.lapponum L. AMOVA analysis shows that most of the variation (55.8%) occurs within populations; variability among groups accounts for 19.7%. An AMOVA analysis based on four groups determined by STRUCTURE analysis shows similar results: variability of 54.1% within the population and variability of 18.9% between the four population groups, based on geographic regions. Within individual geographic groups, which are characterised by the studied populations, the lowest variability (as well as the highest homogeneity) was found in populations located in Belarus. The obtained results are consistent with our expectations that the European Lowland could be a significant geographic barrier for gene flow over large geographic distances for S.lapponum. Both the Scandinavian and Belarusian populations, as well as those coming from NE Poland, are characterised by significant genetic distinctiveness. However, some populations from NE Poland and the Sudetes show similarities with populations from other geographic regions, indicating existing genetic relationships between them. Moreover, the results suggest a fairly clear division of the population into 4 emerging geographic regions, although separated by a geographical barrier: the Polish lowland, which forms part of the larger geographic unit known as the European Lowland.
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Affiliation(s)
- Jacek Urbaniak
- Department of Botany and Plant Ecology, Wrocław University of Environmental and Life Sciences, PolandWrocław University of Environmental and Life SciencesWroclawPoland
| | - Paweł Kwiatkowski
- Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, PolandUniversity of Silesia in KatowiceKatowicePoland
| | - Paweł Pawlikowski
- Department of Plant Ecology and Environmental Conservation, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, PolandUniversity of WarsawWarszawaPoland
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24
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Mamos T, Jażdżewski K, Čiamporová-Zaťovičová Z, Čiampor F, Grabowski M. Fuzzy species borders of glacial survivalists in the Carpathian biodiversity hotspot revealed using a multimarker approach. Sci Rep 2021; 11:21629. [PMID: 34732763 PMCID: PMC8566499 DOI: 10.1038/s41598-021-00320-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/08/2021] [Indexed: 11/21/2022] Open
Abstract
The Carpathians are one of the key biodiversity hotspots in Europe. The mountain chain uplifted during Alpine orogenesis and is characterised by a complex geological history. Its current biodiversity was highly influenced by Pleistocene glaciations. The goal of the current study was to examine the phylogenetic and demographic history of Gammarus balcanicus species complex in the Carpathians using multiple markers as well as to delimit, using an integrative approach, and describe new species hidden so far under the name G. balcanicus. Results showed that divergence of the studied lineages reaches back to the Miocene, which supports the hypothesis of their survival in multiple micro refugia. Moreover, the increase of their diversification rate in the Pleistocene suggests that glaciation was the driving force of their speciation. The climatic changes during and after the Pleistocene also played a major role in the demography of the local Carpathian lineages. Comparison of diversity patterns and phylogenetic relationships of both, the mitochondrial and nuclear markers, provide evidence of putative hybridisation and retention of ancient polymorphism (i.e., incomplete lineage sorting). The morphological examination supported the existence of two morphological types; one we describe as a G. stasiuki sp. nov. and another we redescribe as a G. tatrensis (S. Karaman, 1931).
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Affiliation(s)
- Tomasz Mamos
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237, Lodz, Poland.
| | - Krzysztof Jażdżewski
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237, Lodz, Poland
| | - Zuzana Čiamporová-Zaťovičová
- ZooLab, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23, Bratislava, Slovakia
- Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Fedor Čiampor
- ZooLab, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23, Bratislava, Slovakia
| | - Michał Grabowski
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237, Lodz, Poland
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Xu J, Zang F, Wu Q, Wang Y, Wang B, Huang P, Zang D, Ma Y, Zheng Y. Analysis of the genetic diversity and molecular phylogeography of the endangered wild rose (Rosa rugosa) in China based on chloroplast genes. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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26
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Rendón-Anaya M, Wilson J, Sveinsson S, Fedorkov A, Cottrell J, Bailey MES, Ruņģis D, Lexer C, Jansson S, Robinson KM, Street NR, Ingvarsson PK. Adaptive introgression facilitate adaptation to high latitudes in European aspen (Populus tremula L.). Mol Biol Evol 2021; 38:5034-5050. [PMID: 34329481 PMCID: PMC8557470 DOI: 10.1093/molbev/msab229] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Understanding local adaptation has become a key research area given the ongoing climate challenge and the concomitant requirement to conserve genetic resources. Perennial plants, such as forest trees, are good models to study local adaptation given their wide geographic distribution, largely outcrossing mating systems, and demographic histories. We evaluated signatures of local adaptation in European aspen (Populus tremula) across Europe by means of whole-genome resequencing of a collection of 411 individual trees. We dissected admixture patterns between aspen lineages and observed a strong genomic mosaicism in Scandinavian trees, evidencing different colonization trajectories into the peninsula from Russia, Central and Western Europe. As a consequence of the secondary contacts between populations after the last glacial maximum, we detected an adaptive introgression event in a genome region of ∼500 kb in chromosome 10, harboring a large-effect locus that has previously been shown to contribute to adaptation to the short growing seasons characteristic of Northern Scandinavia. Demographic simulations and ancestry inference suggest an Eastern origin—probably Russian—of the adaptive Nordic allele which nowadays is present in a homozygous state at the north of Scandinavia. The strength of introgression and positive selection signatures in this region is a unique feature in the genome. Furthermore, we detected signals of balancing selection, shared across regional populations, that highlight the importance of standing variation as a primary source of alleles that facilitate local adaptation. Our results, therefore, emphasize the importance of migration–selection balance underlying the genetic architecture of key adaptive quantitative traits.
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Affiliation(s)
- Martha Rendón-Anaya
- Linnean Centre for Plant Biology, Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Jonathan Wilson
- Linnean Centre for Plant Biology, Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Science, Uppsala, Sweden
| | | | - Aleksey Fedorkov
- Institute of Biology, Komi Science Center, Russian Academy of Sciences, Syktyvkar, Russia
| | - Joan Cottrell
- Forest Research, Northern Research Station, Roslin, UK
| | - Mark E S Bailey
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Dainis Ruņģis
- Genetic Resource Centre, Latvian State Forest Research Institute "Silava", LV2169 Salaspils, Latvia
| | - Christian Lexer
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Stefan Jansson
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Kathryn M Robinson
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Nathaniel R Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Pär K Ingvarsson
- Linnean Centre for Plant Biology, Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Science, Uppsala, Sweden
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Boluda CG, Rico VJ, Naciri Y, Hawksworth DL, Scheidegger C. Phylogeographic reconstructions can be biased by ancestral shared alleles: The case of the polymorphic lichen Bryoria fuscescens in Europe and North Africa. Mol Ecol 2021; 30:4845-4865. [PMID: 34252241 DOI: 10.1111/mec.16078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 06/21/2021] [Accepted: 06/29/2021] [Indexed: 11/26/2022]
Abstract
Large phylogeographic studies on lichens are scarce, and none involves a single species within which different lineages show fixed alternative dispersal strategies. We investigated Bryoria fuscescens (including B. capillaris) in Europe and western North Africa by phenotypically characterizing 1400 specimens from 64 populations and genotyping them with 14 microsatellites. We studied population structure and genetic diversity at the local and continental scales, discussed the post-glacial phylogeography, and compared dispersal capacities of phenotypes with and without soralia. Our main hypothesis is that the estimated phylogeography, migration routes, and dispersal capacities may be strongly biased by ancestral shared alleles. Scandinavia is genetically the richest area, followed by the Iberian Peninsula, the Carpathians, and the Alps. Three gene pools were detected: two partially linked to phenotypic characteristics, and the third one genetically related to the American sister species B. pseudofuscescens. The comparison of one gene pool producing soredia and one not, suggested both as panmictic, with similar levels of isolation by distance (IBD). The migration routes were estimated to span from north to south, in disagreement with the assessed glacial refugia. The presence of ancestral shared alleles in distant populations can explain the similar IBD levels found in both gene pools while producing a false signal of panmixia, and also biasing the phylogeographic reconstruction. The incomplete lineage sorting recorded for DNA sequence loci also supports this hypothesis. Consequently, the high diversity in Scandinavia may rather come from recent immigration into northern populations than from an in situ diversification. Similar patterns of ancestral shared polymorphism may bias the phylogeographical reconstruction of other lichen species.
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Affiliation(s)
- Carlos G Boluda
- Departamento de Farmacología, Farmacognosia y Botánica (U.D. Botánica), Facultad de Farmacia, Universidad Complutense, Madrid, Spain.,Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.,Laboratoire de Systématique Végétale et Biodiversité, Conservatoire et Jardin botaniques and Université de Genève, Chambésy, Switzerland
| | - Víctor J Rico
- Departamento de Farmacología, Farmacognosia y Botánica (U.D. Botánica), Facultad de Farmacia, Universidad Complutense, Madrid, Spain
| | - Yamama Naciri
- Laboratoire de Systématique Végétale et Biodiversité, Conservatoire et Jardin botaniques and Université de Genève, Chambésy, Switzerland
| | - David L Hawksworth
- Department of Life Sciences, The Natural History Museum, London, UK.,Comparative Fungal Biology, Royal Botanic Gardens, Kew, UK
| | - Christoph Scheidegger
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
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Kohli M, Djernæs M, Sanchez Herrera M, Sahlen G, Pilgrim E, Simonsen TJ, Olsen K, Ware J. Comparative phylogeography uncovers evolutionary past of Holarctic dragonflies. PeerJ 2021; 9:e11338. [PMID: 34221703 PMCID: PMC8236228 DOI: 10.7717/peerj.11338] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/02/2021] [Indexed: 12/05/2022] Open
Abstract
Here, we investigate the evolutionary history of five northern dragonfly species to evaluate what role the last glaciation period may have played in their current distributions. We look at the population structure and estimate divergence times for populations of the following species: Aeshna juncea (Linnaeus), Aeshna subarctica Walker, Sympetrum danae (Sulzer), Libellula quadrimaculata Linnaeus and Somatochlora sahlbergi Trybom across their Holarctic range. Our results suggest a common phylogeographic pattern across all species except for S. sahlbergi. First, we find that North American and European populations are genetically distinct and have perhaps been separated for more than 400,000 years. Second, our data suggests that, based on genetics, populations from the Greater Beringian region (Beringia, Japan and China) have haplotypes that cluster with North America or Europe depending on the species rather than having a shared geographic affinity. This is perhaps a result of fluctuating sea levels and ice sheet coverage during the Quaternary period that influenced dispersal routes and refugia. Indeed, glacial Beringia may have been as much a transit zone as a refugia for dragonflies. Somatochlora sahlbergi shows no genetic variation across its range and therefore does not share the geographic patterns found in the other circumboreal dragonflies studied here. Lastly, we discuss the taxonomic status of Sympetrum danae, which our results indicate is a species complex comprising two species, one found in Eurasia through Beringia, and the other in North America east and south of Beringia. Through this study we present a shared history among different species from different families of dragonflies, which are influenced by the climatic fluctuations of the past.
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Affiliation(s)
- Manpreet Kohli
- Department of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States
- Department of Biological Sciences, Rutgers, The State University of New Jersey, Newark, New Jersey, United States
| | | | | | - Göran Sahlen
- The Rydberg Laboratory for Applied Sciences, Halmstad University, Halmstad, Sweden
| | - Erik Pilgrim
- Department of Biology, Utah State University, Logan, Utah, United States
| | - Thomas J Simonsen
- Natural History Museum Aarhus, Aarhus, Denmark
- Department of Biology, Aarhus University, Aarhus, Denmark
| | - Kent Olsen
- Natural History Museum Aarhus, Aarhus, Denmark
| | - Jessica Ware
- Department of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States
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Camps GA, Cosacov A, Sérsic AN. Centre-periphery approaches based on geography, ecology and historical climate stability: what explains the variation in morphological traits of Bulnesia sarmientoi? ANNALS OF BOTANY 2021; 127:943-955. [PMID: 33640970 PMCID: PMC8225285 DOI: 10.1093/aob/mcab034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND AND AIMS The centre-periphery hypothesis posits that higher species performance is expected in geographic and ecological centres rather than in peripheral populations. However, this is not the commonly found pattern; therefore, alternative approaches, including the historical dimension of species geographical ranges, should be explored. Morphological functional traits are fundamental determinants of species performance, commonly related to environmental stability and productivity. We tested whether or not historical processes may have shaped variations in tree and leaf traits of the Chaco tree Bulnesia sarmientoi. METHODS Morphological variation patterns were analysed from three centre-periphery approaches: geographical, ecological and historical. Tree (stem and canopy) and leaf (leaf size and specific leaf area) traits were measured in 24 populations across the species range. A principal component analysis was performed on morphological traits to obtain synthetic variables. Linear mixed-effects models were used to test which of the implemented centre-periphery approaches significantly explained trait spatial patterns. KEY RESULTS The patterns retrieved from the three centre-periphery approaches were not concordant. The historical approach revealed that trees were shorter in centre populations than in the periphery. Significant differences in leaf traits were observed between the geographical centre and the periphery, mainly due to low specific leaf area values towards the geographical centre. We did not find any pattern associated with the ecological centre-periphery approach. CONCLUSIONS The decoupled response between leaf and tree traits suggests that these sets of traits respond differently to processes occurring at different times. The geographical and historical approaches showed centres with extreme environments in relation to their respective peripheries, but the historical centre has also been a climatically stable area since the Last Glacial Maximum. The historical approach allowed for the recovery of historical processes underlying variation in tree traits, highlighting that centre-periphery delimitations should be based on a multi-approach framework.
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Affiliation(s)
- Gonzalo A Camps
- Instituto de Fisiología y Recursos Genéticos Vegetales (IFRGV), CIAP, INTA, Córdoba, Argentina
- Laboratorio de Ecología Evolutiva - Biología Floral, Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET-Universidad Nacional de Córdoba, Av. Vélez Sarsfield, Córdoba, Argentina
| | - Andrea Cosacov
- Laboratorio de Ecología Evolutiva - Biología Floral, Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET-Universidad Nacional de Córdoba, Av. Vélez Sarsfield, Córdoba, Argentina
| | - Alicia N Sérsic
- Laboratorio de Ecología Evolutiva - Biología Floral, Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET-Universidad Nacional de Córdoba, Av. Vélez Sarsfield, Córdoba, Argentina
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30
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Marin I, Palatov D. Cryptic refugee on the northern slope of the Greater Caucasian Ridge: Discovery of niphargus (Crustacea: Amphipoda: Niphargidae) in the North Ossetia–Alania, North Caucasus, separated from its relatives in the late Miocene. ZOOL ANZ 2021. [DOI: 10.1016/j.jcz.2021.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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31
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Fabritzek AG, Griebeler EM, Kadereit JW. Hybridization, ecogeographical displacement and the emergence of new lineages - A genotyping-by-sequencing and ecological niche and species distribution modelling study of Sempervivum tectorum L. (Houseleek). J Evol Biol 2021; 34:830-844. [PMID: 33714223 DOI: 10.1111/jeb.13784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/18/2021] [Accepted: 03/03/2021] [Indexed: 11/28/2022]
Abstract
Ecogeographical displacement of homoploid hybrid lineages from their parents is well documented and considered an important mechanism to achieve reproductive isolation. In this study, we investigated the origin of the flowering plant species Sempervivum tectorum in the Massif Central (France) through homoploid hybridization between lineages of the species from the Rhine Gorge area (Germany) and the Pyrenees (France). We used genotyping-by-sequencing genetic data as evidence for the hybrid origin of the Massif Central lineage, and WorldClim climatic data and soil pH and soil temperature data collected by us for ecological niche and species distribution modelling. We could show that the Massif Central lineage shows hybrid admixture and that the niche of this lineage is significantly different from those of the parental lineages. In comparison with the parental niches, different variables of the niche of the hybrid lineage are intermediate, parental-combined or extreme. The different niche of the Massif Central populations thus can plausibly be interpreted as hybridization-derived. Our species distribution modelling for the Last Glacial Maximum and Mid-Holocene showed that the potential distribution of the hybrid lineage at the likely time of its origin in the Quaternary possibly was parapatric in relation to the largely sympatric distributions of the parental lineages. We hypothesize that reproductive isolation of the hybrid lineage from the parental lineages resulted from the segregation of distribution ranges by a differential response of the three lineages to a warming climate.
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Affiliation(s)
- Armin G Fabritzek
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Eva Maria Griebeler
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Joachim W Kadereit
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
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Long-Term Responses of Mediterranean Mountain Forests to Climate Change, Fire and Human Activities in the Northern Apennines (Italy). Ecosystems 2020; 24:1361-1377. [PMID: 33288980 PMCID: PMC7710158 DOI: 10.1007/s10021-020-00587-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/01/2020] [Indexed: 11/11/2022]
Abstract
Fagus sylvatica (beech) dominates the montane forests of the Apennines and builds old-growth high-conservation value stands. However, recent severe drought-induced diebacks raise concern on the future persistence of these forests and of Southern European mesophilous woodlands overall, growing at their dry edge. To explore the history of Apennine beech-dominated forests, we draw on the multiproxy paleoecological record from Lago Verdarolo, which includes a robust vegetation-independent temperature reconstruction. Numerical techniques are used to investigate the drivers of long-term Mediterranean mountain forest dynamics. Specifically, we focus on disentangling the ecological factors that caused the shift from high-diversity mixed forests to beech-dominated stands and on assessing the occurrence of legacy effects on present-day forests. Abrupt climate change largely drove vegetation dynamics during the Late Glacial and Early Holocene. Species-rich mixed Abies alba (silver fir) forests dominated about 10,500—5500 years ago, under rather dry and warmer-than-today conditions (+ 1—2 °C) and limited fire occurrence. Cooler and moister summers and increasing fire activity caused declines in several fire-sensitive temperate deciduous trees (for example, Ulmus, Tilia, Fraxinus) and favored the establishment of fir-beech forests around 5500 years ago. Further enhancement of fire activity and farming around 2000 years ago led to local Abies alba extinction and forest impoverishment. We conclude that the currently widespread monospecific Apennine beech forests are the result of multi-millennial land-use intensification superimposed on Late Holocene cooling and moistening. Given their higher drought-tolerance compared to beech stands, reviving ancient species-rich mixed fir forests represents a feasible and ‘tested’ possibility to adapt forests to climate change.
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Bryophytes are predicted to lag behind future climate change despite their high dispersal capacities. Nat Commun 2020; 11:5601. [PMID: 33154374 PMCID: PMC7645420 DOI: 10.1038/s41467-020-19410-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 10/13/2020] [Indexed: 11/25/2022] Open
Abstract
The extent to which species can balance out the loss of suitable habitats due to climate warming by shifting their ranges is an area of controversy. Here, we assess whether highly efficient wind-dispersed organisms like bryophytes can keep-up with projected shifts in their areas of suitable climate. Using a hybrid statistical-mechanistic approach accounting for spatial and temporal variations in both climatic and wind conditions, we simulate future migrations across Europe for 40 bryophyte species until 2050. The median ratios between predicted range loss vs expansion by 2050 across species and climate change scenarios range from 1.6 to 3.3 when only shifts in climatic suitability were considered, but increase to 34.7–96.8 when species dispersal abilities are added to our models. This highlights the importance of accounting for dispersal restrictions when projecting future distribution ranges and suggests that even highly dispersive organisms like bryophytes are not equipped to fully track the rates of ongoing climate change in the course of the next decades. Bryophytes tend to be sensitive to warming, but their high dispersal ability could help them track climate change. Here the authors combine correlative niche models and mechanistic dispersal models for 40 European bryophyte species under RCP4.5 and RCP8.5, finding that most of these species are unlikely to track climate change over the coming decades.
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Prior CJ, Layman NC, Koski MH, Galloway LF, Busch JW. Westward range expansion from middle latitudes explains the Mississippi River discontinuity in a forest herb of eastern North America. Mol Ecol 2020; 29:4473-4486. [PMID: 32978776 DOI: 10.1111/mec.15650] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 09/01/2020] [Accepted: 09/04/2020] [Indexed: 01/22/2023]
Abstract
It is often expected that temperate plants have expanded their geographical ranges northward from primarily southern refugia. Evidence for this hypothesis is mixed in eastern North American species, and there is increasing support for colonization from middle latitudes. We studied genome-wide patterns of variation in RADseq loci to test hypotheses concerning range expansion in a North American forest herb (Campanula americana). First, spatial patterns of genetic differentiation were determined. Then phylogenetic relationships and divergence times were estimated. Spatial signatures of genetic drift were also studied to identify the directionality of recent range expansion and its geographical origins. Finally, spatially explicit scenarios for the spread of plants across the landscape were compared, using variation in the population mutation parameter and Tajima's D. We found strong longitudinal subdivision, with populations clustering into groups west and east of the Mississippi River. While the southeastern region was probably part of a diverse Pleistocene refugium, there is little evidence that range expansion involved founders from these southern locales. Instead, declines in genetic diversity and the loss of rare alleles support a westward colonization wave from a middle latitude refugium near the southern Appalachian Mountains, with subsequent expansion from a Pleistocene staging ground in the Mississippi River Valley (0.51-1.27 million years ago). These analyses implicate stepping stone colonization from middle latitudes as an important mechanism of species range expansion in eastern North America. This study further demonstrates the utility of population genetics as a tool to infer the routes travelled by organisms during geographical range expansion.
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Affiliation(s)
- Carly J Prior
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Nathan C Layman
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Matthew H Koski
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Laura F Galloway
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Jeremiah W Busch
- School of Biological Sciences, Washington State University, Pullman, WA, USA
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Saladin B, Pellissier L, Graham CH, Nobis MP, Salamin N, Zimmermann NE. Rapid climate change results in long-lasting spatial homogenization of phylogenetic diversity. Nat Commun 2020; 11:4663. [PMID: 32938914 PMCID: PMC7495423 DOI: 10.1038/s41467-020-18343-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 08/14/2020] [Indexed: 11/09/2022] Open
Abstract
Scientific understanding of biodiversity dynamics, resulting from past climate oscillations and projections of future changes in biodiversity, has advanced over the past decade. Little is known about how these responses, past or future, are spatially connected. Analyzing the spatial variability in biodiversity provides insight into how climate change affects the accumulation of diversity across space. Here, we evaluate the spatial variation of phylogenetic diversity of European seed plants among neighboring sites and assess the effects of past rapid climate changes during the Quaternary on these patterns. Our work shows a marked homogenization in phylogenetic diversity across Central and Northern Europe linked to high climate change velocity and large distances to refugia. Our results suggest that the future projected loss in evolutionary heritage may be even more dramatic, as homogenization in response to rapid climate change has occurred among sites across large landscapes, leaving a legacy that has lasted for millennia. How past climate change has affected biodiversity over large spatial scales remains underexplored. Here, the authors find marked homogenization in flowering plant phylogenetic diversity across Central and Northern Europe linked to rapid climate change and large distances to glacial refugia.
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Affiliation(s)
- Bianca Saladin
- Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland.
| | - Loïc Pellissier
- Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland.,Department of Environmental Systems Sciences, Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, 8092, Zurich, Switzerland
| | | | - Michael P Nobis
- Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
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Koch MA, Möbus J, Klöcker CA, Lippert S, Ruppert L, Kiefer C. The Quaternary evolutionary history of Bristol rock cress (Arabis scabra, Brassicaceae), a Mediterranean element with an outpost in the north-western Atlantic region. ANNALS OF BOTANY 2020; 126:103-118. [PMID: 32211750 PMCID: PMC7304472 DOI: 10.1093/aob/mcaa053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 03/19/2020] [Indexed: 05/29/2023]
Abstract
BACKGROUND AND AIMS Bristol rock cress is among the few plant species in the British Isles considered to have a Mediterranean-montane element. Spatiotemporal patterns of colonization of the British Isles since the last interglacial and after the Last Glacial Maximum (LGM) from mainland Europe are underexplored and have not yet included such floristic elements. Here we shed light on the evolutionary history of a relic and outpost metapopulation of Bristol rock cress in the south-western UK. METHODS Amplified fragment length polymorphisms (AFLPs) were used to identify distinct gene pools. Plastome assembly and respective phylogenetic analysis revealed the temporal context. Herbarium material was largely used to exemplify the value of collections to obtain a representative sampling covering the entire distribution range. KEY RESULTS The AFLPs recognized two distinct gene pools, with the Iberian Peninsula as the primary centre of genetic diversity and the origin of lineages expanding before and after the LGM towards mountain areas in France and Switzerland. No present-day lineages are older than 51 ky, which is in sharp contrast to the species stem group age of nearly 2 My, indicating severe extinction and bottlenecks throughout the Pleistocene. The British Isles were colonized after the LGM and feature high genetic diversity. CONCLUSIONS The short-lived perennial herb Arabis scabra, which is restricted to limestone, has expanded its distribution range after the LGM, following corridors within an open landscape, and may have reached the British Isles via the desiccated Celtic Sea at about 16 kya. This study may shed light on the origin of other rare and peculiar species co-occurring in limestone regions in the south-western British Isles.
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Affiliation(s)
- Marcus A Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Im Neuenheimer Feld 345, Heidelberg, Germany
| | - Johanna Möbus
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Im Neuenheimer Feld 345, Heidelberg, Germany
| | - Clara A Klöcker
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Im Neuenheimer Feld 345, Heidelberg, Germany
| | - Stephanie Lippert
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Im Neuenheimer Feld 345, Heidelberg, Germany
| | - Laura Ruppert
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Im Neuenheimer Feld 345, Heidelberg, Germany
| | - Christiane Kiefer
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Im Neuenheimer Feld 345, Heidelberg, Germany
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Tonzo V, Papadopoulou A, Ortego J. Genomic footprints of an old affair: Single nucleotide polymorphism data reveal historical hybridization and the subsequent evolution of reproductive barriers in two recently diverged grasshoppers with partly overlapping distributions. Mol Ecol 2020; 29:2254-2268. [DOI: 10.1111/mec.15475] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Vanina Tonzo
- Department of Integrative Ecology Estación Biológica de Doñana (EBD‐CSIC) Seville Spain
| | - Anna Papadopoulou
- Department of Biological Sciences University of Cyprus Nicosia Cyprus
| | - Joaquín Ortego
- Department of Integrative Ecology Estación Biológica de Doñana (EBD‐CSIC) Seville Spain
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38
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Torres‐Mantelet N, Galián J, León‐Quinto T, López‐López A. Glacial refuges and cryptic speciation in a Southern Palearctic tiger beetle (Coleoptera: Cicindelidae). ZOOL SCR 2020. [DOI: 10.1111/zsc.12427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | - José Galián
- Área de Biología Animal Departamento de Zoología y Antropología Física Facultad de Veterinaria Universidad de Murcia Murcia Spain
| | - Trinidad León‐Quinto
- Área de Zoología Universidad Miguel Hernández de Elche Alicante Spain
- Instituto de Bioingeniería Universidad Miguel Hernández de Elche Alicante Spain
| | - Alejandro López‐López
- Área de Zoología Universidad Miguel Hernández de Elche Alicante Spain
- Área de Biología Animal Departamento de Zoología y Antropología Física Facultad de Veterinaria Universidad de Murcia Murcia Spain
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39
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Denney DA, Jameel MI, Bemmels JB, Rochford ME, Anderson JT. Small spaces, big impacts: contributions of micro-environmental variation to population persistence under climate change. AOB PLANTS 2020; 12:plaa005. [PMID: 32211145 PMCID: PMC7082537 DOI: 10.1093/aobpla/plaa005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 02/06/2020] [Indexed: 05/05/2023]
Abstract
Individuals within natural populations can experience very different abiotic and biotic conditions across small spatial scales owing to microtopography and other micro-environmental gradients. Ecological and evolutionary studies often ignore the effects of micro-environment on plant population and community dynamics. Here, we explore the extent to which fine-grained variation in abiotic and biotic conditions contributes to within-population variation in trait expression and genetic diversity in natural plant populations. Furthermore, we consider whether benign microhabitats could buffer local populations of some plant species from abiotic stresses imposed by rapid anthropogenic climate change. If microrefugia sustain local populations and communities in the short term, other eco-evolutionary processes, such as gene flow and adaptation, could enhance population stability in the longer term. We caution, however, that local populations may still decline in size as they contract into rare microhabitats and microrefugia. We encourage future research that explicitly examines the role of the micro-environment in maintaining genetic variation within local populations, favouring the evolution of phenotypic plasticity at local scales and enhancing population persistence under global change.
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Affiliation(s)
- Derek A Denney
- Department of Plant Biology, University of Georgia, Athens, GA, USA
| | - M Inam Jameel
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Jordan B Bemmels
- Department of Genetics, University of Georgia, Athens, GA, USA
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada
| | - Mia E Rochford
- Department of Plant Biology, University of Georgia, Athens, GA, USA
| | - Jill T Anderson
- Department of Genetics, University of Georgia, Athens, GA, USA
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40
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de Dato GD, Teani A, Mattioni C, Aravanopoulos F, Avramidou EV, Stojnic S, Ganopoulos I, Belletti P, Ducci F. Genetic Analysis by nuSSR Markers of Silver Birch ( Betula pendula Roth) Populations in Their Southern European Distribution Range. FRONTIERS IN PLANT SCIENCE 2020; 11:310. [PMID: 32265963 PMCID: PMC7108150 DOI: 10.3389/fpls.2020.00310] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 03/03/2020] [Indexed: 05/23/2023]
Abstract
In the main distribution area the genetic pattern of silver birch is dominated by two haplotypes: haplotype A located in the western and north-western Europe, and haplotype C in eastern and southeastern Europe, characterized by high levels of neutral genetic variability within populations, and low differentiation among populations. Information about the amount and structure of genetic variation in the southern marginal areas, representing rear populations left during the expansion of this species from southern glacial refugia, are lacking. The general aim of the study was to investigate the existence of the climatic characteristics typical of the environmental niche of the species, jointly to genetic organization, variation and gene flow, in marginal populations on the Italian Apennines and Greek Southern Rhodope and compare them with populations of the southern part of the main distribution range on the Alps and Balkans. Genetic analysis was performed using nuclear microsatellites loci on 311 trees sampled from 14 populations. Environmental analysis was performed on the multivariate analysis of derived climatic variables. The allelic pattern was analyzed to assess genetic diversity, population diversity and differentiation, population structure and gene flow. The geographic and environmental peripherality did not always match, with some Apennine sites at higher elevation enveloped in the environmental niche. In the peripheral populations on the Apennines, we observed a lower genetic diversity and higher differentiation, with evident genetic barriers detected around these sites. These characteristics were not shown in the marginal Greek populations. Unexpectedly, the southern Italian marginal populations showed genetic links with the Greek and central area of the distribution range. The Greek populations also showed evident gene flow with the Alpine and Balkan areas. The disparity of results in these two marginal areas show that it is not the geographic peripherality or even the ecological marginality that may shape the genetic diversity and structure of marginal populations, but primarily their position as part of the continuous range or as disjunct populations. This outcome suggests different considerations on how to manage their gene pools and the role that these rear populations can play in maintaining the biodiversity of this species.
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Affiliation(s)
- Giovanbattista D. de Dato
- Research Centre for Forestry and Wood, Council for Agricultural Research and Economics, Arezzo, Italy
| | - Angela Teani
- Research Centre for Forestry and Wood, Council for Agricultural Research and Economics, Arezzo, Italy
| | - Claudia Mattioni
- Research Institute on Terrestrial Ecosystems, National Research Council, Porano, Italy
| | - Filippos Aravanopoulos
- Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Evangelia V. Avramidou
- Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Srdjan Stojnic
- Institute of Lowland Forestry and Environment, University of Novi Sad, Novi Sad, Serbia
| | - Ioannis Ganopoulos
- Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Piero Belletti
- DI.S.A.F.A., Department of Plant Genetics and Breeding, University of Turin, Grugliasco, Italy
| | - Fulvio Ducci
- Research Centre for Forestry and Wood, Council for Agricultural Research and Economics, Arezzo, Italy
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41
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Vega R, McDevitt AD, Stojak J, Mishta A, Wójcik JM, Kryštufek B, Searle JB. Phylogeographical structure of the pygmy shrew: revisiting the roles of southern and northern refugia in Europe. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blz209] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractSouthern and northern glacial refugia are considered paradigms that explain the complex phylogeographical patterns and processes of European biota. Here, we provide a revisited statistical phylogeographical analysis of the pygmy shrew Sorex minutus Linnaeus, 1766 (Eulipotyphla, Soricidae), examining its genetic diversity, genetic differentiation and demographic history in the Mediterranean peninsulas and in Western and Central Europe. The results showed support for genetically distinct and diverse phylogeographical groups consistent with southern and northern glacial refugia, as expected from previous studies. We also identified geographical barriers concordant with glaciated mountain ranges during the Last Glacial Maximum (LGM), early diversification events dated between the Late Pleistocene and Early Holocene for the main phylogeographical groups, and recent (post-LGM) patterns of demographic expansions. This study is the most comprehensive investigation of this species to date, and the results have implications for the conservation of intraspecific diversity and the preservation of the evolutionary potential of S. minutus.
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Affiliation(s)
- Rodrigo Vega
- Ecology Research Group, Section of Natural and Applied Sciences, School of Human and Life Sciences, Canterbury Christ Church University, Becket, Canterbury, Kent, UK
| | - Allan D McDevitt
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Joanna Stojak
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Alina Mishta
- Schmalhausen Institute of Zoology, National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Jan M Wójcik
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Boris Kryštufek
- Slovenian Museum of Natural History, Prešernova, Ljubljana, Slovenia
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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42
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Korábek O, Juřičková L, Petrusek A. Inferring the sources of postglacial range expansion in two large European land snails. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12368] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ondřej Korábek
- Department of Ecology Faculty of Science Charles University Praha Czechia
| | - Lucie Juřičková
- Department of Zoology Faculty of Science Charles University Praha Czechia
| | - Adam Petrusek
- Department of Ecology Faculty of Science Charles University Praha Czechia
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43
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Napier JD, Fernandez MC, de Lafontaine G, Hu FS. Ice-age persistence and genetic isolation of the disjunct distribution of larch in Alaska. Ecol Evol 2020; 10:1692-1702. [PMID: 32076544 PMCID: PMC7029070 DOI: 10.1002/ece3.6031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/18/2019] [Accepted: 01/06/2020] [Indexed: 01/07/2023] Open
Abstract
Larix laricina (eastern larch, tamarack) is a transcontinental North American conifer with a prominent disjunction in the Yukon isolating the Alaskan distribution from the rest of its range. We investigate whether in situ persistence during the last glacial maximum (LGM) or long-distance postglacial migration from south of the ice sheets resulted in the modern-day Alaskan distribution. We analyzed variation in three chloroplast DNA regions of 840 trees from a total of 69 populations (24 new sampling sites situated on both sides of the Yukon range disjunction pooled with 45 populations from a published source) and conducted ensemble species distribution modeling (SDM) throughout Canada and United States to hindcast the potential range of L. laricina during the LGM. We uncovered the genetic signature of a long-term isolation of larch populations in Alaska, identifying three endemic chlorotypes and low levels of genetic diversity. Range-wide analysis across North America revealed the presence of a distinct Alaskan lineage. Postglacial gene flow across the Yukon divide was unidirectional, from Alaska toward previously glaciated Canadian regions, and with no evidence of immigration into Alaska. Hindcast SDM indicates one of the broadest areas of past climate suitability for L. laricina existed in central Alaska, suggesting possible in situ persistence of larch in Alaska during the LGM. Our results provide the first unambiguous evidence for the long-term isolation of L. laricina in Alaska that extends beyond the last glacial period and into the present interglacial period. The lack of gene flow into Alaska along with the overall probability of larch occurrence in Alaska being currently lower than during the LGM suggests that modern-day Alaskan larch populations are isolated climate relicts of broader glacial distributions, and so are particularly vulnerable to current warming trends.
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Affiliation(s)
- Joseph D. Napier
- Department of Plant BiologyUniversity of IllinoisUrbanaILUSA
- Department of Integrative BiologyThe University of Texas at AustinAustinTXUSA
| | | | - Guillaume de Lafontaine
- Canada Research Chair in Integrative Biology of Northern FloraUniversité du Québec à RimouskiRimouskiQCCanada
| | - Feng Sheng Hu
- Department of Plant BiologyUniversity of IllinoisUrbanaILUSA
- Department of GeologyUniversity of IllinoisUrbanaILUSA
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Abstract
The purpose of this Milankovitch review is to explain the significance of Quaternary DNA studies and the importance of the recent methodological advances that have enabled the study of late Quaternary remains in more detail, and the testing of new assumptions in evolutionary biology and phylogeography to reconstruct the past. The topic is wide, and this review is not intended to be an exhaustive account of all the aDNA work performed in the last three decades on late-Quaternary remains. Instead, it is a selection of relevant studies aimed at illustrating how aDNA has been used to reconstruct not only environments of the past, but also the history of many species including our own.
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45
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Chen J, Li L, Milesi P, Jansson G, Berlin M, Karlsson B, Aleksic J, Vendramin GG, Lascoux M. Genomic data provide new insights on the demographic history and the extent of recent material transfers in Norway spruce. Evol Appl 2019; 12:1539-1551. [PMID: 31462913 PMCID: PMC6708423 DOI: 10.1111/eva.12801] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/28/2019] [Accepted: 04/02/2019] [Indexed: 12/23/2022] Open
Abstract
Primeval forests are today exceedingly rare in Europe, and transfer of forest reproductive material for afforestation and improvement has been very common, especially over the last two centuries. This can be a serious impediment when inferring past population movements in response to past climate changes such as the last glacial maximum (LGM), some 18,000 years ago. In the present study, we genotyped 1,672 individuals from three Picea species (P. abies, P. obovata, and P. omorika) at 400K SNPs using exome capture to infer the past demographic history of Norway spruce (P. abies) and estimate the amount of recent introduction used to establish the Norway spruce breeding program in southern Sweden. Most of these trees belong to P. abies and originate from the base populations of the Swedish breeding program. Others originate from populations across the natural ranges of the three species. Of the 1,499 individuals stemming from the breeding program, a large proportion corresponds to recent introductions from mainland Europe. The split of P. omorika occurred 23 million years ago (mya), while the divergence between P. obovata and P. abies began 17.6 mya. Demographic inferences retrieved the same main clusters within P. abies than previous studies, that is, a vast northern domain ranging from Norway to central Russia, where the species is progressively replaced by Siberian spruce (P. obovata) and two smaller domains, an Alpine domain and a Carpathian one, but also revealed further subdivision and gene flow among clusters. The three main domains divergence was ancient (15 mya), and all three went through a bottleneck corresponding to the LGM. Approximately 17% of P. abies Nordic domain migrated from P. obovata ~103K years ago, when both species had much larger effective population sizes. Our analysis of genomewide polymorphism data thus revealed the complex demographic history of Picea genus in Western Europe and highlighted the importance of material transfer in Swedish breeding program.
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Affiliation(s)
- Jun Chen
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Lili Li
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Pascal Milesi
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Gunnar Jansson
- Forestry Research Institute of Sweden (Skogforsk)UppsalaSweden
| | - Mats Berlin
- Forestry Research Institute of Sweden (Skogforsk)UppsalaSweden
| | - Bo Karlsson
- Forestry Research Institute of Sweden (Skogforsk)EkeboSweden
| | - Jelena Aleksic
- Institute of Molecular Genetics and Genetic EngineeringUniversity of BelgradeBelgradeSerbia
| | - Giovanni G. Vendramin
- Division of Florence, Institute of Biosciences and BioResourcesNational Research Council (IBBR‐CNR)Sesto FiorentinoItaly
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSweden
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Wang Z, Meng S, Rao G. Quaternary climate change and habitat preference shaped the genetic differentiation and phylogeography of Rhodiola sect. Prainia in the southern Qinghai-Tibetan Plateau. Ecol Evol 2019; 9:8305-8319. [PMID: 31380091 PMCID: PMC6662313 DOI: 10.1002/ece3.5406] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/03/2019] [Accepted: 06/05/2019] [Indexed: 11/19/2022] Open
Abstract
There are two long-standing biogeographic hypotheses regarding the glacial survival of plant species in the Qinghai-Tibetan Plateau (QTP): the in situ survival hypothesis and the tabula rasa hypothesis. We tested these two hypotheses in a phylogeographic study of Rhodiola sect. Prainia, a monophyletic section with ecologically divergent lineages. Molecular data from the nuclear internal transcribed spacer, six plastid markers and 13 nuclear microsatellite loci were analyzed for 240 individuals from 19 populations of this section. Environmental data were used to analyze the niches of major phylogenetic lineages within this section and to model changes in their distributions since the Last Glacial Maximum (LGM). We found that Rhodiola sect. Prainia consists of three evolutionary lineages: all populations of R. stapfii, R. prainii populations at the southern edge of the QTP, and R. prainii populations in the interior part of the QTP. During the LGM, the survival of R. prainii in the interior part of the QTP corresponded with the in situ survival hypothesis, while R. stapfii most probably survived the LGM in a manner corresponding with the tabula rasa hypothesis. The evolutionary history of different lineages of this section was shaped by topography, climate change, and lineage-specific habitat preferences.
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Affiliation(s)
- Zi‐Meng Wang
- School of Life SciencesPeking UniversityBeijingChina
| | - Shi‐Yong Meng
- School of Life SciencesPeking UniversityBeijingChina
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47
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Stojak J, Tarnowska E. Polish suture zone as the goblet of truth in post-glacial history of mammals in Europe. MAMMAL RES 2019. [DOI: 10.1007/s13364-019-00433-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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48
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Genomic evidence of survival near ice sheet margins for some, but not all, North American trees. Proc Natl Acad Sci U S A 2019; 116:8431-8436. [PMID: 30962371 DOI: 10.1073/pnas.1901656116] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Temperate species experienced dramatic range reductions during the Last Glacial Maximum, yet refugial populations from which modern populations are descended have never been precisely located. Climate-based models identify only broad areas of potential habitat, traditional phylogeographic studies provide poor spatial resolution, and pollen records for temperate forest communities are difficult to interpret and do not provide species-level taxonomic resolution. Here we harness signals of range expansion from large genomic datasets, using a simulation-based framework to infer the precise latitude and longitude of glacial refugia in two widespread, codistributed hickories (Carya spp.) and to quantify uncertainty in these estimates. We show that one species likely expanded from close to ice sheet margins near the site of a previously described macrofossil for the genus, highlighting support for the controversial notion of northern microrefugia. In contrast, the expansion origin inferred for the second species is compatible with classic hypotheses of distant displacement into southern refugia. Our statistically rigorous, powerful approach demonstrates how refugia can be located from genomic data with high precision and accuracy, addressing fundamental questions about long-term responses to changing climates and providing statistical insight into longstanding questions that have previously been addressed primarily qualitatively.
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49
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Łabiszak B, Zaborowska J, Wachowiak W. Patterns of mtDNA variation reveal complex evolutionary history of relict and endangered peat bog pine ( Pinus uliginosa). AOB PLANTS 2019; 11:plz015. [PMID: 30972216 PMCID: PMC6450798 DOI: 10.1093/aobpla/plz015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 03/13/2019] [Indexed: 06/09/2023]
Abstract
Estimates of genetic differentiation at intra- and interspecific level are often hindered by the lack of suitable molecular markers. Low phylogeographic resolution limits development of appropriate conservation strategies especially in case of endangered forest tree species with small and disjunct distribution. In this study, we assessed fine-scale genetic structure of relict and endangered peat bog pine (Pinus uliginosa) and two other closely related European pine species (Pinus mugo and Pinus uncinata) using a set of 15 newly developed maternally inherited and seed-mediated mitochondrial DNA (mtDNA) markers and two previously known polymorphic mtDNA regions (nad1, nad7). Three main groups, corresponding in general to three investigated species were revealed in the haplotype network analysis. However, only P. uncinata was clearly distinct at all levels of analysis, whereas great genetic similarity and haplotype sharing was observed between P. uliginosa and P. mugo. Strong phylogeographic structure was found in P. uliginosa that showed high differentiation at relatively short geographical distance among populations and the existence of mitochondrial lineages of different evolutionary history. Hybridization with other pine species has likely contributed to genetic differentiation of P. uliginosa as indicated by contemporary distribution of mtDNA haplotypes. The research emphasizes the importance of accurate assessments of genetic structure of endangered species with complex evolutionary history for development of efficient conservation strategies.
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Affiliation(s)
- Bartosz Łabiszak
- Institute of Environmental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Julia Zaborowska
- Institute of Environmental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Witold Wachowiak
- Institute of Environmental Biology, Adam Mickiewicz University, Poznań, Poland
- Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland
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50
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Finsinger W, Schwörer C, Heiri O, Morales-Molino C, Ribolini A, Giesecke T, Haas JN, Kaltenrieder P, Magyari EK, Ravazzi C, Rubiales JM, Tinner W. Fire on ice and frozen trees? Inappropriate radiocarbon dating leads to unrealistic reconstructions. THE NEW PHYTOLOGIST 2019; 222:657-662. [PMID: 30019412 DOI: 10.1111/nph.15354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/29/2018] [Indexed: 06/08/2023]
Affiliation(s)
- Walter Finsinger
- Palaeoecology, ISEM, CNRS, EPHE, IRD, Univ. Montpellier, F-34095, Montpellier, France
| | - Christoph Schwörer
- Institute of Plant Sciences and Oeschger Centre for Climate Change Research, University of Bern, Altenbergrain 21, CH-3013, Bern, Switzerland
| | - Oliver Heiri
- Institute of Plant Sciences and Oeschger Centre for Climate Change Research, University of Bern, Altenbergrain 21, CH-3013, Bern, Switzerland
| | - César Morales-Molino
- Institute of Plant Sciences and Oeschger Centre for Climate Change Research, University of Bern, Altenbergrain 21, CH-3013, Bern, Switzerland
- Palaeoclimate, EPOC (UMR 5805 CNRS/University of Bordeaux), University of Bordeaux, F-33615, Pessac, France
| | - Adriano Ribolini
- Dipartimento di Scienze della Terra, University of Pisa, via S. Maria 53, 56126, Pisa, Italy
| | - Thomas Giesecke
- Department of Palynology and Climate Dynamics, University of Göttingen, Wilhelm-Weber-Str. 2a, D-37073, Göttingen, Germany
| | - Jean Nicolas Haas
- Institute of Botany, Division of Systematics, Palynology and Geobotany, University of Innsbruck, Sternwartestrasse 15, A-6020, Innsbruck, Austria
| | - Petra Kaltenrieder
- Institute of Plant Sciences and Oeschger Centre for Climate Change Research, University of Bern, Altenbergrain 21, CH-3013, Bern, Switzerland
| | - Enikő K Magyari
- MTA-MTM-ELTE Research Group for Paleontology and Department of Environmental and Landscape Geography, Eötvös Lóránd University, Pázmány Péter stny. 1/C, H-1117, Budapest, Hungary
| | - Cesare Ravazzi
- CNR - Institute for the Dynamics of Environmental Processes, U1 - DISAT - Università Milano Bicocca, Piazza della Scienza 1, I-20126, Milano, Italy
| | - Juan Manuel Rubiales
- Departamento de Sistemas y Recursos Naturales, Escuela Técnica Superior de Ingeniería de Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, E-28040, Madrid, Spain
- Departamento de Biodiversidad, Ecología y Evolución, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, C/José Antonio Novais, E-28040, Madrid, Spain
| | - Willy Tinner
- Institute of Plant Sciences and Oeschger Centre for Climate Change Research, University of Bern, Altenbergrain 21, CH-3013, Bern, Switzerland
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