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Zhou Q, Karunarathne P, Andersson-Li L, Chen C, Opgenoorth L, Heer K, Piotti A, Vendramin GG, Nakvasina E, Lascoux M, Milesi P. Recurrent hybridization and gene flow shaped Norway and Siberian spruce evolutionary history over multiple glacial cycles. Mol Ecol 2024; 33:e17495. [PMID: 39148357 DOI: 10.1111/mec.17495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 07/15/2024] [Accepted: 08/02/2024] [Indexed: 08/17/2024]
Abstract
Most tree species underwent cycles of contraction and expansion during the Quaternary. These cycles led to an ancient and complex genetic structure that has since been affected by extensive gene flow and by strong local adaptation. The extent to which hybridization played a role in this multi-layered genetic structure is important to be investigated. To study the effect of hybridization on the joint population genetic structure of two dominant species of the Eurasian boreal forest, Picea abies and P. obovata, we used targeted resequencing and obtained around 480 K nuclear SNPs and 87 chloroplast SNPs in 542 individuals sampled across most of their distribution ranges. Despite extensive gene flow and a clear pattern of Isolation-by-Distance, distinct genetic clusters emerged, indicating the presence of barriers and corridors to migration. Two cryptic refugia located in the large hybrid zone between the two species played a critical role in shaping their current distributions. The two species repeatedly hybridized during the Pleistocene and the direction of introgression depended on latitude. Our study suggests that hybridization helped both species to overcome main shifts in their distribution ranges during glacial cycles and highlights the importance of considering whole species complex instead of separate entities to retrieve complex demographic histories.
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Affiliation(s)
- Qiujie Zhou
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, Uppsala, Sweden
| | - Piyal Karunarathne
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, Uppsala, Sweden
- Institute of Population Genetics, Heinrich-Heine University, Düsseldorf, Universitäts Straße 1, Düsseldorf, Germany
| | - Lili Andersson-Li
- Department of Microbiology, Tumor and Cell Biology, Karolinska L2:02, Solna, Sweden
| | - Chen Chen
- Plant Pathology Group, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Lars Opgenoorth
- Department of Biology, Plant Ecology and Geobotany, Philipps-Universität Marburg, Marburg, Germany
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Katrin Heer
- Faculty of Environment and Natural Resources, Eva Mayr-Stihl Professorship for Forest Genetics, Albert-Ludwigs-Universität Freiburg, Freiburg im Breisgau, Germany
| | - Andrea Piotti
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Sesto Fiorentino, Italy
| | | | - Elena Nakvasina
- Department of Forestry and Forest Management, Northern (Arctic) Federal University Named after M.V. Lomonosov, Arkhangelsk, Russian Federation
| | - Martin Lascoux
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, Uppsala, Sweden
| | - Pascal Milesi
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, Uppsala, Sweden
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2
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Li L, Milesi P, Tiret M, Chen J, Sendrowski J, Baison J, Chen Z, Zhou L, Karlsson B, Berlin M, Westin J, Garcia‐Gil MR, Wu HX, Lascoux M. Teasing apart the joint effect of demography and natural selection in the birth of a contact zone. THE NEW PHYTOLOGIST 2022; 236:1976-1987. [PMID: 36093739 PMCID: PMC9828440 DOI: 10.1111/nph.18480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/23/2022] [Indexed: 05/26/2023]
Abstract
Vast population movements induced by recurrent climatic cycles have shaped the genetic structure of plant species. During glacial periods species were confined to low-latitude refugia from which they recolonized higher latitudes as the climate improved. This multipronged recolonization led to many lineages that later met and formed large contact zones. We utilize genomic data from 5000 Picea abies trees to test for the presence of natural selection during recolonization and establishment of a contact zone in Scandinavia. Scandinavian P. abies is today made up of a southern genetic cluster originating from the Baltics, and a northern one originating from Northern Russia. The contact zone delineating them closely matches the limit between two major climatic regions. We show that natural selection contributed to its establishment and maintenance. First, an isolation-with-migration model with genome-wide linked selection fits the data better than a purely neutral one. Second, many loci show signatures of selection or are associated with environmental variables. These loci, regrouped in clusters on chromosomes, are often related to phenology. Altogether, our results illustrate how climatic cycles, recolonization and selection can establish strong local adaptation along contact zones and affect the genetic architecture of adaptive traits.
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Affiliation(s)
- Lili Li
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
| | - Pascal Milesi
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
| | - Mathieu Tiret
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
| | - Jun Chen
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
- College of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Janek Sendrowski
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
| | - John Baison
- Department Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural SciencesUmeåSE‐90183Sweden
| | - Zhi‐qiang Chen
- Department Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural SciencesUmeåSE‐90183Sweden
| | - Linghua Zhou
- Department Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural SciencesUmeåSE‐90183Sweden
| | | | - Mats Berlin
- SkogforskUppsala Science Park751 83UppsalaSweden
| | - Johan Westin
- Unit for Field‐Based Forest ResearchSwedish University of Agricultural SciencesSE‐922 91VindelnSweden
| | - Maria Rosario Garcia‐Gil
- Department Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural SciencesUmeåSE‐90183Sweden
| | - Harry X. Wu
- Department Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural SciencesUmeåSE‐90183Sweden
- CSIRO National Collection Research AustraliaBlack Mountain LaboratoryCanberraACT2601Australia
| | - Martin Lascoux
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
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Annotation of Siberian Larch (Larix sibirica Ledeb.) Nuclear Genome—One of the Most Cold-Resistant Tree Species in the Only Deciduous GENUS in Pinaceae. PLANTS 2022; 11:plants11152062. [PMID: 35956540 PMCID: PMC9370799 DOI: 10.3390/plants11152062] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 11/17/2022]
Abstract
The recent release of the nuclear, chloroplast and mitochondrial genome assemblies of Siberian larch (Larix sibirica Ledeb.), one of the most cold-resistant tree species in the only deciduous genus of Pinaceae, with seasonal senescence and a rot-resistant valuable timber widely used in construction, greatly contributed to the development of genomic resources for the larch genus. Here, we present an extensive repeatome analysis and the first annotation of the draft nuclear Siberian larch genome assembly. About 66% of the larch genome consists of highly repetitive elements (REs), with the likely wave of retrotransposons insertions into the larch genome estimated to occur 4–5 MYA. In total, 39,370 gene models were predicted, with 87% of them having homology to the Arabidopsis-annotated proteins and 78% having at least one GO term assignment. The current state of the genome annotations allows for the exploration of the gymnosperm and angiosperm species for relative gene abundance in different functional categories. Comparative analysis of functional gene categories across different angiosperm and gymnosperm species finds that the Siberian larch genome has an overabundance of genes associated with programmed cell death (PCD), autophagy, stress hormone biosynthesis and regulatory pathways; genes that may play important roles in seasonal senescence and stress response to extreme cold in larch. Despite being incomplete, the draft assemblies and annotations of the conifer genomes are at a point of development where they now represent a valuable source for further genomic, genetic and population studies.
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Schulte L, Meucci S, Stoof-Leichsenring KR, Heitkam T, Schmidt N, von Hippel B, Andreev AA, Diekmann B, Biskaborn BK, Wagner B, Melles M, Pestryakova LA, Alsos IG, Clarke C, Krutovsky KV, Herzschuh U. Larix species range dynamics in Siberia since the Last Glacial captured from sedimentary ancient DNA. Commun Biol 2022; 5:570. [PMID: 35681049 PMCID: PMC9184489 DOI: 10.1038/s42003-022-03455-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 05/06/2022] [Indexed: 11/19/2022] Open
Abstract
Climate change is expected to cause major shifts in boreal forests which are in vast areas of Siberia dominated by two species of the deciduous needle tree larch (Larix). The species differ markedly in their ecosystem functions, thus shifts in their respective ranges are of global relevance. However, drivers of species distribution are not well understood, in part because paleoecological data at species level are lacking. This study tracks Larix species distribution in time and space using target enrichment on sedimentary ancient DNA extracts from eight lakes across Siberia. We discovered that Larix sibirica, presently dominating in western Siberia, likely migrated to its northern distribution area only in the Holocene at around 10,000 years before present (ka BP), and had a much wider eastern distribution around 33 ka BP. Samples dated to the Last Glacial Maximum (around 21 ka BP), consistently show genotypes of L. gmelinii. Our results suggest climate as a strong determinant of species distribution in Larix and provide temporal and spatial data for species projection in a changing climate. Using ancient sedimentary DNA from up to 50 kya, dramatic distributional shifts are documented in two dominant boreal larch species, likely guided by environmental changes suggesting climate as a strong determinant of species distribution.
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Semerikova SA, Ekart AK. Analysis of Chloroplast DNA Variability Confirms the Existence of Several Pleistocene Lime Refugia in Southern Siberia. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422030127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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6
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Semerikov VL, Semerikova SA, Putintseva YA. Mitochondrial DNA Confirms the American Origin of Modern Firs. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421100112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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7
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Schulte L, Bernhardt N, Stoof-Leichsenring K, Zimmermann HH, Pestryakova LA, Epp LS, Herzschuh U. Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest. Mol Ecol Resour 2021; 21:801-815. [PMID: 33319428 DOI: 10.1111/1755-0998.13311] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 12/07/2020] [Indexed: 01/02/2023]
Abstract
Siberian larch (Larix Mill.) forests dominate vast areas of northern Russia and contribute important ecosystem services to the world. It is important to understand the past dynamics of larches in order to predict their likely response to a changing climate in the future. Sedimentary ancient DNA extracted from lake sediment cores can serve as archives to study past vegetation. However, the traditional method of studying sedimentary ancient DNA-metabarcoding-focuses on small fragments, which cannot resolve Larix to species level nor allow a detailed study of population dynamics. Here, we use shotgun sequencing and hybridization capture with long-range PCR-generated baits covering the complete Larix chloroplast genome to study Larix populations from a sediment core reaching back to 6700 years from the Taymyr region in northern Siberia. In comparison with shotgun sequencing, hybridization capture results in an increase in taxonomically classified reads by several orders of magnitude and the recovery of complete chloroplast genomes of Larix. Variation in the chloroplast reads corroborates an invasion of Larix gmelinii into the range of Larix sibirica before 6700 years ago. Since then, both species have been present at the site, although larch populations have decreased with only a few trees remaining in what was once a forested area. This study demonstrates for the first time that hybridization capture applied directly to ancient DNA of plants extracted from lake sediments can provide genome-scale information and is a viable tool for studying past genomic changes in populations of single species, irrespective of a preservation as macrofossil.
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Affiliation(s)
- Luise Schulte
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany.,Institut für Biochemie and Biologie, Universität Potsdam, Potsdam, Germany
| | - Nadine Bernhardt
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Kathleen Stoof-Leichsenring
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Heike H Zimmermann
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Luidmila A Pestryakova
- Institute of Natural Sciences, North-Eastern Federal University of Yakutsk, Yakutsk, Russia
| | - Laura S Epp
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany
| | - Ulrike Herzschuh
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Forschungsstelle Potsdam, Potsdam, Germany.,Institut für Biochemie and Biologie, Universität Potsdam, Potsdam, Germany.,Institut für Geowissenschaften, Universität Potsdam, Potsdam, Germany
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Polezhaeva MA, Tikhonova NA, Marchuk EA, Modorov MV, Ranyuk MN, Polezhaev AN, Badmayeva NK, Semerikov VL. Genetic structure of a widespread alpine shrub Rhododendron aureum (Ericaceae) across East Asia. JOURNAL OF PLANT RESEARCH 2021; 134:91-104. [PMID: 33398441 DOI: 10.1007/s10265-020-01241-9] [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: 03/10/2020] [Accepted: 11/13/2020] [Indexed: 06/12/2023]
Abstract
The vast territory of East Asia, including southwestern Beringia, is considered to have been almost ice free during the Pleistocene. Cold-resistant flora may have persisted in this region expanding or contracting its range during the climate cooling. Only a few plant genera have been studied with a sampling area across their entire geographic range in East Asia; therefore, the understanding of the biogeographic history of alpine flora in this region remains limited. In the present study, genetic variation and population structure in 21 populations of the alpine shrub Rhododendron aureum across its range in East Asia were assessed using 18 microsatellite loci. Phylogenetic analyses revealed three main genetic groups: Siberia, Northeast, and North Pacific. According to the geographical pattern of genetic diversity, the North Pacific group includes populations from Kamchatka, south of Russian Far East, and territories close to central Japan. This group is the most diverse and likely diverged earlier than the Siberia and Northeast groups. Ecological niche modeling predicts range expansion of this species during the period of cooling and, together with demographic history, suggests that the divergence between the three main genetic groups predated the Last Glacial Maximum. Similar to other cold-resistant species such as Larix sibirica and Juniperus communis, the pattern of genetic diversity of R. aureum supports the survival of the species at high latitudes during the Pleistocene with limited contribution of the southern populations to expansion of the species range to the Northeast region and Siberia.
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Affiliation(s)
- Maria A Polezhaeva
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russia.
| | - Natalya A Tikhonova
- V. N. Sukachev Institute of Forest, Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk, Russia
| | - Elena A Marchuk
- Botanical Garden-Institute, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Makar V Modorov
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russia
| | - Maryana N Ranyuk
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russia
| | - Alexey N Polezhaev
- Institute of the Biological Problems of the North, Far Eastern Branch of the Russian Academy of Sciences, Magadan, Russia
| | - Natalya K Badmayeva
- Institute of General and Experimental Biology, Siberian Branch of the Russian Academy of Sciences, Ulan-Ude, Russia
| | - Vladimir L Semerikov
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russia
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Chen J, Zeng YF, Zhang DY. Dispersal as a result of asymmetrical hybridization between two closely related oak species in China. Mol Phylogenet Evol 2020; 154:106964. [PMID: 32956798 DOI: 10.1016/j.ympev.2020.106964] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/17/2022]
Abstract
Hybridization has played an important role in plant evolution. Less attention has been paid, however, to its role in dispersal. In this study, historical divergence and hybridization were investigated in two closely related Chinese oaks, Quercus mongolica and Q. liaotungensis, to estimate the role that hybridization played in their dispersal. We genotyped 27 Q. mongolica and Q. liaotungensis populations throughout the distributional range of the two oak species, using 14 single-copy nuclear genes and four noncoding chloroplast DNA regions. Bayesian cluster and population tree analyses indicated that there were three groups over all oak populations, namely, Q. mongolica, northwest-northern China (NW-NC) Q. liaotungensis, and northeastern China (NEC) Q. liaotungensis. Approximate Bayesian computation simulation supported an asymmetrical hybridization origin of NEC Q. liaotungensis, after a previous divergence between NW-NC Q. liaotungensis and Q. mongolica. IMa3 analyses suggested that Q. liaotungensis and Q. mongolica diverged in the NW-NC and NEC regions, respectively, and that NEC Q. liaotungensis arose from Q. mongolica, not from NW-NC Q. liaotungensis, and was greatly introgressed by NW-NC Q. liaotungensis. Oak populations in NW-NC and NEC regions held different chloroplast DNA haplotypes, and Q. liaotungensis in NEC shared most haplotypes with Q. mongolica populations, but none with NW-NC Q. liaotungensis populations, suggesting the maternal origin of NEC Q. liaotungensis from Q. mongolica. This study found clear signals of isolation divergence of Q. liaotungensis in NW-NC and Q. mongolica in NEC, and the results suggest that asymmetrical hybridization and introgression from Q. liaotungensis to Q. mongolica, mostly likely via pollen flow, facilitated Q. liaotungensis dispersal to NEC.
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Affiliation(s)
- Jun Chen
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Yan-Fei Zeng
- Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
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10
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Ekart AK, Semerikov VL, Larionova AY, Kravchenko AN. Variability of the mh44 Locus of Mitochondrial DNA in Siberian Spruce Populations. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420070030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Duncan SI, Robertson EP, Fletcher RJ, Austin JD. Urbanization and Population Genetic Structure of the Panama City crayfish (Procambarus econfinae). J Hered 2020; 111:204-215. [PMID: 31746328 DOI: 10.1093/jhered/esz072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 11/18/2019] [Indexed: 11/13/2022] Open
Abstract
For species with geographically restricted distributions, the impacts of habitat loss and fragmentation on long-term persistence may be particularly pronounced. We examined the genetic structure of Panama City crayfish (PCC), Procambarus econfinae, whose historical distribution is limited to an area approximately 145 km2, largely within the limits of Panama City and eastern Bay County, FL. Currently, PCC occupy approximately 28% of its historical range, with suitable habitat composed of fragmented patches in the highly urbanized western portion of the range and managed plantations in the more contiguous eastern portion of the range. We used 1640 anonymous single-nucleotide polymorphisms to evaluate the effects of anthropogenic habitat modification on the genetic diversity and population structure of 161 PCC sampled from across its known distribution. First, we examined urban habitat patches in the west compared with less-developed habitat patches in the east. Second, we used approximate Bayesian computation to model inferences on the demographic history of eastern and western populations. We found anthropogenic habitat modifications explain the genetic structure of PCC range-wide. Clustering analyses revealed significant genetic structure between and within eastern and western regions. Estimates of divergence between east and west were consistent with urban growth in the mid-20th century. PCC have low genetic diversity and high levels of inbreeding and relatedness, indicating populations are small and isolated. Our results suggest that PCC have been strongly affected by habitat loss and fragmentation and management strategies, including legal protection, translocations, or reintroductions, may be necessary to ensure long-term persistence.
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Affiliation(s)
| | - Ellen P Robertson
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL
| | - Robert J Fletcher
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL
| | - James D Austin
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL
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12
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Semerikova SA, Isakov IY, Semerikov VL. Chloroplast DNA Variation Shed Light on the History of Lime Tree (Tilia cordata s. l.) in the Eastern Part of the Range. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420020118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Zimmermann HH, Harms L, Epp LS, Mewes N, Bernhardt N, Kruse S, Stoof-Leichsenring KR, Pestryakova LA, Wieczorek M, Trense D, Herzschuh U. Chloroplast and mitochondrial genetic variation of larches at the Siberian tundra-taiga ecotone revealed by de novo assembly. PLoS One 2019; 14:e0216966. [PMID: 31291259 PMCID: PMC6619608 DOI: 10.1371/journal.pone.0216966] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 04/30/2019] [Indexed: 01/10/2023] Open
Abstract
Larix populations at the tundra-taiga ecotone in northern Siberia are highly under-represented in population genetic studies, possibly due to the remoteness of these regions that can only be accessed at extraordinary expense. The genetic signatures of populations in these boundary regions are therefore largely unknown. We aim to generate organelle reference genomes for the detection of single nucleotide polymorphisms (SNPs) that can be used for paleogenetic studies. We present 19 complete chloroplast genomes and mitochondrial genomic sequences of larches from the southern lowlands of the Taymyr Peninsula (northernmost range of Larix gmelinii (Rupr.) Kuzen.), the lower Omoloy River, and the lower Kolyma River (both in the range of Larix cajanderi Mayr). The genomic data reveal 84 chloroplast SNPs and 213 putatively mitochondrial SNPs. Parsimony-based chloroplast haplotype networks show no spatial structure of individuals from different geographic origins, while the mitochondrial haplotype network shows at least a slight spatial structure with haplotypes from the Omoloy and Kolyma populations being more closely related to each other than to most of the haplotypes from the Taymyr populations. Whole genome alignments with publicly available complete chloroplast genomes of different Larix species show that among official plant barcodes only the rcbL gene contains sufficient polymorphisms, but has to be sequenced completely to distinguish the different provenances. We provide 8 novel mitochondrial SNPs that are putatively diagnostic for the separation of L. gmelinii and L. cajanderi, while 4 chloroplast SNPs have the potential to distinguish the L. gmelinii/L. cajanderi group from other Larix species. Our organelle references can be used for a targeted primer and probe design allowing the generation of short amplicons. This is particularly important with regard to future investigations of, for example, the biogeographic history of Larix by screening ancient sedimentary DNA of Larix.
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MESH Headings
- Chromosome Mapping
- DNA, Ancient
- DNA, Chloroplast/genetics
- DNA, Mitochondrial/genetics
- DNA, Plant/genetics
- Genetic Variation
- Genetics, Population
- Genome, Chloroplast
- Genome, Mitochondrial
- Genome, Plant
- Haplotypes
- History, Ancient
- Larix/classification
- Larix/genetics
- Polymorphism, Single Nucleotide
- Siberia
- Taiga
- Tundra
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Affiliation(s)
- Heike H. Zimmermann
- Polar Terrestrial Environmental Systems Research Group, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- * E-mail: (HHZ); (UH)
| | - Lars Harms
- Scientific Computing, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Laura S. Epp
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Nick Mewes
- Polar Terrestrial Environmental Systems Research Group, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
| | - Nadine Bernhardt
- Polar Terrestrial Environmental Systems Research Group, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
| | - Stefan Kruse
- Polar Terrestrial Environmental Systems Research Group, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
| | - Kathleen R. Stoof-Leichsenring
- Polar Terrestrial Environmental Systems Research Group, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
| | | | - Mareike Wieczorek
- Polar Terrestrial Environmental Systems Research Group, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
| | - Daronja Trense
- Institute for Integrated Natural Sciences, Biology, Koblenz-Landau University, Koblenz, Germany
| | - Ulrike Herzschuh
- Polar Terrestrial Environmental Systems Research Group, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Institute of Environmental Sciences and Geography, University of Potsdam, Potsdam, Germany
- * E-mail: (HHZ); (UH)
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Sedel’nikova TS, Pimenov AV. Karyological Study of Siberian Larch Species Larix sibirica and Larix gmelinii in Taimyr. CYTOL GENET+ 2019. [DOI: 10.3103/s0095452719030046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Yousefzadeh H, Khodadost A, Abdollahi H, Ali SS, Kozlowski G, Bina H. Biogeography and phylogenetic relationships of Hyrcanian wild apple using cpDNA and ITS noncoding sequences. SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2019.1583689] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Hamed Yousefzadeh
- Department of Environmental Science; Faculty of Natural Resources, Tarbiat Modares University, Tehran, Iran
| | - Ali Khodadost
- Department of Forestry, Faculty of Natural Resources, Tarbiat Modares University, Tehran, Iran
| | - Hamid Abdollahi
- Temperate Fruits Research Center, Horticultural Sciences Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Syed Shujait Ali
- Center for Biotechnology and Microbiology (CBM), University of Swat, KPK, Pakistan
| | - Gregor Kozlowski
- Department of Biology and Botanic Garden, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland
- Natural History Museum Fribourg (NHMF), Chemin du Musée 6, Fribourg, CH-1700, Switzerland
| | - Hamid Bina
- Host/Pathogen Interaction & Biotechnology of Fruit Trees Department, Seed and Plant Improvement Institute, Karaj, Iran
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16
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Haselhorst MSH, Parchman TL, Buerkle CA. Genetic evidence for species cohesion, substructure and hybrids in spruce. Mol Ecol 2019; 28:2029-2045. [DOI: 10.1111/mec.15056] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 02/10/2019] [Accepted: 02/11/2019] [Indexed: 12/18/2022]
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17
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Ledent A, Désamoré A, Laenen B, Mardulyn P, McDaniel SF, Zanatta F, Patiño J, Vanderpoorten A. No borders during the post-glacial assembly of European bryophytes. Ecol Lett 2019; 22:973-986. [PMID: 30900805 DOI: 10.1111/ele.13254] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/11/2018] [Accepted: 02/24/2019] [Indexed: 11/28/2022]
Abstract
Climatic fluctuations during the Last Glacial Maximum (LGM) exerted a profound influence on biodiversity patterns, but their impact on bryophytes, the second most diverse group of land plants, has been poorly documented. Approximate Bayesian computations based on coalescent simulations showed that the post-glacial assembly of European bryophytes involves a complex history from multiple sources. The contribution of allochthonous migrants was 95-100% of expanding populations in about half of the 15 investigated species, which is consistent with the globally balanced genetic diversities and extremely low divergence observed among biogeographical regions. Such a substantial contribution of allochthonous migrants in the post-glacial assembly of Europe is unparalleled in other plants and animals. The limited role of northern micro-refugia, which was unexpected based on bryophyte life-history traits, and of southern refugia, is consistent with recent palaeontological evidence that LGM climates in Eurasia were much colder and drier than what palaeoclimatic models predict.
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Affiliation(s)
- A Ledent
- Institute of Botany, University of Liege, Sart Tilman, 4000, Liege, Belgium
| | - A Désamoré
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - B Laenen
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - P Mardulyn
- Evolutionary Biology & Ecology, Université Libre de Bruxelles, 1050, Brussels, Belgium
| | - S F McDaniel
- Biology Department, University of Florida, Gainesville, FL, 32611, USA
| | - F Zanatta
- Institute of Botany, University of Liege, Sart Tilman, 4000, Liege, Belgium
| | - J Patiño
- Plant Conservation and Biogeography Group, Departamento de Botánica, Ecología y Fisiología Vegetal, Universidad de La Laguna, 38071, La Laguna, Spain.,Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), 38071, La Laguna, Spain
| | - A Vanderpoorten
- Institute of Botany, University of Liege, Sart Tilman, 4000, Liege, Belgium
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18
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Vasyutkina EA, Adrianova IY. On the Issue of Larix × lubarskii Sukaczev Origin: Analysis of Polymorphism of Mitochondrial Genome Markers. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419020169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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19
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Kurata S, Sakaguchi S, Ito M. Genetic diversity and population demography of Geranium soboliferum var. kiusianum: a glacial relict plant in the wetlands of Japan. CONSERV GENET 2019. [DOI: 10.1007/s10592-018-01141-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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20
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Epp LS, Kruse S, Kath NJ, Stoof-Leichsenring KR, Tiedemann R, Pestryakova LA, Herzschuh U. Temporal and spatial patterns of mitochondrial haplotype and species distributions in Siberian larches inferred from ancient environmental DNA and modeling. Sci Rep 2018; 8:17436. [PMID: 30498238 PMCID: PMC6265258 DOI: 10.1038/s41598-018-35550-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 11/01/2018] [Indexed: 12/01/2022] Open
Abstract
Changes in species' distributions are classically projected based on their climate envelopes. For Siberian forests, which have a tremendous significance for vegetation-climate feedbacks, this implies future shifts of each of the forest-forming larch (Larix) species to the north-east. However, in addition to abiotic factors, reliable projections must assess the role of historical biogeography and biotic interactions. Here, we use sedimentary ancient DNA and individual-based modelling to investigate the distribution of larch species and mitochondrial haplotypes through space and time across the treeline ecotone on the southern Taymyr peninsula, which at the same time presents a boundary area of two larch species. We find spatial and temporal patterns, which suggest that forest density is the most influential driver determining the precise distribution of species and mitochondrial haplotypes. This suggests a strong influence of competition on the species' range shifts. These findings imply possible climate change outcomes that are directly opposed to projections based purely on climate envelopes. Investigations of such fine-scale processes of biodiversity change through time are possible using paleoenvironmental DNA, which is available much more readily than visible fossils and can provide information at a level of resolution that is not reached in classical palaeoecology.
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Affiliation(s)
- Laura S Epp
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Section, Telegrafenberg A43, 14473, Potsdam, Germany.
| | - Stefan Kruse
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Section, Telegrafenberg A43, 14473, Potsdam, Germany
| | - Nadja J Kath
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Section, Telegrafenberg A43, 14473, Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str 24-25, 14476, Potsdam, Germany
| | - Kathleen R Stoof-Leichsenring
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Section, Telegrafenberg A43, 14473, Potsdam, Germany
| | - Ralph Tiedemann
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str 24-25, 14476, Potsdam, Germany
| | - Luidmila A Pestryakova
- Department for Geography and Biology, North-Eastern Federal University of Yakutsk, Belinskogo 58, 67700, Yakutsk, Russia
| | - Ulrike Herzschuh
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Section, Telegrafenberg A43, 14473, Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str 24-25, 14476, Potsdam, Germany
- Institute of Earth and Environmental Science, University of Potsdam, Karl-Liebknecht-Str 24-25, 14476, Potsdam, Germany
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21
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Vasil’ev AG, Bol’shakov VN, Vasil’eva IA, Evdokimov NG, Sineva NV. Morphogenetic Effects of Drought and Nonselective Elimination in Population of Bank Vole (Clethrionomys glareolus) in Southern Taiga Subzone. RUSS J ECOL+ 2018. [DOI: 10.1134/s1067413618030104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Hantemirova EV, Pimenova EA, Korchagina OS. Polymorphism of Chloroplast DNA and Phylogeography of Green Alder (Alnus alnobetula (Ehrh.) K. Koch s. l.) in Asiatic Russia. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418010052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Hrivnák M, Paule L, Krajmerová D, Kulaç Ş, Şevik H, Turna İ, Tvauri I, Gömöry D. Genetic variation in Tertiary relics: The case of eastern-Mediterranean Abies (Pinaceae). Ecol Evol 2017; 7:10018-10030. [PMID: 29238533 PMCID: PMC5723589 DOI: 10.1002/ece3.3519] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 09/11/2017] [Accepted: 09/28/2017] [Indexed: 01/19/2023] Open
Abstract
The eastern‐Mediterranean Abies taxa, which include both widely distributed species and taxa with minuscule ranges, represent a good model to study the impacts of range size and fragmentation on the levels of genetic diversity and differentiation. To assess the patterns of genetic diversity and phylogenetic relationships among eastern‐Mediterranean Abies taxa, genetic variation was assessed by eight nuclear microsatellite loci in 52 populations of Abies taxa with a focus on those distributed in Turkey and the Caucasus. Both at the population and the taxon level, the subspecies or regional populations of Abies nordmanniana s.l. exhibited generally higher allelic richness, private allelic richness, and expected heterozygosity compared with Abies cilicica s.l. Results of both the structure analysis and distance‐based approaches showed a strong differentiation of the two A. cilicica subspecies from the rest as well as from each other, whereas the subspecies of A. nordmanniana were distinct but less differentiated. ABC simulations were run for a set of scenarios of phylogeny and past demographic changes. For A. ×olcayana, the simulation gave a poor support for the hypothesis of being a taxon resulting from a past hybridization, the same is true for Abies equi‐trojani: both they represent evolutionary branches of Abies bornmuelleriana.
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Affiliation(s)
| | | | | | | | - Hakan Şevik
- Faculty of Engineering and Architecture Kastamonu University Kastamonu Turkey
| | - İbrahim Turna
- Faculty of Forestry Karadeniz Technical University Trabzon Turkey
| | - Irina Tvauri
- Scientific-Research Center of Agriculture Tbilisi Georgia.,Vasil Gulisashvili Forest Institute Agricultural University of Georgia Tbilisi Georgia
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24
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Zimmermann HH, Raschke E, Epp LS, Stoof-Leichsenring KR, Schirrmeister L, Schwamborn G, Herzschuh U. The History of Tree and Shrub Taxa on Bol'shoy Lyakhovsky Island (New Siberian Archipelago) since the Last Interglacial Uncovered by Sedimentary Ancient DNA and Pollen Data. Genes (Basel) 2017; 8:E273. [PMID: 29027988 PMCID: PMC5664123 DOI: 10.3390/genes8100273] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/27/2017] [Accepted: 10/04/2017] [Indexed: 11/21/2022] Open
Abstract
Ecosystem boundaries, such as the Arctic-Boreal treeline, are strongly coupled with climate and were spatially highly dynamic during past glacial-interglacial cycles. Only a few studies cover vegetation changes since the last interglacial, as most of the former landscapes are inundated and difficult to access. Using pollen analysis and sedimentary ancient DNA (sedaDNA) metabarcoding, we reveal vegetation changes on Bol'shoy Lyakhovsky Island since the last interglacial from permafrost sediments. Last interglacial samples depict high levels of floral diversity with the presence of trees (Larix, Picea, Populus) and shrubs (Alnus, Betula, Ribes, Cornus, Saliceae) on the currently treeless island. After the Last Glacial Maximum, Larix re-colonised the island but disappeared along with most shrub taxa. This was probably caused by Holocene sea-level rise, which led to increased oceanic conditions on the island. Additionally, we applied two newly developed larch-specific chloroplast markers to evaluate their potential for tracking past population dynamics from environmental samples. The novel markers were successfully re-sequenced and exhibited two variants of each marker in last interglacial samples. SedaDNA can track vegetation changes as well as genetic changes across geographic space through time and can improve our understanding of past processes that shape modern patterns.
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Affiliation(s)
- Heike H Zimmermann
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Unit, Telegrafenberg A43, 14473 Potsdam, Germany.
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany.
| | - Elena Raschke
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Unit, Telegrafenberg A43, 14473 Potsdam, Germany.
| | - Laura S Epp
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Unit, Telegrafenberg A43, 14473 Potsdam, Germany.
| | - Kathleen R Stoof-Leichsenring
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Unit, Telegrafenberg A43, 14473 Potsdam, Germany.
| | - Lutz Schirrmeister
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Unit, Telegrafenberg A43, 14473 Potsdam, Germany.
| | - Georg Schwamborn
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Unit, Telegrafenberg A43, 14473 Potsdam, Germany.
| | - Ulrike Herzschuh
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Unit, Telegrafenberg A43, 14473 Potsdam, Germany.
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany.
- Institute of Earth and Environmental Sciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany.
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25
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Tsuda Y, Semerikov V, Sebastiani F, Vendramin GG, Lascoux M. Multispecies genetic structure and hybridization in theBetulagenus across Eurasia. Mol Ecol 2016; 26:589-605. [DOI: 10.1111/mec.13885] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 09/19/2016] [Indexed: 01/18/2023]
Affiliation(s)
- Yoshiaki Tsuda
- Department of Ecology and Genetics; Evolutionary Biology Centre; Science for Life Laboratory; Uppsala University; Norbyvägen 18D 75236 Uppsala Sweden
- Institute of Biosciences and Bioresources; Division of Florence; National Research Council; Via Madonna del Piano 10 50019 Sesto Fiorentino (Firenze) Italy
| | - Vladimir Semerikov
- Institute of Plant and Animal Ecology; Ural Branch of Russian Academy of Science; Ekaterinburg 620144 Russia
| | - Federico Sebastiani
- Institute of Biosciences and Bioresources; Division of Florence; National Research Council; Via Madonna del Piano 10 50019 Sesto Fiorentino (Firenze) Italy
| | - Giovanni Giuseppe Vendramin
- Institute of Biosciences and Bioresources; Division of Florence; National Research Council; Via Madonna del Piano 10 50019 Sesto Fiorentino (Firenze) Italy
| | - Martin Lascoux
- Department of Ecology and Genetics; Evolutionary Biology Centre; Science for Life Laboratory; Uppsala University; Norbyvägen 18D 75236 Uppsala Sweden
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26
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The Relationship between Mating System and Genetic Diversity in Diploid Sexual Populations of Cyrtomium falcatum in Japan. PLoS One 2016; 11:e0163683. [PMID: 27706257 PMCID: PMC5051678 DOI: 10.1371/journal.pone.0163683] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 09/11/2016] [Indexed: 11/24/2022] Open
Abstract
The impact of variation in mating system on genetic diversity is a well-debated topic in evolutionary biology. The diploid sexual race of Cyrtomium falcatum (Japanese holly fern) shows mating system variation, i.e., it displays two different types of sexual expression (gametangia formation) in gametophytes: mixed (M) type and separate (S) type. We examined whether there is variation in the selfing rate among populations of this species, and evaluated the relationship between mating system, genetic diversity and effective population size using microsatellites. In this study, we developed eight new microsatellite markers and evaluated genetic diversity and structure of seven populations (four M-type and three S-type). Past effective population sizes (Ne) were inferred using Approximate Bayesian computation (ABC). The values of fixation index (FIS), allelic richness (AR) and gene diversity (h) differed significantly between the M-type (FIS: 0.626, AR: 1.999, h: 0.152) and the S-type (FIS: 0.208, AR: 2.718, h: 0.367) populations (when admixed individuals were removed from two populations). Although evidence of past bottleneck events was detected in all populations by ABC, the current Ne of the M-type populations was about a third of that of the S-type populations. These results suggest that the M-type populations have experienced more frequent bottlenecks, which could be related to their higher colonization ability via gametophytic selfing. Although high population differentiation among populations was detected (FST = 0.581, F’ST = 0.739), there was no clear genetic differentiation between the M- and S-types. Instead, significant isolation by distance was detected among all populations. These results suggest that mating system variation in this species is generated by the selection for single spore colonization during local extinction and recolonization events and there is no genetic structure due to mating system.
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27
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Cytoplasmic DNA disclose high nucleotide diversity and different phylogenetic pattern in Taihangia rupestris Yu et Li. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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28
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Tsuda Y, Chen J, Stocks M, Källman T, Sønstebø JH, Parducci L, Semerikov V, Sperisen C, Politov D, Ronkainen T, Väliranta M, Vendramin GG, Tollefsrud MM, Lascoux M. The extent and meaning of hybridization and introgression between Siberian spruce (Picea obovata) and Norway spruce (Picea abies): cryptic refugia as stepping stones to the west? Mol Ecol 2016; 25:2773-89. [PMID: 27087633 DOI: 10.1111/mec.13654] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 02/23/2016] [Accepted: 04/09/2016] [Indexed: 01/17/2023]
Abstract
Boreal species were repeatedly exposed to ice ages and went through cycles of contraction and expansion while sister species alternated periods of contact and isolation. The resulting genetic structure is consequently complex, and demographic inferences are intrinsically challenging. The range of Norway spruce (Picea abies) and Siberian spruce (Picea obovata) covers most of northern Eurasia; yet their geographical limits and histories remain poorly understood. To delineate the hybrid zone between the two species and reconstruct their joint demographic history, we analysed variation at nuclear SSR and mitochondrial DNA in 102 and 88 populations, respectively. The dynamics of the hybrid zone was analysed with approximate Bayesian computation (ABC) followed by posterior predictive structure plot reconstruction and the presence of barriers across the range tested with estimated effective migration surfaces. To estimate the divergence time between the two species, nuclear sequences from two well-separated populations of each species were analysed with ABC. Two main barriers divide the range of the two species: one corresponds to the hybrid zone between them, and the other separates the southern and northern domains of Norway spruce. The hybrid zone is centred on the Urals, but the genetic impact of Siberian spruce extends further west. The joint distribution of mitochondrial and nuclear variation indicates an introgression of mitochondrial DNA from Norway spruce into Siberian spruce. Overall, our data reveal a demographic history where the two species interacted frequently and where migrants originating from the Urals and the West Siberian Plain recolonized northern Russia and Scandinavia using scattered refugial populations of Norway spruce as stepping stones towards the west.
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Affiliation(s)
- Yoshiaki Tsuda
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden.,CNR, Institute of Biosciences and Bioresources, Via Madonna del Piano 10, 50019, Sesto Fiorentino, Firenze, Italy
| | - Jun Chen
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Michael Stocks
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Thomas Källman
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | | | - Laura Parducci
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Vladimir Semerikov
- Urals Division of the Russian Academy of Sciences, Institute of Plant and Animal Ecology, 8 Marta Str., 202, 620144, Ekaterinburg, Russia
| | - Christoph Sperisen
- Swiss Federal Research Institute for Forest, Snow and Landscape Research (WSL), Zürcherstrasse 111, CH-8903, Birmendsdorf, Switzerland
| | - Dmitry Politov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkin str. 3, 119991, Moscow, Russia
| | - Tiina Ronkainen
- Environmental Change Research Unit (ECRU), Department of Environmental Sciences, University of Helsinki, PO Box 65, FI-00014, Helsinki, Finland
| | - Minna Väliranta
- Environmental Change Research Unit (ECRU), Department of Environmental Sciences, University of Helsinki, PO Box 65, FI-00014, Helsinki, Finland
| | - Giovanni Giuseppe Vendramin
- CNR, Institute of Biosciences and Bioresources, Via Madonna del Piano 10, 50019, Sesto Fiorentino, Firenze, Italy
| | | | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
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29
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Semerikov VL, Putintseva YA, Oreshkova NV, Semerikova SA, Krutovsky KV. Development of new mitochondrial DNA markers in Scots pine (Pinus sylvestris L.) for population and phylogeographic studies. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415120108] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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30
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van Loo M, Hintsteiner W, Pötzelsberger E, Schüler S, Hasenauer H. Intervarietal and intravarietal genetic structure in Douglas-fir: nuclear SSRs bring novel insights into past population demographic processes, phylogeography, and intervarietal hybridization. Ecol Evol 2015; 5:1802-17. [PMID: 26140197 PMCID: PMC4485962 DOI: 10.1002/ece3.1435] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 10/23/2014] [Accepted: 01/21/2015] [Indexed: 01/22/2023] Open
Abstract
Douglas-fir (Pseudotsuga menziesii) is one of numerous wide-range forest tree species represented by subspecies/varieties, which hybridize in contact zones. This study examined the genetic structure of this North American conifer and its two hybridizing varieties, coastal and Rocky Mountain, at intervarietal and intravarietal level. The genetic structure was subsequently associated with the Pleistocene refugial history, postglacial migration and intervarietal hybridization/introgression. Thirty-eight populations from the USA and Canada were genotyped for 13 nuclear SSRs and analyzed with simulations and traditional population genetic structuring methods. Eight genetic clusters were identified. The coastal clusters embodied five refugial populations originating from five distinct refugia. Four coastal refugial populations, three from California and one from western Canada, diverged during the Pleistocene (56.9–40.1 ka). The three Rocky Mountain clusters reflected distinct refugial populations of three glacial refugia. For Canada, ice covered during the Last Glacial Maximum, we present the following three findings. (1) One refugial population of each variety was revealed in the north of the distribution range. Additional research including paleodata is required to support and determine whether both northern populations originated from cryptic refugia situated south or north of the ice-covered area. (2) An interplay between intravarietal gene flow of different refugial populations and intervarietal gene flow by hybridization and introgression was identified. (3) The Canadian hybrid zone displayed predominantly introgressants of the Rocky Mountain into the coastal variety. This study provides new insights into the complex Quaternary dynamics of this conifer essential for understanding its evolution (outside and inside the native range), adaptation to future climates and for forest management.
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Affiliation(s)
- Marcela van Loo
- Institute of Silviculture, University of Natural Resources and Life Sciences Peter Jordan Straße 82, 1190, Wien, Austria
| | - Wolfgang Hintsteiner
- Institute of Silviculture, University of Natural Resources and Life Sciences Peter Jordan Straße 82, 1190, Wien, Austria ; alpS-GmbH Grabenweg 68, 6020, Innsbruck, Austria
| | - Elisabeth Pötzelsberger
- Institute of Silviculture, University of Natural Resources and Life Sciences Peter Jordan Straße 82, 1190, Wien, Austria
| | - Silvio Schüler
- Department of Forest Genetics, Federal Research and Training Centre for Forests, Natural Hazards and Landscapes Hauptstr. 7, 1140, Vienna, Austria
| | - Hubert Hasenauer
- Institute of Silviculture, University of Natural Resources and Life Sciences Peter Jordan Straße 82, 1190, Wien, Austria
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31
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Tsuda Y, Nakao K, Ide Y, Tsumura Y. The population demography ofBetula maximowicziana, a cool-temperate tree species in Japan, in relation to the last glacial period: its admixture-like genetic structure is the result of simple population splitting not admixing. Mol Ecol 2015; 24:1403-18. [DOI: 10.1111/mec.13123] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 02/17/2015] [Accepted: 02/18/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Y. Tsuda
- Program in Plant Ecology and Evolution; Department of Ecology and Genetics; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D 75236 Uppsala Sweden
- Department of Forest Genetics; Forestry and Forest Products Research Institute (FFPRI); Matsunosato 1 Tsukuba Ibaraki 305-8687 Japan
| | - K. Nakao
- Department of Plant Ecology; Forestry and Forest Products Research Institute (FFPRI); Matsunosato 1 Tsukubaa Ibaraki 305-8687 Japan
| | - Y. Ide
- Laboratory of Forest Ecosystem Studies; Department of Ecosystem Studies; Graduate School of Agriculture and Life Sciences; The University of Tokyo; Yayoi 1-1-1 Bunkyo-ku Tokyo 113-8657 Japan
| | - Y. Tsumura
- Department of Forest Genetics; Forestry and Forest Products Research Institute (FFPRI); Matsunosato 1 Tsukuba Ibaraki 305-8687 Japan
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Chen J, Tsuda Y, Stocks M, Källman T, Xu N, Kärkkäinen K, Huotari T, Semerikov VL, Vendramin GG, Lascoux M. Clinal variation at phenology-related genes in spruce: parallel evolution in FTL2 and Gigantea? Genetics 2014; 197:1025-38. [PMID: 24814465 PMCID: PMC4096357 DOI: 10.1534/genetics.114.163063] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 05/07/2014] [Indexed: 12/20/2022] Open
Abstract
Parallel clines in different species, or in different geographical regions of the same species, are an important source of information on the genetic basis of local adaptation. We recently detected latitudinal clines in SNPs frequencies and gene expression of candidate genes for growth cessation in Scandinavian populations of Norway spruce (Picea abies). Here we test whether the same clines are also present in Siberian spruce (P. obovata), a close relative of Norway spruce with a different Quaternary history. We sequenced nine candidate genes and 27 control loci and genotyped 14 SSR loci in six populations of P. obovata located along the Yenisei river from latitude 56°N to latitude 67°N. In contrast to Scandinavian Norway spruce that both departs from the standard neutral model (SNM) and shows a clear population structure, Siberian spruce populations along the Yenisei do not depart from the SNM and are genetically unstructured. Nonetheless, as in Norway spruce, growth cessation is significantly clinal. Polymorphisms in photoperiodic (FTL2) and circadian clock (Gigantea, GI, PRR3) genes also show significant clinal variation and/or evidence of local selection. In GI, one of the variants is the same as in Norway spruce. Finally, a strong cline in gene expression is observed for FTL2, but not for GI. These results, together with recent physiological studies, confirm the key role played by FTL2 and circadian clock genes in the control of growth cessation in spruce species and suggest the presence of parallel adaptation in these two species.
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Affiliation(s)
- Jun Chen
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Yoshiaki Tsuda
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Michael Stocks
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Thomas Källman
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Nannan Xu
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | | | - Tea Huotari
- Finnish Forest Research Institute, 900014, Finland
| | - Vladimir L Semerikov
- Institute of Plant and Animal Ecology, Urals Division of the Russian Academy of Sciences, 620144 Ekaterinburg, Russia
| | - Giovanni G Vendramin
- Consiglio Nazionale delle Ricerche, Institute of Biosciences and Bioresources, 50019 Sesto Fiorentino, Firenze, Italy
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden
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Zhang HX, Zhang ML, Williams DM. Genetic evidence and species distribution modelling reveal the response of Larix sibirica and its related species to Quaternary climatic and ancient historical events. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.02.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Semerikova SA, Semerikov VL. Mitochondrial DNA variation and reticulate evolution of the genus Abies. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414040139] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Vasyutkina EA, Reunova GD, Tupikin AE, Zhuravlev YN. Mitochondrial DNA variation in Olga Bay larch (Larix olgensis A. Henry) from Primorsky Krai of Russia. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414030107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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