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Sandoval-Castellanos E, Hare AJ, Lin AT, Dimopoulos EA, Daly KG, Geiger S, Mullin VE, Wiechmann I, Mattiangeli V, Lühken G, Zinovieva NA, Zidarov P, Çakırlar C, Stoddart S, Orton D, Bulatović J, Mashkour M, Sauer EW, Horwitz LK, Horejs B, Atici L, Özkaya V, Mullville J, Parker Pearson M, Mainland I, Card N, Brown L, Sharples N, Griffiths D, Allen D, Arbuckle B, Abell JT, Duru G, Mentzer SM, Munro ND, Uzdurum M, Gülçur S, Buitenhuis H, Gladyr E, Stiner MC, Pöllath N, Özbaşaran M, Krebs S, Burger J, Frantz L, Medugorac I, Bradley DG, Peters J. Ancient mitogenomes from Pre-Pottery Neolithic Central Anatolia and the effects of a Late Neolithic bottleneck in sheep ( Ovis aries). SCIENCE ADVANCES 2024; 10:eadj0954. [PMID: 38608027 PMCID: PMC11014441 DOI: 10.1126/sciadv.adj0954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 03/11/2024] [Indexed: 04/14/2024]
Abstract
Occupied between ~10,300 and 9300 years ago, the Pre-Pottery Neolithic site of Aşıklı Höyük in Central Anatolia went through early phases of sheep domestication. Analysis of 629 mitochondrial genomes from this and numerous sites in Anatolia, southwest Asia, Europe, and Africa produced a phylogenetic tree with excessive coalescences (nodes) around the Neolithic, a potential signature of a domestication bottleneck. This is consistent with archeological evidence of sheep management at Aşıklı Höyük which transitioned from residential stabling to open pasturing over a millennium of site occupation. However, unexpectedly, we detected high genetic diversity throughout Aşıklı Höyük's occupation rather than a bottleneck. Instead, we detected a tenfold demographic bottleneck later in the Neolithic, which caused the fixation of mitochondrial haplogroup B in southwestern Anatolia. The mitochondrial genetic makeup that emerged was carried from the core region of early Neolithic sheep management into Europe and dominates the matrilineal diversity of both its ancient and the billion-strong modern sheep populations.
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Affiliation(s)
- Edson Sandoval-Castellanos
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, 82152 Martinsried, Germany
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Andrew J. Hare
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Audrey T. Lin
- The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560 USA
| | - Evangelos A. Dimopoulos
- The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Kevin G. Daly
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Sheila Geiger
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Victoria E. Mullin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Ingrid Wiechmann
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Valeria Mattiangeli
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Gesine Lühken
- Institute of Animal Breeding and Genetics, Justus Liebig University of Gießen, Ludwigstr. 21, 35390 Gießen, Germany
| | - Natalia A. Zinovieva
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region, Russia
| | - Petar Zidarov
- Institute of Prehistory, Early History and Medieval Archaeology, Tübingen University, Tübingen, Germany
| | - Canan Çakırlar
- Institute of Archaeology, University of Groningen, 9712 ER Groningen, Netherlands
| | - Simon Stoddart
- Magdalene College, University of Cambridge, Cambridge CB3 0AG, UK
| | - David Orton
- BioArCh, Department of Archaeology, University of York, York YO10 5NG, UK
| | - Jelena Bulatović
- Department of Historical Studies, University of Gothenburg, BOX 200, 40530 Gothenburg, Sweden
| | - Marjan Mashkour
- Unité Archéozoologie, Archéobotanique, Sociétés Pratiques et Environnements (AASPE), CNRS, Muséum National d’Histoire Naturelle, 75020 Paris, France
| | - Eberhard W. Sauer
- School of History, Classics and Archaeology, University of Edinburgh, Old Medical School, Teviot Place, Edinburgh EH8 9AG, UK
| | - Liora Kolska Horwitz
- National Natural History Collections, Faculty of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Barbara Horejs
- OeAI, Austrian Academy of Sciences and HEAS, University of Vienna, Vienna, Austria
| | - Levent Atici
- Department of Anthropology, University of Nevada, Las Vegas, NV 89154, USA
| | - Vecihi Özkaya
- Department of Archaeology, Dicle University, Diyarbakir, Türkiye
| | - Jacqui Mullville
- School of History, Archaeology and Religion, Cardiff University, Cardiff CF10 3EU, UK
| | | | - Ingrid Mainland
- The University of the Highlands and Islands Orkney, Kirkwall, UK
| | - Nick Card
- The University of the Highlands and Islands Orkney, Kirkwall, UK
| | | | - Niall Sharples
- School of History, Archaeology and Religion, Cardiff University, Cardiff CF10 3EU, UK
| | - David Griffiths
- University of Oxford, OUDCE, Rewley House, Oxford OX1 2JA, UK
| | - David Allen
- Hampshire Cultural Trust, Chilcomb House, Winchester, SO23 8RB, UK
| | - Benjamin Arbuckle
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jordan T. Abell
- Department of Geosciences, University of Arizona, Tucson, AZ 85721, USA
| | - Güneş Duru
- Department of Archaeology, Mimar Sinan Fine Arts University, 34381 Şişli/İstanbul, Türkiye
| | - Susan M. Mentzer
- Senckenberg Centre for Human Evolution and Palaeoenvironment, Institute for Archaeological Sciences, Department of Geosciences, Tübingen University, 72074 Tübingen, Germany
| | - Natalie D. Munro
- Department of Anthropology, University of Connecticut, Storrs, CT 06269, USA
| | - Melis Uzdurum
- Department of Archaeology, Ondokuz Mayıs University, 55270 Atakum/Samsun, Türkiye
| | - Sevil Gülçur
- Prehistory Department, Faculty of Letters, Istanbul University, 34134 Istanbul, Türkiye
| | | | - Elena Gladyr
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region, Russia
| | - Mary C. Stiner
- School of Anthropology, University of Arizona, Tucson, AZ 85721, USA
| | - Nadja Pöllath
- Bavarian Natural History Collections, State Collection of Palaeoanatomy Munich, 80333 Munich, Germany
- ArchaeoBioCenter, LMU Munich, 80539 Munich, Germany
| | - Mihriban Özbaşaran
- Prehistory Department, Faculty of Letters, Istanbul University, 34134 Istanbul, Türkiye
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Joachim Burger
- Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Laurent Frantz
- Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, 82152 Martinsried, Germany
- ArchaeoBioCenter, LMU Munich, 80539 Munich, Germany
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Joris Peters
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
- Bavarian Natural History Collections, State Collection of Palaeoanatomy Munich, 80333 Munich, Germany
- ArchaeoBioCenter, LMU Munich, 80539 Munich, Germany
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Krüger M, Mishra A, Spichtinger P, Pöschl U, Berkemeier T. A numerical compass for experiment design in chemical kinetics and molecular property estimation. J Cheminform 2024; 16:34. [PMID: 38520014 PMCID: PMC10960421 DOI: 10.1186/s13321-024-00825-0] [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: 09/01/2023] [Accepted: 03/10/2024] [Indexed: 03/25/2024] Open
Abstract
Kinetic process models are widely applied in science and engineering, including atmospheric, physiological and technical chemistry, reactor design, or process optimization. These models rely on numerous kinetic parameters such as reaction rate, diffusion or partitioning coefficients. Determining these properties by experiments can be challenging, especially for multiphase systems, and researchers often face the task of intuitively selecting experimental conditions to obtain insightful results. We developed a numerical compass (NC) method that integrates computational models, global optimization, ensemble methods, and machine learning to identify experimental conditions with the greatest potential to constrain model parameters. The approach is based on the quantification of model output variance in an ensemble of solutions that agree with experimental data. The utility of the NC method is demonstrated for the parameters of a multi-layer model describing the heterogeneous ozonolysis of oleic acid aerosols. We show how neural network surrogate models of the multiphase chemical reaction system can be used to accelerate the application of the NC for a comprehensive mapping and analysis of experimental conditions. The NC can also be applied for uncertainty quantification of quantitative structure-activity relationship (QSAR) models. We show that the uncertainty calculated for molecules that are used to extend training data correlates with the reduction of QSAR model error. The code is openly available as the Julia package KineticCompass.
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Affiliation(s)
- Matteo Krüger
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Hahn-Meitner-Weg 1, Mainz, 55128, Rhineland Palatinate, Germany
| | - Ashmi Mishra
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Hahn-Meitner-Weg 1, Mainz, 55128, Rhineland Palatinate, Germany
| | - Peter Spichtinger
- Institute for Atmospheric Physics, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 21, Mainz, 55128, Rhineland Palatinate, Germany
| | - Ulrich Pöschl
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Hahn-Meitner-Weg 1, Mainz, 55128, Rhineland Palatinate, Germany
| | - Thomas Berkemeier
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Hahn-Meitner-Weg 1, Mainz, 55128, Rhineland Palatinate, Germany.
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Ong HG, Kim Y, Lee J, Kim B, Kang D, Jung E, Shin J, Kim Y. Approximate Bayesian computation and ecological niche models elucidate the demographic history and current fragmented population distribution of a Korean endemic shrub. Ecol Evol 2023; 13:e10792. [PMID: 38077507 PMCID: PMC10700048 DOI: 10.1002/ece3.10792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 09/15/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023] Open
Abstract
Climatic fluctuations and geological events since the LGM are believed to have significantly impacted the population size, distribution, and mobility of many species that we observe today. In this paper, we determined the processes driving the phylogeographic structure of the Korean endemic white forsythia by combining the use of genome-wide SNPs and predicting paleoclimatic habitats during the LGM (21 kya), Early Holocene (10 kya), Mid-Holocene (6 kya), and Late Holocene (3 kya). Using a maximum of 1897 SNPs retrieved from 124 samples across nine wild populations, five environmental predictors, and the species' natural occurrence records, we aimed to infer the species' demographic history and reconstruct its possible paleodistributions with the use of approximate Bayesian computation and ecological niche models, respectively. Under this integrated framework, we found strong evidence for patterns of range shift and expansion, and population divergence events from the onset of the Holocene, resulting in the formation of its five distinct genetic units. The most highly supported model inferred that after the split of an ancestral population into the southern group and a larger central metapopulation lineage, the latter gave rise to the eastern and northern clusters, before finally dividing into two sub-central groups. While the use of molecular data allowed us to identify and refine the (phylo)genetic relationships of the species' lineages and populations, the use of ecological data helped us infer a past LGM refugium and the directions of post-glacial range dynamics. The time frames of these demographic events were shown to be congruent with climatic and geological events that affected the central Korean Peninsula during these periods. These findings gave us a better understanding of the consequences of past spatiotemporal factors that may have resulted in the current fragmented population distribution of this endangered plant.
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Affiliation(s)
| | - Yong‐In Kim
- On Biological Resource Research Institute (OBRRI)ChuncheonSouth Korea
| | - Jung‐Hoon Lee
- On Biological Resource Research Institute (OBRRI)ChuncheonSouth Korea
| | - Bo‐Yun Kim
- National Institute of Biological Resources (NIBR)IncheonSouth Korea
| | - Dae‐Hyun Kang
- Korea National Park Research InstituteWonjuSouth Korea
| | - Eui‐Kwon Jung
- Department of Life ScienceHallym UniversityChuncheonSouth Korea
| | - Jae‐Seo Shin
- Department of Life ScienceHallym UniversityChuncheonSouth Korea
| | - Young‐Dong Kim
- Multidisciplinary Genome InstituteHallym UniversityChuncheonSouth Korea
- Department of Life ScienceHallym UniversityChuncheonSouth Korea
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Ascunce MS, Toloza AC, González-Oliver A, Reed DL. Nuclear genetic diversity of head lice sheds light on human dispersal around the world. PLoS One 2023; 18:e0293409. [PMID: 37939041 PMCID: PMC10631634 DOI: 10.1371/journal.pone.0293409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 09/26/2023] [Indexed: 11/10/2023] Open
Abstract
The human louse, Pediculus humanus, is an obligate blood-sucking ectoparasite that has coevolved with humans for millennia. Given the intimate relationship between this parasite and the human host, the study of human lice has the potential to shed light on aspects of human evolution that are difficult to interpret using other biological evidence. In this study, we analyzed the genetic variation in 274 human lice from 25 geographic sites around the world by using nuclear microsatellite loci and female-inherited mitochondrial DNA sequences. Nuclear genetic diversity analysis revealed the presence of two distinct genetic clusters I and II, which are subdivided into subclusters: Ia-Ib and IIa-IIb, respectively. Among these samples, we observed the presence of the two most common louse mitochondrial haplogroups: A and B that were found in both nuclear Clusters I and II. Evidence of nuclear admixture was uncommon (12%) and was predominate in the New World potentially mirroring the history of colonization in the Americas. These findings were supported by novel DIYABC simulations that were built using both host and parasite data to define parameters and models suggesting that admixture between cI and cII was very recent. This pattern could also be the result of a reproductive barrier between these two nuclear genetic clusters. In addition to providing new evolutionary knowledge about this human parasite, our study could guide the development of new analyses in other host-parasite systems.
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Affiliation(s)
- Marina S. Ascunce
- Department of Plant Pathology, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- USDA-ARS Center for Medical, Agricultural, and Veterinary Entomology, Gainesville, Florida, United States of America
| | - Ariel C. Toloza
- Centro de Investigaciones de Plagas e Insecticidas (CONICET-UNIDEF), Villa Martelli, Buenos Aires, Argentina
| | - Angélica González-Oliver
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - David L. Reed
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America
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5
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Garrick RC. Genetic signatures of lineage fusion closely resemble population decline. Ecol Evol 2023; 13:e10725. [PMID: 37964788 PMCID: PMC10641302 DOI: 10.1002/ece3.10725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/16/2023] Open
Abstract
Accurate interpretation of the genetic signatures of past demographic events is crucial for reconstructing evolutionary history. Lineage fusion (complete merging, resulting in a single panmictic population) is a special case of secondary contact that is seldom considered. Here, the circumstances under which lineage fusion can be distinguished from population size constancy, growth, bottleneck, and decline were investigated. Multi-locus haplotype data were simulated under models of lineage fusion with different divergence versus sampling lag times (D:L ratios). These pseudo-observed datasets also differed in their allocation of a fixed amount of sequencing resources (number of sampled alleles, haplotype length, number of loci). Distinguishability of lineage fusion versus each of 10 untrue non-fusion scenarios was quantified based on six summary statistics (neutrality tests). Some datasets were also analyzed using extended Bayesian skyline plots. Results showed that signatures of lineage fusion very closely resemble those of decline-high distinguishability was generally limited to the most favorable scenario (D:L = 9), using the most sensitive summary statistics (F S and Z nS), coupled with the optimal sequencing resource allocation (maximizing number of loci). Also, extended Bayesian skyline plots often erroneously inferred population decline. Awareness of the potential for lineage fusion to carry the hallmarks of population decline is critical.
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Affiliation(s)
- Ryan C. Garrick
- Department of BiologyUniversity of MississippiOxfordMississippiUSA
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Jia Y, Liu ML, López-Pujol J, Jia RW, Kou YX, Yue M, Guan TX, Li ZH. The hybridization origin of the Chinese endemic herb genus Notopterygium (Apiaceae): Evidence from population genomics and ecological niche analysis. Mol Phylogenet Evol 2023; 182:107736. [PMID: 36805473 DOI: 10.1016/j.ympev.2023.107736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/03/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023]
Abstract
Hybridization is recognized as a major force in species evolution and biodiversity formation, generally leading to the origin and differentiation of new species. Multiple hybridization events cannot easily be reconstructed, yet they offer the potential to study a number of evolutionary processes. Here, we used nuclear expressed sequence tag-simple sequence repeat and large-scale single nucleotide polymorphism variation data, combined with niche analysis, to investigate the putative independent hybridization events in Notopterygium, a group of perennial herb plants endemic to China. Population genomic analysis indicated that the four studied species are genetically well-delimited and that N. forrestii and N. oviforme have originated by hybridization. According to Approximate Bayesian Computation, the best-fit model involved the formation of N. forrestii from the crossing of N. franchetii and N. incisum, with N. forrestii further backcrossing to N. franchetii to form N. oviforme. The niche analyses indicated that niche divergence [likely triggered by the regional climate changes, particularly the intensification of East Asian winter monsoon, and tectonic movements (affecting both Qinghai-Tibetan Plateau and Qinling Mountains)] may have promoted and maintained the reproductive isolation among hybrid species. N. forrestii shows ecological specialization with respect to their parental species, whereas N. oviforme has completely shifted its niche. These results suggested that the climate and environmental factors together triggered the two-step hybridization of the East Asia herb plants. Our study also emphasizes the power of genome-wide SNPs for investigating suspected cases of hybridization, particularly unravelling old hybridization events.
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Affiliation(s)
- Yun Jia
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China; Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi'an 710061, Shaanxi, China
| | - Mi-Li Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China
| | - Jordi López-Pujol
- Botanic Institute of Barcelona (IBB), CSIC-Ajuntament de Barcelona, Barcelona 08038, Catalonia, Spain; Escuela de Ciencias Ambientales, Universidad Espíritu Santo (UEES), Samborondón 091650, Ecuador
| | - Rui-Wen Jia
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China
| | - Yi-Xuan Kou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China; Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi'an 710061, Shaanxi, China
| | - Tian-Xia Guan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China; Key Laboratory of Hexi Corridor Resources Utilization of Gansu, College of Life Sciences and Engineering, Hexi University, Zhangye 734000, Gansu, China.
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China.
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Kaya S, Kabasakal B, Erdoğan A. Geographic Genetic Structure of Alectoris chukar in Türkiye: Post-LGM-Induced Hybridization and Human-Mediated Contaminations. BIOLOGY 2023; 12:biology12030401. [PMID: 36979093 PMCID: PMC10045126 DOI: 10.3390/biology12030401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 02/19/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
Abstract
Türkiye is considered an important evolutionary area for Chukar partridge (Alectoris chukar), since it is both a potential ancestral area and a diversification center for the species. Using 2 mitochondrial (Cty-b and D-loop) and 13 polymorphic microsatellite markers, we investigated the geographic genetic structure of A. chukar populations to determine how past climatic fluctuations and human activities have shaped the gene pool of this species in Türkiye. Our results indicate, firstly, that only A. chukar of the genus Alectoris is present in Türkiye (Anatolia and Thrace), with no natural or artificial gene flow from congenerics. Secondly, the geographic genetic structure of the species in Türkiye has been shaped by topographic heterogeneity, Pleistocene climatic fluctuations, and artificial transport by humans. Third, there appears to be three genetic clusters: Thracian, Eastern, and Western. Fourth, the post-LGM demographic expansion of the Eastern and Western populations has formed a hybrid zone in Central Anatolia (~8 kyBP). Fifth, the rate of China clade-B contamination in Türkiye is about 8% in mtDNA and about 12% in nuDNA, with the Southeastern Anatolian population having the highest contamination. Sixth, the Thracian population was the most genetically distinct, with the lowest genetic diversity and highest level of inbreeding and no China clad-B contamination. These results can contribute to the conservation regarding A. chukar populations, especially the Thracian population.
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Affiliation(s)
- Sarp Kaya
- First and Emergency Aid Programme, Department of Medical Services and Techniques, Vocational School of Burdur Health Services, Burdur Mehmet Akif Ersoy University, Burdur 15030, Turkey
| | - Bekir Kabasakal
- Department of Biology, Akdeniz University, Antalya 07058, Turkey
- Anesthesia Programme, Department of Medical Services and Techniques, Vocational School of Health Services, Antalya Bilim University, Antalya 07190, Turkey
- Correspondence:
| | - Ali Erdoğan
- Department of Biology, Akdeniz University, Antalya 07058, Turkey
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Korfmann K, Gaggiotti OE, Fumagalli M. Deep Learning in Population Genetics. Genome Biol Evol 2023; 15:6997869. [PMID: 36683406 PMCID: PMC9897193 DOI: 10.1093/gbe/evad008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/19/2022] [Accepted: 01/16/2023] [Indexed: 01/24/2023] Open
Abstract
Population genetics is transitioning into a data-driven discipline thanks to the availability of large-scale genomic data and the need to study increasingly complex evolutionary scenarios. With likelihood and Bayesian approaches becoming either intractable or computationally unfeasible, machine learning, and in particular deep learning, algorithms are emerging as popular techniques for population genetic inferences. These approaches rely on algorithms that learn non-linear relationships between the input data and the model parameters being estimated through representation learning from training data sets. Deep learning algorithms currently employed in the field comprise discriminative and generative models with fully connected, convolutional, or recurrent layers. Additionally, a wide range of powerful simulators to generate training data under complex scenarios are now available. The application of deep learning to empirical data sets mostly replicates previous findings of demography reconstruction and signals of natural selection in model organisms. To showcase the feasibility of deep learning to tackle new challenges, we designed a branched architecture to detect signals of recent balancing selection from temporal haplotypic data, which exhibited good predictive performance on simulated data. Investigations on the interpretability of neural networks, their robustness to uncertain training data, and creative representation of population genetic data, will provide further opportunities for technological advancements in the field.
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Affiliation(s)
- Kevin Korfmann
- Professorship for Population Genetics, Department of Life Science Systems, Technical University of Munich, Germany
| | - Oscar E Gaggiotti
- Centre for Biological Diversity, Sir Harold Mitchell Building, University of St Andrews, Fife KY16 9TF, UK
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Cheng YH, Sun MT, Wang N, Gao CZ, Peng HQ, Zhang JY, Gu MM, Lu DB. Population Genetics of Oncomelania hupensis Snails from New-Emerging Snail Habitats in a Currently Schistosoma japonicum Non-Endemic Area. Trop Med Infect Dis 2023; 8:tropicalmed8010042. [PMID: 36668949 PMCID: PMC9861412 DOI: 10.3390/tropicalmed8010042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/29/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
Schistosomiasis is still one of the most significant neglected tropical diseases worldwide, and China is endemic for Schistosoma japonicum. With its great achievement in schistosomiasis control, the government of China has set the goal to eliminate the parasitic disease at the country level by 2030. However, one major challenge is the remaining huge areas of habitats for the intermediate host Oncomelania hupensis. This is further exacerbated by an increasing number of new emerging snail habitats reported each year. Therefore, population genetics on snails in such areas will be useful in evaluation of snail control effect and/or dispersal. We then sampled snails from new emerging habitats in Taicang of Jiangsu, China, a currently S. japonicum non-endemic area from 2014 to 2017, and performed population genetic analyses based on nine microsatellites. Results showed that all snail populations had low genetic diversity, and most genetic variations originated from within snail populations. The estimated effective population size for the 2015 population was infinitive. All snails could be separated into two clusters, and further DIYABC analysis revealed that both the 2016 and the 2017 populations may derive from the 2015, indicating that the 2017 population must have been missed in the field survey performed in 2016. These findings may have implications in development of more practical guidelines for snail monitoring and control.
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Lesturgie P, Braun CD, Clua E, Mourier J, Thorrold SR, Vignaud T, Planes S, Mona S. Like a rolling stone: Colonization and migration dynamics of the gray reef shark ( Carcharhinus amblyrhynchos). Ecol Evol 2023; 13:e9746. [PMID: 36644707 PMCID: PMC9831972 DOI: 10.1002/ece3.9746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/18/2022] [Accepted: 12/27/2022] [Indexed: 01/13/2023] Open
Abstract
Designing appropriate management plans requires knowledge of both the dispersal ability and what has shaped the current distribution of the species under consideration. Here, we investigated the evolutionary history of the endangered gray reef shark (Carcharhinus amblyrhynchos) across its range by sequencing thousands of RADseq loci in 173 individuals in the Indo-Pacific (IP). We first bring evidence of the occurrence of a range expansion (RE) originating close to the Indo-Australian Archipelago (IAA) where two stepping-stone waves (east and westward) colonized almost the entire IP. Coalescent modeling additionally highlighted a homogenous connectivity (Nm ~ 10 per generation) throughout the range, and isolation by distance model suggested the absence of barriers to dispersal despite the affinity of C. amblyrhynchos to coral reefs. This coincides with long-distance swims previously recorded, suggesting that the strong genetic structure at the IP scale (F ST ~ 0.56 between its ends) is the consequence of its broad current distribution and organization in a large number of demes. Our results strongly suggest that management plans for the gray reef shark should be designed on a range-wide rather than a local scale due to its continuous genetic structure. We further contrasted these results with those obtained previously for the sympatric but strictly lagoon-associated Carcharhinus melanopterus, known for its restricted dispersal ability. Carcharhinus melanopterus exhibits a similar RE dynamic but is characterized by a stronger genetic structure and a nonhomogeneous connectivity largely dependent on local coral reefs availability. This sheds new light on shark evolution, emphasizing the roles of IAA as source of biodiversity and of life-history traits in shaping the extent of genetic structure and diversity.
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Affiliation(s)
- Pierre Lesturgie
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, EPHE‐PSLUniversité PSL, CNRS, SU, UAParisFrance
| | - Camrin D. Braun
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusettsUSA
| | - Eric Clua
- Laboratoire d'Excellence CORAILPapetoaiFrench Polynesia
- EPHE, PSL Research UniversityParisFrance
| | - Johann Mourier
- Laboratoire d'Excellence CORAILPapetoaiFrench Polynesia
- Université de Corse Pasquale Paoli, UMS 3514 Plateforme Marine Stella MareBigugliaFrance
| | - Simon R. Thorrold
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusettsUSA
| | | | - Serge Planes
- Laboratoire d'Excellence CORAILPapetoaiFrench Polynesia
- EPHE, PSL Research UniversityParisFrance
| | - Stefano Mona
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, EPHE‐PSLUniversité PSL, CNRS, SU, UAParisFrance
- EPHE, PSL Research UniversityParisFrance
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11
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The fast invasion of Europe by the box tree moth: an additional example coupling multiple introduction events, bridgehead effects and admixture events. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02887-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AbstractIdentifying the invasion routes of non-native species is crucial to understanding invasions and customizing management strategies. The box tree moth, Cydalima perspectalis, is native to Asia and was recently accidentally introduced into Europe as a result of the ornamental plant trade. Over the last 15 years, it has spread across the continent and has reached the Caucasus and Iran. It is threatening Buxus trees in both urban areas and forests. To investigate the species’ invasion routes, native and invasive box tree moth populations were sampled, and moth’s genetic diversity and structure were compared using microsatellite markers. Our approximate Bayesian computation analyses strongly suggest that invasion pathways were complex. Primary introductions originating from eastern China probably occurred independently twice in Germany and once in the Netherlands. There were also possibly bridgehead effects, where at least three invasive populations may have served as sources for other invasive populations within Europe, with indication of admixture between the two primary invasive populations. The bridgehead populations were likely those in the countries that play a major role in the ornamental plant trade in Europe, notably Germany, the Netherlands, and Italy. All these invasion processes likely facilitated its fast expansion across Europe and illustrate the role played by the ornamental plant trade not only in the moth’s introduction from China but also in the species’ spread across Europe, leading to an invasion with a complex pattern.
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12
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The genetic consequences of captive breeding, environmental change and human exploitation in the endangered peninsular pronghorn. Sci Rep 2022; 12:11253. [PMID: 35788138 PMCID: PMC9253347 DOI: 10.1038/s41598-022-14468-4] [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: 01/29/2022] [Accepted: 06/07/2022] [Indexed: 11/08/2022] Open
Abstract
Endangered species with small population sizes are susceptible to genetic erosion, which can be detrimental to long-term persistence. Consequently, monitoring and mitigating the loss of genetic diversity are essential for conservation. The Peninsular pronghorn (Antilocapra americana peninsularis) is an endangered pronghorn subspecies that is almost entirely held in captivity. Captive breeding has increased the number of pronghorns from 25 founders in 1997 to around 700 individuals today, but it is unclear how the genetic diversity of the captive herd may have changed over time. We therefore generated and analysed data for 16 microsatellites spanning 2009-2021. We detected a decline in heterozygosity and an increase in the proportion of inbred individuals over time. However, these trends appear to have been partially mitigated by a genetically informed breeding management attempt that was implemented in 2018. We also reconstructed the recent demographic history of the Peninsular pronghorn, revealing two sequential population declines putatively linked to the desertification of the Baja California peninsula around 6000 years ago, and hunting and habitat loss around 500 years ago, respectively. Our results provide insights into the genetic diversity of an endangered antelope and indicate the potential for genetically informed management to have positive conservation outcomes.
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13
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Borowiec ML, Dikow RB, Frandsen PB, McKeeken A, Valentini G, White AE. Deep learning as a tool for ecology and evolution. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13901] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marek L. Borowiec
- Entomology, Plant Pathology and Nematology University of Idaho Moscow ID USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho Moscow ID USA
| | - Rebecca B. Dikow
- Data Science Lab, Office of the Chief Information Officer Smithsonian Institution Washington DC USA
| | - Paul B. Frandsen
- Data Science Lab, Office of the Chief Information Officer Smithsonian Institution Washington DC USA
- Department of Plant and Wildlife Sciences Brigham Young University Provo UT USA
| | - Alexander McKeeken
- Entomology, Plant Pathology and Nematology University of Idaho Moscow ID USA
| | | | - Alexander E. White
- Data Science Lab, Office of the Chief Information Officer Smithsonian Institution Washington DC USA
- Department of Botany, National Museum of Natural History Smithsonian Institution Washington DC USA
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14
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Conklin JR, Verkuil YI, Battley PF, Hassell CJ, Ten Horn J, Johnson JA, Tomkovich PS, Baker AJ, Piersma T, Fontaine MC. Global flyway evolution in red knots Calidris canutus and genetic evidence for a Nearctic refugium. Mol Ecol 2022; 31:2124-2139. [PMID: 35106871 PMCID: PMC9545425 DOI: 10.1111/mec.16379] [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: 06/19/2021] [Revised: 12/13/2021] [Accepted: 01/14/2022] [Indexed: 11/30/2022]
Abstract
Present‐day ecology and population structure are the legacies of past climate and habitat perturbations, and this is particularly true for species that are widely distributed at high latitudes. The red knot, Calidris canutus, is an arctic‐breeding, long‐distance migratory shorebird with six recognized subspecies defined by differences in morphology, migration behavior, and annual cycle phenology, in a global distribution thought to have arisen just since the last glacial maximum (LGM). We used nextRAD sequencing of 10,881 single‐nucleotide polymorphisms (SNPs) to assess the neutral genetic structure and phylogeographic history of 172 red knots representing all known global breeding populations. Using population genetics approaches, including model‐based scenario‐testing in an approximate Bayesian computation (ABC) framework, we infer that red knots derive from two main lineages that diverged ca. 34,000 years ago, and thus most probably persisted at the LGM in both Palearctic and Nearctic refugia, followed by at least two instances of secondary contact and admixture. Within two Beringian subspecies (C. c. roselaari and rogersi), we detected previously unknown genetic structure among sub‐populations sharing a migratory flyway, reflecting additional complexity in the phylogeographic history of the region. Conversely, we found very weak genetic differentiation between two Nearctic populations (rufa and islandica) with clearly divergent migratory phenotypes and little or no apparent contact throughout the annual cycle. Together, these results suggest that relative gene flow among migratory populations reflects a complex interplay of historical, geographical, and ecological factors.
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Affiliation(s)
- Jesse R Conklin
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
| | - Yvonne I Verkuil
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
| | - Phil F Battley
- Wildlife and Ecology Group, School of Agriculture and Environment, Massey University, Palmerston North, 4442, New Zealand
| | - Chris J Hassell
- Global Flyway Network, PO Box 3089, Broome, WA, 6725, Australia
| | - Job Ten Horn
- Department of Coastal Systems, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands
| | - James A Johnson
- U.S. Fish & Wildlife Service, Migratory Bird Management, 1011 E. Tudor Road, MS 201, Anchorage, Alaska, 99503, USA
| | - Pavel S Tomkovich
- Zoological Museum, Moscow MV Lomonosov State University, Bolshaya Nikitskaya Str. 6, Moscow, 125009, Russia
| | - Allan J Baker
- Department of Natural History, Royal Ontario Museum, 100 Queens Park, Toronto, ON, M5S 2C6, Canada
| | - Theunis Piersma
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands.,Department of Coastal Systems, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands
| | - Michaël C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands.,MIVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France.,Montpellier Ecology and Evolution of Diseases Network (MEEDiN), Montpellier, France
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15
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Broccard N, Silva NM, Currat M. Simulated patterns of mitochondrial diversity are consistent with partial population turnover in Bronze Age Central Europe. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2022; 177:134-146. [PMID: 36787792 PMCID: PMC9298224 DOI: 10.1002/ajpa.24431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 08/03/2021] [Accepted: 09/24/2021] [Indexed: 11/09/2022]
Abstract
OBJECTIVES The analysis of ancient mitochondrial DNA from osteological remains has challenged previous conclusions drawn from the analysis of mitochondrial DNA from present populations, notably by revealing an absence of genetic continuity between the Neolithic and modern populations in Central Europe. Our study investigates how to reconcile these contradictions at the mitochondrial level using a modeling approach. MATERIALS AND METHODS We used a spatially explicit computational framework to simulate ancient and modern DNA sequences under various evolutionary scenarios of post Neolithic demographic events and compared the genetic diversity of the simulated and observed mitochondrial sequences. We investigated which-if any-scenarios were able to reproduce statistics of genetic diversity similar to those observed, with a focus on the haplogroup N1a, associated with the spread of early Neolithic farmers. RESULTS Demographic fluctuations during the Neolithic transition or subsequent demographic collapses after this period, that is, due to epidemics such as plague, are not sufficient to explain the signal of population discontinuity detected on the mitochondrial DNA in Central Europe. Only a scenario involving a substantial genetic input due to the arrival of migrants after the Neolithic transition, possibly during the Bronze Age, is compatible with observed patterns of genetic diversity. DISCUSSION Our results corroborate paleogenomic studies, since out of the alternative hypotheses tested, the best one that was able to recover observed patterns of mitochondrial diversity in modern and ancient Central European populations was one were immigration of populations from the Pontic steppes during the Bronze Age was explicitly simulated.
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Affiliation(s)
- Nicolas Broccard
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution – Anthropology UnitUniversity of GenevaGenevaSwitzerland
| | - Nuno Miguel Silva
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution – Anthropology UnitUniversity of GenevaGenevaSwitzerland
| | - Mathias Currat
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution – Anthropology UnitUniversity of GenevaGenevaSwitzerland
- Institute of Genetics and Genomics in Geneva (IGE3)University of GenevaGenevaSwitzerland
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16
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Gauffre B, Boissinot A, Quiquempois V, Leblois R, Grillet P, Morin S, Picard D, Ribout C, Lourdais O. Agricultural intensification alters marbled newt genetic diversity and gene flow through density and dispersal reduction. Mol Ecol 2021; 31:119-133. [PMID: 34674328 DOI: 10.1111/mec.16236] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 10/08/2021] [Accepted: 10/18/2021] [Indexed: 11/30/2022]
Abstract
Recent agricultural intensification threatens global biodiversity with amphibians being one of the most impacted groups. Because of their biphasic life cycle, amphibians are particularly vulnerable to habitat loss and fragmentation that often result in small, isolated populations and loss of genetic diversity. Here, we studied how landscape heterogeneity affects genetic diversity, gene flow and demographic parameters in the marbled newt, Triturus marmoratus, over a hedgerow network landscape in Western France. While the northern part of the study area consists of preserved hedged farmland, the southern part was more profoundly converted for intensive arable crops production after WWII. Based on 67 sampled ponds and 10 microsatellite loci, we characterized regional population genetic structure and evaluated the correlation between landscape variables and (i) local genetic diversity using mixed models and (ii) genetic distance using multiple regression methods and commonality analysis. We identified a single genetic population characterized by a spatially heterogeneous isolation-by-distance pattern. Pond density in the surrounding landscape positively affected local genetic diversity while arable crop land cover negatively affected gene flow and connectivity. We used demographic inferences to quantitatively assess differences in effective population density and dispersal between the contrasted landscapes characterizing the northern and southern parts of the study area. Altogether, results suggest recent land conversion affected T. marmoratus through reduction in both effective population density and dispersal due to habitat loss and reduced connectivity.
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Affiliation(s)
- Bertrand Gauffre
- INRAE, UR 1115 PSH, Plantes et Systèmes de culture Horticoles, Avignon, France.,School of Biological Sciences, Monash University, Clayton, Vic., Australia
| | - Alexandre Boissinot
- CNRS, UMR 7372 CEBC - Université de La Rochelle, Villiers-en-Bois, France.,Réserve Naturelle Régionale du Bocage des Antonins - Deux-Sèvres Nature Environnement, Niort, France
| | | | - Raphael Leblois
- CBGP UMR 1062, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier, Montpellier, France.,Institut de Biologie Computationnelle, Univ. Montpellier, Montpelier, France
| | - Pierre Grillet
- CNRS, UMR 7372 CEBC - Université de La Rochelle, Villiers-en-Bois, France
| | - Sophie Morin
- Office Français de la Biodiversité, Villiers-en-Bois, France
| | - Damien Picard
- Département de Biologie, UFR Sciences, Angers, France
| | - Cécile Ribout
- CNRS, UMR 7372 CEBC - Université de La Rochelle, Villiers-en-Bois, France
| | - Olivier Lourdais
- CNRS, UMR 7372 CEBC - Université de La Rochelle, Villiers-en-Bois, France.,School of Life Sciences, Arizona State University, Tempe, AZ, USA
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17
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Kikuchi A, Kyan R, Maki M. Population genetic diversity and conservation priority of prince’s pine Chimaphila umbellata populations around the south margin of their distribution. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01366-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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18
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Smith MM, Gilbert JH, Olson ER, Scribner KT, Van Deelen TR, Van Stappen JF, Williams BW, Woodford JE, Pauli JN. A recovery network leads to the natural recolonization of an archipelago and a potential trailing edge refuge. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2021; 31:e02416. [PMID: 34278627 DOI: 10.1002/eap.2416] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/22/2021] [Indexed: 06/13/2023]
Abstract
Rapid environmental change is reshaping ecosystems and driving species loss globally. Carnivore populations have declined and retracted rapidly and have been the target of numerous translocation projects. Success, however, is complicated when these efforts occur in novel ecosystems. Identifying refuges, locations that are resistant to environmental change, within a translocation framework should improve population recovery and persistence. American martens (Martes americana) are the most frequently translocated carnivore in North America. As elsewhere, martens were extirpated across much of the Great Lakes region by the 1930s and, despite multiple translocations beginning in the 1950s, martens remain of regional conservation concern. Surprisingly, martens were rediscovered in 2014 on the Apostle Islands of Lake Superior after a putative absence of >40 yr. To identify the source of martens to the islands and understand connectivity of the reintroduction network, we collected genetic data on martens from the archipelago and from all regional reintroduction sites. In total, we genotyped 483 individual martens, 43 of which inhabited the Apostle Islands (densities 0.42-1.46 km-2 ). Coalescent analyses supported the contemporary recolonization of the Apostle Islands with progenitors likely originating from Michigan, which were sourced from Ontario. We also identified movements by a first-order relative between the Apostle Islands and the recovery network. We detected some regional gene flow, but in an unexpected direction: individuals moving from the islands to the mainland. Our findings suggest that the Apostle Islands were naturally recolonized by progeny of translocated individuals and now act as a source back to the reintroduction sites on the mainland. We suggest that the Apostle Islands, given its protection from disturbance, complex forest structure, and reduced carnivore competition, will act as a potential refuge for marten along their trailing range boundary and a central node for regional recovery. Our work reveals that translocations, even those occurring along southern range boundaries, can create recovery networks that function like natural metapopulations. Identifying refuges, locations that are resistant to environmental change, within these recovery networks can further improve species recovery, even within novel environments. Future translocation planning should a priori identify potential refuges and sources to improve short-term recovery and long-term persistence.
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Affiliation(s)
- Matthew M Smith
- Department of Forest and Wildlife Ecology, University of Wisconsin, Madison, Wisconsin, 53706, USA
| | - Jonathan H Gilbert
- Great Lakes Indian Fish and Wildlife Commission, Odanah, Wisconsin, 54861, USA
| | - Erik R Olson
- Department of Natural Resources, Northland College, Ashland, Wisconsin, 54806, USA
| | - Kim T Scribner
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, 48824, USA
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Timothy R Van Deelen
- Department of Forest and Wildlife Ecology, University of Wisconsin, Madison, Wisconsin, 53706, USA
| | - Julie F Van Stappen
- Apostle Islands National Lakeshore, National Park Service, Bayfield, Wisconsin, 54814, USA
| | - Bronwyn W Williams
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, 48824, USA
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan, 48824, USA
- Research Laboratory, North Carolina Museum of Natural Sciences, Raleigh, North Carolina, 27699, USA
| | - James E Woodford
- Bureau of Natural Heritage Conservation, Wisconsin Department of Natural Resources, Rhinelander, Wisconsin, 54501, USA
| | - Jonathan N Pauli
- Department of Forest and Wildlife Ecology, University of Wisconsin, Madison, Wisconsin, 53706, USA
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19
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Rico Y, León-Tapia MÁ, Zurita-Solís M, Rodríguez-Gómez F, Vásquez-Morales SG. Influence of Pleistocene climatic oscillations on the phylogeography and demographic history of endemic vulnerable trees (section Magnolia) of the Tropical Montane Cloud Forest in Mexico. PeerJ 2021; 9:e12181. [PMID: 34692249 PMCID: PMC8485838 DOI: 10.7717/peerj.12181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 08/29/2021] [Indexed: 11/20/2022] Open
Abstract
The Tropical Montane Cloud Forest (TMCF) is a highly dynamic ecosystem that has undergone frequent spatial changes in response to the interglacial-glacial cycles of the Pleistocene. These climatic fluctuations between cold and warm cycles have led to species range shifts and contractions-expansions, resulting in complex patterns of genetic structure and lineage divergence in forest tree species. In this study, we sequenced four regions of the chloroplast DNA (trnT-trnL, trnK5-matk, rpl32-trnL, trnS-trnG) for 20 populations and 96 individuals to evaluate the phylogeography, historical demography, and paleodistributions of vulnerable endemic TMCF trees in Mexico: Magnolia pedrazae (north-region), M. schiedeana (central-region), and M. schiedeana population Oaxaca (south-region). Our data recovered 49 haplotypes that showed a significant phylogeographic structure in three regions: north, central, and south. Bayesian Phylogeographic and Ecological Clustering (BPEC) analysis also supported the divergence in three lineages and highlighted the role of environmental factors (temperature and precipitation) in genetic differentiation. Our historical demography analyses revealed demographic expansions predating the Last Interglacial (LIG, ~125,000 years ago), while Approximate Bayesian Computation (ABC) simulations equally supported two contrasting demographic scenarios. The BPEC and haplotype network analyses suggested that ancestral haplotypes were geographically found in central Veracruz. Our paleodistributions modeling showed evidence of range shifts and expansions-contractions from the LIG to the present, which suggested the complex evolutionary dynamics associated to the climatic oscillations of the Pleistocene. Habitat management of remnant forest fragments where large and genetically diverse populations occur in the three TMCF regions analyzed would be key for the conservation of these magnolia populations.
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Affiliation(s)
- Yessica Rico
- Red de Diversidad Biológica del Occidente Mexicano, Instituto de Ecología A.C., Pátzcuaro, Michoacán, México
- CONACYT, Ciudad de México, México
| | - M. Ángel León-Tapia
- Laboratorio de Sistemática Filogenética, Red de Biología Evolutiva, Instituto de Ecología A.C., Xalapa, Veracruz, Mexico
| | - Marisol Zurita-Solís
- Red de Diversidad Biológica del Occidente Mexicano, Instituto de Ecología A.C., Pátzcuaro, Michoacán, México
| | - Flor Rodríguez-Gómez
- Departamento de Ciencias Computacionales, División de Electrónica y Computación, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Suria Gisela Vásquez-Morales
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
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20
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Clonal dynamics in early human embryogenesis inferred from somatic mutation. Nature 2021; 597:393-397. [PMID: 34433967 DOI: 10.1038/s41586-021-03786-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 06/29/2021] [Indexed: 12/19/2022]
Abstract
Cellular dynamics and fate decision in early human embryogenesis remain largely unknown owing to the challenges of performing studies in human embryos1. Here, we explored whole-genomes of 334 single-cell colonies and targeted deep sequences of 379 bulk tissues obtained from various anatomical locations of seven recently deceased adult human donors. Using somatic mutations as an intrinsic barcode, we reconstructed early cellular phylogenies that demonstrate (1) an endogenous mutational rate that is higher in the first cell division but decreases to approximately one per cell per cell division later in life; (2) universal unequal contribution of early cells to embryo proper, resulting from early cellular bottlenecks that stochastically set aside epiblast cells within the embryo; (3) examples of varying degrees of early clonal imbalances between tissues on the left and right sides of the body, different germ layers and specific anatomical parts and organs; (4) emergence of a few ancestral cells that will substantially contribute to adult cell pools in blood and liver; and (5) presence of mitochondrial DNA heteroplasmy in the fertilized egg. Our approach also provides insights into the age-related mutational processes and loss of sex chromosomes in normal somatic cells. In sum, this study provides a foundation for future studies to complete cellular phylogenies in human embryogenesis.
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21
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Lesturgie P, Planes S, Mona S. Coalescence times, life history traits and conservation concerns: An example from four coastal shark species from the Indo-Pacific. Mol Ecol Resour 2021; 22:554-566. [PMID: 34407294 DOI: 10.1111/1755-0998.13487] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/27/2021] [Accepted: 08/12/2021] [Indexed: 11/30/2022]
Abstract
Dispersal abilities play a crucial role in shaping the extent of population genetic structure, with more mobile species being panmictic over large geographical ranges and less mobile ones organized in metapopulations exchanging migrants to different degrees. In turn, population structure directly influences the coalescence pattern of the sampled lineages, but the consequences on the estimated variation of the effective population size (Ne ) over time obtained by means of unstructured demographic models remain poorly understood. However, this knowledge is crucial for biologically interpreting the observed Ne trajectory and further devising conservation strategies in endangered species. Here we investigated the demographic history of four shark species (Carharhinus melanopterus, Carharhinus limbatus, Carharhinus amblyrhynchos, Galeocerdo cuvier) with different degrees of endangered status and life history traits related to dispersal distributed in the Indo-Pacific and sampled off New Caledonia. We compared several evolutionary scenarios representing both structured (metapopulation) and unstructured models and then inferred the Ne variation through time. By performing extensive coalescent simulations, we provided a general framework relating the underlying population structure and the observed Ne dynamics. On this basis, we concluded that the recent decline observed in three out of the four considered species when assuming unstructured demographic models can be explained by the presence of population structure. Furthermore, we also demonstrated the limits of the inferences based on the sole site frequency spectrum and warn that statistics based on linkage disequilibrium will be needed to exclude recent demographic events affecting meta-populations.
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Affiliation(s)
- Pierre Lesturgie
- Institut de Systématique, Evolution, Biodiversité, ISYEB (UMR 7205), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France.,Laboratoire d'Excellence CORAIL, Papetoai, French Polynesia
| | - Stefano Mona
- Institut de Systématique, Evolution, Biodiversité, ISYEB (UMR 7205), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,Laboratoire d'Excellence CORAIL, Papetoai, French Polynesia.,EPHE, PSL Research University, Paris, France
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Recent population expansion in wild gaur (Bos gaurus gaurus) as revealed by microsatellite markers. Mamm Biol 2021. [DOI: 10.1007/s42991-021-00145-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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23
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Abstract
The peopling of Siberia and the Americas is intriguing for archaeologists, linguists, and human geneticists, but despite significant recent developments, many details remain controversial. Here, we provide insights based on genetic diversity within Helicobacter pylori, a bacterium that infects 50% of all humans. H. pylori strains were collected from across eastern Eurasia and the Americas. Sequence analyses indicated that Siberia contains both anciently diverged and recently admixed bacteria, supporting both human persistence over the last glacial maximum and more recent human recolonization. We inferred a single migration across the Bering land bridge, accompanied by a dramatic reduction in effective population size, followed by bidirectional Holocene gene flow between Asia and the Americas. The gastric bacterium Helicobacter pylori shares a coevolutionary history with humans that predates the out-of-Africa diaspora, and the geographical specificities of H. pylori populations reflect multiple well-known human migrations. We extensively sampled H. pylori from 16 ethnically diverse human populations across Siberia to help resolve whether ancient northern Eurasian populations persisted at high latitudes through the last glacial maximum and the relationships between present-day Siberians and Native Americans. A total of 556 strains were cultivated and genotyped by multilocus sequence typing, and 54 representative draft genomes were sequenced. The genetic diversity across Eurasia and the Americas was structured into three populations: hpAsia2, hpEastAsia, and hpNorthAsia. hpNorthAsia is closely related to the subpopulation hspIndigenousAmericas from Native Americans. Siberian bacteria were structured into five other subpopulations, two of which evolved through a divergence from hpAsia2 and hpNorthAsia, while three originated though Holocene admixture. The presence of both anciently diverged and recently admixed strains across Siberia support both Pleistocene persistence and Holocene recolonization. We also show that hspIndigenousAmericas is endemic in human populations across northern Eurasia. The evolutionary history of hspIndigenousAmericas was reconstructed using approximate Bayesian computation, which showed that it colonized the New World in a single migration event associated with a severe demographic bottleneck followed by low levels of recent admixture across the Bering Strait.
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Yue L, Cao LJ, Chen JC, Gong YJ, Lin YH, Hoffmann AA, Wei SJ. Low levels of genetic differentiation with isolation by geography and environment in populations of Drosophila melanogaster from across China. Heredity (Edinb) 2021; 126:942-954. [PMID: 33686193 PMCID: PMC8178374 DOI: 10.1038/s41437-021-00419-8] [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: 10/19/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 01/31/2023] Open
Abstract
The fruit fly, Drosophila melanogaster, is a model species in evolutionary studies. However, population processes of this species in East Asia are poorly studied. Here we examined the population genetic structure of D. melanogaster across China. There were 14 mitochondrial haplotypes with 10 unique ones out of 23 known from around the globe. Pairwise FST values estimated from 15 novel microsatellites ranged from 0 to 0.11, with geographically isolated populations showing the highest level of genetic uniqueness. STRUCTURE analysis identified high levels of admixture at both the individual and population levels. Mantel tests indicated a strong association between genetic distance and geographical distance as well as environmental distance. Full redundancy analysis (RDA) showed that independent effects of environmental conditions and geography accounted for 62.10% and 31.58% of the total explained genetic variance, respectively. When geographic variables were constrained in a partial RDA analysis, the environmental variables bio2 (mean diurnal air temperature range), bio13 (precipitation of the wettest month), and bio15 (precipitation seasonality) were correlated with genetic distance. Our study suggests that demographic history, geographical isolation, and environmental factors have together shaped the population genetic structure of D. melanogaster after its introduction into China.
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Affiliation(s)
- Lei Yue
- grid.418260.90000 0004 0646 9053Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Li-Jun Cao
- grid.418260.90000 0004 0646 9053Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jin-Cui Chen
- grid.418260.90000 0004 0646 9053Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ya-Jun Gong
- grid.418260.90000 0004 0646 9053Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yan-Hao Lin
- grid.418260.90000 0004 0646 9053Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China ,International Department of Beijing No. 80 High School, Beijing, China
| | - Ary Anthony Hoffmann
- grid.1008.90000 0001 2179 088XBio21 Institute, School of BioSciences, The University of Melbourne, Victoria, Australia
| | - Shu-Jun Wei
- grid.418260.90000 0004 0646 9053Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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25
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Clemente F, Unterländer M, Dolgova O, Amorim CEG, Coroado-Santos F, Neuenschwander S, Ganiatsou E, Cruz Dávalos DI, Anchieri L, Michaud F, Winkelbach L, Blöcher J, Arizmendi Cárdenas YO, Sousa da Mota B, Kalliga E, Souleles A, Kontopoulos I, Karamitrou-Mentessidi G, Philaniotou O, Sampson A, Theodorou D, Tsipopoulou M, Akamatis I, Halstead P, Kotsakis K, Urem-Kotsou D, Panagiotopoulos D, Ziota C, Triantaphyllou S, Delaneau O, Jensen JD, Moreno-Mayar JV, Burger J, Sousa VC, Lao O, Malaspinas AS, Papageorgopoulou C. The genomic history of the Aegean palatial civilizations. Cell 2021; 184:2565-2586.e21. [PMID: 33930288 PMCID: PMC8127963 DOI: 10.1016/j.cell.2021.03.039] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 09/17/2020] [Accepted: 03/18/2021] [Indexed: 12/30/2022]
Abstract
The Cycladic, the Minoan, and the Helladic (Mycenaean) cultures define the Bronze Age (BA) of Greece. Urbanism, complex social structures, craft and agricultural specialization, and the earliest forms of writing characterize this iconic period. We sequenced six Early to Middle BA whole genomes, along with 11 mitochondrial genomes, sampled from the three BA cultures of the Aegean Sea. The Early BA (EBA) genomes are homogeneous and derive most of their ancestry from Neolithic Aegeans, contrary to earlier hypotheses that the Neolithic-EBA cultural transition was due to massive population turnover. EBA Aegeans were shaped by relatively small-scale migration from East of the Aegean, as evidenced by the Caucasus-related ancestry also detected in Anatolians. In contrast, Middle BA (MBA) individuals of northern Greece differ from EBA populations in showing ∼50% Pontic-Caspian Steppe-related ancestry, dated at ca. 2,600-2,000 BCE. Such gene flow events during the MBA contributed toward shaping present-day Greek genomes.
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Affiliation(s)
- Florian Clemente
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Martina Unterländer
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece; Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, 55099 Mainz, Germany
| | - Olga Dolgova
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Carlos Eduardo G Amorim
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Francisco Coroado-Santos
- CE3C, Centre for Ecology, Evolution and Environmental Changes, Faculty of Sciences of the University of Lisbon, 1749-016 Lisbon, Portugal
| | - Samuel Neuenschwander
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Vital-IT, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Elissavet Ganiatsou
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece
| | - Diana I Cruz Dávalos
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Lucas Anchieri
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Frédéric Michaud
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Laura Winkelbach
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, 55099 Mainz, Germany
| | - Jens Blöcher
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, 55099 Mainz, Germany
| | - Yami Ommar Arizmendi Cárdenas
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Bárbara Sousa da Mota
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Eleni Kalliga
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece
| | - Angelos Souleles
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece
| | - Ioannis Kontopoulos
- Center for GeoGenetics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | | | - Olga Philaniotou
- Ephor Emerita of Antiquities, Hellenic Ministry of Culture and Sports, 10682 Athens, Greece
| | - Adamantios Sampson
- Department of Mediterranean Studies, University of the Aegean, 85132 Rhodes, Greece
| | - Dimitra Theodorou
- Ephorate of Antiquities of Kozani, Hellenic Ministry of Culture and Sports, 50004 Kozani, Greece
| | - Metaxia Tsipopoulou
- Ephor Emerita of Antiquities, Hellenic Ministry of Culture and Sports, 10682 Athens, Greece
| | - Ioannis Akamatis
- Department of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Paul Halstead
- Department of Archaeology, University of Sheffield, Minalloy House, 10-16 Regent St., Sheffield S1 3NJ, UK
| | - Kostas Kotsakis
- Department of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Dushka Urem-Kotsou
- Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece
| | - Diamantis Panagiotopoulos
- Institute of Classical Archaeology, University of Heidelberg, Marstallhof 4, 69117 Heidelberg, Germany
| | - Christina Ziota
- Ephorate of Antiquities of Florina, Hellenic Ministry of Culture and Sports, 53100 Florina, Greece
| | - Sevasti Triantaphyllou
- Department of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Olivier Delaneau
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - J Víctor Moreno-Mayar
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Center for GeoGenetics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark; National Institute of Genomic Medicine (INMEGEN), 14610 Mexico City, Mexico
| | - Joachim Burger
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, 55099 Mainz, Germany
| | - Vitor C Sousa
- CE3C, Centre for Ecology, Evolution and Environmental Changes, Faculty of Sciences of the University of Lisbon, 1749-016 Lisbon, Portugal
| | - Oscar Lao
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Christina Papageorgopoulou
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece.
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Collin FD, Durif G, Raynal L, Lombaert E, Gautier M, Vitalis R, Marin JM, Estoup A. Extending approximate Bayesian computation with supervised machine learning to infer demographic history from genetic polymorphisms using DIYABC Random Forest. Mol Ecol Resour 2021; 21:2598-2613. [PMID: 33950563 PMCID: PMC8596733 DOI: 10.1111/1755-0998.13413] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 03/29/2021] [Accepted: 04/28/2021] [Indexed: 01/07/2023]
Abstract
Simulation-based methods such as approximate Bayesian computation (ABC) are well-adapted to the analysis of complex scenarios of populations and species genetic history. In this context, supervised machine learning (SML) methods provide attractive statistical solutions to conduct efficient inferences about scenario choice and parameter estimation. The Random Forest methodology (RF) is a powerful ensemble of SML algorithms used for classification or regression problems. Random Forest allows conducting inferences at a low computational cost, without preliminary selection of the relevant components of the ABC summary statistics, and bypassing the derivation of ABC tolerance levels. We have implemented a set of RF algorithms to process inferences using simulated data sets generated from an extended version of the population genetic simulator implemented in DIYABC v2.1.0. The resulting computer package, named DIYABC Random Forest v1.0, integrates two functionalities into a user-friendly interface: the simulation under custom evolutionary scenarios of different types of molecular data (microsatellites, DNA sequences or SNPs) and RF treatments including statistical tools to evaluate the power and accuracy of inferences. We illustrate the functionalities of DIYABC Random Forest v1.0 for both scenario choice and parameter estimation through the analysis of pseudo-observed and real data sets corresponding to pool-sequencing and individual-sequencing SNP data sets. Because of the properties inherent to the implemented RF methods and the large feature vector (including various summary statistics and their linear combinations) available for SNP data, DIYABC Random Forest v1.0 can efficiently contribute to the analysis of large SNP data sets to make inferences about complex population genetic histories.
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Affiliation(s)
| | - Ghislain Durif
- IMAG, Univ Montpellier, CNRS, UMR 5149, Montpellier, France
| | - Louis Raynal
- IMAG, Univ Montpellier, CNRS, UMR 5149, Montpellier, France
| | - Eric Lombaert
- ISA, INRAE, CNRS, Univ Côte d'Azur, Sophia Antipolis, France
| | - Mathieu Gautier
- CBGP, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Renaud Vitalis
- CBGP, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | | | - Arnaud Estoup
- CBGP, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
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27
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Castillo-Chora VDJ, Sánchez-González LA, Mastretta-Yanes A, Prieto-Torres DA, Navarro-Sigüenza AG. Insights into the importance of areas of climatic stability in the evolution and maintenance of avian diversity in the Mesoamerican dry forests. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa202] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
We analysed the phylogeographic structure of five resident bird lineages distributed in the seasonally dry tropical forests (SDTF) of Mesoamerica to test whether they show patterns of synchronous and geographically coincident genetic divergence during the Quaternary. We generated phylogenetic trees, estimated divergence times and analysed the genetic structure of populations (based on sequences of mitochondrial genes), as well as estimating historical distributions (range extension and areas of long-term climate stability) during the Late Pleistocene. We tested and selected the phylogeographic divergence scenarios that best explain the current divergence patterns of taxa using the Approximate Bayesian Computation (ABC) approach. For most species, phylogenetic trees and haplotype networks showed a clear genetic structure associated with geographical distribution. Overall, the divergence times ranged from 0.29–2.0 Mya, suggesting that diversification of populations occurred at different times during the Pleistocene. The palaeodistribution models predicted at least two areas of climatic stability within the current SDTF that probably allowed glacial-interglacial persistence of isolated bird populations along the Mexican Pacific, thus promoting their genetic divergence. The results provide information relevant to the identification of diversification hotspots for the Mesoamerican SDTF avifauna.
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Affiliation(s)
- Vicente De J Castillo-Chora
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, A.P., Mexico City, México
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México
| | - Luis A Sánchez-González
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, A.P., Mexico City, México
| | - Alicia Mastretta-Yanes
- CONACYT—CONABIO, Comisión Nacional para el Conocimiento y Uso de la Biodiversidad, Liga Periférico-Insurgentes Sur No. 4903, Parques del Pedregal, Tlalpan, Mexico City, México
| | - David A Prieto-Torres
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, A.P., Mexico City, México
| | - Adolfo G Navarro-Sigüenza
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, A.P., Mexico City, México
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28
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de Oliveira FFR, Gehara M, Solé M, Lyra M, Haddad CFB, Silva DP, de Magalhães RF, Leite FSF, Burbrink FT. Quaternary climatic fluctuations influence the demographic history of two species of sky-island endemic amphibians in the Neotropics. Mol Phylogenet Evol 2021; 160:107113. [PMID: 33610648 DOI: 10.1016/j.ympev.2021.107113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 01/13/2021] [Accepted: 02/08/2021] [Indexed: 10/22/2022]
Abstract
We evaluated the role of Quaternary climatic fluctuations on the demographic history and population structure of amphibian species endemic to the 'campo rupestre' in the Neotropics, evaluating their distributional shifts, demographic changes, and lineage formation from the end of Pleistocene to present. We chose two anurans endemic to the high-elevation 'campo rupestre' in the Espinhaço Range (ER) in northeastern and southeastern Brazil (Bokermannohyla alvarengai and Bokermannohyla oxente), as models to test the role of Quaternary climatic fluctuations over their distribution range in this region. We collected tissue samples throughout their distribution range and used statistical phylogeography to examine processes of divergence and population demography. We generated spatial-temporal reconstructions using Bayesian inference in a coalescent framework in combination with hind-cast projections of species distribution models (SDMs). We also used the results and literature information to test alternative diversification scenarios via approximate Bayesian computation (ABC). Our results show that Quaternary climatic fluctuations influenced the geographic ranges of both species showing population expansion during the last glacial maximum (LGM) and range contraction during interglacial periods, as inferred from selected ABC models and from past projections of SDMs. We recovered Pleistocene diversification for both species occuring in distinctly unique periods for each taxon. An older and range-restricted lineage was recovered in a geographically isolated geological massif, deserving conservation and further taxonomic study. The diversification and distribution of these amphibian species endemic to the Neotropical 'campo rupestre' were influenced by Quaternary climatic fluctuations. The expansion of cold adapted species restricted to higher elevations during glacial periods and their concomitant retraction during interglacial periods may have been crucial for producing patterns of species richness and endemism along elevation gradients in tropical and subtropical domains. Such processes may influence the evolution of the biota distributed in heterogeneous landscapes with varied topography.
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Affiliation(s)
| | - Marcelo Gehara
- Department of Earth and Environmental Sciences, Rutgers University - Newark, USA
| | - Mirco Solé
- Programa de Pós-graduação em Ecologia e Conservação da Biodiversidade, Universidade Estadual de Santa Cruz, Bahia, Brazil; Herpetology Section, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Mariana Lyra
- Universidade Estadual Paulista (UNESP), Departamento de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Campus Rio Claro, 13506-900 Rio Claro, São Paulo, Brazil
| | - Célio Fernando Baptista Haddad
- Universidade Estadual Paulista (UNESP), Departamento de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Campus Rio Claro, 13506-900 Rio Claro, São Paulo, Brazil
| | - Daniel Paiva Silva
- Instituto Federal Goiano - IF Goiano, Departamento de Biologia, Urutaí, Goiás, Brazil
| | - Rafael Félix de Magalhães
- Departamento de Ciências Naturais, Campus Dom Bosco, Universidade Federal de São João del-Rei, São João del Rei, MG 36301-160, Brazil
| | - Felipe Sá Fortes Leite
- Laboratório Sagarana, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa - UFV, Florestal, Minas Gerais, Brazil
| | - Frank T Burbrink
- Department of Herpetology, American Museum of Natural History, New York, NY, USA
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Kurata S, Sakaguchi S, Hirota SK, Kurashima O, Suyama Y, Nishida S, Ito M. Refugia within refugium of Geranium yesoense (Geraniaceae) in Japan were driven by recolonization into the southern interglacial refugium. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Recent studies have found that geographical fragmentation and recurrent colonization result in complex genetic structures in refugial areas. This phenomenon, known as ‘refugia within refugium’, has been identified from many geographical locations. In Japan, the high-elevation mountains of central Honshu provided an interglacial refugium for alpine plants. Here we focused on the Geranium yesoense complex, which exhibits increased morphological variation in the refugial area, to determine whether this variation was shaped by recurrent colonization, range fragmentation or phenotypic changes independent of population history. We analysed single nucleotide polymorphism data and chloroplast genome sequences. Diversification in the G. yesoense species complex occurred in the mid-Pleistocene. The varieties are distinct entities and suggest the presence of a genetic cluster with highly disjunct distributions, occurring both in northern Japan and in southern refugial areas in central Honshu. Demographic analysis suggests that a single ancestral variety (var. nipponicum) evolved in the alpine region of central Honshu, and that subsequent migration from one of the two diverged northern varieties (var. pseudopratense) led to secondary contact with var. nipponicum during the last glacial period. Recolonization into refugial populations in central Honshu and hybridization between diverged populations have resulted in complex genetic structures among refugial populations.
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Affiliation(s)
- Seikan Kurata
- Laboratory of Plant Evolution and Biodiversity, Department of General Systems Studies, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, Japan
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto, Japan
| | - Shun K Hirota
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, Aza-yomogida, Naruko Onsen, Osaki City, Miyagi, Japan
| | - Osamu Kurashima
- National Museum of Nature and Science, Ueno-koen, Taito-ku, Tokyo, Japan
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, Aza-yomogida, Naruko Onsen, Osaki City, Miyagi, Japan
| | - Sachiko Nishida
- Nagoya University Museum, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Motomi Ito
- Laboratory of Plant Evolution and Biodiversity, Department of General Systems Studies, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, Japan
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30
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Prunier JG, Poesy C, Dubut V, Veyssière C, Loot G, Poulet N, Blanchet S. Quantifying the individual impact of artificial barriers in freshwaters: A standardized and absolute genetic index of fragmentation. Evol Appl 2020; 13:2566-2581. [PMID: 33294009 PMCID: PMC7691472 DOI: 10.1111/eva.13044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 06/02/2020] [Accepted: 06/09/2020] [Indexed: 12/27/2022] Open
Abstract
Fragmentation by artificial barriers is an important threat to freshwater biodiversity. Mitigating the negative aftermaths of fragmentation is of crucial importance, and it is now essential for environmental managers to benefit from a precise estimate of the individual impact of weirs and dams on river connectivity. Although the indirect monitoring of fragmentation using molecular data constitutes a promising approach, it is plagued with several constraints preventing a standardized quantification of barrier effects. Indeed, observed levels of genetic differentiation GD depend on both the age of the obstacle and the effective size of the populations it separates, making comparisons of the actual barrier effect of different obstacles difficult. Here, we developed a standardized genetic index of fragmentation (F INDEX), allowing an absolute and independent assessment of the individual effects of obstacles on connectivity. The F INDEX is the standardized ratio between the observed GD between pairs of populations located on either side of an obstacle and the GD expected if this obstacle completely prevented gene flow. The expected GD is calculated from simulations taking into account two parameters: the number of generations since barrier creation and the expected heterozygosity of the populations, a proxy for effective population size. Using both simulated and empirical datasets, we explored the validity and the limits of the F INDEX. We demonstrated that it allows quantifying effects of fragmentation only from a few generations after barrier creation and provides valid comparisons among obstacles of different ages and populations (or species) of different effective sizes. The F INDEX requires a minimum amount of fieldwork and genotypic data and solves some of the difficulties inherent to the study of artificial fragmentation in rivers and potentially in other ecosystems. This makes the F INDEX promising to support the management of freshwater species affected by barriers, notably for planning and evaluating restoration programs.
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Affiliation(s)
- Jérôme G. Prunier
- Centre National de la Recherche Scientifique (CNRS)Université Paul Sabatier (UPS)UMR 5321Station d’Ecologie Théorique et ExpérimentaleMoulisFrance
| | - Camille Poesy
- Centre National de la Recherche Scientifique (CNRS)Université Paul Sabatier (UPS)UMR 5321Station d’Ecologie Théorique et ExpérimentaleMoulisFrance
| | - Vincent Dubut
- CNRSIRDAvignon UniversitéIMBEAix Marseille UnivMarseille UniversitéFrance
| | - Charlotte Veyssière
- CNRSUPSUMR 5174 EDB (Laboratoire Évolution & Diversité Biologique)École Nationale de Formation Agronomique (ENFA)Toulouse Cedex 4France
| | - Géraldine Loot
- CNRSUPSUMR 5174 EDB (Laboratoire Évolution & Diversité Biologique)École Nationale de Formation Agronomique (ENFA)Toulouse Cedex 4France
| | - Nicolas Poulet
- DRAS, Pôle R&D écohydraulique OFBIMFT‐PPRIMEOffice Français de la BiodiversitéToulouseFrance
| | - Simon Blanchet
- Centre National de la Recherche Scientifique (CNRS)Université Paul Sabatier (UPS)UMR 5321Station d’Ecologie Théorique et ExpérimentaleMoulisFrance
- CNRSUPSUMR 5174 EDB (Laboratoire Évolution & Diversité Biologique)École Nationale de Formation Agronomique (ENFA)Toulouse Cedex 4France
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Hou H, Ye H, Wang Z, Wu J, Gao Y, Han W, Na D, Sun G, Wang Y. Demographic history and genetic differentiation of an endemic and endangered Ulmus lamellosa (Ulmus). BMC PLANT BIOLOGY 2020; 20:526. [PMID: 33203402 PMCID: PMC7672979 DOI: 10.1186/s12870-020-02723-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 10/26/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Ulmus lamellosa (one of the ancient species of Ulmus) is an endemic and endangered plant that has undergone climatic oscillations and geographical changes. The elucidation of its demographic history and genetic differentiation is critical for understanding the evolutionary process and ecological adaption to forests in Northern China. RESULTS Polymorphic haplotypes were detected in most populations of U. lamellosa via DNA sequencing. All haplotypes were divided into three phylogeographic clades fundamentally corresponding to their geographical distribution, namely THM (Taihang Mountains), YM (Yinshan Mountains), and YSM (Yanshan Mountains) groups. The YSM group, which is regarded as ancestral, possessed higher genetic diversity and significant genetic variability in contrast to the YSM and YM groups. Meanwhile, the divergence time of intraspecies haplotypes occurred during the Miocene-Pliocene, which was associated with major Tertiary geological and/or climatic events. Different degrees of gene exchanges were identified between the three groups. During glaciation, the YSM and THM regions might have served as refugia for U. lamellosa. Based on ITS data, range expansion was not expected through evolutionary processes, except for the THM group. A series of mountain uplifts (e.g., Yanshan Mountains and Taihang Mountains) following the Miocene-Pliocene, and subsequently quaternary climatic oscillations in Northern China, further promoted divergence between U. lamellosa populations. CONCLUSIONS Geographical topology and climate change in Northern China played a critical role in establishing the current phylogeographic structural patterns of U. lamellosa. These results provide important data and clues that facilitate the demographic study of tree species in Northern China.
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Affiliation(s)
- Huimin Hou
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Hang Ye
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Zhi Wang
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Jiahui Wu
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Yue Gao
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Wei Han
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Dongchen Na
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Genlou Sun
- Saint Mary’s University, Halifax, Canada
| | - Yiling Wang
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
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32
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Hirsch H, Richardson DM, Pauchard A, Le Roux JJ. Genetic analyses reveal complex introduction histories for the invasive tree
Acacia dealbata
Link around the world. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13186] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Heidi Hirsch
- Centre for Invasion Biology Department of Botany and Zoology Stellenbosch University Matieland South Africa
| | - David M. Richardson
- Centre for Invasion Biology Department of Botany and Zoology Stellenbosch University Matieland South Africa
| | - Aníbal Pauchard
- Laboratorio de Invasiones Biológicas Facultad de Ciencias Forestales Universidad de Concepción Concepción Chile
- Institute of Ecology and Biodiversity (IEB) Santiago Chile
| | - Johannes J. Le Roux
- Centre for Invasion Biology Department of Botany and Zoology Stellenbosch University Matieland South Africa
- Department of Biological Sciences Macquarie University Sydney NSW Australia
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33
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Ghirotto S, Vizzari MT, Tassi F, Barbujani G, Benazzo A. Distinguishing among complex evolutionary models using unphased whole-genome data through random forest approximate Bayesian computation. Mol Ecol Resour 2020; 21:2614-2628. [PMID: 33000507 DOI: 10.1111/1755-0998.13263] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 08/28/2020] [Accepted: 09/07/2020] [Indexed: 01/25/2023]
Abstract
Inferring past demographic histories is crucial in population genetics, and the amount of complete genomes now available should in principle facilitate this inference. In practice, however, the available inferential methods suffer from severe limitations. Although hundreds complete genomes can be simultaneously analysed, complex demographic processes can easily exceed computational constraints, and the procedures to evaluate the reliability of the estimates contribute to increase the computational effort. Here we present an approximate Bayesian computation framework based on the random forest algorithm (ABC-RF), to infer complex past population processes using complete genomes. To this aim, we propose to summarize the data by the full genomic distribution of the four mutually exclusive categories of segregating sites (FDSS), a statistic fast to compute from unphased genome data and that does not require the ancestral state of alleles to be known. We constructed an efficient ABC pipeline and tested how accurately it allows one to recognize the true model among models of increasing complexity, using simulated data and taking into account different sampling strategies in terms of number of individuals analysed, number and size of the genetic loci considered. We also compared the FDSS with the unfolded and folded site frequency spectrum (SFS), and for these statistics we highlighted the experimental conditions maximizing the inferential power of the ABC-RF procedure. We finally analysed real data sets, testing models on the dispersal of anatomically modern humans out of Africa and exploring the evolutionary relationships of the three species of Orangutan inhabiting Borneo and Sumatra.
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Affiliation(s)
- Silvia Ghirotto
- Department of Mathematics and Computer Science, University of Ferrara, Ferrara, Italy
| | - Maria Teresa Vizzari
- Department of Mathematics and Computer Science, University of Ferrara, Ferrara, Italy
| | - Francesca Tassi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Guido Barbujani
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Andrea Benazzo
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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34
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Souza MS, Thomaz AT, Fagundes NJR. River capture or ancestral polymorphism: an empirical genetic test in a freshwater fish using approximate Bayesian computation. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa140] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Abstract
A headwater or river capture is a phenomenon commonly invoked to explain the absence of reciprocal monophyly of genetic lineages among isolated hydrographic basins in freshwater fish. Under the assumption of river capture, a secondary contact between populations previously isolated in different basins explains the observed genetic pattern. However, the absence of reciprocal monophyly could also arise under population isolation through the retention of ancestral of polymorphisms. Here, we applied an approximate Bayesian computation (ABC) framework for estimating the relative probability of scenarios with and without secondary contact. We used Cnesterodon decemmaculatus as a study model because of the multiple possible cases of river capture and the demographic parameters estimated in a previous mitochondrial DNA study that are useful for simulating scenarios to test both hypotheses using the ABC framework. Our results showed that, in general, mitochondrial DNA is useful for distinguishing between these alternative demographic scenarios with reasonable confidence, but in extreme cases (e.g. recent divergence or large population size) there is no power to discriminate between scenarios. Testing hypotheses of drainage rearrangement under a statistically rigorous framework is fundamental for understanding the evolution of freshwater fish fauna as a complement to, or in the absence of, geological evidence.
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Affiliation(s)
- Mateus S Souza
- Postgraduate Program in Animal Biology, Institute of Biosciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
- Laboratory of Medical Genetics and Evolution, Department of Genetics, Institute of Biosciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Andréa T Thomaz
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Nelson J R Fagundes
- Postgraduate Program in Animal Biology, Institute of Biosciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
- Laboratory of Medical Genetics and Evolution, Department of Genetics, Institute of Biosciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
- Postgraduate Program in Genetics and Molecular Biology, Institute of Biosciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
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35
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Bayesian estimation of Lassa virus epidemiological parameters: Implications for spillover prevention using wildlife vaccination. PLoS Negl Trop Dis 2020; 14:e0007920. [PMID: 32956349 PMCID: PMC7529244 DOI: 10.1371/journal.pntd.0007920] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 10/01/2020] [Accepted: 07/20/2020] [Indexed: 12/31/2022] Open
Abstract
Lassa virus is a significant burden on human health throughout its endemic region in West Africa, with most human infections the result of spillover from the primary rodent reservoir of the virus, the natal multimammate mouse, M. natalensis. Here we develop a Bayesian methodology for estimating epidemiological parameters of Lassa virus within its rodent reservoir and for generating probabilistic predictions for the efficacy of rodent vaccination programs. Our approach uses Approximate Bayesian Computation (ABC) to integrate mechanistic mathematical models, remotely-sensed precipitation data, and Lassa virus surveillance data from rodent populations. Using simulated data, we show that our method accurately estimates key model parameters, even when surveillance data are available from only a relatively small number of points in space and time. Applying our method to previously published data from two villages in Guinea estimates the time-averaged R0 of Lassa virus to be 1.74 and 1.54 for rodent populations in the villages of Bantou and Tanganya, respectively. Using the posterior distribution for model parameters derived from these Guinean populations, we evaluate the likely efficacy of vaccination programs relying on distribution of vaccine-laced baits. Our results demonstrate that effective and durable reductions in the risk of Lassa virus spillover into the human population will require repeated distribution of large quantities of vaccine. Lassa virus is a chronic source of illness throughout West Africa, and is considered to be a threat for widespread emergence. Because most human infections result from contact with infected rodents, interventions that reduce the number of rodents infected with Lassa virus represent promising opportunities for reducing the public health burden of this disease. Evaluating how well alternative interventions are likely to perform is complicated by our relatively poor understanding of viral epidemiology within the reservoir population. Here we develop a novel statistical approach that couples mathematical models and viral surveillance data from rodent populations to robustly estimate key epidemiological parameters. Applying our method to existing data from Guinea yields well-resolved parameter estimates and allows us to simulate a variety of rodent vaccination programs. Together, our results demonstrate that rodent vaccination alone is unlikely to be an effective tool for reducing the public health burden of Lassa fever within West Africa.
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36
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Feutry P, Devloo-Delva F, Tran Lu Y A, Mona S, Gunasekera RM, Johnson G, Pillans RD, Jaccoud D, Kilian A, Morgan DL, Saunders T, Bax NJ, Kyne PM. One panel to rule them all: DArTcap genotyping for population structure, historical demography, and kinship analyses, and its application to a threatened shark. Mol Ecol Resour 2020; 20:1470-1485. [PMID: 32492756 DOI: 10.1111/1755-0998.13204] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 01/25/2023]
Abstract
With recent advances in sequencing technology, genomic data are changing how important conservation management decisions are made. Applications such as Close-Kin Mark-Recapture demand large amounts of data to estimate population size and structure, and their full potential can only be realised through ongoing improvements in genotyping strategies. Here we introduce DArTcap, a cost-efficient method that combines DArTseq and sequence capture, and illustrate its use in a high resolution population analysis of Glyphis garricki, a rare, poorly known and threatened euryhaline shark. Clustering analyses and spatial distribution of kin pairs from four different regions across northern Australia and one in Papua New Guinea, representing its entire known range, revealed that each region hosts at least one distinct population. Further structuring is likely within Van Diemen Gulf, the region that included the most rivers sampled, suggesting additional population structuring would be found if other rivers were sampled. Coalescent analyses and spatially explicit modelling suggest that G. garricki experienced a recent range expansion during the opening of the Gulf of Carpentaria following the conclusion of the Last Glacial Maximum. The low migration rates between neighbouring populations of a species that is found only in restricted coastal and riverine habitats show the importance of managing each population separately, including careful monitoring of local and remote anthropogenic activities that may affect their environments. Overall we demonstrated how a carefully chosen SNP panel combined with DArTcap can provide highly accurate kinship inference and also support population structure and historical demography analyses, therefore maximising cost-effectiveness.
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Affiliation(s)
| | - Floriaan Devloo-Delva
- CSIRO Oceans and Atmosphere, Hobart, TAS, Australia.,School of Natural Sciences - Quantitative Marine Science, University of Tasmania, Hobart, TAS, Australia
| | - Adrien Tran Lu Y
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE, Sorbonne Université, Paris, France.,EPHE, PSL University, Paris, France
| | - Stefano Mona
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE, Sorbonne Université, Paris, France.,EPHE, PSL University, Paris, France.,Laboratoire d'Excellence CORAIL, Papetoai, French Polynesia
| | | | - Grant Johnson
- Department of Primary Industry and Fisheries, Aquatic Resource Research Unit, Darwin, NT, Australia
| | | | - Damian Jaccoud
- Diversity Arrays Technology Pty Ltd, University of Canberra, Bruce, ACT, Australia
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, University of Canberra, Bruce, ACT, Australia
| | - David L Morgan
- Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Thor Saunders
- Department of Primary Industry and Fisheries, Aquatic Resource Research Unit, Darwin, NT, Australia
| | - Nicholas J Bax
- CSIRO Oceans and Atmosphere, Hobart, TAS, Australia.,Institute for Marine and Antarctic Science, University of Tasmania, Hobart, TAS, Australia
| | - Peter M Kyne
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
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37
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Currat M, Arenas M, Quilodràn CS, Excoffier L, Ray N. SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal. Bioinformatics 2020; 35:4480-4483. [PMID: 31077292 PMCID: PMC6821363 DOI: 10.1093/bioinformatics/btz311] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/18/2019] [Accepted: 04/29/2019] [Indexed: 01/25/2023] Open
Abstract
SUMMARY SPLATCHE3 simulates genetic data under a variety of spatially explicit evolutionary scenarios, extending previous versions of the framework. The new capabilities include long-distance migration, spatially and temporally heterogeneous short-scale migrations, alternative hybridization models, simulation of serial samples of genetic data and a large variety of DNA mutation models. These implementations have been applied independently to various studies, but grouped together in the current version. AVAILABILITY AND IMPLEMENTATION SPLATCHE3 is written in C++ and is freely available for non-commercial use from the website http://www.splatche.com/splatche3. It includes console versions for Linux, MacOs and Windows and a user-friendly GUI for Windows, as well as detailed documentation and ready-to-use examples.
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Affiliation(s)
- Mathias Currat
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva 1205, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva 1211, Switzerland
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, Vigo 36310, Spain.,Biomedical Research Center (CINBIO), University of Vigo, Vigo 36310, Spain
| | - Claudio S Quilodràn
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva 1205, Switzerland
| | - Laurent Excoffier
- Computational and Molecular Population Genetics Laboratory, Institute of Ecology and Evolution, University of Bern, Bern 3012, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Nicolas Ray
- Institute of Global Health, GeoHealth Group, University of Geneva, Geneva 1205, Switzerland.,Institute for Environmental Sciences, University of Geneva, Geneva 1205, Switzerland
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38
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Binelli G, Montaigne W, Sabatier D, Scotti‐Saintagne C, Scotti I. Discrepancies between genetic and ecological divergence patterns suggest a complex biogeographic history in a Neotropical genus. Ecol Evol 2020; 10:4726-4738. [PMID: 32551056 PMCID: PMC7297752 DOI: 10.1002/ece3.6227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/04/2020] [Indexed: 11/19/2022] Open
Abstract
Phylogenetic patterns and the underlying speciation processes can be deduced from morphological, functional, and ecological patterns of species similarity and divergence. In some cases, though, species retain multiple similarities and remain almost indistinguishable; in other cases, evolutionary convergence can make such patterns misleading; very often in such cases, the "true" picture only emerges from carefully built molecular phylogenies, which may come with major surprises. In addition, closely related species may experience gene flow after divergence, thus potentially blurring species delimitation. By means of advanced inferential methods, we studied molecular divergence between species of the Virola genus (Myristicaceae): widespread Virola michelii and recently described, endemic V. kwatae, using widespread V. surinamensis as a more distantly related outgroup with different ecology and morphology-although with overlapping range. Contrary to expectations, we found that the latter, and not V. michelii, was sister to V. kwatae. Therefore, V. kwatae probably diverged from V. surinamensis through a recent morphological and ecological shift, which brought it close to distantly related V. michelii. Through the modeling of the divergence process, we inferred that gene flow between V. surinamensis and V. kwatae stopped soon after their divergence and resumed later, in a classical secondary contact event which did not erase their ecological and morphological differences. While we cannot exclude that initial divergence occurred in allopatry, current species distribution and the absence of geographical barriers make complete isolation during speciation unlikely. We tentatively conclude that (a) it is possible that divergence occurred in allopatry/parapatry and (b) secondary contact did not suppress divergence.
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Affiliation(s)
| | - William Montaigne
- UMR EcoFoGUniversité des Antilles et de la GuyaneKourouFrench Guiana
| | - Daniel Sabatier
- AMAPIRDCIRADCNRSINRAEUniversité de MontpellierMontpellierFrance
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39
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Xue AT, Hickerson MJ. Comparative phylogeographic inference with genome‐wide data from aggregated population pairs. Evolution 2020; 74:808-830. [DOI: 10.1111/evo.13945] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/24/2020] [Accepted: 01/29/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Alexander T. Xue
- Subprogram in Ecology, Evolutionary Biology, and Behavior, Department of BiologyGraduate Center of City University of New York New York NY 10016
- Subprogram in Ecology, Evolutionary Biology, and Behavior, Department of BiologyCity College of City University of New York New York NY 10031
- Human Genetics Institute of New Jersey and Department of GeneticsRutgers University Piscataway NJ 08854
- Simons Center for Quantitative BiologyCold Spring Harbor Laboratory Cold Spring Harbor NY 11724
| | - Michael J. Hickerson
- Subprogram in Ecology, Evolutionary Biology, and Behavior, Department of BiologyGraduate Center of City University of New York New York NY 10016
- Subprogram in Ecology, Evolutionary Biology, and Behavior, Department of BiologyCity College of City University of New York New York NY 10031
- Division of Invertebrate ZoologyAmerican Museum of Natural History New York NY 10024
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40
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Lee-Six H, Kent DG. Tracking hematopoietic stem cells and their progeny using whole-genome sequencing. Exp Hematol 2020; 83:12-24. [PMID: 32007478 PMCID: PMC7118367 DOI: 10.1016/j.exphem.2020.01.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/07/2020] [Accepted: 01/13/2020] [Indexed: 12/20/2022]
Abstract
Despite decades of progress in our understanding of hematopoiesis through the study of animal models and transplantation in humans, investigating physiological human hematopoiesis directly has remained challenging. Questions on the clonal structure of the human hematopoietic stem cell (HSC) pool, such as "how many HSCs are there?" and "do all HSC clones actively produce all blood cell types in equal proportions?" remain open. These questions have inherent value for understanding normal human physiology, but also directly inform our comprehension of the process by which the system is subverted to drive diseases of the blood, in particular blood cancers and bone marrow failure syndromes. The critical link between normal and abnormal hematopoiesis is perhaps best illustrated by the recent discovery of clonal hematopoiesis in healthy people with no abnormal blood parameters. In such individuals, large clones derived from single cells are present and are dominant relative to their normal counterparts, but their presence does not necessitate abnormal blood cell production. Intriguingly, however, these individuals are also at a significantly greater risk of developing leukemias and of cardiovascular events, underscoring the importance of understanding how blood stem cell clones compete against each other.
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Affiliation(s)
- Henry Lee-Six
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - David G Kent
- York Biomedical Research Institute, Department of Biology, University of York, York, United Kingdom; Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Hills Road, Cambridge, United Kingdom; Department of Haematology, University of Cambridge, Cambridge, United Kingdom.
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41
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Popovic I, Matias AMA, Bierne N, Riginos C. Twin introductions by independent invader mussel lineages are both associated with recent admixture with a native congener in Australia. Evol Appl 2020; 13:515-532. [PMID: 32431733 PMCID: PMC7045716 DOI: 10.1111/eva.12857] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 06/27/2019] [Accepted: 07/24/2019] [Indexed: 01/04/2023] Open
Abstract
Introduced species can impose profound impacts on the evolution of receiving communities with which they interact. If native and introduced taxa remain reproductively semi-isolated, human-mediated secondary contact may promote genetic exchange across newly created hybrid zones, potentially impacting native genetic diversity and invasive species spread. Here, we investigate the contributions of recent divergence histories and ongoing (post-introduction) gene flow between the invasive marine mussel, Mytilus galloprovincialis, and a morphologically indistinguishable and taxonomically contentious native Australian taxon, Mytilus planulatus. Using transcriptome-wide markers, we demonstrate that two contemporary M. galloprovincialis introductions into south-eastern Australia originate from genetically divergent lineages from its native range in the Mediterranean Sea and Atlantic Europe, where both introductions have led to repeated instances of admixture between introduced and endemic populations. Through increased genome-wide resolution of species relationships, combined with demographic modelling, we validate that mussels sampled in Tasmania are representative of the endemic Australian taxon (M. planulatus), but share strong genetic affinities to M. galloprovincialis. Demographic inferences indicate late-Pleistocene divergence times and historical gene flow between the Tasmanian endemic lineage and northern M. galloprovincialis, suggesting that native and introduced taxa have experienced a period of historical isolation of at least 100,000 years. Our results demonstrate that many genomic loci and sufficient sampling of closely related lineages in both sympatric (e.g. Australian populations) and allopatric (e.g. northern hemisphere Mytilus taxa) ranges are necessary to accurately (a) interpret patterns of intraspecific differentiation and to (b) distinguish contemporary invasive introgression from signatures left by recent divergence histories in high dispersal marine species. More broadly, our study fills a significant gap in systematic knowledge of native Australian biodiversity and sheds light on the intrinsic challenges for invasive species research when native and introduced species boundaries are not well defined.
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Affiliation(s)
- Iva Popovic
- School of Biological SciencesUniversity of QueenslandSt LuciaQldAustralia
| | | | - Nicolas Bierne
- Institut des Sciences de l’EvolutionUMR 5554CNRS‐IRD‐EPHE‐UMUniversité de MontpellierMontpellierFrance
| | - Cynthia Riginos
- School of Biological SciencesUniversity of QueenslandSt LuciaQldAustralia
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42
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Ruiz-Suarez S, Leos-Barajas V, Alvarez-Castro I, Morales JM. Using approximate Bayesian inference for a "steps and turns" continuous-time random walk observed at regular time intervals. PeerJ 2020; 8:e8452. [PMID: 32095333 PMCID: PMC7020826 DOI: 10.7717/peerj.8452] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 12/23/2019] [Indexed: 11/20/2022] Open
Abstract
The study of animal movement is challenging because movement is a process modulated by many factors acting at different spatial and temporal scales. In order to describe and analyse animal movement, several models have been proposed which differ primarily in the temporal conceptualization, namely continuous and discrete time formulations. Naturally, animal movement occurs in continuous time but we tend to observe it at fixed time intervals. To account for the temporal mismatch between observations and movement decisions, we used a state-space model where movement decisions (steps and turns) are made in continuous time. That is, at any time there is a non-zero probability of making a change in movement direction. The movement process is then observed at regular time intervals. As the likelihood function of this state-space model turned out to be intractable yet simulating data is straightforward, we conduct inference using different variations of Approximate Bayesian Computation (ABC). We explore the applicability of this approach as a function of the discrepancy between the temporal scale of the observations and that of the movement process in a simulation study. Simulation results suggest that the model parameters can be recovered if the observation time scale is moderately close to the average time between changes in movement direction. Good estimates were obtained when the scale of observation was up to five times that of the scale of changes in direction. We demonstrate the application of this model to a trajectory of a sheep that was reconstructed in high resolution using information from magnetometer and GPS devices. The state-space model used here allowed us to connect the scales of the observations and movement decisions in an intuitive and easy to interpret way. Our findings underscore the idea that the time scale at which animal movement decisions are made needs to be considered when designing data collection protocols. In principle, ABC methods allow to make inferences about movement processes defined in continuous time but in terms of easily interpreted steps and turns.
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Affiliation(s)
- Sofia Ruiz-Suarez
- INIBIOMA (CONICET-Universidad Nacional del Comahue), Rio Negro, Argentina
- Facultad de Ciencias Económicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Vianey Leos-Barajas
- Department of Statistics, North Carolina State University, Raleigh, United States of America
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States of America
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43
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Rocha-Méndez A, Sánchez-González LA, González C, Navarro-Sigüenza AG. The geography of evolutionary divergence in the highly endemic avifauna from the Sierra Madre del Sur, Mexico. BMC Evol Biol 2019; 19:237. [PMID: 31888449 PMCID: PMC6937948 DOI: 10.1186/s12862-019-1564-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/15/2019] [Indexed: 11/30/2022] Open
Abstract
Background Mesoamerica is a remarkable region with a high geological and ecological complexity. Within northern Mesoamerica, the biotic province of the Sierra Madre del Sur (SMS) in southwestern Mexico harbors exceptionally high avian endemism and diversity. Herein, we searched for spatially and temporally concordant phylogeographic patterns, in four bird genera from three distinct avian orders co-distributed across Mesoamerica and investigated their causes through hypothesis testing regarding historical processes. Selected species include endemic and differentiated populations across the montane forests of Mesoamerica, and particularly within the SMS. Results We gathered mitochondrial DNA sequences for at least one locus from 177 individuals across all species. We assessed genetic structure, demographic history, and defined a framework for the coalescent simulations used in biogeographic hypothesis testing temporal and spatial co-variance. Our analyses suggested shared phylogeographic breaks in areas corresponding to the SMS populations, and between the main montane systems in Mesoamerica, with the Central Valley of Oaxaca and the Nicaragua Depression being the most frequently shared breaks among analyzed taxa. Nevertheless, dating analyses and divergence patterns observed were consistent with the hypothesis of broad vicariance across Mesoamerica derived from mechanisms operating at distinct times across taxa in the SMS. Conclusions Our study provides a framework for understanding the evolutionary origins and historical factors enhancing speciation in well-defined regions within Mesoamerica, indicating that the evolutionary history of extant biota inhabiting montane forests is complex and often idiosyncratic.
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Affiliation(s)
- Alberto Rocha-Méndez
- Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Apartado Postal 70-399, 04510, Mexico City, Mexico. .,Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico.
| | - Luis A Sánchez-González
- Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Apartado Postal 70-399, 04510, Mexico City, Mexico
| | - Clementina González
- Instituto de Investigaciones sobre los Recursos Naturales, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Adolfo G Navarro-Sigüenza
- Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Apartado Postal 70-399, 04510, Mexico City, Mexico.,Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
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Fenderson LE, Kovach AI, Llamas B. Spatiotemporal landscape genetics: Investigating ecology and evolution through space and time. Mol Ecol 2019; 29:218-246. [DOI: 10.1111/mec.15315] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/22/2019] [Accepted: 11/13/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Lindsey E. Fenderson
- Australian Centre for Ancient DNA School of Biological Sciences Environment Institute University of Adelaide Adelaide South Australia Australia
- Department of Natural Resources and the Environment University of New Hampshire Durham NH USA
| | - Adrienne I. Kovach
- Department of Natural Resources and the Environment University of New Hampshire Durham NH USA
| | - Bastien Llamas
- Australian Centre for Ancient DNA School of Biological Sciences Environment Institute University of Adelaide Adelaide South Australia Australia
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45
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Pan D, Hülber K, Willner W, Schneeweiss GM. An explicit test of Pleistocene survival in peripheral versus nunatak refugia in two high mountain plant species. Mol Ecol 2019; 29:172-183. [PMID: 31765501 PMCID: PMC7003806 DOI: 10.1111/mec.15316] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 11/20/2019] [Accepted: 11/22/2019] [Indexed: 01/15/2023]
Abstract
Pleistocene climate fluctuations had profound influence on the biogeographical history of many biota. As large areas in high mountain ranges were covered by glaciers, biota were forced either to peripheral refugia (and possibly beyond to lowland refugia) or to interior refugia (nunataks). However, nunatak survival remains controversial as it relies solely on correlative genetic evidence. Here, we test hypotheses of glacial survival using two high alpine plant species (the insect‐pollinated Pedicularis asplenifolia and wind‐pollinated Carex fuliginosa) in the European Alps. Employing the iDDC (integrative Distributional, Demographic and Coalescent) approach, which couples species distribution modelling, spatial and temporal demographic simulation and Approximate Bayesian Computation, we explicitly test three hypotheses of glacial survival: (a) peripheral survival only, (b) nunatak survival only and (c) peripheral plus nunatak survival. In P. asplenifolia the peripheral plus nunatak survival hypothesis was supported by Bayes factors (BF> 100), whereas in C. fuliginosa the peripheral survival only hypothesis, although best supported, could not be unambiguously distinguished from the peripheral plus nunatak survival hypothesis (BF = 5.58). These results are consistent with current habitat preferences (P. asplenifolia extends to higher elevations) and the potential for genetic swamping (i.e., replacement of local genotypes via hybridization with immigrating genotypes [expected to be higher in the wind‐pollinated C. fuliginosa]). Although the persistence of plants on nunataks during glacial periods has been debated and studied over decades, this is one of the first studies to explicitly test the hypothesis instead of solely using correlative evidence.
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Affiliation(s)
- Da Pan
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Karl Hülber
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Wolfgang Willner
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Gerald M Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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Han JH, Weston JF, Heuer C, Gates MC. Estimation of the within-herd transmission rates of bovine viral diarrhoea virus in extensively grazed beef cattle herds. Vet Res 2019; 50:103. [PMID: 31783904 PMCID: PMC6884759 DOI: 10.1186/s13567-019-0723-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 11/06/2019] [Indexed: 11/12/2022] Open
Abstract
Many research groups have developed mathematical models to simulate the dynamics of BVDV infections in cattle herds. However, most models use estimates for within-herd BVDV transmission rates that are either based on expert opinion or adapted from other dairy herd simulation models presented in the literature. There is currently little information on the transmission rates for BVDV in extensively grazed beef herds partly due to the logistical challenges in obtaining longitudinal data of individual animal’s seroconversion, and it may not be appropriate to apply the same transmission rates from intensive dairy herds given the significant differences in herd demographics and management. To address this knowledge gap, we measured BVDV antibody levels in 15 replacement heifers in each of 75 New Zealand beef breeding farms after their first calving and again at pregnancy scanning or weaning to check for seroconversion. Among these, data from 9 farms were used to infer the within-herd BVDV transmission rate with an approximate Bayesian computation method. The most probable within-herd BVDV transmission rate was estimated as 0.11 per persistently infected (PI) animal per day with a 95% highest posterior density interval between 0.03 and 0.34. This suggests that BVDV transmission in extensively grazed beef herds is generally slower than in dairy herds where the transmission rate has been estimated at 0.50 per PI animal per day and therefore may not be sufficient to ensure that all susceptible breeding females gain adequate immunity to the virus before the risk period of early pregnancy for generating new PI calves.
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Affiliation(s)
- Jun-Hee Han
- EpiCentre, School of Veterinary Science, Massey University, Private Bag 11-222, Palmerston North, New Zealand.
| | - Jenny F Weston
- School of Veterinary Science, Massey University, Private Bag 11-222, Palmerston North, New Zealand
| | - Cord Heuer
- EpiCentre, School of Veterinary Science, Massey University, Private Bag 11-222, Palmerston North, New Zealand
| | - M Carolyn Gates
- EpiCentre, School of Veterinary Science, Massey University, Private Bag 11-222, Palmerston North, New Zealand
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Hirano T, Saito T, Tsunamoto Y, Koseki J, Prozorova L, Do VT, Matsuoka K, Nakai K, Suyama Y, Chiba S. Role of ancient lakes in genetic and phenotypic diversification of freshwater snails. Mol Ecol 2019; 28:5032-5051. [DOI: 10.1111/mec.15272] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 09/14/2019] [Accepted: 09/16/2019] [Indexed: 01/17/2023]
Affiliation(s)
- Takahiro Hirano
- Department of Biological Sciences University of Idaho Moscow ID USA
| | - Takumi Saito
- Department of Biology Faculty of Science Toho University Funabashi Japan
| | - Yoshihiro Tsunamoto
- Tohoku Research Center Forestry and Forest Products Research Institute Morioka Japan
| | - Joichiro Koseki
- Graduate School of Life Sciences Tohoku University Sendai Japan
| | - Larisa Prozorova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity Far Eastern Branch Russian Academy of Sciences Vladivostok Russia
| | - Van Tu Do
- Institute of Ecology and Biological Resources Vietnam Academy of Science and Technology Hanoi Vietnam
- Graduate University of Science and Technology Vietnam Academy of Science and Technology Hanoi Vietnam
| | | | | | - Yoshihisa Suyama
- Kawatabi Field Science Center Graduate School of Agricultural Science Tohoku University Osaki Japan
| | - Satoshi Chiba
- Graduate School of Life Sciences Tohoku University Sendai Japan
- Center for Northeast Asian Studies Tohoku University Sendai Japan
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Prentice MB, Bowman J, Murray DL, Klütsch CFC, Khidas K, Wilson PJ. Evaluating evolutionary history and adaptive differentiation to identify conservation units of Canada lynx (Lynx canadensis). Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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Castellanos-Morales G, Ruiz-Mondragón KY, Hernández-Rosales HS, Sánchez-de la Vega G, Gámez N, Aguirre-Planter E, Montes-Hernández S, Lira-Saade R, Eguiarte LE. Tracing back the origin of pumpkins (Cucurbita pepo ssp. pepo L.) in Mexico. Proc Biol Sci 2019; 286:20191440. [PMID: 31409251 PMCID: PMC6710597 DOI: 10.1098/rspb.2019.1440] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 07/23/2019] [Indexed: 11/12/2022] Open
Abstract
Cucurbita pepo is an economically important crop, which consists of cultivated C. pepo ssp. pepo, and two wild taxa (C. pepo ssp. fraterna and C. pepo ssp. ovifera). We aimed at understanding the domestication and the diversity of C. pepo in Mexico. We used two chloroplast regions and nine nuclear microsatellite loci to assess the levels of genetic variation and structure for C. pepo ssp. pepo's landraces sampled in 13 locations in Mexico, five improved varieties, one C. pepo ssp. fraterna population and ornamental C. pepo ssp. ovifera. We tested four hypotheses regarding the origin of C. pepo ssp. pepo's ancestor through approximate Bayesian computation: C. pepo ssp. ovifera as the ancestor; C. pepo ssp. fraterna as the ancestor; an unknown extinct lineage as the ancestor; and C. pepo ssp. pepo as hybrid from C. pepo ssp. ovifera and C. pepo ssp. fraterna ancestors. Cucurbita pepo ssp. pepo showed high genetic variation and low genetic differentiation. Cucurbita pepo ssp. fraterna and C. pepo ssp. pepo shared two chloroplast haplotypes. The three subspecies were well differentiated for microsatellite loci. Cucurbita pepo ssp. fraterna was probably C. pepo ssp. pepo's wild ancestor, but subsequent hybridization between taxa complicate defining C. pepo ssp. pepo's ancestor.
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Affiliation(s)
- Gabriela Castellanos-Morales
- Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur, Unidad Villahermosa, Villahermosa, Tabasco, Mexico
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
- UBIPRO, Facultad de Estudios Superiores, Iztacala, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
| | - Karen Y. Ruiz-Mondragón
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
| | - Helena S. Hernández-Rosales
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
| | - Guillermo Sánchez-de la Vega
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
| | - Niza Gámez
- Facultad de Estudios Superiores, Zaragoza, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
| | - Erika Aguirre-Planter
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
| | - Salvador Montes-Hernández
- Campo Experimental Bajío, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarías (INIFAP), Celaya, Guanajuato, Mexico
| | - Rafael Lira-Saade
- UBIPRO, Facultad de Estudios Superiores, Iztacala, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
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Illera JC, Arenas M, López-Sánchez CA, Obeso JR, Laiolo P. Gradual Distance Dispersal Shapes the Genetic Structure in an Alpine Grasshopper. Genes (Basel) 2019; 10:genes10080590. [PMID: 31387238 PMCID: PMC6724060 DOI: 10.3390/genes10080590] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 08/01/2019] [Accepted: 08/02/2019] [Indexed: 11/16/2022] Open
Abstract
The location of the high mountains of southern Europe has been crucial in the phylogeography of most European species, but how extrinsic (topography of sky islands) and intrinsic features (dispersal dynamics) have interacted to shape the genetic structure in alpine restricted species is still poorly known. Here we investigated the mechanisms explaining the colonisation of Cantabrian sky islands in an endemic flightless grasshopper. We scrutinised the maternal genetic variability and haplotype structure, and we evaluated the fitting of two migration models to understand the extant genetic structure in these populations: Long-distance dispersal (LDD) and gradual distance dispersal (GDD). We found that GDD fits the real data better than the LDD model, with an onset of the expansion matching postglacial expansions after the retreat of the ice sheets. Our findings suggest a scenario with small carrying capacity, migration rates, and population growth rates, being compatible with a slow dispersal process. The gradual expansion process along the Cantabrian sky islands found here seems to be conditioned by the suitability of habitats and the presence of alpine corridors. Our findings shed light on our understanding about how organisms which have adapted to live in alpine habitats with limited dispersal abilities have faced new and suitable environmental conditions.
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Affiliation(s)
- Juan Carlos Illera
- Research Unit of Biodiversity (UMIB, UO-CSIC-PA), Oviedo University, 33600 Mieres, Spain.
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
| | - Carlos A López-Sánchez
- Department of Biology, Organisms and Systems, GIS-Forest Group, Oviedo University, 33600 Mieres, Spain
| | - José Ramón Obeso
- Research Unit of Biodiversity (UMIB, UO-CSIC-PA), Oviedo University, 33600 Mieres, Spain
| | - Paola Laiolo
- Research Unit of Biodiversity (UMIB, UO-CSIC-PA), Oviedo University, 33600 Mieres, Spain
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