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Mansoor S, Hamid S, Tuan TT, Park JE, Chung YS. Advance computational tools for multiomics data learning. Biotechnol Adv 2024:108447. [PMID: 39251098 DOI: 10.1016/j.biotechadv.2024.108447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 09/01/2024] [Accepted: 09/05/2024] [Indexed: 09/11/2024]
Abstract
The burgeoning field of bioinformatics has seen a surge in computational tools tailored for omics data analysis driven by the heterogeneous and high-dimensional nature of omics data. In biomedical and plant science research multi-omics data has become pivotal for predictive analytics in the era of big data necessitating sophisticated computational methodologies. This review explores a diverse array of computational approaches which play crucial roles in processing, normalizing, integrating, and analyzing omics data. Notable methods such similarity-based methods, network-based approaches, correlation-based methods, Bayesian methods, fusion-based methods and multivariate techniques among others are discussed in detail, each offering unique functionalities to address the complexities of multi-omics data. Furthermore, this review underscores the significance of computational tools in advancing our understanding of data and their transformative impact on research.
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Affiliation(s)
- Sheikh Mansoor
- Department of Plant Resources and Environment, Jeju National University, 63243, Republic of Korea
| | - Saira Hamid
- Watson Crick Centre for Molecular Medicine, Islamic University of Science and Technology, Awantipora, Pulwama, J&K, India
| | - Thai Thanh Tuan
- Watson Crick Centre for Molecular Medicine, Islamic University of Science and Technology, Awantipora, Pulwama, J&K, India
| | - Jong Eun Park
- Department of Animal Biotechnology, College of Applied Life Science, Jeju National University, Jeju, Jeju-do, Republic of Korea.
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, 63243, Republic of Korea.
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Zhang HT, Yang TT, Wang WT. A novel hybrid model for species distribution prediction using neural networks and Grey Wolf Optimizer algorithm. Sci Rep 2024; 14:11505. [PMID: 38769379 PMCID: PMC11106298 DOI: 10.1038/s41598-024-62285-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/15/2024] [Indexed: 05/22/2024] Open
Abstract
Neural networks are frequently employed to model species distribution through backpropagation methods, known as backpropagation neural networks (BPNN). However, the complex structure of BPNN introduces parameter settings challenges, such as the determination of connection weights, which can affect the accuracy of model simulation. In this paper, we integrated the Grey Wolf Optimizer (GWO) algorithm, renowned for its excellent global search capacity and rapid convergence, to enhance the performance of BPNN. Then we obtained a novel hybrid algorithm, the Grey Wolf Optimizer algorithm optimized backpropagation neural networks algorithm (GNNA), designed for predicting species' potential distribution. We also compared the GNNA with four prevalent species distribution models (SDMs), namely the generalized boosting model (GBM), generalized linear model (GLM), maximum entropy (MaxEnt), and random forest (RF). These models were evaluated using three evaluation metrics: the area under the receiver operating characteristic curve, Cohen's kappa, and the true skill statistic, across 23 varied species. Additionally, we examined the predictive accuracy concerning spatial distribution. The results showed that the predictive performance of GNNA was significantly improved compared to BPNN, was significantly better than that of GLM and GBM, and was even comparable to that of MaxEnt and RF in predicting species distributions with small sample sizes. Furthermore, the GNNA demonstrates exceptional powers in forecasting the potential non-native distribution of invasive plant species.
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Affiliation(s)
- Hao-Tian Zhang
- School of Mathematics and Computer Science, Northwest Minzu University, Lanzhou, 730030, People's Republic of China
| | - Ting-Ting Yang
- School of Mathematics and Computer Science, Northwest Minzu University, Lanzhou, 730030, People's Republic of China
| | - Wen-Ting Wang
- School of Mathematics and Computer Science, Northwest Minzu University, Lanzhou, 730030, People's Republic of China.
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Polgar G, Iaia M, Righi T, Volta P. The Italian Alpine and Subalpine trouts: Taxonomy, Evolution, and Conservation. BIOLOGY 2022; 11:biology11040576. [PMID: 35453775 PMCID: PMC9026872 DOI: 10.3390/biology11040576] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary In a great part of the world, trout fishing has long inspired human spiritual ideals of immersion into nature and recreation, far removed from the fast-encroaching urbanization. Concurrently, these values and emotions fueled a white-hot business, establishing a florid market of outdoor recreation. Since the 20th century, the trout-culture industry strived to provide anglers with fishing entertainment by stocking massive amounts of non-native trouts in dozens of countries, irrespective of the lakes’ and rivers’ carrying capacity. This had dire consequences on the structural and functional diversity of these ecosystems. “Trout wars” sparked throughout the world between the promoters of stocking activities and the promoters of “wild trout management” and ethics. The “Italian trout war” has been fought on the harsh battleground of trout taxonomy, ecology, distribution, and native vs. non-native interfertile species. Northern Italy, home to the Italian Alpine and subalpine trouts and economic center of the national trout-culture and stocking industry, was particularly affected by this clash. We review here the state of art of this ongoing debate, outlining our scientific view of the taxonomy, evolution, distribution, and sustainable management of the native Italian trouts of northern Italy. Abstract During the last 150 years, the trout-culture industry focused on enhancing trout populations by stocking, in response to the growing anglers’ demand and the habitat degradation associated to the rapid urbanization and hydropower development. The industrialized north of Italy, home to the Italian Alpine and subalpine trout populations, is the source of most of the revenues of the national trout-culture industry. Its rapid growth, and the massive introduction of non-native interfertile trouts eroded the genetic diversity of native lineages, leading to harsh confrontations between scientists, institutions, and sportfishing associations. We review here the state of the art of the taxonomy and distribution of the northern Italian native trouts, presenting both scientific results and historical documentation. We think the only native trouts in this region are Salmo marmoratus, widespread in this region, plus small and fragmented populations of S. ghigii, present only in the South-western Alps. We strongly recommend the interruption of stocking of domesticated interfertile non-native trouts in this area, and recommend the adoption of Evolutionary Significant Units for salmonid fishery management. We further propose future research directions for a sustainable approach to the conservation and ecosystem management of the fishery resources and inland waters of northern Italy.
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Species distribution models for conservation: Identifying translocation sites for eastern quolls under climate change. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Escalante MA, Horníková M, Marková S, Kotlík P. Niche differentiation in a postglacial colonizer, the bank vole Clethrionomys glareolus. Ecol Evol 2021; 11:8054-8070. [PMID: 34188871 PMCID: PMC8216960 DOI: 10.1002/ece3.7637] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/30/2021] [Accepted: 04/13/2021] [Indexed: 01/25/2023] Open
Abstract
Species-level environmental niche modeling has been crucial in efforts to understand how species respond to climate variation and change. However, species often exhibit local adaptation and intraspecific niche differences that may be important to consider in predicting responses to climate. Here, we explore whether phylogeographic lineages of the bank vole originating from different glacial refugia (Carpathian, Western, Eastern, and Southern) show niche differentiation, which would suggest a role for local adaptation in biogeography of this widespread Eurasian small mammal. We first model the environmental requirements for the bank vole using species-wide occurrences (210 filtered records) and then model each lineage separately to examine niche overlap and test for niche differentiation in geographic and environmental space. We then use the models to estimate past [Last Glacial Maximum (LGM) and mid-Holocene] habitat suitability to compare with previously hypothesized glacial refugia for this species. Environmental niches are statistically significantly different from each other for all pairs of lineages in geographic and environmental space, and these differences cannot be explained by habitat availability within their respective ranges. Together with the inability of most of the lineages to correctly predict the distributions of other lineages, these results support intraspecific ecological differentiation in the bank vole. Model projections of habitat suitability during the LGM support glacial survival of the bank vole in the Mediterranean region and in central and western Europe. Niche differences between lineages and the resulting spatial segregation of habitat suitability suggest ecological differentiation has played a role in determining the present phylogeographic patterns in the bank vole. Our study illustrates that models pooling lineages within a species may obscure the potential for different responses to climate change among populations.
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Affiliation(s)
- Marco A. Escalante
- Laboratory of Molecular EcologyInstitute of Animal Physiology and Genetics of the Czech Academy of SciencesLiběchovCzech Republic
| | - Michaela Horníková
- Laboratory of Molecular EcologyInstitute of Animal Physiology and Genetics of the Czech Academy of SciencesLiběchovCzech Republic
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Silvia Marková
- Laboratory of Molecular EcologyInstitute of Animal Physiology and Genetics of the Czech Academy of SciencesLiběchovCzech Republic
| | - Petr Kotlík
- Laboratory of Molecular EcologyInstitute of Animal Physiology and Genetics of the Czech Academy of SciencesLiběchovCzech Republic
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Liu SYV, Tuanmu MN, Rachmawati R, Mahardika GN, Barber PH. Integrating phylogeographic and ecological niche approaches to delimitating cryptic lineages in the blue-green damselfish ( Chromis viridis). PeerJ 2019; 7:e7384. [PMID: 31392097 PMCID: PMC6677123 DOI: 10.7717/peerj.7384] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 06/30/2019] [Indexed: 12/22/2022] Open
Abstract
Species delimitation is challenging in sibling species/cryptic lineages because of the absence of clear diagnostic traits. However, integration of different approaches such as phylogeography and ecological niche comparison offers one potential approach to tease apart recently diverged lineages. In this study, we estimate the ecological niche divergence among lineages in Chromis viridis in a broad-scale phylogeographic framework to test whether the combination of these two approaches can effectively distinguish recently diverged lineages. Results from Cytb and Rag2 analyses identified two cryptic lineages (C. viridis A and C. viridis B) that diverged ∼3 Myr ago. Estimates of ecological niche divergence with 11 environmental parameters across the broad geographic range of these lineages showed overlapping ecological niches and niche conservatism. However, regardless of the incongruence between genetic and ecological niche divergence, the substantial genetic divergence between the two clades of C. viridis in both mtDNA and nuclear loci strong suggest that they are cryptic taxa.
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Affiliation(s)
- Shang Yin Vanson Liu
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Mao-Ning Tuanmu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Rita Rachmawati
- Center for Fisheries Research, Ministry of Marine Affairs and Fisheries, Jakarta, Indonesia.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | | | - Paul H Barber
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
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Khanal L, Chalise MK, Wan T, Jiang X. Riverine barrier effects on population genetic structure of the Hanuman langur (Semnopithecus entellus) in the Nepal Himalaya. BMC Evol Biol 2018; 18:159. [PMID: 30382913 PMCID: PMC6211570 DOI: 10.1186/s12862-018-1280-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 10/24/2018] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Past climatological events and contemporary geophysical barriers shape the distribution, population genetic structure, and evolutionary history of many organisms. The Himalayan region, frequently referred to as the third pole of the Earth, has experienced large-scale climatic oscillations in the past and bears unique geographic, topographic, and climatic areas. The influences of the Pleistocene climatic fluctuations and present-day geographical barriers such as rivers in shaping the demographic history and population genetic structure of organisms in the Nepal Himalaya have not yet been documented. Hence, we examined the effects of late-Quaternary glacial-interglacial cycles and riverine barriers on the genetic composition of Hanuman langurs (Semnopithecus entellus), a colobine primate with a wide range of altitudinal distribution across the Nepalese Himalaya, using the mitochondrial DNA control region (CR, 1090 bp) and cytochrome B (CYTB, 1140 bp) sequences combined with paleodistribution modeling. RESULTS DNA sequences were successfully retrieved from 67 non-invasively collected fecal samples belonging to 18 wild Hanuman langur troops covering the entire distribution range of the species in Nepal. We identified 37 haplotypes from the concatenated CR + CYTB (2230 bp) sequences, with haplotype and nucleotide diversities of 0.958 ± 0.015 and 0.0237 ± 0.0008, respectively. The troops were clustered into six major clades corresponding to their river-isolated spatial distribution, with the significantly high genetic variation among these clades confirming the barrier effects of the snow-fed Himalayan rivers on genetic structuring. Analysis of demographic history projected a decrease in population size with the onset of the last glacial maximum (LGM); and, in accordance with the molecular analyses, paleodistribution modeling revealed a range shift in its suitable habitat downward/southward during the LGM. The complex genetic structure among the populations of central Nepal, and the stable optimal habitat through the last interglacial period to the present suggest that the central mid-hills of Nepal served as glacial refugia for the Hanuman langur. CONCLUSIONS Hanuman langurs of the Nepal Himalaya region exhibit high genetic diversity, with their population genetic structure is strongly shaped by riverine barrier effects beyond isolation by distance; hence, this species demands detailed future phylogenetic study.
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Affiliation(s)
- Laxman Khanal
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650223 China
- Central Department of Zoology, Institute of Science and Technology, Tribhuvan University, Kathmandu, 44613 Nepal
| | - Mukesh Kumar Chalise
- Central Department of Zoology, Institute of Science and Technology, Tribhuvan University, Kathmandu, 44613 Nepal
| | - Tao Wan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan China
| | - Xuelong Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan China
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Laboratory of Ecology and Evolutionary Biology, Yunnan University, Kunming, China
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Lalis A, Mona S, Stoetzel E, Bonhomme F, Souttou K, Ouarour A, Aulagnier S, Denys C, Nicolas V. Out of Africa: demographic and colonization history of the Algerian mouse (Mus spretus Lataste). Heredity (Edinb) 2018; 122:150-171. [PMID: 29795180 DOI: 10.1038/s41437-018-0089-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 02/28/2018] [Accepted: 04/16/2018] [Indexed: 11/09/2022] Open
Abstract
North Africa is now recognized as a major area for the emergence and dispersal of anatomically modern humans from at least 315 kya. The Mediterranean Basin is thus particularly suited to study the role of climate versus human-mediated changes on the evolutionary history of species. The Algerian mouse (Mus spretus Lataste) is an endemic species from this basin, with its distribution restricted to North Africa (from Libya to Morocco), Iberian Peninsula and South of France. A rich paleontological record of M. spretus exists in North Africa, suggesting hypotheses concerning colonization pathways, and the demographic and morphologic history of this species. Here we combined genetic (3 mitochondrial DNA loci and 18 microsatellites) and climatic niche modeling data to infer the evolutionary history of the Algerian mouse. We collected 646 new individuals in 51 localities. Our results are consistent with an anthropogenic translocation of the Algerian mouse from North Africa to the Iberian Peninsula via Neolithic navigators, probably from the Tingitane Peninsula. Once arrived in Spain, suitable climatic conditions would then have favored the dispersion of the Algerian mice to France. The morphological differentiation observed between Spanish, French and North African populations could be explained by a founder effect and possibly local adaptation. This article helps to better understand the role of climate versus human-mediated changes on the evolutionary history of mammal species in the Mediterranean Basin.
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Affiliation(s)
- Aude Lalis
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Paris, France
| | - Stefano Mona
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Paris, France.,EPHE, PSL Research University, Paris, France
| | - Emmanuelle Stoetzel
- Histoire Naturelle de l'Homme Préhistorique, HNHP-UMR 7194-CNRS, MNHN, UPVD, Sorbonne Universités, Paris, France
| | - François Bonhomme
- Institut des Sciences de l'Evolution, ISEM-UMR 4554, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - Karim Souttou
- Department of Agronomy, Faculty of Natural Science and Life, University Ziane Achour, Djelfa, Algeria
| | - Ali Ouarour
- Laboratoire de Biologie et Santé, Faculté des Sciences, Université Abdelmalek Essâadi, Tétouan, Morocco
| | - Stéphane Aulagnier
- Institut National de la Recherche Agronomique, UR35 Comportement et Ecologie de la Faune Sauvage, Caytanet-Tolosan, France
| | - Christiane Denys
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Paris, France
| | - Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Paris, France.
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Khanal L, Chalise MK, He K, Acharya BK, Kawamoto Y, Jiang X. Mitochondrial DNA analyses and ecological niche modeling reveal post-LGM expansion of the Assam macaque (Macaca assamensis) in the foothills of Nepal Himalaya. Am J Primatol 2018. [PMID: 29536562 DOI: 10.1002/ajp.22748] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Genetic diversity of a species is influenced by multiple factors, including the Quaternary glacial-interglacial cycles and geophysical barriers. Such factors are not yet well documented for fauna from the southern border of the Himalayan region. This study used mitochondrial DNA (mtDNA) sequences and ecological niche modeling (ENM) to explore how the late Pleistocene climatic fluctuations and complex geography of the Himalayan region have shaped genetic diversity, population genetic structure, and demographic history of the Nepalese population of Assam macaques (Macaca assamensis) in the Himalayan foothills. A total of 277 fecal samples were collected from 39 wild troops over almost the entire distribution of the species in Nepal. The mtDNA fragment encompassing the complete control region (1121 bp) was recovered from 208 samples, thus defining 54 haplotypes. Results showed low nucleotide diversity (0.0075 ± SD 0.0001) but high haplotype diversity (0.965 ± SD 0.004). The mtDNA sequences revealed a shallow population genetic structure with a moderate but statistically significant effect of isolation by distance. Demographic history analyses using mtDNA sequences suggested a post-pleistocene population expansion. Paleodistribution reconstruction projected that the potential habitat of the Assam macaque was confined to the lower elevations of central Nepal during the Last Glacial Maximum. With the onset of the Holocene climatic optimum, the glacial refugia population experienced eastward range expansion to higher elevations. We conclude that the low genetic diversity and shallow population genetic structure of the Assam macaque population in the Nepal Himalaya region are the consequence of recent demographic and spatial expansion.
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Affiliation(s)
- Laxman Khanal
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, P.R. China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, P.R. China.,Central Department of Zoology, Tribhuvan University, Kathmandu, Nepal
| | - Mukesh K Chalise
- Central Department of Zoology, Tribhuvan University, Kathmandu, Nepal
| | - Kai He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, P.R. China
| | - Bipin K Acharya
- Institute of Remote Sensing and Digital Earth, Chinese Academy of Sciences, Beijing, P.R. China
| | - Yoshi Kawamoto
- Department of Evolution and Phylogeny, Primate Research Institute, Kyoto University, Kyoto, Japan
| | - Xuelong Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, P.R. China.,State Key Laboratory for Conservation and Utilization of Bio-Resources, Laboratory of Ecology and Evolutionary Biology, Yunnan University, Kunming, P.R. China
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Unraveling climate influences on the distribution of the parapatric newts Lissotriton vulgaris meridionalis and L. italicus. Front Zool 2017; 14:55. [PMID: 29255477 PMCID: PMC5727953 DOI: 10.1186/s12983-017-0239-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 10/27/2017] [Indexed: 11/18/2022] Open
Abstract
Background Climate is often considered as a key ecological factor limiting the capability of expansion of most species and the extent of suitable habitats. In this contribution, we implement Species Distribution Models (SDMs) to study two parapatric amphibians, Lissotriton vulgaris meridionalis and L. italicus, investigating if and how climate has influenced their present and past (Last Glacial Maximum and Holocene) distributions. A database of 901 GPS presence records was generated for the two newts. SDMs were built through Boosted Regression Trees and Maxent, using the Worldclim bioclimatic variables as predictors. Results Precipitation-linked variables and the temperature annual range strongly influence the current occurrence patterns of the two Lissotriton species analyzed. The two newts show opposite responses to the most contributing variables, such as BIO7 (temperature annual range), BIO12 (annual precipitation), BIO17 (precipitation of the driest quarter) and BIO19 (precipitation of the coldest quarter). The hypothesis of climate influencing the distributions of these species is also supported by the fact that the co-occurrences within the sympatric area fall in localities characterized by intermediate values of these predictors. Projections to the Last Glacial Maximum and Holocene scenarios provided a coherent representation of climate influences on the past distributions of the target species. Computation of pairwise variables interactions and the discriminant analysis allowed a deeper interpretation of SDMs’ outputs. Further, we propose a multivariate environmental dissimilarity index (MEDI), derived through a transformation of the multivariate environmental similarity surface (MESS), to deal with extrapolation-linked uncertainties in model projections to past climate. Finally, the niche equivalency and niche similarity tests confirmed the link between SDMs outputs and actual differences in the ecological niches of the two species. Conclusions The different responses of the two species to climatic factors have significantly contributed to shape their current distribution, through contractions, expansions and shifts over time, allowing to maintain two wide allopatric areas with an area of sympatry in Central Italy. Moreover, our SDMs hindcasting shows many concordances with previous phylogeographic studies carried out on the same species, thus corroborating the scenarios of potential distribution during the Last Glacial Maximum and the Holocene emerging from the models obtained. Electronic supplementary material The online version of this article (10.1186/s12983-017-0239-4) contains supplementary material, which is available to authorized users.
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Nicolas V, Mataame A, Crochet PA, Geniez P, Fahd S, Ohler A. Phylogeography and ecological niche modeling unravel the evolutionary history of the African green toad,Bufotes boulengeri boulengeri(Amphibia: Bufonidae), through the Quaternary. J ZOOL SYST EVOL RES 2017. [DOI: 10.1111/jzs.12185] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE; Muséum National d'Histoire Naturelle; Sorbonne Universités; Paris France
| | | | - Pierre-André Crochet
- CEFE UMR 5175, CNRS; EPHE; Université de Montpellier; Université Paul-Valéry Montpellier EPHE; Montpellier France
| | - Philippe Geniez
- PSL Research University; CEFE UMR 5175; CNRS, Université de Montpellier, Université Paul-Valéry Montpellier; EPHE; Biogéographie et Ecologie des Vertébrés; Montpellier France
| | - Soumia Fahd
- Laboratoire “Ecologie, Biodiversité et Environnement”; Département de Biologie; Faculté des Sciences de Tétouan; Université Abdelmalek Essaâdi; Tétouan Morocco
| | - Annemarie Ohler
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE; Muséum National d'Histoire Naturelle; Sorbonne Universités; Paris France
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Tóth JP, Varga Z, Verovnik R, Wahlberg N, Váradi A, Bereczki J. Mito-nuclear discordance helps to reveal the phylogeographic patterns of Melitaea ornata (Lepidoptera: Nymphalidae). Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw037] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Ren G, Mateo RG, Liu J, Suchan T, Alvarez N, Guisan A, Conti E, Salamin N. Genetic consequences of Quaternary climatic oscillations in the Himalayas: Primula tibetica as a case study based on restriction site-associated DNA sequencing. THE NEW PHYTOLOGIST 2017; 213:1500-1512. [PMID: 27696413 DOI: 10.1111/nph.14221] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/23/2016] [Indexed: 05/28/2023]
Abstract
The effects of Quaternary climatic oscillations on the demography of organisms vary across regions and continents. In taxa distributed in Europe and North America, several paradigms regarding the distribution of refugia have been identified. By contrast, less is known about the processes that shaped the species' spatial genetic structure in areas such as the Himalayas, which is considered a biodiversity hotspot. Here, we investigated the phylogeographic structure and population dynamics of Primula tibetica by combining genomic phylogeography and species distribution models (SDMs). Genomic data were obtained for 293 samples of P. tibetica using restriction site-associated DNA sequencing (RADseq). Ensemble SDMs were carried out to predict potential present and past distribution ranges. Four distinct lineages were identified. Approximate Bayesian computation analyses showed that each of them have experienced both expansions and bottlenecks since their divergence, which occurred during or across the Quaternary glacial cycles. The two lineages at both edges of the distribution were found to be more vulnerable and responded in different ways to past climatic changes. These results illustrate how past climatic changes affected the demographic history of Himalayan organisms. Our findings highlight the significance of combining genomic approaches with environmental data when evaluating the effects of past climatic changes.
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Affiliation(s)
- Guangpeng Ren
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, 1015, Lausanne, Switzerland
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Rubén G Mateo
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland
- Institute of Earth Surface Dynamics, Geopolis, University of Lausanne, 1015, Lausanne, Switzerland
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Tomasz Suchan
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland
| | - Nadir Alvarez
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland
| | - Antoine Guisan
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland
- Institute of Earth Surface Dynamics, Geopolis, University of Lausanne, 1015, Lausanne, Switzerland
| | - Elena Conti
- Department of Systematic and Evolutionary Botany and Botanic Garden, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, 1015, Lausanne, Switzerland
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14
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Casazza G, Grassi F, Zecca G, Minuto L. Phylogeographic Insights into a Peripheral Refugium: The Importance of Cumulative Effect of Glaciation on the Genetic Structure of Two Endemic Plants. PLoS One 2016; 11:e0166983. [PMID: 27870888 PMCID: PMC5117763 DOI: 10.1371/journal.pone.0166983] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/07/2016] [Indexed: 11/18/2022] Open
Abstract
Quaternary glaciations and mostly last glacial maximum have shaped the contemporary distribution of many species in the Alps. However, in the Maritime and Ligurian Alps a more complex picture is suggested by the presence of many Tertiary paleoendemisms and by the divergence time between lineages in one endemic species predating the Late Pleistocene glaciation. The low number of endemic species studied limits the understanding of the processes that took place within this region. We used species distribution models and phylogeographical methods to infer glacial refugia and to reconstruct the phylogeographical pattern of Silene cordifolia All. and Viola argenteria Moraldo & Forneris. The predicted suitable area for last glacial maximum roughly fitted current known distribution. Our results suggest that separation of the major clades predates the last glacial maximum and the following repeated glacial and interglacial periods probably drove differentiations. The complex phylogeographical pattern observed in the study species suggests that both populations and genotypes extinction was minimal during the last glacial maximum, probably due to the low impact of glaciations and to topographic complexity in this area. This study underlines the importance of cumulative effect of previous glacial cycles in shaping the genetic structure of plant species in Maritime and Ligurian Alps, as expected for a Mediterranean mountain region more than for an Alpine region.
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Affiliation(s)
- Gabriele Casazza
- DISTAV, Università degli studi di Genova, Genova, Italy
- * E-mail:
| | - Fabrizio Grassi
- Dipartimento di Biologia, Università degli studi di Bari, Bari, Italy
| | - Giovanni Zecca
- Dipartimento di Bioscienze, Università degli studi di Milano, Milano, Italy
| | - Luigi Minuto
- DISTAV, Università degli studi di Genova, Genova, Italy
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15
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Dianat M, Darvish J, Cornette R, Aliabadian M, Nicolas V. Evolutionary history of the Persian Jird,Meriones persicus,based on genetics, species distribution modelling and morphometric data. J ZOOL SYST EVOL RES 2016. [DOI: 10.1111/jzs.12145] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Malahat Dianat
- Department of Biology; Faculty of Sciences; Ferdowsi University of Mashhad; Mashhad Iran
| | - Jamshid Darvish
- Department of Biology; Faculty of Sciences; Ferdowsi University of Mashhad; Mashhad Iran
- Rodentology Research Department; Institute of Applied Zoology; Ferdowsi University of Mashhad; Mashhad Iran
- Zoological Innovations Research Department; Institute of Applied Zoology; Ferdowsi University of Mashhad; Mashhad Iran
| | - Raphael Cornette
- Institut de Systématique, Évolution, Biodiversité ISYEB - UMR 7205 - CNRS; MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle; Sorbonne Universités, Paris France
| | - Mansour Aliabadian
- Department of Biology; Faculty of Sciences; Ferdowsi University of Mashhad; Mashhad Iran
- Zoological Innovations Research Department; Institute of Applied Zoology; Ferdowsi University of Mashhad; Mashhad Iran
| | - Violaine Nicolas
- Institut de Systématique, Évolution, Biodiversité ISYEB - UMR 7205 - CNRS; MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle; Sorbonne Universités, Paris France
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16
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Sebasky ME, Keller SR, Taylor DR. Investigating past range dynamics for a weed of cultivation, Silene vulgaris. Ecol Evol 2016; 6:4800-11. [PMID: 27547314 PMCID: PMC4979708 DOI: 10.1002/ece3.2250] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 05/10/2016] [Accepted: 05/16/2016] [Indexed: 11/05/2022] Open
Abstract
Since the last glacial maximum (LGM), many plant and animal taxa have expanded their ranges by migration from glacial refugia. Weeds of cultivation may have followed this trend or spread globally following the expansion of agriculture or ruderal habitats associated with human‐mediated disturbance. We tested whether the range expansion of the weed Silene vulgaris across Europe fit the classical model of postglacial expansion from southern refugia, or followed known routes of the expansion of human agricultural practices. We used species distribution modeling to predict spatial patterns of postglacial expansion and contrasted these with the patterns of human agricultural expansion. A population genetic analysis using microsatellite loci was then used to test which scenario was better supported by spatial patterns of genetic diversity and structure. Genetic diversity was highest in southern Europe and declined with increasing latitude. Locations of ancestral demes from genetic cluster analysis were consistent with areas of predicted refugia. Species distribution models showed the most suitable habitat in the LGM on the southern coasts of Europe. These results support the typical postglacial northward colonization from southern refugia while refuting the east‐to‐west agricultural spread as the main mode of expansion for S. vulgaris. We know that S. vulgaris has recently colonized many regions (including North America and other continents) through human‐mediated dispersal, but there is no evidence for a direct link between the Neolithic expansion of agriculture and current patterns of genetic diversity of S. vulgaris in Europe. Therefore, the history of range expansion of S. vulgaris likely began with postglacial expansion after the LGM, followed by more recent global dispersal by humans.
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Affiliation(s)
- Megan E Sebasky
- Department of Biology University of Virginia Charlottesville Virginia
| | - Stephen R Keller
- Department of Plant Biology University of Vermont Burlington Vermont
| | - Douglas R Taylor
- Department of Biology University of Virginia Charlottesville Virginia
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17
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Nicolas V, Martínez-Vargas J, Hugot JP. Molecular data and ecological niche modelling reveal the evolutionary history of the common and Iberian moles (Talpidae) in Europe. ZOOL SCR 2016. [DOI: 10.1111/zsc.12189] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité; ISYEB UMR 7205 - CNRS; MNHN; UPMC; EPHE; Muséum National d'Histoire Naturelle; Sorbonne Universités; Paris France
| | - Jessica Martínez-Vargas
- Departament de Biologia Animal; de Biologia Vegetal i d'Ecologia; Facultat de Biociències; Universitat Autònoma de Barcelona; E-08193 Bellaterra (Cerdanyola del Vallès) Barcelona Spain
| | - Jean-Pierre Hugot
- Institut de Systématique, Evolution, Biodiversité; ISYEB UMR 7205 - CNRS; MNHN; UPMC; EPHE; Muséum National d'Histoire Naturelle; Sorbonne Universités; Paris France
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18
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Tóth JP, Varga Z, Bereczki J. Long-term survival and diversification of an endemic Melitaeaspecies in mountains of Iran and adjacent areas. J ZOOL SYST EVOL RES 2016. [DOI: 10.1111/jzs.12122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- János P. Tóth
- MTA-DE ‘Lendület’ Behavioural Ecology Research Group; Department of Evolutionary Zoology and Human Biology; University of Debrecen; Debrecen Hungary
| | - Zoltán Varga
- Department of Evolutionary Zoology and Human Biology; Institute of Biology and Ecology; University of Debrecen; Debrecen Hungary
| | - Judit Bereczki
- MTA-DE ‘Lendület’ Behavioural Ecology Research Group; Department of Evolutionary Zoology and Human Biology; University of Debrecen; Debrecen Hungary
- Department of Evolutionary Zoology and Human Biology; Institute of Biology and Ecology; University of Debrecen; Debrecen Hungary
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19
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Splendiani A, Ruggeri P, Giovannotti M, Pesaresi S, Occhipinti G, Fioravanti T, Lorenzoni M, Nisi Cerioni P, Caputo Barucchi V. Alien brown trout invasion of the Italian peninsula: the role of geological, climate and anthropogenic factors. Biol Invasions 2016. [DOI: 10.1007/s10530-016-1149-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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20
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Wan D, Feng J, Jiang D, Mao K, Duan Y, Miehe G, Opgenoorth L. The Quaternary evolutionary history, potential distribution dynamics, and conservation implications for a Qinghai-Tibet Plateau endemic herbaceous perennial, Anisodus tanguticus (Solanaceae). Ecol Evol 2016; 6:1977-95. [PMID: 27099706 PMCID: PMC4831433 DOI: 10.1002/ece3.2019] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 01/27/2016] [Accepted: 01/28/2016] [Indexed: 01/15/2023] Open
Abstract
Various hypotheses have been proposed about the Quaternary evolutionary history of plant species on the Qinghai-Tibet Plateau (QTP), yet only a handful of studies have considered both population genetics and ecological niche context. In this study, we proposed and compared climate refugia hypotheses based on the phylogeographic pattern of Anisodus tanguticus (three plastid DNA fragments and nuclear internal transcribed spacer regions from 32 populations) and present and past species distribution models (SDMs). We detected six plastid haplotypes in two well-differentiated lineages. Although all haplotypes could be found in its western (sampling) area, only haplotypes from one lineage occurred in its eastern area. Meanwhile, most genetic variations existed between populations (F ST = 0.822). The SDMs during the last glacial maximum and last interglacial periods showed range fragmentation in the western area and significant range contraction in the eastern area, respectively, in comparison with current potential distribution. This species may have undergone intraspecific divergence during the early Quaternary, which may have been caused by survival in different refugia during the earliest known glacial in the QTP, rather than geological isolation due to orogenesis events. Subsequently, climate oscillations during the Quaternary resulted in a dynamic distribution range for this species as well as the distribution pattern of its plastid haplotypes and nuclear genotypes. The interglacial periods may have had a greater effect on A. tanguticus than the glacial periods. Most importantly, neither genetic data nor SDM alone can fully reveal the climate refugia history of this species. We also discuss the conservation implications for this important Tibetan folk medicine plant in light of these findings and SDMs under future climate models. Together, our results underline the necessity to combine phylogeographic and SDM approaches in future investigations of the Quaternary evolutionary history of species in topographically complex areas, such as the QTP.
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Affiliation(s)
- Dong‐Shi Wan
- State Key Laboratory of Grassland Agro‐EcosystemSchool of Life SciencesLanzhou UniversityLanzhou730000GansuChina
| | - Jian‐Ju Feng
- College of Plant SciencesXinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim BasinTarimu UniversityAlarXinjiangChina
| | - De‐Chun Jiang
- State Key Laboratory of Grassland Agro‐EcosystemSchool of Life SciencesLanzhou UniversityLanzhou730000GansuChina
| | - Kang‐Shan Mao
- State Key Laboratory of Grassland Agro‐EcosystemSchool of Life SciencesLanzhou UniversityLanzhou730000GansuChina
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of EducationCollege of Life ScienceSichuan UniversityChengdu610064China
| | - Yuan‐Wen Duan
- Key Laboratory of Biodiversity and BiogeographyKunming Institute of BotanyChinese Academy of SciencesLanhei Road 132, HeilongtanKunming650204YunnanChina
| | - Georg Miehe
- Faculty of Biology and GeologyUniversity of Marburg35032MarburgGermany
| | - Lars Opgenoorth
- Faculty of Biology and GeologyUniversity of Marburg35032MarburgGermany
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21
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Bidegaray-Batista L, Sánchez-gracia A, Santulli G, Maiorano L, Guisan A, Vogler AP, Arnedo MA. Imprints of multiple glacial refugia in the Pyrenees revealed by phylogeography and palaeodistribution modelling of an endemic spider. Mol Ecol 2016; 25:2046-64. [DOI: 10.1111/mec.13585] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 01/24/2016] [Accepted: 01/26/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Leticia Bidegaray-Batista
- Institut de Recerca de la Biodiversitat; Universitat de Barcelona; Av. Diagonal 643 08028 Barcelona Spain
- Departament de Biologia Animal; Facultat de Biologia; Universitat de Barcelona; Av. Diagonal 643 08028 Barcelona Spain
- Laboratorio de Etología, Ecología y Evolución; Instituto de Investigaciones Biológicas Clemente Estable; Avenida Italia 3318 11600 Montevideo Uruguay
| | - Alejandro Sánchez-gracia
- Institut de Recerca de la Biodiversitat; Universitat de Barcelona; Av. Diagonal 643 08028 Barcelona Spain
- Departament de Genètica; Facultat de Biologia; Universitat de Barcelona; Av. Diagonal 643 08028 Barcelona Spain
| | - Giulia Santulli
- Institut de Recerca de la Biodiversitat; Universitat de Barcelona; Av. Diagonal 643 08028 Barcelona Spain
- Departament de Biologia Animal; Facultat de Biologia; Universitat de Barcelona; Av. Diagonal 643 08028 Barcelona Spain
| | - Luigi Maiorano
- Department of Ecology and Evolution; University of Lausanne; Biophore Building CH-1015 Lausanne Switzerland
- Department of Biology and Biotechnologies ‘Charles Darwin’; University of Rome ‘La Sapienza’; viale dell'Università 32 00185 Rome Italy
| | - Antoine Guisan
- Department of Ecology and Evolution; University of Lausanne; Biophore Building CH-1015 Lausanne Switzerland
- Institute of Earth Surface Dynamics; University of Lausanne; Geopolis Building CH-1015 Lausanne Switzerland
| | - Alfried P. Vogler
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
- Department of Life Sciences; Imperial College London; Silwood Park Campus Ascot SL5 7PY UK
| | - Miquel A. Arnedo
- Institut de Recerca de la Biodiversitat; Universitat de Barcelona; Av. Diagonal 643 08028 Barcelona Spain
- Departament de Biologia Animal; Facultat de Biologia; Universitat de Barcelona; Av. Diagonal 643 08028 Barcelona Spain
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22
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Fuentes-Hurtado M, Hof AR, Jansson R. Paleodistribution modeling suggests glacial refugia in Scandinavia and out-of-Tibet range expansion of the Arctic fox. Ecol Evol 2016; 6:170-80. [PMID: 26811782 PMCID: PMC4716496 DOI: 10.1002/ece3.1859] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 11/04/2015] [Accepted: 11/06/2015] [Indexed: 11/08/2022] Open
Abstract
Quaternary glacial cycles have shaped the geographic distributions and evolution of numerous species in the Arctic. Ancient DNA suggests that the Arctic fox went extinct in Europe at the end of the Pleistocene and that Scandinavia was subsequently recolonized from Siberia, indicating inability to track its habitat through space as climate changed. Using ecological niche modeling, we found that climatically suitable conditions for Arctic fox were found in Scandinavia both during the last glacial maximum (LGM) and the mid-Holocene. Our results are supported by fossil occurrences from the last glacial. Furthermore, the model projection for the LGM, validated with fossil records, suggested an approximate distance of 2000 km between suitable Arctic conditions and the Tibetan Plateau well within the dispersal distance of the species, supporting the recently proposed hypothesis of range expansion from an origin on the Tibetan Plateau to the rest of Eurasia. The fact that the Arctic fox disappeared from Scandinavia despite suitable conditions suggests that extant populations may be more sensitive to climate change than previously thought.
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Affiliation(s)
- Marcelo Fuentes-Hurtado
- Departamento de Ecosistemas y Medio Ambiente Pontificia Universidad Católica de Chile Santiago Chile
| | - Anouschka R Hof
- Landscape Ecology Group Department of Ecology and Environmental Science Umeå University Umeå Sweden; Department of Wildlife Fish and Environmental Studies Swedish University of Agricultural Sciences (SLU) Umeå Sweden
| | - Roland Jansson
- Landscape Ecology Group Department of Ecology and Environmental Science Umeå University Umeå Sweden
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23
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Tsuda Y, Nakao K, Ide Y, Tsumura Y. The population demography ofBetula maximowicziana, a cool-temperate tree species in Japan, in relation to the last glacial period: its admixture-like genetic structure is the result of simple population splitting not admixing. Mol Ecol 2015; 24:1403-18. [DOI: 10.1111/mec.13123] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 02/17/2015] [Accepted: 02/18/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Y. Tsuda
- Program in Plant Ecology and Evolution; Department of Ecology and Genetics; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D 75236 Uppsala Sweden
- Department of Forest Genetics; Forestry and Forest Products Research Institute (FFPRI); Matsunosato 1 Tsukuba Ibaraki 305-8687 Japan
| | - K. Nakao
- Department of Plant Ecology; Forestry and Forest Products Research Institute (FFPRI); Matsunosato 1 Tsukubaa Ibaraki 305-8687 Japan
| | - Y. Ide
- Laboratory of Forest Ecosystem Studies; Department of Ecosystem Studies; Graduate School of Agriculture and Life Sciences; The University of Tokyo; Yayoi 1-1-1 Bunkyo-ku Tokyo 113-8657 Japan
| | - Y. Tsumura
- Department of Forest Genetics; Forestry and Forest Products Research Institute (FFPRI); Matsunosato 1 Tsukuba Ibaraki 305-8687 Japan
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24
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Jakob SS, Rödder D, Engler JO, Shaaf S, Ozkan H, Blattner FR, Kilian B. Evolutionary history of wild barley (Hordeum vulgare subsp. spontaneum) analyzed using multilocus sequence data and paleodistribution modeling. Genome Biol Evol 2014; 6:685-702. [PMID: 24586028 PMCID: PMC3971598 DOI: 10.1093/gbe/evu047] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Studies of Hordeum vulgare subsp. spontaneum, the wild progenitor of cultivated barley, have mostly relied on materials collected decades ago and maintained since then ex situ in germplasm repositories. We analyzed spatial genetic variation in wild barley populations collected rather recently, exploring sequence variations at seven single-copy nuclear loci, and inferred the relationships among these populations and toward the genepool of the crop. The wild barley collection covers the whole natural distribution area from the Mediterranean to Middle Asia. In contrast to earlier studies, Bayesian assignment analyses revealed three population clusters, in the Levant, Turkey, and east of Turkey, respectively. Genetic diversity was exceptionally high in the Levant, while eastern populations were depleted of private alleles. Species distribution modeling based on climate parameters and extant occurrence points of the taxon inferred suitable habitat conditions during the ice-age, particularly in the Levant and Turkey. Together with the ecologically wide range of habitats, they might contribute to structured but long-term stable populations in this region and their high genetic diversity. For recently collected individuals, Bayesian assignment to geographic clusters was generally unambiguous, but materials from genebanks often showed accessions that were not placed according to their assumed geographic origin or showed traces of introgression from cultivated barley. We assign this to gene flow among accessions during ex situ maintenance. Evolutionary studies based on such materials might therefore result in wrong conclusions regarding the history of the species or the origin and mode of domestication of the crop, depending on the accessions included.
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Affiliation(s)
- Sabine S Jakob
- Leibniz Institute of Plant Genetics and Crop Research (IPK), Gatersleben, Germany
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25
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Mesgaran MB, Cousens RD, Webber BL. Here be dragons: a tool for quantifying novelty due to covariate range and correlation change when projecting species distribution models. DIVERS DISTRIB 2014. [DOI: 10.1111/ddi.12209] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Mohsen B. Mesgaran
- Department of Resource Management & Geography The University of Melbourne Melbourne Vic. 3010 Australia
| | - Roger D. Cousens
- Department of Resource Management & Geography The University of Melbourne Melbourne Vic. 3010 Australia
| | - Bruce L. Webber
- CSIRO Ecosystem Sciences Wembley WA 6913 Australia
- School of Plant Biology The University of Western Australia Crawley WA 6009 Australia
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26
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Bystriakova N, Ansell SW, Russell SJ, Grundmann M, Vogel JC, Schneider H. Present, past and future of the European rock fern Asplenium fontanum: combining distribution modelling and population genetics to study the effect of climate change on geographic range and genetic diversity. ANNALS OF BOTANY 2014; 113:453-465. [PMID: 24284816 PMCID: PMC3906967 DOI: 10.1093/aob/mct274] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 10/10/2013] [Indexed: 06/02/2023]
Abstract
BACKGROUND AND AIMS Climate change is expected to alter the geographic range of many plant species dramatically. Predicting this response will be critical to managing the conservation of plant resources and the effects of invasive species. The aim of this study was to predict the response of temperate homosporous ferns to climate change. METHODS Genetic diversity and changes in distribution range were inferred for the diploid rock fern Asplenium fontanum along a South-North transect, extending from its putative last glacial maximum (LGM) refugia in southern France towards southern Germany and eastern-central France. This study reconciles observations from distribution models and phylogeographic analyses derived from plastid and nuclear diversity. KEY RESULTS Genetic diversity distribution and niche modelling propose that genetic diversity accumulates in the LGM climate refugium in southern France with the formation of a diversity gradient reflecting a slow, post-LGM range expansion towards the current distribution range. Evidence supports the fern's preference for outcrossing, contradicting the expectation that homosporous ferns would populate new sites by single-spore colonization. Prediction of climate and distribution range change suggests that a dramatic loss of range and genetic diversity in this fern is possible. The observed migration is best described by the phalanx expansion model. CONCLUSIONS The results suggest that homosporous ferns reproducing preferentially by outcrossing accumulate genetic diversity primarily in LGM climate refugia and may be threatened if these areas disappear due to global climate change.
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Affiliation(s)
- Nadia Bystriakova
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Stephen W. Ansell
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Stephen J. Russell
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Michael Grundmann
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Johannes C. Vogel
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Harald Schneider
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
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