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Danzey LM, Briceño VF, Cook AM, Nicotra AB, Peyre G, Rossetto M, Yap JYS, Leigh A. Environmental and Biogeographic Drivers behind Alpine Plant Thermal Tolerance and Genetic Variation. Plants (Basel) 2024; 13:1271. [PMID: 38732486 DOI: 10.3390/plants13091271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/26/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
In alpine ecosystems, elevation broadly functions as a steep thermal gradient, with plant communities exposed to regular fluctuations in hot and cold temperatures. These conditions lead to selective filtering, potentially contributing to species-level variation in thermal tolerance and population-level genetic divergence. Few studies have explored the breadth of alpine plant thermal tolerances across a thermal gradient or the underlying genetic variation thereof. We measured photosystem heat (Tcrit-hot) and cold (Tcrit-cold) thresholds of ten Australian alpine species across elevation gradients and characterised their neutral genetic variation. To reveal the biogeographical drivers of present-day genetic signatures, we also reconstructed temporal changes in habitat suitability across potential distributional ranges. We found intraspecific variation in thermal thresholds, but this was not associated with elevation, nor underpinned by genetic differentiation on a local scale. Instead, regional population differentiation and considerable homozygosity within populations may, in part, be driven by distributional contractions, long-term persistence, and migrations following habitat suitability. Our habitat suitability models suggest that cool-climate-distributed alpine plants may be threatened by a warming climate. Yet, the observed wide thermal tolerances did not reflect this vulnerability. Conservation efforts should seek to understand variations in species-level thermal tolerance across alpine microclimates.
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Affiliation(s)
- Lisa M Danzey
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Broadway, NSW 2007, Australia
| | - Verónica F Briceño
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Alicia M Cook
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Broadway, NSW 2007, Australia
| | - Adrienne B Nicotra
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Gwendolyn Peyre
- Department of Civil and Environmental Engineering, University of the Andes, Bogota 111711, Colombia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Gardens Sydney, Sydney, NSW 2000, Australia
- Queensland Alliance of Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia
| | - Jia-Yee S Yap
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Gardens Sydney, Sydney, NSW 2000, Australia
- Queensland Alliance of Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia
| | - Andrea Leigh
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
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Sequeira JJ, Vinuthalakshmi K, Das R, van Driem G, Mustak MS. Corrigendum: The maternal U1 haplogroup in the Koraga tribe as a correlate of their North Dravidian linguistic affinity. Front Genet 2024; 15:1384937. [PMID: 38533206 PMCID: PMC10963611 DOI: 10.3389/fgene.2024.1384937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 02/12/2024] [Indexed: 03/28/2024] Open
Abstract
[This corrects the article DOI: 10.3389/fgene.2023.1303628.].
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Affiliation(s)
| | | | - Ranajit Das
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - George van Driem
- Institut für Sprachwissenschaft, Universität Bern, Bern, Switzerland
| | - Mohammed S. Mustak
- Department of Applied Zoology, Mangalore University, Mangalore, Karnataka, India
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Sequeira JJ, Vinuthalakshmi K, Das R, van Driem G, Mustak MS. The maternal U1 haplogroup in the Koraga tribe as a correlate of their North Dravidian linguistic affinity. Front Genet 2024; 14:1303628. [PMID: 38384360 PMCID: PMC10880486 DOI: 10.3389/fgene.2023.1303628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/31/2023] [Indexed: 02/23/2024] Open
Abstract
Introduction: The Koraga tribe are an isolated endogamous tribal group found in the southwest coastal region of India. The Koraga language shares inherited grammatical features with North Dravidian languages. To seek a possible genetic basis for this exceptionality and understand the maternal lineage pattern, we have aimed to reconstruct the inter-population and intra-population relationships of the Koraga tribal population by using mtDNA markers for the hypervariable regions along with a partial coding region sequence analysis. Methods and Results: Amongst the 96 individuals studied, we observe 11 haplogroups, of which a few are shared and others are unique to the clans Soppu, Oṇṭi and Kuṇṭu. In addition to several deep rooted Indian-specific lineages of macrohaplogroups M and U, we observe a high frequency of the U1 lineage (∼38%), unique to the Koraga. A Bayesian analysis of the U1 clade shows that the Koraga tribe share their maternal lineage with ancestral populations of the Caucasus at the cusp of the Last Glacial Maximum. Discussion: Our study suggests that the U1 lineage found in the Indian subcontinent represents a remnant of a post-glacial dispersal. The presence of West Asian U1 when viewed along with historical linguistics leads us to hypothesise that Koraga represents a mother tongue retained by a vanquished population group that fled southward at the demise of the Indus civilisation as opposed to a father tongue, associated with a particular paternal lineage.
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Affiliation(s)
| | | | - Ranajit Das
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - George van Driem
- Institut für Sprachwissenschaft, Universität Bern, Bern, Switzerland
| | - Mohammed S. Mustak
- Department of Applied Zoology, Mangalore University, Mangalore, Karnataka, India
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Yousefi M, Jouladeh‐Roudbar A, Kafash A. Mapping endemic freshwater fish richness to identify high-priority areas for conservation: An ecoregion approach. Ecol Evol 2024; 14:e10970. [PMID: 38371871 PMCID: PMC10870328 DOI: 10.1002/ece3.10970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/23/2023] [Accepted: 12/06/2023] [Indexed: 02/20/2024] Open
Abstract
Freshwater ecosystems are experiencing accelerating global biodiversity loss. Thus, knowing where these unique ecosystems' species richness reaches a peak can facilitate their conservation planning. By hosting more than 290 freshwater fishes, Iran is a major freshwater fish hotspot in the Middle East. Considering the accelerating rate of biodiversity loss, there is an urgent need to identify species-rich areas and understand the mechanisms driving biodiversity distribution. In this study, we gathered distribution records of all endemic freshwater fishes of Iran (85 species) to develop their richness map and determine the most critical drivers of their richness patterns from an ecoregion approach. We performed a generalized linear model (GLM) with quasi-Poisson distribution to identify contemporary and historical determinants of endemic freshwater fish richness. We also quantified endemic fish similarity among the 15 freshwater ecoregions of Iran. Results showed that endemic freshwater fish richness is highest in the Zagros Mountains while a moderate level of richness was observed between Zagros and Alborz Mountains. High, moderate, and low richness of endemic freshwater fish match with Upper Tigris & Euphrates, Namak, and Kavir & Lut Deserts ecoregions respectively. Kura - South Caspian Drainages and Caspian Highlands were the most similar ecoregions and Orumiyeh was the most unique ecoregion according to endemic fish presence. Precipitation and precipitation change velocity since the Last Glacial Maximum were the most important predictors of endemic freshwater fish richness. Areas identified to have the highest species richness have high priority for the conservation of freshwater fish in Iran, therefore, should be considered in future protected areas development.
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Affiliation(s)
- Masoud Yousefi
- Stiftung Neanderthal MuseumMettmannGermany
- Leibniz Institute for the Analysis of Biodiversity Change (LIB)Museum KoenigBonnGermany
| | | | - Anooshe Kafash
- School of Culture and SocietyAarhus UniversityAarhus CDenmark
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Wu HY, Liu YH, He QX, Ye JW, Tian B. Differential distribution shifts in two subregions of East Asian subtropical evergreen broadleaved forests-a case of Magnoliaceae. Front Plant Sci 2024; 14:1326207. [PMID: 38322424 PMCID: PMC10844446 DOI: 10.3389/fpls.2023.1326207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/27/2023] [Indexed: 02/08/2024]
Abstract
Aim East Asian subtropical evergreen broad-leaved forests (EBLFs) are composed of western and eastern subregions with different topographical and environmental conditions. The distribution shifts over time of plants in the two subregions are predicted to be different, but the difference has seldom been investigated. Methods Potential distributions of 53 Magnoliaceae species (22 in the western and 31 in the eastern subregion) during the last glacial maximum (LGM), present, and the 2070s were predicted using MaxEnt based on 58 environmental variables. The changes in the distribution range size and centroid over time were analyzed. Species-level potential habitats were overlaid to uncover species diversity distribution, and the distributions over time were overlaid to discover long-term refugia. Results At present, the potential distributions are significantly larger than those shown by the occurrence points. During the LGM, 20/22 species in the western subregion experienced increases in range size through downwards and southward migrations, while decreases in range size in the eastern subregion (27/31 species) were accompanied by northward and eastward migrations. In the future, range size declines and northward shifts will both be found; northwestward shifts will exist in most (20/22 species) species in the western subregion, while both northwest- and northeastward shifts will occur in the eastern subregion. The diversity hotspots experienced a slight southward shift in the past and upwards to the mountain region in the future in the western subregion; in the eastern subregion, shrinks occurred in eastern China in the past and shrinks were shown in all regions in the future. Long-term refugia-preserving diversity was found in the mountains across the entire EBLFs region. Main conclusions Significant differences in distribution shifts from past to present and similar distribution shifts from present to future are revealed in the two subregions. Species diversity in both subregions experienced no significant shifts from past to future, and Magnoliaceae plants could be preserved in mountainous regions throughout the EBLFs.
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Affiliation(s)
- Hai-Yang Wu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Yue-Han Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Qiu-Xiang He
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Jun-Wei Ye
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Bin Tian
- National Plateau Wetlands Research Center, Southwest Forestry University, Kunming, China
- Yunnan Key Laboratory of Plateau Wetland Conservation Restoration and Ecological Services, Southwest Forestry University, Kunming, China
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da Silva Coelho FA, Gill S, Tomlin CM, Papavassiliou M, Farley SD, Cook JA, Sonsthagen SA, Sage GK, Heaton TH, Talbot SL, Lindqvist C. Ancient bears provide insights into Pleistocene ice age refugia in Southeast Alaska. Mol Ecol 2023. [PMID: 37096383 DOI: 10.1111/mec.16960] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/28/2023] [Accepted: 04/12/2023] [Indexed: 04/26/2023]
Abstract
During the Late Pleistocene, major parts of North America were periodically covered by ice sheets. However, there are still questions about whether ice-free refugia were present in the Alexander Archipelago along the Southeast (SE) Alaska coast during the last glacial maximum (LGM). Numerous subfossils have been recovered from caves in SE Alaska, including American black (Ursus americanus) and brown (U. arctos) bears, which today are found in the Alexander Archipelago but are genetically distinct from mainland bear populations. Hence, these bear species offer an ideal system to investigate long-term occupation, potential refugial survival and lineage turnover. Here, we present genetic analyses based on 99 new complete mitochondrial genomes from ancient and modern brown and black bears spanning the last ~45,000 years. Black bears form two SE Alaskan subclades, one preglacial and another postglacial, that diverged >100,000 years ago. All postglacial ancient brown bears are closely related to modern brown bears in the archipelago, while a single preglacial brown bear is found in a distantly related clade. A hiatus in the bear subfossil record around the LGM and the deep split of their pre- and postglacial subclades fail to support a hypothesis of continuous occupancy in SE Alaska throughout the LGM for either species. Our results are consistent with an absence of refugia along the SE Alaska coast, but indicate that vegetation quickly expanded after deglaciation, allowing bears to recolonize the area after a short-lived LGM peak.
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Affiliation(s)
| | - Stephanie Gill
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA
| | - Crystal M Tomlin
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA
| | | | - Sean D Farley
- Alaska Department of Fish and Game, Anchorage, Alaska, USA
| | - Joseph A Cook
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Sarah A Sonsthagen
- U.S. Geological Survey, Nebraska Cooperative Fish and Wildlife Research Unit, University of Nebraska-Lincoln, School of Natural Resources, Lincoln, Nebraska, USA
| | - George K Sage
- Far Northwestern Institute of Art and Science, Anchorage, Alaska, USA
| | - Timothy H Heaton
- Department of Earth Sciences, University of South Dakota, Vermillion, South Dakota, USA
| | - Sandra L Talbot
- Far Northwestern Institute of Art and Science, Anchorage, Alaska, USA
| | - Charlotte Lindqvist
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA
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Dantas-Queiroz MV, Hurbath F, de Russo Godoy FM, Lanna FM, Versieux LM, Palma-Silva C. Comparative phylogeography reveals the demographic patterns of neotropical ancient mountain species. Mol Ecol 2023. [PMID: 36934376 DOI: 10.1111/mec.16929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 03/01/2023] [Accepted: 03/07/2023] [Indexed: 03/20/2023]
Abstract
Mountains are renowned for their bountiful biodiversity. Explanations on the origin of such abundant life are usually regarded to their orogenic history. However, ancient mountain systems with geological stability also exhibit astounding levels of number of species and endemism, as illustrated by the Brazilian Quartzitic Mountains (BQM) in Eastern South America. Thus, cycles of climatic changes over the last couple million years are usually assumed to play an important role in the origin of mountainous biota. These climatic oscillations potentially isolated and reconnected adjacent populations, a phenomenon known as flickering connectivity, accelerating speciation events due to range fragmentation, dispersion, secondary contact, and hybridization. To evaluate the role of the climatic fluctuations on the diversification of the BQM biota, we estimated the ancient demography of distinct endemic species of animals and plants using hierarchical approximate Bayesian computation analysis and Ecological Niche Modelling. Additionally, we evaluated if climatic oscillations have driven a genetic spatial congruence in the genetic structure of codistributed species from the Espinhaço Range, one of the main BQM areas. Our results show that the majority of plant lineages underwent a synchronous expansion over the Last Glacial Maximum (LGM, c. 21 thousand years ago), although we could not obtain a clear demographic pattern for the animal lineages. We also obtained a signal of a congruent phylogeographic break between lineages endemic to the Espinhaço Range, suggesting how ancient climatic oscillations might have driven the evolutionary history of the Espinhaço's biota.
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Affiliation(s)
- Marcos Vinicius Dantas-Queiroz
- Programa de Pós-Graduação em Biologia Vegetal, Universidade Estadual Paulista (UNESP), São Paulo, Brazil
- Department of Evolutionary Plant Biology, Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, Czech Republic
| | - Fernanda Hurbath
- Universidade do Estado de Minas Gerais - Unidade Passos, Av. Juca Stockler, 1130, bairro Belo Horizonte, Passos, Brazil
| | - Fernanda Maria de Russo Godoy
- Programa de Pós-Graduação em Biotecnologia e Biodiversidade, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Flávia Mol Lanna
- Department of Evolution, Ecology and Organismal Biology. Museum of Biological Diversity, The Ohio State University, Columbus, Ohio, USA
| | - Leonardo M Versieux
- Departamento de Botânica e Zoologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Clarisse Palma-Silva
- Programa de Pós-Graduação em Biologia Vegetal, Universidade Estadual Paulista (UNESP), São Paulo, Brazil
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
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Rose JP, Sytsma KJ. Phylogeography and genetic variation in Western Jacob's ladder (Polemonium occidentale) provide insights into the origin and conservation of rare species in the Great Lakes region. Mol Ecol 2023; 32:79-94. [PMID: 36217576 DOI: 10.1111/mec.16730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 09/27/2022] [Accepted: 10/06/2022] [Indexed: 12/29/2022]
Abstract
The perennial herb Western Jacob's Ladder (Polemonium occidentale, Polemoniaceae) is widespread in the mountains of western North America but reappears as a disjunct in the Great Lakes Region in Minnesota and Wisconsin, USA as the narrow endemic P. occidentale subsp. lacustre. This distribution is shown by a diverse assemblage of angiosperms. It has been hypothesized that these species became isolated just after the Last Glacial Maximum, but this has not been tested. Additionally, the genetic diversity and population connectivity of the endemic Great Lakes flora has been understudied, with important conservation implications. Using genotyping-by-sequencing, we examined the relationship of P. occidentale subsp. lacustre to its closest relatives, relationships among all known populations, and genetic diversity within these populations. Polemonium occidentale subsp. lacustre represents an isolated, unique lineage that diverged from its closest relatives 1.3 Ma and arrived in the Great Lakes Region by at least 38 ka. Nearly all extant populations diverged prior to the Last Glacial Maximum, are genetically distinct, and show little within-population genetic diversity. Clonality may mitigate reduction in diversity due to drift. Mixed population signal between Wisconsin and some Minnesota populations may be due to gene flow during the Late Pleistocene. While populations of P. occidentale subsp. lacustre may be relictual from a now extinct western relative, it is best treated as a distinct species. Conservation efforts should focus more on ensuring that current populations remain rather than maintaining large populations sizes across a few populations. However, encouraging habitat heterogeneity may accomplish both simultaneously.
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Affiliation(s)
- Jeffrey P Rose
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kenneth J Sytsma
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Wilson TC, Rossetto M, Bain D, Yap JS, Wilson PD, Stimpson ML, Weston PH, Croft L. A turn in species conservation for hairpin banksias: demonstration of oversplitting leads to better management of diversity. Am J Bot 2022; 109:1652-1671. [PMID: 36164832 PMCID: PMC9828017 DOI: 10.1002/ajb2.16074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 06/16/2023]
Abstract
PREMISE Understanding evolutionary history and classifying discrete units of organisms remain overwhelming tasks, and lags in this workload concomitantly impede an accurate documentation of biodiversity and conservation management. Rapid advances and improved accessibility of sensitive high-throughput sequencing tools are fortunately quickening the resolution of morphological complexes and thereby improving the estimation of species diversity. The recently described and critically endangered Banksia vincentia is morphologically similar to the hairpin banksia complex (B. spinulosa s.l.), a group of eastern Australian flowering shrubs whose continuum of morphological diversity has been responsible for taxonomic controversy and possibly questionable conservation initiatives. METHODS To assist conservation while testing the current taxonomy of this group, we used high-throughput sequencing to infer a population-scale evolutionary scenario for a sample set that is comprehensive in its representation of morphological diversity and a 2500-km distribution. RESULTS Banksia spinulosa s.l. represents two clades, each with an internal genetic structure shaped through historical separation by biogeographic barriers. This structure conflicts with the existing taxonomy for the group. Corroboration between phylogeny and population statistics aligns with the hypothesis that B. collina, B. neoanglica, and B. vincentia should not be classified as species. CONCLUSIONS The pattern here supports how morphological diversity can be indicative of a locally expressed suite of traits rather than relationship. Oversplitting in the hairpin banksias is atypical since genomic analyses often reveal that species diversity is underestimated. However, we show that erring on overestimation can yield negative consequences, such as the disproportionate prioritization of a geographically anomalous population.
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Affiliation(s)
- Trevor C. Wilson
- Plant Discovery and Evolution, Australian Institute of Botanical ScienceRoyal Botanic Gardens and Domain TrustSydneyAustralia
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical ScienceThe Royal Botanic Garden SydneyAustralia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical ScienceThe Royal Botanic Garden SydneyAustralia
| | - David Bain
- Ecosystems and Threatened Species, Biodiversity Conservation and ScienceNSW Department of Planning and EnvironmentWollongongAustralia
| | - Jia‐Yee S. Yap
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical ScienceThe Royal Botanic Garden SydneyAustralia
| | - Peter D. Wilson
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical ScienceThe Royal Botanic Garden SydneyAustralia
| | - Margaret L. Stimpson
- Botany, School of Environmental and Rural ScienceUniversity of New EnglandArmidaleNSW2351Australia
| | - Peter H. Weston
- Plant Discovery and Evolution, Australian Institute of Botanical ScienceRoyal Botanic Gardens and Domain TrustSydneyAustralia
| | - Larry Croft
- Centre of Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelong3125VictoriaAustralia
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Wilson TC, Rossetto M, Bain D, Yap JYS, Wilson PD, Stimpson ML, Weston PH, Croft L. A turn in species conservation for hairpin banksias: demonstration of oversplitting leads to better management of diversity. Am J Bot 2022. [PMID: 36164832 DOI: 10.5061/dryad.69p8cz94x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
PREMISE Understanding evolutionary history and classifying discrete units of organisms remain overwhelming tasks, and lags in this workload concomitantly impede an accurate documentation of biodiversity and conservation management. Rapid advances and improved accessibility of sensitive high-throughput sequencing tools are fortunately quickening the resolution of morphological complexes and thereby improving the estimation of species diversity. The recently described and critically endangered Banksia vincentia is morphologically similar to the hairpin banksia complex (B. spinulosa s.l.), a group of eastern Australian flowering shrubs whose continuum of morphological diversity has been responsible for taxonomic controversy and possibly questionable conservation initiatives. METHODS To assist conservation while testing the current taxonomy of this group, we used high-throughput sequencing to infer a population-scale evolutionary scenario for a sample set that is comprehensive in its representation of morphological diversity and a 2500-km distribution. RESULTS Banksia spinulosa s.l. represents two clades, each with an internal genetic structure shaped through historical separation by biogeographic barriers. This structure conflicts with the existing taxonomy for the group. Corroboration between phylogeny and population statistics aligns with the hypothesis that B. collina, B. neoanglica, and B. vincentia should not be classified as species. CONCLUSIONS The pattern here supports how morphological diversity can be indicative of a locally expressed suite of traits rather than relationship. Oversplitting in the hairpin banksias is atypical since genomic analyses often reveal that species diversity is underestimated. However, we show that erring on overestimation can yield negative consequences, such as the disproportionate prioritization of a geographically anomalous population.
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Affiliation(s)
- Trevor C Wilson
- Plant Discovery and Evolution, Australian Institute of Botanical Science, Royal Botanic Gardens and Domain Trust, Sydney, Australia
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Australia
| | - David Bain
- Ecosystems and Threatened Species, Biodiversity Conservation and Science, NSW Department of Planning and Environment, Wollongong, Australia
| | - Jia-Yee S Yap
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Australia
| | - Peter D Wilson
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Australia
| | - Margaret L Stimpson
- Botany, School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia
| | - Peter H Weston
- Plant Discovery and Evolution, Australian Institute of Botanical Science, Royal Botanic Gardens and Domain Trust, Sydney, Australia
| | - Larry Croft
- Centre of Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, 3125, Victoria, Australia
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Motyka M, Kusy D, Bilkova R, Bocak L. Analysis of the Holarctic Dictyoptera aurora Complex (Coleoptera, Lycidae) Reveals Hidden Diversity and Geographic Structure in Müllerian Mimicry Ring. Insects 2022; 13:817. [PMID: 36135518 PMCID: PMC9502218 DOI: 10.3390/insects13090817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 06/16/2023]
Abstract
The elateroid family Lycidae is known for limited dispersal propensity and high species-level endemism. The red net-winged beetle, Dictyoptera aurora (Herbst, 1874), differs from all relatives by the range comprising almost the entire Holarctic region. Based on a five-marker phylogeny and 67 barcode entries (cox1-5' mtDNA) from the whole range, we recovered two genetically distinct species within traditionally defined D. aurora and resurrected the name D. coccinata (Say, 1835) as the oldest available synonym for Nearctic populations. Yet, no reliable morphological trait distinguishes these species except for minute differences in the male genitalia. D. coccinata is a monophylum resulting from a single Miocene dispersal event, ~15.8 million years ago, and genetic divergence implies long-term isolation by the Bering Strait. Far East Asian and west European populations are also genetically distinct, although to a lower extent. Two independent colonization events established the Fennoscandian populations after the last glacial maximum. Besides intrinsic factors, the high morphological similarity might result from stabilizing selection for shared aposematic signals. The rapidly accumulating barcode data provide valuable information on the evolutionary history and the origins of regional faunas.
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Affiliation(s)
| | | | | | - Ladislav Bocak
- Biodiversity & Molecular Evolution, Czech Advanced Technology and Research Institute, Center of the Region Hana, Slechtitelu 27, 779 00 Olomouc, Czech Republic
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Wang Z, Pierce NE. Fine-scale genome-wide signature of Pleistocene glaciation in Thitarodes moths (Lepidoptera: Hepialidae), host of Ophiocordyceps fungus in the Hengduan Mountains. Mol Ecol 2022; 32:2695-2714. [PMID: 35377501 DOI: 10.1111/mec.16457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 02/12/2022] [Accepted: 03/21/2022] [Indexed: 11/28/2022]
Abstract
The Hengduan Mountains region is a biodiversity hotspot known for its topologically complex, deep valleys and high mountains. While landscape and glacial refugia have been evoked to explain patterns of inter-species divergence, the accumulation of intra-species (i.e. population level) genetic divergence across the mountain-valley landscape in this region has received less attention. We used genome-wide restriction site-associated DNA sequencing (RADseq) to reveal signatures of Pleistocene glaciation in populations of Thitarodes shambalaensis (Lepidoptera: Hepialidae), the host moth of parasitic Ophiocordyceps sinensis (Hypocreales: Ophiocordycipitaceae) or "caterpillar fungus" endemic to the glacier of eastern Mt. Gongga. We used moraine history along the glacier valleys to model the distribution and environmental barriers to gene flow across populations of T. shambalaensis. We found that moth populations separated by less than 10 km exhibited valley-based population genetic clustering and isolation-by-distance (IBD), while gene flow among populations was best explained by models using information about their distributions at the local last glacial maximum (LGML , 58 kya), not their contemporary distribution. Maximum likelihood lineage history among populations, and among subpopulations as little as 500 meters apart, recapitulated glaciation history across the landscape. We also found signals of isolated population expansion following the retreat of LGML glaciers. These results reveal the fine-scale, long-term historical influence of landscape and glaciation on the genetic structuring of populations of an endangered and economically important insect species. Similar mechanisms, given enough time and continued isolation, could explain the contribution of glacier refugia to the generation of species diversity among the Hengduan Mountains.
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Affiliation(s)
- Zhengyang Wang
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Naomi E Pierce
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
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Warmuth VM, Burgess MD, Laaksonen T, Manica A, Mägi M, Nord A, Primmer CR, Sætre GP, Winkel W, Ellegren H. Major population splits coincide with episodes of rapid climate change in a forest-dependent bird. Proc Biol Sci 2021; 288:20211066. [PMID: 34727712 PMCID: PMC8564624 DOI: 10.1098/rspb.2021.1066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 10/07/2021] [Indexed: 11/17/2022] Open
Abstract
Climate change influences population demography by altering patterns of gene flow and reproductive isolation. Direct mutation rates offer the possibility for accurate dating on the within-species level but are currently only available for a handful of vertebrate species. Here, we use the first directly estimated mutation rate in birds to study the evolutionary history of pied flycatchers (Ficedula hypoleuca). Using a combination of demographic inference and species distribution modelling, we show that all major population splits in this forest-dependent system occurred during periods of increased climate instability and rapid global temperature change. We show that the divergent Spanish subspecies originated during the Eemian-Weichselian transition 115-104 thousand years ago (kya), and not during the last glacial maximum (26.5-19 kya), as previously suggested. The magnitude and rates of climate change during the glacial-interglacial transitions that preceded population splits in pied flycatchers were similar to, or exceeded, those predicted to occur in the course of the current, human-induced climate crisis. As such, our results provide a timely reminder of the strong impact that episodes of climate instability and rapid temperature changes can have on species' evolutionary trajectories, with important implications for the natural world in the Anthropocene.
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Affiliation(s)
- Vera M. Warmuth
- Department of Evolutionary Biology, Biozentrum Martinsried, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
| | - Malcolm D. Burgess
- Centre for Animal Behaviour, University of Exeter, Exeter, UK
- RSPB Centre for Conservation Science, Sandy, UK
| | - Toni Laaksonen
- Department of Biology, University of Turku, Turku, Finland
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Marko Mägi
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Andreas Nord
- Department of Biology, Section for Evolutionary Ecology, Lund University, Lund, Sweden
| | - Craig R. Primmer
- Organismal and Evolutionary Biology Research Program, University of Helsinki, Finland
- Institute of Biotechnology, Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Finland
| | - Glenn-Peter Sætre
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Wolfgang Winkel
- Institute of Avian Research, ‘Vogelwarte Helgoland’, Wilhelmshaven, Germany
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
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14
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Hammoud C, Kougioumoutzis K, Rijsdijk KF, Simaiakis SM, Norder SJ, Foufopoulos J, Georgopoulou E, Van Loon EE. Past connections with the mainland structure patterns of insular species richness in a continental-shelf archipelago (Aegean Sea, Greece). Ecol Evol 2021; 11:5441-5458. [PMID: 34026019 PMCID: PMC8131802 DOI: 10.1002/ece3.7438] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 11/18/2022] Open
Abstract
Recent research in island biogeography has highlighted the important role of late Quaternary sea-level fluctuations in shaping biogeographic patterns in insular systems but focused on oceanic systems. Through this study, we aim investigate how late Quaternary sea-level fluctuations shaped species richness patterns in continental-shelf island systems. Focusing on the Aegean archipelago, we first compiled maps of the area's geography using published data, under three sea-level stands: (a) current; (b) median sea-level over the last nine glacial-interglacial cycles (MSL); and (c) Last Glacial Maximum (LGM). We gathered taxon-island occurrences for multiple chorotypes of angiosperms, butterflies, centipedes, and reptiles. We investigated the impact of present-day and past geographic settings on chorological groups by analyzing island species-area relationships (ISARs) and using generalized linear mixed models (GLMMs) selection based on multiple metrics of goodness of fit. Our results confirm that the Aegean's geography has changed dramatically since the LGM, whereas the MSL only modestly differs from the present configuration. Apart for centipedes, paleogeographic changes affected both native and endemic species diversity through altering connections between land-bridge islands and the mainland. On land-bridge islands, we detected over-representation of native species and under-representation of endemics. Unlike oceanic islands, sea-level-driven increase of isolation and area contraction did not strongly shape patterns of species richness. Furthermore, the LGM configurations rather than the MSL configuration shaped patterns of endemic species richness. This suggests that even short episodes of increased connectivity with continental populations are sufficient to counteract the genetic differentiation of insular populations. On the other hand, the over-representation of native nonendemic species on land-bridge islands reflected MSL rather than LGM mainland connections. Our study shows that in terms of processes affecting species richness patterns, continental archipelagos differ fundamentally from oceanic systems because episodic connections with the mainland have profound effects on the biota of land-bridge islands.
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Affiliation(s)
- Cyril Hammoud
- Invertebrate UnitDepartment of BiologyRoyal Museum for Central AfricaTervurenBelgium
- Limnology UnitDepartment of BiologyGhent UniversityGhentBelgium
| | - Konstantinos Kougioumoutzis
- Department of BiologySection of Ecology and TaxonomyNational & Kapodistrian University of AthensAthensGreece
| | - Kenneth F. Rijsdijk
- Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
| | | | - Sietze J. Norder
- Leiden University Centre for LinguisticsLeiden UniversityLeidenThe Netherlands
| | | | | | - Emiel E. Van Loon
- Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
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15
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Jin DP, Park JS, Choi BH. Historical migration and taxonomic entity of Korean endemic shrub Lespedeza maritima (Fabaceae) based on microsatellite loci. AoB Plants 2021; 13:plab009. [PMID: 33767807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 02/11/2021] [Indexed: 06/12/2023]
Abstract
Various plant species are endemic to the Korean Peninsula, but their evolutionary divergence and establishment are poorly understood. One of these, Lespedeza maritima, has been proposed as either a hybrid (L. cyrtobotrya × L. maximowiczii) or a synonym of L. thunbergii. A distinct taxon, L. uekii, has been proposed for inland populations. We investigated genetic diversity and structure in L. maritima and related taxa to resolve this. Genotypes of L. maritima (n = 244, including L. uekii) were determined using 12 microsatellite loci, then compared with those of related species. Genetic diversity within L. maritima was estimated, and Bayesian clustering analysis was used to represent its genetic structure and that of related taxa. Its distribution during the last glacial maximum (LGM) was predicted using ecological niche modelling (ENM). Neighbour-joining (NJ) analysis and principal coordinate analysis (PCoA) were used to investigate relationships among species. Bayesian tree based on nuclear ribosomal internal transcribed spacers (nrITS) was also reconstructed to show relationships and divergence time among species. Morphological features were examined using flower characteristics. In result, expected heterozygosity (H E) and allelic richness (A R) within L. maritima were higher in southern than northern populations. Bayesian clustering analysis largely assigned populations to two clusters (K = 2) (south vs. north). The ENM showed that L. maritima occurred around the East China Sea and Korean Strait land bridge during the LGM. Compared with other Lespedeza species, L. maritima was assigned to an independent cluster (K = 2-5), supported by the NJ, PCoA, Bayesian tree and morphological examination results. Lespedeza maritima and L. uekii were clustered to one clade on Bayesian tree. Given results, current L. maritima populations derive from post-LGM colonization away from southern refugia. The type L. uekii, which grows inland, is thought synonym of L. maritima. In addition, L. maritima is considered a distinct species, compared with related taxa.
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Affiliation(s)
- Dong-Pil Jin
- Department of Biological Sciences, Inha University, 100, Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Jong-Soo Park
- Department of Biological Sciences, Inha University, 100, Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Byoung-Hee Choi
- Department of Biological Sciences, Inha University, 100, Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
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Jin DP, Park JS, Choi BH. Historical migration and taxonomic entity of Korean endemic shrub Lespedeza maritima (Fabaceae) based on microsatellite loci. AoB Plants 2021; 13:plab009. [PMID: 33767807 PMCID: PMC7983312 DOI: 10.1093/aobpla/plab009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 02/11/2021] [Indexed: 07/06/2023]
Abstract
Various plant species are endemic to the Korean Peninsula, but their evolutionary divergence and establishment are poorly understood. One of these, Lespedeza maritima, has been proposed as either a hybrid (L. cyrtobotrya × L. maximowiczii) or a synonym of L. thunbergii. A distinct taxon, L. uekii, has been proposed for inland populations. We investigated genetic diversity and structure in L. maritima and related taxa to resolve this. Genotypes of L. maritima (n = 244, including L. uekii) were determined using 12 microsatellite loci, then compared with those of related species. Genetic diversity within L. maritima was estimated, and Bayesian clustering analysis was used to represent its genetic structure and that of related taxa. Its distribution during the last glacial maximum (LGM) was predicted using ecological niche modelling (ENM). Neighbour-joining (NJ) analysis and principal coordinate analysis (PCoA) were used to investigate relationships among species. Bayesian tree based on nuclear ribosomal internal transcribed spacers (nrITS) was also reconstructed to show relationships and divergence time among species. Morphological features were examined using flower characteristics. In result, expected heterozygosity (H E) and allelic richness (A R) within L. maritima were higher in southern than northern populations. Bayesian clustering analysis largely assigned populations to two clusters (K = 2) (south vs. north). The ENM showed that L. maritima occurred around the East China Sea and Korean Strait land bridge during the LGM. Compared with other Lespedeza species, L. maritima was assigned to an independent cluster (K = 2-5), supported by the NJ, PCoA, Bayesian tree and morphological examination results. Lespedeza maritima and L. uekii were clustered to one clade on Bayesian tree. Given results, current L. maritima populations derive from post-LGM colonization away from southern refugia. The type L. uekii, which grows inland, is thought synonym of L. maritima. In addition, L. maritima is considered a distinct species, compared with related taxa.
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Affiliation(s)
- Dong-Pil Jin
- Department of Biological Sciences, Inha University, 100, Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Jong-Soo Park
- Department of Biological Sciences, Inha University, 100, Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Byoung-Hee Choi
- Department of Biological Sciences, Inha University, 100, Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
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17
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Avila-Cervantes J, Arias C, Venegas-Anaya M, Vargas M, Larsson HCE, McMillan WO. Effect of the Central American Isthmus on gene flow and divergence of the American crocodile (Crocodylus acutus). Evolution 2021; 75:245-259. [PMID: 33314048 DOI: 10.1111/evo.14139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 11/13/2020] [Accepted: 11/25/2020] [Indexed: 01/22/2023]
Abstract
The final formation of the Central American Isthmus (CAI) about 3.5 million years ago altered global ocean circulation, connected North and South America terrestrial biotas, and established the Caribbean Sea. The nature of this event creates a natural scenario to test vicariance, divergence, and speciation by allopatry. Studies have shown the effect of the CAI on marine and terrestrial species, but none have examined a large-bodied amphibious taxon. We used RAD sequencing on populations of the American crocodile (Crocodylus acutus) to study the genomic variation of C. acutus on both sides of the CAI, infer its demographic history, and measure the effect of the opening of the Panama Canal. Our results showed three genomic clusters: (1) Caribbean and the Panama Canal, (2) Pacific coast, and (3) Coiba island. The estimated divergence times between the Caribbean and Pacific populations are about 20,000 years ago, which is younger than the formation of the CAI, coinciding with the Last Glacial Maximum. We hypothesize the glacial/interglacial cycles facilitated gene flow between the Caribbean and Pacific crocodile populations after the formation of the CAI, masking any genomic divergence the CAI may have caused. There is no evidence of gene flow associated with the opening of the Panama Canal.
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Affiliation(s)
- Jose Avila-Cervantes
- McGill University, Redpath Museum 859 Sherbrooke Street West, Montreal, Quebec, H3A 0C4, Canada
| | - Carlos Arias
- Smithsonian Tropical Research Institute, Roosevelt Ave. Tupper Bldg. 401, Panama, Rep. of Panama
| | - Miryam Venegas-Anaya
- Smithsonian Tropical Research Institute, Roosevelt Ave. Tupper Bldg. 401, Panama, Rep. of Panama
| | - Marta Vargas
- Smithsonian Tropical Research Institute, Roosevelt Ave. Tupper Bldg. 401, Panama, Rep. of Panama
| | - Hans C E Larsson
- McGill University, Redpath Museum 859 Sherbrooke Street West, Montreal, Quebec, H3A 0C4, Canada
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Roosevelt Ave. Tupper Bldg. 401, Panama, Rep. of Panama
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18
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Sun J, Ma PC, Cheng HZ, Wang CZ, Li YL, Cui YQ, Yao HB, Wen SQ, Wei LH. Post- last glacial maximum expansion of Y-chromosome haplogroup C2a-L1373 in northern Asia and its implications for the origin of Native Americans. Am J Phys Anthropol 2021; 174:363-374. [PMID: 33241578 DOI: 10.1002/ajpa.24173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 10/10/2020] [Accepted: 11/04/2020] [Indexed: 02/05/2023]
Abstract
OBJECTIVES Subbranches of Y-chromosome haplogroup C2a-L1373 are founding paternal lineages in northern Asia and Native American populations. Our objective was to investigate C2a-L1373 differentiation in northern Asia and its implications for Native American origins. MATERIALS AND METHODS Sequences of rare subbranches (n = 43) and ancient individuals (n = 37) of C2a-L1373 (including P39 and MPB373), were used to construct phylogenetic trees with age estimation by BEAST software. RESULTS C2a-L1373 expanded rapidly approximately 17.7,000-14.3,000 years ago (kya) after the last glacial maximum (LGM), generating numerous sublineages which became founding paternal lineages of modern northern Asian and Native American populations (C2a-P39 and C2a-MPB373). The divergence pattern supports possible initiation of differentiation in low latitude regions of northern Asia and northward diffusion after the LGM. There is a substantial gap between the divergence times of C2a-MPB373 (approximately 22.4 or 17.7 kya) and C2a-P39 (approximately 14.3 kya), indicating two possible migration waves. DISCUSSION We discussed the decreasing time interval of "Beringian standstill" (2.5 ky or smaller) and its reduced significance. We also discussed the multiple possibilities for the peopling of the Americas: the "Long-term Beringian standstill model," the "Short-term Beringian standstill model," and the "Multiple waves of migration model." Our results support the argument from ancient DNA analyses that the direct ancestor group of Native Americans is an admixture of "Ancient Northern Siberians" and Paleolithic communities from the Amur region, which appeared during the post-LGM era, rather than ancient populations in greater Beringia, or an adjacent region, before the LGM.
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Affiliation(s)
- Jin Sun
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
- Xingyi Normal University for Nationalities, Xingyi, China
| | - Peng-Cheng Ma
- School of Life Sciences, Jilin University, Changchun, China
| | - Hui-Zhen Cheng
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | - Chi-Zao Wang
- Department of Radiology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Yong-Lan Li
- School of Ethnology and Anthropology, Inner Mongolia Normal University, Hohhot, China
| | - Yin-Qiu Cui
- School of Life Sciences, Jilin University, Changchun, China
| | - Hong-Bin Yao
- Key Laboratory of Evidence Science of Gansu Province, Gansu University of Political Science and Law, Lanzhou, China
| | - Shao-Qing Wen
- Institute of Archaeological Science, Fudan University, Shanghai, China
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
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19
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Branco C, Ray N, Currat M, Arenas M. Influence of Paleolithic range contraction, admixture and long-distance dispersal on genetic gradients of modern humans in Asia. Mol Ecol 2020; 29:2150-2159. [PMID: 32436243 DOI: 10.1111/mec.15479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 12/29/2022]
Abstract
Cavalli-Sforza and coauthors originally explored the genetic variation of modern humans throughout the world and observed an overall east-west genetic gradient in Asia. However, the specific environmental and population genetics processes causing this gradient were not formally investigated and promoted discussion in recent studies. Here we studied the influence of diverse environmental and population genetics processes on Asian genetic gradients and identified which could have produced the observed gradient. To do so, we performed extensive spatially-explicit computer simulations of genetic data under the following scenarios: (a) variable levels of admixture between Paleolithic and Neolithic populations, (b) migration through long-distance dispersal (LDD), (c) Paleolithic range contraction induced by the last glacial maximum (LGM), and (d) Neolithic range expansions from one or two geographic origins (the Fertile Crescent and the Yangzi and Yellow River Basins). Next, we estimated genetic gradients from the simulated data and we found that they were sensible to the analysed processes, especially to the range contraction induced by LGM and to the number of Neolithic expansions. Some scenarios were compatible with the observed east-west genetic gradient, such as the Paleolithic expansion with a range contraction induced by the LGM or two Neolithic range expansions from both the east and the west. In general, LDD increased the variance of genetic gradients among simulations. We interpreted the obtained gradients as a consequence of both allele surfing caused by range expansions and isolation by distance along the vast east-west geographic axis of this continent.
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Affiliation(s)
- Catarina Branco
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.,Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain
| | - Nicolas Ray
- GeoHealth Group, Institute of Global Health, University of Geneva, Geneva, Switzerland.,Institute for Environmental Sciences, University of Geneva, Geneva, Switzerland
| | - Mathias Currat
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.,Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain
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20
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De la Rosa-Conroy L, Gasca-Pineda J, Bello-Bedoy R, Eguiarte LE, Arteaga MC. Genetic patterns and changes in availability of suitable habitat support a colonisation history of a North American perennial plant. Plant Biol (Stuttg) 2020; 22:233-242. [PMID: 31603263 DOI: 10.1111/plb.13053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/14/2019] [Indexed: 06/10/2023]
Abstract
Climatic fluctuations during the Pleistocene influenced the geographical distribution of plant species across the southern region of California. Following an integrative approach, we combined genetic data analysis with Environmental Niche Models (ENMs) to assess the historical range expansion of Yucca schidigera, a long-lived desert perennial native of the Baja California Peninsula. We genotyped 240 individuals with seven nuclear microsatellite to investigate genetic diversity distribution across 13 populations. Indeed, we used Environmental Niche Models to examine the changes on the distribution of suitable climatic conditions for this species during the LIG (~120 ka), LGM (~22 ka) and Mid Holocene (~6 ka). We detected high genetic diversity across Y. schidigera populations (AR = 9.94 ± 0.38 SE; Hexp = 0.791 ± 0.011 SE) with genetic variation decreasing significantly with latitude (allelic richness: R 2 = 0.38, P = 0.023; expected heterocigosity: R2 = 0.32, P = 0.042). We observed low, but significant genetic differentiation (FST = 0.0678; P < 0.001) which was consistent with the parapatric distribution of the three genetic groupings detected by the Bayesian clustering algorithm. The ENMs suggest that suitable habitat for this species increased since the LGM. Our results support a range expansion of Y. schidigera across northwestern Baja California during the late Quaternary. Genetic data suggest that colonization of the current distribution followed a southward directionality as suitable climatic conditions became widely available in this region. High genetic variation across our sample suggests large historic effective population sizes for this section of the geographical range.
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Affiliation(s)
- L De la Rosa-Conroy
- Departamento de Biología de la Conservación, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, México
| | - J Gasca-Pineda
- Departamento de Biología de la Conservación, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, México
| | - R Bello-Bedoy
- Facultad de Ciencias, Universidad Autónoma de Baja California, Ensenada, Baja California, México
| | - L E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - M C Arteaga
- Departamento de Biología de la Conservación, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, México
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21
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Napier JD, Fernandez MC, de Lafontaine G, Hu FS. Ice-age persistence and genetic isolation of the disjunct distribution of larch in Alaska. Ecol Evol 2020; 10:1692-1702. [PMID: 32076544 PMCID: PMC7029070 DOI: 10.1002/ece3.6031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/18/2019] [Accepted: 01/06/2020] [Indexed: 01/07/2023] Open
Abstract
Larix laricina (eastern larch, tamarack) is a transcontinental North American conifer with a prominent disjunction in the Yukon isolating the Alaskan distribution from the rest of its range. We investigate whether in situ persistence during the last glacial maximum (LGM) or long-distance postglacial migration from south of the ice sheets resulted in the modern-day Alaskan distribution. We analyzed variation in three chloroplast DNA regions of 840 trees from a total of 69 populations (24 new sampling sites situated on both sides of the Yukon range disjunction pooled with 45 populations from a published source) and conducted ensemble species distribution modeling (SDM) throughout Canada and United States to hindcast the potential range of L. laricina during the LGM. We uncovered the genetic signature of a long-term isolation of larch populations in Alaska, identifying three endemic chlorotypes and low levels of genetic diversity. Range-wide analysis across North America revealed the presence of a distinct Alaskan lineage. Postglacial gene flow across the Yukon divide was unidirectional, from Alaska toward previously glaciated Canadian regions, and with no evidence of immigration into Alaska. Hindcast SDM indicates one of the broadest areas of past climate suitability for L. laricina existed in central Alaska, suggesting possible in situ persistence of larch in Alaska during the LGM. Our results provide the first unambiguous evidence for the long-term isolation of L. laricina in Alaska that extends beyond the last glacial period and into the present interglacial period. The lack of gene flow into Alaska along with the overall probability of larch occurrence in Alaska being currently lower than during the LGM suggests that modern-day Alaskan larch populations are isolated climate relicts of broader glacial distributions, and so are particularly vulnerable to current warming trends.
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Affiliation(s)
- Joseph D. Napier
- Department of Plant BiologyUniversity of IllinoisUrbanaILUSA
- Department of Integrative BiologyThe University of Texas at AustinAustinTXUSA
| | | | - Guillaume de Lafontaine
- Canada Research Chair in Integrative Biology of Northern FloraUniversité du Québec à RimouskiRimouskiQCCanada
| | - Feng Sheng Hu
- Department of Plant BiologyUniversity of IllinoisUrbanaILUSA
- Department of GeologyUniversity of IllinoisUrbanaILUSA
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Morrison BD, Heath K, Greenberg JA. Spatial scale affects novel and disappeared climate change projections in Alaska. Ecol Evol 2019; 9:12026-12044. [PMID: 31844515 PMCID: PMC6854118 DOI: 10.1002/ece3.5511] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 07/02/2019] [Accepted: 07/08/2019] [Indexed: 11/23/2022] Open
Abstract
The formation of novel and disappeared climates between the last glacial maximum (LGM) and the present is important to consider to understand the expansion and contraction of species niches and distributions, as well as the formation and loss of communities and ecological interactions over time. Our choice in climate data resolution has the potential to complicate predictions of the ecological impacts of climate change, since climate varies from local to global scales and this spatial variation is reflected in climate data. To address this issue, we downscaled LGM and modern (1975-2005) 30-year averaged climate data to 60-m resolution for the entire state of Alaska for 10 different climate variables, and then upsampled each variable to coarser resolutions (60 m to 12 km). We modeled the distributions of novel and disappeared climates to evaluate the locations and fractional area of novel and disappeared climates for each of our climate variables and resolutions. Generally, novel and disappeared climates were located in southern Alaska, although there were cases where some disappeared climates existed within coastal and interior Alaska. Climate resolution affected the fractional area of novel and disappeared climates in three patterns: As the spatial resolution of climate became coarser, the fractional area of novel and disappeared climates (a) increased, (b) decreased, or (c) had no explainable relationship. Overall, we found the use of coarser climate data increased the fractional area of novel and disappeared climates due to decreased environmental variability and removal of climate extremes. Our results reinforce the importance of downscaling coarse climate data and suggest that studies analyzing the effects of climate change on ecosystems may overestimate or underestimate their conclusions when utilizing coarse climate data.
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Affiliation(s)
- Bailey D. Morrison
- Environmental and Climate Sciences DepartmentBrookhaven National LaboratoryUptonNew York
| | - Katy Heath
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinois
| | - Jonathan A. Greenberg
- Department of Natural Resources and Environmental ScienceUniversity of Nevada, RenoRenoNevada
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Yamaura Y, Narita A, Kusumoto Y, Nagano AJ, Tezuka A, Okamoto T, Takahara H, Nakamura F, Isagi Y, Lindenmayer D. Genomic reconstruction of 100 000-year grassland history in a forested country: population dynamics of specialist forbs. Biol Lett 2019; 15:20180577. [PMID: 31138096 PMCID: PMC6548723 DOI: 10.1098/rsbl.2018.0577] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Grassland ecosystems worldwide have been extensively converted to other land uses and are globally imperiled. Because many grasslands have been maintained by human activities, understanding their origin and history is fundamentally important to better contemporary management. However, existing methods to reconstruct past vegetation can produce contrasting views on grassland history. Here, we inferred demographic histories of 40 populations of four grassland forb species throughout Japan using high-resolution genome sequences and model-flexible demographic simulation based on the site frequency spectrum. Although two species showed a slight decline in population size between 100 000–10 000 years ago, our results suggest that population sizes of studied species have been maintained within the range of 0.5–2.0 times the most recent estimates for at least 100 000 years across Japan. Our results suggest that greater than 90% declines in Japanese grasslands and subsequent losses of grassland species in the last 100 years are geologically and biologically important and will have substantial consequences for Japanese biota and culture. People have had critical roles in maintaining disturbance-dependent grassland ecosystems and biota in this warm and wet forested country. In these contexts, disturbances associated with forest harvesting and traditional extensive farming have the potential to maintain grassland ecosystems and can provide important opportunities to reconcile resource production and conservation of grassland biodiversity.
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Affiliation(s)
- Yuichi Yamaura
- 1 Graduate School of Agriculture, Hokkaido University , Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589 , Japan.,2 Department of Forest Vegetation, Forestry and Forest Products Research Institute , 1 Matunosato, Tsukuba, Ibaraki 305-8687 , Japan.,3 Fenner School of Environment and Society, Australian National University , Canberra, ACT 2601 , Australia
| | - Ayu Narita
- 4 Graduate School of Agriculture, Kyoto University , Kyoto 606-8502 , Japan.,5 Forestry Research Institute, Hokkaido Research Organization , Bibai, Hokkaido 079-0198 , Japan
| | - Yoshinobu Kusumoto
- 6 Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization , 3-1-3 Kannondai, Tsukuba, Ibaraki 305-8604 , Japan.,7 Western Region Agricultural Research Center, National Agriculture and Food Research Organization , 2575 Senyu-cho, Zentsuji, Kagawa 765-0053 , Japan
| | - Atsushi J Nagano
- 8 Department of Plant Life Science, Faculty of Agriculture, Ryukoku University , Otsu, Shiga 520-2194 , Japan
| | - Ayumi Tezuka
- 8 Department of Plant Life Science, Faculty of Agriculture, Ryukoku University , Otsu, Shiga 520-2194 , Japan
| | - Toru Okamoto
- 9 Kansai Research Center, Forestry and Forest Products Research Institute , 68 Nagaikyutaroh, Momoyama, Fushimi, Kyoto, Kyoto 612-0855 , Japan
| | - Hikaru Takahara
- 10 Graduate School of Life and Environmental Sciences, Kyoto Prefectural University , 1-5 Hangi, Shimogamo, Sakyo, Kyoto 606-8522 , Japan
| | - Futoshi Nakamura
- 1 Graduate School of Agriculture, Hokkaido University , Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589 , Japan
| | - Yuji Isagi
- 4 Graduate School of Agriculture, Kyoto University , Kyoto 606-8502 , Japan
| | - David Lindenmayer
- 3 Fenner School of Environment and Society, Australian National University , Canberra, ACT 2601 , Australia
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Diringer B, Pretell K, Avellan R, Chanta C, Cedeño V, Gentile G. Genetic structure, phylogeography, and demography of Anadara tuberculosa (Bivalvia) from East Pacific as revealed by mtDNA: Implications to conservation. Ecol Evol 2019; 9:4392-4402. [PMID: 31031914 PMCID: PMC6476791 DOI: 10.1002/ece3.4937] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 09/27/2018] [Accepted: 11/20/2018] [Indexed: 11/22/2022] Open
Abstract
Wild populations of the pustulose ark, Anadara tuberculosa (Bivalvia), an emblematic species of the East Pacific mangrove ecosystem declined in South American countries (Colombia, Ecuador, and Peru) mainly due to overharvesting and habitat loss or degradation. Understanding the genetic aspects of geographic variations and population structure of A. tuberculosa, currently unknown, appears as a priority to fishery authorities in order to elaborate integrated and collaborative conservation policies for fishery management, aquaculture, and stock enhancement programs. We used mtDNA sequence data to investigate haplotype diversity, genetic structure, and demography of A. tuberculosa. Results indicate genetic homogeneity of populations distributed north and south of the equator, respectively. However, statistically significant differentiation emerged between northern and southern populations with pairwise ф ST values ranging between 0.036 and 0.092. The oceanic current system acting in the area (Panama Current and Humboldt Current) might play a role in limiting the larval dispersal of the species, still poorly understood. Demography reconstruction supported recent population expansion, possibly started after last glacial maximum. Our results would suggest separate and independent management of populations north and south of the equator.
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Affiliation(s)
- Benoit Diringer
- IncabiotecTumbesPeru
- Universidad Nacional de TumbesTumbesPeru
| | - Krizia Pretell
- Universidad Nacional de TumbesTumbesPeru
- Cienciactiva‐ConcytecLimaPeru
| | | | | | - Virna Cedeño
- IncabiotecTumbesPeru
- Universidad Nacional de TumbesTumbesPeru
- Concepto AzulGuayaquilEcuador
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Koparde P, Mehta P, Mukherjee S, Robin VV. Quaternary climatic fluctuations and resulting climatically suitable areas for Eurasian owlets. Ecol Evol 2019; 9:4864-4874. [PMID: 31031949 PMCID: PMC6476768 DOI: 10.1002/ece3.5086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 02/24/2019] [Accepted: 02/26/2019] [Indexed: 11/10/2022] Open
Abstract
AIM The nested pattern in the geographical distribution of three Indian owlets, resulting in a gradient of endemicity, is hypothesized to be an impact of historical climate change. In current time, the Forest Owlet Athene blewitti is endemic to central India, and its range is encompassed within the ranges of the Jungle Owlet Glaucidium radiatum (distributed through South Asia) and Spotted Owlet Athene brama (distributed through Iran, South and Southeast Asia). Another phylogenetically close species, Little Owl Athene noctua, which is largely Palearctic in distribution, is hypothesized to have undergone severe range reduction during the Last Glacial Maximum, showing a postglacial expansion. The present study tests hypotheses on the possible role of Quaternary climatic fluctuations in shaping geographical ranges of owlets. METHODS We used primary field observations, open access data, and climatic niche modeling to construct climatic niches of four owlets for four periods, the Last Interglacial (~120-140 Ka), Last Glacial Maximum (~22 Ka), Mid-Holocene (~6 Ka), and Current (1960-1990). We performed climatic niche extent, breadth, and overlap analyses and tested if climatically suitable areas for owlets are nested in a relatively stable climate. RESULTS Climatically suitable areas for all owlets examined underwent cycles of expansion and reduction or a gradual expansion or reduction since the Last Interglacial. The Indian owlets show significant climatic niche overlap in the current period. Climatically suitable areas for Little Owl shifted southwards during the Last Glacial Maximum and expanded northwards in the postglaciation period. For each owlet, the modeled climatic niches were nested in climatically stable areas. MAIN CONCLUSIONS The study highlights the impact of Quaternary climate change in shaping the present distribution of owlets. This is relevant to the current scenario of climate change and global warming and can help inform conservation strategies, especially for the extremely range-restricted Forest Owlet.
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Affiliation(s)
- Pankaj Koparde
- Division of Conservation BiologySálim Ali Centre for Ornithology and Natural HistoryCoimbatoreIndia
- Manipal Academy of Higher EducationManipalIndia
- Indian Institute of Science Education and Research (IISER)TirupatiIndia
| | - Prachi Mehta
- Wildlife Research and Conservation SocietyPuneIndia
| | - Shomita Mukherjee
- Division of Conservation BiologySálim Ali Centre for Ornithology and Natural HistoryCoimbatoreIndia
| | - V. V. Robin
- Indian Institute of Science Education and Research (IISER)TirupatiIndia
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Ye JW, Zhang ZK, Wang HF, Bao L, Ge JP. Phylogeography of Schisandra chinensis (Magnoliaceae) Reveal Multiple Refugia With Ample Gene Flow in Northeast China. Front Plant Sci 2019; 10:199. [PMID: 30858859 PMCID: PMC6397880 DOI: 10.3389/fpls.2019.00199] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/05/2019] [Indexed: 05/14/2023]
Abstract
Temperate conifers and broadleaved mixed forests in northeast China are ideal to investigate the genetic consequences of climate changes during the last glacial maximum (LGM), 29 - 16 kya. As previous studies were focused on tree species with long generation time; here, the evolutionary history of Schisandra chinensis, a climber species with a generation time of five years, was investigated using chloroplast DNA (cpDNA), nuclear single copy gene (nSCG), and nuclear single sequence repeats (nSSRs, i.e., microsatellite) markers, along with ecological niche modeling (ENM), which predicted a suitable habitat in Korea Peninsula (KP) during the LGM. Private haplotypes and high genetic diversity of both cpDNA and nSCG were mainly found in KP and Changbai Mt. (CB). Although no significant phylogeographic structure was detected in the cpDNA and nSCG, three nSSRs clusters roughly distributed in west (CB and KP), east (north China), and north (Xiaoxing'an Range, XR) regions were found in Structure analysis. The approximate Bayesian computation analysis showed the west cluster diverged at 35.45 kya, and the other two clusters at 19.85 kya. The genetic diversity calculated for each of the three markers showed no significant correlation with latitude. Genetic differentiation of nSSRs was also not correlated with geographic distance. Migrate analysis estimated extensive gene flow between almost all genetic cluster pairs and BOTTLENECK analysis showed that few populations experienced severe bottlenecks. Overall, results indicate that S. chinensis survived the LGM in situ in multiple refugia, which likely include two macrorefugia (KP and CB) and two microrefugia (XR and north China). Extensive postglacial gene flow among the three nSSRs clusters led to uniformly distributed genetic diversity and low genetic differentiation.
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Affiliation(s)
- Jun-Wei Ye
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Ze-Kun Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Hong-Fang Wang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Lei Bao
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Jian-Ping Ge
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
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Glasnović P, Temunović M, Lakušić D, Rakić T, Grubar VB, Surina B. Understanding biogeographical patterns in the western Balkan Peninsula using environmental niche modelling and geostatistics in polymorphic Edraianthus tenuifolius. AoB Plants 2018; 10:ply064. [PMID: 30425822 PMCID: PMC6220721 DOI: 10.1093/aobpla/ply064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 10/09/2018] [Indexed: 06/09/2023]
Abstract
The Balkan Peninsula represents one of the three southern European glacial refugia where biodiversity persisted throughout the climatically unstable Quaternary. This study considered the 'refugia within refugia' model, which assumes the environmental heterogeneity over time and space in larger refugia. To better understand patterns shaped during the Quaternary climatic oscillations, the present and last glacial maximum (LGM) environmental conditions and current morphological variability of Edraianthus tenuifolius, an endemic plant of the western Balkans with a well-known therphical structure, were considered. Potential present and LGM distributions were studied through environmental niche modelling using 161 data of occurrences and six bioclimatic variables, hindcasting the model to LGM conditions using three different global circulation models. To test the geographical variability of the reproductive region, 41 characters of 667 inflorescences from 35 populations within the distribution range were measured. Geographical patterns, using geostatistics together with univariate and multivariate statistical approaches, were analysed. The environmental niche model suggested the current potential distribution in correspondence to its known occurrences. The hindcast to LGM conditions suggested two separate areas of environmental suitability, one in the present-day northern Adriatic coast of Croatia (Istrian Peninsula, Kvarner) and another on the present-day south-eastern Adriatic coast (southern Dalmatia, Montenegro and northern Albania). Morphological variability showed a similar pattern, where southern populations separated from northern populations according to a major split in the central part of its distribution range (central Dalmatia). On other levels, stronger barriers were predicted to separate northern populations from the eastern Istrian Peninsula and the Kvarner area. The results suggested congruent biogeographical patterns to the already known phylogeographical structure. Both environmental niche modelling and the geographical variability of morphological characters suggested spatial partitioning, indicating the potential presence of two separate refugia during the LGM.
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Affiliation(s)
- Peter Glasnović
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška, Koper, Slovenia
| | - Martina Temunović
- Faculty of Forestry, Department of Forest Genetics, Dendrology and Botany, University of Zagreb, Svetošimunska, Zagreb, Croatia
| | - Dmitar Lakušić
- Faculty of Biology, Institute of Botany and Botanical Garden ‘Jevremovac’, University of Belgrade, Takovska, Belgrade, Serbia
| | - Tamara Rakić
- Faculty of Biology, Institute of Botany and Botanical Garden ‘Jevremovac’, University of Belgrade, Takovska, Belgrade, Serbia
| | | | - Boštjan Surina
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška, Koper, Slovenia
- Natural History Museum Rijeka, Lorenzov Prolaz, Rijeka, Croatia
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28
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Branco C, Arenas M. Selecting among Alternative Scenarios of Human Evolution by Simulated Genetic Gradients. Genes (Basel) 2018; 9:E506. [PMID: 30340387 DOI: 10.3390/genes9100506] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/11/2018] [Accepted: 10/16/2018] [Indexed: 11/16/2022] Open
Abstract
Selecting among alternative scenarios of human evolution is nowadays a common methodology to investigate the history of our species. This strategy is usually based on computer simulations of genetic data under different evolutionary scenarios, followed by a fitting of the simulated data with the real data. A recent trend in the investigation of ancestral evolutionary processes of modern humans is the application of genetic gradients as a measure of fitting, since evolutionary processes such as range expansions, range contractions, and population admixture (among others) can lead to different genetic gradients. In addition, this strategy allows the analysis of the genetic causes of the observed genetic gradients. Here, we review recent findings on the selection among alternative scenarios of human evolution based on simulated genetic gradients, including pros and cons. First, we describe common methodologies to simulate genetic gradients and apply them to select among alternative scenarios of human evolution. Next, we review previous studies on the influence of range expansions, population admixture, last glacial period, and migration with long-distance dispersal on genetic gradients for some regions of the world. Finally, we discuss this analytical approach, including technical limitations, required improvements, and advice. Although here we focus on human evolution, this approach could be extended to study other species.
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Koch JB, Vandame R, Mérida‐Rivas J, Sagot P, Strange J. Quaternary climate instability is correlated with patterns of population genetic variability in Bombus huntii. Ecol Evol 2018; 8:7849-7864. [PMID: 30250668 PMCID: PMC6145020 DOI: 10.1002/ece3.4294] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 05/03/2018] [Accepted: 05/18/2018] [Indexed: 11/20/2022] Open
Abstract
Climate oscillations have left a significant impact on the patterns of genetic diversity observed in numerous taxa. In this study, we examine the effect of Quaternary climate instability on population genetic variability of a bumble bee pollinator species, Bombus huntii in western North America. Pleistocene and contemporary B. huntii habitat suitability (HS) was estimated with an environmental niche model (ENM) by associating 1,035 locality records with 10 bioclimatic variables. To estimate genetic variability, we genotyped 380 individuals from 33 localities at 13 microsatellite loci. Bayesian inference was used to examine population structure with and without a priori specification of geographic locality. We compared isolation by distance (IBD) and isolation by resistance (IBR) models to examine population differentiation within and among the Bayesian inferred genetic clusters. Furthermore, we tested for the effect of environmental niche stability (ENS) on population genetic diversity with linear regression. As predicted, high-latitude B. huntii habitats exhibit low ENS when compared to low-latitude habitats. Two major genetic clusters of B. huntii inhabit western North America: (a) a north genetic cluster predominantly distributed north of 28°N and (b) a south genetic cluster distributed south of 28°N. In the south genetic cluser, both IBD and IBR models are significant. However, in the north genetic cluster, IBD is significant but not IBR. Furthermore, the IBR models suggest that low-latitude montane populations are surrounded by habitat with low HS, possibly limiting dispersal, and ultimately gene flow between populations. Finally, we detected high genetic diversity across populations in regions that have been climatically unstable since the last glacial maximum (LGM), and low genetic diversity across populations in regions that have been climatically stable since the LGM. Understanding how species have responded to climate change has the potential to inform management and conservation decisions of both ecological and economic concerns.
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Affiliation(s)
- Jonathan B. Koch
- Department of BiologyUtah State UniversityLoganUtah
- Pollinating Insects Research UnitUSDA‐ARS‐PWALoganUtah
| | - Rémy Vandame
- Departamento Agricultura Sociedad y AmbienteEl Colegio de la Frontera SurSan Cristóbal de Las CasasChiapasMexico
| | - Jorge Mérida‐Rivas
- Departamento Agricultura Sociedad y AmbienteEl Colegio de la Frontera SurSan Cristóbal de Las CasasChiapasMexico
| | - Philippe Sagot
- Departamento Agricultura Sociedad y AmbienteEl Colegio de la Frontera SurSan Cristóbal de Las CasasChiapasMexico
| | - James Strange
- Pollinating Insects Research UnitUSDA‐ARS‐PWALoganUtah
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Li Q, Kou X, Beierkuhnlein C, Liu S, Ge J. Global patterns of nonanalogous climates in the past and future derived from thermal and hydraulic factors. Glob Chang Biol 2018; 24:2463-2475. [PMID: 29476633 DOI: 10.1111/gcb.14104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 01/28/2018] [Accepted: 01/30/2018] [Indexed: 06/08/2023]
Abstract
Nonanalogous climates (NACs), climates without modern analogs on Earth, challenge our understanding of eco-evolutionary processes that shape global biodiversity, particularly because of their propensity to promote novel ecosystems. However, NAC studies are generally inadequate and partial. Specifically, systematic comparisons between the future and the past are generally lacking, and hydraulic NACs tend to be underemphasized. In the present study, by adopting a frequency distribution-based method that facilitates the procedures of contributions parsing and conducting multiple comparisons, we provide a global overview of multidimensional NACs for both the past and the future within a unified framework. We show that NACs are globally prevalent, covering roughly half of the land area across the time-periods under investigation, and have a high degree of spatial structure. Patterns of NACs differ dramatically between the past and the future. Hydraulic NACs are more complex both in spatial patterns and in major contributions of variables than are thermal NACs. However, hydraulic NACs are more predictable than originally thought. Generally, hydraulic NACs in the future (2100 AD) exhibit comparable predictability to thermal NACs in the last glacial maximum (LGM) (21k BP). Identifying these NAC patterns has potential implications on climate-adaptive managements and preparing in advance to possibly frequent novel ecosystems. However, a learning-from-the-past strategy might be of limited utility for management under present circumstances.
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Affiliation(s)
- Qin Li
- College of Life Sciences, Beijing Normal University, Beijing, China
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Xiaojun Kou
- College of Life Sciences, Beijing Normal University, Beijing, China
- Key Laboratory for Biodiversity Science and Ecological Engineering of Ministry of Education, Beijing Normal University, Beijing, China
| | - Carl Beierkuhnlein
- Department of Biogeography, BayCEER, GIB, University of Bayreuth, Bayreuth, Germany
| | - Shirong Liu
- Key Laboratory of China's State Forestry Administration for Forest Ecology and Environment, Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Jianping Ge
- College of Life Sciences, Beijing Normal University, Beijing, China
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Kohlmann B, Arriaga-Jiménez A, Rös M. Dung beetle vicariant speciation in the mountains of Oaxaca, Mexico, with a description of a new species of Phanaeus (Coleoptera, Geotrupidae, Scarabaeidae). Zookeys 2018:67-93. [PMID: 29670437 PMCID: PMC5904386 DOI: 10.3897/zookeys.743.23029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/11/2018] [Indexed: 11/12/2022] Open
Abstract
An analysis of vicariant speciation of Geotrupes and Phanaeus (Coleoptera, Geotrupidae, Scarabaeidae) from the mountains of Oaxaca, Mexico is undertaken. The new species of dung beetle (Coleoptera: Scarabaeidae) from Oaxaca, Mexico, Phanaeusdionysiussp. n. is described. Photos of the habitus and a distribution map are provided. Phanaeusmalyi Arnaud is revalidated. An updated key for the Phanaeusendymion species group and new localities are also presented. An updated key for the Geotrupes of Oaxaca and new locality records are also submitted.
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Affiliation(s)
- Bert Kohlmann
- Universidad EARTH, AP 4442-1000, San José, Costa Rica
| | | | - Matthias Rös
- CONACYT, CIIDIR-Oaxaca, Instituto Politécnico Nacional, México
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32
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Pfanzelt S, Albach DC, von Hagen KB. Tabula rasa in the Patagonian Channels? The phylogeography of Oreobolus obtusangulus (Cyperaceae). Mol Ecol 2017; 26:4027-4044. [PMID: 28437593 DOI: 10.1111/mec.14156] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 04/06/2017] [Indexed: 11/29/2022]
Abstract
The extent of the Pleistocene glaciations in the Patagonian Channel region (southwesternmost South America) and their impact on the vegetation there are largely unknown. Whether the regional flora was wiped out completely (tabula rasa) or survived in ice-free pockets (in situ survival) is still an open question. The molecular imprint of either scenario should still be visible in extant populations. Therefore, DNA sequence data of Oreobolus obtusangulus Gaudich. (Cyperaceae) were analysed. This species is an abundant constituent of Patagonian cushion peat bogs, one of the Patagonian Channel region's major vegetation types. Three hundred and eighty-four individuals from 48 populations were sequenced for two chloroplast (ycf3-psaA and trnQUUG -psbK intergenic spacers) and 14 nuclear loci containing simple sequence repeats (SSRs; microsatellites). Phylogenetic reconstructions and the geographic distribution of genetic diversity revealed that the species was split into three main lineages whose general distributions comprise three separate major regions, that is, south-central Chile, Fuego-Patagonia and the East Patagonian Andes, which probably constitute glacial refugia. Postglacial migration fronts formed a suture zone with high levels of genetic diversity in the Northwest Patagonian Andes, where remnants of a supposedly ancestral lineage were also found to be locally restricted to a single population (Huinay). The heavily glaciated Patagonian Channels were likely recolonized from the northwest, and partly from the south. Although the westernmost Patagonian Channel population (Estero Bachem) harboured private SSR alleles (singletons) and showed slightly elevated genetic diversity, it remained unclear whether this population actually survived in situ. This study helps fill a major gap in reconstructing the Pleistocene vegetation history of West and Andean Patagonia.
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Affiliation(s)
- Simon Pfanzelt
- Institute of Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Dirk C Albach
- Institute of Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Klaus Bernhard von Hagen
- Institute of Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
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Patel RP, Förster DW, Kitchener AC, Rayan MD, Mohamed SW, Werner L, Lenz D, Pfestorf H, Kramer-Schadt S, Radchuk V, Fickel J, Wilting A. Two species of Southeast Asian cats in the genus Catopuma with diverging histories: an island endemic forest specialist and a widespread habitat generalist. R Soc Open Sci 2016; 3:160350. [PMID: 27853549 PMCID: PMC5098974 DOI: 10.1098/rsos.160350] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 09/13/2016] [Indexed: 06/06/2023]
Abstract
Background. The bay cat Catopuma badia is endemic to Borneo, whereas its sister species the Asian golden cat Catopuma temminckii is distributed from the Himalayas and southern China through Indochina, Peninsular Malaysia and Sumatra. Based on morphological data, up to five subspecies of the Asian golden cat have been recognized, but a taxonomic assessment, including molecular data and morphological characters, is still lacking. Results. We combined molecular data (whole mitochondrial genomes), morphological data (pelage) and species distribution projections (up to the Late Pleistocene) to infer how environmental changes may have influenced the distribution of these sister species over the past 120 000 years. The molecular analysis was based on sequenced mitogenomes of 3 bay cats and 40 Asian golden cats derived mainly from archival samples. Our molecular data suggested a time of split between the two species approximately 3.16 Ma and revealed very low nucleotide diversity within the Asian golden cat population, which supports recent expansion of the population. Discussion. The low nucleotide diversity suggested a population bottleneck in the Asian golden cat, possibly caused by the eruption of the Toba volcano in Northern Sumatra (approx. 74 kya), followed by a continuous population expansion in the Late Pleistocene/Early Holocene. Species distribution projections, the reconstruction of the demographic history, a genetic isolation-by-distance pattern and a gradual variation of pelage pattern support the hypothesis of a post-Toba population expansion of the Asian golden cat from south China/Indochina to Peninsular Malaysia and Sumatra. Our findings reject the current classification of five subspecies for the Asian golden cat, but instead support either a monotypic species or one comprising two subspecies: (i) the Sunda golden cat, distributed south of the Isthmus of Kra: C. t. temminckii and (ii) Indochinese, Indian, Himalayan and Chinese golden cats, occurring north of the Isthmus: C. t. moormensis.
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Affiliation(s)
- Riddhi P. Patel
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Strasse 17, 10315 Berlin, Germany
- Freie Universität Berlin, Kaiserswerther Strasse 16–18, 14195 Berlin, Germany
| | - Daniel W. Förster
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Strasse 17, 10315 Berlin, Germany
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK
- Institute of Geography, School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH8 9XP, UK
| | - Mark D. Rayan
- WWF Malaysia, 1 Jalan PJS 5/28A, Petaling Jaya Commercial Centre (PJCC), 46150 Petaling Jaya, Selangor, Malaysia
| | - Shariff W. Mohamed
- WWF Malaysia, 1 Jalan PJS 5/28A, Petaling Jaya Commercial Centre (PJCC), 46150 Petaling Jaya, Selangor, Malaysia
| | - Laura Werner
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Strasse 17, 10315 Berlin, Germany
| | - Dorina Lenz
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Strasse 17, 10315 Berlin, Germany
| | - Hans Pfestorf
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Strasse 17, 10315 Berlin, Germany
| | - Stephanie Kramer-Schadt
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Strasse 17, 10315 Berlin, Germany
| | - Viktoriia Radchuk
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Strasse 17, 10315 Berlin, Germany
| | - Jörns Fickel
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Strasse 17, 10315 Berlin, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24–25, 14476 Potsdam, Germany
| | - Andreas Wilting
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Strasse 17, 10315 Berlin, Germany
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Meachen JA, Brannick AL, Fry TJ. Extinct Beringian wolf morphotype found in the continental U.S. has implications for wolf migration and evolution. Ecol Evol 2016; 6:3430-8. [PMID: 27252837 PMCID: PMC4870223 DOI: 10.1002/ece3.2141] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/22/2016] [Accepted: 03/27/2016] [Indexed: 11/08/2022] Open
Abstract
Pleistocene diversity was much higher than today, for example there were three distinct wolf morphotypes (dire, gray, Beringian) in North America versus one today (gray). Previous fossil evidence suggested that these three groups overlapped ecologically, but split the landscape geographically. The Natural Trap Cave (NTC) fossil site in Wyoming, USA is an ideally placed late Pleistocene site to study the geographical movement of species from northern to middle North America before, during, and after the last glacial maximum. Until now, it has been unclear what type of wolf was present at NTC. We analyzed morphometrics of three wolf groups (dire, extant North American gray, Alaskan Beringian) to determine which wolves were present at NTC and what this indicates about wolf diversity and migration in Pleistocene North America. Results show NTC wolves group with Alaskan Beringian wolves. This provides the first morphological evidence for Beringian wolves in mid‐continental North America. Their location at NTC and their radiocarbon ages suggest that they followed a temporary channel through the glaciers. Results suggest high levels of competition and diversity in Pleistocene North American wolves. The presence of mid‐continental Beringian morphotypes adds important data for untangling the history of immigration and evolution of Canis in North America.
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Affiliation(s)
- Julie A Meachen
- Anatomy Department Des Moines University 3200 Grand Ave Des Moines Iowa 50312
| | | | - Trent J Fry
- Anatomy Department Des Moines University 3200 Grand Ave Des Moines Iowa 50312
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Shintaku Y, Motokawa M. Geographic Variation in Skull Morphology of the Large Japanese Field Mice, Apodemus speciosus (Rodentia: Muridae) Revealed by Geometric Morphometric Analysis. Zoolog Sci 2016; 33:132-45. [PMID: 27032678 DOI: 10.2108/zs150082] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We analyzed geographic variation in skull morphology of the large Japanese field mouse (Apodemus speciosus) and determined changes in skull morphology that occurred during the evolutionary history of A. speciosus in relation to the estimated distribution range in the last glacial maximum (LGM). We analyzed 1,416 specimens from 78 localities using geometric morphometric techniques applied to the dorsal side of the cranium and mandible. While large variations within and among the populations in Honshu, Shikoku, and Kyushu were observed, geographic patterns were not observed. Hokkaido and peripheral island populations showed shared differentiation from the Honshu, Shikoku, and Kyushu populations with a larger skull and distinct mandible shape. In addition, these two groups also differed from each other in accumulated random shape variation. Common characteristics found in Hokkaido and peripheral island populations were considered to be the ancestral states, which were retained by geographic isolation from the main islands. Random variations in Hokkaido and the peripheral island populations were formed through stochastic processes in relation to their isolation. Characteristic morphologies widely found in the populations of Honshu, Shikoku, and Kyushu were considered to be derived states that expanded after separation from the peripheral islands. Complex geomorphology and a shift in distribution range related to climate change and altitudinal distribution are suggested to have formed the complex geographic variation in this species.
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Affiliation(s)
- Yuta Shintaku
- 1 Wildlife Research Center, Kyoto University, 2-24 Tanaka Sekidencho, Sakyo, Kyoto 606-8203, Japan.,2 Japan Monkey Centre, 26 Kanrin, Inuyama, Aichi 484-0081, Japan
| | - Masaharu Motokawa
- 3 The Kyoto University Museum, Kyoto University, Sakyo, Kyoto 606-8501, Japan
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Cotton JM, Cerling TE, Hoppe KA, Mosier TM, Still CJ. Climate, CO2, and the history of North American grasses since the Last Glacial Maximum. Sci Adv 2016; 2:e1501346. [PMID: 27051865 PMCID: PMC4820366 DOI: 10.1126/sciadv.1501346] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 02/09/2016] [Indexed: 06/01/2023]
Abstract
The spread of C4 grasses in the late Neogene is one of the most important ecological transitions of the Cenozoic, but the primary driver of this global expansion is widely debated. We use the stable carbon isotopic composition (δ(13)C) of bison and mammoth tissues as a proxy for the relative abundance of C3 and C4 vegetation in their grazing habitat to determine climatic and atmospheric CO2 controls on C4 grass distributions from the Last Glacial Maximum (LGM) to the present. We predict the spatial variability of grass δ(13)C in North America using a mean of three different methods of classification and regression tree (CART) machine learning techniques and nine climatic variables. We show that growing season precipitation and temperature are the strongest predictors of all single climate variables. We apply this CART analysis to high-resolution gridded climate data and Coupled Model Intercomparison Project (CMIP5) mean paleoclimate model outputs to produce predictive isotope landscape models ("isoscapes") for the current, mid-Holocene, and LGM average δ(13)C of grass-dominated areas across North America. From the LGM to the present, C4 grass abundances substantially increased in the Great Plains despite concurrent increases in atmospheric CO2. These results suggest that changes in growing season precipitation rather than atmospheric CO2 were critically important in the Neogene expansion of C4 grasses.
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Affiliation(s)
- Jennifer M. Cotton
- Department of Geology and Geophysics, University of Utah, Salt Lake City, UT 84112, USA
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97330, USA
- Department of Geological Sciences, California State University, Northridge, Northridge, CA 91330, USA
| | - Thure E. Cerling
- Department of Geology and Geophysics, University of Utah, Salt Lake City, UT 84112, USA
| | - Kathryn A. Hoppe
- Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98195, USA
- Department of Geology, Green River Community College, Auburn, WA 98092, USA
| | - Thomas M. Mosier
- School of Mechanical, Industrial and Manufacturing Engineering, Oregon State University, Corvallis, OR 97330, USA
| | - Christopher J. Still
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97330, USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Leite YL, Costa LP, Loss AC, Rocha RG, Batalha-Filho H, Bastos AC, Quaresma VS, Fagundes V, Paresque R, Passamani M, Pardini R. Neotropical forest expansion during the last glacial period challenges refuge hypothesis. Proc Natl Acad Sci U S A 2016; 113:1008-13. [PMID: 26755597 DOI: 10.1073/pnas.1513062113] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The forest refuge hypothesis (FRH) has long been a paradigm for explaining the extreme biological diversity of tropical forests. According to this hypothesis, forest retraction and fragmentation during glacial periods would have promoted reproductive isolation and consequently speciation in forest patches (ecological refuges) surrounded by open habitats. The recent use of paleoclimatic models of species and habitat distributions revitalized the FRH, not by considering refuges as the main drivers of allopatric speciation, but instead by suggesting that high contemporary diversity is associated with historically stable forest areas. However, the role of the emerged continental shelf on the Atlantic Forest biodiversity hotspot of eastern South America during glacial periods has been ignored in the literature. Here, we combined results of species distribution models with coalescent simulations based on DNA sequences to explore the congruence between scenarios of forest dynamics through time and the genetic structure of mammal species cooccurring in the central region of the Atlantic Forest. Contrary to the FRH predictions, we found more fragmentation of suitable habitats during the last interglacial (LIG) and the present than in the last glacial maximum (LGM), probably due to topography. We also detected expansion of suitable climatic conditions onto the emerged continental shelf during the LGM, which would have allowed forests and forest-adapted species to expand. The interplay of sea level and land distribution must have been crucial in the biogeographic history of the Atlantic Forest, and forest refuges played only a minor role, if any, in this biodiversity hotspot during glacial periods.
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Alves I, Arenas M, Currat M, Sramkova Hanulova A, Sousa VC, Ray N, Excoffier L. Long-Distance Dispersal Shaped Patterns of Human Genetic Diversity in Eurasia. Mol Biol Evol 2015; 33:946-58. [PMID: 26637555 PMCID: PMC4776706 DOI: 10.1093/molbev/msv332] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Most previous attempts at reconstructing the past history of human populations did not explicitly take geography into account or considered very simple scenarios of migration and ignored environmental information. However, it is likely that the last glacial maximum (LGM) affected the demography and the range of many species, including our own. Moreover, long-distance dispersal (LDD) may have been an important component of human migrations, allowing fast colonization of new territories and preserving high levels of genetic diversity. Here, we use a high-quality microsatellite data set genotyped in 22 populations to estimate the posterior probabilities of several scenarios for the settlement of the Old World by modern humans. We considered models ranging from a simple spatial expansion to others including LDD and a LGM-induced range contraction, as well as Neolithic demographic expansions. We find that scenarios with LDD are much better supported by data than models without LDD. Nevertheless, we show evidence that LDD events to empty habitats were strongly prevented during the settlement of Eurasia. This unexpected absence of LDD ahead of the colonization wave front could have been caused by an Allee effect, either due to intrinsic causes such as an inbreeding depression built during the expansion or due to extrinsic causes such as direct competition with archaic humans. Overall, our results suggest only a relatively limited effect of the LGM contraction on current patterns of human diversity. This is in clear contrast with the major role of LDD migrations, which have potentially contributed to the intermingled genetic structure of Eurasian populations.
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Affiliation(s)
- Isabel Alves
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland Population and Conservation Genetics Group, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Miguel Arenas
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Mathias Currat
- Anthropology, Genetics and Peopling History Lab, Department of Genetics & Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - Anna Sramkova Hanulova
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Vitor C Sousa
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nicolas Ray
- EnviroSPACE Lab, Institute for Environmental Sciences, University of Geneva, Geneva, Switzerland
| | - Laurent Excoffier
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Abstract
North American tree species, subspecies and genetic varieties have primarily evolved in a landscape of extensive continental ice and restricted temperate climate environments. Here, we reconstruct the refugial history of western North American trees since the last glacial maximum using species distribution models, validated against 3571 palaeoecological records. We investigate how modern subspecies structure and genetic diversity corresponds to modelled glacial refugia, based on a meta-analysis of allelic richness and expected heterozygosity for 473 populations of 22 tree species. We find that species with strong genetic differentiation into subspecies had widespread and large glacial refugia, whereas species with restricted refugia show no differentiation among populations and little genetic diversity, despite being common over a wide range of environments today. In addition, a strong relationship between allelic richness and the size of modelled glacial refugia (r(2) = 0.55) suggest that population bottlenecks during glacial periods had a pronounced effect on the presence of rare alleles.
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Affiliation(s)
- David R Roberts
- Department of Renewable Resources, University of Alberta, 751 General Services Building, Edmonton, Alberta, Canada T6G 2H1
| | - Andreas Hamann
- Department of Renewable Resources, University of Alberta, 751 General Services Building, Edmonton, Alberta, Canada T6G 2H1
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Dalmaris E, Ramalho CE, Poot P, Veneklaas EJ, Byrne M. A climate change context for the decline of a foundation tree species in south-western Australia: insights from phylogeography and species distribution modelling. Ann Bot 2015; 116:941-52. [PMID: 25851142 PMCID: PMC4640123 DOI: 10.1093/aob/mcv044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 03/05/2015] [Indexed: 05/06/2023]
Abstract
BACKGROUND AND AIMS A worldwide increase in tree decline and mortality has been linked to climate change and, where these represent foundation species, this can have important implications for ecosystem functions. This study tests a combined approach of phylogeographic analysis and species distribution modelling to provide a climate change context for an observed decline in crown health and an increase in mortality in Eucalyptus wandoo, an endemic tree of south-western Australia. METHODS Phylogeographic analyses were undertaken using restriction fragment length polymorphism analysis of chloroplast DNA in 26 populations across the species distribution. Parsimony analysis of haplotype relationships was conducted, a haplotype network was prepared, and haplotype and nucleotide diversity were calculated. Species distribution modelling was undertaken using Maxent models based on extant species occurrences and projected to climate models of the last glacial maximum (LGM). KEY RESULTS A structured pattern of diversity was identified, with the presence of two groups that followed a climatic gradient from mesic to semi-arid regions. Most populations were represented by a single haplotype, but many haplotypes were shared among populations, with some having widespread distributions. A putative refugial area with high haplotype diversity was identified at the centre of the species distribution. Species distribution modelling showed high climatic suitability at the LGM and high climatic stability in the central region where higher genetic diversity was found, and low suitability elsewhere, consistent with a pattern of range contraction. CONCLUSIONS Combination of phylogeography and paleo-distribution modelling can provide an evolutionary context for climate-driven tree decline, as both can be used to cross-validate evidence for refugia and contraction under harsh climatic conditions. This approach identified a central refugial area in the test species E. wandoo, with more recent expansion into peripheral areas from where it had contracted at the LGM. This signature of contraction from lower rainfall areas is consistent with current observations of decline on the semi-arid margin of the range, and indicates low capacity to tolerate forecast climatic change. Identification of a paleo-historical context for current tree decline enables conservation interventions to focus on maintaining genetic diversity, which provides the evolutionary potential for adaptation to climate change.
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Affiliation(s)
- Eleftheria Dalmaris
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia and
| | - Cristina E Ramalho
- Science and Conservation Division, Western Australian Department of Parks and Wildlife, Locked Bag 104, Bentley Delivery Centre, Bentley, 6983 WA, Australia
| | - Pieter Poot
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia and Science and Conservation Division, Western Australian Department of Parks and Wildlife, Locked Bag 104, Bentley Delivery Centre, Bentley, 6983 WA, Australia
| | - Erik J Veneklaas
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia and
| | - Margaret Byrne
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia and Science and Conservation Division, Western Australian Department of Parks and Wildlife, Locked Bag 104, Bentley Delivery Centre, Bentley, 6983 WA, Australia
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Cerón-Souza I, Gonzalez EG, Schwarzbach AE, Salas-Leiva DE, Rivera-Ocasio E, Toro-Perea N, Bermingham E, McMillan WO. Contrasting demographic history and gene flow patterns of two mangrove species on either side of the Central American Isthmus. Ecol Evol 2015; 5:3486-99. [PMID: 26380680 PMCID: PMC4569042 DOI: 10.1002/ece3.1569] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 04/12/2015] [Indexed: 11/18/2022] Open
Abstract
Comparative phylogeography offers a unique opportunity to understand the interplay between past environmental events and life-history traits on diversification of unrelated but co-distributed species. Here, we examined the effects of the quaternary climate fluctuations and palaeomarine currents and present-day marine currents on the extant patterns of genetic diversity in the two most conspicuous mangrove species of the Neotropics. The black (Avicennia germinans, Avicenniaceae) and the red (Rhizophora mangle, Rhizophoraceae) mangroves have similar geographic ranges but are very distantly related and show striking differences on their life-history traits. We sampled 18 Atlantic and 26 Pacific locations for A. germinans (N = 292) and R. mangle (N = 422). We performed coalescence simulations using microsatellite diversity to test for evidence of population change associated with quaternary climate fluctuations. In addition, we examined whether patterns of genetic variation were consistent with the directions of major marine (historical and present day) currents in the region. Our demographic analysis was grounded within a phylogeographic framework provided by the sequence analysis of two chloroplasts and one flanking microsatellite region in a subsample of individuals. The two mangrove species shared similar biogeographic histories including: (1) strong genetic breaks between Atlantic and Pacific ocean basins associated with the final closure of the Central American Isthmus (CAI), (2) evidence for simultaneous population declines between the mid-Pleistocene and early Holocene, (3) asymmetric historical migration with higher gene flow from the Atlantic to the Pacific oceans following the direction of the palaeomarine current, and (4) contemporary gene flow between West Africa and South America following the major Atlantic Ocean currents. Despite the remarkable differences in life-history traits of mangrove species, which should have had a strong influence on seed dispersal capability and, thus, population connectivity, we found that vicariant events, climate fluctuations and marine currents have shaped the distribution of genetic diversity in strikingly similar ways.
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Affiliation(s)
- Ivania Cerón-Souza
- Smithsonian Tropical Research Institute Apartado, 0843-03092, Panama ; University of Puerto Rico - Rio Piedras Campus PO BOX 23360, San Juan, Puerto Rico, 00931-3360
| | - Elena G Gonzalez
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, MNCN-CSIC José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Andrea E Schwarzbach
- Department of Biomedicine, University of Texas One West University Blvd., Brownsville, Texas, 78520
| | - Dayana E Salas-Leiva
- Department of Biological Sciences, Florida International University Miami, Florida, 33199 ; USDA-ARS-SHRS, National Germplasm Repository Miami, Florida, 33158
| | - Elsie Rivera-Ocasio
- Department of Biology, University of Puerto Rico-Bayamon Parque Industrial Minillas Carr 174, Bayamón, Puerto Rico, 00959-1911
| | - Nelson Toro-Perea
- Departamento de Biología, Sección de Genética, Universidad del Valle AA 25360, Cali, Colombia
| | - Eldredge Bermingham
- Patricia and Phillip Frost Museum of Science, 3280 South Miami Avenue Miami, Florida
| | - W Owen McMillan
- Smithsonian Tropical Research Institute Apartado, 0843-03092, Panama
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Kimura MK, Uchiyama K, Nakao K, Moriguchi Y, San Jose-Maldia L, Tsumura Y. Evidence for cryptic northern refugia in the last glacial period in Cryptomeria japonica. Ann Bot 2014; 114:1687-1700. [PMID: 25355521 PMCID: PMC4649686 DOI: 10.1093/aob/mcu197] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 08/26/2014] [Indexed: 05/31/2023]
Abstract
BACKGROUND AND AIMS Distribution shifts and natural selection during past climatic changes are important factors in determining the genetic structure of forest species. In particular, climatic fluctuations during the Quaternary appear to have caused changes in the distribution ranges of plants, and thus strongly affected their genetic structure. This study was undertaken to identify the responses of the conifer Cryptomeria japonica, endemic to the Japanese Archipelago, to past climatic changes using a combination of phylogeography and species distribution modelling (SDM) methods. Specifically, this study focused on the locations of refugia during the last glacial maximum (LGM). METHODS Genetic diversity and structure were examined using 20 microsatellite markers in 37 populations of C. japonica. The locations of glacial refugia were assessed using STRUCTURE analysis, and potential habitats under current and past climate conditions were predicted using SDM. The process of genetic divergence was also examined using the approximate Bayesian computation procedure (ABC) in DIY ABC to test the divergence time between the gene pools detected by the STRUCTURE analysis. KEY RESULTS STRUCTURE analysis identified four gene pools: northern Tohoku district; from Chubu to Chugoku district; from Tohoku to Shikoku district on the Pacific Ocean side of the Archipelago; and Yakushima Island. DIY ABC analysis indicated that the four gene pools diverged at the same time before the LGM. SDM also indicated potential northern cryptic refugia. CONCLUSIONS The combined evidence from microsatellites and SDM clearly indicates that climatic changes have shaped the genetic structure of C. japonica. The gene pool detected in northern Tohoku district is likely to have been established by cryptic northern refugia on the coast of the Japan Sea to the west of the Archipelago. The gene pool in Yakushima Island can probably be explained simply by long-term isolation from the other gene pools since the LGM. These results are supported by those of SDM and the predicted divergence time determined using ABC analysis.
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Affiliation(s)
- Megumi K Kimura
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, 305-8687, Japan
| | - Kentaro Uchiyama
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, 305-8687, Japan
| | - Katsuhiro Nakao
- Department of Forest Vegetation, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, 305-8687, Japan
| | - Yoshinari Moriguchi
- Graduate School of Science and Technology, Niigata University, 8050, Igarashi 2-Nocho, Nishi-ku Niigata 950-2181, Japan
| | - Lerma San Jose-Maldia
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, 305-8687, Japan
| | - Yoshihiko Tsumura
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, 305-8687, Japan
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Raes N, Cannon CH, Hijmans RJ, Piessens T, Saw LG, van Welzen PC, Slik JW. Historical distribution of Sundaland's Dipterocarp rainforests at Quaternary glacial maxima. Proc Natl Acad Sci U S A 2014; 111:16790-5. [PMID: 25385612 DOI: 10.1073/pnas.1403053111] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The extent of Dipterocarp rainforests on the emergent Sundaland landmass in Southeast Asia during Quaternary glaciations remains a key question. A better understanding of the biogeographic history of Sundaland could help explain current patterns of biodiversity and support the development of effective forest conservation strategies. Dipterocarpaceae trees dominate the rainforests of Sundaland, and their distributions serve as a proxy for rainforest extent. We used species distribution models (SDMs) of 317 Dipterocarp species to estimate the geographic extent of appropriate climatic conditions for rainforest on Sundaland at the last glacial maximum (LGM). The SDMs suggest that the climate of central Sundaland at the LGM was suitable to sustain Dipterocarp rainforest, and that the presence of a previously suggested transequatorial savannah corridor at that time is unlikely. Our findings are supported by palynologic evidence, dynamic vegetation models, extant mammal and termite communities, vascular plant fatty acid stable isotopic compositions, and stable carbon isotopic compositions of cave guano profiles. Although Dipterocarp species richness was generally lower at the LGM, areas of high species richness were mostly found off the current islands and on the emergent Sunda Shelf, indicating substantial species migration and mixing during the transitions between the Quaternary glacial maxima and warm periods such as the present.
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de Lafontaine G, Amasifuen Guerra CA, Ducousso A, Sánchez-Goñi MF, Petit RJ. Beyond skepticism: uncovering cryptic refugia using multiple lines of evidence. New Phytol 2014; 204:450-454. [PMID: 25312609 DOI: 10.1111/nph.13089] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- Guillaume de Lafontaine
- INRA, UMR 1202 BIOGECO, F-33610, Cestas, France
- Univ. Bordeaux, UMR 1202 BIOGECO, F-33600, Pessac, France
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research, Institute for Systems and Integrative Biology, Université Laval, 1030 avenue de la Médecine, Québec, QC, Canada, G1V 0A6
| | | | - Alexis Ducousso
- INRA, UMR 1202 BIOGECO, F-33610, Cestas, France
- Univ. Bordeaux, UMR 1202 BIOGECO, F-33600, Pessac, France
| | | | - Rémy J Petit
- INRA, UMR 1202 BIOGECO, F-33610, Cestas, France
- Univ. Bordeaux, UMR 1202 BIOGECO, F-33600, Pessac, France
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Huntley B. Extreme temporal interpolation of sparse data is not a sufficient basis to substantiate a claim to have uncovered Pleistocene forest microrefugia. New Phytol 2014; 204:447-449. [PMID: 25312608 DOI: 10.1111/nph.12941] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- Brian Huntley
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham, DH1 3LE, UK
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Becklin KM, Medeiros JS, Sale KR, Ward JK. Evolutionary history underlies plant physiological responses to global change since the last glacial maximum. Ecol Lett 2014; 17:691-9. [PMID: 24636555 PMCID: PMC4097002 DOI: 10.1111/ele.12271] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 12/13/2013] [Accepted: 02/19/2014] [Indexed: 11/28/2022]
Abstract
Assessing family- and species-level variation in physiological responses to global change across geologic time is critical for understanding factors that underlie changes in species distributions and community composition. Here, we used stable carbon isotopes, leaf nitrogen content and stomatal measurements to assess changes in leaf-level physiology in a mixed conifer community that underwent significant changes in composition since the last glacial maximum (LGM) (21 kyr BP). Our results indicate that most plant taxa decreased stomatal conductance and/or maximum photosynthetic capacity in response to changing conditions since the LGM. However, plant families and species differed in the timing and magnitude of these physiological responses, and responses were more similar within families than within co-occurring species assemblages. This suggests that adaptation at the level of leaf physiology may not be the main determinant of shifts in community composition, and that plant evolutionary history may drive physiological adaptation to global change over recent geologic time.
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Affiliation(s)
- Katie M. Becklin
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
| | | | - Kayla R. Sale
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
| | - Joy K. Ward
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
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Groom SVC, Stevens MI, Schwarz MP. Parallel responses of bees to Pleistocene climate change in three isolated archipelagos of the southwestern Pacific. Proc Biol Sci 2014; 281:20133293. [PMID: 24807250 DOI: 10.1098/rspb.2013.3293] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The impacts of glacial cycles on the geographical distribution and size of populations have been explored for numerous terrestrial and marine taxa. However, most studies have focused on high latitudes, with only a few focused on the response of biota to the last glacial maximum (LGM) in equatorial regions. Here, we examine how population sizes of key bee fauna in the southwest Pacific archipelagos of Fiji, Vanuatu and Samoa have fluctuated over the Quaternary. We show that all three island faunas suffered massive population declines, roughly corresponding in time to the LGM, followed by rapid expansion post-LGM. Our data therefore suggest that Pleistocene climate change has had major impacts across a very broad tropical region. While other studies indicate widespread Holarctic effects of the LGM, our data suggest a much wider range of latitudes, extending to the tropics, where these climate change repercussions were important. As key pollinators, the inferred changes in these bee faunas may have been critical in the development of the diverse Pacific island flora. The magnitude of these responses indicates future climate change scenarios may have alarming consequences for Pacific island systems involving pollinator-dependent plant communities and agricultural crops.
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Affiliation(s)
- Scott V C Groom
- School of Biological Sciences, Flinders University, , GPO Box 2100, Adelaide, South Australia 5001, Australia, South Australian Museum, , GPO Box 234, Adelaide, South Australia 5000, Australia, School of Pharmacy and Medical Sciences, University of South Australia, , Adelaide, South Australia 5000, Australia
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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. Ann Bot 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] [What about the content of this article? (0)] [Affiliation(s)] [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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