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Patterson CW, Drury JP. Interspecific behavioural interference and range dynamics: current insights and future directions. Biol Rev Camb Philos Soc 2023; 98:2012-2027. [PMID: 37364865 DOI: 10.1111/brv.12993] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/28/2023]
Abstract
Novel biotic interactions in shifting communities play a key role in determining the ability of species' ranges to track suitable habitat. To date, the impact of biotic interactions on range dynamics have predominantly been studied in the context of interactions between different trophic levels or, to a lesser extent, exploitative competition between species of the same trophic level. Yet, both theory and a growing number of empirical studies show that interspecific behavioural interference, such as interspecific territorial and mating interactions, can slow down range expansions, preclude coexistence, or drive local extinction, even in the absence of resource competition. We conducted a systematic review of the current empirical research into the consequences of interspecific behavioural interference on range dynamics. Our findings demonstrate there is abundant evidence that behavioural interference by one species can impact the spatial distribution of another. Furthermore, we identify several gaps where more empirical work is needed to test predictions from theory robustly. Finally, we outline several avenues for future research, providing suggestions for how interspecific behavioural interference could be incorporated into existing scientific frameworks for understanding how biotic interactions influence range expansions, such as species distribution models, to build a stronger understanding of the potential consequences of behavioural interference on the outcome of future range dynamics.
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Affiliation(s)
| | - Jonathan P Drury
- Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK
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2
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Nizamani MM, Papeş M, Wang H, Harris AJ. How does spatial extent and environmental limits affect the accuracy of species richness estimates from ecological niche models? A case study with North American Pinaceae and Cactaceae. Ecol Evol 2023; 13:e10007. [PMID: 37091570 PMCID: PMC10121319 DOI: 10.1002/ece3.10007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 03/13/2023] [Accepted: 03/31/2023] [Indexed: 04/25/2023] Open
Abstract
Measuring species richness at varying spatial extents can be challenging, especially at large extents where exhaustive species surveys are difficult or impossible. Our work aimed at determining the reliability of species richness estimates from stacked ecological niche models at different spatial extents for taxonomic groups with vastly different environmental dependencies and interactions. To accomplish this, we generated ecological niche models for the species of Cactaceae and Pinaceae that occur within 180 published floras from North America north of Mexico. We overlaid or stacked the resulting species' potential distribution estimates over the bounding boxes representing each of the 180 floras to generate predictions of species richness. In general, our stacked models of Cactaceae and Pinaceae were poor predictors of species richness. The relationships between observed and predicted values improved noticeably with the size of spatial extents. However, the stacked models tended to overpredict the richness of Cactaceae and over- and underpredict the richness of Pinaceae. Cactaceae stacked models showed higher sensitivity and lower specificity than those for Pinaceae. We conclude that stacked ecological niche models may be somewhat poor predictors of species richness at smaller spatial extents and should be used with caution for this purpose. Perhaps more importantly, abilities to compensate for their limitations or apply corrections to their reliability may vary with taxonomic groups.
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Affiliation(s)
- Mir Muhammad Nizamani
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed LaboratorySanyaChina
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical CropsHainan UniversityHaikouChina
| | - Monica Papeş
- Department of Ecology and Evolutionary BiologyUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Hua‐Feng Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed LaboratorySanyaChina
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical CropsHainan UniversityHaikouChina
| | - AJ Harris
- South China Botanical Garden, Chinese Academy of ScienceGuangzhouChina
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3
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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] [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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4
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Luo X, Zhou H, Cao D, Yan F, Chen P, Wang J, Woeste K, Chen X, Fei Z, An H, Malvolti M, Ma K, Liu C, Ebrahimi A, Qiao C, Ye H, Li M, Lu Z, Xu J, Cao S, Zhao P. Domestication and selection footprints in Persian walnuts (Juglans regia). PLoS Genet 2022; 18:e1010513. [PMID: 36477175 PMCID: PMC9728896 DOI: 10.1371/journal.pgen.1010513] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022] Open
Abstract
Walnut (Juglans) species are economically important hardwood trees cultivated worldwide for both edible nuts and high-quality wood. Broad-scale assessments of species diversity, evolutionary history, and domestication are needed to improve walnut breeding. In this study, we sequenced 309 walnut accessions from around the world, including 55 Juglans relatives, 98 wild Persian walnuts (J. regia), 70 J. regia landraces, and 86 J. regia cultivars. The phylogenetic tree indicated that J. regia samples (section Dioscaryon) were monophyletic within Juglans. The core areas of genetic diversity of J. regia germplasm were southwestern China and southern Asia near the Qinghai-Tibet Plateau and the Himalayas, and the uplift of the Himalayas was speculated to be the main factor leading to the current population dynamics of Persian walnut. The pattern of genomic variation in terms of nucleotide diversity, linkage disequilibrium, single nucleotide polymorphisms, and insertions/deletions revealed the domestication and selection footprints in Persian walnut. Selective sweep analysis, GWAS, and expression analysis further identified two transcription factors, JrbHLH and JrMYB6, that influence the thickness of the nut diaphragm as loci under selection during domestication. Our results elucidate the domestication and selection footprints in Persian walnuts and provide a valuable resource for the genomics-assisted breeding of this important crop.
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Affiliation(s)
- Xiang Luo
- College of Agriculture, Henan University, Kaifeng, Henan, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Huijuan Zhou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
- Xi’an Botanical Garden of Shaanxi Province, Xi’an, China
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Da Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, Ghent, Belgium
| | - Feng Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Pengpeng Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Jiangtao Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Keith Woeste
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
| | - Xin Chen
- Shandong Institute of Pomology, National Germplasm Repository of Walnut and Chestnut, Tai’an, China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, US Department of Agriculture (USDA) Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, New York, United States of America
| | - Hong An
- Bioinformatics and Analytics Core, University of Missouri, Columbia, Missouri, United States of America
| | - Maria Malvolti
- Research Institute on Terrestrial Ecosystems, National Research Council, Porano, Terni, Italy
| | - Kai Ma
- Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Chaobin Liu
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, Ghent, Belgium
| | - Aziz Ebrahimi
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
| | - Chengkui Qiao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Mengdi Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Zhenhua Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Jiabao Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- * E-mail: (JX); (SC); (PZ)
| | - Shangying Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- * E-mail: (JX); (SC); (PZ)
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
- * E-mail: (JX); (SC); (PZ)
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5
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Szép E, Trubenová B, Csilléry K. Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. Mol Ecol Resour 2022; 22:2941-2955. [PMID: 35765749 PMCID: PMC9796524 DOI: 10.1111/1755-0998.13676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 06/02/2022] [Accepted: 06/16/2022] [Indexed: 01/01/2023]
Abstract
Spatially explicit population genetic models have long been developed, yet have rarely been used to test hypotheses about the spatial distribution of genetic diversity or the genetic divergence between populations. Here, we use spatially explicit coalescence simulations to explore the properties of the island and the two-dimensional stepping stone models under a wide range of scenarios with spatio-temporal variation in deme size. We avoid the simulation of genetic data, using the fact that under the studied models, summary statistics of genetic diversity and divergence can be approximated from coalescence times. We perform the simulations using gridCoal, a flexible spatial wrapper for the software msprime (Kelleher et al., 2016, Theoretical Population Biology, 95, 13) developed herein. In gridCoal, deme sizes can change arbitrarily across space and time, as well as migration rates between individual demes. We identify different factors that can cause a deviation from theoretical expectations, such as the simulation time in comparison to the effective deme size and the spatio-temporal autocorrelation across the grid. Our results highlight that FST , a measure of the strength of population structure, principally depends on recent demography, which makes it robust to temporal variation in deme size. In contrast, the amount of genetic diversity is dependent on the distant past when Ne is large, therefore longer run times are needed to estimate Ne than FST . Finally, we illustrate the use of gridCoal on a real-world example, the range expansion of silver fir (Abies alba Mill.) since the last glacial maximum, using different degrees of spatio-temporal variation in deme size.
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Affiliation(s)
- Enikő Szép
- IST Austria (Institute of Science and Technology Austria)KlosterneuburgAustria
| | - Barbora Trubenová
- IST Austria (Institute of Science and Technology Austria)KlosterneuburgAustria,Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Katalin Csilléry
- Biodiversity and Conservation BiologySwiss Federal Research Institute WSLBirmensdorfSwitzerland
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6
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Chapin KJ, Jones MR, Winkler DE, Rink G, Massatti R. Evolutionary dynamics inform management interventions of a hanging garden obligate, Carex specuicola. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.941002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Uncovering the historical and contemporary processes shaping rare species with complex distributions is of growing importance due to threats such as habitat destruction and climate change. Species restricted to specialized, patchy habitat may persist by virtue of life history characteristics facilitating ongoing gene flow and dispersal, but they could also reflect the remnants of formerly widespread, suitable habitat that existed during past climate regimes. If formerly widespread species did not rely upon traits facilitating high dispersibility to persist, contemporary populations could be at high risk of extirpation or extinction. Fortunately, genomic investigations provide an opportunity to illuminate such alternative scenarios while simultaneously offering guidance for future management interventions. Herein, we test the role of these mechanisms in shaping patterns of genomic diversity and differentiation across a highly restricted and rare ecosystem: desert hanging gardens. We focus on Carex specuicola (Cyperaceae), a hanging garden obligate narrowly distributed in the Four Corners region of the southwestern United States that is listed as Threatened under the United States Endangered Species Act. Population structure and diversity analyses reveal that hanging garden populations are shaped by strong genetic drift, but that individuals in gardens are occasionally more closely related to individuals at other gardens than to individuals within the same garden. Similarly, gardens separated by long geographic distances may contain individuals that are more closely related compared to individuals in gardens separated by short geographic distances. Demographic modeling supports historical gene flow between some contemporary garden pairs, which is corroborated by low estimates of inbreeding coefficients and recent divergence times. As such, multiple lines of evidence support dispersal and gene flow across C. specuicola populations at both small and large spatial scales, indicating that even if C. specuicola was formerly more widespread, it may be well suited to persist in hanging gardens so long as suitable habitat remains available. Analyses like those demonstrated herein may be broadly applicable for understanding the short- and long-term evolutionary processes influencing rare species, and especially those having complex distributions across heterogeneous landscapes.
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7
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Bemmels JB, Haddrath O, Colbourne RM, Robertson HA, Weir JT. Legacy of supervolcanic eruptions on population genetic structure of brown kiwi. Curr Biol 2022; 32:3389-3397.e8. [PMID: 35728597 DOI: 10.1016/j.cub.2022.05.064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/09/2022] [Accepted: 05/31/2022] [Indexed: 10/18/2022]
Abstract
Supervolcanoes are volcanoes capable of mega-colossal eruptions that emit more than 1,000 km3 of ash and other particles.1 The earth's most recent mega-colossal eruption was the Oruanui eruption of the Taupo supervolcano 25,580 years before present (YBP) on the central North Island of New Zealand.2 This eruption blanketed major swaths of the North Island in thick layers of ash and igneous rock,2,3 devastating habitats and likely causing widespread population extinctions.4-7 An additional devastating super-colossal eruption (>100 km3) of the Taupo supervolcano occurred approximately 1,690 YBP.8 The impacts of such massive but ephemeral natural disasters on contemporary population genetic structure remain underexplored. Here, we combined data for 4,951 SNPs with spatially explicit demographic and coalescent models within an approximate Bayesian computation framework to test the drivers of genetic structure in brown kiwi (Apteryx mantelli). Our results strongly support the importance of eruptions of the Taupo supervolcano in restructuring pre-existing geographic patterns of population differentiation and genetic diversity. Range shifts due to climatic oscillations-a frequent explanation for genetic structure9-are insufficient to fully explain the empirical data. Meanwhile, recent range contraction and fragmentation due to historically documented anthropogenic habitat alteration adds no explanatory power to our models. Our results support a major role for cycles of destruction and post-volcanic recolonization in restructuring the population genomic landscape of brown kiwi and highlight how ancient and ephemeral mega-disasters may leave a lasting legacy on patterns of intraspecific genetic variation.
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Affiliation(s)
- Jordan B Bemmels
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada; Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.
| | - Oliver Haddrath
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada; Department of Natural History, Royal Ontario Museum, Toronto, ON M5S 2C6, Canada
| | - Rogan M Colbourne
- Department of Conservation, PO Box 10420, Wellington 6140, New Zealand
| | - Hugh A Robertson
- Department of Conservation, PO Box 10420, Wellington 6140, New Zealand
| | - Jason T Weir
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada; Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada; Department of Natural History, Royal Ontario Museum, Toronto, ON M5S 2C6, Canada.
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8
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Massatti R, Winkler DE. Spatially explicit management of genetic diversity using ancestry probability surfaces. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rob Massatti
- US Geological Survey, Southwest Biological Science Center Flagstaff AZ USA
| | - Daniel E. Winkler
- US Geological Survey, Southwest Biological Science Center Tucson AZ USA
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9
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Stunz E, Fetcher N, Lavretsky P, Mohl JE, Tang J, Moody ML. Landscape Genomics Provides Evidence of Ecotypic Adaptation and a Barrier to Gene Flow at Treeline for the Arctic Foundation Species Eriophorum vaginatum. FRONTIERS IN PLANT SCIENCE 2022; 13:860439. [PMID: 35401613 PMCID: PMC8987161 DOI: 10.3389/fpls.2022.860439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Global climate change has resulted in geographic range shifts of flora and fauna at a global scale. Extreme environments, like the Arctic, are seeing some of the most pronounced changes. This region covers 14% of the Earth's land area, and while many arctic species are widespread, understanding ecotypic variation at the genomic level will be important for elucidating how range shifts will affect ecological processes. Tussock cottongrass (Eriophorum vaginatum L.) is a foundation species of the moist acidic tundra, whose potential decline due to competition from shrubs may affect ecosystem stability in the Arctic. We used double-digest Restriction Site-Associated DNA sequencing to identify genomic variation in 273 individuals of E. vaginatum from 17 sites along a latitudinal gradient in north central Alaska. These sites have been part of 30 + years of ecological research and are inclusive of a region that was part of the Beringian refugium. The data analyses included genomic population structure, demographic models, and genotype by environment association. Genome-wide SNP investigation revealed environmentally associated variation and population structure across the sampled range of E. vaginatum, including a genetic break between populations north and south of treeline. This structure is likely the result of subrefugial isolation, contemporary isolation by resistance, and adaptation. Forty-five candidate loci were identified with genotype-environment association (GEA) analyses, with most identified genes related to abiotic stress. Our results support a hypothesis of limited gene flow based on spatial and environmental factors for E. vaginatum, which in combination with life history traits could limit range expansion of southern ecotypes northward as the tundra warms. This has implications for lower competitive attributes of northern plants of this foundation species likely resulting in changes in ecosystem productivity.
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Affiliation(s)
- Elizabeth Stunz
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, United States
| | - Ned Fetcher
- Institute for Environmental Science and Sustainability, Wilkes University, Wilkes-Barre, PA, United States
| | - Philip Lavretsky
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, United States
| | - Jonathon E. Mohl
- Department of Mathematical Sciences, Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX, United States
| | - Jianwu Tang
- Marine Biological Laboratory, The Ecosystems Center, Woods Hole, MA, United States
| | - Michael L. Moody
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, United States
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Sousa R, Vasconcelos J, Vera-Escalona I, Pinto AR, Hawkins SJ, Freitas M, Delgado J, González JA, Riera R. Pleistocene expansion, anthropogenic pressure and ocean currents: Disentangling the past and ongoing evolutionary history of Patella aspera Röding, 1798 in the archipelago of Madeira. MARINE ENVIRONMENTAL RESEARCH 2021; 172:105485. [PMID: 34715642 DOI: 10.1016/j.marenvres.2021.105485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 09/12/2021] [Accepted: 09/18/2021] [Indexed: 06/13/2023]
Abstract
AIMS Rising sea-level following the Last Glacial Maximum lead to fragmentation of coastal limpet populations between islands of the Archipelago of Madeira. This fragmentation is reinforced by recent heavy exploitation reducing effective population size on Madeira Island. We use the limpet P. aspera to understand how the role of processes at different time scales (i.e. changes in the sea level and overexploitation) can influence the genetic composition of an extant species, relating these processes to reproductive phenology and seasonal shifts in ocean currents. LOCATION Madeira Island, Porto Santo and Desertas (Archipelago of Madeira, NE Atlantic Ocean). TAXON The limpet Patella aspera. METHODS Twelve microsatellite genetic markers were used. A power analysis was used to evaluate the power of the microsatellite markers to detect a signal of population differentiation. Long-term past migrations were assessed using a Bayesian Markov Montecarlo approach in the software MIGRATE-n to estimate mutation-scaled migration rates (M = m/μ; m, probability of a lineage immigrating per generation; μ, mutation rate). Two scenarios were evaluated using an Approximate Bayesian Computation (ABC) in the software DIYABC 2.1 (i) Scenario 1: considered a population scenario from a reduced Ne at time t3 to a higher Ne at time t2; and (ii) Scenario 2 considering a reduction of Ne from a time t3 to a time t2. RESULTS Colonization of the archipelago by Portuguese settlers six centuries ago probably led to an important decrease in the genetic diversity of the species (Ne). Contemporary gene flow strongly support a pattern of high asymmetric connectivity explained by the reproductive phenology of the species and spatio-temporal seasonal changes in the ocean currents. Spatio-temporal reconstructions using Bayesian methods, including coalescent and Approximate Bayesian Computation (ABC) approaches, suggest changes in the migration patterns from highly symmetric to highly asymmetric connectivity with subtle population differentiation as consequence of post-glacial maximum sea level rise during the Holocene. MAIN CONCLUSIONS Our results suggest that anthropogenic activity could have had serious effects on the genetic diversity of heavily exploited littoral species since the end of the Pleistocene, probably accelerating in recent years.
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Affiliation(s)
- Ricardo Sousa
- Observatório Oceânico da Madeira, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (OOM/ARDITI) - Edifício Madeira Tecnopolo, Funchal, Madeira, Portugal; Direção Regional do Mar (DRM)/ Direção de Serviços de Monitorização, Estudos e Investigação do Mar (DSEIMar), 9004-562, Funchal, Madeira, Portugal; MARE - Marine and Environmental Sciences Centre, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI), Edifício Madeira Tecnopolo Piso 0, Caminho da Penteada, 9020-105, Funchal, Madeira, Portugal
| | - Joana Vasconcelos
- MARE - Marine and Environmental Sciences Centre, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI), Edifício Madeira Tecnopolo Piso 0, Caminho da Penteada, 9020-105, Funchal, Madeira, Portugal; Faculdade de Ciências de Vida, Universidade da Madeira, Campus Universitário da Madeira, Caminho da Penteada, 9020-020, Funchal, Madeira, Portugal; Departamento de Ecología, Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Casilla 297, Concepción, Chile
| | - Iván Vera-Escalona
- CIBAS, Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Casilla 297, Concepción, Chile; IU-ECOAQUA, Group of Biodiversity and Conservation (BIOCON), Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Ana Rita Pinto
- Direção Regional do Mar (DRM)/ Direção de Serviços de Monitorização, Estudos e Investigação do Mar (DSEIMar), 9004-562, Funchal, Madeira, Portugal
| | - S J Hawkins
- Marine Biological Association of the UK, Plymouth, PL1 2PB, UK; School of Ocean and Earth Science, University of Southampton, National Oceanography Centre, Southampton, SO14 3ZH, UK
| | - Mafalda Freitas
- Observatório Oceânico da Madeira, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (OOM/ARDITI) - Edifício Madeira Tecnopolo, Funchal, Madeira, Portugal; Direção Regional do Mar (DRM)/ Direção de Serviços de Monitorização, Estudos e Investigação do Mar (DSEIMar), 9004-562, Funchal, Madeira, Portugal; MARE - Marine and Environmental Sciences Centre, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI), Edifício Madeira Tecnopolo Piso 0, Caminho da Penteada, 9020-105, Funchal, Madeira, Portugal
| | - João Delgado
- Direção Regional do Mar (DRM)/ Direção de Serviços de Monitorização, Estudos e Investigação do Mar (DSEIMar), 9004-562, Funchal, Madeira, Portugal; Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Porto, Portugal
| | - José A González
- Ecología Marina Aplicada y Pesquerías (i-UNAT), Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Rodrigo Riera
- Departamento de Ecología, Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Casilla 297, Concepción, Chile; IU-ECOAQUA, Group of Biodiversity and Conservation (BIOCON), Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain.
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Ortego J, Knowles LL. Geographical isolation versus dispersal: Relictual alpine grasshoppers support a model of interglacial diversification with limited hybridization. Mol Ecol 2021; 31:296-312. [PMID: 34651368 DOI: 10.1111/mec.16225] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/21/2021] [Accepted: 10/08/2021] [Indexed: 01/25/2023]
Abstract
Alpine biotas are paradigmatic of the countervailing roles of geographical isolation and dispersal during diversification. In temperate regions, repeated distributional shifts driven by Pleistocene climatic oscillations produced both recurrent pulses of population fragmentation and opportunities for gene flow during range expansions. Here, we test whether a model of divergence in isolation vs. with gene flow is more likely in the diversification of flightless alpine grasshoppers of the genus Podisma from the Iberian Peninsula. The answer to this question can also provide key insights about the pace of evolution. Specifically, if the data fit a divergence in isolation model, this suggests rapid evolution of reproductive isolation. Genomic data confirm a Pleistocene origin of the species complex, and multiple analytical approaches revealed limited asymmetric historical hybridization between two taxa. Genomic-based demographic reconstructions, spatial patterns of genetic structure and range shifts inferred from palaeodistribution modelling suggest severe range contraction accompanied by declines in effective population sizes during interglacials (i.e., contemporary populations confined to sky islands are relicts) and expansions during the coldest stages of the Pleistocene in each taxon. Although limited hybridization during secondary contact leads to phylogenetic uncertainty if gene flow is not accommodated when estimating evolutionary relationships, all species exhibit strong genetic cohesiveness. Our study lends support to the notion that the accumulation of incipient differences during periods of isolation were sufficient to lead to lineage persistence, but also that the demographic changes, dispersal constraints and spatial distribution of the sky islands themselves mediated species diversification in temperate alpine biotas.
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Affiliation(s)
- Joaquín Ortego
- Department of Integrative Ecology, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
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Larsson DJ, Pan D, Schneeweiss GM. Addressing alpine plant phylogeography using integrative distributional, demographic and coalescent modeling. ALPINE BOTANY 2021; 132:5-19. [PMID: 35368907 PMCID: PMC8933363 DOI: 10.1007/s00035-021-00263-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 07/05/2021] [Indexed: 06/14/2023]
Abstract
Phylogeographic studies of alpine plants have evolved considerably in the last two decades from ad hoc interpretations of genetic data to statistical model-based approaches. In this review we outline the developments in alpine plant phylogeography focusing on the recent approach of integrative distributional, demographic and coalescent (iDDC) modeling. By integrating distributional data with spatially explicit demographic modeling and subsequent coalescent simulations, the history of alpine species can be inferred and long-standing hypotheses, such as species-specific responses to climate change or survival on nunataks during the last glacial maximum, can be efficiently tested as exemplified by available case studies. We also discuss future prospects and improvements of iDDC.
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Affiliation(s)
- Dennis J. Larsson
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Da Pan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Gerald M. Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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13
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Dolby GA. The hidden landscape: Evidence that sea-level change shaped the present population genomic patterns of marginal marine species. Mol Ecol 2021; 30:1357-1360. [PMID: 33545743 DOI: 10.1111/mec.15826] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 01/28/2021] [Indexed: 11/29/2022]
Abstract
Oftentimes, to understand the genetic relatedness and diversity of today's populations requires considering the ancient landscape on which those populations evolved. Nowhere is this clearer than along Earth's coastline, which has been in its present-day configuration for only about 6.5% of the past 800,000 years (Dolby et al., 2020; Miller et al., 2005). During ice ages when glaciers expanded in the Northern Hemisphere, they stored enough of the planet's water to drop global sea level by ~120 m below present levels ("lowstand", Figure 1a), and there have been at least eight of these 100,000-year cycles preceding today. When glaciers melted, ocean water reflooded shorelines, shifting and re-forming marginal marine habitats globally and shaping the relatedness of populations (Dolby et al., 2016). In a From the Cover article in this issue of Molecular Ecology, Stiller et al. (2020) integrate population genomic analysis of leafy seadragons in southern Australia with estimates of available seabed area to reveal that the expansion of habitat that accompanied this reflooding led to strong demographic expansions. With statistical models, they also show that western populations were eliminated and then recolonized because the continental shelf there is narrow, leaving little available habitat when sea level was low (Figure 1b). Their results document the dynamic and interrelated nature of a hidden, changing landscape and the evolution of species inhabiting it.
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Affiliation(s)
- Greer A Dolby
- Center for Mechanisms of Evolution, Biodesign Institute, School of Life Sciences, Arizona State University, Tempe, AZ, USA
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14
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Graciá E. Biotic interactions matter in phylogeography research: Integrative analysis of demographic, genetic and distribution data to account for them. Mol Ecol 2020; 29:4503-4505. [PMID: 33070388 DOI: 10.1111/mec.15697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 10/08/2020] [Indexed: 11/28/2022]
Abstract
It is well established that biotic-interspecific interactions, such as competition, mutualism, parasitism or predation, modulate species dynamics in demographic and evolutionary terms. It is also acknowledged that biotic interactions can even have major effects on local population dynamics and scale-up to determine wider species' ranges (Wisz et al., 2013). Notwithstanding, the study of biotic interactions has been mostly ignored in biogeography and phylogeography research, for which it has been long assumed that abiotic factors (e.g. climate) mostly drive the ecological and evolutionary processes that underlie species' distribution. Consequently, our knowledge is scarce about the role of biotic interactions in determining spatial patterns of genetic diversity and structure. In a From the Cover article in this issue of Molecular Ecology, Ortego & Knowles (2020) address the study of positive and negative plant-plant interactions and test whether their demographic consequences translate into broadscale patterns of genomic variation in two oak species from the iconic California Floristic Province. The integrative approach undertaken in this study reveals that some models that incorporate competition or facilitation better explain genomic patterns than null models in which species respond only to variations in environmental suitability. These findings highlight the relevance of biologically informed model-based approaches for inferring the evolutionary consequences of species' range dynamics, which is of particular importance in today's global change context.
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Affiliation(s)
- Eva Graciá
- Department of Applied Biology, Universidad Miguel Hernández, Elche, Spain
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