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Banerjee AK, Feng H, Guo W, Harms NE, Xie H, Liang X, Xing F, Lin Y, Shao H, Guo Z, Ng WL, Huang Y. Glacial vicariance and oceanic circulation shape population structure of the coastal legume Derris trifoliata in the Indo-West Pacific. AMERICAN JOURNAL OF BOTANY 2022; 109:1016-1034. [PMID: 35419829 DOI: 10.1002/ajb2.1851] [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: 03/07/2022] [Revised: 03/17/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
PREMISE The phylogeography of coastal plant species is shaped by contemporary and historical biogeographic processes. In this study, we aim to decipher the phylogeography of Derris trifoliata, a woody legume of relatively recent origin and wide distribution, in coastal areas in the Indo-West Pacific (IWP) region. METHODS Genetic diversity and population structure were assessed by analyzing six nuclear and three chloroplast DNA sequences from 30 populations across the species' range. Phylogeography was inferred by estimating gene flow, divergence time, historical population size changes, and historical habitat suitability using paleoclimatic niche modeling. RESULTS High genetic diversity was observed at the species level. The populations of three oceanic regions included in this study (i.e., Indian Ocean, South China Sea, and Pacific Ocean) formed distinct clades and likely diverged during the late Pleistocene. Potential barriers to gene flow were identified, including the Sunda and Sahul shelves, geographic distance, and current patterns of oceanic circulation. Analysis of changes in population size supported the bottleneck model, which was strengthened by estimates of habitat suitability across paleoclimatic conditions. CONCLUSIONS The once widespread distribution of D. trifoliata was fragmented by changes in climatic suitability and biogeographic barriers that arose following sea-level changes during the Pleistocene. In addition, contemporary patterns of oceanic circulation and geographic distance between populations appear to maintain genetic differentiation across its distribution in the IWP.
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Affiliation(s)
- Achyut Kumar Banerjee
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Hui Feng
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Wuxia Guo
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
- Department of Bioengineering, Zunyi Medical University, Zhuhai, 519041 Guangdong, China
| | - Nathan E Harms
- US Army Engineer Research and Development Center, Lewisville, TX 75057, USA
| | - Hongxian Xie
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Xinru Liang
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Fen Xing
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Yuting Lin
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Huiyu Shao
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Zixiao Guo
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Wei Lun Ng
- China-ASEAN College of Marine Sciences, Xiamen University, Malaysia, 43900 Sepang, Selangor, Malaysia
| | - Yelin Huang
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
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Prazeres M, Morard R, Roberts TE, Doo SS, Jompa J, Schmidt C, Stuhr M, Renema W, Kucera M. High dispersal capacity and biogeographic breaks shape the genetic diversity of a globally distributed reef-dwelling calcifier. Ecol Evol 2020; 10:5976-5989. [PMID: 32607205 PMCID: PMC7319125 DOI: 10.1002/ece3.6335] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 04/08/2020] [Accepted: 04/14/2020] [Indexed: 12/23/2022] Open
Abstract
Understanding the role of dispersal and adaptation in the evolutionary history of marine species is essential for predicting their response to changing conditions. We analyzed patterns of genetic differentiation in the key tropical calcifying species of large benthic foraminifera Amphistegina lobifera to reveal the evolutionary processes responsible for its biogeographic distribution. We collected specimens from 16 sites encompassing the entire range of the species and analyzed hypervariable fragments of the 18S SSU rDNA marker. We identified six hierarchically organized genotypes with mutually exclusive distribution organized along a longitudinal gradient. The distribution is consistent with diversification occurring in the Indo-West Pacific (IWP) followed by dispersal toward the periphery. This pattern can be explained by: (a) high dispersal capacity of the species, (b) habitat heterogeneity driving more recent differentiation in the IWP, and (c) ecological-scale processes such as niche incumbency reinforcing patterns of genotype mutual exclusion. The dispersal potential of this species drives the ongoing range expansion into the Mediterranean Sea, indicating that A. lobifera is able to expand its distribution by tracking increases in temperature. The genetic structure reveals recent diversification and high rate of extinction in the evolutionary history of the clade suggesting a high turnover rate of the diversity at the cryptic level. This diversification dynamic combined with high dispersal potential, allowed the species to maintain a widespread distribution over periods of geological and climatic upheaval. These characteristics are likely to allow the species to modify its geographic range in response to ongoing global warming without requiring genetic differentiation.
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Affiliation(s)
- Martina Prazeres
- Marine Biodiversity GroupNaturalis Biodiversity CenterLeidenThe Netherlands
| | | | - T. Edward Roberts
- Marine Biodiversity GroupNaturalis Biodiversity CenterLeidenThe Netherlands
| | - Steve S. Doo
- Leibniz Centre for Tropical Marine ResearchBremenGermany
- Department of BiologyCalifornia State UniversityNorthridgeCAUSA
| | | | | | - Marleen Stuhr
- Leibniz Centre for Tropical Marine ResearchBremenGermany
- Interuniversity Institute for Marine Sciences (IUI)EilatIsrael
- Bar‐Ilan University (BIU)Ramat GanIsrael
| | - Willem Renema
- Marine Biodiversity GroupNaturalis Biodiversity CenterLeidenThe Netherlands
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Otwoma LM, Diemel V, Reuter H, Kochzius M, Meyer A. Genetic population structure of the convict surgeonfish Acanthurus triostegus: a phylogeographic reassessment across its range. JOURNAL OF FISH BIOLOGY 2018; 93:597-608. [PMID: 29956317 DOI: 10.1111/jfb.13686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 06/05/2018] [Indexed: 06/08/2023]
Abstract
This study investigates the genetic population structure and connectivity of Acanthurus triostegus in five Indo-Pacific biogeographic regions (western and eastern Indian Ocean, western, central and eastern Pacific Ocean), using a mitochondrial DNA marker spanning the ATPase8 and ATPase6 gene regions. In order to assess the phylogeography and genetic population structure of A. triostegus across its range, 35 individuals were sampled from five localities in the western Indian Ocean and complemented with 227 sequences from two previous studies. Results from the overall analysis of molecular variance (AMOVA) without a priori grouping showed evidence of significant differentiation in the Indo-Pacific, with 25 (8.3%) out of 300 pairwise ΦST comparisons being significant. However, the hierarchical AMOVA grouping of Indian and Pacific Ocean populations failed to support the vicariance hypothesis, showing a lack of a genetic break between the two ocean basins. Instead, the correlation between pairwise ΦST values and geographic distance showed that dispersal of A. triostegus in the Indo-Pacific Ocean follows an isolation-by-distance model. Three haplogroups could be deduced from the haplotype network and phylogenetic tree, with haplogroup 1 and 2 dominating the Indian and the Pacific Ocean, respectively, while haplogroup 3 exclusively occurring in the Hawaiian Archipelago of the central Pacific Ocean.
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Affiliation(s)
- Levy M Otwoma
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
- Kenya Marine and Fisheries Research Institute (KMFRI), Mombasa, Kenya
- Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Valeska Diemel
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
| | - Hauke Reuter
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
- Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | | | - Achim Meyer
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
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Coryell RL, Turnham KE, de Jesus Ayson EG, Lavilla‐Pltogo C, Alcala AC, Sotto F, Gonzales B, Nishiguchi MK. Phylogeographic patterns in the Philippine archipelago influence symbiont diversity in the bobtail squid -Vibrio mutualism. Ecol Evol 2018; 8:7421-7435. [PMID: 30151160 PMCID: PMC6106162 DOI: 10.1002/ece3.4266] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/20/2018] [Accepted: 04/23/2018] [Indexed: 12/05/2022] Open
Abstract
Marine microbes encounter a myriad of biotic and abiotic factors that can impact fitness by limiting their range and capacity to move between habitats. This is especially true for environmentally transmitted bacteria that cycle between their hosts and the surrounding habitat. As geologic history, biogeography, and other factors such as water temperature, salinity, and physical barriers can inhibit bacterial movement to novel environments, we chose to examine the genetic architecture of Euprymna albatrossae (Mollusca: Cephalopoda) and their Vibrio fischeri symbionts in the Philippine archipelago using a combined phylogeographic approach. Eleven separate sites in the Philippine islands were examined using haplotype estimates that were examined via nested clade analysis to determine the relationship between E. albatrossae and V. fischeri populations and their geographic location. Identical analyses of molecular variance (AMOVA) were used to estimate variation within and between populations for host and symbiont genetic data. Host animals demonstrated a significant amount of variation within island groups, while symbiont variation was found within individual populations. Nested clade phylogenetic analysis revealed that hosts and symbionts may have colonized this area at different times, with a sudden change in habitat. Additionally, host data indicate restricted gene flow, whereas symbionts show range expansion, followed by periodic restriction to genetic flow. These differences between host and symbiont networks indicate that factors "outside the squid" influence distribution of Philippine V. fischeri. Our results shed light on how geography and changing environmental factors can impact marine symbiotic associations at both local and global scales.
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Affiliation(s)
- Randy L. Coryell
- Department of BiologyNew Mexico State UniversityLas CrucesNew Mexico
| | - Kira E. Turnham
- Department of BiologyNew Mexico State UniversityLas CrucesNew Mexico
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Neiva J, Paulino C, Nielsen MM, Krause-Jensen D, Saunders GW, Assis J, Bárbara I, Tamigneaux É, Gouveia L, Aires T, Marbà N, Bruhn A, Pearson GA, Serrão EA. Glacial vicariance drives phylogeographic diversification in the amphi-boreal kelp Saccharina latissima. Sci Rep 2018; 8:1112. [PMID: 29348650 PMCID: PMC5773594 DOI: 10.1038/s41598-018-19620-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 01/04/2018] [Indexed: 11/08/2022] Open
Abstract
Glacial vicariance is regarded as one of the most prevalent drivers of phylogeographic structure and speciation among high-latitude organisms, but direct links between ice advances and range fragmentation have been more difficult to establish in marine than in terrestrial systems. Here we investigate the evolution of largely disjunct (and potentially reproductively isolated) phylogeographic lineages within the amphi-boreal kelp Saccharina latissima s. l. Using molecular data (COI, microsatellites) we confirm that S. latissima comprises also the NE Pacific S. cichorioides complex and is composed of divergent lineages with limited range overlap and genetic admixture. Only a few genetic hybrids were detected throughout a Canadian Arctic/NW Greenland contact zone. The degree of genetic differentiation and sympatric isolation of phylogroups suggest that S. latissima s. l. represents a complex of incipient species. Phylogroup distributions compared with paleo-environmental reconstructions of the cryosphere further suggest that diversification within S. latissima results from chronic glacial isolation in disjunct persistence areas intercalated with ephemeral interglacial poleward expansions and admixture at high-latitude (Arctic) contact zones. This study thus supports a role for glaciations not just in redistributing pre-existing marine lineages but also as a speciation pump across multi-glacial cycles for marine organisms otherwise exhibiting cosmopolite amphi-boreal distributions.
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Affiliation(s)
- João Neiva
- CCMAR- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal.
| | - Cristina Paulino
- CCMAR- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
| | - Mette M Nielsen
- Department of Bioscience, Aarhus University, Silkeborg, Denmark
| | - Dorte Krause-Jensen
- Department of Bioscience, Aarhus University, Silkeborg, Denmark
- Arctic Research Centre, Aarhus University, Aarhus, Denmark
| | - Gary W Saunders
- Centre for Environmental and Molecular Algal Research, University of New Brunswick, Fredericton, Canada
| | - Jorge Assis
- CCMAR- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
| | - Ignacio Bárbara
- Biocost Research Group, Universidade de A Coruña, A Coruña, Spain
| | - Éric Tamigneaux
- NSERC Industrial Research Chair for Colleges in Marine Macroalgae, Cégep de la Gaspésie et des Îles, Grande-Rivière, Québec, Canada
| | - Licínia Gouveia
- CCMAR- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
| | - Tânia Aires
- CCMAR- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
| | - Núria Marbà
- Department of Global Change Research, IMEDEA (CSIC-UIB), Esporles, Spain
| | - Annette Bruhn
- Department of Bioscience, Aarhus University, Silkeborg, Denmark
| | - Gareth A Pearson
- CCMAR- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
| | - Ester A Serrão
- CCMAR- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal.
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Stefanni S, Castilho R, Sala-Bozano M, Robalo JI, Francisco SM, Santos RS, Marques N, Brito A, Almada VC, Mariani S. Establishment of a coastal fish in the Azores: recent colonisation or sudden expansion of an ancient relict population? Heredity (Edinb) 2015; 115:527-37. [PMID: 26174025 PMCID: PMC4806900 DOI: 10.1038/hdy.2015.55] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 04/21/2015] [Accepted: 05/06/2015] [Indexed: 11/25/2022] Open
Abstract
The processes and timescales associated with ocean-wide changes in the distribution of marine species have intrigued biologists since Darwin's earliest insights into biogeography. The Azores, a mid-Atlantic volcanic archipelago located >1000 km off the European continental shelf, offers ideal opportunities to investigate phylogeographic colonisation scenarios. The benthopelagic sparid fish known as the common two-banded seabream (Diplodus vulgaris) is now relatively common along the coastline of the Azores archipelago, but was virtually absent before the 1990 s. We employed a multiple genetic marker approach to test whether the successful establishment of the Azorean population derives from a recent colonisation from western continental/island populations or from the demographic explosion of an ancient relict population. Results from nuclear and mtDNA sequences show that all Atlantic and Mediterranean populations belong to the same phylogroup, though microsatellite data indicate significant genetic divergence between the Azorean sample and all other locations, as well as among Macaronesian, western Iberian and Mediterranean regions. The results from Approximate Bayesian Computation indicate that D. vulgaris has likely inhabited the Azores for ∼ 40 (95% confidence interval (CI): 5.5-83.6) to 52 (95% CI: 6.32-89.0) generations, corresponding to roughly 80-150 years, suggesting near-contemporary colonisation, followed by a more recent demographic expansion that could have been facilitated by changing climate conditions. Moreover, the lack of previous records of this species over the past century, together with the absence of lineage separation and the presence of relatively few private alleles, do not exclude the possibility of an even more recent colonisation event.
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Affiliation(s)
- S Stefanni
- CNR-ISSIA, Via de Marini 6,
Genova, Italy
- LARSyS Associated Laboratory and Centre
of IMAR of the University of the Azores, Department of Oceanography and
Fisheries, Horta, Portugal
| | - R Castilho
- Centre of Marine Sciences, CCMAR,
Universidade do Algarve, Faro, Portugal
| | - M Sala-Bozano
- School of Biology and Environmental
Science, University College Dublin, Belfield, Ireland,
UK
| | - J I Robalo
- MARE–Marine and Environmental
Sciences Centre, ISPA-IU, Lisboa, Portugal
| | - S M Francisco
- MARE–Marine and Environmental
Sciences Centre, ISPA-IU, Lisboa, Portugal
| | - R S Santos
- LARSyS Associated Laboratory and Centre
of IMAR of the University of the Azores, Department of Oceanography and
Fisheries, Horta, Portugal
| | - N Marques
- LARSyS Associated Laboratory and Centre
of IMAR of the University of the Azores, Department of Oceanography and
Fisheries, Horta, Portugal
| | - A Brito
- BIOECOMAC, Departamento de
Biología Animal (Ciencias Marinas), Universidad de La Laguna,
Tenerife, Canary Islands
| | - V C Almada
- MARE–Marine and Environmental
Sciences Centre, ISPA-IU, Lisboa, Portugal
| | - S Mariani
- Ecosystems and Environment Research
Centre, School of Environment and Life Science, University of Salford,
Salford, UK
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Liu R, Zheng XM, Zhou L, Zhou HF, Ge S. Population genetic structure of Oryza rufipogon and Oryza nivara: implications for the origin of O. nivara. Mol Ecol 2015; 24:5211-28. [PMID: 26340227 DOI: 10.1111/mec.13375] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 08/30/2015] [Accepted: 09/01/2015] [Indexed: 12/25/2022]
Abstract
Ecological speciation plays a primary role in driving species divergence and adaptation. Oryza rufipogon and Oryza nivara are two incipient species at the early stage of speciation with distinct differences in morphology, life history traits and habitat preference, and therefore provide a unique model for the study of ecological speciation. However, the population genetic structure of the ancestral O. rufipogon has been controversial despite substantial study, and the origin of the derivative O. nivara remains unclear. Here, based on sequences of 10 nuclear and two chloroplast loci from 26 wild populations across the entire geographic ranges of the two species, we conducted comprehensive analyses using population genetics, phylogeography and species distribution modelling (SDM) approaches. In addition to supporting the two previously reported major subdivisions, we detected four genetically distinct groups within O. rufipogon and found no correlation between the genetic groups and either species identity or geographical regions. The SDM clearly showed substantial change in the distribution range of O. rufipogon in history, demonstrating that the repeated extinction and colonization of local populations due to multiple glacial-interglacial cycles during the Quaternary was most likely the main factor shaping the confounding population genetic structure of O. rufipogon. Moreover, we found significant differences between the two species in climate preferences, suggestive of an important role for climatic factors in the adaptation, persistence and expansion of O. nivara. Finally, based on the genetic pattern and dynamics of the O. nivara populations, we hypothesize that O. nivara might have independently originated multiple times from different O. rufipogon populations.
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Affiliation(s)
- Rong Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Ming Zheng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Lian Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hai-Fei Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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