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Sylvain FÉ, Bouslama S, Holland A, Leroux N, Mercier PL, Val AL, Derome N. Bacterioplankton Communities in Dissolved Organic Carbon-Rich Amazonian Black Water. Microbiol Spectr 2023; 11:e0479322. [PMID: 37199657 PMCID: PMC10269884 DOI: 10.1128/spectrum.04793-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/04/2023] [Indexed: 05/19/2023] Open
Abstract
The Amazon River basin sustains dramatic hydrochemical gradients defined by three water types: white, clear, and black waters. In black water, important loads of allochthonous humic dissolved organic matter (DOM) result from the bacterioplankton degradation of plant lignin. However, the bacterial taxa involved in this process remain unknown, since Amazonian bacterioplankton has been poorly studied. Its characterization could lead to a better understanding of the carbon cycle in one of the Earth's most productive hydrological systems. Our study characterized the taxonomic structure and functions of Amazonian bacterioplankton to better understand the interplay between this community and humic DOM. We conducted a field sampling campaign comprising 15 sites distributed across the three main Amazonian water types (representing a gradient of humic DOM), and a 16S rRNA metabarcoding analysis based on bacterioplankton DNA and RNA extracts. Bacterioplankton functions were inferred using 16S rRNA data in combination with a tailored functional database from 90 Amazonian basin shotgun metagenomes from the literature. We discovered that the relative abundances of fluorescent DOM fractions (humic-, fulvic-, and protein-like) were major drivers of bacterioplankton structure. We identified 36 genera for which the relative abundance was significantly correlated with humic DOM. The strongest correlations were found in the Polynucleobacter, Methylobacterium, and Acinetobacter genera, three low abundant but omnipresent taxa that possessed several genes involved in the main steps of the β-aryl ether enzymatic degradation pathway of diaryl humic DOM residues. Overall, this study identified key taxa with DOM degradation genomic potential, the involvement of which in allochthonous Amazonian carbon transformation and sequestration merits further investigation. IMPORTANCE The Amazon basin discharge carries an important load of terrestrially derived dissolved organic matter (DOM) to the ocean. The bacterioplankton from this basin potentially plays important roles in transforming this allochthonous carbon, which has consequences on marine primary productivity and global carbon sequestration. However, the structure and function of Amazonian bacterioplanktonic communities remain poorly studied, and their interactions with DOM are unresolved. In this study, we (i) sampled bacterioplankton in all the main Amazon tributaries, (ii) combined information from the taxonomic structure and functional repertory of Amazonian bacterioplankton communities to understand their dynamics, (iii) identified the main physicochemical parameters shaping bacterioplanktonic communities among a set of >30 measured environmental parameters, and (iv) characterized how bacterioplankton structure varies according to the relative abundance of humic compounds, a by-product from the bacterial degradation process of allochthonous DOM.
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Affiliation(s)
| | - Sidki Bouslama
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
| | - Aleicia Holland
- La Trobe University, School of Life Science, Department of Ecology, Environment and Evolution, Centre for Freshwater Ecosystems, Albury/Wodonga Campus, Victoria, Australia
| | - Nicolas Leroux
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
| | - Pierre-Luc Mercier
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
| | - Adalberto Luis Val
- Instituto Nacional de Pesquisas da Amazônia, Laboratório de Ecofisiologia e Evolução Molecular, Manaus, Brazil
| | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
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Carvalho PS, Santana DJ, Zaher H, Myers EA. Effects of Environmental Variation in Structuring Population Genetic Variation in the False-Water Cobras (Xenodontinae: Hydrodynastes). Evol Biol 2023. [DOI: 10.1007/s11692-023-09601-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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Gates K, Sandoval-Castillo J, Brauer CJ, Unmack PJ, Laporte M, Bernatchez L, Beheregaray LB. Environmental selection, rather than neutral processes, best explain regional patterns of diversity in a tropical rainforest fish. Heredity (Edinb) 2023:10.1038/s41437-023-00612-x. [PMID: 36997655 DOI: 10.1038/s41437-023-00612-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 03/14/2023] [Accepted: 03/14/2023] [Indexed: 03/31/2023] Open
Abstract
AbstractTo conserve the high functional and genetic variation in hotspots such as tropical rainforests, it is essential to understand the forces driving and maintaining biodiversity. We asked to what extent environmental gradients and terrain structure affect morphological and genomic variation across the wet tropical distribution of an Australian rainbowfish, Melanotaenia splendida splendida. We used an integrative riverscape genomics and morphometrics framework to assess the influence of these factors on both putative adaptive and non-adaptive spatial divergence. We found that neutral genetic population structure was largely explainable by restricted gene flow among drainages. However, environmental associations revealed that ecological variables had a similar power to explain overall genetic variation, and greater power to explain body shape variation, than the included neutral covariables. Hydrological and thermal variables were the strongest environmental predictors and were correlated with traits previously linked to heritable habitat-associated dimorphism in rainbowfishes. In addition, climate-associated genetic variation was significantly associated with morphology, supporting heritability of shape variation. These results support the inference of evolved functional differences among localities, and the importance of hydroclimate in early stages of diversification. We expect that substantial evolutionary responses will be required in tropical rainforest endemics to mitigate local fitness losses due to changing climates.
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Sylvain FÉ, Leroux N, Normandeau É, Holland A, Bouslama S, Mercier PL, Luis Val A, Derome N. Genomic and Environmental Factors Shape the Active Gill Bacterial Community of an Amazonian Teleost Holobiont. Microbiol Spectr 2022; 10:e0206422. [PMID: 36445161 PMCID: PMC9769777 DOI: 10.1128/spectrum.02064-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022] Open
Abstract
Fish bacterial communities provide functions critical for their host's survival in contrasting environments. These communities are sensitive to environmental-specific factors (i.e., physicochemical parameters, bacterioplankton), and host-specific factors (i.e., host genetic background). The relative contribution of these factors shaping Amazonian fish bacterial communities is largely unknown. Here, we investigated this topic by analyzing the gill bacterial communities of 240 wild flag cichlids (Mesonauta festivus) from 4 different populations (genetic clusters) distributed across 12 sites in 2 contrasting water types (ion-poor/acidic black water and ion-rich/circumneutral white water). Transcriptionally active gill bacterial communities were characterized by a 16S rRNA metabarcoding approach carried on RNA extractions. They were analyzed using comprehensive data sets from the hosts genetic background (Genotyping-By-Sequencing), the bacterioplankton (16S rRNA) and a set of 34 environmental parameters. Results show that the taxonomic structure of 16S rRNA gene transcripts libraries were significantly different between the 4 genetic clusters and also between the 2 water types. However, results suggest that the contribution of the host's genetic background was relatively weak in comparison to the environment-related factors in structuring the relative abundance of different active gill bacteria species. This finding was also confirmed by a mixed-effects modeling analysis, which indicated that the dissimilarity between the taxonomic structure of bacterioplanktonic communities possessed the best explicative power regarding the dissimilarity between gill bacterial communities' structure, while pairwise fixation indexes (FST) from the hosts' genetic data only had a weak explicative power. We discuss these results in terms of bacterial community assembly processes and flag cichlid fish ecology. IMPORTANCE Host-associated microbial communities respond to factors specific to the host physiology, genetic backgrounds, and life history. However, these communities also show different degrees of sensitivity to environment-dependent factors, such as abiotic physico-chemical parameters and ecological interactions. The relative importance of host- versus environment-associated factors in shaping teleost bacterial communities is still understudied and is paramount for their conservation and aquaculture. Here, we studied the relative importance of host- and environment-associated factors structuring teleost bacterial communities using gill samples from a wild Amazonian teleost model (Mesonauta festivus) sampled in contrasting habitats along a 1500 km section of the Amazonian basin, thus ensuring high genetic diversity. Results showed that the contribution of the host's genetic background was weak compared to environment-related bacterioplanktonic communities in shaping gill bacterial assemblages, thereby suggesting that our understanding of teleost microbiome assembly could benefit from further studies focused on the ecological interplay between host-associated and free-living communities.
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Affiliation(s)
| | - Nicolas Leroux
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
| | - Éric Normandeau
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
| | - Aleicia Holland
- La Trobe University, School of Life Science, Department of Ecology, Environment and Evolution, Centre for Freshwater Ecosystems, Wodonga, Victoria, Australia
| | - Sidki Bouslama
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
| | - Pierre-Luc Mercier
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
| | - Adalberto Luis Val
- Instituto Nacional de Pesquisas da Amazônia (INPA), Laboratório de Ecofisiologia e Evolução Molecular, Manaus, Amazonas, Brazil
| | - Nicolas Derome
- Instituto Nacional de Pesquisas da Amazônia (INPA), Laboratório de Ecofisiologia e Evolução Molecular, Manaus, Amazonas, Brazil
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Leroux N, Sylvain FÉ, Normandeau E, Holland A, Val AL, Derome N. Evolution of an Amazonian Fish Is Driven by Allopatric Divergence Rather Than Ecological Divergence. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.875961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Lowland central Amazonia is characterized by heterogeneous riverscapes dominated by two chemically divergent water types: black (ion-poor, rich in dissolved organic carbonate and acidic) and white (rich in nutrient and turbid) waters. Recent phylogeographic and genomic studies have associated the ecotone formed by these environments to an ecologically driven genetic divergence between fish present in both water types. With the objective of better understanding the evolutionary forces behind the central Amazonian teleostean diversification, we sampled 240 Mesonauta festivus from 12 sites on a wide area of the Amazonian basin. These sites included three confluences of black and white water environments to seek for repeated evidences of ecological divergence at the junction of these ecotones. Results obtained through our genetic assessment based on 41,268 single nucleotide polymorphism (SNPs) contrast with previous findings and support a low influence of diverging water physicochemical characteristics on the genetic structuration of M. festivus populations. Conversely, we detected patterns of isolation by downstream water current and evidence of past events of vicariance potentially linked to the Amazon River formation. Using a combination of population genetics, phylogeographic analysis and environmental association models, we decomposed the spatial and environmental genetic variances to assess which evolutionary forces shaped inter-population differences in M. festivus’ genome. Our sampling design, comprising three confluences of black and white water rivers, supports the main role of evolution by allopatry. While an ecologically driven evolution admittedly played a role in Amazonian fish diversification, we argue that neutral evolutionary processes explain most of the divergence between M. festivus populations.
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Hay AC, Sandoval-Castillo J, Cooke GM, Chao NL, Beheregaray LB. Riverscape Genomics Clarifies Neutral and Adaptive Evolution in an Amazonian Characin Fish (Triportheus albus). Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.825406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Understanding the role of natural selection in the evolution of wild populations is challenging due to the spatial complexity of natural systems. The richest diversity of freshwater fishes in the world is found in the Amazon Basin, a system where marked hydrochemical differences exist at the interface of major rivers with distinct “water colors” (i.e., black, white, and clear water). We hypothesize that divergent natural selection associated with these “aquatic ecotones” influences population-level adaptive divergence in the non-migratory Amazonian fish fauna. This hypothesis was tested using a landscape genomics framework to compare the relative contribution of environmental and spatial factors to the evolutionary divergence of the Amazonian characin fish Triportheus albus. The framework was based on spatial data, in situ hydrochemical measurements, and 15,251 filtered SNPs (single nucleotide polymorphisms) for T. albus sampled from three major Amazonian rivers. Gradient Forest, redundancy analysis (RDA) and BayPass analyses were used to test for signals of natural selection, and model-based and model-free approaches were used to evaluate neutral population differentiation. After controlling for a signal of neutral hierarchical structure which was consistent with the expectations for a dendritic system, variation in turbidity and pH were key factors contributing to adaptive divergence. Variation in genes involved in acid-sensitive ion transport pathways and light-sensitive photoreceptor pathways was strongly associated with pH and turbidity variability. This study improves our understanding of how natural selection and neutral evolution impact on the distribution of aquatic biodiversity from the understudied and ecologically complex Amazonia.
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7
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Fouquet A, Cornuault J, Rodrigues MT, Werneck FP, Hrbek T, Acosta-Galvis AR, Massemin D, J. R. Kok P, Ernst R. Diversity, biogeography and reproductive evolution in the genus Pipa (Amphibia: Anura: Pipidae). Mol Phylogenet Evol 2022; 170:107442. [DOI: 10.1016/j.ympev.2022.107442] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/22/2021] [Accepted: 02/16/2022] [Indexed: 11/29/2022]
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8
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Borghezan EDA, Pires THDS, Ikeda T, Zuanon J, Kohshima S. A Review on Fish Sensory Systems and Amazon Water Types With Implications to Biodiversity. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2020.589760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The Amazon has the highest richness of freshwater organisms in the world, which has led to a multitude of hypotheses on the mechanisms that generated this biodiversity. However, most of these hypotheses focus on the spatial distance of populations, a framework that fails to provide an explicit mechanism of speciation. Ecological conditions in Amazon freshwaters can be strikingly distinct, as it has been recognized since Alfred Russel Wallace’s categorization into black, white, and blue (= clear) waters. Water types reflect differences in turbidity, dissolved organic matter, electrical conductivity, pH, amount of nutrients and lighting environment, characteristics that directly affect the sensory abilities of aquatic organisms. Since natural selection drives evolution of sensory systems to function optimally according to environmental conditions, the sensory systems of Amazon freshwater organisms are expected to vary according to their environment. When differences in sensory systems affect chances of interbreeding between populations, local adaptations may result in speciation. Here, we briefly present the limnologic characteristics of Amazonian water types and how they are expected to influence photo-, chemical-, mechano-, and electro-reception of aquatic organisms, focusing on fish. We put forward that the effect of different water types on the adaptation of sensory systems is an important mechanism that contributed to the evolution of fish diversity. We point toward underexplored research perspectives on how divergent selection may act on sensory systems and thus contribute to the origin and maintenance of the biodiversity of Amazon aquatic environments.
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9
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Bogotá-Gregory JD, Lima FCT, Correa SB, Silva-Oliveira C, Jenkins DG, Ribeiro FR, Lovejoy NR, Reis RE, Crampton WGR. Biogeochemical water type influences community composition, species richness, and biomass in megadiverse Amazonian fish assemblages. Sci Rep 2020; 10:15349. [PMID: 32948815 PMCID: PMC7501869 DOI: 10.1038/s41598-020-72349-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 08/26/2020] [Indexed: 11/09/2022] Open
Abstract
Amazonian waters are classified into three biogeochemical categories by dissolved nutrient content, sediment type, transparency, and acidity-all important predictors of autochthonous and allochthonous primary production (PP): (1) nutrient-poor, low-sediment, high-transparency, humic-stained, acidic blackwaters; (2) nutrient-poor, low-sediment, high-transparency, neutral clearwaters; (3) nutrient-rich, low-transparency, alluvial sediment-laden, neutral whitewaters. The classification, first proposed by Alfred Russel Wallace in 1853, is well supported but its effects on fish are poorly understood. To investigate how Amazonian fish community composition and species richness are influenced by water type, we conducted quantitative year-round sampling of floodplain lake and river-margin habitats at a locality where all three water types co-occur. We sampled 22,398 fish from 310 species. Community composition was influenced more by water type than habitat. Whitewater communities were distinct from those of blackwaters and clearwaters, with community structure correlated strongly to conductivity and turbidity. Mean per-sampling event species richness and biomass were significantly higher in nutrient-rich whitewater floodplain lakes than in oligotrophic blackwater and clearwater river-floodplain systems and light-limited whitewater rivers. Our study provides novel insights into the influences of biogeochemical water type and ecosystem productivity on Earth's most diverse aquatic vertebrate fauna and highlights the importance of including multiple water types in conservation planning.
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Affiliation(s)
| | - Flávio C T Lima
- Museu de Zoologia da Universidade Estadual de Campinas, Cidade Universitária, Campinas, São Paulo, 13083-863, Brazil
| | - Sandra B Correa
- Department of Wildlife, Fisheries and Aquaculture, Mississippi State University, Box 9680, Starkville, MS, 39762, USA
| | - Cárlison Silva-Oliveira
- Instituto Nacional de Pesquisas da Amazonia, Coleção de Peixes, Av. André Araújo, 2936, Petrópolis, Manaus, Amazonas, 69.067-375, Brazil
| | - David G Jenkins
- Department of Biology, University of Central Florida, 4100 Libra Dr, Orlando, FL, 32816, USA
| | - Frank R Ribeiro
- Coleção Ictiológica da Universidade Federal do Oeste do Pará. Campus Amazônia, Avenida Mendonça Furtado, 2946, Fátima, Santarém, Pará, CEP 68040-470, Brazil
| | - Nathan R Lovejoy
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Roberto E Reis
- Pontifícia Universidade Católica do Rio Grande do Sul, Avenida Ipiranga 6681, Porto Alegre, Rio Grande do Sul, 90619-900, Brazil
| | - William G R Crampton
- Department of Biology, University of Central Florida, 4100 Libra Dr, Orlando, FL, 32816, USA.
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Sylvain F, Holland A, Audet‐Gilbert É, Luis Val A, Derome N. Amazon fish bacterial communities show structural convergence along widespread hydrochemical gradients. Mol Ecol 2019; 28:3612-3626. [DOI: 10.1111/mec.15184] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 07/13/2019] [Accepted: 07/15/2019] [Indexed: 12/30/2022]
Affiliation(s)
| | - Aleicia Holland
- Department of Ecology, Environment and Evolution School of Life Science La Trobe University Bundoora Vic. Australia
| | - Émie Audet‐Gilbert
- Institut de Biologie Intégrative et des Systèmes Université Laval Québec City QC Canada
| | - Adalberto Luis Val
- Laboratório de Ecofisiologia e Evolução Molecular Instituto Nacional de Pesquisas da Amazônia (INPA) Manaus Brazil
| | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes Université Laval Québec City QC Canada
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Pires THS, Borghezan EA, Cunha SLR, Leitão RP, Pinto KS, Zuanon J. Sensory drive in colourful waters: morphological variation suggests combined natural and sexual selection in an Amazonian fish. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Tiago H S Pires
- Laboratório de Ecologia Comportamental e Evolutiva - LECE, Instituto Nacional de Pesquisas da Amazônia - INPA., Petrópolis, Manaus AM, Brazil
| | - Elio A Borghezan
- Laboratório de Ecologia Comportamental e Evolutiva - LECE, Instituto Nacional de Pesquisas da Amazônia - INPA., Petrópolis, Manaus AM, Brazil
- Wildlife Research Center of Kyoto University., Sakyo-ku, Kyoto, Japan
| | - Sergio L R Cunha
- Laboratório de Ecologia Comportamental e Evolutiva - LECE, Instituto Nacional de Pesquisas da Amazônia - INPA., Petrópolis, Manaus AM, Brazil
- Laboratório de Ecologia de Ecossistemas Aquáticos - LEEA, Universidade Federal do Ceará/UFC, Fortaleza CE, Brazil
| | - Rafael P Leitão
- Laboratório de Ecologia de Peixes, Departamento de Biologia Geral - ICB, Universidade Federal de Minas Gerais/UFMG, Pampulha, Belo Horizonte MG, Brazil
| | - Kalebe S Pinto
- Laboratório de Ecologia Comportamental e Evolutiva - LECE, Instituto Nacional de Pesquisas da Amazônia - INPA., Petrópolis, Manaus AM, Brazil
| | - Jansen Zuanon
- Laboratório de Ecologia Comportamental e Evolutiva - LECE, Instituto Nacional de Pesquisas da Amazônia - INPA., Petrópolis, Manaus AM, Brazil
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12
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Rodríguez-Zárate CJ, Sandoval-Castillo J, van Sebille E, Keane RG, Rocha-Olivares A, Urteaga J, Beheregaray LB. Isolation by environment in the highly mobile olive ridley turtle ( Lepidochelys olivacea) in the eastern Pacific. Proc Biol Sci 2019; 285:rspb.2018.0264. [PMID: 29720414 DOI: 10.1098/rspb.2018.0264] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/10/2018] [Indexed: 11/12/2022] Open
Abstract
Spatial and temporal scales at which processes modulate genetic diversity over the landscape are usually overlooked, impacting the design of conservation management practices for widely distributed species. We examine processes shaping population divergence in highly mobile species by re-assessing the case of panmixia in the iconic olive ridley turtle from the eastern Pacific. We implemented a biophysical model of connectivity and a seascape genetic analysis based on nuclear DNA variation of 634 samples collected from 27 nesting areas. Two genetically distinct populations largely isolated during reproductive migrations and mating were detected, each composed of multiple nesting sites linked by high connectivity. This pattern was strongly associated with a steep environmental gradient and also influenced by ocean currents. These findings relate to meso-scale features of a dynamic oceanographic interface in the eastern tropical Pacific (ETP) region, a scenario that possibly provides different cost-benefit solutions and selective pressures for sea turtles during both the mating and migration periods. We reject panmixia and propose a new paradigm for olive ridley turtles where reproductive isolation due to assortative mating is linked to its environment. Our study demonstrates the relevance of integrative approaches for assessing the role of environmental gradients and oceanographic currents as drivers of genetic differentiation in widely distributed marine species. This is relevant for the conservation management of species of highly mobile behaviour, and assists the planning and development of large-scale conservation strategies for the threatened olive ridley turtles in the ETP.
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Affiliation(s)
| | | | - Erik van Sebille
- Institute for Marine and Atmospheric Research, Utrecht University, 3584 CC, The Netherlands.,Grantham Institute and Department of Physics, Imperial College London, London SW7 2AZ, UK
| | - Robert G Keane
- Geographic Information Systems, Flinders University, Adelaide, South Adelaide 5001, Australia
| | - Axayácatl Rocha-Olivares
- Laboratorio de Ecología Molecular, Departamento de Oceanografía Biológica, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada Baja California 22860, Mexico
| | | | - Luciano B Beheregaray
- Molecular Ecology Laboratory, Flinders University, Adelaide, South Adelaide 5001, Australia
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Carvalho TP, Arce H M, Reis RE, Sabaj MH. Molecular phylogeny of Banjo catfishes (Ostaryophisi: Siluriformes: Aspredinidae): A continental radiation in South American freshwaters. Mol Phylogenet Evol 2018; 127:459-467. [PMID: 29723648 DOI: 10.1016/j.ympev.2018.04.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 04/27/2018] [Accepted: 04/27/2018] [Indexed: 10/17/2022]
Abstract
The family Aspredinidae is a moderately diverse and broadly distributed group of freshwater fishes endemic to South America. Commonly known as Banjo Catfishes, Aspredinidae currently includes 44 valid species divided among 13 genera. The first species-comprehensive hypothesis on phylogenetic relationships among aspredinids is presented. The phylogeny is based on DNA sequence data for five gene fragments (mitochondrial 16S and COI; nuclear RAG1, MYH6 and SH3PX3) from 114 individuals representing 31 species in 12 aspredinid genera. Analyses of molecular data support the monophyly of most genera (Bunocephalus excepted) and several higher-level relationships previously proposed by morphological studies. Based on the molecular phylogeny, a new suprageneric classification for Aspredinidae is proposed with the new monotypic subfamily Pseudobunocephalinae as the sister taxon to all other aspredinids.
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Affiliation(s)
- Tiago P Carvalho
- Laboratório de Ictiologia, Departamento de Zoologia, Universidade Federal do Rio Grande do Sul. Av. Bento Gonçalves, 9500, 91501-970 Porto Alegre, RS, Brazil; Department of Ichthyology, The Academy of Natural Sciences of Philadelphia, Drexel University, 1900 Benjamin Franklin Parkway, 19103-1195 Philadelphia, PA, USA.
| | - Mariangeles Arce H
- Department of Ichthyology, The Academy of Natural Sciences of Philadelphia, Drexel University, 1900 Benjamin Franklin Parkway, 19103-1195 Philadelphia, PA, USA.
| | - Roberto E Reis
- PUCRS, Laboratório de Sistemática de Vertebrados, Av. Ipiranga, 6681, 90619-900 Porto Alegre, RS, Brazil.
| | - Mark H Sabaj
- Department of Ichthyology, The Academy of Natural Sciences of Philadelphia, Drexel University, 1900 Benjamin Franklin Parkway, 19103-1195 Philadelphia, PA, USA.
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14
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Pires THS, Borghezan EA, Machado VN, Powell DL, Röpke CP, Oliveira C, Zuanon J, Farias IP. Testing Wallace's intuition: water type, reproductive isolation and divergence in an Amazonian fish. J Evol Biol 2018; 31:882-892. [PMID: 29577482 DOI: 10.1111/jeb.13272] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 03/14/2018] [Accepted: 03/16/2018] [Indexed: 01/20/2023]
Abstract
Alfred Russel Wallace proposed classifying Amazon rivers based on their colour and clarity: white, black and clear water. Wallace also proposed that black waters could mediate diversification and yield distinct fish species. Here, we bring evidence of speciation mediated by water type in the sailfin tetra (Crenuchus spilurus), a fish whose range encompasses rivers of very distinct hydrochemical conditions. Distribution of the two main lineages concords with Wallace's water types: one restricted to the acidic and nutrient-poor waters of the Negro River (herein Rio Negro lineage) and a second widespread throughout the remaining of the species' distribution (herein Amazonas lineage). These lineages occur over a very broad geographical range, suggesting that despite occurring in regions separated by thousands of kilometres, individuals of the distinct lineages fail to occupy each other's habitats, hundreds of metres apart and not separated by physical barrier. Reproductive isolation was assessed in isolated pairs exposed to black-water conditions. All pairs with at least one individual of the lineage not native to black waters showed significantly lower spawning success, suggesting that the water type affected the fitness and contributed to reproductive isolation. Our results endorse Wallace's intuition and highlight the importance of ecological factors in shaping diversity of the Amazon fish fauna.
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Affiliation(s)
- Tiago H S Pires
- Laboratório de Ecologia Comportamental e Evolutiva/LECE, Instituto Nacional de Pesquisas da Amazônia/INPA, Manaus, AM, Brazil
| | - Elio A Borghezan
- Laboratório de Ecologia Comportamental e Evolutiva/LECE, Instituto Nacional de Pesquisas da Amazônia/INPA, Manaus, AM, Brazil
| | - Valeria N Machado
- Laboratório de Evolução e Genética Animal/LEGAL, Universidade Federal do Amazonas/UFAM, Manaus, AM, Brazil
| | - Daniel L Powell
- Department of Biology, Texas A&M University. TAMU, College Station, TX, USA
| | - Cristhiana P Röpke
- Departamento de Ciências Pesqueiras, Faculdade de Ciências Agrárias, Universidade Federal do Amazonas, Manaus, AM, Brazil
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil
| | - Jansen Zuanon
- Laboratório de Ecologia Comportamental e Evolutiva/LECE, Instituto Nacional de Pesquisas da Amazônia/INPA, Manaus, AM, Brazil
| | - Izeni P Farias
- Laboratório de Evolução e Genética Animal/LEGAL, Universidade Federal do Amazonas/UFAM, Manaus, AM, Brazil
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15
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Thom G, Amaral FRD, Hickerson MJ, Aleixo A, Araujo-Silva LE, Ribas CC, Choueri E, Miyaki CY. Phenotypic and Genetic Structure Support Gene Flow Generating Gene Tree Discordances in an Amazonian Floodplain Endemic Species. Syst Biol 2018; 67:700-718. [DOI: 10.1093/sysbio/syy004] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 01/23/2018] [Indexed: 01/25/2023] Open
Affiliation(s)
- Gregory Thom
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, Rua do Matão, 277, Cidade Universitária, São Paulo, SP 05508-090, Brazil
| | - Fabio Raposo Do Amaral
- Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Laboratório de Genética Evolutiva, Universidade Federal de São Paulo, Rua Professor Artur Riedel, 275, Diadema, SP 09972–270, Brazil
| | - Michael J Hickerson
- Department of Biology, Marshak Science Building, City College of New York, 160, Convent Avenue, 10031 New York, NY, USA
| | - Alexandre Aleixo
- Departamento de Ornitologia, Museu Paraense Emílio Goeldi (MPEG), Caixa Postal 399, Belém, PA 66040-170, Brazil
| | - Lucas E Araujo-Silva
- Departamento de Ornitologia, Museu Paraense Emílio Goeldi (MPEG), Caixa Postal 399, Belém, PA 66040-170, Brazil
| | - Camila C Ribas
- Coordenação de biodiversidade, Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo 2936, Manaus, AM 69060-001, Brazil
| | - Erik Choueri
- Coordenação de biodiversidade, Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo 2936, Manaus, AM 69060-001, Brazil
| | - Cristina Y Miyaki
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, Rua do Matão, 277, Cidade Universitária, São Paulo, SP 05508-090, Brazil
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16
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Jardim de Queiroz L, Torrente-Vilara G, Quilodran C, Rodrigues da Costa Doria C, Montoya-Burgos JI. Multifactorial genetic divergence processes drive the onset of speciation in an Amazonian fish. PLoS One 2017; 12:e0189349. [PMID: 29261722 PMCID: PMC5738069 DOI: 10.1371/journal.pone.0189349] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 11/24/2017] [Indexed: 11/19/2022] Open
Abstract
Understanding the processes that drive population genetic divergence in the Amazon is challenging because of the vast scale, the environmental richness and the outstanding biodiversity of the region. We addressed this issue by determining the genetic structure of the widespread Amazonian common sardine fish Triportheus albus (Characidae). We then examined the influence, on this species, of all previously proposed population-structuring factors, including isolation-by-distance, isolation-by-barrier (the Teotônio Falls) and isolation-by-environment using variables that describe floodplain and water characteristics. The population genetics analyses revealed an unusually strong structure with three geographical groups: Negro/Tapajós rivers, Lower Madeira/Central Amazon, and Upper Madeira. Distance-based redundancy analyses showed that the optimal model for explaining the extreme genetic structure contains all proposed structuring factors and accounts for up to 70% of the genetic structure. We further quantified the contribution of each factor via a variance-partitioning analysis. Our results demonstrate that multiple factors, often proposed as individual drivers of population divergence, have acted in conjunction to divide T. albus into three genetic lineages. Because the conjunction of multiple long-standing population-structuring processes may lead to population reproductive isolation, that is, the onset of speciation, we suggest that the multifactorial population-structuring processes highlighted in this study could account for the high speciation rate characterising the Amazon Basin.
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Affiliation(s)
| | - Gislene Torrente-Vilara
- Department of Marine Sciences, Universidade Federal de São Paulo, Campus Baixada Santista, Santos/SP, Brazil
| | - Claudio Quilodran
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Switzerland
| | | | - Juan I. Montoya-Burgos
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Switzerland
- * E-mail:
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17
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The Role of Geographical and Ecological Factors on Population Divergence of the Neotropical otter Lontra longicaudis (Carnivora, Mustelidae). Evol Biol 2017. [DOI: 10.1007/s11692-017-9428-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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18
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Brauer CJ, Hammer MP, Beheregaray LB. Riverscape genomics of a threatened fish across a hydroclimatically heterogeneous river basin. Mol Ecol 2016; 25:5093-5113. [DOI: 10.1111/mec.13830] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/15/2016] [Accepted: 08/23/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Chris J. Brauer
- Molecular Ecology Laboratory School of Biological Sciences Flinders University Adelaide SA 5042 Australia
| | - Michael P. Hammer
- Natural Sciences, Museum and Art Gallery of the Northern Territory Darwin NT 0801 Australia
| | - Luciano B. Beheregaray
- Molecular Ecology Laboratory School of Biological Sciences Flinders University Adelaide SA 5042 Australia
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19
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Röpke CP, Amadio SA, Winemiller KO, Zuanon J. Seasonal dynamics of the fish assemblage in a floodplain lake at the confluence of the Negro and Amazon Rivers. JOURNAL OF FISH BIOLOGY 2016; 89:194-212. [PMID: 26563716 DOI: 10.1111/jfb.12791] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 08/06/2015] [Indexed: 06/05/2023]
Abstract
The temporal effect of discharge and limnology on fish composition and species diversity in a floodplain lake at the confluence of the Amazon and Negro Rivers was evaluated. Species richness, abundance and assemblage composition were strongly influenced by seasonal discharge of the Amazon and Negro Rivers, which affects lateral connectivity, water conductivity and temperature. As a consequence, temporal β-diversity was high in the lake and the assemblage was dominated by seasonally transient species. Relatively large species known to feed on resources within the floodplain were captured almost exclusively during the flood period. During the dry season, the assemblage was dominated by fishes adapted to harsh conditions of high temperature and low dissolved oxygen concentrations. An open system with high spatial and temporal heterogeneity created by the meeting of two large rivers with different water chemistry, Lago Catalão has a dynamic fish assemblage. Given its high temporal β-diversity and abundance of fishes, many of great importance in local fisheries, Lago Catalão and other floodplain lakes in this region merit special attention for conservation.
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Affiliation(s)
- C P Röpke
- Programa de Pós-Graduação em Biologia de Água Doce e Pesca Interior, Instituto Nacional de Pesquisas da Amazônia - INPA, Cx. Postal 2223, 69080-971, Manaus, Amazonas, Brasil
| | - S A Amadio
- Coordenação de Biodiversidade, CBIO/Instituto Nacional de Pesquisas da Amazônia - INPA, Manaus, Amazonas, Brasil
| | - K O Winemiller
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, 77843-2258, U.S.A
| | - J Zuanon
- Coordenação de Biodiversidade, CBIO/Instituto Nacional de Pesquisas da Amazônia - INPA, Manaus, Amazonas, Brasil
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20
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Thomaz AT, Christie MR, Knowles LL. The architecture of river networks can drive the evolutionary dynamics of aquatic populations. Evolution 2016; 70:731-9. [DOI: 10.1111/evo.12883] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 02/01/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Andréa T. Thomaz
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor Michigan 48109
| | - Mark R. Christie
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor Michigan 48109
- Department of Biological Science; Purdue University; West Lafayette Indiana 47907
- Department of Forestry and Natural Resources; Purdue University; West Lafayette Indiana 47907
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor Michigan 48109
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21
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Edwards T, Tollis M, Hsieh P, Gutenkunst RN, Liu Z, Kusumi K, Culver M, Murphy RW. Assessing models of speciation under different biogeographic scenarios; an empirical study using multi-locus and RNA-seq analyses. Ecol Evol 2016; 6:379-96. [PMID: 26843925 PMCID: PMC4729248 DOI: 10.1002/ece3.1865] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 11/01/2015] [Accepted: 11/02/2015] [Indexed: 12/30/2022] Open
Abstract
Evolutionary biology often seeks to decipher the drivers of speciation, and much debate persists over the relative importance of isolation and gene flow in the formation of new species. Genetic studies of closely related species can assess if gene flow was present during speciation, because signatures of past introgression often persist in the genome. We test hypotheses on which mechanisms of speciation drove diversity among three distinct lineages of desert tortoise in the genus Gopherus. These lineages offer a powerful system to study speciation, because different biogeographic patterns (physical vs. ecological segregation) are observed at opposing ends of their distributions. We use 82 samples collected from 38 sites, representing the entire species' distribution and generate sequence data for mtDNA and four nuclear loci. A multilocus phylogenetic analysis in *BEAST estimates the species tree. RNA‐seq data yield 20,126 synonymous variants from 7665 contigs from two individuals of each of the three lineages. Analyses of these data using the demographic inference package ∂a∂i serve to test the null hypothesis of no gene flow during divergence. The best‐fit demographic model for the three taxa is concordant with the *BEAST species tree, and the ∂a∂i analysis does not indicate gene flow among any of the three lineages during their divergence. These analyses suggest that divergence among the lineages occurred in the absence of gene flow and in this scenario the genetic signature of ecological isolation (parapatric model) cannot be differentiated from geographic isolation (allopatric model).
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Affiliation(s)
- Taylor Edwards
- School of Natural Resources and the Environment The University of Arizona Tucson Arizona 85721; University of Arizona Genetics Core University of Arizona Tucson Arizona 85721
| | - Marc Tollis
- School of Life Sciences Arizona State University Tempe Arizona 85287
| | - PingHsun Hsieh
- Department of Ecology and Evolutionary Biology The University of Arizona Tucson Arizona 85721
| | - Ryan N Gutenkunst
- Department of Ecology and Evolutionary Biology The University of Arizona Tucson Arizona 85721; Department of Molecular and Cellular Biology The University of Arizona Tucson Arizona 85721
| | - Zhen Liu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China
| | - Kenro Kusumi
- School of Life Sciences Arizona State University Tempe Arizona 85287
| | - Melanie Culver
- School of Natural Resources and the Environment The University of Arizona Tucson Arizona 85721; Arizona Cooperative Fish & Wildlife Research Unit USGS University of Arizona Tucson Arizona 85721
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China; Centre for Biodiversity and Conservation Biology Royal Ontario Museum Toronto ON Canada
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22
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Weir JT, Faccio MS, Pulido-Santacruz P, Barrera-Guzmán AO, Aleixo A. Hybridization in headwater regions, and the role of rivers as drivers of speciation in Amazonian birds. Evolution 2015; 69:1823-34. [DOI: 10.1111/evo.12696] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 04/29/2015] [Accepted: 04/29/2015] [Indexed: 01/19/2023]
Affiliation(s)
- Jason T. Weir
- Department of Biological Sciences; University of Toronto Scarborough; Toronto Canada
- Department of Ecology and Evolutionary Biology; University of Toronto; Toronto Canada
| | - Maya S. Faccio
- Department of Ecology and Evolutionary Biology; University of Toronto; Toronto Canada
| | | | | | - Alexandre Aleixo
- Department of Zoology; Museu Paraense Emílio Goeldi; Belém Brazil
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23
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Beheregaray LB, Cooke GM, Chao NL, Landguth EL. Ecological speciation in the tropics: insights from comparative genetic studies in Amazonia. Front Genet 2015; 5:477. [PMID: 25653668 PMCID: PMC4301025 DOI: 10.3389/fgene.2014.00477] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 12/29/2014] [Indexed: 11/26/2022] Open
Abstract
Evolution creates and sustains biodiversity via adaptive changes in ecologically relevant traits. Ecologically mediated selection contributes to genetic divergence both in the presence or absence of geographic isolation between populations, and is considered an important driver of speciation. Indeed, the genetics of ecological speciation is becoming increasingly studied across a variety of taxa and environments. In this paper we review the literature of ecological speciation in the tropics. We report on low research productivity in tropical ecosystems and discuss reasons accounting for the rarity of studies. We argue for research programs that simultaneously address biogeographical and taxonomic questions in the tropics, while effectively assessing relationships between reproductive isolation and ecological divergence. To contribute toward this goal, we propose a new framework for ecological speciation that integrates information from phylogenetics, phylogeography, population genomics, and simulations in evolutionary landscape genetics (ELG). We introduce components of the framework, describe ELG simulations (a largely unexplored approach in ecological speciation), and discuss design and experimental feasibility within the context of tropical research. We then use published genetic datasets from populations of five codistributed Amazonian fish species to assess the performance of the framework in studies of tropical speciation. We suggest that these approaches can assist in distinguishing the relative contribution of natural selection from biogeographic history in the origin of biodiversity, even in complex ecosystems such as Amazonia. We also discuss on how to assess ecological speciation using ELG simulations that include selection. These integrative frameworks have considerable potential to enhance conservation management in biodiversity rich ecosystems and to complement historical biogeographic and evolutionary studies of tropical biotas.
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Affiliation(s)
- Luciano B Beheregaray
- Molecular Ecology Lab, School of Biological Sciences, Flinders University Adelaide, SA, Australia
| | - Georgina M Cooke
- The Australian Museum, The Australian Museum Research Institute Sydney, NSW, Australia
| | - Ning L Chao
- Departamento de Ciências Pesqueiras, Universidade Federal do Amazonas Manaus, Brazil ; National Museum of Marine Biology and Aquarium Pintung, Taiwan
| | - Erin L Landguth
- Division of Biological Sciences, University of Montana Missoula, MT, USA
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