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Raffard A, Cucherousset J, Montoya JM, Richard M, Acoca-Pidolle S, Poésy C, Garreau A, Santoul F, Blanchet S. Intraspecific diversity loss in a predator species alters prey community structure and ecosystem functions. PLoS Biol 2021; 19:e3001145. [PMID: 33705375 PMCID: PMC7987174 DOI: 10.1371/journal.pbio.3001145] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/23/2021] [Accepted: 02/15/2021] [Indexed: 01/09/2023] Open
Abstract
Loss in intraspecific diversity can alter ecosystem functions, but the underlying mechanisms are still elusive, and intraspecific biodiversity-ecosystem function (iBEF) relationships have been restrained to primary producers. Here, we manipulated genetic and functional richness of a fish consumer (Phoxinus phoxinus) to test whether iBEF relationships exist in consumer species and whether they are more likely sustained by genetic or functional richness. We found that both genotypic and functional richness affected ecosystem functioning, either independently or interactively. Loss in genotypic richness reduced benthic invertebrate diversity consistently across functional richness treatments, whereas it reduced zooplankton diversity only when functional richness was high. Finally, losses in genotypic and functional richness altered functions (decomposition) through trophic cascades. We concluded that iBEF relationships lead to substantial top-down effects on entire food chains. The loss of genotypic richness impacted ecological properties as much as the loss of functional richness, probably because it sustains "cryptic" functional diversity.
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Affiliation(s)
- Allan Raffard
- CNRS, Université Toulouse III Paul Sabatier, Station d’Écologie Théorique et Expérimentale du CNRS à Moulis, UMR-5321, Moulis, France
- EcoLab, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - Julien Cucherousset
- CNRS, Université Toulouse III Paul Sabatier, UMR-5174 EDB (Laboratoire Evolution & Diversité Biologique), Toulouse, France
| | - José M. Montoya
- CNRS, Université Toulouse III Paul Sabatier, Station d’Écologie Théorique et Expérimentale du CNRS à Moulis, UMR-5321, Moulis, France
| | - Murielle Richard
- CNRS, Université Toulouse III Paul Sabatier, Station d’Écologie Théorique et Expérimentale du CNRS à Moulis, UMR-5321, Moulis, France
| | - Samson Acoca-Pidolle
- CNRS, Université Toulouse III Paul Sabatier, Station d’Écologie Théorique et Expérimentale du CNRS à Moulis, UMR-5321, Moulis, France
| | - Camille Poésy
- CNRS, Université Toulouse III Paul Sabatier, Station d’Écologie Théorique et Expérimentale du CNRS à Moulis, UMR-5321, Moulis, France
| | - Alexandre Garreau
- CNRS, Université Toulouse III Paul Sabatier, Station d’Écologie Théorique et Expérimentale du CNRS à Moulis, UMR-5321, Moulis, France
| | - Frédéric Santoul
- EcoLab, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - Simon Blanchet
- CNRS, Université Toulouse III Paul Sabatier, Station d’Écologie Théorique et Expérimentale du CNRS à Moulis, UMR-5321, Moulis, France
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Kulbaba MW, Shaw RG. Lifetime Fitness through Female and Male Function: Influences of Genetically Effective Population Size and Density. Am Nat 2021; 197:434-447. [PMID: 33755534 DOI: 10.1086/713067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractAn individual's lifetime fitness and patterns of mating between individuals are interdependent features of sexual organisms. Mating systems (outcrossing vs. selfing or mating between close relatives) can affect the distribution of offspring fitness, which generally declines with inbreeding, which in turn is related to a population's genetically effective size (Ne). Fitness and mating patterns are also expected to vary with proximity of mates (i.e., population density). Consequently, density and Ne may influence demographic and genetic changes over generations and interact in their effects. Here, we report an experiment designed to assess the influence of these two population-level properties on mating system and lifetime fitness. In experimental arrays under quasi-natural conditions, we varied the density and Ne of the hermaphroditic annual legume Chamaecrista fasciculata. We recorded components of fitness for each individual and employed microsatellite markers to estimate outcrossing and assign paternity. We used aster analyses to estimate lifetime fitness for genetic families using female (seeds set) and male (seeds sired) reproduction as fitness measures. With estimates from these analyses, we assessed the evidence for a trade-off between fitness attained through female versus male function, but we found none. Lifetime fitness increased with density, especially under high Ne. Outcrossing rates increased with density under high Ne but declined modestly with density under low Ne. Our results show that density and Ne have strong direct effects on fitness and mating systems, with negative fitness effects of low Ne limiting the positive effects of increasing density. These findings highlight the importance of the interactive effects of density and Ne on lifetime fitness.
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53
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Wan K, Guo L, Ye C, Zhu J, Zhang M, Yu X. Accumulation of antibiotic resistance genes in full-scale drinking water biological activated carbon (BAC) filters during backwash cycles. WATER RESEARCH 2021; 190:116744. [PMID: 33401101 DOI: 10.1016/j.watres.2020.116744] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/14/2020] [Accepted: 12/11/2020] [Indexed: 06/12/2023]
Abstract
Biological activated carbon (BAC) filtration, a process widely used in drinking water treatment, was recently reported to harbor antibiotic resistance genes (ARGs). This emerging contamination is poorly understood. This study was conducted to investigate the occurrence of ARGs and bacterial community in full-scale BAC filters during the backwash cycle using high-throughput qPCR and high-throughput sequencing. A total of 178 ARGs were detected in all biofilm samples, with relative abundance ranging from 0.1 to 1.37 copies per 16S rRNA and absolute abundance ranging from 4.48 × 107 to 3.09 × 109 copies/g carbon. Biofilms sampled from different filters shared most detected ARGs and dominant genera including Bryobacter, Pedomicrobium, Reyranella, and Terrimonas, though their bacterial community structure differed significantly. After backwashing, the relative ARGs abundance increased by 1.5- to 3.8-folds and the absolute ARGs abundance increased by 0.90- to 1.12-logs in all biofilm samples during filter ripening, indicating that ARGs accumulated in filters during this period. Redundancy analysis suggested that such ARGs accumulation was mainly driven by horizontal gene transfer in winter, but highly correlated with the increasing relative abundance of genera Bryobacter and Acidibacter in summer. It was observed that 80.6 %-89.3% of the detected ARGs persisted in the filters despite of the backwashing. Given the high richness and relative abundance of ARGs in BAC filter and the ineffectiveness of backwashing in ARG removal, more stringent downstream disinfection strategies are deserved and more research is necessary to assess potential human health risks due to the persistence of ARGs in drinking water.
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Affiliation(s)
- Kun Wan
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Lizheng Guo
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Chengsong Ye
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Jianwen Zhu
- Hangzhou Water Group Company, Ltd, Hangzhou 310009, China
| | - Menglu Zhang
- College of Environmental Science and Engineering, Fujian Normal University, Fuzhou 350007, China
| | - Xin Yu
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, China.
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Hu Y, Fan H, Chen Y, Chang J, Zhan X, Wu H, Zhang B, Wang M, Zhang W, Yang L, Hou X, Shen X, Pan T, Wu W, Li J, Hu H, Wei F. Spatial patterns and conservation of genetic and phylogenetic diversity of wildlife in China. SCIENCE ADVANCES 2021; 7:eabd5725. [PMID: 33523945 PMCID: PMC10671236 DOI: 10.1126/sciadv.abd5725] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
Genetic diversity and phylogenetic diversity reflect the evolutionary potential and history of species, respectively. However, the levels and spatial patterns of genetic and phylogenetic diversity of wildlife at the regional scale have largely remained unclear. Here, we performed meta-analyses of genetic diversity in Chinese terrestrial vertebrates based on three genetic markers and investigated their phylogenetic diversity based on a dated phylogenetic tree of 2461 species. We detected strong positive spatial correlations among mitochondrial DNA-based genetic diversity, phylogenetic diversity, and species richness. Moreover, the terrestrial vertebrates harbored higher genetic and phylogenetic diversity in South China and Southwest China than in other regions. Last, climatic factors (precipitation and temperature) had significant positive effects while altitude and human population density had significant negative impacts on levels of mitochondrial DNA-based genetic diversity in most cases. Our findings will help guide national-level genetic diversity conservation plans and a post-2020 biodiversity conservation framework.
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Affiliation(s)
- Yibo Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Huizhong Fan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Youhua Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jiang Chang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Xiangjiang Zhan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Hua Wu
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Baowei Zhang
- School of Life Sciences, Anhui University, Hefei, China
| | - Meng Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenyan Zhang
- University of Chinese Academy of Sciences, Beijing, China
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Lin Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xian Hou
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xing Shen
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Tao Pan
- School of Life Sciences, Anhui University, Hefei, China
| | - Wei Wu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun Li
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Haihua Hu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangdong, China
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Lu Y, Xu P, Li Q, Wang Y, Wu C. Planning priority conservation areas for biodiversity under climate change in topographically complex areas: A case study in Sichuan province, China. PLoS One 2020; 15:e0243425. [PMID: 33362279 PMCID: PMC7757871 DOI: 10.1371/journal.pone.0243425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 11/22/2020] [Indexed: 11/24/2022] Open
Abstract
Identifying priority conservation areas plays a significant role in conserving biodiversity under climate change, but uncertainties create challenges for conservation planning. To reduce uncertainties in the conservation planning framework, we developed an adaptation index to assess the effect of topographic complexity on species adaptation to climate change, which was incorporated into the conservation framework as conservation costs. Meanwhile, the species distributions were predicted by the Maxent model, and the priority conservation areas were optimized during different periods in Sichuan province by the Marxan model. Our results showed that the effect of topographic complexity was critical for species adaptation, but the adaptation index decreased with the temperature increase. Based on the conservation targets and costs, the distributions of priority conservation areas were mainly concentrated in mountainous areas around the Sichuan Basin where may be robust to the adaptation to climate change. In the future, the distributions of priority conservation areas had no evident changes, accounting for about 26% and 28% of the study areas. Moreover, most species habitats could be conserved in terms of conservation targets in these priority conservation areas. Therefore, our approach could achieve biodiversity conservation goals and be highly practical. More importantly, quantifying the effect of topography also is critical for options for planning conservation areas in response to climate change.
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Affiliation(s)
- Yafeng Lu
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences and Ministry of Water Resources, Chengdu, China
| | - Pei Xu
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences and Ministry of Water Resources, Chengdu, China
| | - Qinwen Li
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences and Ministry of Water Resources, Chengdu, China
| | - Yukuan Wang
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences and Ministry of Water Resources, Chengdu, China
| | - Cheng Wu
- Power China Kunming Engineering Corporation Limited, Kuming, China
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Mayer‐Pinto M, Ledet J, Crowe TP, Johnston EL. Sublethal effects of contaminants on marine habitat-forming species: a review and meta-analysis. Biol Rev Camb Philos Soc 2020; 95:1554-1573. [PMID: 32614143 PMCID: PMC7689725 DOI: 10.1111/brv.12630] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 06/08/2020] [Accepted: 06/10/2020] [Indexed: 12/24/2022]
Abstract
Contaminants may affect ecosystem functioning by reducing the fitness of organisms and these impacts may cascade through ecosystems, particularly if the sensitive organisms are also habitat-forming species. Understanding how sub-lethal effects of toxicants can affect the quality and functions of biogenic habitats is critical if we are to establish effective guidelines for protecting ecosystems. We carried out a global systematic review and meta-analysis critically evaluating contaminant effects on properties of habitat-formers linked to ecosystem functioning. We reviewed a total of 95 publications. However, 40% of publications initially captured by the literature search were identified as having flaws in experimental design and ~11% did not present results in an appropriate way and thus were excluded from the quantitative meta-analysis. We quantitatively reviewed 410 studies from 46 publications, of which 313 (~76%) were on plants and seaweeds, that is macro-algae, saltmarsh plants and seagrasses, 58 (~14%) studied corals and 39 (~10%) looked at toxicant impacts on bivalves, with 70% of those on mussels and the remaining studies on oysters. Response variables analysed were photosynthetic efficiency, amount of chlorophyll a (as a proxy for primary production) and growth of plants, seaweeds and corals as well as leaf area of plants. We also analysed filtration, growth and respiration rates of bivalves. Our meta-analysis found that chemical contaminants have a significant negative impact on most of the analysed functional variables, with the exception of the amount of chlorophyll a. Metals were the most widely harmful type of contaminant, significantly decreasing photosynthetic efficiency of kelps, leaf area of saltmarsh plants, growth of fucoids, corals and saltmarsh plants and the filtration rates of bivalves. Organic contaminants decreased the photosynthetic efficiency of seagrass, but had no significant effects on bivalve filtration. We did not find significant effects of polycyclic aromatic hydrocarbons on any of the analysed functional variables or habitat-forming taxa, but this could be due to the low number of studies available. A meta-regression revealed that relationships between concentrations of metal contaminants and the magnitude of functional responses varied with the type of metal and habitat-former. Increasing concentrations of contaminants significantly increased the negative effects on the photosynthetic efficiency of habitat-formers. There was, however, no apparent relationship between ecologically relevant concentrations of metals and effect sizes of photosynthetic efficiency of corals and seaweeds. A qualitative analysis of all relevant studies found slightly different patterns when compared to our quantitative analysis, emphasising the need for studies to meet critical inclusion criteria for meta-analyses. Our study highlights links between effects of contaminants at lower levels of organisation (i.e. at the biochemical and/or physiological level of individuals) and ecological, large-scale impacts, through effects on habitat-forming species. Contaminants can clearly reduce the functioning of many habitat-forming marine species. We therefore recommend the adoption of routine measures of functional endpoints in monitoring and conservation programs to complement structural measures.
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Affiliation(s)
- Mariana Mayer‐Pinto
- Centre for Marine Scince and Innovation, Evolution & Ecology Research Centre, School of Biological, Earth and Environmental SciencesUniversity of New South WalesSydneyNew South Wales2052Australia
- Sydney Institute of Marine SciencesMosmanNew South Wales2088Australia
| | - Janine Ledet
- Centre for Marine Scince and Innovation, Evolution & Ecology Research Centre, School of Biological, Earth and Environmental SciencesUniversity of New South WalesSydneyNew South Wales2052Australia
| | - Tasman P. Crowe
- Earth Institute and School of Biology & Environmental Science, Science Centre WestUniversity College DublinBelfieldDublin 4Ireland
| | - Emma L. Johnston
- Centre for Marine Scince and Innovation, Evolution & Ecology Research Centre, School of Biological, Earth and Environmental SciencesUniversity of New South WalesSydneyNew South Wales2052Australia
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Martin GK, Beisner BE, Chain FJJ, Cristescu ME, Del Giorgio PA, Derry AM. Freshwater zooplankton metapopulations and metacommunities respond differently to environmental and spatial variation. Ecology 2020; 102:e03224. [PMID: 33067865 DOI: 10.1002/ecy.3224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/22/2020] [Accepted: 08/17/2020] [Indexed: 11/09/2022]
Abstract
Theory predicts that population genetic structure and metacommunity structure are linked by the common processes of drift and migration, but how population genetic structure and metacommunity structure are related in nature is still unknown. Deeper understanding of the processes influencing both genetic and community diversity is vital for better predicting how environmental change will impact biodiversity patterns. We examined how crustacean zooplankton and rotifer species' metapopulation genetic structure and metacommunities respond to environmental and spatial variation both within and across four regions of boreal Canada. Metapopulation and metacommunity variation partitioning results were compared within and across the four regions. Metapopulations and metacommunities responded differently to environmental variation and spatial structure both within and across regions, as metapopulations were influenced by different environmental variables compared to metacommunities. At larger spatial scales both metapopulations and metacommunities exhibited greater spatial and environmental structuring, again responding to a different subset of environmental variables. Our findings suggest that even though both genetic and species diversity are linked by the same processes, regional variation in environmental characteristics and spatial structure influence resulting biodiversity patterns differently. To date, no other empirical research has explored relationships between entire metapopulation and metacommunity assemblages at large regional spatial scales.
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Affiliation(s)
- Gillian K Martin
- Department of Biological Sciences, Groupe de Recherche Interuniversitaire en Limnologie (GRIL), University of Québec at Montreal, Québec, H2X 3Y7, Canada
| | - Beatrix E Beisner
- Department of Biological Sciences, Groupe de Recherche Interuniversitaire en Limnologie (GRIL), University of Québec at Montreal, Québec, H2X 3Y7, Canada
| | - Frédéric J J Chain
- Department of Biological Science, University of Massachusetts Lowell, Massachusetts, 01854, USA
| | - Melania E Cristescu
- Department of Biology, Groupe de Recherche Interuniversitaire en Limnologie (GRIL), McGill University, Québec, H3A 1B1, Canada
| | - Paul A Del Giorgio
- Department of Biological Sciences, Groupe de Recherche Interuniversitaire en Limnologie (GRIL), University of Québec at Montreal, Québec, H2X 3Y7, Canada
| | - Alison M Derry
- Department of Biological Sciences, Groupe de Recherche Interuniversitaire en Limnologie (GRIL), University of Québec at Montreal, Québec, H2X 3Y7, Canada
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Kollars NM, DuBois K, Stachowicz JJ. Sequential disturbances alter the outcome of inter‐genotypic interactions in a clonal plant. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13690] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Nicole M. Kollars
- Center for Population Biology University of California Davis CA USA
- Department of Evolution and Ecology University of California Davis CA USA
| | - Katherine DuBois
- Department of Evolution and Ecology University of California Davis CA USA
- Bodega Marine Laboratory Bodega Bay CA USA
| | - John J. Stachowicz
- Center for Population Biology University of California Davis CA USA
- Department of Evolution and Ecology University of California Davis CA USA
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Abstract
This research deals with the development of capacity-building through marine bioresearch from a scientific standpoint, particularly through a new approach based on publication and authorship metrics. By using a 50-y dataset on the discovery of marine natural products, this study draws verifiable conclusions on capacity-building, a process that is often difficult to quantify. This is a stepping-stone toward evidence-based capacity building for bioprospecting as originally envisioned in the framework of high-level international fora, such as the Convention on Biological Diversity and, more recently, the Nagoya Protocol. The Convention on Biological Diversity, and the Nagoya Protocol in particular, provide a framework for the fair and equitable sharing of benefits arising from the utilization of biological resources and traditional knowledge, and ultimately aim to promote capacity-building in the developing world. However, measuring capacity-building is a challenging task due to its intangible nature. By compiling and analyzing a database of scientific peer-reviewed publications over a period of 50 y (1965 to 2015), we investigated capacity-building in global marine natural product discovery. We used publication and authorship metrics to assess how the capacity to become scientifically proficient, prolific, and independent has changed in bioprospecting countries. Our results show that marine bioprospecting is a dynamically growing field of research with continuously increasing numbers of participating countries, publications, and scientists. Yet despite longstanding efforts to promote equitability and scientific independence, not all countries have similarly increased their capacity to explore marine biodiversity within their national jurisdiction areas. Although developing countries show an increasing trend in the number of publications, a few developed countries still account for almost one-half of all publications in the field. Multiple lines of evidence suggest that economic capacity affects how well countries with species-rich marine ecosystems can scientifically explore those resources. Overall, the capacity-building data analyzed here provides a timely contribution to the ongoing international debate about access to and benefit-sharing of biological resources for countries exploring biodiversity within and outside their national jurisdiction areas.
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Machine learning approaches identify male body size as the most accurate predictor of species richness. BMC Biol 2020; 18:105. [PMID: 32854698 PMCID: PMC7453550 DOI: 10.1186/s12915-020-00835-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/22/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A major challenge in biodiversity science is to understand the factors contributing to the variability of species richness -the number of different species in a community or region - among comparable taxonomic lineages. Multiple biotic and abiotic factors have been hypothesized to have an effect on species richness and have been used as its predictors, but identifying accurate predictors is not straightforward. Spiders are a highly diverse group, with some 48,000 species in 120 families; yet nearly 75% of all species are found within just the ten most speciose families. Here we use a Random Forest machine learning algorithm to test the predictive power of different variables hypothesized to affect species richness of spider genera. RESULTS We test the predictive power of 22 variables from spiders' morphological, genetic, geographic, ecological and behavioral landscapes on species richness of 45 genera selected to represent the phylogenetic and biological breath of Araneae. Among the variables, Random Forest analyses find body size (specifically, minimum male body size) to best predict species richness. Multiple Correspondence analysis confirms this outcome through a negative relationship between male body size and species richness. Multiple Correspondence analyses furthermore establish that geographic distribution of congeneric species is positively associated with genus diversity, and that genera from phylogenetically older lineages are species poorer. Of the spider-specific traits, neither the presence of ballooning behavior, nor sexual size dimorphism, can predict species richness. CONCLUSIONS We show that machine learning analyses can be used in deciphering the factors associated with diversity patterns. Since no spider-specific biology could predict species richness, but the biologically universal body size did, we believe these conclusions are worthy of broader biological testing. Future work on other groups of organisms will establish whether the detected associations of species richness with small body size and wide geographic ranges hold more broadly.
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Chu X, Zhang D, Buckling A, Zhang Q. Warmer temperatures enhance beneficial mutation effects. J Evol Biol 2020; 33:1020-1027. [PMID: 32424908 PMCID: PMC7496171 DOI: 10.1111/jeb.13642] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/23/2020] [Accepted: 05/12/2020] [Indexed: 12/17/2022]
Abstract
Temperature determines the rates of all biochemical and biophysical processes, and is also believed to be a key driver of macroevolutionary patterns. It is suggested that physiological constraints at low temperatures may diminish the fitness advantages of otherwise beneficial mutations; by contrast, relatively high, benign, temperatures allow beneficial mutations to efficiently show their phenotypic effects. To experimentally test this "mutational effects" mechanism, we examined the fitness effects of mutations across a temperature gradient using bacterial genotypes from the early stage of a mutation accumulation experiment with Escherichia coli. While the incidence of beneficial mutations did not significantly change across environmental temperatures, the number of mutations that conferred strong beneficial fitness effects was greater at higher temperatures. The results therefore support the hypothesis that warmer temperatures increase the chance and magnitude of positive selection, with implications for explaining the geographic patterns in evolutionary rates and understanding contemporary evolution under global warming.
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Affiliation(s)
- Xiao‐Lin Chu
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijingChina
| | - Da‐Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijingChina
| | | | - Quan‐Guo Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijingChina
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Zizka VMA, Weiss M, Leese F. Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. METABARCODING AND METAGENOMICS 2020. [DOI: 10.3897/mbmg.4.51925] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Genetic diversity is the most basal level of biodiversity and determines the evolutionary capacity of species to adapt to changing environments, yet it is typically neglected in routine biomonitoring and stressor impact assessment. For a comprehensive analysis of stressor impacts on genetic diversity, it is necessary to assess genetic variants simultaneously in many individuals and species. Such an assessment is not as straightforward and usually limited to one or few focal species. However, nowadays species diversity can be assessed by analysing thousands of individuals of a community simultaneously with DNA metabarcoding. Recent bioinformatic advances also allow for the extraction of exact sequence variants (ESVs or haplotypes) in addition to Operational Taxonomic Units (OTUs). By using this new capability, we here evaluated if the analysis of intraspecific mitochondrial diversity in addition to species diversity can provide insights into responses of stream macrozoobenthic communities to environmental stressors. For this purpose, we analysed macroinvertebrate bulk samples of three German river systems with different stressor levels using DNA metabarcoding. While OTU and haplotype number were negatively correlated with stressor impact, this association was not as clear when studying haplotype diversity across all taxa. However, stressor responses were found for sensitive EPT (Ephemeroptera, Plecoptera, Trichoptera) taxa and those exceedingly resistant to organic stress. An increase in haplotype number per OTU and haplotype diversity of sensitive taxa was observed with an increase in ecosystem quality and stability, while the opposite pattern was detected for pollution resistant taxa. However, this pattern was less prominent than expected based on the strong differences in stressor intensity between sites. To compare genetic diversity among communities in river systems, we focussed on OTUs, which were present in all systems. As OTU composition differed strongly between rivers, this led to the exclusion of a high number of OTUs, especially in diverse river systems of good quality, which potentially diminished the increase in intraspecific diversity. To better understand responses of intraspecific genetic diversity to environmental stressors, for example in river ecosystems, it would be important to increase OTU overlap between compared sites, e.g. by sampling a narrower stressor gradient, and to perform calibrated studies controlling for the number of individuals and their haplotypes. However, this pioneer study shows that the extraction of haplotypes from DNA metabarcoding datasets is a promising source of information to simultaneously assess intraspecific diversity changes in response to environmental impacts for a metacommunity.
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Blanchet S, Prunier JG, Paz‐Vinas I, Saint‐Pé K, Rey O, Raffard A, Mathieu‐Bégné E, Loot G, Fourtune L, Dubut V. A river runs through it: The causes, consequences, and management of intraspecific diversity in river networks. Evol Appl 2020; 13:1195-1213. [PMID: 32684955 PMCID: PMC7359825 DOI: 10.1111/eva.12941] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/14/2020] [Accepted: 02/19/2020] [Indexed: 01/01/2023] Open
Abstract
Rivers are fascinating ecosystems in which the eco-evolutionary dynamics of organisms are constrained by particular features, and biologists have developed a wealth of knowledge about freshwater biodiversity patterns. Over the last 10 years, our group used a holistic approach to contribute to this knowledge by focusing on the causes and consequences of intraspecific diversity in rivers. We conducted empirical works on temperate permanent rivers from southern France, and we broadened the scope of our findings using experiments, meta-analyses, and simulations. We demonstrated that intraspecific (genetic) diversity follows a spatial pattern (downstream increase in diversity) that is repeatable across taxa (from plants to vertebrates) and river systems. This pattern can result from interactive processes that we teased apart using appropriate simulation approaches. We further experimentally showed that intraspecific diversity matters for the functioning of river ecosystems. It indeed affects not only community dynamics, but also key ecosystem functions such as litter degradation. This means that losing intraspecific diversity in rivers can yield major ecological effects. Our work on the impact of multiple human stressors on intraspecific diversity revealed that-in the studied river systems-stocking of domestic (fish) strains strongly and consistently alters natural spatial patterns of diversity. It also highlighted the need for specific analytical tools to tease apart spurious from actual relationships in the wild. Finally, we developed original conservation strategies at the basin scale based on the systematic conservation planning framework that appeared pertinent for preserving intraspecific diversity in rivers. We identified several important research avenues that should further facilitate our understanding of patterns of local adaptation in rivers, the identification of processes sustaining intraspecific biodiversity-ecosystem function relationships, and the setting of reliable conservation plans.
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Affiliation(s)
- Simon Blanchet
- Centre National pour la Recherche ScientifiqueStation d'Écologie Théorique et Expérimentale du CNRS à MoulisUniversité Toulouse III Paul SabatierUMR‐5321MoulisFrance
- Centre National pour la Recherche ScientifiqueLaboratoire Evolution & Diversité BiologiqueInstitut de Recherche pour le DéveloppementUniversité Toulouse III Paul SabatierUMR‐5174 EDBToulouseFrance
| | - Jérôme G. Prunier
- Centre National pour la Recherche ScientifiqueStation d'Écologie Théorique et Expérimentale du CNRS à MoulisUniversité Toulouse III Paul SabatierUMR‐5321MoulisFrance
| | - Ivan Paz‐Vinas
- Centre National pour la Recherche ScientifiqueLaboratoire Evolution & Diversité BiologiqueInstitut de Recherche pour le DéveloppementUniversité Toulouse III Paul SabatierUMR‐5174 EDBToulouseFrance
- Laboratoire Ecologie Fonctionnelle et EnvironnementUniversité de ToulouseUPSCNRSINPUMR‐5245 ECOLABToulouseFrance
| | - Keoni Saint‐Pé
- Centre National pour la Recherche ScientifiqueLaboratoire Evolution & Diversité BiologiqueInstitut de Recherche pour le DéveloppementUniversité Toulouse III Paul SabatierUMR‐5174 EDBToulouseFrance
| | - Olivier Rey
- IHPEUniv. MontpellierCNRSIfremerUniv. Perpignan Via DomitiaPerpignanFrance
| | - Allan Raffard
- Centre National pour la Recherche ScientifiqueStation d'Écologie Théorique et Expérimentale du CNRS à MoulisUniversité Toulouse III Paul SabatierUMR‐5321MoulisFrance
| | - Eglantine Mathieu‐Bégné
- Centre National pour la Recherche ScientifiqueLaboratoire Evolution & Diversité BiologiqueInstitut de Recherche pour le DéveloppementUniversité Toulouse III Paul SabatierUMR‐5174 EDBToulouseFrance
- IHPEUniv. MontpellierCNRSIfremerUniv. Perpignan Via DomitiaPerpignanFrance
| | - Géraldine Loot
- Centre National pour la Recherche ScientifiqueLaboratoire Evolution & Diversité BiologiqueInstitut de Recherche pour le DéveloppementUniversité Toulouse III Paul SabatierUMR‐5174 EDBToulouseFrance
| | - Lisa Fourtune
- Centre National pour la Recherche ScientifiqueLaboratoire Evolution & Diversité BiologiqueInstitut de Recherche pour le DéveloppementUniversité Toulouse III Paul SabatierUMR‐5174 EDBToulouseFrance
- PEIRENEEA 7500Université de LimogesLimogesFrance
| | - Vincent Dubut
- Aix Marseille UniversitéCNRSIRDAvignon UniversitéIMBEMarseilleFrance
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64
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Karbstein K, Prinz K, Hellwig F, Römermann C. Plant intraspecific functional trait variation is related to within-habitat heterogeneity and genetic diversity in Trifolium montanum L. Ecol Evol 2020; 10:5015-5033. [PMID: 32551078 PMCID: PMC7297743 DOI: 10.1002/ece3.6255] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 03/11/2020] [Accepted: 03/17/2020] [Indexed: 11/23/2022] Open
Abstract
Intraspecific trait variation (ITV), based on available genetic diversity, is one of the major means plant populations can respond to environmental variability. The study of functional trait variation and diversity has become popular in ecological research, for example, as a proxy for plant performance influencing fitness. Up to now, it is unclear which aspects of intraspecific functional trait variation (iFDCV) can be attributed to the environment or genetics under natural conditions. Here, we examined 260 individuals from 13 locations of the rare (semi-)dry calcareous grassland species Trifolium montanum L. in terms of iFDCV, within-habitat heterogeneity, and genetic diversity. The iFDCV was assessed by measuring functional traits (releasing height, biomass, leaf area, specific leaf area, leaf dry matter content, Fv/Fm, performance index, stomatal pore surface, and stomatal pore area index). Abiotic within-habitat heterogeneity was derived from altitude, slope exposure, slope, leaf area index, soil depth, and further soil factors. Based on microsatellites, we calculated expected heterozygosity (He) because it best-explained, among other indices, iFDCV. We performed multiple linear regression models quantifying relationships among iFDCV, abiotic within-habitat heterogeneity and genetic diversity, and also between separate functional traits and abiotic within-habitat heterogeneity or genetic diversity. We found that abiotic within-habitat heterogeneity influenced iFDCV twice as strong compared to genetic diversity. Both aspects together explained 77% of variation in iFDCV ( R adj 2 = .77, F 2, 10 = 21.66, p < .001). The majority of functional traits (releasing height, biomass, specific leaf area, leaf dry matter content, Fv/Fm, and performance index) were related to abiotic habitat conditions indicating responses to environmental heterogeneity. In contrast, only morphology-related functional traits (releasing height, biomass, and leaf area) were related to genetics. Our results suggest that both within-habitat heterogeneity and genetic diversity affect iFDCV and are thus crucial to consider when aiming to understand or predict changes of plant species performance under changing environmental conditions.
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Affiliation(s)
- Kevin Karbstein
- Institute of Ecology and SystematicsFriedrich‐Schiller‐University JenaJenaGermany
- Present address:
Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium)University of GoettingenAlbrecht‐von‐Haller Institute for Plant SciencesGoettingenGermany
| | - Kathleen Prinz
- Institute of Ecology and SystematicsFriedrich‐Schiller‐University JenaJenaGermany
- Present address:
Landschaftspflegeverband Suedharz/Kyffhaeuser e.V.NordhausenGermany
| | - Frank Hellwig
- Institute of Ecology and SystematicsFriedrich‐Schiller‐University JenaJenaGermany
| | - Christine Römermann
- Institute of Ecology and SystematicsFriedrich‐Schiller‐University JenaJenaGermany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
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65
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Evolutionary history and past climate change shape the distribution of genetic diversity in terrestrial mammals. Nat Commun 2020; 11:2557. [PMID: 32444801 PMCID: PMC7244709 DOI: 10.1038/s41467-020-16449-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 04/30/2020] [Indexed: 11/08/2022] Open
Abstract
Knowledge of global patterns of biodiversity, ranging from intraspecific genetic diversity (GD) to taxonomic and phylogenetic diversity, is essential for identifying and conserving the processes that shape the distribution of life. Yet, global patterns of GD and its drivers remain elusive. Here we assess existing biodiversity theories to explain and predict the global distribution of GD in terrestrial mammal assemblages. We find a strong positive covariation between GD and interspecific diversity, with evolutionary time, reflected in phylogenetic diversity, being the best predictor of GD. Moreover, we reveal the negative effect of past rapid climate change and the positive effect of inter-annual precipitation variability in shaping GD. Our models, explaining almost half of the variation in GD globally, uncover the importance of deep evolutionary history and past climate stability in accumulating and maintaining intraspecific diversity, and constitute a crucial step towards reducing the Wallacean shortfall for an important dimension of biodiversity. The drivers of genetic diversity (GD) are poorly understood at the global scale. Here the authors show, for terrestrial mammals, that within-species GD covaries with phylogenetic diversity and is higher in locations with more stable past climates. They also interpolate GD for data-poor locations such as the tropics.
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66
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Kumar A, Dewan S, Lochan R, Sharma DK. Spatial genetic structure of black francolin ( Francolinus francolinus asiae) in the North-Western Himalayan region based on mitochondrial control region. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:163-170. [PMID: 32340511 DOI: 10.1080/24701394.2020.1757664] [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] [Indexed: 10/24/2022]
Abstract
Due to specific habitat preferences and behavioural limitations, black francolin is not uniformly distributed across the northwestern Himalayan landscape, rather is confined to certain land mosaic. The habitable zones are further reduced due to several manmade threats as logging and forest fire leading to sparse distribution. Overall 54 samples were used for partial sequence analysis of mitochondrial control region. A well evident divergence pattern was observed as individuals collected from low altitude, terrai region significantly distanced from high altitude sampled individuals. Also, the individuals at lower elevation sites exhibited higher genetic diversity in comparison to the samples collected at higher elevations. This indicates that patchy distribution and low dispersal rate have resulted in fine-scale patterns of genetic diversity among the black francolin population. Further, habitat loss and forest fragmentation could lead to more small and isolated populations that could suffer from reduced genetic diversity and may be higher extinction rates.
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Affiliation(s)
- Anand Kumar
- Department of Zoology, HNB Garhwal University, Badshahithaul, New Tehri, India
| | - Saurabh Dewan
- Department of Zoology and Biotechnology, HNB Garhwal University, Srinagar, India
| | - Rajeev Lochan
- Department of Zoology and Biotechnology, HNB Garhwal University, Srinagar, India
| | - Dinesh K Sharma
- Department of Zoology, HNB Garhwal University, Badshahithaul, New Tehri, India
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67
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Cruz-Salazar B, García-Bautista M, Ruiz-Montoya L. Genetic Structure Associated with the Ecological Traits of Four Species of Phyllostomid Bats Inhabiting Selva El Ocote Biosphere Reserve, Chiapas, México. ACTA CHIROPTEROLOGICA 2020. [DOI: 10.3161/15081109acc2019.21.2.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Bárbara Cruz-Salazar
- Consejo Nacional de Ciencia y Tecnología, Universidad Autónoma de Tlaxcala, Carretera Federal Puebla-Tlaxcala Km 1.5, La Loma Xicohténcatl, CP 90062, Tlaxcala de Xicohténcatl, Tlaxcala, México
| | - Maricela García-Bautista
- Consejo Nacional de Ciencia y Tecnología, Universidad Autónoma de Tlaxcala, Carretera Federal Puebla-Tlaxcala Km 1.5, La Loma Xicohténcatl, CP 90062, Tlaxcala de Xicohténcatl, Tlaxcala, México
| | - Lorena Ruiz-Montoya
- Consejo Nacional de Ciencia y Tecnología, Universidad Autónoma de Tlaxcala, Carretera Federal Puebla-Tlaxcala Km 1.5, La Loma Xicohténcatl, CP 90062, Tlaxcala de Xicohténcatl, Tlaxcala, México
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68
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Manel S, Guerin PE, Mouillot D, Blanchet S, Velez L, Albouy C, Pellissier L. Global determinants of freshwater and marine fish genetic diversity. Nat Commun 2020; 11:692. [PMID: 32041961 PMCID: PMC7010757 DOI: 10.1038/s41467-020-14409-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 01/06/2020] [Indexed: 01/18/2023] Open
Abstract
Genetic diversity is estimated to be declining faster than species diversity under escalating threats, but its spatial distribution remains poorly documented at the global scale. Theory predicts that similar processes should foster congruent spatial patterns of genetic and species diversity, but empirical studies are scarce. Using a mined database of 50,588 georeferenced mitochondrial DNA barcode sequences (COI) for 3,815 marine and 1,611 freshwater fish species respectively, we examined the correlation between genetic diversity and species diversity and their global distributions in relation to climate and geography. Genetic diversity showed a clear spatial organisation, but a weak association with species diversity for both marine and freshwater species. We found a predominantly positive relationship between genetic diversity and sea surface temperature for marine species. Genetic diversity of freshwater species varied primarily across the regional basins and was negatively correlated with average river slope. The detection of genetic diversity patterns suggests that conservation measures should consider mismatching spatial signals across multiple facets of biodiversity. Biogeographic patterns of genetic diversity are poorly documented, especially for fish species. Here the authors show that (mitochondrial) genetic diversity has global spatial organization patterns with different environmental drivers for marine and freshwater fishes, where genetic diversity is only partly congruent with species richness.
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Affiliation(s)
- Stéphanie Manel
- CEFE, Univ. Montpellier, CNRS, EPHE-PSL University, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France.
| | - Pierre-Edouard Guerin
- CEFE, Univ. Montpellier, CNRS, EPHE-PSL University, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - David Mouillot
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France.,Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - Simon Blanchet
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS); Station d'Ecologie Théorique et Expérimentale, UMR 5321, F-09200, Moulis, France
| | - Laure Velez
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
| | - Camille Albouy
- IFREMER, unité Ecologie et Modèle pour l'Halieutique, Nantes, France
| | - Loïc Pellissier
- Swiss Federal Research Institute WSL, CH-8903, Birmensdorf, Switzerland.,Landscape Ecology, Institute of Terrestrial Ecosystems, Department of Environmental System Science, ETH Zürich, CH-8092, Zürich, Switzerland
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69
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Abstract
Biodiversity has always responded dynamically to environmental perturbations in the geological past, through changes to the abundances and distributions of genes and species, to the composition of biological communities, and to the cover and locations of different ecosystem types. This is how the 'nature' that exists today has survived. The same is true in the Anthropocene. The entire planet surface has been altered by humans, ranging from direct vegetation transformation and removal of most of the world's megafauna, through to atmospheric changes in greenhouse gasses and consequent climatic changes and ocean acidification. These anthropogenic perturbations have led to the establishment of genes and species in new locations, thus generating novel communities and ecosystems. In this historical context, recent biological changes should be seen as responses to multiple drivers of change, rather than being a problem per se. These changes are the means by which the biosphere is adjusting to and will ultimately survive the Anthropocene. Thus, management and conservation of the biological world, and our place in it, requires a transition from trying to minimize biological change to one in which we facilitate dynamism that accelerates the rates at which species and ecosystems adjust to human-associated drivers of change. This article is part of the theme issue 'Climate change and ecosystems: threats, opportunities and solutions'.
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Affiliation(s)
- Chris D Thomas
- Leverhulme Centre for Anthropocene Biodiversity, Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
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70
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Abstract
How biodiversity is maintained in ecosystems is a central issue in ecology. According to the evolutionary theory, heritable variations between individuals are important for the generation of species diversity, linking both intra and interspecific variations. The present food web model shows that intraspecific variations via natural selection also play crucial roles in maintaining the stability of large communities with diverse species. In particular, our computations indicate that larger communities need more intraspecific variation to be maintained and are powerfully stabilized when multiple traits are variable. Consequently, these variations are likely to be maintained in larger communities. Hence, intra and interspecific diversities may support each other during evolution.
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Affiliation(s)
- Akihiko Mougi
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, Matsue, Japan
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71
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Agrawal AA. A scale‐dependent framework for trade‐offs, syndromes, and specialization in organismal biology. Ecology 2020; 101:e02924. [DOI: 10.1002/ecy.2924] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/24/2019] [Accepted: 09/26/2019] [Indexed: 02/02/2023]
Affiliation(s)
- Anurag A. Agrawal
- Department of Ecology and Evolutionary Biology Cornell University Ithaca New York 14853 USA
- Department of Entomology Cornell University Ithaca New York 14853 USA
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72
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Krueger-Hadfield SA, Blakeslee AMH, Fowler AE. Incorporating Ploidy Diversity into Ecological and Community Genetics. JOURNAL OF PHYCOLOGY 2019; 55:1198-1207. [PMID: 31349373 DOI: 10.1111/jpy.12906] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 07/11/2019] [Indexed: 06/10/2023]
Abstract
Studies in ecological and community genetics have advanced our understanding of the role of intraspecific diversity in structuring communities and ecosystems. However, in near-shore marine communities, these studies have mostly been restricted to seagrasses, marsh plants, and oysters. Yet, macroalgae are critically important ecosystem engineers in these communities. Greater intraspecific diversity in a macroalgal ecosystem engineer should result in higher primary and secondary production and community resilience. The paucity of studies investigating the consequences of macroalgal intraspecific genetic variation might be due, in part, to the complexity of macroalgal life cycles. The majority of macroalgae have seemingly subtle, but in actuality, profoundly different life cycles than the more typical animal and angiosperm models. Here, we develop a novel genetic diversity metric, PHD , that incorporates the ratio of gametophytic to sporophytic thalli in natural populations. This metric scales from 0 to 1 like many common genetic diversity metrics, such as genotypic richness, enabling comparisons among metrics. We discuss PHD and examples from the literature, with specific reference to the widespread, red seaweed Agarophyton vermiculophyllum. We also discuss a sex diversity metric, PFM , which also scales from 0 to 1, but fewer studies have identified males and females in natural populations. Nevertheless, by incorporating these novel metrics into the repertoire of diversity metrics, we can explore the role of genetic diversity in community and ecosystem dynamics with an emphasis on the unique biology of many macroalgae, as well as other haplodiplontic taxa such as ferns, foraminiferans, and some fungi.
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Affiliation(s)
- Stacy A Krueger-Hadfield
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd CH464, Birmingham, Alabama, 35294, USA
| | - April M H Blakeslee
- Department of Biology, East Carolina University, E 10th Street, Greenville, North Carolina, 27858, USA
| | - Amy E Fowler
- Department of Environmental Science and Policy, George Mason University, 4400 University Dr, Fairfax, Virginia, 22030, USA
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73
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Fan (樊海英) H, Zhang (张清臣) Q, Rao (饶娟娟) J, Cao (曹静文) J, Lu (卢欣) X. Genetic Diversity–Area Relationships across Bird Species. Am Nat 2019; 194:736-740. [DOI: 10.1086/705346] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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74
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Wollenberg Valero KC, Marshall JC, Bastiaans E, Caccone A, Camargo A, Morando M, Niemiller ML, Pabijan M, Russello MA, Sinervo B, Werneck FP, Sites JW, Wiens JJ, Steinfartz S. Patterns, Mechanisms and Genetics of Speciation in Reptiles and Amphibians. Genes (Basel) 2019; 10:genes10090646. [PMID: 31455040 PMCID: PMC6769790 DOI: 10.3390/genes10090646] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/21/2019] [Accepted: 08/05/2019] [Indexed: 12/22/2022] Open
Abstract
In this contribution, the aspects of reptile and amphibian speciation that emerged from research performed over the past decade are reviewed. First, this study assesses how patterns and processes of speciation depend on knowing the taxonomy of the group in question, and discuss how integrative taxonomy has contributed to speciation research in these groups. This study then reviews the research on different aspects of speciation in reptiles and amphibians, including biogeography and climatic niches, ecological speciation, the relationship between speciation rates and phenotypic traits, and genetics and genomics. Further, several case studies of speciation in reptiles and amphibians that exemplify many of these themes are discussed. These include studies of integrative taxonomy and biogeography in South American lizards, ecological speciation in European salamanders, speciation and phenotypic evolution in frogs and lizards. The final case study combines genomics and biogeography in tortoises. The field of amphibian and reptile speciation research has steadily moved forward from the assessment of geographic and ecological aspects, to incorporating other dimensions of speciation, such as genetic mechanisms and evolutionary forces. A higher degree of integration among all these dimensions emerges as a goal for future research.
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Affiliation(s)
| | - Jonathon C Marshall
- Department of Zoology, Weber State University, 1415 Edvalson Street, Dept. 2505, Ogden, UT 84401, USA
| | - Elizabeth Bastiaans
- Department of Biology, State University of New York, College at Oneonta, Oneonta, NY 13820, USA
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Arley Camargo
- Centro Universitario de Rivera, Universidad de la República, Ituzaingó 667, Rivera 40000, Uruguay
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC, CENPAT-CONICET) Bv. Brown 2915, Puerto Madryn U9120ACD, Argentina
| | - Matthew L Niemiller
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Maciej Pabijan
- Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, ul. Gronostajowa 9, 30-387 Kraków, Poland
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC V1V 1V7, Canada
| | - Barry Sinervo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Coastal Biology Building, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | - Fernanda P Werneck
- Programa de Coleções Científicas Biológicas, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus 69060-000, Brazil
| | - Jack W Sites
- Department of Biological and Marine Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, UK
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Sebastian Steinfartz
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstrasse 33, 04103 Leipzig, Germany
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75
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Eisenhauer N, Schielzeth H, Barnes AD, Barry K, Bonn A, Brose U, Bruelheide H, Buchmann N, Buscot F, Ebeling A, Ferlian O, Freschet GT, Giling DP, Hättenschwiler S, Hillebrand H, Hines J, Isbell F, Koller-France E, König-Ries B, de Kroon H, Meyer ST, Milcu A, Müller J, Nock CA, Petermann JS, Roscher C, Scherber C, Scherer-Lorenzen M, Schmid B, Schnitzer SA, Schuldt A, Tscharntke T, Türke M, van Dam NM, van der Plas F, Vogel A, Wagg C, Wardle DA, Weigelt A, Weisser WW, Wirth C, Jochum M. A multitrophic perspective on biodiversity-ecosystem functioning research. ADV ECOL RES 2019; 61:1-54. [PMID: 31908360 PMCID: PMC6944504 DOI: 10.1016/bs.aecr.2019.06.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Concern about the functional consequences of unprecedented loss in biodiversity has prompted biodiversity-ecosystem functioning (BEF) research to become one of the most active fields of ecological research in the past 25 years. Hundreds of experiments have manipulated biodiversity as an independent variable and found compelling support that the functioning of ecosystems increases with the diversity of their ecological communities. This research has also identified some of the mechanisms underlying BEF relationships, some context-dependencies of the strength of relationships, as well as implications for various ecosystem services that mankind depends upon. In this paper, we argue that a multitrophic perspective of biotic interactions in random and non-random biodiversity change scenarios is key to advance future BEF research and to address some of its most important remaining challenges. We discuss that the study and the quantification of multitrophic interactions in space and time facilitates scaling up from small-scale biodiversity manipulations and ecosystem function assessments to management-relevant spatial scales across ecosystem boundaries. We specifically consider multitrophic conceptual frameworks to understand and predict the context-dependency of BEF relationships. Moreover, we highlight the importance of the eco-evolutionary underpinnings of multitrophic BEF relationships. We outline that FAIR data (meeting the standards of findability, accessibility, interoperability, and reusability) and reproducible processing will be key to advance this field of research by making it more integrative. Finally, we show how these BEF insights may be implemented for ecosystem management, society, and policy. Given that human well-being critically depends on the multiple services provided by diverse, multitrophic communities, integrating the approaches of evolutionary ecology, community ecology, and ecosystem ecology in future BEF research will be key to refine conservation targets and develop sustainable management strategies.
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Affiliation(s)
- Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Holger Schielzeth
- Department of Population Ecology, Institute of Ecology and Evolution, Friedrich Schiller University Jena, Jena, Germany
| | - Andrew D Barnes
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Kathryn Barry
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, Johannisallee 21-23, 04103 Leipzig, Germany
| | - Aletta Bonn
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Ulrich Brose
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- EcoNetLab, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger-Str. 159, 07743 Jena, Germany
| | - Helge Bruelheide
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Biology / Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle (Saale), Germany
| | - Nina Buchmann
- Institute of Agricultural Sciences, ETH Zurich, Universitätstr. 2, 8092 Zurich, Switzerland
| | - François Buscot
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- UFZ - Helmholtz Centre for Environmental Research, Soil Ecology Department, Theodor-Lieser-Straße 4, 06120 Halle Saale, Germany
| | - Anne Ebeling
- Institute of Ecology and Evolution, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany
| | - Olga Ferlian
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Grégoire T Freschet
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 (CNRS - Université de Montpellier - Université Paul-Valéry Montpellier - EPHE), 1919 Route de Mende, Montpellier 34293, France
| | - Darren P Giling
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Ecology and Evolution, Friedrich Schiller University Jena, Dornburger Straße 159, 07743 Jena, Germany
| | - Stephan Hättenschwiler
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 (CNRS - Université de Montpellier - Université Paul-Valéry Montpellier - EPHE), 1919 Route de Mende, Montpellier 34293, France
| | - Helmut Hillebrand
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute for Chemistry and Biology of Marine Environments [ICBM], Carl-von-Ossietzky University Oldenburg, Schleusenstrasse 1, 26382 Wilhelmshaven, Germany
| | - Jes Hines
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Forest Isbell
- Department of Ecology, Evolution and Behavior, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN 55108, USA
| | - Eva Koller-France
- Karlsruher Institut für Technologie (KIT), Institut für Geographie und Geoökologie, Reinhard-Baumeister-Platz 1, 76131 Karlsruhe, Germany
| | - Birgitta König-Ries
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Computer Science, Friedrich Schiller Universität Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Hans de Kroon
- Radboud University, Institute for Water and Wetland Research, Animal Ecology and Physiology & Experimental Plant Ecology, PO Box 9100, 6500 GL Nijmegen, The Netherlands
| | - Sebastian T Meyer
- Terrestrial Ecology Research Group, Technical University of Munich, School of Life Sciences Weihenstephan, Hans-Carl-von-Carlowitz-Platz 2, 85354 Freising, Germany
| | - Alexandru Milcu
- Ecotron Européen de Montpellier, Centre National de la Recherche Scientifique (CNRS), Unité Propre de Service 3248, Campus Baillarguet, Montferrier-sur-Lez, France
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 (CNRS - Université de Montpellier - Université Paul-Valéry Montpellier - EPHE), 1919 Route de Mende, Montpellier 34293, France
| | - Jörg Müller
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Glashüttenstraße 5, 96181 Rauhenebrach, Germany
- Bavarian Forest National Park, Freyunger Str. 2, 94481 Grafenau, Germany
| | - Charles A Nock
- Geobotany, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
- Department of Renewable Resources, University of Alberta, 751 General Services Building, Edmonton, Canada, T6G 2H1
| | - Jana S Petermann
- Department of Biosciences, University of Salzburg, Hellbrunner Str. 34, 5020 Salzburg, Austria
| | - Christiane Roscher
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- UFZ - Helmholtz Centre for Environmental Research, Department Physiological Diversity, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Christoph Scherber
- Institute of Landscape Ecology, University of Münster, Heisenbergstr. 2, 48149 Münster, Germany
| | - Michael Scherer-Lorenzen
- Geobotany, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
| | - Bernhard Schmid
- Department of Geography, University of Zürich, 190 Winterthurerstrasse, 8057, Zürich, Switzerland
| | | | - Andreas Schuldt
- Forest Nature Conservation, Faculty of Forest Sciences and Forest Ecology, University of Göttingen, Buesgenweg 3, 37077 Goettingen, Germany
| | - Teja Tscharntke
- Agroecology, Dept. of Crop Sciences, University of Göttingen, Germany
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Germany
| | - Manfred Türke
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Biological and Medical Imaging (IBMI), Helmholtz Zentrum München (HMGU) - German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Nicole M van Dam
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger-Str. 159, 07743 Jena, Germany
| | - Fons van der Plas
- Institute of Biology, Leipzig University, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Anja Vogel
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Ecology and Evolution, Friedrich Schiller University Jena, Dornburger Straße 159, 07743 Jena, Germany
| | - Cameron Wagg
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, E3B 8B7, Fredericton, Canada
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, 190 Winterthurerstrasse, 8057, Zürich, Switzerland
| | - David A Wardle
- Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798
| | - Alexandra Weigelt
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, Johannisallee 21-23, 04103 Leipzig, Germany
| | - Wolfgang W Weisser
- Terrestrial Ecology Research Group, Technical University of Munich, School of Life Sciences Weihenstephan, Hans-Carl-von-Carlowitz-Platz 2, 85354 Freising, Germany
| | - Christian Wirth
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, Johannisallee 21-23, 04103 Leipzig, Germany
| | - Malte Jochum
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
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Xie P, Zhao G, Niu J, Wang J, Zhou Q, Guo Y, Ma X. Comprehensive analysis of population genetics of Phoxinus phoxinus ujmonensis in the Irtysh River: Abiotic and biotic factors. Ecol Evol 2019; 9:7997-8012. [PMID: 31380067 PMCID: PMC6662318 DOI: 10.1002/ece3.5320] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 05/14/2019] [Accepted: 05/15/2019] [Indexed: 12/25/2022] Open
Abstract
As a widely distributed species along the Irtysh River, Phoxinus phoxinus ujmonensis (Kaschtschenko, 1899) was used as a model to investigate genetic diversity and population structure as well as the influence of environmental factors on population genetics. In this study, we specifically developed 12 polymorphic microsatellite loci. The analysis of microsatellite and mtDNA markers revealed a high and a moderate genetic diversity across seven populations, respectively. Moderate differentiation was also detected among several populations, indicating the impact of habitat fragmentation and divergence. The absence of isolation by distance implied an extensive gene flow, while the presence of isolation by adaptation implied that these populations might be in the process of adapting to divergent habitats. Correlation analysis showed that abiotic factors like dissolved oxygen, pH, total dissolved solids, and conductivity in water as well as biotic factors like plankton diversity and fish species diversity had impact on genetic diversity and divergence in P. phoxinus ujmonensis populations. The results of this study will provide an insight into the effect of environmental factors on genetic diversity and contribute to the study of population genetics of sympatric species.
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Affiliation(s)
- Peng Xie
- College of FisheriesHuazhong Agricultural UniversityWuhanChina
| | - Guang Zhao
- College of FisheriesHuazhong Agricultural UniversityWuhanChina
| | - Jian‐Gong Niu
- Fisheries Research Institute of Xinjiang Uygur Autonomous RegionUrumqiChina
| | - Jun Wang
- Institute of International Rivers and Eco‐securityYunnan UniversityKunmingChina
| | - Qiong Zhou
- College of FisheriesHuazhong Agricultural UniversityWuhanChina
| | - Yan Guo
- Fisheries Research Institute of Xinjiang Uygur Autonomous RegionUrumqiChina
| | - Xu‐Fa Ma
- College of FisheriesHuazhong Agricultural UniversityWuhanChina
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Gregory AC, Zayed AA, Conceição-Neto N, Temperton B, Bolduc B, Alberti A, Ardyna M, Arkhipova K, Carmichael M, Cruaud C, Dimier C, Domínguez-Huerta G, Ferland J, Kandels S, Liu Y, Marec C, Pesant S, Picheral M, Pisarev S, Poulain J, Tremblay JÉ, Vik D, Babin M, Bowler C, Culley AI, de Vargas C, Dutilh BE, Iudicone D, Karp-Boss L, Roux S, Sunagawa S, Wincker P, Sullivan MB. Marine DNA Viral Macro- and Microdiversity from Pole to Pole. Cell 2019; 177:1109-1123.e14. [PMID: 31031001 PMCID: PMC6525058 DOI: 10.1016/j.cell.2019.03.040] [Citation(s) in RCA: 397] [Impact Index Per Article: 79.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/05/2019] [Accepted: 03/20/2019] [Indexed: 01/04/2023]
Abstract
Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow, and metabolic outputs. However, ecosystem-level impacts of viral community diversity remain difficult to assess due to classification issues and few reference genomes. Here, we establish an ∼12-fold expanded global ocean DNA virome dataset of 195,728 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions. Across the zones, local and global patterns and drivers in viral community diversity were established for both macrodiversity (inter-population diversity) and microdiversity (intra-population genetic variation). These patterns sometimes, but not always, paralleled those from macro-organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. Such further understanding of ocean viruses is critical for broader inclusion in ecosystem models.
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Affiliation(s)
- Ann C Gregory
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Ahmed A Zayed
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Nádia Conceição-Neto
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, KU Leuven-University of Leuven, Leuven, Belgium; Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, KU Leuven-University of Leuven, Leuven, Belgium
| | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, UK
| | - Ben Bolduc
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Mathieu Ardyna
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, 06230 Villefranche-sur-mer, France
| | - Ksenia Arkhipova
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, the Netherlands
| | - Margaux Carmichael
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M ECOMAP, 29680 Roscoff, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Corinne Cruaud
- CEA-Institut de Biologie François Jacob, Genoscope, Evry 91057, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Céline Dimier
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, 06230 Villefranche-sur-mer, France; Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | | | - Joannie Ferland
- Département de biologie, Québec Océan and Takuvik Joint International Laboratory (UMI 3376), Université Laval (Canada)-CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Stefanie Kandels
- Structural and Computational Biology, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Directors' Research, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Yunxiao Liu
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Claudie Marec
- Département de biologie, Québec Océan and Takuvik Joint International Laboratory (UMI 3376), Université Laval (Canada)-CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Stéphane Pesant
- PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, 28359 Bremen, Germany; MARUM, Bremen University, 28359 Bremen, Germany
| | - Marc Picheral
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, 06230 Villefranche-sur-mer, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Sergey Pisarev
- Shirshov Institute of Oceanology of Russian Academy of Sciences, 36 Nakhimovsky prosp, 117997 Moscow, Russia
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Jean-Éric Tremblay
- Département de biologie, Québec Océan and Takuvik Joint International Laboratory (UMI 3376), Université Laval (Canada)-CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Dean Vik
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Marcel Babin
- Département de biologie, Québec Océan and Takuvik Joint International Laboratory (UMI 3376), Université Laval (Canada)-CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Chris Bowler
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Alexander I Culley
- Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec, QC G1V 0A6, Canada
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M ECOMAP, 29680 Roscoff, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, the Netherlands; Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Simon Roux
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, 8093 Zurich, Switzerland
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH 43210, USA.
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Incorporating Rarity and Accessibility Factors into the Cultural Ecosystem Services Assessment in Mountainous Areas: A Case Study in the Upper Reaches of the Minjiang River. SUSTAINABILITY 2019. [DOI: 10.3390/su11082203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cultural ecosystem services (CES) are not only a key source for supporting the development of economy but also maintain the ecological security in mountainous areas. However, there are limited numbers of studies that focus on establishing the assessment model for the CES at a regional scale. We combined the topographic factors and accessibility factors to quantify the distribution of CES and tested the approach with data on road and topography in the upper reaches of the Minjiang River. The results showed that the areas with high CES were located in the southwestern part of the study area, where it was convenient traffic and rare topography. Results from our approach were likely to support the development of local tourism industry because the distribution of CES was consistent with current hotspots for scenic spots. Meanwhile, we found that the area with high rarity and low accessibility should improve accessibility in order to enhance the capacity of CES. The assumptions applied in our approach highlighted the impacts of complex topography on CES, which could be suitable for the area with a lack of data. Moreover, our approach provided an effective way to assess CES for creating management strategies and enhancing capacity in mountainous areas.
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79
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Wan K, Zhang M, Ye C, Lin W, Guo L, Chen S, Yu X. Organic carbon: An overlooked factor that determines the antibiotic resistome in drinking water sand filter biofilm. ENVIRONMENT INTERNATIONAL 2019; 125:117-124. [PMID: 30711652 DOI: 10.1016/j.envint.2019.01.054] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 01/17/2019] [Accepted: 01/17/2019] [Indexed: 06/09/2023]
Abstract
Biofilter, an essential water treatment process, is reported to be the harbor of bacterial antibiotic resistance genes (ARGs). Due to the oligotrophic characteristic of source water, filter biofilm is largely influenced by the concentration of organic carbon. The objective of this study was to investigate the effect of organic carbon concentration on shaping bacterial antibiotic resistome in filter biofilm. Our study was based on pilot-scale sand filters, and we investigated the antibiotic resistome using high-throughput qPCR. A total of 180 resistance genes from eight categories of antibiotics were detected in 15 biofilm samples of three sand filters. The results indicated that higher concentration of influent organic carbon led to lower diversity of bacterial community and richness of antibiotic resistance genes (ARGs) in biofilm. We discovered a negative correlation (p ≤ 0.01) between the richness of ARGs and the corresponding TOC level. Moreover, the absolute abundance of ARGs was positively correlated (p ≤ 0.05) with the abundance of 16S rRNA gene and was determined by the organic carbon concentration. Sand filters with gradient influent organic carbon concentration led to the formation of different antibiotic resistomes and canonical correspondence analysis (CCA) indicated that difference in bacterial community composition was likely the main reason behind this difference. We also observed a similar trend in the relative abundance of ARGs, which increased with the depth of sand filters. However, this trend was more pronounced in filters with low organic carbon concentrations. Overall, this study revealed that the organic carbon concentration determined the absolute abundance of ARGs and also shaped the diversity and relative abundance of ARGs in drinking water sand filters. These results may provide new insights into the mechanism of persistent bacterial antibiotic resistance in drinking water treatment.
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Affiliation(s)
- Kun Wan
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Menglu Zhang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Chengsong Ye
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China
| | - Wenfang Lin
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China
| | - Lizheng Guo
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Sheng Chen
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Xin Yu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China.
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80
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Costanzi J, Steifetten Ø. Island biogeography theory explains the genetic diversity of a fragmented rock ptarmigan ( Lagopus muta) population. Ecol Evol 2019; 9:3837-3849. [PMID: 31015970 PMCID: PMC6468070 DOI: 10.1002/ece3.5007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 01/31/2019] [Accepted: 02/04/2019] [Indexed: 01/20/2023] Open
Abstract
The island biogeography theory is one of the major theories in ecology, and its applicability to natural systems is well documented. The core model of the theory, the equilibrium model of island biogeography, predicts that species diversity on an island is positively related to the size of the island, but negatively related by the island's distance to the mainland. In recent years, ecologists have begun to apply this model when investigating genetic diversity, arguing that genetic and species diversity might be influenced by similar ecological processes. However, most studies have focused on oceanic islands, but knowledge on how the theory applies to islands located on the mainland (e.g., mountain islands, forest islands) is scarce. In this study, we examined how the size and degree of isolation of mountain islands would affect the genetic diversity of an alpine bird, the rock ptarmigan (Lagopus muta). Within our study area, we defined the largest contiguous mountain area as the mainland, while smaller mountains surrounding the mainland were defined as islands. We found that the observed heterozygosity (H o) was significantly higher, and the inbreeding coefficient (F is) significantly lower, on the mainland compared to islands. There was a positive significant relationship between the unbiased expected heterozygosity (H n.b.) and island size (log km2), but a negative significant relationship between H o and the cost distance to the mainland. Our results are consistent with the equilibrium model of island biogeography and show that the model is well suited for investigating genetic diversity among islands, but also on islands located on the mainland.
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Affiliation(s)
- Jean‐Marc Costanzi
- Department of Natural Sciences and Environmental HealthUniversity of South‐Eastern NorwayBø i TelemarkNorway
| | - Øyvind Steifetten
- Department of Natural Sciences and Environmental HealthUniversity of South‐Eastern NorwayBø i TelemarkNorway
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81
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Caron H, Molino J, Sabatier D, Léger P, Chaumeil P, Scotti‐Saintagne C, Frigério J, Scotti I, Franc A, Petit RJ. Chloroplast DNA variation in a hyperdiverse tropical tree community. Ecol Evol 2019; 9:4897-4905. [PMID: 31031952 PMCID: PMC6476754 DOI: 10.1002/ece3.5096] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 02/11/2019] [Accepted: 03/01/2019] [Indexed: 01/05/2023] Open
Abstract
We investigate chloroplast DNA variation in a hyperdiverse community of tropical rainforest trees in French Guiana, focusing on patterns of intraspecific and interspecific variation. We test whether a species genetic diversity is higher when it has congeners in the community with which it can exchange genes and if shared haplotypes are more frequent in genetically diverse species, as expected in the presence of introgression.We sampled a total of 1,681 individual trees from 472 species corresponding to 198 genera and sequenced them at a noncoding chloroplast DNA fragment.Polymorphism was more frequent in species that have congeneric species in the study site than in those without congeners (30% vs. 12%). Moreover, more chloroplast haplotypes were shared with congeners in polymorphic species than in monomorphic ones (44% vs. 28%).Despite large heterogeneities caused by genus-specific behaviors in patterns of hybridization, these results suggest that the higher polymorphism in the presence of congeners is caused by local introgression rather than by incomplete lineage sorting. Our findings suggest that introgression has the potential to drive intraspecific genetic diversity in species-rich tropical forests.
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Affiliation(s)
- Henri Caron
- BIOGECOINRA, Univ. BordeauxCestasFrance
- INRAUMR 0745 EcoFoG (Ecologie des forêts de Guyane)KourouFrance
| | | | - Daniel Sabatier
- AMAP, IRD, Cirad, CNRS, INRAUniversité de MontpellierMontpellierFrance
| | | | | | - Caroline Scotti‐Saintagne
- INRAUMR 0745 EcoFoG (Ecologie des forêts de Guyane)KourouFrance
- INRA, UR629 Ecologie des Forêts MéditerranéennesURFMAvignonFrance
| | | | - Ivan Scotti
- INRAUMR 0745 EcoFoG (Ecologie des forêts de Guyane)KourouFrance
- INRA, UR629 Ecologie des Forêts MéditerranéennesURFMAvignonFrance
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Gu QH, Husemann M, Wu HH, Dong J, Zhou CJ, Wang XF, Gao YN, Zhang M, Zhu GR, Nie GX. Phylogeography of Bellamya (Mollusca: Gastropoda: Viviparidae) snails on different continents: contrasting patterns of diversification in China and East Africa. BMC Evol Biol 2019; 19:82. [PMID: 30898091 PMCID: PMC6429760 DOI: 10.1186/s12862-019-1397-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 02/22/2019] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Species diversity is determined by both local environmental conditions that control differentiation and extinction and the outcome of large-scale processes that affect migration. The latter primarily comprises climatic change and dynamic landscape alteration. In the past few million years, both Southeast Asia and Eastern Africa experienced drastic climatic and geological oscillations: in Southeast Asia, especially in China, the Tibetan Plateau significantly rose up, and the flow of the Yangtze River was reversed. In East Africa, lakes and rivers experienced frequent range expansions and regressions due to the African mega-droughts. To test how such climatic and geological histories of both regions relate to their respective regional species and genetic diversity, a large scale comparative phylogeographic study is essential. Bellamya, a species rich freshwater snail genus that is widely distributed across China and East Africa, represents a suitable model system to address this question. We sequenced mitochondrial and nuclear DNA for members of the genus from China and used published sequences from Africa and some other locations in Asia to investigate their phylogeny and distribution of genetic diversity. RESULTS Our phylogenetic analysis revealed two monophyletic groups, one in China and one in East Africa. Within the Chinese group, Bellamya species show little genetic differentiation. In contrast, we observe fairly deep divergence among the East African lakes with almost every lake possessing its unique clade. Our results show that strong divergence does not necessarily depend on intrinsic characteristics of a species, but rather is related to the landscape dynamics of a region. CONCLUSION Our phylogenetic results suggest that the Bellamya in China and East Africa are independent phylogenetic clades with different evolutionary trajectories. The different climate and geological histories likely contributed to the diverging evolutionary patterns. Repeated range expansions and regressions of lakes likely contributed to the great divergence of Bellamya in East Africa, while reversal of the river courses and intermingling of different lineages had an opposite effect on Bellamya diversification in China.
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Affiliation(s)
- Qian H. Gu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, No. 36 Lushan Road, Changsha City, 410081 Hunan People’s Republic of China
| | - Martin Husemann
- Centrum für Naturkunde, Universität Hamburg, 20146 Hamburg, Germany
| | - Hui H. Wu
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007 Henan People’s Republic of China
| | - Jing Dong
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007 Henan People’s Republic of China
| | - Chuan J. Zhou
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007 Henan People’s Republic of China
| | - Xian F. Wang
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007 Henan People’s Republic of China
| | - Yun N. Gao
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007 Henan People’s Republic of China
| | - Man Zhang
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007 Henan People’s Republic of China
| | - Guo R. Zhu
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007 Henan People’s Republic of China
| | - Guo X. Nie
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007 Henan People’s Republic of China
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83
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Zhu R, Wang Q, Guan W, Mao Y, Tian B, Cheng J, El‐Kassaby YA. Conservation of genetic diversity hotspots of the high-valued relic yellowhorn ( Xanthoceras sorbifolium) considering climate change predictions. Ecol Evol 2019; 9:3251-3263. [PMID: 30962890 PMCID: PMC6434555 DOI: 10.1002/ece3.4944] [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: 08/29/2018] [Revised: 12/22/2018] [Accepted: 01/07/2019] [Indexed: 11/25/2022] Open
Abstract
Genetic structure and major climate factors may contribute to the distribution of genetic diversity of a highly valued oil tree species Xanthoceras sorbifolium (yellowhorn). Long-term over utilization along with climate change is affecting the viability of yellowhorn wild populations. To preserve the species known and unknown valuable gene pools, the identification of genetic diversity "hotspots" is a prerequisite for their consideration as in situ conservation high priority. Chloroplast DNA (cpDNA) diversity was high among 38 natural populations (H d = 0.717, K = 4.616, Tajmas' D = -0.22) and characterized by high genetic divergence (F ST = 0.765) and relatively low gene flow (N m = 0.03), indicating populations isolation reflecting the species' habitat fragmentation and inbreeding depression. Six out of the studied 38 populations are defined as genetic diversity "hotspots." The number and geographic direction of cpDNA mutation steps supported the species southwest to northeast migration history. Climatic factors such as extreme minimum temperature over 30 years indicated that the identified genetic "hotspots" are expected to experience 5°C temperature increase in next following 50 years. The results identified vulnerable genetic diversity "hotspots" and provided fundamental information for the species' future conservation and breeding activities under the anticipated climate change. More specifically, the role of breeding as a component of a gene resource management strategy aimed at fulfilling both utilization and conservation goals.
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Affiliation(s)
- Ren‐Bin Zhu
- Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglunChina
- College of Resource and EnvironmentNorthwest A&F UniversityYanglingChina
| | - Qing Wang
- School of Nature ConservationBeijing Forestry UniversityBeijingChina
- Department of Forest and Conservation Sciences, Faculty of ForestryThe University of British ColumbiaVancouverBritish ColumbiaCanada
| | - Wen‐Bin Guan
- School of Nature ConservationBeijing Forestry UniversityBeijingChina
| | - Yanjia Mao
- Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglunChina
| | - Bin Tian
- Key Laboratory of Biodiversity Conservation in Southwest ChinaState Forestry Administration, Southwest Forestry UniversityKunmingChina
| | - Ji‐Min Cheng
- College of Resource and EnvironmentNorthwest A&F UniversityYanglingChina
- Institute of Soil and Water ConservationChinese Academy of Sciences and Ministry of Water resourcesYanglingChina
| | - Yousry A. El‐Kassaby
- Department of Forest and Conservation Sciences, Faculty of ForestryThe University of British ColumbiaVancouverBritish ColumbiaCanada
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84
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Dakos V, Matthews B, Hendry AP, Levine J, Loeuille N, Norberg J, Nosil P, Scheffer M, De Meester L. Ecosystem tipping points in an evolving world. Nat Ecol Evol 2019; 3:355-362. [DOI: 10.1038/s41559-019-0797-2] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 01/04/2019] [Indexed: 02/08/2023]
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85
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Reisch C, Schmid C. Species and genetic diversity are not congruent in fragmented dry grasslands. Ecol Evol 2019; 9:664-671. [PMID: 30680146 PMCID: PMC6342089 DOI: 10.1002/ece3.4791] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 10/15/2018] [Accepted: 11/09/2018] [Indexed: 01/19/2023] Open
Abstract
Biological diversity comprises both species diversity (SD) and genetic diversity (GD), and it has been postulated that both levels of diversity depend on similar mechanisms. Species-genetic diversity correlations (SGDC) are therefore supposed to be generally positive. However, in contrast to theory, empirical data are contradictory. Furthermore, there is a pronounced lack of multispecies studies including also the ecological factors potentially driving species and genetic diversity. We analyzed the relationship between the species diversity of dry grasslands and the genetic diversity of several dry grassland plant species, therefore, in the context of habitat fragmentation and habitat conditions. Our study revealed a lack of correlation between species and genetic diversity. We demonstrated previously that SD mainly depends on habitat conditions (vegetation height and cover of litter), whereas GD is significantly affected by habitat fragmentation (distance to the nearest dry grassland in 1830 and connectivity in 2013). This seems to be the main reason why SD and GD are not congruent in fragmented grasslands. Our results support, hence, the observation that positive SGDCs can mainly be found in natural, island-like study systems in equilibrium and at similar levels of heterogeneity. In fragmented dry grassland ecosystems, which differ in heterogeneity, this state of equilibrium may not have been reached mitigating the positive relationship between SD and GD. From our study, it can be concluded that in fragmented dry grasslands, the protection of SD does not necessarily ensure the conservation of GD.
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Affiliation(s)
- Christoph Reisch
- Institute of Plant SciencesUniversity of RegensburgRegensburgGermany
| | - Christoph Schmid
- Research Unit Comparative Microbiome AnalysisGerman Research Center for Environmental HealthNeuherbergGermany
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86
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Pfeiffer VW, Ford BM, Housset J, McCombs A, Blanco‐Pastor JL, Gouin N, Manel S, Bertin A. Partitioning genetic and species diversity refines our understanding of species-genetic diversity relationships. Ecol Evol 2018; 8:12351-12364. [PMID: 30619550 PMCID: PMC6308885 DOI: 10.1002/ece3.4530] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 07/27/2018] [Accepted: 08/03/2018] [Indexed: 12/24/2022] Open
Abstract
Disentangling the origin of species-genetic diversity correlations (SGDCs) is a challenging task that provides insight into the way that neutral and adaptive processes influence diversity at multiple levels. Genetic and species diversity are comprised by components that respond differently to the same ecological processes. Thus, it can be useful to partition species and genetic diversity into their different components to infer the mechanisms behind SGDCs. In this study, we applied such an approach using a high-elevation Andean wetland system, where previous evidence identified neutral processes as major determinants of the strong and positive covariation between plant species richness and AFLP genetic diversity of the common sedge Carex gayana. To tease apart putative neutral and non-neutral genetic variation of C. gayana, we identified loci putatively under selection from a dataset of 1,709 SNPs produced using restriction site-associated DNA sequencing (RAD-seq). Significant and positive relationships between local estimates of genetic and species diversities (α-SGDCs) were only found with the putatively neutral loci datasets and with species richness, confirming that neutral processes were primarily driving the correlations and that the involved processes differentially influenced local species diversity components (i.e., richness and evenness). In contrast, SGDCs based on genetic and community dissimilarities (β-SGDCs) were only significant with the putative non-neutral datasets. This suggests that selective processes influencing C. gayana genetic diversity were involved in the detected correlations. Together, our results demonstrate that analyzing distinct components of genetic and species diversity simultaneously is useful to determine the mechanisms behind species-genetic diversity relationships.
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Affiliation(s)
- Vera Wilder Pfeiffer
- Nelson Institute for Environmental ScienceUniversity of Wisconsin – MadisonMadisonWisconsin
| | - Brett Michael Ford
- Department of BiologyUniversity of British ColumbiaKelownaBritish ColumbiaCanada
| | - Johann Housset
- Alcina ForetsMontpellierFrance
- Centre d’étude de la forêtUniversité du Québec à MontréalMontréalQuebecCanada
| | - Audrey McCombs
- Department of Statistics, Ecology and Evolutionary Biology ProgramIowa State UniversityAmesIowa
| | | | - Nicolas Gouin
- Departamento de BiologíaFacultad de CienciasUniversidad de La SerenaLa SerenaChile
- Centro de Estudios Avanzados en Zonas ÁridasLa SerenaChile
- Instituto de Investigación Multidisciplinar en Ciencia y TecnologíaUniversidad de La SerenaLa SerenaChile
| | - Stéphanie Manel
- EPHEPSL Research UniversityCNRSUM, SupAgro, IRDINRAUMR 5175 CEFEMontpellierFrance
| | - Angéline Bertin
- Departamento de BiologíaFacultad de CienciasUniversidad de La SerenaLa SerenaChile
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87
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Marchesini A, Vernesi C, Battisti A, Ficetola GF. Deciphering the drivers of negative species-genetic diversity correlation in Alpine amphibians. Mol Ecol 2018; 27:4916-4930. [PMID: 30346071 DOI: 10.1111/mec.14902] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 09/26/2018] [Accepted: 10/01/2018] [Indexed: 01/08/2023]
Abstract
The evolutionary and ecological importance of neutral and adaptive genetic diversity is widely recognized. Nevertheless, genetic diversity is rarely assessed for conservation planning, which often implicitly assumes a positive correlation between species and genetic diversity. Multiple drivers can cause the co-variation between the genetic diversity of one species and the richness of the whole communities, and explicit tests are needed to identify the processes that can determine species-genetic diversity correlations (SGDCs). Here, we tested whether intrapopulation genetic diversity (at neutral loci) and species richness co-vary in the amphibian communities of a southern Alpine region (Trentino, Italy), using the common frog (Rana temporaria) as focal species for the study of genetic diversity. We also analysed ecological similarity, niche overlap and interspecific interactions between the species, to unravel the processes determining SGDC. The neutral genetic diversity of common frogs was negatively related to species richness. The negative SGDC was probably due to an opposite influence of environmental gradients on the two levels of biodiversity, since the focal species and the other amphibians differ in ecological preferences, particularly in terms of thermal optimum. Conversely, we did not find evidence for a role of interspecific interactions in the negative SGDC. Our findings stress that species richness cannot be used as a universal proxy for genetic diversity, and only combining SGDC with analyses on the determinants of biodiversity can allow to identify the processes determining the relationships between genetic and species diversity.
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Affiliation(s)
- Alexis Marchesini
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy.,Department of Agronomy, Food, Natural Resources, Animals, & Environment (DAFNAE), University of Padua, Legnaro (PD), Italy
| | - Cristiano Vernesi
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
| | - Andrea Battisti
- Department of Agronomy, Food, Natural Resources, Animals, & Environment (DAFNAE), University of Padua, Legnaro (PD), Italy
| | - Gentile Francesco Ficetola
- Departement of Environmental Science and Policy, Università degli Studi di Milano, Milano, Italy.,Univ. Grenoble Alpes, CNRS, Laboratoire d'Ecologie Alpine (LECA), Université Grenoble-Alpes, Grenoble, France
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88
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89
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Raffard A, Santoul F, Cucherousset J, Blanchet S. The community and ecosystem consequences of intraspecific diversity: a meta-analysis. Biol Rev Camb Philos Soc 2018; 94:648-661. [PMID: 30294844 DOI: 10.1111/brv.12472] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 09/12/2018] [Accepted: 09/14/2018] [Indexed: 12/12/2022]
Abstract
Understanding the relationships between biodiversity and ecosystem functioning has major implications. Biodiversity-ecosystem functioning relationships are generally investigated at the interspecific level, although intraspecific diversity (i.e. within-species diversity) is increasingly perceived as an important ecological facet of biodiversity. Here, we provide a quantitative and integrative synthesis testing, across diverse plant and animal species, whether intraspecific diversity is a major driver of community dynamics and ecosystem functioning. We specifically tested (i) whether the number of genotypes/phenotypes (i.e. intraspecific richness) or the specific identity of genotypes/phenotypes (i.e. intraspecific variation) in populations modulate the structure of communities and the functioning of ecosystems, (ii) whether the ecological effects of intraspecific richness and variation are strong in magnitude, and (iii) whether these effects vary among taxonomic groups and ecological responses. We found a non-linear relationship between intraspecific richness and community and ecosystem dynamics that follows a saturating curve shape, as observed for biodiversity-function relationships measured at the interspecific level. Importantly, intraspecific richness modulated ecological dynamics with a magnitude that was equal to that previously reported for interspecific richness. Our results further confirm, based on a database containing more than 50 species, that intraspecific variation also has substantial effects on ecological dynamics. We demonstrated that the effects of intraspecific variation are twice as high as expected by chance, and that they might have been underestimated previously. Finally, we found that the ecological effects of intraspecific variation are not homogeneous and are actually stronger when intraspecific variation is manipulated in primary producers than in consumer species, and when they are measured at the ecosystem rather than at the community level. Overall, we demonstrated that the two facets of intraspecific diversity (richness and variation) can both strongly affect community and ecosystem dynamics, which reveals the pivotal role of within-species biodiversity for understanding ecological dynamics.
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Affiliation(s)
- Allan Raffard
- CNRS, Station d'Écologie Théorique et Expérimentale du CNRS à Moulis UMR-5321, Université Toulouse III Paul Sabatier, 2 route du CNRS, F-09200, Moulis, France.,EcoLab, Université de Toulouse, CNRS, INPT, UPS, 31062 Toulouse, France
| | - Frédéric Santoul
- EcoLab, Université de Toulouse, CNRS, INPT, UPS, 31062 Toulouse, France
| | - Julien Cucherousset
- CNRS, IRD, UPS, Laboratoire Évolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse, 118 route de Narbonne, Toulouse 31062, France
| | - Simon Blanchet
- CNRS, Station d'Écologie Théorique et Expérimentale du CNRS à Moulis UMR-5321, Université Toulouse III Paul Sabatier, 2 route du CNRS, F-09200, Moulis, France.,CNRS, IRD, UPS, Laboratoire Évolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse, 118 route de Narbonne, Toulouse 31062, France
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90
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Fan D, Huang J, Hu H, Sun Z, Cheng S, Kou Y, Zhang Z. Evolutionary Hotspots of Seed Plants in Subtropical China: A Comparison With Species Diversity Hotspots of Woody Seed Plants. Front Genet 2018; 9:333. [PMID: 30177954 PMCID: PMC6109751 DOI: 10.3389/fgene.2018.00333] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 08/02/2018] [Indexed: 11/13/2022] Open
Abstract
Genetic diversity is a fundamental level of biodiversity. However, it is frequently neglected in conservation prioritization because intraspecific genetic diversity is difficult to measure at large scales. In this study, we synthesized population genetic or phylogeographic datasets of 33 seed plants in subtropical China into multi-species genetic landscapes. The genetic landscapes identified 18 evolutionary hotspots with high within-population genetic diversity (WGD), and among-population genetic diversity (AGD), or both. The western subtropical China is rich in AGD (possessing four major AGD hotspots), deserving a high conservation priority. We found that WGD was positively correlated with longitude, with most WGD hotspots locating in east subtropical China. The results showed that the locations of 12 of 18 evolutionary hotspots corresponded approximately to those of previously identified species diversity (SD) hotspots, however, a positive and significant correlation existed only between AGD and SD, not between WGD and SD. Therefore, spatial patterns of species richness in plants in subtropical China cannot generally be used as surrogate for their intraspecific diversity. This study identified multi-species evolutionary hotspots and correlated multi-species genetic diversity with SD across subtropical China for the first time, providing profound implications for the conservation of biodiversity in this important ecoregion.
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Affiliation(s)
- Dengmei Fan
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Jihong Huang
- Key Laboratory of Forest Ecology and Environment, The State Forestry and Grassland Administration, Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Huili Hu
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Zhixia Sun
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China.,Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Shanmei Cheng
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Yixuan Kou
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Zhiyong Zhang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
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91
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Rhoades OK, Best RJ, Stachowicz JJ. Assessing Feeding Preferences of a Consumer Guild: Partitioning Variation Among versus Within Species. Am Nat 2018; 192:287-300. [PMID: 30125236 DOI: 10.1086/698325] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Interspecific variation in resource use is critical to understanding species diversity, coexistence, and ecosystem functioning. A growing body of research describes analogous intraspecific variation and its potential importance for population dynamics and community outcomes. However, the magnitude of intraspecific variation relative to interspecific variation in key dimensions of consumer-resource interactions remains unknown, hampering our understanding of the importance of this variation for population and community processes. In this study, we examine feeding preference through repeated laboratory choice feeding assays of 444 wild-caught individuals of eight invertebrate grazer species on rocky reefs in northern California. Between-species variation accounted for 25%-33% of the total variation in preference for the preferred resource, while between-individual variation accounted for 4%-5% of total variation. For two of the eight species, between-individual variation was significantly different from zero and on average contributed 14% and 17% of the total diet variation, even after accounting for differences due to size and sex. Therefore, even with clearly distinguishable between-species differences in mean preference, diet variation between and within individuals can contribute to the dietary niche width of species and guilds, which may be overlooked by focusing solely on species' mean resource use patterns.
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92
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Escobar S, Pintaud J, Balslev H, Bernal R, Moraes Ramírez M, Millán B, Montúfar R. Genetic structuring in a Neotropical palm analyzed through an Andean orogenesis-scenario. Ecol Evol 2018; 8:8030-8042. [PMID: 30250682 PMCID: PMC6144996 DOI: 10.1002/ece3.4216] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 04/22/2018] [Accepted: 04/30/2018] [Indexed: 12/27/2022] Open
Abstract
Andean orogenesis has driven the development of very high plant diversity in the Neotropics through its impact on landscape evolution and climate. The analysis of the intraspecific patterns of genetic structure in plants would permit inferring the effects of Andean uplift on the evolution and diversification of Neotropical flora. In this study, using microsatellite markers and Bayesian clustering analyses, we report the presence of four genetic clusters for the palm Oenocarpus bataua var. bataua which are located within four biogeographic regions in northwestern South America: (a) Chocó rain forest, (b) Amotape-Huancabamba Zone, (c) northwestern Amazonian rain forest, and (d) southwestern Amazonian rain forest. We hypothesize that these clusters developed following three genetic diversification events mainly promoted by Andean orogenic events. Additionally, the distinct current climate dynamics among northwestern and southwestern Amazonia may maintain the genetic diversification detected in the western Amazon basin. Genetic exchange was identified between the clusters, including across the Andes region, discarding the possibility of any cluster to diversify as a distinct intraspecific variety. We identified a hot spot of genetic diversity in the northern Peruvian Amazon around the locality of Iquitos. We also detected a decrease in diversity with distance from this area in westward and southward direction within the Amazon basin and the eastern Andean foothills. Additionally, we confirmed the existence and divergence of O. bataua var. bataua from var. oligocarpus in northern South America, possibly expanding the distributional range of the latter variety beyond eastern Venezuela, to the central and eastern Andean cordilleras of Colombia. Based on our results, we suggest that Andean orogenesis is the main driver of genetic structuring and diversification in O. bataua within northwestern South America.
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Affiliation(s)
- Sebastián Escobar
- Facultad de Ciencias Exactas y NaturalesPontificia Universidad Católica del EcuadorQuitoEcuador
- Department of Bioscience, Ecoinformatics and Biodiversity GroupAarhus UniversityAarhusDenmark
| | | | - Henrik Balslev
- Department of Bioscience, Ecoinformatics and Biodiversity GroupAarhus UniversityAarhusDenmark
| | - Rodrigo Bernal
- Instituto de Ciencias NaturalesUniversidad Nacional de ColombiaBogotáColombia
| | | | - Betty Millán
- Museo de Historia NaturalUniversidad Nacional Mayor de San Marcos (UNMSM)LimaPerú
| | - Rommel Montúfar
- Facultad de Ciencias Exactas y NaturalesPontificia Universidad Católica del EcuadorQuitoEcuador
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93
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Delord C, Lassalle G, Oger A, Barloy D, Coutellec M, Delcamp A, Evanno G, Genthon C, Guichoux E, Le Bail P, Le Quilliec P, Longin G, Lorvelec O, Massot M, Reveillac E, Rinaldo R, Roussel J, Vigouroux R, Launey S, Petit EJ. A cost‐and‐time effective procedure to develop
SNP
markers for multiple species: A support for community genetics. Methods Ecol Evol 2018. [DOI: 10.1111/2041-210x.13034] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Chrystelle Delord
- ESE, Ecology and Ecosystem HealthAgrocampus OuestINRA Rennes France
- HYDRECO Guyane SARLLaboratoire‐Environnement de Petit Saut Kourou France
| | - Gilles Lassalle
- ESE, Ecology and Ecosystem HealthAgrocampus OuestINRA Rennes France
| | - Adrien Oger
- ESE, Ecology and Ecosystem HealthAgrocampus OuestINRA Rennes France
| | - Dominique Barloy
- ESE, Ecology and Ecosystem HealthAgrocampus OuestINRA Rennes France
| | | | | | - Guillaume Evanno
- ESE, Ecology and Ecosystem HealthAgrocampus OuestINRA Rennes France
| | | | | | | | | | | | - Olivier Lorvelec
- ESE, Ecology and Ecosystem HealthAgrocampus OuestINRA Rennes France
| | | | - Elodie Reveillac
- ESE, Ecology and Ecosystem HealthAgrocampus OuestINRA Rennes France
| | | | | | - Regis Vigouroux
- HYDRECO Guyane SARLLaboratoire‐Environnement de Petit Saut Kourou France
| | - Sophie Launey
- ESE, Ecology and Ecosystem HealthAgrocampus OuestINRA Rennes France
| | - Eric J. Petit
- ESE, Ecology and Ecosystem HealthAgrocampus OuestINRA Rennes France
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94
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Connolly RM, Smith TM, Maxwell PS, Olds AD, Macreadie PI, Sherman CDH. Highly Disturbed Populations of Seagrass Show Increased Resilience but Lower Genotypic Diversity. FRONTIERS IN PLANT SCIENCE 2018; 9:894. [PMID: 30008728 PMCID: PMC6034141 DOI: 10.3389/fpls.2018.00894] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 06/07/2018] [Indexed: 06/08/2023]
Abstract
The response of seagrass systems to a severe disturbance provides an opportunity to quantify the degree of resilience in different meadows, and subsequently to test whether there is a genetic basis to resilience. We used existing data on levels of long-standing disturbance from poor water quality, and the responses of seagrass (Zostera muelleri) after an extreme flood event in Moreton Bay, Queensland, Australia. Sites were grouped into high and low disturbance categories, in which seagrass showed high and low resilience, respectively, as determined by measuring rates of key feedback processes (nutrient removal, suppression of sediment resuspension, and algal grazing), and physiological and morphological traits. Theoretically, meadows with higher genotypic diversity would be expected to have greater resilience. However, because the more resilient meadows occur in areas historically exposed to high disturbance, the alternative is also possible, that selection will have resulted in a narrower, less diverse subset of genotypes than in less disturbed meadows. Levels of genotypic and genetic diversity (allelic richness) based on 11 microsatellite loci, were positively related (R2 = 0.58). Genotypic diversity was significantly lower at highly disturbed sites (R = 0.49) than at less disturbed sites (R = 0.61). Genotypic diversity also showed a negative trend with two morphological characteristics known to confer resilience on seagrass in Moreton Bay, leaf chlorophyll concentrations and seagrass biomass. Genetic diversity did not differ between disturbed and undisturbed sites. We postulate that the explanation for these results is historical selection for genotypes that confer protection against disturbance, reducing diversity in meadows that contemporarily show greater resilience.
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Affiliation(s)
- Rod M. Connolly
- Australian Rivers Institute – Coast and Estuaries, School of Environment and Science, Griffith University, Southport, QLD, Australia
| | - Timothy M. Smith
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
- School of Life and Environmental Sciences, University of Newcastle, Ourimbah, NSW, Australia
| | - Paul S. Maxwell
- Australian Rivers Institute – Coast and Estuaries, School of Environment and Science, Griffith University, Southport, QLD, Australia
- Healthy Land and Water, Brisbane, QLD, Australia
| | - Andrew D. Olds
- Australian Rivers Institute – Coast and Estuaries, School of Environment and Science, Griffith University, Southport, QLD, Australia
- School of Science and Engineering, University of the Sunshine Coast, Maroochydore, QLD, Australia
| | - Peter I. Macreadie
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Craig D. H. Sherman
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
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95
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Mazur M, Zielińska M, Boratyńska K, Romo A, Salva-Catarineu M, Marcysiak K, BoratyŃski A. Taxonomic and geographic differentiation of Juniperus phoenicea agg. based on cone, seed, and needle characteristics. SYST BIODIVERS 2018. [DOI: 10.1080/14772000.2018.1439120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Małgorzata Mazur
- Department of Botany, Kazimierz Wielki University, Ossolińskich 12, 85-093 Bydgoszcz, Poland
| | - Monika Zielińska
- Department of Botany, Kazimierz Wielki University, Ossolińskich 12, 85-093 Bydgoszcz, Poland
| | - Krystyna Boratyńska
- Polish Academy of Sciences, Institute of Dendrology, Parkowa 5, 62-035 Kórnik, Poland
| | - Angel Romo
- Spanish Research Council (Consejo Superior de Investigaciones Científicas: IBB, CSIC-ICUB). Botanical Institute, Passeig Migdia s/n, 08038 Barcelona, Spain
| | | | - Katarzyna Marcysiak
- Department of Botany, Kazimierz Wielki University, Ossolińskich 12, 85-093 Bydgoszcz, Poland
| | - Adam BoratyŃski
- Polish Academy of Sciences, Institute of Dendrology, Parkowa 5, 62-035 Kórnik, Poland
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96
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Koricheva J, Hayes D. The relative importance of plant intraspecific diversity in structuring arthropod communities: A meta‐analysis. Funct Ecol 2018. [DOI: 10.1111/1365-2435.13062] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Julia Koricheva
- School of Biological SciencesRoyal Holloway University of London Egham Surrey UK
| | - Dexter Hayes
- School of Biological SciencesRoyal Holloway University of London Egham Surrey UK
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97
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Valencia-Cuevas L, Mussali-Galante P, Cano-Santana Z, Pujade-Villar J, Equihua-Martínez A, Tovar-Sánchez E. Genetic variation in foundation species governs the dynamics of trophic interactions. Curr Zool 2018; 64:13-22. [PMID: 29492034 PMCID: PMC5809035 DOI: 10.1093/cz/zox015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 10/11/2016] [Accepted: 02/27/2017] [Indexed: 11/25/2022] Open
Abstract
Various studies have demonstrated that the foundation species genetic diversity can have direct effects that extend beyond the individual or population level, affecting the dependent communities. Additionally, these effects may be indirectly extended to higher trophic levels throughout the entire community. Quercus castanea is an oak species with characteristics of foundation species beyond presenting a wide geographical distribution and being a dominant element of Mexican temperate forests. In this study, we analyzed the influence of population (He) and individual (HL) genetic diversity of Q. castanea on its canopy endophagous insect community and associated parasitoids. Specifically, we studied the composition, richness (S) and density of leaf-mining moths (Lepidoptera: Tischeridae, Citheraniidae), gall-forming wasps (Hymenoptera: Cynipidae), and canopy parasitoids of Q. castanea. We sampled 120 trees belonging to six populations (20/site) through the previously recognized gradient of genetic diversity. In total, 22 endophagous insect species belonging to three orders (Hymenoptera, Lepidoptera, and Diptera) and 20 parasitoid species belonging to 13 families were identified. In general, we observed that the individual genetic diversity of the host plant (HL) has a significant positive effect on the S and density of the canopy endophagous insect communities. In contrast, He has a significant negative effect on the S of endophagous insects. Additionally, indirect effects of HL were observed, affecting the S and density of parasitoid insects. Our results suggest that genetic variation in foundation species can be one of the most important factors governing the dynamics of tritrophic interactions that involve oaks, herbivores, and parasitoids.
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Affiliation(s)
- Leticia Valencia-Cuevas
- Laboratorio de Marcadores Moleculares, Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca, Morelos, CP 62209, México
| | - Patricia Mussali-Galante
- Laboratorio de Investigaciones Ambientales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca, Morelos, CP 62209, México
| | - Zenón Cano-Santana
- Departamento de Ecología y Recursos Naturales, Facultad de Ciencias, Universidad Nacional Autónoma de México, Delegación Coyoacán, DF 04510, México
| | - Juli Pujade-Villar
- Departamento de Biología Animal, Universitat de Barcelona, Facultat de Biología, Av. Diagonal, 645, Barcelona 08028, España
| | | | - Efraín Tovar-Sánchez
- Laboratorio de Marcadores Moleculares, Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca, Morelos, CP 62209, México
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98
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On the proportional abundance of species: Integrating population genetics and community ecology. Sci Rep 2017; 7:16815. [PMID: 29196682 PMCID: PMC5711905 DOI: 10.1038/s41598-017-17070-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 11/21/2017] [Indexed: 11/09/2022] Open
Abstract
The frequency of genes in interconnected populations and of species in interconnected communities are affected by similar processes, such as birth, death and immigration. The equilibrium distribution of gene frequencies in structured populations is known since the 1930s, under Wright’s metapopulation model known as the island model. The equivalent distribution for the species frequency (i.e. the species proportional abundance distribution (SPAD)), at the metacommunity level, however, is unknown. In this contribution, we develop a stochastic model to analytically account for this distribution (SPAD). We show that the same as for genes SPAD follows a beta distribution, which provides a good description of empirical data and applies across a continuum of scales. This stochastic model, based upon a diffusion approximation, provides an alternative to neutral models for the species abundance distribution (SAD), which focus on number of individuals instead of proportions, and demonstrate that the relative frequency of genes in local populations and of species within communities follow the same probability law. We hope our contribution will help stimulate the mathematical and conceptual integration of theories in genetics and ecology.
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99
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Aavik T, Helm A. Restoration of plant species and genetic diversity depends on landscape-scale dispersal. Restor Ecol 2017. [DOI: 10.1111/rec.12634] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Tsipe Aavik
- Institute of Ecology and Earth Sciences; University of Tartu, Lai 40; 51005, Tartu Estonia
| | - Aveliina Helm
- Institute of Ecology and Earth Sciences; University of Tartu, Lai 40; 51005, Tartu Estonia
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100
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Cahill AE, De Jode A, Dubois S, Bouzaza Z, Aurelle D, Boissin E, Chabrol O, David R, Egea E, Ledoux JB, Mérigot B, Weber AAT, Chenuil A. A multispecies approach reveals hot spots and cold spots of diversity and connectivity in invertebrate species with contrasting dispersal modes. Mol Ecol 2017; 26:6563-6577. [PMID: 29087018 DOI: 10.1111/mec.14389] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 09/18/2017] [Indexed: 12/18/2022]
Abstract
Genetic diversity is crucial for species' maintenance and persistence, yet is often overlooked in conservation studies. Species diversity is more often reported due to practical constraints, but it is unknown if these measures of diversity are correlated. In marine invertebrates, adults are often sessile or sedentary and populations exchange genes via dispersal of gametes and larvae. Species with a larval period are expected to have more connected populations than those without larval dispersal. We assessed the relationship between measures of species and genetic diversity, and between dispersal ability and connectivity. We compiled data on genetic patterns and life history traits in nine species across five phyla. Sampling sites spanned 600 km in the northwest Mediterranean Sea and focused on a 50-km area near Marseilles, France. Comparative population genetic approaches yielded three main results. (i) Species without larvae showed higher levels of genetic structure than species with free-living larvae, but the role of larval type (lecithotrophic or planktotrophic) was negligible. (ii) A narrow area around Marseilles, subject to offshore advection, limited genetic connectivity in most species. (iii) We identified sites with significant positive contributions to overall genetic diversity across all species, corresponding with areas near low human population densities. In contrast, high levels of human activity corresponded with a negative contribution to overall genetic diversity. Genetic diversity within species was positively and significantly linearly related to local species diversity. Our study suggests that local contribution to overall genetic diversity should be taken into account for future conservation strategies.
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Affiliation(s)
- Abigail E Cahill
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France.,Biology Department, Albion College, Albion, MI, USA
| | - Aurélien De Jode
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France
| | - Sophie Dubois
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France
| | - Zoheir Bouzaza
- Département de Biologie, Faculté des Sciences de la Nature et de la Vie, Université Abdelhamid Ibn Badis, Mostaganem, Algérie
| | - Didier Aurelle
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France
| | - Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France
| | - Olivier Chabrol
- CNRS, Centrale Marseille, I2M, UMR7373, Aix-Marseille Université, Marseille, France
| | - Romain David
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France
| | - Emilie Egea
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France
| | - Jean-Baptiste Ledoux
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Porto, Portugal.,Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain
| | - Bastien Mérigot
- UMR MARBEC (CNRS, Ifremer, IRD, UM), Université de Montpellier, Sète, France
| | - Alexandra Anh-Thu Weber
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France.,Zoological Institute, University of Basel, Basel, Switzerland
| | - Anne Chenuil
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France
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