Ecological Archives E096-203-D1
Camille Albouy, Frida Ben Rais Lasram, Laure Velez, François Guilhaumon, Christine N. Meynard, Séverine Boyer, Laura Benestan, Nicolas Mouquet, Emmanuel Douzery, Roland Aznar, Marc Troussellier, Samuel Somot, Fabien Leprieur, François Le Loc’h, and David Mouillot. 2015. FishMed: traits phylogeny, current and projected species distribution of Mediterranean fishes, and environmental data. Ecology 96:2312. http://dx.doi.org/10.1890/14-2279.1
Introduction
Impressive progresses in ecology and biogeography have occurred over the last decade to forecast potential impacts of climate change on biodiversity (Guisan and Hofer 2003, Araújo and New 2007, Mouillot et al. 2011, Thuiller et al. 2013, Albouy et al. 2014a) including the multi-faceted aspect (Thuiller et al. 2011, Guilhaumon et al. 2014). The developments of programming and geographical information system (GIS) were pivotal tools to analyze the massive data sets compiling information about species occurrences, traits and phylogenies. The database FishMed proposes three main biodiversity facets described hereafter (taxonomy, functions, and phylogeny) of 635 fish species recorded in Mediterranean Sea along with their geographic distribution and projected values of sea surface temperature (SST). FishMed was the source of several published studies on the biodiversity of coastal Mediterranean fish assemblages under climate change (Mouillot et al. 2011, Albouy et al. 2012, 2013, 2014a-b).
The first part of FishMed combines the current geographical distributions of 635 Mediterranean fish species and two sets of predicted future distributions for coastal species (n = 288) obtained by species distribution modeling (SDM) for the middle and the end of the 21st century (Albouy et al. 2012, Albouy et al. 2013). These two projected distribution data sets were obtained by using an ensemble forecasting approach based on future SST according to the IPPC/SRES A2 scenario (Albouy et al. 2013) implemented with the Mediterranean climatic model NEMOMED8 under the A2 socio-economic hypothesis (Somot et al. 2006, Beuvier et al. 2010).
In the second part of FishMed, we provide a list of 12 biological and ecological traits for the 635 fish species that embraces many aspects of their functional roles (Albouy et al. 2014b). For each species, maximal and common lengths, vertical distribution, habitat, migration types, reproduction mode, sex shift, semelparity, diet type (larvae and adults), social behavior, species geographic origin, and minimum and maximum depths where the species can be encountered have been gathered fromseveral sources (Whitehead et al. 1986, Louisy 2005, Froese and Pauly 2012).
The third part of FishMed contains phylogenetic information (phylogenetic tree) obtained by assembling a DNA supermatrix composed of four mitochondrial genes (12S ribosomal DNA, 16S ribosomal DNA, cytochrome c oxidase subunit I, and cytochrome b) and two nuclear genes (rhodopsin and recombination activating gene I), including 62% of Mediterranean teleost species plus 9 outgroups (Meynard et al. 2012). Maximum likelihood and Bayesian phylogenetic and dating analyses were calibrated using 20 fossil species. An additional 124 fish species were grafted onto the chronogram according to their taxonomic affinity, checking for the effects of taxonomic coverage in subsequent diversification analyses (Meynard et al. 2012).
Finally the FishMed database provides SST variables predicted by the regional ocean model NEMOMED8 (Beuvier et al. 2010) for the 21st century (2040–2059 and 2080–2099 periods) under the A2 socio-economic hypothesis (Somot et al. 2006). IPCC/SRES A2 scenario was considered as conservative for future prediction of global warming (IPCC, 2007). The period 1961–1980 was considered as a baseline to calibrate the species distribution models (SDM) and the SST daily data were averaged to infer monthly data, leading to 8 synthetic variables determined by a k-means clustering analysis. Projected SST values for the middle (2040–2059) and the end of the 21st century (2080–2099) were obtained from NEMOMED8. It is worth noting that the projected climatic conditions provided here are based on one specific simulation of the Mediterranean Sea physics for the 21st century (i.e., one scenario, one forcing, one ocean model, one run) and therefore do not take into account the different uncertainties associated to any climate change projection. Consequently, the goal is not to give a robust estimate of the future Mediterranean Sea conditions but an illustration of its possible evolution.
This database might be of interest in the context of global anthropogenic changes as coastal Mediterranean ecosystems are currently recognized as one of the most impacted ecosystems on earth (Coll et al. 2012).
Metadata
Class I. Data set descriptors
A. Data set identity: A taxonomic functional and phylogenetic database on Mediterranean fish species.
B. Data set identification code: FishMed.zip
C. Data set description
Principal Investigators:
Camille Albouy, Département de biologie, chimie et géographie, Université du Québec à Rimouski, 300 Allée des Ursulines, G5L 3A1 Rimouski Québec, Canada. Email: [email protected].
Laure Velez, UMR 9190 MARBEC (CNRS-IFREMER-IRD-UM), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier, France. Email: [email protected].
Frida Ben Rais Lasram, Laboratoire Écosystèmes et Ressources Aquatiques UR13AGRO1, Institut National Agronomique de Tunisie, 43 avenue Charles Nicolle, 1082 Tunis, Tunisia. Email: [email protected].
Christine N. Meynard: Virginia Institute of Marine Science, College of William & Mary, P.O. Box 1346, Gloucester Point, VA 23062, USA. Email: [email protected].
Abstract: The FishMed database provides traits, phylogeny, current and projected species distribution of Mediterranean fishes, and associated SST from the regional oceanic model NEMOMED8. Data for the current geographical distributions of 635 Mediterranean fish species were compiled from a published expert knowledge atlas of fishes of the northern Atlantic and the Mediterranean (FNAM) edited between 1984 and 1986 and from an updated exotic fish species list. Two future sets of projected species distributions were obtained for the middle and end of the 21st century by using an ensemble forecasting approach for 288 coastal Mediterranean fish species based on SST according to the IPPC/SRES A2 scenario implemented with the Mediterranean climatic model NEMOMED8. The functional part of the database encompasses 12 biological and ecological traits (maximal and common lengths, vertical distribution, habitat, migration type, mode of reproduction, sex shift, semelparity, diet type (larvae and adults), social behavior, species origin and depth) for the 635 fish species. To build the phylogeny we inferred the timing and geographic origins of Mediterranean teleost species diversity using nucleotide sequences collected from GenBank including 62% of Mediterranean teleost species plus nine outgroups. Maximum likelihood Bayesian phylogenetic and dating analyses were calibrated using 20 fossil species. An additional 124 fish species were grafted onto the chronogram according to their taxonomic affinity to obtain a phylogenetic tree including 498 species. Finally we also present the associated SST data for the observed period (1961–1980) and for the middle (2040–2059) and the end of the 21st century (2080–2099) obtained from NEMOMED8 according to the IPCC A2 scenario. The FishMed database might be of interest in the context of global anthropogenic changes as coastal Mediterranean ecosystems are currently recognized as one of the most impacted ecosystems on earth.
D. Key words: climate change; coastal fishes; functional diversity; Mediterranean fish species; Mediterranean Sea; NEMOMED8, species distribution models; phylogenetic diversity; taxonomic diversity.
Class II. Research origin descriptors
A. Overall project description
Identity: BIODIVMED
Originators:
David Mouillot, UMR 9190 MARBEC (CNRS-IFREMER-IRD-UM), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier, France.
François Le Loc’h, UMR 6539 Laboratoire des Sciences de l’Environnement Marin, CNRS-UBO-IRD-IFREMER, Institut Universitaire Européen de la Mer, Place Nicolas Copernic, Pointe du Diable, Technopole Brest-Iroise, 29280 Plouzané, France.
Period of Study: 2009–2012
Objectives: The goal of the BIODIVMED project is to model the ecological Mediterranean fish species niches, depending on climatic scenarios and to predict their future areas of distributions and therefore the expected fish biodiversity dynamic. This would permit (i) to assess which Mediterranean endemic species sees its IUCN status modified following the expected new range of temperature due to global climatic change (ii) to assess the effectiveness of the current MPA network and to propose conservation solutions for Mediterranean fish biodiversity (iii) to elaborate a strategy for selecting future locations of MPAs based on expected species shifts (iv) to assess the impact of these range modifications on the trophic functioning of exploited ecosystems.
Abstract: The Mediterranean Sea concentrates synergetic effects eroding fish biodiversity such as global warming, exotic species invasions and fish overexploitation. Consequently, an ever-increasing number of MPAs along the Mediterranean coast was created to counteract biodiversity erosion and to maintain resource sustainability. Within this context, the primary objective of the BIODIVMED project was the evaluation of the Mediterranean fish biodiversity evolution to test the relevance of the actual and future spatial distribution of MPAs. A second objective was to integrate both local (overfishing, alien invasions) and global influences (climate change) on the functioning of Mediterranean coastal marine ecosystems. During the "Convention on Biological Diversity" in 2004, the partners agreed to protect 10% of each major marine ecoregion before 2010 including the Mediterranean Sea. Presently, MPAs cover only 0.4% of the Mediterranean Sea surface and should be extended. The originality of this project lies in the coupling of (i) species distribution model to predict changes in spatial distributions of species with increasing temperature and (ii) trophic models to predict the flow of material depending on the structure of the assemblages as well as overfished species. This project is an important step towards a comprehensive approach to the protection of fish biodiversity in the Mediterranean Sea and an essential tool for decision support for future political and societal choices.
Sources of funding: The majority of this research was funded by the “Fondation pour la Recherche sur la Biodiversité” (FRB) and the “Fondation TOTAL”.
B. Brief subproject description
Study site:
The Mediterranean Sea, at the margins of three continents (Africa, Europe and Asia), has remarkable habitat diversity and has experienced major colonization events, which together have shaped highly heterogeneous patterns of species diversity (Ben Rais Lasram et al. 2009). The Mediterranean Sea is the largest (2.97 million km²) and deepest (mean 1460 m, maximum 5267 m) enclosed sea on earth and is indubitably a marine biodiversity hotspot. Despite representing 0.32% of the global oceanic volume, the Mediterranean Sea harbours a high level of endemism of 20% (over 17,000 compiled marine species; Coll et al., 2012). Like all marine ecosystems, the Mediterranean Sea is highly affected by anthropogenic activities including intensification in the exploitation of fisheries, a high concentration of aquaculture and a heavy deposition of pesticides and fertilizers from agriculture (Coll et al. 2012). Beyond these local pressures, the Mediterranean Sea is also one of the most responsive regions to climate change (Giorgi 2006).
Objectives:
One of the main goals in ecology is to understand the effects of climate change on biodiversity and ecosystem functioning. This subproject, within a multi-components biodiversity approach, aimed to forecast expected changes in the structure of Mediterranean coastal fish assemblages under climate change (Albouy et al. 2012, Albouy et al. 2013). The originality of this work was to consider the dynamics of species size structure, species diversity, phylogenetic diversity and functional diversity in coastal fish assemblages at different scales in the Mediterranean basin. The two last components of biodiversity are largely ignored in climate change projections whereas they are essential to maintain the viability of ecosystems and associated services beyond the number of species (Albouy et al. 2014a, Cadotte et al. 2008).
Main results:
We projected future geographic ranges of Mediterranean coastal fish through the implementation of SDMs based on a regional climate model (NEMOMED8-IPPC/SRES A2 scenario). The main results of this subproject were that for the end of the century (i) 54 species would lose their climatic niche, (ii) 70.4% of the continental shelf area would experience a reduction in species richness particularly in the Western Mediterranean basin and in the Aegean Sea, and (iii) the average maximum size of fish assemblages would increase over 74.8% of the continental shelf (Albouy et al 2013). The small size species, mainly belonging to the Gobiidae family, not targeted by fishing activities, would be the species most threatened by climate change, while larger species would be the most vulnerable to fishing effort (Albouy et al. 2013). Our projections at the whole Mediterranean scale showed a decrease of 13.6% for the phylogenetic diversity (PD) of coastal fish and 3% for their functional diversity (FD) by the end of this century and these decreases suggested a significant erosion of some lineages like the Gobiidae family (Albouy et al. 2014a). While the erosion of PD and FD was partly due to the loss of species richness (fewer species implies less lineage and functions) fish assemblages, especially in the western basin, would lose more phylogenetic and functional diversities than expected simply due to the erosion of species richness.
Main conclusions:
Beyond changes in species richness, the Mediterranean coastal fish assemblages might be modified, in the functions that they play in ecosystem and in the amount evolutionary history they support. This subproject paves the way towards the biogeography of ecosystem functioning using parsimonious and hybrid models to integrate different components of biodiversity, physical oceanography, and the level of resource exploitations to infer the future of marine system functioning facing multiple pressures that are already there.
Class III. Data set status and accessibility
A. Status
Latest update: September 2014 for all data files.
Latest Archive date: September 2014
Metadata status: Metadata are complete to last update and are stored with data.
B. Accessibility
1. Storage location and medium: All data are stored in non-proprietary digital form by all co-authors in multiple back-ups. The data set is also available via direct contact to the authors (below).
2. Contact person: Camille Albouy, email: [email protected].
3. Copyright restrictions: None.
4. Proprietary restrictions: Users are requested to acknowledge their use of the data set in publications, research proposals, websites, and other outlets with citation of this data paper. This data set is freely available for non-commercial scientific use, given the appropriate scholarly citation.
5. Costs: None.
Class IV. Data structural descriptors
Presence absence data (observed and future)
A. Data Set File
1. Identity: Presence_absence_data.zip
2. Size: 1.7 Mo (compressed)
3. Format and storage mode: Files compressed and submitted together in a zipped directory.
4. Header information: Names of each of the three files.
Observed_grid_1980.csv; number of columns: 637; number of rows: 27095;
Projected_grid_2040_2059.csv; number of columns: 290; number of rows: 8154;
Projected_grid_2080_2099.csv; number of columns: 290; number of rows: 8154;
B. Variable information
Each file encompasses in the header columns: the latitude, the longitude, and the species names. Each row corresponds to a grid cell, of the whole Mediterranean Sea for the observed data set, and of the Mediterranean continental shelf (0–200 m) for the projected data set. We included all the species in the observed data set (Observed_grid_1980.csv), however, we only included the species present on the continental shelf for the projected data set. Species distribution maps were digitalized and geo-referenced from a published atlas of fish of the northern Atlantic and the Mediterranean (FNAM; Whitehead et al. 1986), from the list of exotic fish species of the CIESM atlas (Golani et al. 2002) and data provided in Quignard and Tomasini (2000). Digitalized data were refined using the species bathymetric range (Froese and Pauly 2010, Louisy 2005). From this work a presence/absence matrix was computed using a 0.1° resolution grid covering the whole Mediterranean Sea for observed data and only the continental shelf for projected data. For more information about the projection method please read the following publications:
Albouy, C., F. Guilhaumon, M. B. Araújo, D. Mouillot, and F. Leprieur. 2012. Combining projected changes in species richness and composition reveals climate change impacts on coastal Mediterranean fish assemblages. Global Change Biology 18:2995–3003.
Albouy, C., F. Guilhaumon, F. Leprieur, F. Ben Rais Lasram, S. Somot, R. Aznar, L. Velez, F. Le Loc'h, and D. Mouillot. 2013. Projected climate change and the changing biogeography of coastal Mediterranean fishes. Journal of Biogeography 40:534–547.
Functional data set
A. Data Set File
1. Identity: Functional_data.zip.
2. Size: 24 Ko.
3. Format and storage mode: csv file, file compressed.
4. Header information: See variable names in Section B.
5. Special characters/fields: Missing data denoted as “NA”.
B. Variable information
Each row (635 + 1 for the header) of the data set corresponds to a Mediterranean fish species. Information on the species are summarized in 28 columns: the id number of the species, the taxonomy (Super class, Order, Family, Genus, Species), the IUCN Red list categories, the common and maximum length (in cm), the minimum and maximum depth (in meter), the trophic level and the following traits with their modalities: vertical distribution (3 modalities) migration (3 modalities), habitat (3 modalities), reproduction (3 modalities), sex reversal (4 modalities), semelparity (2 modalities), larvae (3 modalities), social behavior (3 modalities), diet type (3 modalities) and geographical origin (4 modalities). For more details on each trait see Table 1). Biological and ecological traits for the previous 635 species are gathered from different sources (Whitehead et al. 1986; Louisy, 2005; Froese and Pauly, 2012).
Table 1. List of ecological and biological traits
Modalities variables |
Vertical distribution |
Habitats |
Migration |
Reproduction |
Semelparity |
Diet_type of adults |
Social behavior |
Sex reversal |
Origin |
Diet type of larvae |
Depth |
Trophic level |
Length |
A |
Demersal |
Soft |
Catadromous |
Oviparous |
Yes |
Carnivorous |
Solitary |
Protogynous |
Lessepssian |
Planktotrophic |
Minimum |
— |
Maximum |
B |
Benthic |
Rocky |
Amphidromous |
Viviparous |
No |
Omnivorous |
Gregarious |
Hermaphrodism |
Endemic |
Leicitotrophic |
Maximum |
— |
Common— |
C |
Pelagic |
Posidonia |
Oceanodromous |
Ovoviviparous |
— |
Herbivorous |
Both |
Protandrous |
Atlantic |
no |
|
— |
— |
D |
— |
— |
Anadromous |
— |
— |
— |
— |
no |
Ubiquist |
— |
|
— |
— |
Units |
— |
— |
— |
— |
— |
— |
— |
— |
|
— |
Meters |
— |
Cm |
Phylogenetic data set
A. Data Set File
1. Identity: Phylogenetic_data.zip
2. Size: 57 ko (compressed).
3. Format and storage mode: Files compressed and submitted together in a zipped directory.
4. Header information: Names of each five files.
chronogram.tre
Med_405tax_g2.trd
Med_417tax_g1.trd
Med_474tax_f.trd
Med_498tax_o.trd
B. Variable information
We assembled a DNA supermatrix composed of four mitochondrial genes (12S ribosomal DNA, 16S ribosomal DNA, cytochrome c oxidase subunit I and cytochrome b) and two nuclear genes (rhodopsin and recombination activating gene I), including 62% of Mediterranean teleost species plus nine outgroups. Maximum likelihood and Bayesian phylogenetic and dating analyses were calibrated using 20 fossil constraints. An additional 124 species were grafted onto the chronogram according to their taxonomic affinity, checking for the effects of taxonomic coverage in subsequent diversification analyses. The files provided above contain the following in newick format: chronogram.tre contains the dated phylogeny of the species for which there was DNA sequence data (see Meynard et al. 2012) the other chronograms contain nested sets of species with decreasing taxonomic precision represented in the tree in the following order: Med_405tax_g2.trd adds species that have at least two congeners represented in the original chronogram grafted into the tree as polytomies at the congener’s node; Med_417tax_g1.trd adds species with at least one congener represented in the tree and added as polytomies at the congener’s node; following the same procedure, Med_474tax_f.trd adds species that have their family represented in the chronogram and Med_498tax_o.trd adds those that have species in the same order represented in the chronogram. The most complete tree therefore contains 498 species but many polytomies.
Contact person: Christine N. Meynard: Virginia Institute of Marine Science, College of William & Mary, P.O. Box 1346, Gloucester Point, VA 23062, USA. Email: [email protected].
CLIMATE DATA
A. Data Set File
1. Identity: Climate_data.zip
2. Size: 1.1 Mo (compressed).
3. Format and storage mode: Files compressed and submitted together in a zipped directory.
4. Header information: Names of each of the three files.
Observed_climate_data_1960_1980.csv; number of columns: 17; number of rows: 8154;
Projected_climate_data_2040_2059.csv; number of columns: 17; number of rows: 8154;
Projected_climate_data_2080_2099.csv; number of columns: 17; number of rows: 8154;
B. Variable information
Each file encompasses in the header columns the latitude, the longitude, and the variables names (see details below), each row corresponds to a grid cell of the Mediterranean continental shelf (0–200 m). We averaged daily SST values predicted by NEMOMED8 to infer monthly data, leading to 15 variables: 12 monthly averaged SST values, the absolute minimum SST, the absolute maximum SST and the absolute range of SST (i.e., the difference between the absolute maximum and minimum SST). We used the data from the period 1961–1980 as a baseline to calibrate the species distribution models. Several SST variables were considered because fish are ectothermic and thus highly dependent on the precise characteristics of their thermal environment for breeding and developmental success (Mann and Blackburn 1991). Projected SST values were obtained from NEMOMED8 for the middle (2040–2059) and the end of the 21st century (2080–2099) according to the IPCC/SRES A2 scenario (Somot et al, 2006; Beuvier et al, 2010). This scenario was considered as conservative for future prediction of global warming and it assumes a very heterogeneous world that preserves local identities, and which results from a continuously growing human population and an atmospheric CO2 concentration of 815 ppm by (IPCC 2007). The A2 scenario is a standard for regional climate studies and it is the only available scenario implemented by NEMOMED8.
Class V. Supplemental descriptors
A. Data Acquisition
A1. Data Forms and Location:
Original data forms reside at the UMR MARBEC, located at the University of Montpellier place Eugène Bataillon 34095 Montpellier cedex 5, France.
A2. Competing Interests:
The authors declare that they have no competing interests.
B. Quality Assurance/Quality Control Procedures
Data were double checked upon entry.
C. History of Data Set Usage
The data set is original and unpublished.
D. Publications and Results
Albouy, C., F. Guilhaumon, M. B. Araújo, D. Mouillot, and F. Leprieur. 2012. Combining projected changes in species richness and composition reveals climate change impacts on coastal Mediterranean fish assemblages. Global Change Biology 18:2995–3003.
Albouy, C., F. Guilhaumon, F. Leprieur, F. Ben Rais Lasram, S. Somot, R. Aznar, L. Velez, F. Le Loc'h, and D. Mouillot. 2013. Projected climate change and the changing biogeography of coastal Mediterranean fishes. Journal of Biogeography 40:534–547.
Albouy, C., F. Leprieur, F. Le Loc'h, N. Mouquet, C. Meynard, E. Douzery, and D. Mouillot. 2014a. Projected impacts of climate warming on the functional and phylogenetic components of coastal Mediterranean fish biodiversity. Ecography (In press) Doi 10.1111/ecog.01254.
Albouy, C., L. Velez, M. Coll, F. Colloca, F. Le Loc'h, D. Mouillot, and D. Gravel. 2014b. From projected species distribution to food-web structure under climate change. Global Change Biology 20:730–741.
Elleouet, J., C. Albouy, F. Ben Rais Lasram, D. Mouillot, and F. Leprieur. 2014. A trait-based approach for assessing and mapping niche overlap between native and exotic species: the Mediterranean coastal fish fauna as a case study. Diversity and Distributions 20:1333–1344.
Guilhaumon, F., C. Albouy, J. Claudet, L. Velez, F. Ben Rais Lasram, J.-A. Tomasini, E. J. P. Douzery, C. N. Meynard, N. Mouquet, M. Troussellier, M. B. Araújo, and D. Mouillot. 2014. Representing taxonomic, phylogenetic and functional diversity: new challenges for Mediterranean marine-protected areas. Diversity and Distributions 21(2):175–187.
Meynard, C. N., D. Mouillot, N. Mouquet, and E. J. P. Douzery. 2012. A Phylogenetic Perspective on the Evolution of Mediterranean Teleost Fishes. PLoS ONE 7.
Mouillot, D., C. Albouy, F. Guilhaumon, F. B. R. Lasram, M. Coll, V. Devictor, C. N. Meynard, D. Pauly, J. A. Tomasini, M. Troussellier, L. Velez, R. Watson, E. J. P. Douzery, and N. Mouquet. 2011. Protected and Threatened Components of Fish Biodiversity in the Mediterranean Sea. Current Biology 21:1044–1050.
Acknowledgments
We are grateful to the two anonymous referees for all the remarks and suggestions that improved the manuscript. We would like to thank Amel Berima and Rob Domvile and the RCMP for English Editing. This work was partly funded by the “Fondation TOTAL”, the ‘Fondation pour la Recherche sur la Biodiversité.’ (project BIODIVMED). C.A. was supported by a RAQ post-doctoral fellowship. D.M. was supported by a Marie Curie International Outgoing Fellowship (FISHECO) with agreement number IOF-GA-2009-236316.
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