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Maglietta R, Saccotelli L, Fanizza C, Telesca V, Dimauro G, Causio S, Lecci R, Federico I, Coppini G, Cipriano G, Carlucci R. Environmental variables and machine learning models to predict cetacean abundance in the Central-eastern Mediterranean Sea. Sci Rep 2023; 13:2600. [PMID: 36788321 PMCID: PMC9929343 DOI: 10.1038/s41598-023-29681-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
Although the Mediterranean Sea is a crucial hotspot in marine biodiversity, it has been threatened by numerous anthropogenic pressures. As flagship species, Cetaceans are exposed to those anthropogenic impacts and global changes. Assessing their conservation status becomes strategic to set effective management plans. The aim of this paper is to understand the habitat requirements of cetaceans, exploiting the advantages of a machine-learning framework. To this end, 28 physical and biogeochemical variables were identified as environmental predictors related to the abundance of three odontocete species in the Northern Ionian Sea (Central-eastern Mediterranean Sea). In fact, habitat models were built using sighting data collected for striped dolphins Stenella coeruleoalba, common bottlenose dolphins Tursiops truncatus, and Risso's dolphins Grampus griseus between July 2009 and October 2021. Random Forest was a suitable machine learning algorithm for the cetacean abundance estimation. Nitrate, phytoplankton carbon biomass, temperature, and salinity were the most common influential predictors, followed by latitude, 3D-chlorophyll and density. The habitat models proposed here were validated using sighting data acquired during 2022 in the study area, confirming the good performance of the strategy. This study provides valuable information to support management decisions and conservation measures in the EU marine spatial planning context.
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Affiliation(s)
- Rosalia Maglietta
- Institute of Intelligent Industrial Technologies and Systems for Advanced Manufacturing, National Research Council, via Amendola 122/D-I, 70126, Bari, Italy.
| | - Leonardo Saccotelli
- Ocean Predictions and Applications Division, Centro Euro-Mediterraneo sui Cambiamenti Climatici, Lecce, Italy
| | - Carmelo Fanizza
- Jonian Dolphin Conservation, viale Virgilio 102, 74121, Taranto, Italy
| | - Vito Telesca
- School of Engineering, University of Basilicata, viale Ateneo Lucano 10, 85100, Potenza, Italy
| | - Giovanni Dimauro
- Department of Computer Science, University of Bari, via Orabona 4, 70125, Bari, Italy
| | - Salvatore Causio
- Ocean Predictions and Applications Division, Centro Euro-Mediterraneo sui Cambiamenti Climatici, Lecce, Italy
| | - Rita Lecci
- Ocean Predictions and Applications Division, Centro Euro-Mediterraneo sui Cambiamenti Climatici, Lecce, Italy
| | - Ivan Federico
- Ocean Predictions and Applications Division, Centro Euro-Mediterraneo sui Cambiamenti Climatici, Lecce, Italy
| | - Giovanni Coppini
- Ocean Predictions and Applications Division, Centro Euro-Mediterraneo sui Cambiamenti Climatici, Lecce, Italy
| | - Giulia Cipriano
- Department of Biology, University of Bari, via Orabona 4, 70125, Bari, Italy
| | - Roberto Carlucci
- Department of Biology, University of Bari, via Orabona 4, 70125, Bari, Italy
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He M, Fang DA, Chen YJ, Sun HB, Luo H, Ren YF, Li TY. Genetic Diversity Evaluation and Conservation of Topmouth Culter ( Culter alburnus) Germplasm in Five River Basins in China. BIOLOGY 2022; 12:biology12010012. [PMID: 36671705 PMCID: PMC9854899 DOI: 10.3390/biology12010012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/09/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
To study the genetic diversity of Culter alburnus (C. alburnus) populations, we analyzed the genetic diversity of five C. alburnus populations from Songhua Lake (SH), Huaihe River (HH), Changjiang River (CJ), Taihu Lake (TH), and Gehu Lake (GH) based on mitochondrial COI gene sequences. The results showed that the average contents of bases T, C, A, and G in the 526 bp COI gene sequence were 25.3%, 18.1%, 28.1%, and 28.6%, respectively, which showed AT bias. A total of 115 polymorphic sites were detected in the five populations, and 11 haplotypes (Hap) were defined. The nucleotide diversity (Pi) of the five populations ranged from 0.00053 to 0.01834, and the haplotype diversity (Hd) ranged from 0.280 to 0.746, with the highest genetic diversity in the TH population, followed by the SH population, with lower genetic diversity in the HH, CJ and GH populations. The analysis of the fixation index (Fst) and the genetic distance between populations showed that there was significant genetic differentiation between the SH population and the other populations, and the genetic distances between all of them were far; the genetic diversity within populations was higher than that between populations. Neutral tests, mismatch distributions, and Bayesian skyline plot (BSP) analyses showed that the C. alburnus populations have not experienced population expansion and are relatively stable in historical dynamics.
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Affiliation(s)
- Miao He
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Di-An Fang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
- Correspondence:
| | - Yong-jin Chen
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Hai-bo Sun
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Hui Luo
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Ya-fei Ren
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Tian-you Li
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
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3
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Çetin C, Furman A, Kalkan E, Bilgin R. Mitonuclear genetic patterns of divergence in the marbled crab, Pachygrapsus marmoratus (Fabricius, 1787) along the Turkish seas. PLoS One 2022; 17:e0266506. [PMID: 35381029 PMCID: PMC8982882 DOI: 10.1371/journal.pone.0266506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 03/22/2022] [Indexed: 12/03/2022] Open
Abstract
Biogeographical transition zones present good opportunities for studying the effect of the past ice ages on genetic structure of species because secondary contact zones of post-glacial lineages can be formed. In this study, we investigated the population genetic structure of the marbled rock crab, Pachygrapsus marmoratus along the coasts of Turkey. We genotyped 334 individuals from the Black Sea, the Turkish Straits System (TSS), the Aegean, and the Eastern Mediterranean basins. In order to reveal its evolutionary history and its population connectivity, we used mitochondrial CO1 region and five microsatellite loci. CO1 analyzes also included 610 additional samples from Genbank, which covered most of its distribution range. Both microsatellites and mtDNA showed decreased diversity in sampling sites of the TSS and the Black Sea as compared to those along the Aegean and the Levantine coasts. There is an especially strong geographical pattern in distributions of haplotypes in mtDNA, most probably as a result of genetic drift in the Black Sea and the Sea of Marmara (SoM). Microsatellite data analyses revealed two genetically distinct clusters of P. marmoratus (clusters C and M). While individuals belonging to cluster C are present in all the sampling locations, those belonging to cluster M are only detected along the Mediterranean coasts including the Aegean and the Levantine basins. These clusters shared similar haplotypes in the Mediterranean. Haplotypes of two sympatric clusters could be similar due to incomplete lineage sorting of ancestral polymorphisms. In order to retrieve the complex demographic history and to investigate evolutionary processes resulting in sympatric clusters in the Aegean Sea and the Levantine basin, mitochondrial markers with faster mutation rates than CO1 and/or SNP data will be useful.
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Affiliation(s)
- Cansu Çetin
- Institute of Environmental Sciences, Boğaziçi University, Bebek, Istanbul, Turkey
- Institute of Integrative Biology (IBZ), ETH Zürich, Zürich, Switzerland
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- * E-mail:
| | - Andrzej Furman
- Institute of Environmental Sciences, Boğaziçi University, Bebek, Istanbul, Turkey
| | - Evrim Kalkan
- Institute of Marine Sciences, Middle East Technical University, Erdemli-Mersin, Turkey
| | - Raşit Bilgin
- Institute of Environmental Sciences, Boğaziçi University, Bebek, Istanbul, Turkey
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Population Genetic Structure of Chlorops oryzae (Diptera, Chloropidae) in China. INSECTS 2022; 13:insects13040327. [PMID: 35447769 PMCID: PMC9032139 DOI: 10.3390/insects13040327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/18/2022] [Accepted: 03/24/2022] [Indexed: 02/04/2023]
Abstract
Frequent outbreaks have made Chlorops oryzae one of the major pests of rice in some regions. In order to understand the ecological adaptation of C. oryzae at the molecular level, and provide a scientific basis for formulating management strategies, we used two molecular markers, COI and ITS1 sequences, to systematically analyze the genetic structure of 31 populations. The higher haplotype diversity and lower nucleotide diversity indicated that the C. oryzae populations experienced rapid expansion after a “Bottleneck effect”. The results of the mismatch distribution, neutrality test (Fu’s Fs < 0, p < 0.001), and haplotype network analysis suggested that the population has recently undergone an expansion. Although genetic differentiation among C. oryzae populations was found to have existed at low/medium levels (Fst: 0.183 for COI, 0.065 for ITS1), the frequent gene flow presented as well (Nm: 2.23 for COI, 3.60 for ITS1) was supposed to be responsible for frequent local outbreaks.
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Ben Chehida Y, Loughnane R, Thumloup J, Kaschner K, Garilao C, Rosel PE, Fontaine MC. No leading-edge effect in North Atlantic harbor porpoises: Evolutionary and conservation implications. Evol Appl 2021; 14:1588-1611. [PMID: 34178106 PMCID: PMC8210799 DOI: 10.1111/eva.13227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/19/2021] [Accepted: 02/24/2021] [Indexed: 01/12/2023] Open
Abstract
Understanding species responses to past environmental changes can help forecast how they will cope with ongoing climate changes. Harbor porpoises are widely distributed in the North Atlantic and were deeply impacted by the Pleistocene changes with the split of three subspecies. Despite major impacts of fisheries on natural populations, little is known about population connectivity and dispersal, how they reacted to the Pleistocene changes, and how they will evolve in the future. Here, we used phylogenetics, population genetics, and predictive habitat modeling to investigate population structure and phylogeographic history of the North Atlantic porpoises. A total of 925 porpoises were characterized at 10 microsatellite loci and one quarter of the mitogenome (mtDNA). A highly divergent mtDNA lineage was uncovered in one porpoise off Western Greenland, suggesting that a cryptic group may occur and could belong to a recently discovered mesopelagic ecotype off Greenland. Aside from it and the southern subspecies, spatial genetic variation showed that porpoises from both sides of the North Atlantic form a continuous system belonging to the same subspecies (Phocoena phocoena phocoena). Yet, we identified important departures from random mating and restricted dispersal forming a highly significant isolation by distance (IBD) at both mtDNA and nuclear markers. A ten times stronger IBD at mtDNA compared with nuclear loci supported previous evidence of female philopatry. Together with the lack of spatial trends in genetic diversity, this IBD suggests that migration-drift equilibrium has been reached, erasing any genetic signal of a leading-edge effect that accompanied the predicted recolonization of the northern habitats freed from Pleistocene ice. These results illuminate the processes shaping porpoise population structure and provide a framework for designing conservation strategies and forecasting future population evolution.
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Affiliation(s)
- Yacine Ben Chehida
- Groningen Institute for Evolutionary Life Sciences (GELIFES)University of GroningenGroningenThe Netherlands
| | - Roisin Loughnane
- Groningen Institute for Evolutionary Life Sciences (GELIFES)University of GroningenGroningenThe Netherlands
| | - Julie Thumloup
- Groningen Institute for Evolutionary Life Sciences (GELIFES)University of GroningenGroningenThe Netherlands
| | - Kristin Kaschner
- Department of Biometry and Environmental System AnalysisFaculty of Environment and Natural ResourcesUniversity of FreiburgFreiburgGermany
| | | | - Patricia E. Rosel
- Southeast Fisheries Science CenterNational Marine Fisheries ServiceNOAALafayetteLAUSA
| | - Michael C. Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES)University of GroningenGroningenThe Netherlands
- Laboratoire MIVEGEC (Université de Montpellier, CNRS, IRD)Montpellier Cedex 5France
- Centre de Recherche en Écologie et Évolution de la Santé (CREESMontpellier Cedex 5France
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6
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Morin PA, Forester BR, Forney KA, Crossman CA, Hancock-Hanser BL, Robertson KM, Barrett-Lennard LG, Baird RW, Calambokidis J, Gearin P, Hanson MB, Schumacher C, Harkins T, Fontaine MC, Taylor BL, Parsons KM. Population structure in a continuously distributed coastal marine species, the harbor porpoise, based on microhaplotypes derived from poor-quality samples. Mol Ecol 2021; 30:1457-1476. [PMID: 33544423 DOI: 10.1111/mec.15827] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 01/20/2021] [Accepted: 01/27/2021] [Indexed: 12/24/2022]
Abstract
Harbor porpoise in the North Pacific are found in coastal waters from southern California to Japan, but population structure is poorly known outside of a few local areas. We used multiplexed amplicon sequencing of 292 loci and genotyped clusters of single nucleotide polymoirphisms as microhaplotypes (N = 271 samples) in addition to mitochondrial (mtDNA) sequence data (N = 413 samples) to examine the genetic structure from samples collected along the Pacific coast and inland waterways from California to southern British Columbia. We confirmed an overall pattern of strong isolation-by-distance, suggesting that individual dispersal is restricted. We also found evidence of regions where genetic differences are larger than expected based on geographical distance alone, implying current or historical barriers to gene flow. In particular, the southernmost population in California is genetically distinct (FST = 0.02 [microhaplotypes]; 0.31 [mtDNA]), with both reduced genetic variability and high frequency of an otherwise rare mtDNA haplotype. At the northern end of our study range, we found significant genetic differentiation of samples from the Strait of Georgia, previously identified as a potential biogeographical boundary or secondary contact zone between harbor porpoise populations. Association of microhaplotypes with remotely sensed environmental variables indicated potential local adaptation, especially at the southern end of the species' range. These results inform conservation and management for this nearshore species, illustrate the value of genomic methods for detecting patterns of genetic structure within a continuously distributed marine species, and highlight the power of microhaplotype genotyping for detecting genetic structure in harbor porpoises despite reliance on poor-quality samples.
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Affiliation(s)
- Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, USA
| | - Brenna R Forester
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Karin A Forney
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Moss Landing, CA, USA.,Moss Landing Marine Laboratories, San Jose State University, Moss Landing, CA, USA
| | - Carla A Crossman
- Biology Department, Saint Mary's University, Halifax, NS, Canada.,Cetacean Research Program, Vancouver Aquarium, Vancouver, BC, Canada
| | | | - Kelly M Robertson
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, USA
| | | | | | | | - Pat Gearin
- Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA, USA
| | - M Bradley Hanson
- Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA, USA
| | | | | | - Michael C Fontaine
- MIVEGEC Research Unit (Université de Montpellier, CNRS, IRD) & Centre for Research on the Ecology and Evolution of Diseases (CREES), Centre IRD de Montpellier, Montpellier, France.,Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Barbara L Taylor
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, USA
| | - Kim M Parsons
- Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA, USA.,Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA, USA
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7
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Ben Chehida Y, Thumloup J, Vishnyakova K, Gol'din P, Fontaine MC. Genetic homogeneity in the face of morphological heterogeneity in the harbor porpoise from the Black Sea and adjacent waters (Phocoena phocoena relicta). Heredity (Edinb) 2020; 124:469-484. [PMID: 31772318 PMCID: PMC7028986 DOI: 10.1038/s41437-019-0284-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 11/08/2019] [Accepted: 11/10/2019] [Indexed: 01/31/2023] Open
Abstract
Absence of genetic differentiation is usually taken as an evidence of panmixia, but can also reflect other situations, including even nearly complete demographic independence among large-sized populations. Deciphering which situation applies has major practical implications (e.g., in conservation biology). The endangered harbor porpoises in the Black Sea illustrates this point well. While morphological heterogeneity suggested that population differentiation may exist between individuals from the Black and Azov seas, no genetic study provided conclusive evidence or covered the entire subspecies range. Here, we assessed the genetic structure at ten microsatellite loci and a 3904 base-pairs mitochondrial fragment in 144 porpoises across the subspecies range (i.e., Aegean, Marmara, Black, and Azov seas). Analyses of the genetic structure, including FST, Bayesian clustering, and multivariate analyses revealed a nearly complete genetic homogeneity. Power analyses rejected the possibility of underpowered analyses (power to detect FST ≥ 0.008 at microsatellite loci). Simulations under various demographic models, evaluating the evolution of FST, showed that a time-lag effect between demographic and genetic subdivision is also unlikely. With a realistic effective population size of 1000 individuals, the expected "gray zone" would be at most 20 generations under moderate levels of gene flow (≤10 migrants per generation). After excluding alternative hypotheses, panmixia remains the most likely hypothesis explaining the genetic homogeneity in the Black Sea porpoises. Morphological heterogeneity may thus reflect other processes than population subdivision (e.g., plasticity, selection). This study illustrates how combining empirical and theoretical approaches can contribute to understanding patterns of weak population structure in highly mobile marine species.
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Affiliation(s)
- Yacine Ben Chehida
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands
| | - Julie Thumloup
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands
| | - Karina Vishnyakova
- Ukrainian Scientific Centre of Ecology of Sea, 89 Frantsuzsky Blvd, Odesa, 65009, Ukraine
| | - Pavel Gol'din
- Schmalhausen Institute of Zoology, National Academy of Sciences of Ukraine, 15 Bogdan Khmelnytskyi Street, Kiev, 01030, Ukraine
| | - Michael C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands.
- Laboratoire MIVEGEC (Université de Montpellier, UMR CNRS 5290, IRD 229), Centre IRD de Montpellier, 911 Avenue Agropolis, BP 64501, Montpellier Cedex 5, 34394, France.
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8
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Jay F, Boitard S, Austerlitz F. An ABC Method for Whole-Genome Sequence Data: Inferring Paleolithic and Neolithic Human Expansions. Mol Biol Evol 2020; 36:1565-1579. [PMID: 30785202 DOI: 10.1093/molbev/msz038] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Species generally undergo a complex demographic history consisting, in particular, of multiple changes in population size. Genome-wide sequencing data are potentially highly informative for reconstructing this demographic history. A crucial point is to extract the relevant information from these very large data sets. Here, we design an approach for inferring past demographic events from a moderate number of fully sequenced genomes. Our new approach uses Approximate Bayesian Computation, a simulation-based statistical framework that allows 1) identifying the best demographic scenario among several competing scenarios and 2) estimating the best-fitting parameters under the chosen scenario. Approximate Bayesian Computation relies on the computation of summary statistics. Using a cross-validation approach, we show that statistics such as the lengths of haplotypes shared between individuals, or the decay of linkage disequilibrium with distance, can be combined with classical statistics (e.g., heterozygosity and Tajima's D) to accurately infer complex demographic scenarios including bottlenecks and expansion periods. We also demonstrate the importance of simultaneously estimating the genotyping error rate. Applying our method on genome-wide human-sequence databases, we finally show that a model consisting in a bottleneck followed by a Paleolithic and a Neolithic expansion is the most relevant for Eurasian populations.
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Affiliation(s)
- Flora Jay
- Laboratoire EcoAnthropologie et Ethnobiologie, CNRS/MNHN/Université Paris Diderot, Paris, France.,Laboratoire de Recherche en Informatique, CNRS/Université Paris-Sud/Université Paris-Saclay, Orsay, France
| | - Simon Boitard
- GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, Castanet Tolosan, France
| | - Frédéric Austerlitz
- Laboratoire EcoAnthropologie et Ethnobiologie, CNRS/MNHN/Université Paris Diderot, Paris, France
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9
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Autenrieth M, Hartmann S, Lah L, Roos A, Dennis AB, Tiedemann R. High-quality whole-genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena). Mol Ecol Resour 2018; 18:1469-1481. [PMID: 30035363 DOI: 10.1111/1755-0998.12932] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 07/04/2018] [Accepted: 07/05/2018] [Indexed: 11/27/2022]
Abstract
The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found across the Northern hemisphere. It occurs in coastal waters and inhabits basins that vary broadly in salinity, temperature and food availability. These diverse habitats could drive subtle differentiation among populations, but examination of this would be best conducted with a robust reference genome. Here, we report the first harbour porpoise genome, assembled de novo from an individual originating in the Kattegat Sea (Sweden). The genome is one of the most complete cetacean genomes currently available, with a total size of 2.39 Gb and 50% of the total length found in just 34 scaffolds. Using 122 of the longest scaffolds, we were able to show high levels of synteny with the genome of the domestic cattle (Bos taurus). Our draft annotation comprises 22,154 predicted genes, which we further annotated through matches to the NCBI nucleotide database, GO categorization and motif prediction. Within the predicted genes, we have confirmed the presence of >20 genes or gene families that have been associated with adaptive evolution in other cetaceans. Overall, this genome assembly and draft annotation represent a crucial addition to the genomic resources currently available for the study of porpoises and Phocoenidae evolution, phylogeny and conservation.
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Affiliation(s)
- Marijke Autenrieth
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Stefanie Hartmann
- Institute of Biochemistry and Biology, Evolutionary Adaptive Genomics, University of Potsdam, Potsdam, Germany
| | - Ljerka Lah
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Anna Roos
- Swedish Museum of Natural History, Stockholm, Sweden
| | - Alice B Dennis
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Ralph Tiedemann
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
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10
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Sharma R, Goossens B, Heller R, Rasteiro R, Othman N, Bruford MW, Chikhi L. Genetic analyses favour an ancient and natural origin of elephants on Borneo. Sci Rep 2018; 8:880. [PMID: 29343863 PMCID: PMC5772424 DOI: 10.1038/s41598-017-17042-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 11/18/2017] [Indexed: 12/02/2022] Open
Abstract
The origin of the elephant on the island of Borneo remains elusive. Research has suggested two alternative hypotheses: the Bornean elephant stems either from a recent introduction in the 17th century or from an ancient colonization several hundreds of thousands years ago. Lack of elephant fossils has been interpreted as evidence for a very recent introduction, whereas mtDNA divergence from other Asian elephants has been argued to favor an ancient colonization. We investigated the demographic history of Bornean elephants using full-likelihood and approximate Bayesian computation analyses. Our results are at odds with both the recent and ancient colonization hypotheses, and favour a third intermediate scenario. We find that genetic data favour a scenario in which Bornean elephants experienced a bottleneck during the last glacial period, possibly as a consequence of the colonization of Borneo, and from which it has slowly recovered since. Altogether the data support a natural colonization of Bornean elephants at a time when large terrestrial mammals could colonise from the Sunda shelf when sea levels were much lower. Our results are important not only in understanding the unique history of the colonization of Borneo by elephants, but also for their long-term conservation.
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Affiliation(s)
- Reeta Sharma
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, P-2780-156, Oeiras, Portugal.
| | - Benoit Goossens
- Organisms and Environment Division, School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK.
- Danau Girang Field Centre, c/o Sabah Wildlife Department, Wisma Muis, 88100, Kota Kinabalu, Sabah, Malaysia.
- Sabah Wildlife Department, Wisma Muis, 88100, Kota Kinabalu, Sabah, Malaysia.
- Sustainable Places Research Institute, Cardiff University, 33 Park Place, Cardiff, CF10 3BA, UK.
| | - Rasmus Heller
- Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen Ø, Denmark
| | - Rita Rasteiro
- Department of Genetics and Genome Biology, University of Leicester, Adrian Building, University Road, Leicester, LE1 7RH, United Kingdom
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Nurzhafarina Othman
- Organisms and Environment Division, School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
- Danau Girang Field Centre, c/o Sabah Wildlife Department, Wisma Muis, 88100, Kota Kinabalu, Sabah, Malaysia
| | - Michael W Bruford
- Organisms and Environment Division, School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
- Sustainable Places Research Institute, Cardiff University, 33 Park Place, Cardiff, CF10 3BA, UK
| | - Lounès Chikhi
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, P-2780-156, Oeiras, Portugal
- CNRS, Université Paul Sabatier, ENFA, UMR 5174 EDB (Laboratoire Evolution & Diversité Biologique), 118 route de Narbonne, F-31062, Toulouse, France
- Université Paul Sabatier, UMR 5174 EDB, F-31062, Toulouse, France
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11
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Hohenlohe PA, Hand BK, Andrews KR, Luikart G. Population Genomics Provides Key Insights in Ecology and Evolution. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_20] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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12
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Chen M, Fontaine MC, Ben Chehida Y, Zheng J, Labbé F, Mei Z, Hao Y, Wang K, Wu M, Zhao Q, Wang D. Genetic footprint of population fragmentation and contemporary collapse in a freshwater cetacean. Sci Rep 2017; 7:14449. [PMID: 29089536 PMCID: PMC5663847 DOI: 10.1038/s41598-017-14812-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 10/16/2017] [Indexed: 02/07/2023] Open
Abstract
Understanding demographic trends and patterns of gene flow in an endangered species is crucial for devising conservation strategies. Here, we examined the extent of population structure and recent evolution of the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis). By analysing genetic variation at the mitochondrial and nuclear microsatellite loci for 148 individuals, we identified three populations along the Yangtze River, each one connected to a group of admixed ancestry. Each population displayed extremely low genetic diversity, consistent with extremely small effective size (≤92 individuals). Habitat degradation and distribution gaps correlated with highly asymmetric gene-flow that was inefficient in maintaining connectivity between populations. Genetic inferences of historical demography revealed that the populations in the Yangtze descended from a small number of founders colonizing the river from the sea during the last Ice Age. The colonization was followed by a rapid population split during the last millennium predating the Chinese Modern Economy Development. However, genetic diversity showed a clear footprint of population contraction over the last 50 years leaving only ~2% of the pre-collapsed size, consistent with the population collapses reported from field studies. This genetic perspective provides background information for devising mitigation strategies to prevent this species from extinction.
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Affiliation(s)
- Minmin Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology of Chinese Academy of Sciences, Wuhan, 430072, China.,Research Center of Aquatic Organism Conservation and Water Ecosystem Restoration in Anhui Province, College of Life Science, Anqing Normal University, Anqing, 246133, China
| | - Michael C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands.
| | - Yacine Ben Chehida
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands
| | - Jinsong Zheng
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology of Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Frédéric Labbé
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands.,Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Biological Sciences, University of Notre Dame, Galvin Life Sciences Center, Notre Dame, IN, 46556, USA
| | - Zhigang Mei
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology of Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yujiang Hao
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology of Chinese Academy of Sciences, Wuhan, 430072, China
| | - Kexiong Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology of Chinese Academy of Sciences, Wuhan, 430072, China
| | - Min Wu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology of Chinese Academy of Sciences, Wuhan, 430072, China
| | - Qingzhong Zhao
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology of Chinese Academy of Sciences, Wuhan, 430072, China
| | - Ding Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology of Chinese Academy of Sciences, Wuhan, 430072, China.
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13
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Cabrera AA, Palsbøll PJ. Inferring past demographic changes from contemporary genetic data: A simulation-based evaluation of the ABC methods implemented indiyabc. Mol Ecol Resour 2017; 17:e94-e110. [DOI: 10.1111/1755-0998.12696] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 06/12/2017] [Accepted: 06/20/2017] [Indexed: 01/19/2023]
Affiliation(s)
- Andrea A. Cabrera
- Marine Evolution and Conservation; Groningen Institute of Evolutionary Life Sciences; University of Groningen; Groningen The Netherlands
| | - Per J. Palsbøll
- Marine Evolution and Conservation; Groningen Institute of Evolutionary Life Sciences; University of Groningen; Groningen The Netherlands
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14
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Fontaine MC, Thatcher O, Ray N, Piry S, Brownlow A, Davison NJ, Jepson P, Deaville R, Goodman SJ. Mixing of porpoise ecotypes in southwestern UK waters revealed by genetic profiling. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160992. [PMID: 28405389 PMCID: PMC5383846 DOI: 10.1098/rsos.160992] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 01/30/2017] [Indexed: 06/07/2023]
Abstract
Contact zones between ecotypes are windows for understanding how species may react to climate changes. Here, we analysed the fine-scale genetic and morphological variation in harbour porpoises (Phocoena phocoena) around the UK by genotyping 591 stranded animals at nine microsatellite loci. The data were integrated with a prior study to map at high resolution the contact zone between two previously identified ecotypes meeting in the northern Bay of Biscay. Clustering and spatial analyses revealed that UK porpoises are derived from two genetic pools with porpoises from the southwestern UK being genetically differentiated, and having larger body sizes compared to those of other UK areas. Southwestern UK porpoises showed admixed ancestry between southern and northern ecotypes with a contact zone extending from the northern Bay of Biscay to the Celtic Sea and Channel. Around the UK, ancestry blends from one genetic group to the other along a southwest--northeast axis, correlating with body size variation, consistent with previously reported morphological differences between the two ecotypes. We also detected isolation by distance among juveniles but not in adults, suggesting that stranded juveniles display reduced intergenerational dispersal. The fine-scale structure of this admixture zone raises the question of how it will respond to future climate change and provides a reference point for further study.
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Affiliation(s)
- Michaël C. Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Oliver Thatcher
- Institute of Zoology, Zoological Society of London, London NW1 4RY, UK
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Nicolas Ray
- EnviroSPACE Laboratory, Institute for Environmental Sciences, University of Geneva, Carouge, Switzerland
| | - Sylvain Piry
- INRA, UMR CBGP, 34988 Montferrier-sur-Lez Cedex, France
| | - Andrew Brownlow
- Scottish Marine Animal Stranding Scheme, SRUC Veterinary Services, Drummondhill, Stratherrick Road, Inverness IV2 4JZ, UK
| | - Nicholas J. Davison
- Scottish Marine Animal Stranding Scheme, SRUC Veterinary Services, Drummondhill, Stratherrick Road, Inverness IV2 4JZ, UK
- Animal and Plant Health Agency, Polwhele, Truro, Cornwall TR4 9AD, UK
| | - Paul Jepson
- Institute of Zoology, Zoological Society of London, London NW1 4RY, UK
| | - Rob Deaville
- Institute of Zoology, Zoological Society of London, London NW1 4RY, UK
| | - Simon J. Goodman
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
- Institute of Zoology, Zoological Society of London, London NW1 4RY, UK
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15
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Aimé C, Austerlitz F. Different kinds of genetic markers permit inference of Paleolithic and Neolithic expansions in humans. Eur J Hum Genet 2016; 25:360-365. [PMID: 28000700 DOI: 10.1038/ejhg.2016.191] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/12/2016] [Accepted: 11/22/2016] [Indexed: 11/09/2022] Open
Abstract
Recent population genetic studies have provided valuable insights on the demographic history of our species. However, some issues such as the dating of the first demographic expansions in human populations remain puzzling. Indeed, although a few genetic studies argued that the first human expansions were concomitant with the Neolithic transition, many others found signals of expansion events starting during the Palaeolithic. Here we performed a simulation study to show that these contradictory findings may result from the differences in the genetic markers used, especially if two successive expansion events occurred. For a large majority of replicates for each scenario tested, microsatellite data allow only detecting the recent expansion event in that case, whereas sequence data allow only detecting the ancient expansion. Combined with previous real data analyses, our results bring support to the ideas that (i) a first human expansions started during the Palaeolithic period, (ii) a second expansion event occurred later, concomitantly with the Neolithic transition.
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Affiliation(s)
- Carla Aimé
- UMR 7206, EcoAnthropologie et Ethnobiologie, CNRS/MNHN/Université Paris Diderot, Paris, France.,UMR 5554, Institut des Sciences de l'Évolution, CNRS-Université de Montpellier, Montpellier, France
| | - Frédéric Austerlitz
- UMR 7206, EcoAnthropologie et Ethnobiologie, CNRS/MNHN/Université Paris Diderot, Paris, France
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16
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Fontaine MC. Harbour Porpoises, Phocoena phocoena, in the Mediterranean Sea and Adjacent Regions: Biogeographic Relicts of the Last Glacial Period. ADVANCES IN MARINE BIOLOGY 2016; 75:333-358. [PMID: 27770989 DOI: 10.1016/bs.amb.2016.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The harbour porpoise, Phocoena phocoena, is one of the best studied cetacean species owing to its common distribution along the coastal waters of the Northern Hemisphere. In European waters, strandings are common and bycatch mortalities in commercial fisheries reach alarming numbers. Lethal interactions resulting from human activities together with ongoing environmental changes raise serious concerns about population viability throughout the species' range. These concerns foster the need to fill critical gaps in knowledge of harbour porpoise biology, including population structure, feeding ecology, habitat preference and evolutionary history, that are critical information for planning effective management and conservation efforts. While the species is distributed fairly continuously in the North Atlantic Ocean, it becomes fragmented in the south-eastern part with isolated populations occurring along the Atlantic coasts of the Iberian Peninsula, Northwest Africa and the Black Sea. The latter population is separated from Atlantic populations by the Mediterranean Sea, where the species is almost entirely absent. Understanding the evolutionary history of these populations occurring in marginal habitats holds the potential to reveal fundamental aspects of the species' biology such as the factors determining its distribution, ecological niche, and how past and recent environmental variation have shaped the current population structure. This information can be critical for understanding the future evolution of the species in consideration of ongoing environmental changes. This chapter summarizes the recent advances in our knowledge regarding the populations bordering the Mediterranean Sea with a special emphasis on their ecological and evolutionary history, which has recently been reconstructed from genetic analyses.
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Affiliation(s)
- M C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands.
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17
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Boissin E, Micu D, Janczyszyn-Le Goff M, Neglia V, Bat L, Todorova V, Panayotova M, Kruschel C, Macic V, Milchakova N, Keskin Ç, Anastasopoulou A, Nasto I, Zane L, Planes S. Contemporary genetic structure and postglacial demographic history of the black scorpionfish, Scorpaena porcus, in the Mediterranean and the Black Seas. Mol Ecol 2016; 25:2195-209. [PMID: 26989881 DOI: 10.1111/mec.13616] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 02/09/2016] [Accepted: 03/11/2016] [Indexed: 12/24/2022]
Abstract
Understanding the distribution of genetic diversity in the light of past demographic events linked with climatic shifts will help to forecast evolutionary trajectories of ecosystems within the current context of climate change. In this study, mitochondrial sequences and microsatellite loci were analysed using traditional population genetic approaches together with Bayesian dating and the more recent approximate Bayesian computation scenario testing. The genetic structure and demographic history of a commercial fish, the black scorpionfish, Scorpaena porcus, was investigated throughout the Mediterranean and Black Seas. The results suggest that the species recently underwent population expansions, in both seas, likely concomitant with the warming period following the Last Glacial Maximum, 20 000 years ago. A weak contemporaneous genetic differentiation was identified between the Black Sea and the Mediterranean Sea. However, the genetic diversity was similar for populations of the two seas, suggesting a high number of colonizers entered the Black Sea during the interglacial period and/or the presence of a refugial population in the Black Sea during the glacial period. Finally, within seas, an east/west genetic differentiation in the Adriatic seems to prevail, whereas the Black Sea does not show any structured spatial genetic pattern of its population. Overall, these results suggest that the Black Sea is not that isolated from the Mediterranean, and both seas revealed similar evolutionary patterns related to climate change and changes in sea level.
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Affiliation(s)
- E Boissin
- EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, Perpignan, F-66360, France.,Laboratoire d'Excellence CRIOBE, BP 1013, 98729, Papetoai, Moorea, Polynésie Française
| | - D Micu
- National Institute of Marine Research and Development, Grigore Antipa, Constanta, 900581, Romania
| | - M Janczyszyn-Le Goff
- EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, Perpignan, F-66360, France.,Laboratoire d'Excellence CRIOBE, BP 1013, 98729, Papetoai, Moorea, Polynésie Française
| | - V Neglia
- EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, Perpignan, F-66360, France.,Laboratoire d'Excellence CRIOBE, BP 1013, 98729, Papetoai, Moorea, Polynésie Française
| | - L Bat
- Department of Marine Biology and Ecology, Faculty of Fisheries, Sinop University, Sinop, TR57000, Turkey
| | - V Todorova
- IO-BAS - Institute of Oceanology, PO Box 152, Varna, 9000, Bulgaria
| | - M Panayotova
- IO-BAS - Institute of Oceanology, PO Box 152, Varna, 9000, Bulgaria
| | - C Kruschel
- University of Zadar, Ul. Mihovila Pavlinovića, Zadar, 23000, Croatia
| | - V Macic
- Institute of Marine Biology Kotor (IBMK), Dobrota bb, PO Box 69, Kotor, 85330, Montenegro
| | - N Milchakova
- Institute of Marine Biological Research (IMBR), 2 Nakhimov ave., Sevastopol, 299011, Russia
| | - Ç Keskin
- Faculty of Fisheries, Istanbul University, Ordu St 200, Istanbul, TR-34470, Turkey
| | - A Anastasopoulou
- Hellenic Centre for Marine Research, 46.7 km Athinon-Souniou Av., Anavyssos, 19013, Greece
| | - I Nasto
- Department of Biology, Faculty of Technical Sciences, Vlora University, Vlora, 9401, Albania
| | - L Zane
- Department of Biology, University of Padova, via U. Bassi/58B, Padova, I-35121, Italy
| | - S Planes
- EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, Perpignan, F-66360, France.,Laboratoire d'Excellence CRIOBE, BP 1013, 98729, Papetoai, Moorea, Polynésie Française
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18
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Hughes MR, Dodd JA, Maitland PS, Adams CE. Lake bathymetry and species occurrence predict the distribution of a lacustrine apex predator. JOURNAL OF FISH BIOLOGY 2016; 88:1648-54. [PMID: 26899559 DOI: 10.1111/jfb.12919] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 01/20/2016] [Indexed: 05/25/2023]
Abstract
This study examined the abiotic and biotic characteristics of ecosystems that allow expression of a life history called ferox trout, the colloquial name given to brown trout Salmo trutta adopting a piscivorous life history strategy, an apex predator in post-glacial lakes in northern Europe. One hundred and ninety-two lakes in Scotland show evidence of currently, or historically, supporting ferox S. trutta; their presence was predicted in logistic models by larger and deeper lakes with a large catchment that also support populations of Arctic charr Salvelinus alpinus.
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Affiliation(s)
- M R Hughes
- Scottish Centre for Ecology and the Natural Environment, Institute of Biomedical and Life Sciences, University of Glasgow, Loch Lomond, Glasgow, G63 OAW, Scotland, U.K
| | - J A Dodd
- Scottish Centre for Ecology and the Natural Environment, Institute of Biomedical and Life Sciences, University of Glasgow, Loch Lomond, Glasgow, G63 OAW, Scotland, U.K
| | - P S Maitland
- Fish Conservation Centre, Gladshot, Haddington, East Lothian, EH41 4NR, Scotland, U.K
| | - C E Adams
- Scottish Centre for Ecology and the Natural Environment, Institute of Biomedical and Life Sciences, University of Glasgow, Loch Lomond, Glasgow, G63 OAW, Scotland, U.K
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19
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Tonay AM, Yazıcı Ö, Dede A, Bilgin S, Danyer E, Aytemiz I, Maracı Ö, Öztürk AA, Öztürk B, Bilgin R. Is there a distinct harbor porpoise subpopulation in the Marmara Sea? Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:558-564. [PMID: 27159712 DOI: 10.3109/24701394.2016.1155118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Genetic population structure of geographically isolated endangered Black Sea harbor porpoise (Phocoena phocoena relicta) is little known in Turkish waters, especially in the Turkish Straits System (TSS- Marmara Sea, Bosphorus and Dardanelles), which connects the Black Sea and the Aegean Sea. Mitochondrial DNA sequences of 70 new individuals sampled in the Turkish Black Sea, TSS and Aegean Sea, revealed five new haplotypes from the Black Sea. The findings support the idea that harbor porpoises from the Black Sea dispersed into the Aegean through the TSS. Considering signatures of population expansion, all subpopulations showed a signature of population expansion. The network data and the Фst calculations indicated that the Marmara Sea subpopulation was significantly differentiated from all of the other subpopulations, and supports the notion of its isolated. The finding of a potential management unit (MU) within an already heavily impacted subpopulation as a whole suggests that the individuals of P. p. relicta inhabiting the Marmara Sea require a very rigorous conservation strategy to ensure the survival of this subpopulation, represented by its unique haplotype.
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Affiliation(s)
- Arda M Tonay
- a Faculty of Fisheries , Istanbul University , Laleli , Istanbul , Turkey.,b Turkish Marine Research Foundation (TUDAV) , Beykoz , Istanbul , Turkey
| | - Özge Yazıcı
- c Institute of Environment Sciences , Boğaziçi University , Bebek , Istanbul , Turkey
| | - Ayhan Dede
- a Faculty of Fisheries , Istanbul University , Laleli , Istanbul , Turkey.,b Turkish Marine Research Foundation (TUDAV) , Beykoz , Istanbul , Turkey
| | - Sabri Bilgin
- d Faculty of Fisheries , Sinop University , Sinop , Turkey
| | - Erdem Danyer
- b Turkish Marine Research Foundation (TUDAV) , Beykoz , Istanbul , Turkey.,e Faculty of Veterinary , Istanbul University , Avcılar , Istanbul , Turkey
| | - Işıl Aytemiz
- b Turkish Marine Research Foundation (TUDAV) , Beykoz , Istanbul , Turkey.,e Faculty of Veterinary , Istanbul University , Avcılar , Istanbul , Turkey
| | - Öncü Maracı
- c Institute of Environment Sciences , Boğaziçi University , Bebek , Istanbul , Turkey
| | - Ayaka A Öztürk
- a Faculty of Fisheries , Istanbul University , Laleli , Istanbul , Turkey.,b Turkish Marine Research Foundation (TUDAV) , Beykoz , Istanbul , Turkey
| | - Bayram Öztürk
- a Faculty of Fisheries , Istanbul University , Laleli , Istanbul , Turkey.,b Turkish Marine Research Foundation (TUDAV) , Beykoz , Istanbul , Turkey
| | - Raşit Bilgin
- c Institute of Environment Sciences , Boğaziçi University , Bebek , Istanbul , Turkey
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20
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Botta F, Eriksen C, Fontaine MC, Guillot G. Enhanced computational methods for quantifying the effect of geographic and environmental isolation on genetic differentiation. Methods Ecol Evol 2015. [DOI: 10.1111/2041-210x.12424] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Filippo Botta
- Applied Mathematics and Computer Science Department Technical University of Denmark Copenhagen Denmark
- Now at Centre for Macro‐Ecology Copenhagen University Copenhagen Denmark
| | - Casper Eriksen
- Applied Mathematics and Computer Science Department Technical University of Denmark Copenhagen Denmark
| | - Michaël C. Fontaine
- Marine Evolution and Conservation Groningen Institute for Evolutionary Life Sciences University of Groningen The Netherlands
| | - Gilles Guillot
- Applied Mathematics and Computer Science Department Technical University of Denmark Copenhagen Denmark
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21
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Paris JR, King RA, Stevens JR. Human mining activity across the ages determines the genetic structure of modern brown trout (Salmo trutta L.) populations. Evol Appl 2015; 8:573-85. [PMID: 26136823 PMCID: PMC4479513 DOI: 10.1111/eva.12266] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 04/13/2015] [Indexed: 01/09/2023] Open
Abstract
Humans have exploited the earth's metal resources for thousands of years leaving behind a legacy of toxic metal contamination and poor water quality. The southwest of England provides a well-defined example, with a rich history of metal mining dating to the Bronze Age. Mine water washout continues to negatively impact water quality across the region where brown trout (Salmo trutta L.) populations exist in both metal-impacted and relatively clean rivers. We used microsatellites to assess the genetic impact of mining practices on trout populations in this region. Our analyses demonstrated that metal-impacted trout populations have low genetic diversity and have experienced severe population declines. Metal-river trout populations are genetically distinct from clean-river populations, and also from one another, despite being geographically proximate. Using approximate Bayesian computation (ABC), we dated the origins of these genetic patterns to periods of intensive mining activity. The historical split of contemporary metal-impacted populations from clean-river fish dated to the Medieval period. Moreover, we observed two distinct genetic populations of trout within a single catchment and dated their divergence to the Industrial Revolution. Our investigation thus provides an evaluation of contemporary population genetics in showing how human-altered landscapes can change the genetic makeup of a species.
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Affiliation(s)
- Josephine R Paris
- Biosciences, College of Life and Environmental Sciences, University of Exeter Exeter, UK
| | - R Andrew King
- Biosciences, College of Life and Environmental Sciences, University of Exeter Exeter, UK
| | - Jamie R Stevens
- Biosciences, College of Life and Environmental Sciences, University of Exeter Exeter, UK
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22
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Nyman T, Valtonen M, Aspi J, Ruokonen M, Kunnasranta M, Palo JU. Demographic histories and genetic diversities of Fennoscandian marine and landlocked ringed seal subspecies. Ecol Evol 2014; 4:3420-34. [PMID: 25535558 PMCID: PMC4228616 DOI: 10.1002/ece3.1193] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 07/21/2014] [Accepted: 07/22/2014] [Indexed: 11/18/2022] Open
Abstract
Island populations are on average smaller, genetically less diverse, and at a higher risk to go extinct than mainland populations. Low genetic diversity may elevate extinction probability, but the genetic component of the risk can be affected by the mode of diversity loss, which, in turn, is connected to the demographic history of the population. Here, we examined the history of genetic erosion in three Fennoscandian ringed seal subspecies, of which one inhabits the Baltic Sea 'mainland' and two the 'aquatic islands' composed of Lake Saimaa in Finland and Lake Ladoga in Russia. Both lakes were colonized by marine seals after their formation c. 9500 years ago, but Lake Ladoga is larger and more contiguous than Lake Saimaa. All three populations suffered dramatic declines during the 20th century, but the bottleneck was particularly severe in Lake Saimaa. Data from 17 microsatellite loci and mitochondrial control-region sequences show that Saimaa ringed seals have lost most of the genetic diversity present in their Baltic ancestors, while the Ladoga population has experienced only minor reductions. Using Approximate Bayesian computing analyses, we show that the genetic uniformity of the Saimaa subspecies derives from an extended founder event and subsequent slow erosion, rather than from the recent bottleneck. This suggests that the population has persisted for nearly 10,000 years despite having low genetic variation. The relatively high diversity of the Ladoga population appears to result from a high number of initial colonizers and a high post-colonization population size, but possibly also by a shorter isolation period and/or occasional gene flow from the Baltic Sea.
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Affiliation(s)
- Tommi Nyman
- Department of Biology, University of Eastern FinlandPO Box 111, Joensuu, FI-80101, Finland
- Institute for Systematic Botany, University of Zurich, Zollikerstrasse 107Zurich, CH-8008, Switzerland
| | - Mia Valtonen
- Department of Biology, University of Eastern FinlandPO Box 111, Joensuu, FI-80101, Finland
| | - Jouni Aspi
- Department of Biology, University of OuluPO Box 3000, Oulu, FI-90014, Finland
| | - Minna Ruokonen
- Department of Biology, University of OuluPO Box 3000, Oulu, FI-90014, Finland
| | - Mervi Kunnasranta
- Department of Biology, University of Eastern FinlandPO Box 111, Joensuu, FI-80101, Finland
| | - Jukka U Palo
- Laboratory of Forensic Biology, Hjelt Institute, University of HelsinkiPO Box 40, Helsinki, FI-00014, Finland
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23
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Spurgin LG, Wright DJ, van der Velde M, Collar NJ, Komdeur J, Burke T, Richardson DS. Museum DNA reveals the demographic history of the endangered Seychelles warbler. Evol Appl 2014; 7:1134-43. [PMID: 25553073 PMCID: PMC4231601 DOI: 10.1111/eva.12191] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 06/30/2014] [Indexed: 01/10/2023] Open
Abstract
The importance of evolutionary conservation – how understanding evolutionary forces can help guide conservation decisions – is widely recognized. However, the historical demography of many endangered species is unknown, despite the fact that this can have important implications for contemporary ecological processes and for extinction risk. Here, we reconstruct the population history of the Seychelles warbler (Acrocephalus sechellensis) – an ecological model species. By the 1960s, this species was on the brink of extinction, but its previous history is unknown. We used DNA samples from contemporary and museum specimens spanning 140 years to reconstruct bottleneck history. We found a 25% reduction in genetic diversity between museum and contemporary populations, and strong genetic structure. Simulations indicate that the Seychelles warbler was bottlenecked from a large population, with an ancestral Ne of several thousands falling to <50 within the last century. Such a rapid decline, due to anthropogenic factors, has important implications for extinction risk in the Seychelles warbler, and our results will inform conservation practices. Reconstructing the population history of this species also allows us to better understand patterns of genetic diversity, inbreeding and promiscuity in the contemporary populations. Our approaches can be applied across species to test ecological hypotheses and inform conservation.
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Affiliation(s)
- Lewis G Spurgin
- School of Biological Sciences, University of East Anglia Norwich, Norfolk, UK ; Behavioural Ecology and Self-organization Group, Centre for Ecological and Evolutionary Studies, University of Groningen Groningen, The Netherlands
| | - David J Wright
- School of Biological Sciences, University of East Anglia Norwich, Norfolk, UK ; Department of Animal and Plant Sciences, NERC Biomolecular Analysis Facility, University of Sheffield Sheffield, UK
| | - Marco van der Velde
- Behavioural Ecology and Self-organization Group, Centre for Ecological and Evolutionary Studies, University of Groningen Groningen, The Netherlands
| | - Nigel J Collar
- School of Biological Sciences, University of East Anglia Norwich, Norfolk, UK ; BirdLife International Cambridge, UK
| | - Jan Komdeur
- Behavioural Ecology and Self-organization Group, Centre for Ecological and Evolutionary Studies, University of Groningen Groningen, The Netherlands
| | - Terry Burke
- Department of Animal and Plant Sciences, NERC Biomolecular Analysis Facility, University of Sheffield Sheffield, UK
| | - David S Richardson
- School of Biological Sciences, University of East Anglia Norwich, Norfolk, UK ; Nature Seychelles Roche Caiman, Mahé, Republic of Seychelles
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Chakraborty D, Sinha A, Ramakrishnan U. Mixed fortunes: ancient expansion and recent decline in population size of a subtropical montane primate, the Arunachal macaque Macaca munzala. PLoS One 2014; 9:e97061. [PMID: 25054863 PMCID: PMC4108313 DOI: 10.1371/journal.pone.0097061] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 04/14/2014] [Indexed: 11/18/2022] Open
Abstract
Quaternary glacial oscillations are known to have caused population size fluctuations in many temperate species. Species from subtropical and tropical regions are, however, considerably less studied, despite representing most of the biodiversity hotspots in the world including many highly threatened by anthropogenic activities such as hunting. These regions, consequently, pose a significant knowledge gap in terms of how their fauna have typically responded to past climatic changes. We studied an endangered primate, the Arunachal macaque Macaca munzala, from the subtropical southern edge of the Tibetan plateau, a part of the Eastern Himalaya biodiversity hotspot, also known to be highly threatened due to rampant hunting. We employed a 534 bp-long mitochondrial DNA sequence and 22 autosomal microsatellite loci to investigate the factors that have potentially shaped the demographic history of the species. Analysing the genetic data with traditional statistical methods and advance Bayesian inferential approaches, we demonstrate a limited effect of past glacial fluctuations on the demographic history of the species before the last glacial maximum, approximately 20,000 years ago. This was, however, immediately followed by a significant population expansion possibly due to warmer climatic conditions, approximately 15,000 years ago. These changes may thus represent an apparent balance between that displayed by the relatively climatically stable tropics and those of the more severe, temperate environments of the past. This study also draws attention to the possibility that a cold-tolerant species like the Arunachal macaque, which could withstand historical climate fluctuations and grow once the climate became conducive, may actually be extremely vulnerable to anthropogenic exploitation, as is perhaps indicated by its Holocene ca. 30-fold population decline, approximately 3,500 years ago. Our study thus provides a quantitative appraisal of these demographically important events, emphasising the ability to potentially infer the occurrence of two separate historical events from contemporary genetic data.
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Affiliation(s)
- Debapriyo Chakraborty
- Nature Conservation Foundation, Gokulam Park, Mysore, India
- National Centre for Biological Sciences, GKVK Campus, Bangalore, India
- * E-mail:
| | - Anindya Sinha
- Nature Conservation Foundation, Gokulam Park, Mysore, India
- National Centre for Biological Sciences, GKVK Campus, Bangalore, India
- National Institute of Advanced Studies, Indian Institute of Science Campus, Bangalore, India
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, GKVK Campus, Bangalore, India
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25
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Schwerdtner Máñez K, Holm P, Blight L, Coll M, MacDiarmid A, Ojaveer H, Poulsen B, Tull M. The future of the oceans past: towards a global marine historical research initiative. PLoS One 2014; 9:e101466. [PMID: 24988080 PMCID: PMC4079652 DOI: 10.1371/journal.pone.0101466] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 06/05/2014] [Indexed: 11/29/2022] Open
Abstract
Historical research is playing an increasingly important role in marine sciences. Historical data are also used in policy making and marine resource management, and have helped to address the issue of shifting baselines for numerous species and ecosystems. Although many important research questions still remain unanswered, tremendous developments in conceptual and methodological approaches are expected to contribute to a comprehensive understanding of the global history of human interactions with life in the seas. Based on our experiences and knowledge from the "History of Marine Animal Populations" project, this paper identifies the emerging research topics for future historical marine research. It elaborates on concepts and tools which are expected to play a major role in answering these questions, and identifies geographical regions which deserve future attention from marine environmental historians and historical ecologists.
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Affiliation(s)
- Kathleen Schwerdtner Máñez
- Department of Social Sciences, Leibniz Center for Tropical Marine Ecology, Bremen, Germany
- Asia Research Center, Murdoch University, Murdoch, Western Australia, Australia
| | - Poul Holm
- Trinity Long Room Hub Arts and Humanities Research Institute, Trinity College Dublin, Dublin, Ireland
| | - Louise Blight
- World Wildlife Fund (WWF) -Canada, Vancouver, British Columbia, Canada
| | - Marta Coll
- Renewable Marine Resources Department, Institute of Marine Science, Barcelona, Spain
- Laboratoire Écosystèmes Marins Exploités, Sète Cedex, France
| | - Alison MacDiarmid
- Marine Ecology, National Institute of Water and Atmospheric Research, Kilbirnie, Wellington, New Zealand
| | - Henn Ojaveer
- Estonian Marine Institute, University Tartu, Tartu, Estonia
| | - Bo Poulsen
- Faculty of Social Sciences, Aalborg University, Aalborg Ø, Denmark
| | - Malcolm Tull
- Murdoch Business School, Murdoch University, Murdoch, Western Australia, Australia
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26
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Fontaine MC, Roland K, Calves I, Austerlitz F, Palstra FP, Tolley KA, Ryan S, Ferreira M, Jauniaux T, Llavona A, Öztürk B, Öztürk AA, Ridoux V, Rogan E, Sequeira M, Siebert U, Vikingsson GA, Borrell A, Michaux JR, Aguilar A. Postglacial climate changes and rise of three ecotypes of harbour porpoises,Phocoena phocoena, in western Palearctic waters. Mol Ecol 2014; 23:3306-21. [DOI: 10.1111/mec.12817] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 05/11/2014] [Accepted: 05/21/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Michaël C. Fontaine
- Department of Biological Sciences; University of Notre Dame; Notre Dame IN 46556 USA
- Ecologie, Systématique et Evolution; UMR8079; Université Paris-Sud; F-91405 Orsay France
- CNRS; 91405 Orsay France
- AgroParisTech; F-91405 Orsay France
- Eco-Anthropologie et Ethnobiologie; UMR 7206 CNRS; MNHN; Sorbonne Paris Cité; Université Paris Diderot; F-75005 Paris France
| | - Kathleen Roland
- INRA; UMR 1064 CBGP; Campus international de Baillarguet CS30016 F-34988 Montferrier-sur-Lez Cedex France
- Research Unit in Environmental and Evolutionary Biology (URBE); Narilis (Namur Research Institute for Lifesciences); University of Namur (FUNDP); Rue de Bruxelles 61 B-5000 Namur Belgium
| | - Isabelle Calves
- INRA; UMR 1064 CBGP; Campus international de Baillarguet CS30016 F-34988 Montferrier-sur-Lez Cedex France
- Laboratoire LEMAR (UMR CNRS/UBO/IRD/Ifremer 6539); Institut Universitaire Européen de la Mer; Technopôle Brest-Iroise; Rue Dumont d'Urville 29280 Plouzané France
| | - Frederic Austerlitz
- Eco-Anthropologie et Ethnobiologie; UMR 7206 CNRS; MNHN; Sorbonne Paris Cité; Université Paris Diderot; F-75005 Paris France
| | - Friso P. Palstra
- Eco-Anthropologie et Ethnobiologie; UMR 7206 CNRS; MNHN; Sorbonne Paris Cité; Université Paris Diderot; F-75005 Paris France
| | - Krystal A. Tolley
- Applied Biodiversity Research; South African National Biodiversity Institute; Private Bag X7 Claremont 7735 Cape Town South Africa
- Department of Botany & Zoology; Stellenbosch University; Private Bag X1 Matieland 7602 South Africa
| | - Sean Ryan
- Department of Biological Sciences; University of Notre Dame; Notre Dame IN 46556 USA
| | - Marisa Ferreira
- Departmento de Biologia; Sociedade Portuguesa de Vida Selvagem & Molecular and Environmental Biology Centre (CBMA); Universidade de Minho; Campus de Gualtar 4710-047 Braga Portugal
| | - Thierry Jauniaux
- Department of Pathology; University of Liège; Sart Tilman B43 4000 Liège Belgium
| | - Angela Llavona
- C.E.M.MA. Coordinadora para o Estudio dos Mamíferos MAriños; Apartado 15 36380 Nigrán Pontevedra Spain
| | - Bayram Öztürk
- Faculty of Fisheries; Istanbul University; Ordu Cad. No.200 34320 Laleli-Istanbul Turkey
- Turkish Marine Research Foundation (TUDAV) PK 10; 34820 Beykoz-Istanbul Turkey
| | - Ayaka A. Öztürk
- Faculty of Fisheries; Istanbul University; Ordu Cad. No.200 34320 Laleli-Istanbul Turkey
- Turkish Marine Research Foundation (TUDAV) PK 10; 34820 Beykoz-Istanbul Turkey
| | - Vincent Ridoux
- Littoral Environnement et Sociétés; UMR 7266; Université de La Rochelle/CNRS; F-17000 La Rochelle France
- Observatoire PELAGIS - Systèmes d'Observation pour la Conservation des Mammifères et des Oiseaux Marins; UMS 3462 Université de La Rochelle/CNRS; F-17000 La Rochelle France
| | - Emer Rogan
- School of Biological; Earth and Environmental Sciences; University College Cork; Cork Ireland
| | - Marina Sequeira
- Instituto da Conservação da Natureza e das Florestas; Rua de Santa Marta 55 1169-230 Lisboa Portugal
| | - Ursula Siebert
- Institute for Terrestrial and Aquatic Wildlife Research; University of Veterinary Medicine Hannover, Foundation; Werftstr. 6 25761 Büsum Germany
| | | | - Asunción Borrell
- Department of Animal Biology and IRBio; Faculty of Biology; University of Barcelona; Diagonal 643 08071 Barcelona Spain
| | - Johan R. Michaux
- INRA; UMR 1064 CBGP; Campus international de Baillarguet CS30016 F-34988 Montferrier-sur-Lez Cedex France
| | - Alex Aguilar
- Department of Animal Biology and IRBio; Faculty of Biology; University of Barcelona; Diagonal 643 08071 Barcelona Spain
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Aimé C, Verdu P, Ségurel L, Martinez-Cruz B, Hegay T, Heyer E, Austerlitz F. Microsatellite data show recent demographic expansions in sedentary but not in nomadic human populations in Africa and Eurasia. Eur J Hum Genet 2014; 22:1201-7. [PMID: 24518830 DOI: 10.1038/ejhg.2014.2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 12/10/2013] [Accepted: 12/12/2013] [Indexed: 11/09/2022] Open
Abstract
The transition from hunting and gathering to plant and animal domestication was one of the most important cultural and technological revolutions in human history. According to archeologists and paleoanthropologists, this transition triggered major demographic expansions. However, few genetic studies have found traces of Neolithic expansions in the current repartition of genetic polymorphism, pointing rather toward Paleolithic expansions. Here, we used microsatellite autosomal data to investigate the past demographic history of 87 African and Eurasian human populations with contrasted lifestyles (nomadic hunter-gatherers, semi-nomadic herders and sedentary farmers). Likely due to the combination of a higher mutation rate and the possibility to analyze several loci as independent replicates of the coalescent process, the analysis of microsatellite data allowed us to infer more recent expansions than previous genetic studies, potentially resulting from the Neolithic transition. Despite the variability in their location and environment, we found consistent expansions for all sedentary farmers, while we inferred constant population sizes for all hunter-gatherers and most herders that could result from constraints linked to a nomadic or semi-nomadic lifestyle and/or competition for land between herders and farmers. As an exception, we inferred expansions for Central Asian herders. This might be linked with the arid environment of this area that may have been more favorable to nomadic herders than to sedentary farmers. Alternatively, current Central Asian herders may descent from populations who have first experienced a transition from hunter-gathering to sedentary agropastoralism, and then a second transition to nomadic herding.
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Affiliation(s)
- Carla Aimé
- Laboratoire d'Eco-Anthropologie et Ethnobiologie, UMR 7206, Muséum National d'Histoire Naturelle-Centre National de la Recherche Scientifique-Université Paris 7 Diderot, Paris, France
| | - Paul Verdu
- Laboratoire d'Eco-Anthropologie et Ethnobiologie, UMR 7206, Muséum National d'Histoire Naturelle-Centre National de la Recherche Scientifique-Université Paris 7 Diderot, Paris, France
| | - Laure Ségurel
- Laboratoire d'Eco-Anthropologie et Ethnobiologie, UMR 7206, Muséum National d'Histoire Naturelle-Centre National de la Recherche Scientifique-Université Paris 7 Diderot, Paris, France
| | - Begoña Martinez-Cruz
- Integrative Ecology Group, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
| | - Tatyana Hegay
- Academy of Sciences, Institute of Immunology, Tashkent, Uzbekistan
| | - Evelyne Heyer
- Laboratoire d'Eco-Anthropologie et Ethnobiologie, UMR 7206, Muséum National d'Histoire Naturelle-Centre National de la Recherche Scientifique-Université Paris 7 Diderot, Paris, France
| | - Frédéric Austerlitz
- Laboratoire d'Eco-Anthropologie et Ethnobiologie, UMR 7206, Muséum National d'Histoire Naturelle-Centre National de la Recherche Scientifique-Université Paris 7 Diderot, Paris, France
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28
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Aimé C, Laval G, Patin E, Verdu P, Ségurel L, Chaix R, Hegay T, Quintana-Murci L, Heyer E, Austerlitz F. Human genetic data reveal contrasting demographic patterns between sedentary and nomadic populations that predate the emergence of farming. Mol Biol Evol 2013; 30:2629-44. [PMID: 24063884 DOI: 10.1093/molbev/mst156] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Demographic changes are known to leave footprints on genetic polymorphism. Together with the increased availability of large polymorphism data sets, coalescent-based methods allow inferring the past demography of populations from their present-day patterns of genetic diversity. Here, we analyzed both nuclear (20 noncoding regions) and mitochondrial (HVS-I) resequencing data to infer the demographic history of 66 African and Eurasian human populations presenting contrasting lifestyles (nomadic hunter-gatherers, nomadic herders, and sedentary farmers). This allowed us to investigate the relationship between lifestyle and demography and to address the long-standing debate about the chronology of demographic expansions and the Neolithic transition. In Africa, we inferred expansion events for farmers, but constant population sizes or contraction events for hunter-gatherers. In Eurasia, we inferred higher expansion rates for farmers than herders with HVS-I data, except in Central Asia and Korea. Although isolation and admixture processes could have impacted our demographic inferences, these processes alone seem unlikely to explain the contrasted demographic histories inferred in populations with different lifestyles. The small expansion rates or constant population sizes inferred for herders and hunter-gatherers may thus result from constraints linked to nomadism. However, autosomal data revealed contraction events for two sedentary populations in Eurasia, which may be caused by founder effects. Finally, the inferred expansions likely predated the emergence of agriculture and herding. This suggests that human populations could have started to expand in Paleolithic times, and that strong Paleolithic expansions in some populations may have ultimately favored their shift toward agriculture during the Neolithic.
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Affiliation(s)
- Carla Aimé
- Laboratoire Eco-Anthropologie et Ethnobiologie, UMR 7206, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Université Paris 7 Diderot, Paris, France
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29
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Models with a porpoise. Proc Natl Acad Sci U S A 2012; 109:15078-9. [PMID: 22949681 DOI: 10.1073/pnas.1213189109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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30
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Alfonsi E, Hassani S, Carpentier FG, Le Clec’h JY, Dabin W, Van Canneyt O, Fontaine MC, Jung JL. A European melting pot of harbour porpoise in the French Atlantic coasts inferred from mitochondrial and nuclear data. PLoS One 2012; 7:e44425. [PMID: 22984507 PMCID: PMC3440431 DOI: 10.1371/journal.pone.0044425] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 08/02/2012] [Indexed: 11/21/2022] Open
Abstract
Field surveys have reported a global shift in harbour porpoise distribution in European waters during the last 15 years, including a return to the Atlantic coasts of France. In this study, we analyzed genetic polymorphisms at a fragment of the mitochondrial control region (mtDNA CR) and 7 nuclear microsatellite loci, for 52 animals stranded and by-caught between 2000 and 2010 along the Atlantic coasts of France. The analysis of nuclear and mitochondrial loci provided contrasting results. The mtDNA revealed two genetically distinct groups, one closely related to the Iberian and African harbour porpoises, and the second related to individuals from the more northern waters of Europe. In contrast, nuclear polymorphisms did not display such a distinction. Nuclear markers suggested that harbour porpoises behaved as a randomly mating population along the Atlantic coasts of France. The difference between the two kinds of markers can be explained by differences in their mode of inheritance, the mtDNA being maternally inherited in contrast to nuclear loci that are bi-parentally inherited. Our results provide evidence that a major proportion of the animals we sampled are admixed individuals from the two genetically distinct populations previously identified along the Iberian coasts and in the North East Atlantic. The French Atlantic coasts are clearly the place where these two previously separated populations of harbour porpoises are now admixing. The present shifts in distribution of harbour porpoises along this coast is likely caused by habitat changes that will need to be further studied.
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Affiliation(s)
- Eric Alfonsi
- Laboratoire BioGeMME (Biologie et Génétique des Mammifères Marins dans leur Environnement), Université Européenne de Bretagne & Université de Bretagne Occidentale, Brest, France
- Laboratoire d’Etude des Mammifères Marins, Océanopolis, Brest, France
- LEMAR, Université Européenne de Bretagne & Université de Bretagne Occidentale, Brest, France
| | - Sami Hassani
- Laboratoire d’Etude des Mammifères Marins, Océanopolis, Brest, France
| | - François-Gilles Carpentier
- Laboratoire BioGeMME (Biologie et Génétique des Mammifères Marins dans leur Environnement), Université Européenne de Bretagne & Université de Bretagne Occidentale, Brest, France
| | | | - Willy Dabin
- Observatoire PELAGIS, UMS 3462, CNRS-Université de La Rochelle, La Rochelle, France
| | - Olivier Van Canneyt
- Observatoire PELAGIS, UMS 3462, CNRS-Université de La Rochelle, La Rochelle, France
| | - Michael C. Fontaine
- Laboratoire d’Ecologie, Systématique et Evolution, Université Paris-Sud – CNRS, Orsay, France
- Ecoanthropologie et d’Ethnobiologie, UMR 5145, CNRS-MNHN-Université Paris 7 Musée de l’Homme, Paris, France
| | - Jean-Luc Jung
- Laboratoire BioGeMME (Biologie et Génétique des Mammifères Marins dans leur Environnement), Université Européenne de Bretagne & Université de Bretagne Occidentale, Brest, France
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