A Phylogenetic Perspective on the Evolution of Mediterranean Teleost Fishes
Publication Date
May 08, 2012
Journal
PLOS ONE
Authors
Christine N. Meynard, David Mouillot, Nicolas Mouquet & Emmanuel J. P. Douzery
Volume
7
Issue
5
Pages
e36443
DOI
https://dx.plos.org/10.1371/journal.pone.0036443
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0036443
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/22590545
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3348158
Europe PMC
http://europepmc.org/abstract/MED/22590545
Web of Science
000305335500013
Scopus
84860701740
Mendeley
http://www.mendeley.com/research/phylogenetic-perspective-evolution-mediterranean-teleost-fishes
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Mendeley | Further Information

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/330839", "https://ndownloader.figshare.com/files/330985", "https://ndownloader.figshare.com/files/331083"], "description"=>"<div><p>The Mediterranean Sea is a highly diverse, highly studied, and highly impacted biogeographic region, yet no phylogenetic reconstruction of fish diversity in this area has been published to date. Here, we infer the timing and geographic origins of Mediterranean teleost species diversity using nucleotide sequences collected from GenBank. 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 9 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. We then interpreted the time-line of teleost diversification in light of Mediterranean historical biogeography, distinguishing non-endemic natives, endemics and exotic species. Results show that the major Mediterranean orders are of Cretaceous origin, specifically ∼100–80 Mya, and most Perciformes families originated 80–50 Mya. Two important clade origin events were detected. The first at 100–80 Mya, affected native and exotic species, and reflects a global diversification period at a time when the Mediterranean Sea did not yet exist. The second occurred during the last 50 Mya, and is noticeable among endemic and native species, but not among exotic species. This period corresponds to isolation of the Mediterranean from Indo-Pacific waters before the Messinian salinity crisis. The Mediterranean fish fauna illustrates well the assembly of regional faunas through origination and immigration, where dispersal and isolation have shaped the emergence of a biodiversity hotspot.</p> </div>", "links"=>[], "tags"=>["phylogenetic", "mediterranean", "teleost", "fishes"], "article_id"=>125329, "categories"=>["Inorganic Chemistry", "Ecology", "Evolutionary Biology"], "users"=>["Christine N. Meynard", "David Mouillot", "Nicolas Mouquet", "Emmanuel J. P. Douzery"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0036443.s001", "https://dx.doi.org/10.1371/journal.pone.0036443.s002", "https://dx.doi.org/10.1371/journal.pone.0036443.s003"], "stats"=>{"downloads"=>17, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Phylogenetic_Perspective_on_the_Evolution_of_Mediterranean_Teleost_Fishes/125329", "title"=>"A Phylogenetic Perspective on the Evolution of Mediterranean Teleost Fishes", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-05-08 01:28:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/641370"], "description"=>"<p>Phylogenetic relationships and divergence time estimates of Mediterranean teleosts, inferred from a supermatrix of 6 mitochondrial and nuclear genes. The global phylogeny is given on the upper left, with black branches indicating the part of the tree that is represented on the right panel. Color codes on species names indicate the origin of the species: green  =  extra-Mediterranean species; red  =  exotic species; blue  =  endemic species; black  =  non-endemic native. The green dashed boxes around nodes indicate the 95% credibility interval for the estimated node age. Maximum likelihood node bootstrap support is indicated using different types of circles: back circle  =  >90%, double circle  =  70–90%, single white circle  =  50–70%, no circle  = <50%. Letters at the bottom indicate geologic time references: UJ  =  Upper Jurassic; LC  =  Lower Cretaceous; UC  =  Upper Cretaceous; P  =  Paleocene; E  =  Eocene; O  =  Oligocene; M = Miocene. Numbers in the phylogeny correspond to the calibration described in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036443#pone-0036443-t001\" target=\"_blank\">Table 1</a>. Note that node 20 appears on the left panel of <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036443#pone-0036443-g001\" target=\"_blank\">Figure 1d</a> as this node links <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036443#pone-0036443-g001\" target=\"_blank\">Figure 1b and 1d</a>. We also show with dashed red lines important biogeographic events: peak temperatures (PT) that occurred during the Cenomanian (93–100 Mya); the Cretaceous-Paleogene (KP) mass extinction some 65 Mya, and the Messinian salinity crisis (MSC) some 7–5 Mya. On the right hand side, names in upper case correspond to teleost orders while names in lower case correspond to families. For clarity, names alternate between black and grey.</p>", "links"=>[], "tags"=>["phylogeny", "mediterranean", "teleost"], "article_id"=>311859, "categories"=>["Inorganic Chemistry", "Ecology", "Evolutionary Biology"], "users"=>["Christine N. Meynard", "David Mouillot", "Nicolas Mouquet", "Emmanuel J. P. Douzery"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036443.g001", "stats"=>{"downloads"=>3, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Dated_phylogeny_of_Mediterranean_teleost_fishes_/311859", "title"=>"Dated phylogeny of Mediterranean teleost fishes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-08 00:30:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/641444"], "description"=>"<p>Histograms are shown for (a) all species found in the Mediterranean Sea, (b) exotics only, (c) non-endemic natives, and (d) endemics. Dashed lines indicate the median based on the mean (M) node age estimates as well as based on the lower (L) and upper (U) bounds for each node's 95% credibility interval. Asterisks near the letters indicate significantly different ages than those expected by a random draw of the same number of species from the global chronogram (P<0.05, two-tailed bootstrap test).</p>", "links"=>[], "tags"=>["ages", "diversification"], "article_id"=>311939, "categories"=>["Inorganic Chemistry", "Ecology", "Evolutionary Biology"], "users"=>["Christine N. Meynard", "David Mouillot", "Nicolas Mouquet", "Emmanuel J. P. Douzery"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036443.g002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Histograms_of_the_ages_of_the_diversification_events_/311939", "title"=>"Histograms of the ages of the diversification events.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-08 00:32:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/641583"], "description"=>"*<p>Notice that this node corresponds to the bifurcation between two genera and not to the family Labridae.</p><p>Node numbers correspond to the numbers shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036443#pone-0036443-g001\" target=\"_blank\">Figure 1</a>.</p>", "links"=>[], "tags"=>["calibration"], "article_id"=>312078, "categories"=>["Inorganic Chemistry", "Ecology", "Evolutionary Biology"], "users"=>["Christine N. Meynard", "David Mouillot", "Nicolas Mouquet", "Emmanuel J. P. Douzery"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036443.t001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Nodes_used_for_calibration_in_the_phylogeny_/312078", "title"=>"Nodes used for calibration in the phylogeny.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-08 00:34:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/641494"], "description"=>"<p>Shown for (a) the backbone raw dated phylogeny; (b) adding species represented by at least two congeners in the backbone; (c) adding species represented by at least one congener; (d) adding species represented by a member of its family and (e) adding species represented by a member of its order. We also show with dashed red lines important biogeographic events: PT =  peak temperatures during the Cenomanian (93–100 Mya); KP =  Cretaceous-Paleogene mass extinction some 65 Mya; MSC =  Messinian Salinity Crisis (7–5 Mya).</p>", "links"=>[], "tags"=>["ecology", "marine and aquatic sciences", "Evolutionary biology"], "article_id"=>311990, "categories"=>["Inorganic Chemistry", "Ecology", "Evolutionary Biology"], "users"=>["Christine N. Meynard", "David Mouillot", "Nicolas Mouquet", "Emmanuel J. P. Douzery"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036443.g003", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Lineage_through_time_plots_/311990", "title"=>"Lineage-through-time plots.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-08 00:33:10"}

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Relative Metric

{"start_date"=>"2012-01-01T00:00:00Z", "end_date"=>"2012-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Evolutionary biology", "average_usage"=>[366, 574, 695, 795, 885, 973, 1063, 1148, 1233, 1319, 1389, 1459, 1533, 1611, 1685, 1754, 1820, 1882, 1937, 2001, 2071, 2129, 2219, 2273, 2335]}, {"subject_area"=>"/Biology and life sciences/Molecular biology", "average_usage"=>[324, 551, 679, 782, 879, 971, 1064, 1154, 1245, 1328, 1406, 1476, 1541, 1617, 1683, 1754, 1818, 1893, 1962, 2025, 2092, 2164, 2227, 2294, 2355]}, {"subject_area"=>"/Biology and life sciences/Organisms", "average_usage"=>[331, 557, 677, 777, 868, 960, 1050, 1136, 1223, 1307, 1390, 1466, 1536, 1603, 1673, 1741, 1814, 1889, 1954, 2028, 2096, 2164, 2233, 2305, 2362]}, {"subject_area"=>"/Computer and information sciences/Data management", "average_usage"=>[392, 619, 725, 831, 919, 1031, 1118, 1228, 1305, 1394, 1526, 1617, 1696, 1788, 1856, 1933, 2027, 2089, 2201, 2276, 2344, 2418, 2493, 2573, 2665]}, {"subject_area"=>"/Earth sciences", "average_usage"=>[368, 548, 649, 749, 833, 915, 993, 1071, 1153, 1240, 1315, 1388, 1456, 1520, 1597, 1673, 1747, 1826, 1892, 1975, 2036, 2101, 2178, 2256, 2319]}, {"subject_area"=>"/Earth sciences/Geography", "average_usage"=>[335, 517, 611, 697, 777, 866, 931, 1004, 1074, 1183, 1251, 1324, 1396, 1474, 1553, 1608, 1670, 1744, 1819, 1875, 1930, 2011, 2092, 2162, 2218]}, {"subject_area"=>"/Earth sciences/Paleontology", "average_usage"=>[512, 778, 908, 1007, 1121, 1219, 1313, 1420, 1525, 1602, 1663, 1754, 1803, 1885, 1950, 2033, 2125, 2230, 2316, 2410, 2481, 2569, 2659, 2753, 2831]}, {"subject_area"=>"/Ecology and environmental sciences", "average_usage"=>[348, 541, 638, 730, 827, 907, 993, 1074, 1152, 1232, 1310, 1379, 1442, 1507, 1576, 1648, 1715, 1786, 1854, 1926, 1991, 2059, 2125, 2181, 2249]}, {"subject_area"=>"/Ecology and environmental sciences/Biogeography", "average_usage"=>[366, 546, 656, 734, 830, 901, 986, 1076, 1161, 1245, 1325, 1404, 1474, 1538, 1609, 1670, 1740, 1818, 1889, 1954, 2030, 2090, 2147, 2218, 2304]}]}
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Net::HTTPTooManyRequests

Source
Scopus
Time
2019-09-27 15:05:26 UTC
Target URL
https://api.elsevier.com/content/search/index:SCOPUS?query=DOI(10.1371%2Fjournal.pone.0036443)
Trace

/app/models/concerns/networkable.rb:21:in `get_result'
/app/models/source.rb:165:in `get_data'
/app/models/retrieval_status.rb:47:in `perform_get_data'
/app/jobs/source_job.rb:52:in `block (2 levels) in perform'
/app/jobs/source_job.rb:51:in `block in perform'
/app/jobs/source_job.rb:35:in `each'
/app/jobs/source_job.rb:35:in `perform'