Temporal Patterns of Diversification across Global Cichlid Biodiversity (Acanthomorpha: Cichlidae)
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{"title"=>"Temporal Patterns of Diversification across Global Cichlid Biodiversity (Acanthomorpha: Cichlidae)", "type"=>"journal", "authors"=>[{"first_name"=>"Caleb D.", "last_name"=>"McMahan"}, {"first_name"=>"Prosanta", "last_name"=>"Chakrabarty"}, {"first_name"=>"John S.", "last_name"=>"Sparks"}, {"first_name"=>"Wm. Leo", "last_name"=>"Smith"}, {"first_name"=>"Matthew P.", "last_name"=>"Davis"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"563054539", "sgr"=>"84893766107", "issn"=>"1932-6203", "pmid"=>"23990936", "scopus"=>"2-s2.0-84893766107", "doi"=>"10.1371/journal.pone.0071162", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)"}, "id"=>"8846ca1c-b757-3aa8-9520-c69b85abe9e7", "abstract"=>"The contrasting distribution of species diversity across the major lineages of cichlids makes them an ideal group for investigating macroevolutionary processes. In this study, we investigate whether different rates of diversification may explain the disparity in species richness across cichlid lineages globally. We present the most taxonomically robust time-calibrated hypothesis of cichlid evolutionary relationships to date. We then utilize this temporal framework to investigate whether both species-rich and depauperate lineages are associated with rapid shifts in diversification rates and if exceptional species richness can be explained by clade age alone. A single significant rapid rate shift increase is detected within the evolutionary history of the African subfamily Pseudocrenilabrinae, which includes the haplochromins of the East African Great Lakes. Several lineages from the subfamilies Pseudocrenilabrinae {(Australotilapiini,} Oreochromini) and Cichlinae {(Heroini)} exhibit exceptional species richness given their clade age, a net rate of diversification, and relative rates of extinction, indicating that clade age alone is not a sufficient explanation for their increased diversity. Our results indicate that the Neotropical Cichlinae includes lineages that have not experienced a significant rapid burst in diversification when compared to certain African lineages (rift lake). Neotropical cichlids have remained comparatively understudied with regard to macroevolutionary patterns relative to African lineages, and our results indicate that of Neotropical lineages, the tribe Heroini may have an elevated rate of diversification in contrast to other Neotropical cichlids. These findings provide insight into our understanding of the diversification patterns across taxonomically disparate lineages in this diverse clade of freshwater fishes and one of the most species-rich families of vertebrates.", "link"=>"http://www.mendeley.com/research/temporal-patterns-diversification-across-global-cichlid-biodiversity-acanthomorpha-cichlidae", "reader_count"=>78, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Researcher"=>22, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>21, "Student > Postgraduate"=>3, "Student > Master"=>15, "Other"=>3, "Student > Bachelor"=>7, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Researcher"=>22, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>21, "Student > Postgraduate"=>3, "Student > Master"=>15, "Other"=>3, "Student > Bachelor"=>7, "Professor"=>1}, "reader_count_by_subject_area"=>{"Environmental Science"=>8, "Biochemistry, Genetics and Molecular Biology"=>6, "Agricultural and Biological Sciences"=>63, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>63}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Environmental Science"=>{"Environmental Science"=>8}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>5, "Brazil"=>3, "United Kingdom"=>1, "Switzerland"=>1, "Germany"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1175301"], "description"=>"<p>Area curves indicate 95% confidence intervals for upper and lower bounds of species diversity given clade age for A; low (<i>r</i> = 0.0828, <i>eps</i>  = 0) and high (<i>r</i> = 0.062, <i>eps</i>  = 0.9) relative rates of extinction (<i>eps</i>) given a constant net rate of diversification (<i>r</i>) across cichlids, and B; the estimated background rate of diversification (<i>r</i> = 0.069) and relative rate of extinction (<i>eps</i>  = 0.41) from the MEDUSA analysis (Fig. 2). White circles indicate the mean clade age for each tribe from the temporal hypothesis of cichlid evolutionary relationships (Fig. 1). Lineages appearing to the left of the curves indicate exceptional species richness given clade age.</p>", "links"=>[], "tags"=>["ecology", "biodiversity", "Evolutionary biology", "Zoology", "Ichthyology", "richness", "cichlid", "tribes", "75"], "article_id"=>776712, "categories"=>["Biological Sciences"], "users"=>["Caleb D. McMahan", "Prosanta Chakrabarty", "John S. Sparks", "Wm. Leo Smith", "Matthew P. Davis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0071162.g003", "stats"=>{"downloads"=>2, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Clade_age_vs_species_richness_in_cichlid_tribes_with_greater_than_or_equal_to_75_species_/776712", "title"=>"Clade age vs. species richness in cichlid tribes with greater than or equal to 75 species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-19 04:53:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1175299"], "description"=>"<p>C1 indicates Acanthomorpha calibration; C2 indicates †<i>Mahengechromis</i> calibration; C3 indicates †<i>Gymnogeophagus eocenicus</i> calibration; C4 indicates †<i>Plesioheros</i> and †<i>Trembichthys</i> calibration. Horizontal gray bars indicate age range of 95% HPD. * at nodes indicates BPP ≤95.</p>", "links"=>[], "tags"=>["ecology", "biodiversity", "Evolutionary biology", "Zoology", "Ichthyology", "phylogeny", "cichlid", "fishes", "mitochondrial", "genes"], "article_id"=>776710, "categories"=>["Biological Sciences"], "users"=>["Caleb D. McMahan", "Prosanta Chakrabarty", "John S. Sparks", "Wm. Leo Smith", "Matthew P. Davis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0071162.g001", "stats"=>{"downloads"=>4, "page_views"=>41, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Temporal_phylogeny_of_cichlid_fishes_based_on_two_mitochondrial_16S_COI_and_two_nuclear_genes_TMO_H3_/776710", "title"=>"Temporal phylogeny of cichlid fishes based on two mitochondrial (16S, COI) and two nuclear genes (TMO, H3).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-19 04:53:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1175304", "https://ndownloader.figshare.com/files/1175306", "https://ndownloader.figshare.com/files/1175308", "https://ndownloader.figshare.com/files/1175311", "https://ndownloader.figshare.com/files/1175312"], "description"=>"<div><p>The contrasting distribution of species diversity across the major lineages of cichlids makes them an ideal group for investigating macroevolutionary processes. In this study, we investigate whether different rates of diversification may explain the disparity in species richness across cichlid lineages globally. We present the most taxonomically robust time-calibrated hypothesis of cichlid evolutionary relationships to date. We then utilize this temporal framework to investigate whether both species-rich and depauperate lineages are associated with rapid shifts in diversification rates and if exceptional species richness can be explained by clade age alone. A single significant rapid rate shift increase is detected within the evolutionary history of the African subfamily Pseudocrenilabrinae, which includes the haplochromins of the East African Great Lakes. Several lineages from the subfamilies Pseudocrenilabrinae (Australotilapiini, Oreochromini) and Cichlinae (Heroini) exhibit exceptional species richness given their clade age, a net rate of diversification, and relative rates of extinction, indicating that clade age alone is not a sufficient explanation for their increased diversity. Our results indicate that the Neotropical Cichlinae includes lineages that have not experienced a significant rapid burst in diversification when compared to certain African lineages (rift lake). Neotropical cichlids have remained comparatively understudied with regard to macroevolutionary patterns relative to African lineages, and our results indicate that of Neotropical lineages, the tribe Heroini may have an elevated rate of diversification in contrast to other Neotropical cichlids. These findings provide insight into our understanding of the diversification patterns across taxonomically disparate lineages in this diverse clade of freshwater fishes and one of the most species-rich families of vertebrates.</p></div>", "links"=>[], "tags"=>["ecology", "biodiversity", "Evolutionary biology", "Zoology", "Ichthyology", "patterns", "diversification", "cichlid"], "article_id"=>776715, "categories"=>["Biological Sciences"], "users"=>["Caleb D. McMahan", "Prosanta Chakrabarty", "John S. Sparks", "Wm. Leo Smith", "Matthew P. Davis"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0071162.s001", "https://dx.doi.org/10.1371/journal.pone.0071162.s002", "https://dx.doi.org/10.1371/journal.pone.0071162.s003", "https://dx.doi.org/10.1371/journal.pone.0071162.s004", "https://dx.doi.org/10.1371/journal.pone.0071162.s005"], "stats"=>{"downloads"=>71, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Temporal_Patterns_of_Diversification_across_Global_Cichlid_Biodiversity_Acanthomorpha_Cichlidae_/776715", "title"=>"Temporal Patterns of Diversification across Global Cichlid Biodiversity (Acanthomorpha: Cichlidae)", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-08-19 04:53:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1175303"], "description"=>"<p>Divergence times of cichlid lineages, as seen in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071162#pone-0071162-g001\" target=\"_blank\">Figures 1</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071162#pone-0071162-g002\" target=\"_blank\">2</a>.</p>", "links"=>[], "tags"=>["ecology", "biodiversity", "Evolutionary biology", "Zoology", "Ichthyology", "times", "cichlid", "seen"], "article_id"=>776714, "categories"=>["Biological Sciences"], "users"=>["Caleb D. McMahan", "Prosanta Chakrabarty", "John S. Sparks", "Wm. Leo Smith", "Matthew P. Davis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0071162.t001", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Divergence_times_of_cichlid_lineages_as_seen_in_Figures_1_and_2_/776714", "title"=>"Divergence times of cichlid lineages, as seen in Figures 1 and 2.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-19 04:53:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1175300"], "description"=>"<p>Red clades indicate rate shifts in diversification, with lineages in blue undergoing a background rate of diversification.</p>", "links"=>[], "tags"=>["ecology", "biodiversity", "Evolutionary biology", "Zoology", "Ichthyology", "phylogeny", "cichlids", "pruned", "subfamily", "tribes"], "article_id"=>776711, "categories"=>["Biological Sciences"], "users"=>["Caleb D. McMahan", "Prosanta Chakrabarty", "John S. Sparks", "Wm. Leo Smith", "Matthew P. Davis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0071162.g002", "stats"=>{"downloads"=>7, "page_views"=>49, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Temporal_phylogeny_of_cichlids_pruned_to_subfamily_for_Ptychochrominae_Etroplinae_tribes_for_Pseudocrenilabrinae_Cichlinae_/776711", "title"=>"Temporal phylogeny of cichlids pruned to subfamily for Ptychochrominae, Etroplinae, tribes for Pseudocrenilabrinae, Cichlinae.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-19 04:53:05"}

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Relative Metric

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