DNA and Morphology Unite Two Species and 10 Million Year Old Fossils
Publication Date
December 20, 2012
Journal
PLOS ONE
Authors
Simon F. K. Hills, James S. Crampton, Steven A. Trewick & Mary Morgan Richards
Volume
7
Issue
12
Pages
e52083
DOI
https://dx.plos.org/10.1371/journal.pone.0052083
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0052083
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/23284880
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3527379
Europe PMC
http://europepmc.org/abstract/MED/23284880
Web of Science
000312794500087
Scopus
84871516442
Mendeley
http://www.mendeley.com/research/dna-morphology-unite-two-species-10-million-year-old-fossils
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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/521859"], "description"=>"a<p>voucher numbers with an M prefix denote specimens from the Museum of New Zealand Te Papa Tongarewa collection, voucher numbers with no letter prefix are from the collection of the National Institute of Water and Atmospheric Research (NIWA). Underlined voucher numbers indicate specimens that were not included in morphometric analyses.</p>b<p>coordinates are given in decimal degrees, rounded to 3 decimal places.</p>", "links"=>[], "tags"=>["variability", "mitochondrial", "dna"], "article_id"=>192353, "categories"=>["Evolutionary Biology"], "users"=>["Simon F. K. Hills", "James S. Crampton", "Steven A. Trewick", "Mary Morgan-Richards"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0052083.t001", "stats"=>{"downloads"=>8, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Specimens_of_Alcithoe_wilsonae_and_A_knoxi_used_to_determine_population_variability_in_mitochondrial_DNA_first_35_and_shell_morphometrics_/192353", "title"=>"Specimens of <i>Alcithoe wilsonae</i> and <i>A. knoxi</i> used to determine population variability in mitochondrial DNA (first 35), and shell morphometrics.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-12-20 00:39:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/521802"], "description"=>"<p>The distribution for the marginal prior on the <i>A. fusus</i> node recovers a bimodal distribution that appears to result from leakage into the <i>A. arabica</i> node calibration. However, the posterior distribution on the <i>A. fusus</i> node shows that the anomalous secondary peak in the marginal distribution has little effect on the analysis in the presence of sequence data.</p>", "links"=>[], "tags"=>["posterior", "distributions", "calibrated", "nodes", "illustrates", "node"], "article_id"=>192293, "categories"=>["Evolutionary Biology"], "users"=>["Simon F. K. Hills", "James S. Crampton", "Steven A. Trewick", "Mary Morgan-Richards"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0052083.g008", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_prior_and_posterior_distributions_on_the_calibrated_Alcithoe_fusus_and_A_arabica_nodes_illustrates_an_interaction_between_the_two_node_calibrations_but_this_interaction_has_little_effect_with_the_addition_of_sequence_data_/192293", "title"=>"Comparison of prior and posterior distributions on the calibrated <i>Alcithoe fusus</i> and <i>A. arabica</i> nodes illustrates an interaction between the two node calibrations, but this interaction has little effect with the addition of sequence data.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-20 00:38:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/521148"], "description"=>"<p>Morphological ambiguity results in a range of phylogenetic hypotheses for the placement of <i>A. knoxi</i>, ranging from (A) <i>A</i>. <i>knoxi</i> representing a distinct lineage (genus <i>Teremelon</i>) sister to the <i>Alcithoe</i> lineage, to (B) <i>A. knoxi</i> is a form of <i>A. wilsonae</i> nested within the modern diversity of <i>Alcithoe</i>. The node that would be calibrated at approximately 10my based on the <i>A. knoxi</i> fossils is shown (arrows). Calibration (A) would set a maximum limit of the origin of the modern <i>Alcithoe</i> at no earlier then 10mya, whereas (B) would allow the diversification of the extant <i>Alcithoe</i> to have occurred earlier.</p>", "links"=>[], "tags"=>["phylogenetic", "positions"], "article_id"=>191649, "categories"=>["Evolutionary Biology"], "users"=>["Simon F. K. Hills", "James S. Crampton", "Steven A. Trewick", "Mary Morgan-Richards"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0052083.g002", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Potential_phylogenetic_positions_of_Alcithoe_knoxi_/191649", "title"=>"Potential phylogenetic positions of <i>Alcithoe knoxi</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-20 00:27:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/521417"], "description"=>"<p>(A) Histograms showing the distribution specimens arrayed according to their scores on the morphometric discriminant function axis. Bold arrows indicate the positions of group means. (B) Landmarks used in the geometric morphometric analysis. Black-filled landmarks are type 1 and type 2 landmarks (<i>sensu </i><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052083#pone.0052083-Bookstein2\" target=\"_blank\">[26]</a>); white-filled landmarks are semilandmarks (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052083#pone.0052083.s001\" target=\"_blank\">Table S1</a> for explanation). The “comb” used to locate semilandmarks 6–9 is shown with a dotted line. This comb was located using the anterior extremity of the outer lip (semilandmark 5) and the suture at the posterior limit of the outer lip (landmark 10), and the anterior half of the comb was divided into eighths in order to locate semilandmarks 6–9. (C) The deformation (i.e. translation of landmarks) inferred from the change from mean <i>A. wilsonae</i> to mean <i>A. knoxi</i> (right). For clarity, translations have been exaggerated by a factor of two.</p>", "links"=>[], "tags"=>["reveals", "overlapping", "means"], "article_id"=>191913, "categories"=>["Evolutionary Biology"], "users"=>["Simon F. K. Hills", "James S. Crampton", "Steven A. Trewick", "Mary Morgan-Richards"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0052083.g004", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Morphometric_analysis_of_Alcithoe_wilsonae_and_A_knoxi_reveals_overlapping_distributions_but_different_means_of_shell_shape_/191913", "title"=>"Morphometric analysis of <i>Alcithoe wilsonae</i> and <i>A. knoxi</i> reveals overlapping distributions, but different means of shell shape.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-20 00:31:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/521257"], "description"=>"<p>The theoretical extent of the range of these species is indicated by the dotted line. <i>A. wilsonae</i> generally occupies depths from 50 m to 450 m and <i>A. knoxi</i> is found between approximately 400 and 750 meters. Approximate locations of sample sites of the DNA sequenced specimens are indicated with circles, boxes indicate the locations of samples only used for morphometric analysis. Inset – A sample of the morphological variation of <i>A. wilsonae</i> (A) M190111, (B) M190079, (C) M177177, and the <i>A. knoxi</i> form (D) 30037. The sampling locations of these specimens are indicated with the corresponding lower case letter.</p>", "links"=>[], "tags"=>["geographic"], "article_id"=>191759, "categories"=>["Evolutionary Biology"], "users"=>["Simon F. K. Hills", "James S. Crampton", "Steven A. Trewick", "Mary Morgan-Richards"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0052083.g003", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Approximate_geographic_range_of_A_wilsonae_and_A_knoxi_/191759", "title"=>"Approximate geographic range of <i>A. wilsonae</i> and <i>A. knoxi</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-20 00:29:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/521555"], "description"=>"<p>Each haplotype differs by a single nucleotide, unsampled haplotypes are represented by black dots. (See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052083#pone-0052083-t001\" target=\"_blank\">Table 1</a> for sample codes.).</p>", "links"=>[], "tags"=>["573", "bp", "mtdna", "27", "demonstrates"], "article_id"=>192049, "categories"=>["Evolutionary Biology"], "users"=>["Simon F. K. Hills", "James S. Crampton", "Steven A. Trewick", "Mary Morgan-Richards"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0052083.g006", "stats"=>{"downloads"=>2, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Haplotype_network_based_on_573_bp_of_mtDNA_nad_2_of_27_Alcithoe_wilsonae_open_ovals_and_8_Alcithoe_knoxi_filled_ovals_demonstrates_the_lack_of_genetic_structure_related_to_morphology_/192049", "title"=>"Haplotype network (based on 573 bp of mtDNA <i>nad</i>2) of 27 <i>Alcithoe wilsonae</i> (open ovals) and 8 <i>Alcithoe knoxi</i> (filled ovals) demonstrates the lack of genetic structure related to morphology.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-20 00:34:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/521074"], "description"=>"<p>Fossil species are shown on the left, extant species on the right. Bars show occurrence in the fossil record in the time bins indicated, with resolution at the level of recognised New Zealand geological stages <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052083#pone.0052083-Cooper1\" target=\"_blank\">[56]</a>. Numbers by the fossil species indicate the number of discrete sampling events, as recorded in the FRED database <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052083#pone.0052083-Crampton4\" target=\"_blank\">[57]</a>. <i>Alcithoe knoxi</i> is known from two collections in Tongaporutuan and is found in the extant fauna, but no fossils have yet been identified from the intervening time, as indicated by a dashed line. Abbreviations are given for New Zealand fossil record stages (Tt – Tongaporutuan, Tk – Kapitean, Wo – Opoitian, Wp – Waipipian, Wm – Mangapanian, Wn – Nukumaruan, Wc – Castlecliffian, Wq – Haweran).</p>", "links"=>[], "tags"=>["zealand", "11"], "article_id"=>191575, "categories"=>["Evolutionary Biology"], "users"=>["Simon F. K. Hills", "James S. Crampton", "Steven A. Trewick", "Mary Morgan-Richards"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0052083.g001", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_New_Zealand_Alcithoe_of_the_last_11_million_years_/191575", "title"=>"The New Zealand <i>Alcithoe</i> of the last 11 million years.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-20 00:26:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/521497"], "description"=>"<p>Scores of specimens on the morphometric first principal component axis plotted against water depth indicates a correlation between depth and morphology. The first principal component explains 66% of the total shape variation in the dataset. Open circles represent <i>A. wilsonae</i> specimens, filled circles represent <i>A. knoxi</i> specimens.</p>", "links"=>[], "tags"=>["morphometric", "benthic", "snail"], "article_id"=>191994, "categories"=>["Evolutionary Biology"], "users"=>["Simon F. K. Hills", "James S. Crampton", "Steven A. Trewick", "Mary Morgan-Richards"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0052083.g005", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_morphometric_shape_with_depth_of_collection_of_two_benthic_snail_taxa_Alcithoe_wilsonae_and_A_knoxi_/191994", "title"=>"Comparison of morphometric shape with depth of collection of two benthic snail taxa, <i>Alcithoe wilsonae</i> and <i>A. knoxi.</i>", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-20 00:33:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/281581"], "description"=>"<div><p>Species definition and delimitation is a non-trivial problem in evolutionary biology that is particularly problematic for fossil organisms. This is especially true when considering the continuity of past and present species, because species defined in the fossil record are not necessarily equivalent to species defined in the living fauna. Correctly assigned fossil species are critical for sensitive downstream analysis (e.g., diversification studies and molecular-clock calibration). The marine snail genus <em>Alcithoe</em> exemplifies many of the problems with species identification. The paucity of objective diagnostic characters, prevalence of morphological convergence between species and considerable variability within species that are observed in <em>Alcithoe</em> are typical of a broad range of fossilised organisms. Using a synthesis of molecular and morphometric approaches we show that two taxa currently recognised as distinct are morphological variants of a single species. Furthermore, we validate the fossil record for one of these morphotypes by finding a concordance between the palaeontological record and divergence time of the lineage inferred using molecular-clock analysis. This work demonstrates the utility of living species represented in the fossil record as candidates for molecular-clock calibration, as the veracity of fossil species assignment can be more rigorously tested.</p> </div>", "links"=>[], "tags"=>["dna", "morphology", "10", "fossils"], "article_id"=>115519, "categories"=>["Evolutionary Biology"], "users"=>["Simon F. K. Hills", "James S. Crampton", "Steven A. Trewick", "Mary Morgan-Richards"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0052083", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/DNA_and_Morphology_Unite_Two_Species_and_10_Million_Year_Old_Fossils__/115519", "title"=>"DNA and Morphology Unite Two Species and 10 Million Year Old Fossils", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-12-20 01:31:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/521884"], "description"=>"<p>Three models were tested: simple, regression independent of nominal taxonomic grouping; parallel, regression slope is independent of taxonomic grouping, but the intercept is not; non-parallel, slope and intercept depend on taxonomic grouping. The <i>p</i>-values on <i>F</i>-statistics indicate the probability that the simpler model in each comparison is adequate; significant <i>p</i>-values indicate that the more complex model is preferred (see text). In each comparison the more complex model is supported and, overall, the non-parallel model is preferred, indicating a correlation between depth and morphology.</p>", "links"=>[], "tags"=>["linear", "regression"], "article_id"=>192380, "categories"=>["Evolutionary Biology"], "users"=>["Simon F. K. Hills", "James S. Crampton", "Steven A. Trewick", "Mary Morgan-Richards"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0052083.t002", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Results_of_general_linear_modelling_of_the_regression_between_shell_shape_and_water_depth_/192380", "title"=>"Results of general linear modelling of the regression between shell shape and water depth.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-12-20 00:39:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/521922"], "description"=>"<p>Results from AMOVA of <i>A. wilsonae</i> nad2 DNA sequneces, low Phi<sub>PT</sub> values indicate high levels of genetic exchange between populations.</p>", "links"=>[], "tags"=>["amova", "nad2", "dna", "levels"], "article_id"=>192413, "categories"=>["Evolutionary Biology"], "users"=>["Simon F. K. Hills", "James S. Crampton", "Steven A. Trewick", "Mary Morgan-Richards"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0052083.t003", "stats"=>{"downloads"=>8, "page_views"=>53, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Results_from_AMOVA_of_A_wilsonae_nad2_DNA_sequneces_low_Phi_PT_values_indicate_high_levels_of_genetic_exchange_between_populations_/192413", "title"=>"Results from AMOVA of <i>A. wilsonae</i> nad2 DNA sequneces, low Phi<sub>PT</sub> values indicate high levels of genetic exchange between populations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-12-20 00:40:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/521698"], "description"=>"<p> <b>bp of mtDNA sequence indicates that </b><b><i>A. wilsonae/knoxi</i></b><b> diverged from the </b><b><i>A. arabica</i></b><b> lineage approximately 8 million years ago.</b> All nodes are recovered with a posterior support of at least 0.93 and had >90% bootstrap support under Maximum likelihood, with the exception of the <i>A lutea</i>/<i>A. fissurata</i> node (0.58). Node age estimates are given in millions of years before present. 95% confidence intervals are depicted by boxes centred on nodes. Nodes calibrated using soft priors based on fossil data are indicated with filled boxes.</p>", "links"=>[], "tags"=>["phylogeny", "derived"], "article_id"=>192191, "categories"=>["Evolutionary Biology"], "users"=>["Simon F. K. Hills", "James S. Crampton", "Steven A. Trewick", "Mary Morgan-Richards"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0052083.g007", "stats"=>{"downloads"=>1, "page_views"=>36, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Molecular_clock_analysis_of_the_Alcithoe_phylogeny_derived_from_4696_/192191", "title"=>"Molecular-clock analysis of the <i>Alcithoe</i> phylogeny derived from 4696", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-20 00:36:31"}

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Relative Metric

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