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Accuracy of phylogenetic reconstructions from continuous characters analyzed under parsimony and its parametric correlates
<p>Quantitative traits are a source of evolutionary information often difficult to handle in cladistics. Tools exist to analyze this kind of data without subjective discretization, avoiding biases in the delimitation of categorical states. Nonetheless, the ability of continuous characters to accurately infer relationships is incompletely understood, particularly under parsimony analysis. This study evaluates the accuracy of phylogenetic reconstructions from simulated matrices of continuous characters evolving under alternative evolutionary processes and analyzed by parsimony. We sampled 100 empirical trees to simulate 9,000 matrices, each containing between 25 and 50 taxa and 50 and 150 continuous characters evolving under three evolutionary processes: Brownian-Motion (BM), Ornstein-Uhlenbeck (OU) and Early-Burst (EB) with variable parametrizations. Our cladogram comparisons revealed that continuous character matrices, when discretized objectively and analyzed by parsimony in TNT, carry phylogenetic signals to infer species relationships, regardless of the evolutionary models and parameterization schemes. Interestingly, implementing Equal Weighting (EW) or Implied Weighting (IW) with varying penalization strengths against homoplasies did not affect cladogram reconstructions on the basis of continuous characters. Finally, the accuracy of continuous characters in resolving species relationships is skewed toward apical nodes of the recovered trees. Our findings provide general insights of the utility of quantitative traits in cladistics and demonstrate that their effectiveness in estimating shallower nodes is independent of the underlying evolutionary model, parameters and weighting schemes.</p>
Figure 3 in Exploring phylogenetic relationships of Pteraspidiformes heterostracans (stem-gnathostomes) using continuous and discrete characters
Figure 3. Cartoons of selected characters and character states. Numbers signify characters, bracketed numbers represent character states e.g. 1(0), where 1 is the characters and (0) is the character state.
Figure 6. Most parsimonious result from a in Exploring phylogenetic relationships of Pteraspidiformes heterostracans (stem-gnathostomes) using continuous and discrete characters
Figure 6. Most parsimonious result from a phylogenetic analysis of discrete (1—64) and discretized continuous characters identified through gap coding (88—100). A, strict consensus of 30 most parsimonious trees with equally weighted characters (tree length 346). B, most parsimonious solution with implied weighted characters (k = 3) (tree length 27.86). Psammosteidae taxa in bold (for which quantitative characters have been treated as inapplicable, i.e. non-homologous).
Figure 2 in Exploring phylogenetic relationships of Pteraspidiformes heterostracans (stem-gnathostomes) using continuous and discrete characters
Figure 2. Reconstruction of a hypothetical Pteraspidiformes (adapted from Blieck 1984). A, dorsal and ventral view of Pteraspidiformes headshield with plates labelled. B, D, E, measurements used in phylogenetic analysis. C, dorsal headshield sensory canals. Anatomical abbreviations: SOC, supraorbital canal; OrbC, orbital canal; PinC, pineal canal; LDC, lateral dorsal canal; MDC, medial dorsal canal; TC, transverse commissures; MTC, median transverse commissures. Measurement abbreviations: DSL, dorsal shield length; DSW, dorsal shield width, not including the cornual plate width; DPL, dorsal plate length; DPW, dorsal plate width; RPL, rostral plate length; RPW, rostral plate width; PPL, pineal plate length; PPW, pineal plate width; BPL, brachial plate length; BOL, branchial opening distance from anterior of dorsal plate; CPL, cornual plate length; OrbPL, orbital plate length; OrbPAPL, orbital plate anterior process length; OrbPMPL, orbital plate medial process length; OrbPPPL, orbital plate posterior process length; Orb—Orb, orbital opening to orbital opening length; DSBW, dorsal spine base width; DSBL, dorsal spine base length; DPEB, dorsal plate embayment; DPEL, distance to beginning of embayment from anterior end of dorsal plate; DPEW, dorsal plate embayment narrowest width.
Figure 1. Previous Pteraspidiformes phylogenies. A in Exploring phylogenetic relationships of Pteraspidiformes heterostracans (stem-gnathostomes) using continuous and discrete characters
Figure 1. Previous Pteraspidiformes phylogenies. A, Blieck's (1984) Pteraspidiformes phylogeny for all the then-known taxa. B, Janvier's (1996) phylogeny for the major clades of Pteraspidiformes. C, Ilyes & Elliott's (1994) phylogeny for the Western USA taxa. D, Perǹegre's (2002) phylogeny to determine the position of Doryaspis. E, Perǹegre & Goujet's (2007) phylogeny to determine the position of Gigantaspis. F, Perǹegre & Elliott's (2008) most recent Pteraspidiformes phylogeny with the identification of major families. The Psammosteidae are highlighted when included in an analysis.
Figure 7. Pteraspidiformes phylogeny with genera plotted against their stratigraphical occurrences. A in Exploring phylogenetic relationships of Pteraspidiformes heterostracans (stem-gnathostomes) using continuous and discrete characters
Figure 7. Pteraspidiformes phylogeny with genera plotted against their stratigraphical occurrences. A, discrete and continuous character analysis with implied weighting (k = 3). B, discretized analysis with implied weighting (k = 3). Colours relate to palaeobiogeographical provinces.
Figure 4. Results from the phylogenetic analysis using discrete data only. A in Exploring phylogenetic relationships of Pteraspidiformes heterostracans (stem-gnathostomes) using continuous and discrete characters
Figure 4. Results from the phylogenetic analysis using discrete data only. A, strict consensus of 275 most parsimonious trees with equal character weights; length 276 steps, consistency index (CI) = 0.35, retention index (RI) = 0.59, and rescaled consistency index (RC) = 0.22. B, strict consensus of four most parsimonious trees with implied character weighting (k = 3) (tree length 23.11). Psammosteidae taxa in bold.
Figure 5 in Exploring phylogenetic relationships of Pteraspidiformes heterostracans (stem-gnathostomes) using continuous and discrete characters
Figure 5. Phylogenetic results from data sets containing discrete (1—64) and continuous (66, 68, 70, 72, 77, 80, 82, 86) characters. A, most parsimonious tree with equally weighted characters (tree length 319.36). B, most parsimonious tree with implied weighting (k = 3) (tree length 26.53). Psammosteidae taxa in bold (for which quantitative characters have been treated as inapplicable, i.e. nonhomologous).
FIGURE 1. A in A novel distance that reduces information loss in continuous characters with few observations
FIGURE 1. A. An interval and its components; B. Possible relationships between two intervals and A, B, and C in the Character X's space; C. DBI's behavior according to the possible relationships between the intervals of any two objects. For this, a mobile test interval of range X with its upper limit placed at Y was discreetly displaced by D units W times. For each of these W steps the DBI between the test interval and a fixed interval of range F with its lower limit placed at H were computed. The Left section shows the DBI for non-overlapped intervals; the Central section shows the DBI for partially overlapped intervals; and the Right section shows the DBI for fully overlapped intervals. Dashed lines show the results between intervals with different relative ranges (i.e., interval sizes). The asterisks show the paired distances between A, B, and C using DBI.
FIGURE 8 in Continuous character variation within the Glossopleura-Anoria-Sonoraspis plexus: Dolichometopid trilobites from the Cadiz Formation (Cambrian: Miaolingian, Wuliuan), California
FIGURE 8. Matrix characters for phylogenetic analysis shown on an unspecified species of dolichometopid trilobite (Glossopleura sp.). First number is character number (see Appendix for descriptions and matrix); number in parentheses is character state demonstrated by illustrated form. (Drawing courtesy of Sam Gon III.)
FIGURE 3 in Continuous character variation within the Glossopleura-Anoria-Sonoraspis plexus: Dolichometopid trilobites from the Cadiz Formation (Cambrian: Miaolingian, Wuliuan), California
FIGURE 3. Relative eye position and length for dolichometopids in this study, by taxon and formation group (most traditional Glossopleura species blended). This version of the data shows the intermixing of Glossopleura and traditional Anoria and Sonorapis. Note that within taxa, eye position may vary greatly. Only eye length shows possible distinction between genera. Anoria tontoensis from the Bright Angel Formation (along with one specimen of A. bessus from the Gordon Shale) is smaller-eyed and separates from Glossopleura (including G. mckeei) but only at an arbitrary EL/GL of 0.380. A. lodensis, G. mohavensis, and S. californica all plot within Glossopleura.
FIGURE 2 in Continuous character variation within the Glossopleura-Anoria-Sonoraspis plexus: Dolichometopid trilobites from the Cadiz Formation (Cambrian: Miaolingian, Wuliuan), California
FIGURE 2. Relative eye position and length for dolichometopids measured in this study, showing low degree to which the studied specimens demonstrate large, posteriorly positioned eyes (toward upper right; historically features attributed to Glossopleura) or smaller, more anteriorly positioned eyes (toward lower left, normally attributed to Anoria and Sonoraspis). Data set equation shows a shallow slope and very weak correlation.
FIGURE 9 in Continuous character variation within the Glossopleura-Anoria-Sonoraspis plexus: Dolichometopid trilobites from the Cadiz Formation (Cambrian: Miaolingian, Wuliuan), California
FIGURE 9. Phylogenetic analysis of 12 dolichometopid taxa for which there are relatively complete specimens, plus two outgroup taxa. A) Strict consensus of 40 MPTs of 41 steps. B) Strict consensus of 4 MPTs of 38 steps, after removal of the less well represented taxon G. bion. C) Strict consensus of 2 MPTs of 35 steps with just 8 dolichometopid taxa, after assuming the following synonymies: G. mckeei = G. boccar; S. californica = G. mohavensis; and G. producta = G. boccar. See text.
FIGURE 4 in Continuous character variation within the Glossopleura-Anoria-Sonoraspis plexus: Dolichometopid trilobites from the Cadiz Formation (Cambrian: Miaolingian, Wuliuan), California
FIGURE 4. Comparison of cranial measurements (in mm) in dolichometopids assigned to Glossopleura (blue), Sonoraspis (red), and Anoria (black). A) Eye length relative to glabella length. B) Eye position as represented by mid-ocular distance versus glabella length. Genera coded by color as noted above. Species denoted by symbols as listed alphabetically here: Glossopleura bion (filled blue squares), G. boccar (open blue diamonds), G. campbelli (open blue circles), G. gigantea (open blue ovals), G. lodensis (blue stars), G. mckeei (open blue triangles), G. mohavensis (blue dashes), G. producta (filled blue triangles), G. similaris (open inverted blue triangles), G. stephenensis (filled inverted blue triangles), G. utahensis (vertical blue bars), G. walcotti (filled blue diamonds), G. yatesi (filled blue circles); Sonoraspis californica (filled red squares), S. gomezi (open red squares), S. nelsoni (red pluses); Anoria baton (black pluses), A. bessus (black X), and A. tontoensis (filled black circles),
FIGURE 11 in Continuous character variation within the Glossopleura-Anoria-Sonoraspis plexus: Dolichometopid trilobites from the Cadiz Formation (Cambrian: Miaolingian, Wuliuan), California
FIGURE 11. Some representative dolichometopids from other formations included in this study. A–B and D–E) Glossopleura boccar. C) Glossopleura similaris(?) F) Anoria tontoensis. G–H) Glossopleura mohavensis. A) USNM 62703, type of Glossopleura boccar, from the Stephen Formation. B) USNM 62702, specimen originally assigned to G. stephenensis, from the Stephen Formation. C) KUMIP 314054, G. similaris(?), from the Spence Shale (Langston Formation). D) SGDS 1975, G. boccar, from the Chisholm Formation. E) USNM 62714, specimen originally assigned to G. mckeei, from the Bright Angel Formation. F) USNM 62685, Anoria tontoensis, from the Bright Angel Formation. G) LACMIP 10782, specimen originally assigned to "Sonoraspis nelsoni", from the Monola Formation. H) LACMIP 2469/24444.1, specimen originally assigned to "Sonoraspis californica", from the Pole Canyon Formation. (Image in D courtesy of Andrew R.C. Milner. G and H courtesy LACM: Hendy, A., Walker, L., Mertz, W. [2020]. LACM Invertebrate Paleontology. Version 1.9. Natural History Museum of Los Angeles County. Occurrence dataset https://doi.org/ 10.15468/6nxzen accessed via GBIF.org on 2021-03-23.) All scale bars equal 1 cm.
FIGURE 10. Dolichometopid trilobite specimens from the Cadiz Formation, California. A in Continuous character variation within the Glossopleura-Anoria-Sonoraspis plexus: Dolichometopid trilobites from the Cadiz Formation (Cambrian: Miaolingian, Wuliuan), California
FIGURE 10. Dolichometopid trilobite specimens from the Cadiz Formation, California. A) Glossopleura lodensis (USNM 78400a), note eight thoracic segments, elongate T5 pleural spines, anteriorly expanded glabella, and long eyes (impression, lighting from left). B) Glossopleura mohavensis (USNM 78400b), note eight thoracic segments (dorsal exoskeleton, lighting from left). C) Glossopleura mohavensis (LACM 10785; "Sonoraspis californica"), note wide glabella, eight thoracic segments, and axial spine bases (impression, lighting from left). D) Glossopleura mohavensis (LACM 10786; "Sonoraspis californica"), note wide glabella, eight thoracic segments, and axial spine bases (impression, lighting from left). E) Glossopleura mohavensis (MWC 7769), note eight thoracic segments (dorsal exoskeleton, lighting from left). F) Glossopleura mohavensis (MWC 7779), (dorsal exoskeleton, lighting from left). A and B from the Bristol Mountains; C and D from near Section A of Foster (1994) (type section; north of Route 66), Marble Mountains; E and F from UCR 7359, near Section B of Foster (1994) (south of Route 66), Marble Mountains. All scale bars = 1 cm.
FIGURE 6 in Continuous character variation within the Glossopleura-Anoria-Sonoraspis plexus: Dolichometopid trilobites from the Cadiz Formation (Cambrian: Miaolingian, Wuliuan), California
FIGURE 6. Anterior expansion of glabella in dolichometopids. A) Comparing AGW/MGW and AGW/PGW, showing Anoria and Sonoraspis less expanded but well mixed with Glossopleura specimens. B) Full data set statistics.
FIGURE 1 in Continuous character variation within the Glossopleura-Anoria-Sonoraspis plexus: Dolichometopid trilobites from the Cadiz Formation (Cambrian: Miaolingian, Wuliuan), California
FIGURE 1. Measurements taken of dolichometopid cephala for this study. Abbreviations: AGW, anterior glabella width; CW, cephalon width; EL, eye length; GL, glabella length; MGW, mid-glabella width; MOD, midocular distance; PGW, posterior glabella width.
Linked collectors and determiners for: Phylogenetic analysis of the Belostoma plebejum group sensu Nieser (Insecta, Hemiptera, Belostomatidae): the effect of adding continuous characters on its accuracy.
Natural history specimen data linked to collectors and determiners held within, "Phylogenetic analysis of the Belostoma plebejum group sensu Nieser (Insecta, Hemiptera, Belostomatidae): the effect of adding continuous characters on its accuracy". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/0367aa61-0794-47f5-84b8-8abde5050c40">https://bionomia.net/dataset/0367aa61-0794-47f5-84b8-8abde5050c40</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/0367aa61-0794-47f5-84b8-8abde5050c40">https://gbif.org/dataset/0367aa61-0794-47f5-84b8-8abde5050c40</a>. Formatted as a Frictionless Data package.
Fig. 3. Dibolostethus Hoffman, 2009 somatic characters continued. A, E. Dibolostethus sicarius Hoffman, 2009 in A review of the previously monotypic tribe Dibolostethini (Chelodesmidae: Chelodesminae) with description of two new species and a summary of the Chelodesmidae of the Tropical Andes Biodiversity Hotspot
Fig. 3. Dibolostethus Hoffman, 2009 somatic characters continued. A, E. Dibolostethus sicarius Hoffman, 2009, holotype, ♂ (VMNH110810). B–D. D. kattani Means, Bouzan, Martínez-Torres & Ivanov sp. nov., holotype, ♂ (ICN-MD-1317-1). A. Coxa 2, mesal view, red arrow = gonopore. B. Left leg 4, posterior view, red arrow = tibial ventro-apical projection. C. Left leg of 5th leg pair showing incrassate femur, red arrow = tibial ventro-apical projection. D. Body ring 5, lateral view, red circle = anterior pair of sternal projections. E. Prefemur 5, red arrow = basal pore. Abbreviations: Cx = coxa; Pf = prefemur.
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