Differences between hard and soft phylogenetic data

Robert S. Sansom, Matthew A. Wills

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

When building the tree of life, variability of phylogenetic signal is often accounted for by partitioning gene sequences and testing for differences. The same considerations, however, are rarely applied to morphological data, potentially undermining its use in evolutionary contexts. Here, we apply partition heterogeneity tests to 59 animal datasets to demonstrate that significant differences exist between the phylogenetic signal conveyed by ‘hard’ and ‘soft’ characters (bones, teeth and shells versus myology, integument etc). Furthermore, the morphological partitions differ significantly in their consistency relative to independent molecular trees. The observed morphological differences correspond with missing data biases, and as such their existence presents a problemnot only for phylogeny reconstruction, but also for interpretations of fossil data. Evolutionary inferences drawn from clades inwhich hard, readily fossilizable characters are relatively less consistent and different from other morphology (mammals, bivalves) may be less secure. More secure inferences might be drawn from the fossil record of clades that exhibit fewer differences, or exhibit more consistent hard characters (fishes, birds). In all cases, it will be necessary to consider the impact of missing data on empirical data, and the differences that exist between morphological modules.

Original languageEnglish
Article number20172150
JournalProceedings of the Royal Society B: Biological Sciences
Volume284
Issue number1869
DOIs
Publication statusPublished - 20 Dec 2017

Fingerprint

Mammals
Bivalvia
Birds
Phylogeny
Fish
Tooth
Bone
Fishes
Animals
Genes
phylogenetics
Bone and Bones
phylogeny
Testing
fossils
shell (molluscs)
integument
teeth
testing
bones

Keywords

  • Heterogeneity
  • Missing data
  • Morphology
  • Partition
  • Phylogenetics

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Environmental Science(all)
  • Agricultural and Biological Sciences(all)

Cite this

Differences between hard and soft phylogenetic data. / Sansom, Robert S.; Wills, Matthew A.

In: Proceedings of the Royal Society B: Biological Sciences, Vol. 284, No. 1869, 20172150, 20.12.2017.

Research output: Contribution to journalArticle

@article{a2cfdee6b6244b809d83a9fd5dc42122,
title = "Differences between hard and soft phylogenetic data",
abstract = "When building the tree of life, variability of phylogenetic signal is often accounted for by partitioning gene sequences and testing for differences. The same considerations, however, are rarely applied to morphological data, potentially undermining its use in evolutionary contexts. Here, we apply partition heterogeneity tests to 59 animal datasets to demonstrate that significant differences exist between the phylogenetic signal conveyed by ‘hard’ and ‘soft’ characters (bones, teeth and shells versus myology, integument etc). Furthermore, the morphological partitions differ significantly in their consistency relative to independent molecular trees. The observed morphological differences correspond with missing data biases, and as such their existence presents a problemnot only for phylogeny reconstruction, but also for interpretations of fossil data. Evolutionary inferences drawn from clades inwhich hard, readily fossilizable characters are relatively less consistent and different from other morphology (mammals, bivalves) may be less secure. More secure inferences might be drawn from the fossil record of clades that exhibit fewer differences, or exhibit more consistent hard characters (fishes, birds). In all cases, it will be necessary to consider the impact of missing data on empirical data, and the differences that exist between morphological modules.",
keywords = "Heterogeneity, Missing data, Morphology, Partition, Phylogenetics",
author = "Sansom, {Robert S.} and Wills, {Matthew A.}",
year = "2017",
month = "12",
day = "20",
doi = "10.1098/rspb.2017.2150",
language = "English",
volume = "284",
journal = "Philosophical transactions B: Biological Sciences",
issn = "0962-8436",
publisher = "The Royal Society",
number = "1869",

}

TY - JOUR

T1 - Differences between hard and soft phylogenetic data

AU - Sansom, Robert S.

AU - Wills, Matthew A.

PY - 2017/12/20

Y1 - 2017/12/20

N2 - When building the tree of life, variability of phylogenetic signal is often accounted for by partitioning gene sequences and testing for differences. The same considerations, however, are rarely applied to morphological data, potentially undermining its use in evolutionary contexts. Here, we apply partition heterogeneity tests to 59 animal datasets to demonstrate that significant differences exist between the phylogenetic signal conveyed by ‘hard’ and ‘soft’ characters (bones, teeth and shells versus myology, integument etc). Furthermore, the morphological partitions differ significantly in their consistency relative to independent molecular trees. The observed morphological differences correspond with missing data biases, and as such their existence presents a problemnot only for phylogeny reconstruction, but also for interpretations of fossil data. Evolutionary inferences drawn from clades inwhich hard, readily fossilizable characters are relatively less consistent and different from other morphology (mammals, bivalves) may be less secure. More secure inferences might be drawn from the fossil record of clades that exhibit fewer differences, or exhibit more consistent hard characters (fishes, birds). In all cases, it will be necessary to consider the impact of missing data on empirical data, and the differences that exist between morphological modules.

AB - When building the tree of life, variability of phylogenetic signal is often accounted for by partitioning gene sequences and testing for differences. The same considerations, however, are rarely applied to morphological data, potentially undermining its use in evolutionary contexts. Here, we apply partition heterogeneity tests to 59 animal datasets to demonstrate that significant differences exist between the phylogenetic signal conveyed by ‘hard’ and ‘soft’ characters (bones, teeth and shells versus myology, integument etc). Furthermore, the morphological partitions differ significantly in their consistency relative to independent molecular trees. The observed morphological differences correspond with missing data biases, and as such their existence presents a problemnot only for phylogeny reconstruction, but also for interpretations of fossil data. Evolutionary inferences drawn from clades inwhich hard, readily fossilizable characters are relatively less consistent and different from other morphology (mammals, bivalves) may be less secure. More secure inferences might be drawn from the fossil record of clades that exhibit fewer differences, or exhibit more consistent hard characters (fishes, birds). In all cases, it will be necessary to consider the impact of missing data on empirical data, and the differences that exist between morphological modules.

KW - Heterogeneity

KW - Missing data

KW - Morphology

KW - Partition

KW - Phylogenetics

UR - http://www.scopus.com/inward/record.url?scp=85038871297&partnerID=8YFLogxK

U2 - 10.1098/rspb.2017.2150

DO - 10.1098/rspb.2017.2150

M3 - Article

VL - 284

JO - Philosophical transactions B: Biological Sciences

JF - Philosophical transactions B: Biological Sciences

SN - 0962-8436

IS - 1869

M1 - 20172150

ER -