A Bayesian approach to dynamic homology of morphological characters and the ancestral phenotype of jawed vertebrates
Abstract
Phylogenetic analysis of morphological data proceeds from a fixed set of primary homology statements, the character-by-taxon matrix. However, there are cases where multiple conflicting homology statements can be justified from comparative anatomy. The upper jaw bones of placoderms have traditionally been considered homologous to the palatal vomer-dermopalatine series of osteichthyans. The discovery of 'maxillate' placoderms led to the alternative hypothesis that 'core' placoderm jaw bones are premaxillae and maxillae lacing external (facial) laminae. We introduce a BEAST2 package for simultaneous inference of homology and phylogeny, and find strong evidence for the latter hypothesis. Phenetic analysis of reconstructed ancestors suggests that maxillate placoderms are the most plesiomorphic known gnathostomes, and the shared cranial architecture of arthrodire placoderms, maxillate placoderms and osteichthyans is inherited. We suggest that the gnathostome ancestor possessed maxillae and premaxillae with facial and palatal laminae, and that these bones underwent divergent evolutionary trajectories in placoderms and osteichthyans.
Data availability
Taxon sources, character list, the data matrix in nexus format and the BEAST2 xml file are available for review at https://figshare.com/s/e40652290467d2a436fd.
Article and author information
Author details
Funding
Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Vidi 864.14.009)
- Benedict King
- Martin Rücklin
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2020, King & Rücklin
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 1,259
- views
-
- 215
- downloads
-
- 9
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Further reading
-
- Evolutionary Biology
The ovules or seeds (fertilized ovules) with wings are widespread and especially important for wind dispersal. However, the earliest ovules in the Famennian of the Late Devonian are rarely known about the dispersal syndrome and usually surrounded by a cupule. From Xinhang, Anhui, China, we now report a new taxon of Famennian ovules, Alasemenia tria gen. et sp. nov. Each ovule of this taxon possesses three integumentary wings evidently extending outwards, folding inwards along abaxial side and enclosing most part of nucellus. The ovule is borne terminally on smooth dichotomous branches and lacks a cupule. Alasemenia suggests that the integuments of the earliest ovules without a cupule evolved functions in probable photosynthetic nutrition and wind dispersal. It indicates that the seed wing originated earlier than other wind dispersal mechanisms such as seed plume and pappus, and that three- or four-winged seeds were followed by seeds with less wings. Mathematical analysis shows that three-winged seeds are more adapted to wind dispersal than seeds with one, two or four wings under the same condition.
-
- Evolutionary Biology
The Xerces Blue (Glaucopsyche xerces) is considered to be the first butterfly to become extinct in historical times. It was notable for its chalky lavender wings with conspicuous white spots on the ventral wings. The last individuals were collected in their restricted habitat, in the dunes near the Presidio military base in San Francisco, in 1941. We sequenced the genomes of four 80- to 100-year-old Xerces Blue, and seven historical and one modern specimens of its closest relative, the Silvery Blue (Glaucopsyche lygdamus). We compared these to a novel annotated genome of the Green-Underside Blue (Glaucopsyche alexis). Phylogenetic relationships inferred from complete mitochondrial genomes indicate that Xerces Blue was a distinct species that diverged from the Silvery Blue lineage at least 850,000 years ago. Using nuclear genomes, both species experienced population growth during the Eemian interglacial period, but the Xerces Blue decreased to a very low effective population size subsequently, a trend opposite to that observed in the Silvery Blue. Runs of homozygosity and deleterious load in the former were significantly greater than in the later, suggesting a higher incidence of inbreeding. These signals of population decline observed in Xerces Blue could be used to identify and monitor other insects threatened by human activities, whose extinction patterns are still not well known.