Biology subjects

Keating, J. N.

Publications and source records attributed to Keating, J. N..

5 recordsLinked to original sources

bioRxiv2024

Estimating ancestral states of complex characters: a case study on the evolution of feathers

Feathers are a key novelty underpinning the evolutionary success of birds, yet the origin of feathers remains poorly understood. Debates about feather evolution hinge upon whether filamentous integument has evolved once or multiple time independently on the lineage leading to modern birds. These contradictory results stem from subjective methodological differences in statistical ancestral state estimates. Here we conduct a comprehensive comparison of ancestral state estimation methodologies applied to stem-group birds, testing the role of outgroup inclusion, tree time scaling method, model choice and character coding strategy. Models are compared based on their Akaike Information Criteria (AIC), mutual information, as well as the uncertainty of marginal ancestral state estimates. Our results demonstrate that ancestral state estimates of stem-bird integument are strongly influenced by tree time scaling method, outgroup selection and model choice, while character coding strategy seems to have less effect on the ancestral estimates produced. We identify the best fitting models using AIC scores and a leave-one-out cross-validation approach (LOOCV). Our analyses broadly support the independent origin of filamentous integument in dinosaurs and pterosaurs and support a younger evolutionary origin of feathers than has been suggested previously. More generally, our study highlights that special care must be taken in selecting the outgroup, tree and model when conducting ASE analyses. With respect to model selection, our results suggest that considering a LOOCV approach, may yield more reliable results than simply comparing AIC scores when the analyses involve a limited number of taxa.

paleontology↗

bioRxiv2024

Independent origins of spicules reconcile the evolutionary history of sponges

Sponges (Porifera) play a critical role in global biogeochemical processes. However, their evolutionary timeline remains unclear hampering our understanding of Neoproterozoic paleoecology. Molecular data suggest a Tonian or Cryogenian origin, while the oldest confirmed sponge fossils, represented by siliceous spicules, date to the Ediacaran. To understand this 150-million-year discrepancy, we compiled a new phylogenomic dataset, revised fossil evidence, derived a new dated sponge phylogeny, and tested whether ancestral sponges were aspiculated or not. We infer the last common sponge ancestor to have been early Ediacaran in age and aspiculated. Siliceous spicules evolved independently at least four times, and calcareous spicules at least two times in crown sponges. We performed a diversification rate analysis showing that siliceous spicules did not drive species radiations. Our study reconciles molecular and fossil evidence, indicating that while sponges emerged in the early Ediacaran, they are largely absent from the Neoproterozoic fossil record because they had not yet evolved spicules. TeaserSponges emerged in the Precambrian, were soft-bodied and did not produce mineralized spicules, which emerged multiple times independently.

evolutionary biology↗

bioRxiv2023

What is the best method for estimating ancestral states from discrete characters?

Ancestral state estimation is a formal phylogenetic method for inferring the nature of ancestors and performing tests of character evolution. As such, it is among the most important tools available to evolutionary biologists. However, there are a profusion of methods available, the accuracy of which remains unclear. Here I use a simulation approach to test between parsimony and likelihood methods for estimating ancestral states from discrete binary characters. I simulate 500 characters using 15 different Markov generating models, a range of tree sizes (8-256 tips) and three topologies representing end members of tree symmetry and branch length heterogeneity. Simulated tip states were subjected to ancestral state estimation under the Equal Rates (ER) and All-Rates-Different (ARD) models, as well as under parsimony assuming accelerated transformations (ACCTRAN). The results demonstrate that both parsimony and likelihood approaches obtain high accuracy applied to trees with more tips. Parsimony performs poorly when trees contain long branches, whereas the ER model performs well across simulations and is reasonably robust to model violation. The ER model frequently outperforms the ARD model, even when data are simulated using unequal rates. Furthermore, the ER model exhibits less transition rate error when compared to ER models. These results suggest that ARD models may be overparameterized when character data is limited. Surprisingly, the difference in likelihood-based information criteria between models was found to be a poor predictor of difference in model error; better fitting models are not necessarily more accurate. However, there is a strong correlation between model uncertainty and model error; likelihood models with more certain ancestral state estimates are typically more accurate. Using empirical morphological datasets, I demonstrate that applying different methods often results in substantively different ancestral state estimates. The results of the simulation study highlight the importance of incorporating fossils in ancestral state estimation. Fossils increase the total number of tips, break long branches and are closer to internal nodes, thereby lowering average branch length and overall branch length heterogeneity of trees. These factors will all contribute to increasing the accuracy of ancestral state estimates, irrespective of the method used.

evolutionary biology↗

bioRxiv2023

Hagfish genome illuminates vertebrate whole genome duplications and their evolutionary consequences

Whole genome duplications (WGDs) are major events that drastically reshape genome architecture and are causally associated with organismal innovations and radiations1. The 2R Hypothesis suggests that two WGD events (1R and 2R) occurred during early vertebrate evolution2, 3. However, the veracity and timing of the 2R event relative to the divergence of gnathostomes (jawed vertebrates) and cyclostomes (jawless hagfishes and lampreys) is unresolved4-6 and whether these WGD events underlie vertebrate phenotypic diversification remains elusive7. Here we present the genome of the inshore hagfish, Eptatretus burgeri. Through comparative analysis with lamprey and gnathostome genomes, we reconstruct the early events in cyclostome genome evolution, leveraging insights into the ancestral vertebrate genome. Genome-wide synteny and phylogenetic analyses support a scenario in which 1R occurred in the vertebrate stem-lineage during the early Cambrian, and the 2R event occurred in the gnathostome stem-lineage in the late Cambrian after its divergence from cyclostomes. We find that the genome of stem-cyclostomes experienced two additional, independent genome duplications (herein CR1 and CR2). Functional genomic and morphospace analyses demonstrate that WGD events generally contribute to developmental evolution with similar changes in the regulatory genome of both vertebrate groups. However, appreciable morphological diversification occurred only after the 2R event, questioning the general expectation that WGDs lead to leaps of morphological complexity7.

genomics↗

bioRxiv2022

A Phylogeny for Heterostraci (stem-gnathostomes)

The armoured jawless fishes (ostracoderms) are major and widespread components of middle Palaeozoic ecosystems. As successive plesia on the gnathostome lineage, they reveal the early sequences of vertebrate evolution, including the assembly of the vertebrate skeleton. This is predicated however, on understanding of their diversity and interrelationships. The largest ostracoderm clade, the Pteraspidimorphi, is often reconstructed as sister taxon to other boney vertebrates yet they lack a phylogenetic framework, in particular the heterostracans. Problematic heterostracans with a tessellate headshield ( tessellate-basal model) are often regarded as the plesiomorphic condition for the clade but no phylogenetic analysis has included these taxa. Here we review the Heterostraci and present their first comprehensive phylogenetic analysis (131 heterostracan taxa and 12 outgroup taxa). Heterostraci and Ordovician Pteraspidimorphi are recovered as sister-group to all other boney jawless vertebrates in parsimony analyses, however, in no instances do we recover a monophyletic Pteraspidimorphi. Tree visualization reveals lack of resolution results from two conflicting solutions for the heterostracan root. Stratigraphic congruences provides support for the macromeric Ctenaspisdidae as sister taxon to all other Heterostraci rather than the "tesselate-basal" model. The results presented here are the first phylogenetic hypotheses of heterostracan relationships and it is hoped a first step into an accurate interpretation of character evolution and polarity in this crucial episode of vertebrate evolution.

paleontology↗