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Dryad

Data from: Body size evolution in otters distinguished from terrestrial mustelids

Cite this dataset

Harano, Tomohiro; Kutsukake, Nobuyuki (2024). Data from: Body size evolution in otters distinguished from terrestrial mustelids [Dataset]. Dryad. https://doi.org/10.5061/dryad.2jm63xsvt

Abstract

Some taxa of mammals live in water, all of which evolved from land-dwelling ancestors. In the family Mustelidae (Mammalia: Carnivora), most species live on land, while otters, comprising the subfamily Lutrinae, inhabit aquatic environments, which include the almost exclusively aquatic sea otters (Enhydra lutris). Thus, the transition from a terrestrial to an aquatic lifestyle has occurred within this family. Despite potentially different selection pressures on body size in aquatic and terrestrial habitats, no divergence in the evolutionary pattern of body size between otters and other mustelids has previously been shown using models of trait evolution on a phylogeny. We applied models that explicitly incorporated lineage-specific directional selection to the evolution of body mass in living mustelids. Using a simulation-based likelihood and approximate Bayesian computation approach, we demonstrated lineage-specific directional selection for larger body mass in otters, which is distinct from other mustelids. There was no evidence of a difference between sea otters and other otters in the strength of directional selection for larger body mass. Additionally, our analyses supported no difference in the rate at which body mass evolves in both directions between otters and other mustelids. These findings suggest that the evolution of body mass in otters is associated with selective advantages of larger size rather than the relaxation of constraints on body size in aquatic habitats, like other aquatic mammals such as sirenians, cetaceans, and pinnipeds.

README: Data from: Body size evolution in otters distinguished from terrestrial mustelids

Code files

The codes stored in this repository were used to run Markov chain Monte Carlo (MCMC) computations using a simulation-based likelihood. The parameters of the evolutionary models described in the article were estimated from the posterior distributions of the parameters obtained by running five independent MCMC chains. The codes were written in the C language, and the computations were performed using a MacPro (OS 10.6.7, 2 × 2.93 GHz Quad-Core Intel Xeon).

(1) First model directional selection_phylo1_MCMC_code.c

This file contains the code used to estimate the parameters of the first model with directional selection using the phylogenetic tree provided in the file entitled "Phylogeny_phylo1.txt".

The parameter descriptions displayed when this code is run are as follows:

MRCA: the trait value for the most recent common ancestor of all species, denoted as θ0 in the article.

sel: the effect of branch-specific directional selection in all branches of Lutrinae, denoted as drslOTT in the article.

ev_change: the background evolutionary rate in a Brownian motion (BM)-like model across the phylogeny, denoted as μ0 in the article.

(2) Second model directional selection_phylo1_MCMC_code.c

This file contains the code used to estimate the parameters of the second model with directional selection using the phylogenetic tree provided in the file entitled "Phylogeny_phylo1.txt".

The parameter descriptions displayed when this code is run are as follows:

MRCA: the trait value for the most recent common ancestor of all species, denoted as θ0 in the article.

sel: the effect of branch-specific directional selection in the branches of Lutrinae except for the terminal branch reaching the sea otter, denoted as drslOTT in the article.

sel_2: the effect of branch-specific directional selection in the terminal branch reaching the sea otter, denoted as drslSEA in the article.

ev_change: the background evolutionary rate in a BM-like model across the phylogeny, denoted as μ0 in the article.

(3) Model different evolutionary rates_phylo1_MCMC_code.c

This file contains the code used to estimate the parameters of the model with different evolutionary rates using the phylogenetic tree provided in the file entitled "Phylogeny_phylo1.txt".

The parameter descriptions displayed when this code is run are as follows:

MRCA: the trait value for the most recent common ancestor of all species, denoted as θ0 in the article.

ev_change: the evolutionary rate in a BM-like model in the branches of the phylogeny except for Lutrinae, denoted as μTER in the article.

ev_change_2: the evolutionary rate in a BM-like model in all branches of Lutrinae, denoted as μOTT in the article.

(4) First model directional selection_phylo2_MCMC_code.c

This file contains the code used to estimate the parameters of the first model with directional selection using the alternative phylogenetic tree provided in the file entitled "Alternative_phylogeny _phylo2.txt".

The parameter descriptions displayed when this code is run are as follows:

MRCA: the trait value for the most recent common ancestor of all species, denoted as θ0 in the article.

sel: the effect of branch-specific directional selection in all branches of Lutrinae, denoted as drslOTT in the article.

ev_change: the background evolutionary rate in a BM-like model across the phylogeny, denoted as μ0 in the article.

(5) Second model directional selection_phylo2_MCMC_code.c

This file contains the code used to estimate the parameters of the second model with directional selection using the alternative phylogenetic tree provided in the file entitled "Alternative_phylogeny _phylo2.txt".

The parameter descriptions displayed when this code is run are as follows:

MRCA: the trait value for the most recent common ancestor of all species, denoted as θ0 in the article.

sel: the effect of branch-specific directional selection in the branches of Lutrinae except for the terminal branch reaching the sea otter, denoted as drslOTT in the article.

sel_2: the effect of branch-specific directional selection in the terminal branch reaching the sea otter, denoted as drslSEA in the article.

ev_change: the background evolutionary rate in a BM-like model across the phylogeny, denoted as μ0 in the article.

(6) Model different evolutionary rates_phylo2_MCMC_code.c

This file contains the code used to estimate the parameters of the model with different evolutionary rates using the alternative phylogenetic tree provided in the file entitled "Alternative_phylogeny _phylo2.txt".

The parameter descriptions displayed when this code is run are as follows:

MRCA: the trait value for the most recent common ancestor of all species, denoted as θ0 in the article.

ev_change: the evolutionary rate in a BM-like model in the branches of the phylogeny except for Lutrinae, denoted as μTER in the article.

ev_change_2: the evolutionary rate in a BM-like model in all branches of Lutrinae, denoted as μOTT in the article.

Phylogenetic tree files

The phylogenetic trees used in this study can be viewed in the files stored in this repository. The phylogenetic trees in Newick format are provided in the following files.

(7) Phylogeny_phylo1.txt

This file contains the phylogenetic tree of the mustelid species used in this study, as shown in Figure 1 in the article.

(8) Alternative_phylogeny_phylo2.txt

This file contains the alternative phylogenetic tree of the mustelid species used in this study, as shown in Supporting information Figure S1 in the article.