DOI: 10.5061/dryad.2jm63xsvt
title: Data from: Body size evolution in otters distinguished from terrestrial mustelids

description: 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.
description: # 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.