DOI: 10.5061/dryad.zkh1893pf
title: Data from: Distinctive increase in offspring size in sea otters: evolutionary changes in and beyond the trade-off against offspring number

description: Offspring size and number, key fitness components, are expected to evolve
 under a trade-off between them. In mammals, the evolution of larger
 offspring size may be promoted in aquatic environments, where the
 selective advantages of large body size are more pronounced than in
 terrestrial environments. A transition from a fully terrestrial to an
 aquatic lifestyle has occurred within the family Mustelidae (Mammalia:
 Carnivora). Sea otters (Enhydra lutris) are unique in this family for
 giving birth in water, with offspring living almost exclusively in the
 aquatic environment. Controlling for phylogeny and adult body mass, we
 identified a trade-off between neonate mass and litter size (i.e.,
 offspring number per litter) across species in the Mustelidae. Using
 models of trait evolution on the phylogeny of this family, we revealed
 lineage-specific directional selection in sea otters favoring larger
 neonate mass and smaller litter size relative to adult mass. These results
 support the unique evolution of larger offspring size in sea otters,
 resulting in a decreased litter size through the trade-off. Furthermore,
 we revealed lineage-specific directional selection in sea otters favoring
 larger total litter mass relative to adult mass, as well as larger neonate
 mass after excluding the effect of the trade-off against litter size.
 Lineage-specific directional selection in sea otters favoring larger
 neonate mass and litter mass cannot be solely attributed to the prolonged
 gestation period. This study suggests that sea otters have undergone
 distinctive evolutionary changes, investing more resources in offspring
 size than can be allocated merely by reducing offspring number.
description: # Data from:Distinctive increase in offspring size in sea otters:
 evolutionary changes in and beyond the trade-off against offspring number
 **Short summary of the study** Controlling for phylogeny and adult body
 mass, we identified the trade-off between neonate mass and litter size
 across the family Mustelidae. Using models of trait evolution on the
 phylogeny, we revealed lineage-specific directional selection in sea
 otters favoring larger neonate mass and smaller litter size relative to
 adult mass, which deviates from the evolutionary patterns observed for
 each trait across the Mustelidae. Furthermore, we revealed
 lineage-specific directional selection in sea otters favoring larger total
 litter mass relative to adult mass, as well as larger neonate mass even
 after excluding the effect of the trade-off against litter size.
 Lineage-specific directional selection in sea otters favoring larger
 neonate mass and litter mass cannot be solely attributed to the prolonged
 gestation period. Our findings suggest that sea otters have undergone
 distinctive evolutionary changes in the trade-offs among life history
 traits. ## Data description The phylogenetic tree, data and code files
 used to conduct the analyses in the article with the above-mentioned title
 are stored in this repository. ### Phylogenetic tree files The
 phylogenetic trees in Newick format are provided in the following files.
 These files were used when running the codes described in the file
 entitled "PGLS_R_code_Sea_otter_lifehistory_evolution.txt" in R
 version 4.2.2. (1) phylo1_Sea_otter_lifehistory_evolution.txt This file
 contains the primary tree of the mustelid species used in this study, as
 shown in Figure 1 in the article. (2)
 phylo2_Sea_otter_lifehistory_evolution.txt This file contains the
 alternative tree of the mustelid species used in this study, as shown in
 Supplementary Figure S1 in the article. ### Data and code files used to
 conduct phylogenetic generalized least squares (PGLS) analyses (3)
 Dataset_Sea_otter_lifehistory_evolution.csv This file contains the dataset
 of the traits used when running the codes described in the file entitled
 "PGLS_R_code_Sea_otter_lifehistory_evolution.txt" in R version
 4.2.2. The variable descriptions are as follows: * Species: species
 scientific names, corresponding to those in the phylogenetic trees given
 in the file entitled "Phylogeny_phylo1.txt" and
 "Phylogeny_phylo2.txt" * Adult_mass: Adult body mass (g) *
 Neonate_mass: Neonate body mass (g) * Litter_size: Litter size *
 Litter_mass: Litter mass, which was calculated as neonate mass multiplied
 by litter size * Gestation_period: Gestation period (days) (4)
 PGLS_R_code_Sea_otter_lifehistory_evolution This file contains the codes
 to run the following PGLS models (A-N) in R version 4.2.2. (A) PGLS model
 used to examine the relationship between adult mass and neonate mass using
 the primary tree. The results are shown in Table 1A in the article. (B)
 PGLS model used to examine the relationship between adult mass and litter
 size using the primary tree. The results are shown in Table 1B in the
 article. (C) PGLS model used to examine the relationship between adult
 mass and litter mass using the primary tree. The results are shown in
 Table 1C in the article. (D) PGLS model used to examine the relationship
 between adult mass and gestation period using the primary tree. The
 results are shown in Table 1D in the article. (E) PGLS model used to
 examine the trade-off relationships between neonate mass and litter size
 after controlling for adult body mass using the primary tree. The results
 are shown in Table 2A in the article. (F) PGLS model used to examine the
 relationship between neonate mass and gestation period while controlling
 for adult body mass using the primary tree. The results are shown in Table
 2B in the article. (G) PGLS model used to examine the relationship between
 litter mass and gestation period while controlling for adult body mass
 using the primary tree. The results are shown in Table 2C in the article.
 (H) PGLS model used to examine the relationship between adult mass and
 neonate mass using the alternative tree. The results are shown in
 Supplementary Table S2A in the article. (I) PGLS model used to examine the
 relationship between adult mass and litter size using the alternative
 tree. The results are shown in Supplementary Table S2B in the article. (J)
 PGLS model used to examine the relationship between adult mass and litter
 mass using the alternative tree. The results are shown in Supplementary
 Table S2C in the article. (K) PGLS model used to examine the relationship
 between adult mass and gestation period using the alternative tree. The
 results are shown in Supplementary Table S2D in the article. (L) PGLS
 model used to examine the trade-off relationships between neonate mass and
 litter size after controlling for adult body mass using the alternative
 tree. The results are shown in Supplementary Table S3A in the article. (M)
 PGLS model used to examine the relationship between neonate mass and
 gestation period while controlling for adult body mass using the
 alternative tree. The results are shown in Supplementary Table S3B in the
 article. (N) PGLS model used to examine the relationship between litter
 mass and gestation period while controlling for adult body mass using the
 alternative tree. The results are shown in Supplementary Table S3C in the
 article. * Packages and software R version 4.2.2 R Development Core Team.
 2022. R: a language and environment for statistical computing. R
 Foundation for Statistical Computing, Vienna.
 [https://www.R-project.org](https://www.R-project.org). ape package in R
 Paradis E, Schliep K. 2018 ape 5.0: an environment for modern
 phylogenetics and evolutionary analyses in R. Bioinformatics 35, 526–528.
 nlme package in R Pinheiro J, Bates D, DebRoy S, Sarkar D, R Core Team.
 2019 nlme: Linear and Nonlinear Mixed Effects Models. R package version
 3.1–141. ### Code files used to conduct an approach that combined
 simulation-based likelihood and approximate Bayesian computation (ABC) The
 following files contain codes to run Markov chain Monte Carlo (MCMC)
 computations using the approximate likelihood based on the simulation of
 trait evolution. 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). The parameter descriptions displayed when these
 codes are run are as follows: * MRCA: the trait value for the most recent
 common ancestor of all species, denoted as θ0 in the article. * drsl_OTT:
 the effect of lineage-specific directional selection in the branches of
 Lutrinae except for the terminal branch leading to the sea otter, denoted
 as drslOTT in the article. * drsl_SEA: the effect of lineage-specific
 directional selection in the terminal branch leading to the sea otter,
 denoted as drslSEA in the article. * mu_0: the background evolutionary
 rate in a Brownian motion (BM)-like model across the phylogeny, denoted as
 μ0 in the article. 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. (5)
 Neonate_mass_phylo1_MCMC_code.c This file contains the code used to
 estimate the parameters in the analysis of lineage-specific directional
 selection in the evolution of neonate mass relative to adult mass using
 the primary tree. Parameter estimation results are summarized in Table 3A
 in the article. (6) Litter_size_phylo1_MCMC_code.c This file contains the
 code used to estimate the parameters in the analysis of lineage-specific
 directional selection in the evolution of litter size relative to adult
 mass using the primary tree. Parameter estimation results are summarized
 in Table 3B in the article. (7) Litter_mass_phylo1_MCMC_code.c This file
 contains the code used to estimate the parameters in the analysis of
 lineage-specific directional selection in the evolution of litter mass
 relative to adult mass using the primary tree. Parameter estimation
 results are summarized in Table 3C in the article. (8)
 Gestation_period_phylo1_MCMC_code.c This file contains the code used to
 estimate the parameters in the analysis of lineage-specific directional
 selection in the evolution of gestation period relative to adult mass
 using the primary tree. Parameter estimation results are summarized in
 Table 3D in the article. (9)
 Neonate_mass_corrected_for_litter_size_phylo1_MCMC_code.c This file
 contains the code used to estimate the parameters in the analysis of
 lineage-specific directional selection in the evolution of neonate mass
 corrected for adult mass and litter size using the primary tree. Parameter
 estimation results are summarized in Table 3E in the article. (10)
 Neonate_mass_corrected_for_gestation_phylo1_MCMC_code.c This file contains
 the code used to estimate the parameters in the analysis of
 lineage-specific directional selection in the evolution of neonate mass
 corrected for adult mass and gestation period using the primary tree.
 Parameter estimation results are summarized in Table 3F in the article.
 (11) Litter_mass_corrected_for_gestation_phylo1_MCMC_code.c This file
 contains the code used to estimate the parameters in the analysis of
 lineage-specific directional selection in the evolution of neonate mass
 corrected for adult mass and gestation period using the primary tree.
 Parameter estimation results are summarized in Table 3G in the article.
 (12) Neonate_mass_phylo2_MCMC_code.c This file contains the code used to
 estimate the parameters in the analysis of lineage-specific directional
 selection in the evolution of neonate mass relative to adult mass using
 the alternative tree. Parameter estimation results are summarized in
 Supplementary Table S4A in the article. (13)
 Litter_size_phylo2_MCMC_code.c This file contains the code used to
 estimate the parameters in the analysis of lineage-specific directional
 selection in the evolution of litter size relative to adult mass using the
 alternative tree. Parameter estimation results are summarized in
 Supplementary Table S4B in the article. (14)
 Litter_mass_phylo2_MCMC_code.c This file contains the code used to
 estimate the parameters in the analysis of lineage-specific directional
 selection in the evolution of litter mass relative to adult mass using the
 alternative tree. Parameter estimation results are summarized in
 Supplementary Table S4C in the article. (15)
 Gestation_period_phylo2_MCMC_code.c This file contains the code used to
 estimate the parameters in the analysis of lineage-specific directional
 selection in the evolution of gestation period relative to adult mass
 using the alternative tree. Parameter estimation results are summarized in
 Supplementary Table S4D in the article. (16)
 Neonate_mass_corrected_for_litter_size_phylo2_MCMC_code.c This file
 contains the code used to estimate the parameters in the analysis of
 lineage-specific directional selection in the evolution of neonate mass
 corrected for adult mass and litter size using the alternative tree.
 Parameter estimation results are summarized in Supplementary Table S4E in
 the article. (17) Neonate_mass_corrected_for_gestation_phylo2_MCMC_code.c
 This file contains the code used to estimate the parameters in the
 analysis of lineage-specific directional selection in the evolution of
 neonate mass corrected for adult mass and gestation period using the
 alternative tree. Parameter estimation results are summarized in
 Supplementary Table S4F in the article. (18)
 Litter_mass_corrected_for_gestation_phylo2_MCMC_code.c This file contains
 the code used to estimate the parameters in the analysis of
 lineage-specific directional selection in the evolution of neonate mass
 corrected for adult mass and gestation period using the alternative tree.
 Parameter estimation results are summarized in Supplementary Table S4G in
 the article.