1 Motivation & goals

This document contains the analyses for the manuscript “Putting the energetic-savings hypothesis underground: fossorial and non-fossorial amphibians have similar metabolic rates” by Danilo Giacometti and Glenn Tattersall.

In this study, our main goal to test whether fossorial amphibians evolved reduced metabolic rates compared to non-fossorial and aquatic ones. To do so, we collated a dataset of amphibian metabolic rates (VO2) measured across a range of temperatures (5, 10, 15, 20, and 25 ºC). We classified the species in our dataset as fossorial, non-fossorial, or aquatic based on species-specific descriptions of habitat usage available in the literature. Within a Bayesian framework, we control for temperature, body mass, and phylogenetic effects over VO2 to test the extent to which lifestyle affects metabolism in Amphibians.


2 Packages

library(ape)
library(geiger)
library(phytools)
library(picante)
library(nlme)
library(ggplot2)
library(ggbeeswarm)
library(pander)
library(kableExtra)
library(tidyverse)
library(Thermimage)
library(caper)
library(nlme)
library(cowplot)
library(gridExtra)
library(fitdistrplus)
library(grid)
library(AICcmodavg)
library(phyr)
library(car)
library(ggridges)
library(rr2)
library(forecast)
library(EBImage)
library(ggtree)
library(ggpubr)
library(gmodels)

3 Standardised theme for plots

Function by Glenn Tattersall

ggtheme <- function(base_size=12, base_line=0.3) {
  theme(
    
    text =        element_text(size=base_size),
    line =        element_line(size=base_line, linetype="solid"),
    
    axis.text.x = element_text(size=base_size*0.8, colour='black',  hjust=0.5, vjust=1, angle=0),
    axis.text.y = element_text(size=base_size*0.8, colour='black', hjust=1, vjust=0.5, angle=0),
    axis.line.x = element_line(size=base_line),
    axis.line.y = element_line(size=base_line),
    
    axis.title.x =  element_text(size = base_size, vjust = 1, margin=unit(c(3,0,0,0),"mm")),
    axis.title.y =  element_text(size = base_size, angle = 90, vjust = 0.5, margin=unit(c(0,3,0,0),"mm")),
    axis.ticks = element_line(size=base_line),
    axis.ticks.length = unit(0.3, "lines"),
    
    panel.background = element_blank(),
    panel.grid.minor = element_blank(),
    panel.grid.major = element_blank(),
    panel.border     = element_rect(fill=NA, colour=NA, size=base_line),
    panel.spacing    = unit(1, "lines"),
    
    legend.background = element_rect(fill="transparent", colour="transparent"),
    legend.key =       element_rect(fill="transparent", colour="transparent"),
    legend.text=       element_text(size=base_size),
    
    strip.background =  element_blank(),
    strip.text.x =      element_text(size = base_size * 0.8),
    strip.text.y =      element_text(size = base_size * 0.8, angle = -90),
    strip.switch.pad.grid = unit(0, "mm"),
    strip.switch.pad.wrap = unit(0, "mm"),
    
    plot.margin =       unit(c(0.5, 0.5, 0.5, 0.5), "cm"),
    plot.title =        element_text(size = base_size * 1.2),
    plot.background =   element_rect(colour = "transparent", fill="transparent", size=base_line)
  )}


4 Dataset

4.1 Metabolic rates

This spreadsheet contains whole-organism rates of oxygen consumption (V̇O2; mL O2/h at) at rest of Amphibian species reported in Feder & Burggren (1992), papers that have cited this book chapter until 2022, and papers that were published after the synthesis by Kreiman et al. 2019.

d <- read.csv("VO2-across-temps.csv")

d$Order<-as.factor(d$Order)
d$Lifestyle<-as.factor(d$Lifestyle)
d$Lifestyle<-relevel(d$Lifestyle, ref="Non-fossorial")
d$Lifestyle2<-as.factor(d$Lifestyle2)
d$Lifestyle2<-relevel(d$Lifestyle2, ref="Non-fossorial")
d$Microhabitat<-as.factor(d$Microhabitat)
d$Microhabitat<-relevel(d$Microhabitat, ref="Aquatic")
d$TemperatureCont<-as.numeric(d$Temperature)
d$Temperature<-as.factor(d$Temperature)

str(d)
## 'data.frame':    563 obs. of  14 variables:
##  $ Species        : chr  "Acris_crepitans" "Acris_crepitans" "Acris_crepitans" "Acris_crepitans" ...
##  $ Family         : chr  "Hylidae" "Hylidae" "Hylidae" "Hylidae" ...
##  $ Order          : Factor w/ 3 levels "Anura","Caudata",..: 1 1 1 1 1 1 1 1 1 1 ...
##  $ Latitude       : num  35.2 35.2 35.2 35.2 35.2 ...
##  $ Longitude      : num  -83.5 -83.5 -83.5 -83.5 -83.5 ...
##  $ AbsLat         : num  35.2 35.2 35.2 35.2 35.2 ...
##  $ Temperature    : Factor w/ 5 levels "5","10","15",..: 1 3 3 3 3 3 5 5 5 4 ...
##  $ VO2            : num  0.0459 0.0335 0.0612 0.0838 0.1155 ...
##  $ BodyMass       : num  1.94 0.5 0.9 1.27 1.5 ...
##  $ VO2Mass        : num  0.0237 0.067 0.068 0.066 0.077 ...
##  $ Lifestyle      : Factor w/ 2 levels "Non-fossorial",..: 1 1 1 1 1 1 1 1 1 1 ...
##  $ Lifestyle2     : Factor w/ 3 levels "Non-fossorial",..: 1 1 1 1 1 1 1 1 1 1 ...
##  $ Microhabitat   : Factor w/ 4 levels "Aquatic","Arboreal",..: 4 4 4 4 4 4 4 4 4 2 ...
##  $ TemperatureCont: num  5 15 15 15 15 15 25 25 25 20 ...
kable(d) %>% kable_styling() %>% scroll_box(width = "100%", height = "500px")
Species Family Order Latitude Longitude AbsLat Temperature VO2 BodyMass VO2Mass Lifestyle Lifestyle2 Microhabitat TemperatureCont
Acris_crepitans Hylidae Anura 35.22 -83.540 35.22 5 0.04590 1.9350 0.0237209 Non-fossorial Non-fossorial Terrestrial 5
Acris_crepitans Hylidae Anura 35.22 -83.540 35.22 15 0.03350 0.5000 0.0670000 Non-fossorial Non-fossorial Terrestrial 15
Acris_crepitans Hylidae Anura 35.22 -83.540 35.22 15 0.06120 0.9000 0.0680000 Non-fossorial Non-fossorial Terrestrial 15
Acris_crepitans Hylidae Anura 35.22 -83.540 35.22 15 0.08380 1.2700 0.0659843 Non-fossorial Non-fossorial Terrestrial 15
Acris_crepitans Hylidae Anura 35.22 -83.540 35.22 15 0.11550 1.5000 0.0770000 Non-fossorial Non-fossorial Terrestrial 15
Acris_crepitans Hylidae Anura 35.22 -83.540 35.22 15 0.11800 1.7350 0.0680115 Non-fossorial Non-fossorial Terrestrial 15
Acris_crepitans Hylidae Anura 35.22 -83.540 35.22 25 0.11700 0.5000 0.2340000 Non-fossorial Non-fossorial Terrestrial 25
Acris_crepitans Hylidae Anura 35.22 -83.540 35.22 25 0.25350 1.5000 0.1690000 Non-fossorial Non-fossorial Terrestrial 25
Acris_crepitans Hylidae Anura 35.22 -83.540 35.22 25 0.32880 1.8550 0.1772507 Non-fossorial Non-fossorial Terrestrial 25
Agalychnis_callidryas Hylidae Anura 15.15 -87.440 15.15 20 0.33700 5.6500 0.0596460 Non-fossorial Non-fossorial Arboreal 20
Agalychnis_callidryas Hylidae Anura 15.15 -87.440 15.15 20 0.34770 5.7000 0.0610000 Non-fossorial Non-fossorial Arboreal 20
Allobates_talamancae Aromobatidae Anura 8.90 -83.530 8.90 20 0.02500 0.8700 0.0287356 Non-fossorial Non-fossorial Terrestrial 20
Ambystoma_gracile Ambystomatidae Caudata 47.94 -124.230 47.94 15 0.63520 30.3900 0.0209016 Fossorial Fossorial Fossorial 15
Ambystoma_jeffersonianum Ambystomatidae Caudata 43.12 -79.950 43.12 15 0.31580 8.9200 0.0354036 Fossorial Fossorial Fossorial 15
Ambystoma_macrodactylum Ambystomatidae Caudata 49.59 -121.370 49.59 15 0.10980 3.4100 0.0321994 Fossorial Fossorial Fossorial 15
Ambystoma_macrodactylum Ambystomatidae Caudata 49.59 -121.370 49.59 15 0.45140 3.7000 0.1220000 Fossorial Fossorial Fossorial 15
Ambystoma_maculatum Ambystomatidae Caudata 47.75 -78.680 47.75 5 0.31570 13.1000 0.0240992 Fossorial Fossorial Fossorial 5
Ambystoma_maculatum Ambystomatidae Caudata 47.75 -78.680 47.75 5 0.36310 11.7500 0.0309021 Fossorial Fossorial Fossorial 5
Ambystoma_maculatum Ambystomatidae Caudata 47.75 -78.680 47.75 10 0.58750 11.7500 0.0500000 Fossorial Fossorial Fossorial 10
Ambystoma_maculatum Ambystomatidae Caudata 47.75 -78.680 47.75 10 0.60450 11.9000 0.0507983 Fossorial Fossorial Fossorial 10
Ambystoma_maculatum Ambystomatidae Caudata 47.75 -78.680 47.75 15 0.36250 15.8300 0.0228996 Fossorial Fossorial Fossorial 15
Ambystoma_maculatum Ambystomatidae Caudata 47.75 -78.680 47.75 15 1.23960 11.7500 0.1054979 Fossorial Fossorial Fossorial 15
Ambystoma_maculatum Ambystomatidae Caudata 47.75 -78.680 47.75 15 1.31990 13.4000 0.0985000 Fossorial Fossorial Fossorial 15
Ambystoma_maculatum Ambystomatidae Caudata 47.75 -78.680 47.75 20 0.05180 0.5120 0.1011719 Fossorial Fossorial Fossorial 20
Ambystoma_maculatum Ambystomatidae Caudata 47.75 -78.680 47.75 25 1.54400 11.7500 0.1314043 Fossorial Fossorial Fossorial 25
Ambystoma_maculatum Ambystomatidae Caudata 47.75 -78.680 47.75 25 1.67700 12.9000 0.1300000 Fossorial Fossorial Fossorial 25
Ambystoma_mexicanum Ambystomatidae Caudata 19.14 -98.980 19.14 20 0.96140 43.7000 0.0220000 Non-fossorial Aquatic Aquatic 20
Ambystoma_opacum Ambystomatidae Caudata 34.87 -83.690 34.87 15 0.46400 5.8000 0.0800000 Fossorial Fossorial Fossorial 15
Ambystoma_talpoideum Ambystomatidae Caudata 32.97 -87.240 32.97 15 0.56000 7.0000 0.0800000 Fossorial Fossorial Fossorial 15
Ambystoma_tigrinum Ambystomatidae Caudata 36.27 -115.030 36.27 5 0.27600 23.0000 0.0120000 Fossorial Fossorial Fossorial 5
Ambystoma_tigrinum Ambystomatidae Caudata 36.27 -115.030 36.27 10 0.88950 15.0000 0.0593000 Fossorial Fossorial Fossorial 10
Ambystoma_tigrinum Ambystomatidae Caudata 36.27 -115.030 36.27 15 0.13800 10.7800 0.0128015 Fossorial Fossorial Fossorial 15
Ambystoma_tigrinum Ambystomatidae Caudata 36.27 -115.030 36.27 15 1.32130 16.4900 0.0801274 Fossorial Fossorial Fossorial 15
Ambystoma_tigrinum Ambystomatidae Caudata 36.27 -115.030 36.27 15 1.54840 35.0000 0.0442400 Fossorial Fossorial Fossorial 15
Ambystoma_tigrinum Ambystomatidae Caudata 36.27 -115.030 36.27 25 0.89100 8.1000 0.1100000 Fossorial Fossorial Fossorial 25
Ambystoma_tigrinum Ambystomatidae Caudata 36.27 -115.030 36.27 25 1.56750 14.9000 0.1052013 Fossorial Fossorial Fossorial 25
Ambystoma_tigrinum Ambystomatidae Caudata 36.27 -115.030 36.27 25 1.78850 35.0000 0.0511000 Fossorial Fossorial Fossorial 25
Ambystoma_tigrinum Ambystomatidae Caudata 36.27 -115.030 36.27 25 1.97800 23.0000 0.0860000 Fossorial Fossorial Fossorial 25
Ambystoma_tigrinum Ambystomatidae Caudata 36.27 -115.030 36.27 25 3.19080 16.4900 0.1934991 Fossorial Fossorial Fossorial 25
Amietia_delalandii Pyxicephalidae Anura -26.25 27.580 26.25 20 6.83830 15.6525 0.4368823 Non-fossorial Aquatic Aquatic 20
Amietophrynus_rangeri Bufonidae Anura -28.88 27.140 28.88 20 8.95850 69.0990 0.1296473 Non-fossorial Non-fossorial Terrestrial 20
Amphiuma_means Amphiumidae Caudata 31.83 -82.520 31.83 5 0.88400 352.0000 0.0025114 Non-fossorial Aquatic Aquatic 5
Amphiuma_means Amphiumidae Caudata 31.83 -82.520 31.83 5 1.65000 500.0000 0.0033000 Non-fossorial Aquatic Aquatic 5
Amphiuma_means Amphiumidae Caudata 31.83 -82.520 31.83 10 2.80000 500.0000 0.0056000 Non-fossorial Aquatic Aquatic 10
Amphiuma_means Amphiumidae Caudata 31.83 -82.520 31.83 15 2.51300 408.0000 0.0061593 Non-fossorial Aquatic Aquatic 15
Amphiuma_means Amphiumidae Caudata 31.83 -82.520 31.83 15 2.53100 375.0000 0.0067493 Non-fossorial Aquatic Aquatic 15
Amphiuma_means Amphiumidae Caudata 31.83 -82.520 31.83 15 3.10000 500.0000 0.0062000 Non-fossorial Aquatic Aquatic 15
Amphiuma_means Amphiumidae Caudata 31.83 -82.520 31.83 20 2.32400 83.0000 0.0280000 Non-fossorial Aquatic Aquatic 20
Amphiuma_means Amphiumidae Caudata 31.83 -82.520 31.83 20 5.05000 500.0000 0.0101000 Non-fossorial Aquatic Aquatic 20
Amphiuma_means Amphiumidae Caudata 31.83 -82.520 31.83 25 5.03800 376.0000 0.0133989 Non-fossorial Aquatic Aquatic 25
Amphiuma_means Amphiumidae Caudata 31.83 -82.520 31.83 25 9.25000 500.0000 0.0185000 Non-fossorial Aquatic Aquatic 25
Amphiuma_tridactylum Amphiumidae Caudata 32.54 -91.120 32.54 15 2.45200 652.0000 0.0037607 Non-fossorial Aquatic Aquatic 15
Amphiuma_tridactylum Amphiumidae Caudata 32.54 -91.120 32.54 25 9.86000 493.0000 0.0200000 Non-fossorial Aquatic Aquatic 25
Anaxyrus_americanus Bufonidae Anura 46.86 -80.510 46.86 5 0.60810 25.2000 0.0241310 Non-fossorial Non-fossorial Terrestrial 5
Anaxyrus_americanus Bufonidae Anura 46.86 -80.510 46.86 15 2.09340 19.0000 0.1101789 Non-fossorial Non-fossorial Terrestrial 15
Anaxyrus_americanus Bufonidae Anura 46.86 -80.510 46.86 20 1.37770 27.0000 0.0510259 Non-fossorial Non-fossorial Terrestrial 20
Anaxyrus_americanus Bufonidae Anura 46.86 -80.510 46.86 20 1.38000 27.0300 0.0510544 Non-fossorial Non-fossorial Terrestrial 20
Anaxyrus_americanus Bufonidae Anura 46.86 -80.510 46.86 20 1.39000 50.0000 0.0278000 Non-fossorial Non-fossorial Terrestrial 20
Anaxyrus_americanus Bufonidae Anura 46.86 -80.510 46.86 25 2.58730 21.1000 0.1226209 Non-fossorial Non-fossorial Terrestrial 25
Anaxyrus_americanus Bufonidae Anura 46.86 -80.510 46.86 25 2.93710 40.4000 0.0727005 Non-fossorial Non-fossorial Terrestrial 25
Anaxyrus_boreas Bufonidae Anura 36.41 -106.700 36.41 5 4.09080 72.7000 0.0562696 Non-fossorial Non-fossorial Terrestrial 5
Anaxyrus_boreas Bufonidae Anura 36.41 -106.700 36.41 10 0.55480 40.2000 0.0138010 Non-fossorial Non-fossorial Terrestrial 10
Anaxyrus_boreas Bufonidae Anura 36.41 -106.700 36.41 10 0.62440 47.3000 0.0132008 Non-fossorial Non-fossorial Terrestrial 10
Anaxyrus_boreas Bufonidae Anura 36.41 -106.700 36.41 10 0.72830 57.8000 0.0126003 Non-fossorial Non-fossorial Terrestrial 10
Anaxyrus_boreas Bufonidae Anura 36.41 -106.700 36.41 15 3.87060 68.7000 0.0563406 Non-fossorial Non-fossorial Terrestrial 15
Anaxyrus_boreas Bufonidae Anura 36.41 -106.700 36.41 20 0.25000 2.5000 0.1000000 Non-fossorial Non-fossorial Terrestrial 20
Anaxyrus_boreas Bufonidae Anura 36.41 -106.700 36.41 20 1.05200 57.8000 0.0182007 Non-fossorial Non-fossorial Terrestrial 20
Anaxyrus_boreas Bufonidae Anura 36.41 -106.700 36.41 20 1.30250 40.2000 0.0324005 Non-fossorial Non-fossorial Terrestrial 20
Anaxyrus_boreas Bufonidae Anura 36.41 -106.700 36.41 20 2.31770 47.3000 0.0490000 Non-fossorial Non-fossorial Terrestrial 20
Anaxyrus_boreas Bufonidae Anura 36.41 -106.700 36.41 25 2.64000 27.3000 0.0967033 Non-fossorial Non-fossorial Terrestrial 25
Anaxyrus_boreas Bufonidae Anura 36.41 -106.700 36.41 25 5.58120 53.8000 0.1037398 Non-fossorial Non-fossorial Terrestrial 25
Anaxyrus_cognatus Bufonidae Anura 36.92 -103.970 36.92 5 1.27920 45.2000 0.0283009 Fossorial Non-fossorial Terrestrial 5
Anaxyrus_cognatus Bufonidae Anura 36.92 -103.970 36.92 10 1.97900 39.5800 0.0500000 Fossorial Non-fossorial Terrestrial 10
Anaxyrus_cognatus Bufonidae Anura 36.92 -103.970 36.92 15 3.84810 50.5000 0.0762000 Fossorial Non-fossorial Terrestrial 15
Anaxyrus_cognatus Bufonidae Anura 36.92 -103.970 36.92 20 4.47250 39.5800 0.1129990 Fossorial Non-fossorial Terrestrial 20
Anaxyrus_cognatus Bufonidae Anura 36.92 -103.970 36.92 25 2.95870 40.2000 0.0735995 Fossorial Non-fossorial Terrestrial 25
Anaxyrus_debilis Bufonidae Anura 29.88 -102.510 29.88 15 0.08450 0.6600 0.1280303 Fossorial Non-fossorial Terrestrial 15
Anaxyrus_terrestris Bufonidae Anura 31.91 -83.540 31.91 5 0.65270 21.4000 0.0305000 Non-fossorial Non-fossorial Terrestrial 5
Anaxyrus_terrestris Bufonidae Anura 31.91 -83.540 31.91 15 1.33600 16.6000 0.0804819 Non-fossorial Non-fossorial Terrestrial 15
Anaxyrus_terrestris Bufonidae Anura 31.91 -83.540 31.91 15 7.50000 102.0000 0.0735294 Non-fossorial Non-fossorial Terrestrial 15
Anaxyrus_terrestris Bufonidae Anura 31.91 -83.540 31.91 20 15.10000 102.0000 0.1480392 Non-fossorial Non-fossorial Terrestrial 20
Anaxyrus_terrestris Bufonidae Anura 31.91 -83.540 31.91 25 2.24250 19.8000 0.1132576 Non-fossorial Non-fossorial Terrestrial 25
Anaxyrus_terrestris Bufonidae Anura 31.91 -83.540 31.91 25 30.42000 102.0000 0.2982353 Non-fossorial Non-fossorial Terrestrial 25
Anaxyrus_woodhousii Bufonidae Anura 37.93 -103.400 37.93 10 1.27390 67.4000 0.0189006 Fossorial Non-fossorial Terrestrial 10
Anaxyrus_woodhousii Bufonidae Anura 37.93 -103.400 37.93 15 2.72550 69.0000 0.0395000 Fossorial Non-fossorial Terrestrial 15
Anaxyrus_woodhousii Bufonidae Anura 37.93 -103.400 37.93 20 4.41290 64.8000 0.0681003 Fossorial Non-fossorial Terrestrial 20
Anaxyrus_woodhousii Bufonidae Anura 37.93 -103.400 37.93 25 1.01700 9.0000 0.1130000 Fossorial Non-fossorial Terrestrial 25
Anaxyrus_woodhousii Bufonidae Anura 37.93 -103.400 37.93 25 2.23000 56.3000 0.0396092 Fossorial Non-fossorial Terrestrial 25
Aneides_ferreus Plethodontidae Caudata 43.67 -123.160 43.67 15 0.07430 2.7300 0.0272161 Fossorial Fossorial Fossorial 15
Aneides_ferreus Plethodontidae Caudata 43.67 -123.160 43.67 25 0.21180 3.2000 0.0661875 Fossorial Fossorial Fossorial 25
Aneides_flavipunctatus Plethodontidae