Research Article |
Corresponding author: H. Mauricio Ortega-Andrade ( mauricio.ortega@ikiam.edu.ec ) Academic editor: Robert Whittaker
© 2024 Arjen A. W. van der Kamp, H. Mauricio Ortega-Andrade.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
van der Kamp AAW, Ortega-Andrade HM (2024) Phylogeny, historical biogeography and climate niche differentiation in extant species of Ceratophryidae (Anura, Hyloidea) frogs in South America. Frontiers of Biogeography 17: e132672. https://doi.org/10.21425/fob.17.132672
|
Ceratophryidae is a family of frogs containing twelve extant species distributed in South America. Several studies have been carried out concerning the systematics, morphology, karyotypes, and behaviour within this monophyletic family. However, little is known about the historical biogeography and the divergence in time of this group. Here, we present an updated phylogeny, along with a calibrated chronogram, to analyse the historical biogeographical pattern and climate niche differentiation among extant species of Ceratophryidae (Anura: Hyloidea) frogs in South America. A phylogeny based on morphological and genetic data was obtained from 256 morphological characters, six mitochondrial and eight nuclear genes for up to a total of 8428 characters in the homological matrix. Our results indicate that the genus Ceratophrys is sister to the clade Chacophrys + Lepidobatrachus. The divergence of the crown group of Ceratophryidae is estimated to have occurred 19.2 Ma at the beginning of the Miocene, with recent cladogenetic events related to the late Miocene (10.18–13.70 Ma) and the Pliocene (~5.3–2.6 Ma). Moreover, the Cerrado region is estimated to be the ancestral area of the family, as well for the genera Chacophrys and Lepidobatrachus. In addition, temperature seasonality and annual precipitation play a major role in the niche differentiation of extant species within Ceratophryidae. In conclusion, our data suggest multiple dispersal and vicariance events originating from the Cerrado region in the early Miocene, and recognize the role of the environment in the differentiation of the ecological niches among extant species of this family in South America.
Ceratophryidae is hypothesized to have originated in the semi-arid Cerrado region in the early Miocene (~19.2 million years ago), from where species have diversified by independent dispersal and vicariance events across other South American regions.
Ceratophrys frogs are phylogenetically recovered as the sister taxon to the clade comprising Chacophrys and Lepidobatrachus.
Three lineages of Lepidobatrachus and four lineages from Ceratophrys diverged in the Pliocene, around 5.3 to 2.6 million years ago.
Niche differentiation among extant species of Ceratophryidae appears to reflect roles for temperature seasonality and annual precipitation.
ancestral area reconstruction, biogeography, Ceratophrys, Cerrado, Chacophrys, chronogram, divergence time estimation, Lepidobatrachus, precipitation, seasonality
Ceratophryidae
(Anura: Hyloidea) (
Herpetologists have for a long time been interested in the biology of Ceratophryidae, for ecological, morphological and behavioural reasons. For example, larva from Ceratophryidae have an unique mechanism for sound production underwater (
The fossil records of Ceratophryidae have undergone extensive examination. Various studies have attempted to estimate the divergence times within Ceratophryidae. Notably,
Several studies have delved into evolutionary radiations through phylogenetic analysis at a biogeographical scale in amphibians (
We aim to investigate the phylogeny, historical biogeographic pattern and climate niche differentiation in extant species of Ceratophryidae (Anura: Hyloidea) frogs in South America. We focus on the following research questions: (1) How are the three genera of Ceratophryidae phylogenetically related to each other based on morphological and genetic characters? (2) What are the divergence times of species within the Ceratophryidae family? (3) What is the biogeographical ancestral area of Ceratophryidae species in South America? (4) Which environmental variable(s) play a major role in niche differentiation among extant species of Ceratophryidae?
Data from eleven of the twelve frog species of the family Ceratophryidae are included. Ceratophrys testudo was excluded, as this species has not been collected since the holotype (
The phylogenetic tree of Ceratophryidae was constructed by first analysing a concatenated matrix with 8172 bp DNA sequences from GenBank. The six mitochondrial gene sequences used include portions of cytochrome oxidase subunit I (COI) gene, cytochrome b (cytb) gene, 12S rRNA gene, the intermediate partition sequence tRNAVal gene, 16S rRNA gene and NADH dehydrogenase subunit 1 (ND1) gene. The eight nuclear gene sequences include the Seven In Absentia Homolog 1 (SIAH1) gene, Tyrosinase precursor (TYR) gene, Recombination activating protein 1 (RAG-1) gene, Ribosomal protein L3 (RPL3) gene, Proopiomelanocortin A (POMC) gene, Chemokine receptor 4 (CXCR4) gene, lactose dehydrogenase beta chain gene (lactose_dh) and Fibrinogen A alpha polypeptide gene (fib_A) (Suppl. material
Genes were selected based on the number of species with available sequences in GenBank (https://www.ncbi.nlm.nih.gov/genbank/; accessed in March 2023). Sequences for every gene were separately aligned with the MAFFT v.7.450 (
IQ-TREE v.1.6.12 (
We employed BEAST v. 2.7.4 (
Two independent runs were made, and sampled values were joined and analysed for convergence. Tracer v.1.7.2 (
The divergence time reconstruction inferred for the phylogenies is the key input for biogeographical analysis (
The maximum number of areas in ancestral ranges was restricted to three, in accordance with the current distributional range codified for each species across the designated regions. We estimated the probabilities of ancestral areas for each node, drawing from a subset comprising 1000 randomly selected trees in RASP v.4.4., utilizing the chronogram and trees derived from BEAST2 software as input files (
Biogeographic map for species in the Ceratophryidae family. (A) Map of South America with convex hull polygons representing the occurrences for every species of Ceratophrys. (B) The Gran Chaco region with convex hull polygons that represent the occurrences for species of Lepidobatrachus and Chacophrys.
The nineteen bioclimatic variables were downloaded from the WorldClim2 database (http://www.worldclim.com/version2; accessed in December 2023), with a 30 seconds (~1 km2) spatial resolution (
The genetic and the combined analysis (genetic + morphology) show a similar phylogeny, where the monophyly of Ceratophrys, Chacophrys and Lepidobatrachus is well supported for Ceratophryidae (Fig.
Estimates of relative contributions of the environmental variables by Jackknife test for extant Ceratophryidae species in South America. Blue colors correspond to high percentage of environmental importance of variables, green are medium values and white are lower values.
Bioclimatic variables | Ceratophrys aurita | Ceratophrys calcarata | Ceratophrys cornuta | Ceratophrys cranwelli | Ceratophrys joazeirensis | Ceratophrys ornata | Ceratophrys stolzmanni | Chacophrys pierottii | Lepidobatrachus asper | Lepidobatrachus laevis | Lepidobatrachus llanensis |
BIO1 = Annual Mean Temperature | 5.2 | 2.7 | 1.1 | 0.2 | 6.6 | 4.3 | 0 | 0 | 0 | 0 | 0.4 |
BIO2 = Mean Diurnal Range | 8.6 | 0.2 | 1.4 | 0.1 | 0 | 0.7 | 4.8 | 0 | 0.3 | 0 | 0.1 |
BIO3 = Isothermality (BIO2/BIO7) (×100) | 6.9 | 2.9 | 15.3 | 0.8 | 0 | 11.1 | 0 | 0.4 | 0 | 0 | 0.8 |
BIO4 = Temperature Seasonality (standard deviation ×100) | 45.7 | 0.3 | 3.7 | 55.2 | 0.8 | 54.9 | 1.2 | 50.6 | 46.6 | 47.4 | 47.3 |
BIO5 = Max Temperature of Warmest Month | 0.1 | 2.8 | 0.7 | 5.7 | 0 | 0.1 | 0.1 | 11.1 | 16.4 | 31.7 | 12.4 |
BIO6 = Min Temperature of Coldest Month | 0 | 3.9 | 1.1 | 0.2 | 0 | 0.1 | 1.1 | 0.3 | 0 | 0 | 0 |
BIO7 = Temperature Annual Range (BIO5-BIO6) | 0 | 0.6 | 0.2 | 0 | 0 | 0.2 | 30.2 | 0.2 | 0.4 | 0 | 0.7 |
BIO8 = Mean Temperature of Wettest Quarter | 0 | 1.1 | 0.6 | 12.1 | 0 | 3.3 | 0.1 | 22.2 | 24.6 | 0.4 | 17.8 |
BIO9 = Mean Temperature of Driest Quarter | 0 | 2.4 | 4.8 | 0.1 | 7.9 | 0.1 | 0 | 0.1 | 0.6 | 0 | 0 |
BIO10 = Mean Temperature of Warmest Quarter | 0 | 0.5 | 2.8 | 2.2 | 0 | 3.3 | 0 | 0.2 | 0.2 | 0 | 0.5 |
BIO11 = Mean Temperature of Coldest Quarter | 0 | 64.7 | 2 | 0 | 13.2 | 0.1 | 0.2 | 0 | 0 | 0 | 0 |
BIO12 = Annual Precipitation | 0 | 0.5 | 2.8 | 0 | 37.8 | 0.6 | 2.1 | 0.3 | 1.8 | 0.7 | 0.2 |
BIO13 = Precipitation of Wettest Month | 0 | 0.2 | 2.7 | 0.3 | 0 | 0.1 | 0.5 | 0 | 1.8 | 0.6 | 0 |
BIO14 = Precipitation of Driest Month | 29 | 0.2 | 31 | 0.2 | 0 | 14.1 | 0.8 | 7.7 | 0 | 4.6 | 0.1 |
BIO15 = Precipitation Seasonality (Coefficient of Variation) | 1.7 | 1.1 | 0.4 | 11.6 | 0 | 0.6 | 17.7 | 2.3 | 1.2 | 0.7 | 8.5 |
BIO16 = Precipitation of Wettest Quarter | 0 | 7.4 | 21.7 | 0.1 | 0 | 0 | 0 | 0.2 | 0 | 0 | 0 |
BIO17 = Precipitation of Driest Quarter | 0 | 5.5 | 0.1 | 0.3 | 32.1 | 0 | 0 | 0 | 0.9 | 0.2 | 0 |
BIO18 = Precipitation of Warmest Quarter | 0.1 | 0.1 | 4.6 | 10.3 | 0 | 6.2 | 8.2 | 0.2 | 4.5 | 13 | 4.1 |
BIO19 = Precipitation of Coldest Quarter | 2.7 | 2.8 | 2.9 | 0.6 | 1.8 | 0.2 | 32.9 | 4.2 | 0.6 | 0.6 | 7 |
The divergence times are shown in Table
Ancestral Area Reconstruction for extant species of Ceratophryidae in South America. A dispersal-extinction-cladogenesis model (DEC) for Ceratophryidae reconstructed with RASP v.4.4. software. The condensed tree is a chronogram based on 10,001 trees derived from genetic data reconstructed by Bayesian inference analysis in BEAST2 for Ceratophryidae. Biogeographical region categories are based on
Time of divergence in Ceratophryidae. Results by node numbers (shown in Fig.
Node number | Clade | UFB | Height | 95% HPD |
---|---|---|---|---|
1 | Outgroup | N/A | 131.79 | - |
2 | Outgroup | N/A | 71.67 | 66.36–77.01 |
3 | Outgroup | N/A | 64.08 | 59.26–68.83 |
4 | Outgroup | N/A | 54.78 | 39.84–66.50 |
5 | Ceratophryidae | 100 | 19.18 | 14.72–24.05 |
6 | Chacophrys + Lepidobatrachus | 91 | 13.70 | 8.15–19.50 |
7 | Lepidobatrachus | 100 | 4.95 | 4.00–6.47 |
8 | Lepidobatrachus | 100 | 3.46 | 2.03–5.01 |
9 | Ceratophrys | 96 | 17.16 | 12.53–21.74 |
10 | Ceratophrys | 100 | 10.38 | 5.12–15–78 |
11 | Ceratophrys | 82 | 14.71 | 10.41–19.20 |
12 | Ceratophrys | 100 | 10.18 | 6.67–13.90 |
13 | Ceratophrys | 100 | 4.84 | 2.08–8.16 |
14 | Ceratophrys | 100 | 4.24 | 4.00–4.72 |
The Dispersal-extinction-cladogenesis model (DEC = –30.38 lnL; AICc = 65.76; AICc_wt = 39%) was the best among other biogeographical models (Table
Comparative statistics of biogeographic models. Abbreviations: -lnL = log-likelihood; d = dispersal rate; e = extinction rate; j = founder-event speciation; AICc = corrected Akaike Information Criterion; AICc_wt = weighted AICc percentage values; DEC = Dispersal Extinction Cladogenesis model; DIVALIKE = BioGeoBEARS implementation of DIVA model; BAYAREALIKE = BioGeoBEARS implementation of BayArea model.
Model | -lnL | d | e | j | AICc | AICc_wt |
---|---|---|---|---|---|---|
DEC | -30.38 | 0.021 | 0.44 | 0 | 65.76 | 39% |
DEC+J | -30.35 | 0.024 | 0.66 | 0.00001 | 68.88 | 8% |
DIVALIKE | -30.69 | 0.015 | 0.21 | 0 | 66.38 | 29% |
DIVALIKE+J | -30.36 | 0.013 | 0.28 | 0.025 | 68.9 | 8% |
BAYAREALIKE | -31.93 | 0.012 | 0.16 | 0 | 68.85 | 8% |
BAYAREALIKE+J | -30.51 | 0.011 | 0.27 | 0.041 | 69.2 | 7% |
The Jackknife resampling test shows the environmental importance of Temperature Seasonality (BIO4) for several species of Ceratophryidae (C. aurita, C. cranwelli, C. ornata, Ch. pierottii, L. asper, L. laevis and L. llanensis). Mean Temperature of Coldest Quarter (BIO11) is environmentally important for C. calcarata, Precipitation of Driest month (BIO14) for C. cornuta, Annual Precipitation (BIO12) for C. joazeirensis and Precipitation of Coldest Quarter (BIO19) for C. stolzmanni (Table
The environmental PCA analysis for Chacophrys and Lepidobatrachus displays overlap between the four species (Fig.
The pPCA shows that the first principal component has the greatest multivariate load from Precipitation Seasonality (BIO15, positive load) and overall precipitation (BIO12; negative load). The second PC is mostly accumulated by Temperature Seasonality (BIO4; negative load) and Isothermality (BIO3; positive load) and. C. cornuta is highly related with precipitation variables and Temperature seasonality, located far from all other members of this family in the environmental space (Fig.
Scatter plot of the Principal Components Analysis (PCA) and correlation matrix for the nineteen environmental variables from WorldClim2 for Ceratophryidae. PCA for extant (A) species of Chacophrys, Lepidobatrachus, and (B) Ceratophrys in South America. Values in the x-axis are the percentage of variance explained mostly by the principal component 1 (PC1) and on the y-axis principal component 2 (PC2). The colored dots represent individual occurrences per species in the PCA and are surrounded by 95% ellipses. (C) Correlation plot with positive (blue) or negative (red) direction that show the collinearity between environmental variables. Variables names are detailed in Table
Phylomorphospace of Phylogenetic Principal Components for extant Ceratophrys species in South America. (A) Phylogenetic PCA for Ceratophryidae species to represent the environmental niche differentiation data based on the phylogenetic chronogram. Tip colors indicate (B) Biogeographical region categories based on
We present for the first time a phylogeny based on both genetic and morphological characters, as well as a calibrated chronogram, to explore the historical biogeographic patterns and the evolutionary role of environmental variables in the diversification of Ceratophryidae in South America.
The phylogenetic tree (Fig.
All nodes within Lepidobatrachus in our phylogeny (Fig.
Our chronogram mostly agreed with previous studies in estimating divergence times in Anura, despite the inclusion of only a few representatives of Ceratophryidae in those analyses (
The ancestral area for Ceratophryidae reveals that the Cerrado (area A; Fig.
The node related with extant Ceratophrys species (node 9) has a high marginal probability to assign the Cerrado region as the ancestral area (A = 61.89%), but low probability to support the RASP route in the speciation events (10.5%; Table
Cocoon production is observed in all species of Ceratophryidae, but is unknown for the species C. testudo, C. calcarata and C. cornuta (
Three species of Ceratophrys (C. cornuta, C. calcarata and C. aurita) inhabit areas with a high average precipitation. C. cornuta is distributed in tropical humid environments, separated from all other species in the environmental space (Fig.
We present the first calibrated chronogram hypothesis, providing divergence time estimations for Ceratophryidae. Within this family, Ceratophrys emerges as the sister taxon to the clade comprising Chacophrys and Lepidobatrachus. Our chronogram revealed a pronounced surge in species radiation within this clade during the Miocene, around 19.2 million years ago (Ma). Notably, three lineages of Lepidobatrachus and four lineages from Ceratophrys diverged in the Pliocene, around 5.3 to 2.6 Ma. Ceratophryidae is hypothesized to have originated in the semi-arid Cerrado region, from where species have diversified by dispersal and vicariance events across other South American regions, exhibiting distinct environmental niches shaped by variation in temperature seasonality and annual precipitation in extant species. The biogeography, evolution, and niche adaptation of extant Ceratophryidae species are linked with their likely origin in semi-arid ecosystems in the Cerrado region, exhibiting marked temperature seasonality across South America (
Special thanks to Pim van Hooft for the supervision of this project. Also, many thanks to Andrea Belén Salgado-Revelo, Andersson David Ocampos-Valarezo, Walter Armando Quilumbaquin-Alba and María José Sánchez-Carvajal for their help with the technical issues and Angel Andrés Ojeda-Montesdeoca and Stan Vandenhouwe for providing useful comments. This work was supported by the following projects: “On the quest of the golden fleece in Amazonia: The first herpetological DNA - barcoding expedition to unexplored areas on the Napo watershed, Ecuador” (TWAS-16-095 RG/BIO/LA_I and SENESCYT-PIC-17-BENS-001) granted to HMOA, from The World Academy of Sciences and la Secretaría de Educación Superior, Ciencia, Tecnología e Innovación SENESCYT, and by Erasmus+ CBHE consortium “NB-lab” (Grant number: 619346-EPP-12020-1-DE-EPPKA2-CBHE-JP.
Conceptualization, methodology, formal analysis, investigation, validation, formal analysis, data curation, visualization, supervision, HMOA, AvdK; writing original draft preparation, AvdK, HMOA; writing—review and editing, AvdK, HMOA; project administration, funding acquisition, HMOA. Both authors have read and agreed to the published version of the manuscript and declared not conflict of interest.
Supplemental material is available in ZENODO repository.
fig. S1: Phylogeny base only in genetic data (.png)
table S3: Environmental data for Principal components analysis (.xlsx)
table S4: Phylogenetic Principal Components Analysis (.xlsx)
appendix S1: BEAUti (.xml) file with the chronogram model parameters (.xml)
appendix S2: RASP v.4.3 output of the ancestral area reconstruction (.docx)
appendix S3: Tree file of the calibrated chronogram by BEAST v. 2.7.4 (.tree)