Cryptic diversity of a widespread global pathogen reveals expanded threats to amphibian conservation

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.Biodiversity loss is one major outcome of human-mediated ecosystem disturbance. One way that humans have triggered wildlife declines is by transporting disease-causing agents to remote areas of the world. Amphibians have been hit particularly hard by disease due in part to a globally distributed pathogenic chytrid fungus (Batrachochytrium dendrobatidis [Bd]). Prior research has revealed important insights into the biology and distribution of Bd; however, there are still many outstanding questions in this system. Although we know that there are multiple divergent lineages of Bd that differ in pathogenicity, we know little about how these lineages are distributed around the world and where lineages may be coming into contact. Here, we implement a custom genotyping method for a global set of Bd samples. This method is optimized to amplify and sequence degraded DNA from noninvasive skin swab samples. We describe a divergent lineage of Bd, which we call BdASIA3, that appears to be widespread in Southeast Asia. This lineage co-occurs with the global panzootic lineage (BdGPL) in multiple localities. Additionally, we shed light on the global distribution of BdGPL and highlight the expanded range of another lineage, BdCAPE. Finally, we argue that more monitoring needs to take place where Bd lineages are coming into contact and where we know little about Bd lineage diversity. Monitoring need not use expensive or difficult field techniques but can use archived swab samples to further explore the history—and predict the future impacts—of this devastating pathogen

Data from: The evolution of reproductive diversity in Afrobatrachia: a phylogenetic comparative analysis of an extensive radiation of African frogs

The reproductive modes of anurans (frogs and toads) are the most diverse of terrestrial vertebrates, and a major challenge is identifying selective factors that promote the evolution or retention of reproductive modes across clades. Terrestrialized anuran breeding strategies have evolved repeatedly from the plesiomorphic fully aquatic reproductive mode, a process thought to occur through intermediate reproductive stages. Several selective forces have been proposed for the evolution of terrestrialized reproductive traits, but factors such as water systems and co-evolution with ecomorphologies have not been investigated. We examined these topics in a comparative phylogenetic framework using Afrobatrachian frogs, an ecologically and reproductively diverse clade representing more than half of the total frog diversity found in Africa (∼400 species). We infer direct development has evolved twice independently from terrestrialized reproductive modes involving subterranean or terrestrial oviposition, supporting evolution through intermediate stages. We also detect associations between specific ecomorphologies and oviposition sites, and demonstrate arboreal species exhibit an overall shift towards using lentic water systems for breeding. These results indicate that changes in microhabitat use associated with ecomorphology, which allow access to novel sites for reproductive behavior, oviposition, or larval development, may also promote reproductive mode diversity in anurans

Data from: Historical biogeography resolves the origins of endemic Arabian toad lineages (Anura: Bufonidae): evidence for ancient vicariance and dispersal events with the Horn of Africa and South Asia

Background: The Arabian Peninsula is home to a unique fauna that has assembled and evolved throughout the course of major geophysical events, including the separation of the Arabian Plate from Africa and subsequent collision with Eurasia. Opportunities for faunal exchanges with particular continents occurred in temporally distinct periods, and the presence of African, Western Eurasian, and South Asian derived taxa on the Arabian Peninsula signifies the complexity of these historical biogeographic events. The six true toad species (family Bufonidae) endemic to Arabian Peninsula present a considerable taxonomic and biogeographic challenge because they are part of a global bufonid radiation, including several genera surrounding the Arabian Peninsula, and difficult to discriminate morphologically. As they could be derived from African, Western Eurasian, or South Asian toad groups, elucidating their evolutionary relationships has important implications for historical biogeography. Here, we analyze a global molecular data set of 243 bufonid lineages, with an emphasis on new sampling from the Horn of Africa, Western Eurasia, South Asia, and the Arabian Peninsula, to reconstruct the evolutionary relationships of the Arabian species. We produce a robust time-calibrated phylogeny to infer the biogeographic history of this group on and around the Arabian Peninsula. Results: Our phylogenetic analyses indicate two of the endemic Arabian toad species, “Bufo” tihamicus and “Bufo” arabicus, evolved independently within the African genus Amietophrynus. We confirm the Arabian species Duttaphrynus dhufarensis is of South Asian origin, but do not find evidence for the Asian genus Duttaphrynus being present in the Horn of Africa, discrediting a previously proposed Asian bufonid dispersal event to Africa. We also do not find evidence of the African genus Amietophrynus occurring in South Asia, suggesting that unlike many other vertebrate taxa, toads have not used the Arabian Peninsula as a stepping-stone for trans-continental dispersal. Our divergence dating estimates strongly suggest the formation of the Red Sea drove simultaneous divergences between two of the Arabian species (A. tihamicus comb. nov. and A. arabicus comb. nov.) and their xclosest mainland African relatives in the Early Miocene. We estimate the divergence of D. dhufarensis with its closest South Asian relatives occurred in the mid to Late Miocene, suggesting the temporary or permanent land connections between the Arabian plate and Eurasia facilitated dispersal of this lineage to the Arabian Peninsula. Conclusions: The Arabian bufonid assemblage, despite being comparatively depauperate with respect to surrounding continents, exemplifies the faunal pattern of the Arabian Peninsula, namely being a complex admixture of African, Western Eurasian, and South Asian elements. The historical biogeographic patterns exhibited by Arabian toads and their allies are concordant with studies of other vertebrate taxa, building support for the role of major geological events in driving simultaneous vicariance and dispersal events around the Arabian Peninsula. Although many taxa or groups exhibiting disjunct Afro-Arabian distributions appear to have dispersed more recently from the Horn of Africa via a southern land bridge or overwater dispersal, both Amietophrynus tihamicus and A. arabicus likely represent true African relicts resulting from vicariance associated with the Red Sea formation, a pattern that so far is rare among the vertebrate species investigated

Power_Analyses_3_ConvertToBayesTraits&Inputs

Includes python script to convert simulation output files to BayesTraits binary input format (Simulation_Outputs_processing_for_BayesTraits.py). Instructions for usage and details of conversion are annotated at the top of the script. The results of this conversion process are in the directory "3_BayesTraits_inputs", which contains subdirectories of the relevant character comparisons, each with 500 input files. These subdirectories contain a tree file, and will need the "BayesTraitsV2" executable placed within. These subdirectories are the focus of the next bundle of scripts

SuperCRUNCH: A bioinformatics toolkit for creating and manipulating supermatrices and other large phylogenetic datasets

Phylogenies with extensive taxon sampling have become indispensable for many types of ecological and evolutionary studies. Many large-scale trees are based on a 'supermatrix' approach, which involves amalgamating thousands of published sequences for a group. Constructing up-to-date supermatrices can be challenging, especially as new sequences may become available almost constantly. Additionally, genomic datasets (composed of thousands of loci) are becoming common in phylogenetics and phylogeography, and present novel challenges for constructing such datasets. Here we present SuperCRUNCH, a Python toolkit for assembling large phylogenetic datasets. It can be applied to GenBank sequences, unpublished sequences or combinations of GenBank and unpublished data. SuperCRUNCH constructs local databases and uses them to conduct rapid searches for user-specified sets of taxa and loci. Sequences are parsed into putative loci and passed through rigorous filtering steps. A post-filtering step allows for selection of one sequence per taxon (i.e. species-level supermatrix) or retention of all sequences per taxon (i.e. population-level dataset). Importantly, SuperCRUNCH can generate 'vouchered' population-level datasets, in which voucher information is used to generate multi-locus phylogeographic datasets. SuperCRUNCH offers many options for taxonomy resolution, similarity filtering, sequence selection, alignment and file manipulation. We demonstrate the range of features available in SuperCRUNCH by generating a variety of phylogenetic datasets. Output datasets include traditional species-level supermatrices, large-scale phylogenomic matrices and phylogeographic datasets. Finally, we briefly compare the ability of SuperCRUNCH to construct species-level supermatrices relative to alternative approaches. SuperCRUNCH generated a large-scale supermatrix (1,400 taxa and 66 loci) from 16 GB of GenBank data in ~1.5 hr, and generated population-level datasets (<350 samples, <10 loci) in <1 min. It outperformed alternative methods for supermatrix construction in terms of taxa, loci and sequences recovered. SuperCRUNCH is a modular bioinformatics toolkit that can be used to assemble datasets for any taxonomic group and scale (kingdoms to individuals). It allows rapid construction of supermatrices, greatly simplifying the process of updating large phylogenies with new data. It is also designed to produce population-level datasets. SuperCRUNCH streamlines the major tasks required to process phylogenetic data, including filtering, alignment, trimming and formatting. SuperCRUNCH is open-source, documented and available at https://github.com/dportik/SuperCRUNCH.12 month embargo; published online: 11 April 2020This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Power_Analyses_2_SimulationResults

The resulting output files from the previous step. The directory contains 500 files, each with independent simulations for characters 1-4 (note number of states varies across characters) across all taxa included

Afrobatrachia_Sequence_Alignment

A nexus format sequence alignment of the five nuclear markers (FICD, KIAA2013, POMC, RAG1, TYR) and 16S data, along with relevant MrBayes style partitions and models defined. The alignment contains 186 taxa and 3700 bp

Analysis_3_exponential

Input file for BEAST v1.8.1 for Analysis 3