DOI: 10.5061/dryad.f7m0cfxsj
title: Diversification history of clown tree frogs in Neotropical rainforests (Anura, Hylidae, Dendropsophus leucophyllatus group)

description: General consensus emphasizes that no single biological process can explain
 the patterns of species’ distributions and diversification in the
 Neotropics. Instead, the interplay of several processes across space and
 time must be taken into account. Here we investigated the phylogenetic
 relationships and biogeographic history of tree frogs in the Dendropsophus
 leucophyllatus species group (Amphibia: Hylidae), which is distributed
 across Amazonia and the Atlantic rainforests. Using Next Generation
 Sequencing (NGS) and double digest restriction-site associated DNA
 (ddRADseq), we inferred phylogenetic relationships, species limits, and
 temporal and geographic patterns of diversification relative to the
 history of these biomes. Our results indicate that the D. leucophyllatus
 species group includes at least 14 independent lineages, which are
 currently arranged into ten described species. Therefore, a significant
 portion of species in the group are still unnamed. Different processes
 were associated to the group diversification history. For instance, the
 Andes uplift likely caused allopatric speciation for Cis-Andean species,
 whereas it may also be responsible for changes in the Amazonian landscape
 triggering parapatric speciation by local adaptation to ecological
 factors. Meanwhile, Atlantic Forest ancestors unable to cross the dry
 diagonal biomes after the rainforest’s retraction, evolved in isolation
 into different species. Diversification in the group began in the early
 Miocene, when connections between Atlantic Forest and the Andes (Pacific
 Dominion) by way of a south corridor were possible. The historical
 scenario in Amazonia, characterized by several speciation events and
 habitat heterogeneity, helped promoting species diversification, resulting
 in the highest species diversity for the group. This marked species
 diversification did not happen in Atlantic Forest, where speciation is
 very recent (late Pliocene and Pleistocene), despite its remarkable
 climatic heterogeneity.
description: We
 collected genomic data from 196 specimens representing ten of 14 currently
 recognized species of the <i>Dendropsophus leucophyllatus</i>
 group (we failed to sample <i>D. manonegra</i>, <i>D.
 salli</i>,<i> D. vraemi</i>, and<i> D.
 nekronastes</i>), sampled from 100 localities distributed in the
 Neotropical rainforests (see Appendix A, Table A1), plus three outgroup
 taxa: <i>D. minutus</i>, <i>D. anceps</i> and
 <i>D. marmoratus</i>. All species were represented by at least
 two individuals from each locality; except for <i>D.
 leucophyllatus</i> and <i>D. triangulum</i> for which at
 least six individuals were collected from each locality in order to better
 infer the lineages limits and relationships within these taxa. The
 complete list of samples used in this study is provided in Appendix A
 (Table A1). Genomic DNA was
 extracted from muscle or liver samples of each individual using a Qiagen
 DNeasy Blood and Tissue Kit and following manufacturer’s protocol. Two
 reduced representation libraries were constructed using the Double Digest
 Restriction Associated DNA Sequencing approach (ddRADseq) following the
 protocol from Peterson et al. (2012). DNA was double digested with
 restriction enzymes <i>EcoR1</i> and <i>MseI</i>.
 Unique barcodes (10 bp) and Illumina adaptors were ligated to the digested
 fragments. Individuals were pooled together for each library and DNA
 fragments between 350–450 bp were size selected using Pippin Prep (Sage
 Science). Fragments were amplified by PCR, with 8 cycles. After each step,
 we performed a cleanup using AMPure beads (1.6x, except after Pippin Prep)
 and quantified the material with Qubit high sensitivity assay. Libraries
 were sequenced in an Illumina 2500 platform at the Center for Applied
 Genomics (Toronto, Canada) to generate 150 bp single-end reads.
description: The upload files here are the input files used for all the
 analyses used in this manuscript.