10.5061/DRYAD.F7M0CFXSJ
Pirani, Renata
0000-0002-0241-7278
University of Nevada Reno
Peloso, Pedro
Universidade Federal do Pará
Prado, Joyce
University of Sao Paulo
Polo, Érico
Federal University of Amazonas
Knowles, Lacey
University of Michigan–Ann Arbor
Ron, Santiago
Pontificia Universidad Católica del Ecuador
Rodrigues, Miguel
University of Sao Paulo
Sturaro, Marcelo
Federal University of Sao Paulo
Werneck, Fernanda
Instituto Nacional de Pesquisas da Amazônia
Diversification history of clown tree frogs in Neotropical rainforests
(Anura, Hylidae, Dendropsophus leucophyllatus group)
Dryad
dataset
2020
National Council for Scientific and Technological Development
https://ror.org/03swz6y49
400770/2014-8
National Council for Scientific and Technological Development
https://ror.org/03swz6y49
475559/2013-4
National Council for Scientific and Technological Development
https://ror.org/03swz6y49
140088/2018-0
Conselho Nacional de Desenvolvimento Científico e Tecnológico- Science
without borders*
2014/22444-0
Society of Systematic Biologists
https://ror.org/0575b2v60
Graduate Student Research Award 2017
Society for the Study of Evolution
https://ror.org/057kr0a20
2017 Travel Award
National Council for Scientific and Technological Development
https://ror.org/03swz6y49
400252/2014-7
National Council for Scientific and Technological Development
https://ror.org/03swz6y49
BJT 313680/2014-0
National Council for Scientific and Technological Development
https://ror.org/03swz6y49
PQ 302501/2019-3
National Council for Scientific and Technological Development
https://ror.org/03swz6y49
PDJ 150279/2015-9
National Council for Scientific and Technological Development
https://ror.org/03swz6y49
150406/2016-9
National Council for Scientific and Technological Development
https://ror.org/03swz6y49
475559/2013-4
National Council for Scientific and Technological Development
https://ror.org/03swz6y49
425571/2018-1
National Council for Scientific and Technological Development
https://ror.org/03swz6y49
Productivity fellowship PQ 305535/2017-0
Coordenação de Aperfeicoamento de Pessoal de Nível Superior
https://ror.org/00x0ma614
88881.169862/2018-01
Fundação de Amparo à Pesquisa do Estado do Amazonas
https://ror.org/026d6ma13
062.00665/2015
Fundação de Amparo à Pesquisa do Estado do Amazonas
https://ror.org/026d6ma13
062.01110/2017
Fundação de Amparo à Pesquisa do Estado do Amazonas
https://ror.org/026d6ma13
062.00962/2018
National Academy of Sciences
https://ror.org/038mfx688
Enhanced Engagement in Research from the U.S. National Academy of
Sciences and U.S. Agency of International Development-PEER NAS/USAID *
AID-OAA-A-11-00012
L’Oreal-UNESCO For Women In Science Program*
Brazil 2016 and IRT 2017
National Council for Scientific and Technological Development
https://ror.org/03swz6y49
2003/10335-8
São Paulo Research Foundation
https://ror.org/02ddkpn78
BIOTA [2013/50297‐0
National Council for Scientific and Technological Development
https://ror.org/03swz6y49
2011/50146-6
National Council for Scientific and Technological Development
https://ror.org/03swz6y49
2013/50297-0
National Science Foundation
https://ror.org/021nxhr62
DEB 1343578
Secretaría de Educación Superior, Ciencia, Tecnología e Innovación
https://ror.org/056c6e777
Arca de Noé Initiative
L’Oreal-UNESCO For Women In Science Program
Brazil 2016 and IRT 2017
2020-09-21T00:00:00Z
2020-09-21T00:00:00Z
en
https://doi.org/10.1016/j.ympev.2020.106877
https://doi.org/10.1016/j.ympev.2020.106877
4695514 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
We collected genomic data from 196 specimens representing ten of 14
currently recognized species of the Dendropsophus leucophyllatus group (we
failed to sample D. manonegra, D. salli, D. vraemi, and D. nekronastes),
sampled from 100 localities distributed in the Neotropical rainforests
(see Appendix A, Table A1), plus three outgroup taxa: D. minutus, D.
anceps and D. marmoratus. All species were represented by at least two
individuals from each locality; except for D. leucophyllatus and D.
triangulum 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 EcoR1 and
MseI. 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.
The upload files here are the input files used for all the analyses used
in this manuscript.