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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

oalescent-based species delimitation meets deep learning: Insights from a highly fragmented cactus syste

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Author(s):
Perez, Manolo F. [1, 2] ; Bonatelli, Isabel A. S. [1, 3] ; Romeiro-Brito, Monique [1] ; Franco, Fernando F. [1] ; Taylor, Nigel P. [4] ; Zappi, Daniela C. [5] ; Moraes, Evandro M. [1]
Total Authors: 7
Affiliation:
[1] Univ Fed Sao Carlos, Dept Biol, Sorocaba - Brazil
[2] Univ Fed Sao Carlos, Dept Genet & Evolucao, Sao Carlos - Brazil
[3] Univ Fed Sao Paulo, Dept Ecol & Biol Evolut, Diadema - Brazil
[4] Univ Gibraltar, The Alameda - Gibraltar
[5] Univ Brasilia, Inst Ciencias Biol, Programa Pos Grad Bot, Brasilia, DF - Brazil
Total Affiliations: 5
Document type: Journal article
Source: MOLECULAR ECOLOGY RESOURCES; v. 22, n. 3 OCT 2021.
Web of Science Citations: 0
Abstract

Delimiting species boundaries is a major goal in evolutionary biology. An increasing volume of literature has focused on the challenges of investigating cryptic diversity within complex evolutionary scenarios of speciation, including gene flow and demographic fluctuations. New methods based on model selection, such as approximate Bayesian computation, approximate likelihoods, and machine learning are promising tools arising in this field. Here, we introduce a framework for species delimitation using the multispecies coalescent model coupled with a deep learning algorithm based on convolutional neural networks (CNNs). We compared this strategy with a similar ABC approach. We applied both methods to test species boundary hypotheses based on current and previous taxonomic delimitations as well as genetic data (sequences from 41 loci) in Pilosocereus aurisetus, a cactus species complex with a sky-island distribution and taxonomic uncertainty. To validate our method, we also applied the same strategy on data from widely accepted species from the genus Drosophila. The results show that our CNN approach has a high capacity to distinguish among the simulated species delimitation scenarios, with higher accuracy than ABC. For the cactus data set, a splitter hypothesis without gene flow showed the highest probability in both CNN and ABC approaches, a result agreeing with previous taxonomic classifications and in line with the sky-island distribution and low dispersal of P. aurisetus. Our results highlight the cryptic diversity within the P. aurisetus complex and show that CNNs are a promising approach for distinguishing complex evolutionary histories, even outperforming the accuracy of other model-based approaches such as ABC. (AU)

FAPESP's process: 12/22857-8 - GENETIC STRUCTURE OF CACTACEAE SPECIES OF PILOSOCEREUS AURISETUS GROUP USING MICROSATELLITES MARKERS DEVELOPED BY NEXT GENERATION SEQUENCING
Grantee:Isabel Aparecida da Silva Bonatelli
Support Opportunities: Scholarships in Brazil - Doctorate
FAPESP's process: 15/06160-5 - Phylogeny of the Pilosocereus genus (Cactaceae) and coalescent-based species delimitation in the Pilosocereus aurisetus group using multilocus data
Grantee:Evandro Marsola de Moraes
Support Opportunities: Regular Research Grants
FAPESP's process: 12/22943-1 - Multiloci phylogeography of PILOSOCEREUS AURISETUS group (Cactaceae)
Grantee:Manolo Fernandez Perez
Support Opportunities: Scholarships in Brazil - Doctorate