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Admixture may be extensive among hyperdominant Amazon rainforest tree species

Citation

Larson, Drew; Vargas, Oscar; Vicentini, Alberto; Dick, Christopher W. (2021), Admixture may be extensive among hyperdominant Amazon rainforest tree species, Dryad, Dataset, https://doi.org/10.5061/dryad.fj6q573t4

Abstract

Admixture is a mechanism by which species of long-lived plants may acquire novel alleles. However, the potential role of admixture in the origin and maintenance of tropical plant diversity is unclear. We ask whether admixture occurs in an ecologically important clade of Eschweilera (Parvifolia clade, Lecythidaceae), which includes some of the most widespread and abundant tree species in Amazonian forests.

Using target capture sequencing, we conducted a detailed phylogenomic investigation of 33 species in the Parvifolia clade and investigated specific hypotheses of admixture within a robust phylogenetic framework. We assembled target loci from raw sequence reads, conducted tree-based paralog trimming, and estimated species trees using maximum likelihood approaches. In addition, we called single nucleotide polymorphisms for members of the Parvifolia clade and used a Bayesian clustering approach to estimate the ancestry of individuals. We distinguished between population structure and evidence of admixture using a test based on rooted gene trees. We also investigated overlap in geographical range, phenology, and morphology of species, including those we found to admix.

We found strong evidence of admixture among three ecologically dominant species, E. coriacea, E. wachenheimii and E. parviflora, but a lack of evidence for admixture among other lineages. Accepted species were largely distinguishable from one another, as was geographic structure within species.

We show that hybridization may play a role in the evolution of the most widespread and ecologically variable Amazonian tree species. While admixture occurs among some species of Eschweilera, it has not led to widespread erosion of most species’ genetic or morphological identities. Therefore, current morphological based species circumscriptions appear to provide a useful characterization of the clade’s lineage diversity.

Usage Notes

The dataset is organized according to the major types of analyses conducted:

Map Information about datasets used to produce maps
SNP_calling Files relating to calling single nucleotide polymorphisms
Trimming_and_assembly Files related to read trimming and gene assembly
Phenology Dataset on flowering times
RT_tests Input and output files related to rooted triplet tests
STRUCTURE Input and output files related to Bayesian clustering analyses
R_scripts_and_plotting Input data for R scripts
Tree_analyses Files related to various stages of tree based analyses, including species trees

Please see the included README file for further details.

Funding

Conselho Nacional de Desenvolvimento Científico e Tecnológico, Award: AEX 01300.006387/2017‐42

Instituto Nacional de Pesquisas da Amazônia