DOI: 10.5061/dryad.qv9s4mwnd
title: Patterns in the genetic structure of 49 lowland rain forest tree species co-distributed on opposite sides of the Northern Andes

description: The Andes are a major dispersal barrier for lowland rain forest plants and
 animals, yet hundreds of lowland tree species are distributed on both
 sides of the Northern Andes, raising questions about how the Andes
 influenced their biogeographic histories and population genetic structure.
 To explore these questions, we generated standardized datasets of
 thousands of SNPs from paired populations of 49 tree species
 co-distributed in rain forest tree communities located in Panama and
 Amazonian Ecuador and calculated genetic diversity (π) and absolute
 genetic divergence (dXY) within and between populations, respectively. We
 predicted (1) higher genetic diversity in the ancestral source region
 (east or west of the Andes) for each taxon, and (2) correlation of genetic
 statistics with species attributes, including elevational range and
 life-history strategy. We found that genetic diversity was higher in
 putative ancestral source regions, possibly reflecting founder events
 during colonization. We found little support for a relationship between
 genetic divergence and species attributes except that species with higher
 elevational range limits exhibited higher dXY, implying older divergence
 times. One possible explanation for this pattern is that dispersal through
 mountain passes declined in importance relative to dispersal via
 alternative lowland routes as the Andes experienced uplift. We found no
 difference in mean genetic diversity between populations in Central
 America and the Amazon. Overall, our results suggest that dispersal across
 the Andes has left enduring signatures in the genetic structure of
 widespread rain forest trees. We outline additional hypotheses to be
 tested with species-specific case studies.
description: The data consist of called genotypes of single nucleotide
 polymorphisms (SNPs) for 49 tropical rain forest tree species. Individuals
 were sampled from Yasuni, Ecuador and Barro Colorado Island (BCI), Panama,
 and sequenced using a double-digest Restriction-Associated DNA (ddRAD)
 approach. Data are presented as standard Variant Call Format
 (VCF) files.
description: # Patterns in the genetic structure of 49 lowland rain forest tree species
 co-distributed on opposite sides of the northern Andes
 ## Description of the data
 and file structure The data consist of called genotypes of single
 nucleotide polymorphisms (SNPs) for 49 tropical rain forest tree species.
 Individuals were sampled from Yasuni, Ecuador and Barro Colorado Island
 (BCI), Panama, and sequenced using a double-digest Restriction-Associated
 DNA (ddRAD) approach. Data are presented as standard Variant Call Format
 (VCF) files. Each VCF file contains genotype data for a single species
 from two populations (Ecuador and Panama). The VCF files are named as
 XXXXXX.vcf, where XXXXXX is a six-character code for each species. Species
 codes are provided at the end of this document. Within the VCF file, the
 individual samples (listed at the end of the header lines beginning with
 #) are named as XXXXXX_YY_ZZZ where: * XXXXXX is the six-character species
 code * YY is one of [EC, PA], denoting that the sample is from Ecuador or
 Panama, respectively * ZZZ is a three-digit internal lab code denoting
 extraction number (not meaningful for analysis) The six-digit species
 codes are as follows: CODE GENUS SPECIFIC_EPITHET FAMILY ANDIIN Andira
 inermis Fabaceae APEIME Apeiba membranacea Malvaceae APEITI Apeiba
 tibourbou Malvaceae ASTRGR Astronium graveolens Anacardiaceae CASEAC
 Casearia aculeata Salicaceae CASEAR Casearia arborea Salicaceae CASESY
 Casearia sylvestris Salicaceae CEIBPE Ceiba pentandra Malvaceae CELTSC
 Celtis schippii Cannabaceae CINNTR Cinnamomum triplinerve Lauraceae CUPACI
 Cupania cinerea Sapindaceae DENDAR Dendropanax arboreus Araliaceae DIOSAR
 Diospyros artanthifolia Ebenaceae ERYTMA Erythroxylum macrophyllum
 Erythroxylaceae FICUMA Ficus maxima Moraceae GUARGR Guarea grandifolia
 Meliaceae HASSFL Hasseltia floribunda Salicaceae INGAMA Inga marginata
 Fabaceae INGANO Inga nobilis Fabaceae INGAPU Inga punctata Fabaceae INGARU
 Inga ruiziana Fabaceae INGASA Inga sapindoides Fabaceae INGASP Inga
 spectabilis Fabaceae INGATH Inga thibaudiana Fabaceae INGAUM Inga
 umbellifera Fabaceae JACACO Jacaranda copaia Bignoniaceae LACIAG Lacistema
 aggregatum Lacistemataceae LAETPR Laetia procera Salicaceae MARGNO
 Margaritaria nobilis Phyllanthaceae MICOEL Miconia elata Melastomataceae
 NECTLI Nectandra lineata Lauraceae OCOTOB Ocotea oblonga Lauraceae PALIGU
 Palicourea guianensis Rubiaceae PEREXA Perebea xanthochyma Moraceae PIPEAE
 Piper aequale Piperaceae PIPEAR Piper arboreum Piperaceae PIPERE Piper
 reticulatum Piperaceae PLATPI Platymiscium pinnatum Fabaceae POSOLA
 Posoqueria latifolia Rubiaceae POULAR Poulsenia armata Moraceae POURBI
 Pourouma bicolor Urticaceae POUTRE Pouteria reticulata Sapotaceae PTERRO
 Pterocarpus rohrii Fabaceae STERAP Sterculia apetala Malvaceae TREMMI
 Trema micrantha Cannabaceae TRICPA Trichilia pallida Meliaceae TURPOC
 Turpinia occidentalis Staphyleaceae URERBA Urera baccifera Urticaceae
 VISMBA Vismia baccifera Hypericaceae