DOI: 10.5061/dryad.3k506
title: Data from: Impacts of selective logging on inbreeding and gene flow in two Amazonian timber species with contrasting ecological and reproductive characteristics

description: Selective logging in Brazil allows for the removal of up to 90% of trees
 above 50 cm diameter of a given timber species, independent of a species’
 life history characteristics or how quickly it will recover. The genetic
 and demographic effects of selective logging on two Amazonian timber
 species (Dipteryx odorata Leguminosae, Jacaranda copaia Bignoniaceae) with
 contrasting ecological and reproductive characteristics were assessed in
 the same forest. Genetic diversity and gene flow were characterized by
 genotyping adults and seed sampled before and after logging, using
 hypervariable microsatellite markers. Overall, there were no short term
 genetic impacts on the J. copaia population, with commercial application
 of current Brazilian forest management regulations. In contrast, for D.
 odorata selective logging showed a range of genetic impacts, with a 10%
 loss of alleles, and reductions in siring by pollen from trees within the
 546 ha study area (23% to 11%) and in the number of pollen donors per
 progeny array (2.8 to 1.6), illustrating the importance of the surrounding
 landscape. Asynchrony in flowering between D. odorata trees led to trees
 with no breeding partners, which could limit the species reproduction and
 regeneration under current regulations. The results are summarised with
 other published studies from the same site and the implications for forest
 management discussed. The different types and levels of impacts associated
 with each species support the idea that ecological and genetic information
 by species, ecological guild or reproductive group are essential in
 helping to derive sustainable logging guidelines for tropical forests.
description: Input for Fdash for
 Dipteryx odorataSource of information:
 Genotypes from lab experiments, here is the input for Fdash software for
 genetic diversity of polyploid analysis. Input contains genotypes of pre-
 and post-logging adults, pre- and post-logging progenies. First column
 contains id of population, second column onwards contains genotypes of
 Do03, Do17, Do18, Do25, Do08, Do19 and Do20 loci. abbreviations: adultos
 corresponds to pre-logging adults sample, adultospos (post-logging adults
 sample), filhotespre (pre-logging progenies sample) and filhotespos
 (post-logging progenies sample).Do_Input_Fdash.txtInput for Spagedi for Dipteryx odorataSource of information: Genotypes from lab experiments. Here is the input for Spagedi software for spatial genetic diversity analysis, divide into two parts, first part contains pre-logging adult input and second part contains post-logging adult input. First column contains id of sample, second and third column contains x and y coordinates, forth column onwards contains genotypes of Do03, Do17, Do18, Do25, Do08, Do19 and Do20 loci.Do_InputSpagedi.txtInput for paternity software for pre-logging Dipteryx odorataSource of information: Genotypes from lab experiments. Here is the input for Orchard software for paternity analysis, divide into two parts, first part contains pre-logging progenies input and second part contains pre-logging candidate father input. Pre-logging progenies input contains first column contains id of progeny, second column onwards contains genotypes of Do03, Do17, Do18, Do25, Do08, Do19 and Do20 loci and last column contains name of known mother. Pre-logging candidate father input contains first column contains id of individual, second column onwards contains genotypes of Do03, Do17, Do18, Do25, Do08, Do19 and Do20 loci and last two columns contains X and Y coordinates.DoPre_InputOrchard.txtInput for paternity software for post-logging Dipteryx odorataSource of information: Genotypes from lab experiments. Here is the input for Orchard software for paternity analysis, divide into two parts, first part contains post-logging progenies input and second part contains post-logging candidate father input. Post-logging progenies input contains first column contains id of progeny, second column onwards contains genotypes of Do03, Do17, Do18, Do25, Do08, Do19 and Do20 loci and last column contains name of known mother. Post-logging candidate father input contains first column contains id of individual, second column onwards contains genotypes of Do03, Do17, Do18, Do25, Do08, Do19 and Do20 loci and last two columns contains X and Y coordinates.DoPost_InputOrchard.txtInput for MLTR software for Jacaranda copaiaSource of information: Genotypes from lab experiments. Here is the input for MLTR software for mating system analysis. Input contains genotypes of pre- and post-logging progenies. First column contains id of known mother, second column contains group id (a=pre-logging, b=post-logging), third column onwards contains genotypes of the progeny of JC03, JC09, JC21, JC05, JC28 loci.JcInputMltr.txtInput for Spagedi software for Jacaranda copaiaSource of information: Genotypes from lab experiments. Here is the input for Spagedi software for spatial genetic diversity analysis, divide into two parts, first part contains pre-logging adults input and second part contains post-logging adults input. First column contains id of individual, second column contains field id, third column contains measure of diameter at breast height (DBH) in cm, and fifth column onwards contains genotypes of JC03, JC09, JC21, JC05, JC28 loci.JcInputGdaSpagedi.txtInput for Cervus software for Jacaranda copaiaSource of information: Genotypes from lab experiments. Here is the input for Cervus software for paternity analysis, divide into three parts. First part contains pre-logging progenies and pre-logging adults genotypes first column contains id of individual, second column onwards contains genotypes of JC03, JC09, JC21, JC05, JC28 loci. Second part contains list of progenies with known mother and third part is the list of candidate fathers.JcPreInputCervus.txtInput for Cervus software for Jacaranda copaiaSource of information: Genotypes from lab experiments. Here is the input for Cervus software for paternity analysis, divide into three parts. First part contains post-logging progenies and post-logging adults genotypes first column contains id of individual, second column onwards contains genotypes of JC03, JC09, JC21, JC05, JC28 loci. Second part contains list of progenies with known mother and third part is the list of candidate fathers.JcPostInputCervus.txt