Population genetic and geographic data of six Neotropical plant species
Data files
May 18, 2022 version files 16.56 GB
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Db_populations.snps.genepop
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Db_populations.snps.vcf
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Db.gds
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Db.txt
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Db01_MIN.fastq.gz
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Db02_MIN.fastq.gz
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Db02_SAN.fastq.gz
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Db03_MIN.fastq.gz
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Db03_SAN.fastq.gz
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Db04_MIN.fastq.gz
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Db04_SAN.fastq.gz
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Db05_MIN.fastq.gz
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Db06_MIN.fastq.gz
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Db06_SAN.fastq.gz
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Db07_MIN.fastq.gz
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Db07_SAN.fastq.gz
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Db08_MIN.fastq.gz
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Db08_SAN.fastq.gz
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Db09_MIN.fastq.gz
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Db09_SAN.fastq.gz
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Db10_MIN.fastq.gz
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Db10_SAN.fastq.gz
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Db11_MIN.fastq.gz
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Db11_SAN.fastq.gz
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Db12_MIN.fastq.gz
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Db12_SAN.fastq.gz
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Db13_MIN.fastq.gz
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Db13_SAN.fastq.gz
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Db14_MIN.fastq.gz
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Db14_SAN.fastq.gz
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Db15_MIN.fastq.gz
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Db15_SAN.fastq.gz
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Db16_MIN.fastq.gz
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Db16_SAN.fastq.gz
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Db17_MIN.fastq.gz
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Db18_MIN.fastq.gz
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Db19_MIN.fastq.gz
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Db20_MIN.fastq.gz
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Db20_SAN.fastq.gz
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Db21_SAN.fastq.gz
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Db22_SAN.fastq.gz
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Dbrochidodroma.csv
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Dbrochidodroma.txt
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Dt_03.fastq.gz
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Dt_08.fastq.gz
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Dt_populations.snps.genepop
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Dt_populations.snps.vcf
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Dt.gds
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Dt.txt
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Dt01_PAH.fastq.gz
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Dt02_BEL.fastq.gz
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Dt02_PAH.fastq.gz
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Dt03_BEL.fastq.gz
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Dt03_PAH.fastq.gz
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Dt07_BEL.fastq.gz
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Dt07_PAH.fastq.gz
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Dt09_BEL.fastq.gz
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Dt09_PAH.fastq.gz
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Dt10_PAH.fastq.gz
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Dt11_BEL.fastq.gz
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Dt11_PAH.fastq.gz
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Dt12_BEL.fastq.gz
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Dt12_PAH.fastq.gz
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Dt13_BEL.fastq.gz
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Dt14_BEL.fastq.gz
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Dt14_PAH.fastq.gz
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Dt15_BEL.fastq.gz
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Dt15_PAH.fastq.gz
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Dt16_BEL.fastq.gz
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Dt17_BEL.fastq.gz
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Dt18_BEL.fastq.gz
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Dt19_BEL.fastq.gz
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Dt19_PAH.fastq.gz
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Dt20_PAH.fastq.gz
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Dt22_PAH.fastq.gz
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Dt23_PAH.fastq.gz
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Dtenuis.csv
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Dtenuis.txt
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DtI_SAN.fastq.gz
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DtIII_SAN.fastq.gz
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DtIV_SAN.fastq.gz
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DtIX_SAN.fastq.gz
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DtV_SAN.fastq.gz
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DtVI_SAN.fastq.gz
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DtVIII_SAN.fastq.gz
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DtX_SAN.fastq.gz
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Mrubescens.csv
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Mrubescens.txt
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Mt_05.fastq.gz
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Mt_09.fastq.gz
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Mt_10.fastq.gz
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Mt_27.fastq.gz
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Mt_populations.snps.genepop
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Mt_populations.snps.vcf
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Mt.gds
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Mt.txt
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Mt01_BEL.fastq.gz
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Mt01_PAH.fastq.gz
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Mt02_PAH.fastq.gz
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Mt03_PAH.fastq.gz
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Mt04_BEL.fastq.gz
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Mt04_PAH.fastq.gz
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Mt05_BEL.fastq.gz
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Mt05_PAH.fastq.gz
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Mt06_PAH.fastq.gz
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Mt07_BEL.fastq.gz
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Mt08_BEL.fastq.gz
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Mt08_PAH.fastq.gz
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Mt09_PAH.fastq.gz
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Mt09_SAN.fastq.gz
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Mt10_BEL.fastq.gz
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Mt10.6_SAN.fastq.gz
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Mt10.8_SAN.fastq.gz
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Mt11.5_SAN.fastq.gz
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Mt12_BEL.fastq.gz
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Mt12_PAH.fastq.gz
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Mt13_BEL.fastq.gz
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Mt13_SAN.fastq.gz
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Mt14_BEL.fastq.gz
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Mt14_PAH.fastq.gz
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Mt14_SAN.fastq.gz
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Mt15_BEL.fastq.gz
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Mt16_BEL.fastq.gz
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Mt17_BEL.fastq.gz
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Mt17_PAH.fastq.gz
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Mt18_BEL.fastq.gz
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Mt18_PAH.fastq.gz
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Mt19_PAH.fastq.gz
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Mt20_PAH.fastq.gz
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Mt21_BEL.fastq.gz
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Mt22_BEL.fastq.gz
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Mt6.5_SAN.fastq.gz
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Mt9.6_SAN.fastq.gz
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Mt9.7_SAN.fastq.gz
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Mtomentosa.csv
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Mtomentosa.txt
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Nl_populations.snps.genepop
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Nl_populations.snps.vcf
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Nl.gds
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Nl.txt
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Nl01_BEL.fastq.gz
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Nl01_SAN.fastq.gz
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Nl02_BEL.fastq.gz
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Nl02_SAN.fastq.gz
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Nl03_PAH.fastq.gz
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Nl04_SAN.fastq.gz
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Nl05_PAH.fastq.gz
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Nl05_SAN.fastq.gz
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Nl06_PAH.fastq.gz
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Nl06_SAN.fastq.gz
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Nl07_BEL.fastq.gz
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Nl08_BEL.fastq.gz
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Nl08_PAH.fastq.gz
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Nl08_SAN.fastq.gz
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Nl09_BEL.fastq.gz
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Nl09_PAH.fastq.gz
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Nl10_BEL.fastq.gz
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Nl10_PAH.fastq.gz
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Nl10_SAN.fastq.gz
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Nl11_BEL.fastq.gz
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Nl11_PAH.fastq.gz
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Nl11_SAN.fastq.gz
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Nl12_BEL.fastq.gz
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Nl12_PAH.fastq.gz
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Nl12_SAN.fastq.gz
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Nl13_PAH.fastq.gz
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Nl13_SAN.fastq.gz
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Nl14_BEL.fastq.gz
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Nl14_PAH.fastq.gz
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Nl15_BEL.fastq.gz
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Nl15_PAH.fastq.gz
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Nl15_SAN.fastq.gz
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Nl16_BEL.fastq.gz
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Nl16_PAH.fastq.gz
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Nl17_BEL.fastq.gz
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Nl17_SAN.fastq.gz
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Nl18_BEL.fastq.gz
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Nl18_PAH.fastq.gz
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Nl19_BEL.fastq.gz
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Nl19_PAH.fastq.gz
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Nl19_SAN.fastq.gz
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Nl20_SAN.fastq.gz
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Nl21_BEL.fastq.gz
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Nl21_PAH.fastq.gz
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Nl21_SAN.fastq.gz
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Nl22_PAH.fastq.gz
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Nl23_PAH.fastq.gz
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Nl23_SAN.fastq.gz
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Nl24_PAH.fastq.gz
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Nl25_SAN.fastq.gz
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Nlongiped.txt
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Nlongipedunculoides.csv
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Om_01.fastq.gz
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Om_02.fastq.gz
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Om_03.fastq.gz
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Om_04.fastq.gz
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Om_06.fastq.gz
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Om_08.fastq.gz
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Om_11.fastq.gz
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Om_12.fastq.gz
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Om_13.fastq.gz
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Om_15.fastq.gz
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Om_16.fastq.gz
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Om_17.fastq.gz
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Om_18.fastq.gz
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Om_19.fastq.gz
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Om_20.fastq.gz
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Om_21.fastq.gz
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Om_22.fastq.gz
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Om_23.fastq.gz
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Om_24.fastq.gz
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Om_25.fastq.gz
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Om_27.fastq.gz
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Om_28.fastq.gz
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Om_populations.snps.genepop
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Om_populations.snps.vcf
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Om.gds
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Om.txt
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Om01_BEL.fastq.gz
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Om01_PAH.fastq.gz
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Om01_SAN.fastq.gz
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Om02_BEL.fastq.gz
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Om03_PAH.fastq.gz
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Om03_SAN.fastq.gz
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Om04_PAH.fastq.gz
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Om04_SAN.fastq.gz
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Om06_BEL.fastq.gz
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Om06_PAH.fastq.gz
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Om06_SAN.fastq.gz
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Om07_BEL.fastq.gz
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Om07_PAH.fastq.gz
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Om08_BEL.fastq.gz
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Om08_PAH.fastq.gz
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Om09_BEL.fastq.gz
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Om09_SAN.fastq.gz
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Om10_BEL.fastq.gz
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Om10_PAH.fastq.gz
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Om11_BEL.fastq.gz
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Om12_PAH.fastq.gz
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Om12_SAN.fastq.gz
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Om13_BEL.fastq.gz
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Om13_SAN.fastq.gz
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Om14_BEL.fastq.gz
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Om14_PAH.fastq.gz
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Om15_PAH.fastq.gz
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Om15_SAN.fastq.gz
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Om16_BEL.fastq.gz
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Om16_SAN.fastq.gz
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Om17_BEL.fastq.gz
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Om17_PAH.fastq.gz
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Om18_BEL.fastq.gz
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Om18_SAN.fastq.gz
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Om19_PAH.fastq.gz
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Om20_BEL.fastq.gz
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Om20_PAH.fastq.gz
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Om20_SAN.fastq.gz
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Om21_SAN.fastq.gz
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Om22_PAH.fastq.gz
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Om22_SAN.fastq.gz
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Pd_01.fastq.gz
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Pd_03.fastq.gz
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Pd_08.fastq.gz
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Pd_09.fastq.gz
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Pd_10.fastq.gz
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Pd_13.fastq.gz
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Pd_15.fastq.gz
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Pd_20.fastq.gz
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Pd_populations.snps.genepop
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Pd_populations.snps.vcf
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Pd.gds
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Pd.txt
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Pd01_BEL.fastq.gz
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Pd01_SAN.fastq.gz
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Pd02_BEL.fastq.gz
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Pd02_SAN.fastq.gz
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Pd03_BEL.fastq.gz
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Pd04_BEL.fastq.gz
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Pd05_BEL.fastq.gz
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Pd05_SAN.fastq.gz
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Pd06_BEL.fastq.gz
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Pd07_BEL.fastq.gz
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Pd07_SAN.fastq.gz
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Pd08_SAN.fastq.gz
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Pd09_SAN.fastq.gz
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Pd10_BEL.fastq.gz
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Pd10_SAN.fastq.gz
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Pd11_BEL.fastq.gz
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Pd12_SAN.fastq.gz
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Pd13_BEL.fastq.gz
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Pd14_SAN.fastq.gz
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Pd15_BEL.fastq.gz
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Pd16_BEL.fastq.gz
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Pd16_SAN.fastq.gz
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Pd17_SAN.fastq.gz
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Pd18_BEL.fastq.gz
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Pd18_SAN.fastq.gz
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Pd19_BEL.fastq.gz
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Pd19_SAN.fastq.gz
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Pd20_BEL.fastq.gz
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Pd21_BEL.fastq.gz
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Pd22_SAN.fastq.gz
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Pdemissa.csv
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Pdemissa.txt
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README.txt
Abstract
We examined population genetic structure and fine-scale spatial genetic structure (FSGS) in six perennial understory angiosperms in Andean cloud forests of northwestern Ecuador. Species belong to three families (Gesneriaceae, Melastomataceae, and Rubiaceae), and within each family we paired one insect-pollinated with one hummingbird-pollinated species, predicting that insect-pollinated species have greater population differentiation (as quantified with the FST statistic) and stronger FSGS (as quantified with the SP statistic) than hummingbird-pollinated species.
Methods
- GPS coordinates of 30–42 individuals per species from 2–3 sites in northwestern Ecuador were taken with a Garmin GPSMAP device.
- Genetic data is stored in fastq format and corresponds to quality filtered 2B-RAD sequencing reads (raw reads were generated at the BYU DNA Sequencing Center).
- These filtered reads were processed as described in the manuscript methods for estimating population genetic parameters in the 'de novo' Stacks v2.3e pipeline.
- The genepop file was used in GenoDive v3.0 to estimate population genetic structure parameters and the vcf file was used in the R program SNPRelate to produce the gds files and perform a PCA.
- The input files for SPAGeDi v. 1.3a are stored for each species in the corresponnding txt file, used for FSGS analyses.
- Db=Drymonia brochidodroma, Dt=Drymonia tenuis, Mt=Meriania tomentosa, Om=Miconia rubescens (for the synonym Ossaea micrantha), Nl=Notopleura longipedunculoides, Pd=Palicourea demissa.