Nothofagus hybridization and population structure reveals high fluctuating asymmetry in putative hybrids and surprisingly little differentiation between species
Data files
Dec 29, 2025 version files 151.82 KB
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FieldData_2022_appendixA.csv
2.04 KB
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FieldData_2023_appendixB.csv
5.19 KB
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intergenic.fasta
40.56 KB
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MatK_nothofagus.fasta
41.27 KB
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Microsatellite_reads_appendixC.csv
10.24 KB
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rbcl.fasta
47.86 KB
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README.md
4.65 KB
Abstract
Interspecific hybridization is documented in various tree species, such as the Nothofagus (N. pumilio and N. antarctica), located in Chile. Hybridization can sometimes lead to developmental instability, resulting in increasing leaf fluctuating asymmetry. However, the extent of Nothofagus hybridization throughout Chile and its impact on leaf fluctuating asymmetry between N. pumilio and N. antarctica hybrids remains unexplored. We collected N. pumilio, N. antarctica, and putative hybrid leaves for morphological and chloroplast DNA analyses and conducted population genetic analysis on N. pumilio, N. antarctica, N. betuloides, N. dombeyi, and N. obliqua using microsatellite markers (eight loci). The putative hybrids with intermediate phenotypes displayed significantly higher fluctuating asymmetry than morphologically unambiguous N. pumilio and N. antarctica, suggesting a higher developmental instability. However, despite clear phenotypic differences, our DNA analyses of this sympatric population did not show the two species or their putative hybrids to be genetically differentiated; all three groups shared the same mtDNA and almost identical microsatellite composition. Our microsatellite analyses of five Nothofagus species found high allelic variation within species and subpopulations, but surprisingly low structure between species and populations. Further studies are needed to determine whether the N. pumilio and N. antarctica genomes are distinct enough to be classified as distinct species under the phylogenetic species concept.
https://doi.org/10.5061/dryad.79cnp5j6m
Description of the data and file structure
Datasets from paper: Nothofagus hybridization and population structure reveal high fluctuating asymmetry in putative hybrids and surprisingly little differentiation between species.
Files and variables
File: FieldData_2022_appendixA.csv
Description: Collection of information for individuals used in the morphological analyses.
Variables
- Individual: Individual label
- Latitude: GPS coordinates
- Longitude: GPS coordinates
- DBH (cm): diameter of trunk at breast height in the field
- Height (m): height of the tree in the field
- Species: Nothofagus antarctica, Nothofagus pumilio, or putative hybrid
File: FieldData_2023_appendixB.csv
Description: Collection sites for individuals used in population genetic analyses
Variables
- ID: individual plant ID
- Latitude: GPS coordinate
- Longitude: GPS Coordinate
- Species: Species identity
File: Microsatellite_reads_appendixC.csv
Description:
Variables
- ID: individual label
- Species: the species of the individual
- Collection Group: location information
- location: location
- 6fam1: 1st allele of microsatellite Npum1
- 6fam1_2: 2nd allele of microsatellite Npum1
- 6fam2: 1st allele of microsatellite Npum9
- 6fam2_2: 2nd allele of microsatellite Npum9
- vic1: 1st allele of microsatellite Npum3
- vic1_2: 2nd allele of microsatellite Npum1
- vic2: 1st allele of microsatellite Npum11
- vic2_2: 2nd allele of microsatellite Npum11
- ned1: 1st allele of microsatellite Npum10
- ned1_2: 2nd allele of microsatellite Npum10
- ned2: 1st allele of microsatellite Npum18
- ned2_2: 2nd allele of microsatellite Npum18
- pet1: 1st allele of microsatellite Npum13
- pet1_2: 2nd allele of microsatellite Npum13
- pet2: 1st allele of microsatellite oak_pum43
- pet2_2: 2nd allele of microsatellite oak_pum43
File: intergenic.fasta
Description: Chloroplast DNA sequences from the intergenic region and rbcl from our Nothofagus antarctica and N. pumilio samples aligned against existing GenBank sequences. Individual labels refer to labels in Appendix B.
File: MatK_nothofagus.fasta
Description: Chloroplast DNA sequences from the MatK gene from our Nothofagus antarctica and N. pumilio samples aligned against existing GenBank sequences. Individual labels refer to labels in Appendix B.
File: rbcl.fasta
Description: Chloroplast DNA sequences from the rbcl gene from our Nothofagus antarctica and N. pumilio samples aligned against existing GenBank sequences. Individual labels refer to labels in Appendix B.
Access information
Other publicly accessible locations of the data:
- Genbank accession number PV239901-PV239906 for chloroplast markers for one representative N. pumilio and one N. antarctica
Data was derived from the following sources:
- For Chloroplast sequencing fasta files we have new collections (Sanger sequencing) and for fasta files Genbank access: AB015464, AJ581438, U92859, U92860, AY263924, LC677699, L13341, L13342, L13343, L13344, L13345, L13346, L13347, L13348, L13349, L13350, L13351, L13352, L13353, L13354, L13355, L13356, L13357, L13358, L13359, L13360, L13361, L13362, L13363, L13339, AF015686, AF015687, AF015688, AF015689, AF015690, AF015691, AF015692, AF015693, AF015694, AF015695, AF015696, AF015697, AF015698, AF015699, AF015701, AF015703, AF015704, AF015705, AF015706, AF015707, AF015708, AF015709, AF015710.
Code/Software:
Structure_Clean.R: This R script reads STRUCTURE output files, extracts individual ancestry (Q) values, and saves them as a CSV for a chosen number of clusters (K). It then plots these ancestry proportions as stacked bar plots using ggplot2 and exports the figure as a PDF.
Nothofagus_Rcode_clean.R: This script performs exploratory plots, ANOVA, and Tukey post-hoc tests to compare multiple leaf traits among species, visualizing results with density plots and boxplots. It also runs species-specific linear regressions to examine relationships between leaf dimensions (length, width, area) and visualizes them with scatter plots and fitted lines.
Fst_calculations.R: This code loads the hierfstat package and checks its citation and version. It then calculates allelic richness, allele counts, and basic population genetic statistics (including F-statistics) from genetic data.
We collected leaf samples from Nothofagus antarctica and N. pumillo and putative hybrids in the forests near Estancia Pingo Salvaje, Chile (-51.5359, -72.5669) in December 2023: 10 N. pumilio, 11 N. antarctica, and 23 putative hybrid individuals (appendix A)
During the following March, October, and November, we collected additional samples from 125 trees in 14 populations in northern (41-42 °S) and southern regions (51-53 °S; Figure 2A). In the southern region, we sampled 33 N. pumilio, 29 N. antarctica, 29 N. betuloides, and 6 N. dombeyi trees. In the Northern region, we sampled 1 N. pumilio, 2 N. antarctica, 16 N. dombeyi, and 9 N. nitida. (appendix B)
For the samples from Estancia, we collected 3 chloroplast genes (Matk, rbcL, and atpB-rbcL intergenic spacer regions) as well as genotype data for 8 microsatellites.
For the remaining samples, we collected genotype data for 8 microsatellites (Appendix C)