Data from: Genomic diversity and structure of a Neotropical microendemic fig tree
Data files
Mar 14, 2024 version files 2.79 MB
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1.0-Fprin_snps_71.vcf.gz
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2.0-Fprin_ind_71.csv
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README.md
Abstract
Genetic diversity is a key component of evolution and unraveling factors that promote genetic differentiation in space and time is a central question in evolutionary biology. One of the most diverse and ecologically important tree genera in tropical forests worldwide is Ficus (Moraceae). It has been suggested that, given the great dispersal capacity of pollinating fig wasps (Chalcidoidea; Agaonidae), the spatial genetic structure, particularly in monoecious fig species, should be weak. However, no studies have addressed the factors that determine the genetic structure of Ficus species in regions of high geological, geographic, and climatic complexity, such as the Mexican Transition Zone. Using nuclear single nucleotide polymorphisms (5,311 SNPs) derived from low-coverage whole genomes and 17 populations, we analyzed the population genomics of Ficus pringlei to characterize neutral and adaptive genetic variation and structure and its association with geographic barriers such as the Trans-Mexican Volcanic Belt, environmental heterogeneity, and wind connectivity. From genomic data of 71 individuals, high genetic diversity, and the identification of three genomic lineages were recorded (North, South, and Churumuco). The results suggest that genetic variation is primarily determined by climatic heterogeneity. Ficus pringlei populations from the north and south of the Trans-Mexican Volcanic Belt also exhibited minimal genetic differentiation (FST= 0.021), indicating that this mountain range may not act as an insurmountable barrier to gene flow. Wind connectivity is also highlighted in structuring putative adaptive genetic variation, underscoring the intricate complexity of the various factors influencing genetic variation in the species. This study provides information on the possible mechanisms underlying the genetic variation of endemic species of the tropical dry forest of Western Mexico, such as F. pringlei.
README: Data from: Genomic diversity and structure of a Neotropical microendemic fig tree
The dataset contains genomic data from 71 individuals of Ficus pringlei, a tree species found in the tropical dry forest of western Mexico. The study aims to investigate the genetic structure and variation of F. pringlei and understand the factors influencing it. The researchers utilized nuclear single nucleotide polymorphisms (SNPs) to analyze the population genomics of the species.
The experimental procedures involved collecting genetic samples from the individuals and performing SNP analysis to characterize both neutral and adaptive genetic variation. The researchers examined the association between genetic structure and geographic barriers, such as the Trans-Mexican Volcanic Belt, as well as environmental factors like climatic conditions.
Description of the data and file structure
File 1 Name: 1.0-Fprin_snps_71.vcf.gz.
File Description: Final filtered vcf for 71 individuals genotyped at 5,311 SNPs
File 2 Name: 2.0-Fprin_ind_71.csv
Description: Individual, site, and coordinates, environmental data, MEM, and wind connectivity values between individuals for 71 individuals in 1.0-Fprin_snps_71.vcf.gz
DATA-SPECIFIC INFORMATION FOR: 2.0-Fprin_ind_71.csv
- Number of variables: 33
- Number of cases/rows: 71
Variable List:
ID: Number of individuals
Name_vcf: Name of individual in 1.0-Fprin_snps_71.vcf.gz.
Localities: ID of the collection locality
Individual: ID of individuals
Longitude: in decimal degrees
Latitude: in decimal degrees
bio1: annual mean temperature in Celsius degree (1910 -2009, Cuervo-Robayo et al., 2014)
bio2: annual mean diurnal range in Celsius degree (1910 -2009, Cuervo-Robayo et al., 2014)
bio3: isothermality in percent (1910 -2009, Cuervo-Robayo et al., 2014)
bio4: temperature seasonality (1910 -2009, Cuervo-Robayo et al., 2014)
bio5: max temperature of warmest month in Celsius degree (1910 -2009, Cuervo-Robayo et al., 2014)
bio6: min temperature of coldest month in Celsius degree (1910 -2009, Cuervo-Robayo et al., 2014)
bio7: annual temperature range in Celsius degree (1910 -2009, Cuervo-Robayo et al., 2014)
bio8: mean temperature of wettest quarter in Celsius degree (1910 -2009, Cuervo-Robayo et al., 2014)
bio9: mean temperature of driest quarter in Celsius degree (1910 -2009, Cuervo-Robayo et al., 2014)
bio10: mean temperature of warmest quarter in Celsius degree (1910 -2009, Cuervo-Robayo et al., 2014)
bio11: mean temperature of coldest quarter in Celsius degree (1910 -2009, Cuervo-Robayo et al., 2014)
bio12: annual precipitation in millimeters (1910 -2009, Cuervo-Robayo et al., 2014)
bio13 precipitation of wettest month in millimeters (1910 -2009, Cuervo-Robayo et al., 2014)
bio14: precipitation of driest month in millimeters (1910 -2009, Cuervo-Robayo et al., 2014)
bio15: precipitation seasonality in percent (1910 -2009, Cuervo-Robayo et al., 2014)
bio16: precipitation of wettest quarter in millimeters (1910 -2009, Cuervo-Robayo et al., 2014)
bio17: precipitation of driest quarter in millimeters (1910 -2009, Cuervo-Robayo et al., 2014)
bio18: precipitation of warmest quarter in millimeters (1910 -2009, Cuervo-Robayo et al., 2014)
bio19: precipitation of coldest quarter in millimeters (1910 -2009, Cuervo-Robayo et al., 2014)
MEM1: first Moran's eigenvector map vector
MEM2: second Moran's eigenvector map vector
MEM3: third Moran's eigenvector map vector
MEM4: fourth Moran's eigenvector map vector
MEM5: fifth Moran's eigenvector map vector
MEM6: sixth Moran's eigenvector map vector
MEM7: seventh Moran's eigenvector map vectorwind: wind connectivity values between individual