Data from: Genetic effects of anthropogenic habitat fragmentation on remnant animal and plant populations: a meta-analysis
Data files
Aug 23, 2019 version files 194.19 KB
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DataS1.zip
194.19 KB
Jan 03, 2025 version files 3.70 MB
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DataS1_TableS1_PublishedDataReferences.csv
28.67 KB
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DataS1_TableS2_PublishedData.csv
3.63 MB
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DataS1_TableS3_CalculatedEffectSizesPerSpeciesAndResponse.csv
24.10 KB
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MetadataS1_Table_PublishedData_ColumnExplanation.csv
3.63 KB
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MetadataS2_Table_CalculatedEffectSizesPerSpeciesAndResponse_ColumnExplanation.csv
3.54 KB
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README.md
9.43 KB
Abstract
Habitat loss and fragmentation are among the biggest threats to biodiversity. Anthropogenic habitat fragmentation leads to small and isolated remnant plant and animal populations. The combination of increased random genetic drift, inbreeding, and reduced gene flow may substantially reduce genetic variation of remnant populations. However, the magnitude of these responses may depend on several poorly understood factors including organism group, habitat type of both the fragment and the surrounding matrix, life‐history traits, and time since fragmentation. We compiled data for 83 plant and 52 animal species and conducted a meta‐analysis following best practices to evaluate how these factors mediate the effects of anthropogenic habitat fragmentation. We calculated 206 effect sizes as correlations between one of four measures of population‐level genetic diversity and fragment area. All analyses were repeated using models of increasing complexity (traditional random‐effects models, multilevel models accounting for non‐independent data, and multilevel models additionally correcting for phylogenetic relatedness). We confirmed that anthropogenic habitat fragmentation has overall negative effects on genetic diversity of organisms. Our meta‐analysis shows, however, that plant species responded in general stronger to fragmentation than animal species and that the largest negative impacts of fragmentation occurred in tropical and temperate forest fragments, surrounded by a non‐forest matrix. In contrast, we found only weak responses in non‐forest fragments. Genetic diversity measured as mean number of alleles (A) showed the strongest response to fragmentation. Expected heterozygosity (He) and percentage of polymorphic loci (PLP) showed similar but weaker responses. In contrast, our meta‐analysis indicated that inbreeding (Fis) was not measurably affected by anthropogenic habitat fragmentation. Additionally, our models revealed that effects on genetic diversity became stronger with age of fragments: We found significant negative responses for fragments older than 50 yr but not for those more recently isolated. Our meta‐analyses also showed that currently animals are underrepresented in the literature on genetic effects of anthropogenic fragmentation, as are certain geographical regions and habitat types. We expect that future field studies using state‐of‐the‐art approaches will provide further evidence of negative genetic effects, which may reinforce the here reported patterns, even for groups not yet studied.
https://doi.org/10.5061/dryad.44k7304
Description of the data and file structure
This dataset supports the analysis published in Schlaepfer et al. 2018 Genetic effects of anthropogenic habitat fragmentation on remnant animal and plant populations: a meta-analysis. Ecosphere (https://doi.org/10.1002/ecs2.2488).
This dataset contains five files:
- DataS1_TableS1_PublishedDataReferences.csv. References of studies used in meta-analysis
- DataS1_TableS2_PublishedData.csv. Prepared set of extracted data. Data file is in ‘long-format’, i.e., each row contains data for one combination of fragment, genetic measure (A, He, Sh, PLP, and Fis), species, genetic marker, and study
- MetadataS1_Table_PublishedData_ColumnExplanation.csv. Explanation of columns for Table S2
- DataS1_TableS3_CalculatedEffectSizesPerSpeciesAndResponse.csv. Calculated effect sizes for main analysis
- MetadataS2_Table_CalculatedEffectSizesPerSpeciesAndResponse_ColumnExplanation.csv. Explanation of columns for Table S3
The R code utilized for the analysis is available from https://github.com/dschlaep/GeneticEffects_of_Fragmentation [https://doi.org/10.5281/zenodo.1402234]
Description of how the the R code uses the files:
- DataS1_TableS2_PublishedData.csv is a
csv
-representation of underlying data used for the analysis. It was produced by the code fileStep5g_Manuscript_SupplementaryTables.R
with the logical flagdo_Data1_TablesS1and2
. Thus, this table is produced by the variabledat0_final
as output of the code fileStep1c_Moderators.R
and is loaded in the subsequent steps asdatl
. - The code file
0_Run_all_analyses.R
is the master file which documents and executes all code; it also identifies the figures and tables of the manuscripts. There are six steps: (i) data preparation, (ii) calculate effect sizes, (iii) fit meta-analysis models, (iv) produce miscellaneous output figures, (v) prepare data for output, and (vi) produce main results, figures, and tables. Each of these steps is controlled by a logical flag in the0_Run_all_analyses.R
and executes a subset of the other code files.
Files and variables
File: DataS1_TableS2_PublishedData.csv
Description: Prepared set of extracted data. Data file is in ‘long-format’, i.e., each row contains data for one combination of fragment, genetic measure (A, He, Sh, PLP, and Fis), species, genetic marker, and study
Variables
NA indicates that a value was not provided by the original study.
- ID_effect: Unique identifier of effects as combination of study, species, and genetic marker
- ID_article: Unique identifier of study (see Data S1 for full reference)
- Paper_Nr: Internal study identifier
- ID_unit: Internal unique identifier for each combination of study and species
- FirstAuthor: Last name of first author of study
- is_fragment: Does the row describe data from a fragment (TRUE) or from a control area (FALSE)?
- is_standardized: Are the genetic data standardized?
- Fragment_area_ha: Fragment area in hectares
- Fragment_area_rank: Per effect rank of fragment area
- Fragment_area_source: Explanation of fragment area source
- Pop_size_n: Population size in numbers of individuals
- Pop_size_rank: Per effect rank of population size
- Pop_size_source: Explanation of population size source
- Response: Genetic measure (A, He, Sh, PLP, and Fis)
- Value: Value of genetic measure
- Ind_sampled_nPERfragment: Number of individuals that were sampled to determine genetic measure
- Pub_Year: Publication year of study
- Study_type: Type of study (field survey or experiment)
- Marker: Genetic marker type (AFLP, Isozymes, ISSR, etc.)
- Marker_cat: Class of genetic marker (codominant, dominant, proteins, uniparental)
- Effect_longitude: Average longitude of study fragments (WGS84)
- Effect_latitude: Average latitude of study fragments (WGS84)
- EffectAgeCat2_ord_yrs: Absolute age of fragmentation in years
- Habitat2: Classification of fragment habitat (6 categories)
- Habitat3: Classification of fragment habitat (2 categories)
- Matrix2: lassification of matrix habitat (3 categories)
- Organism_group4: Organism groups (animals, nonwoody-plants, woody-plants)
- Organism_group5: Organism groups (arthropods&herps, mammals&birds, nonwoody-plants, woody-plants)
- Kingdom: Taxonomy
- Phylum: Taxonomy
- Class: Taxonomy
- Order: Taxonomy
- Family: Taxonomy
- Genus: Taxonomy
- Species_resolved: Taxonomy
- Plants_Lifeform: Plant traits (see Appendix S2: Table S2)
- Plants_Sex: Plant traits (see Appendix S2: Table S2)
- Plants_Self_compatibility: Plant traits (see Appendix S2: Table S2)
- Plants_Mating_system: Plant traits (see Appendix S2: Table S2)
- Plants_Pollination_syndrome: Plant traits (see Appendix S2: Table S2)
- Plants_Pollination_vector: Plant traits (see Appendix S2: Table S2)
- Plants_Seed_dispersal_vector: Plant traits (see Appendix S2: Table S2)
- Animals_Length_cat: Animal traits (see Appendix S2: Table S3)
- Animals_Mass_cat: Animal traits (see Appendix S2: Table S3)
- Animals_Generation_cat: Animal traits (see Appendix S2: Table S3)
- Animals_Dispersal_ability: Animal traits (see Appendix S2: Table S3)
- Animals_Trophic_group: Animal traits (see Appendix S2: Table S3)
- SpeciesAgeCat2_ord_yrs: Life span in years
- Effect_NGenSinceFrag_ord: Relative age of fragmentation in number of generations since start of fragmentation
- Effect_NlifeSinceFrag_ord: Relative age of fragmentation in number of lifespans since start of fragmentation
File: DataS1_TableS3_CalculatedEffectSizesPerSpeciesAndResponse.csv
Description: Calculated effect sizes for main analysis
Variables
- Organism group: Organism groups (animals, nonwoody-plants, woody-plants)
- Species: Taxonomy
- Response: Genetic measure (A, He, Sh, PLP, and Fis)
- Marker: Genetic marker type (AFLP, Isozymes, ISSR, etc.)
- Effect size (z of Pearson cor): Effect size
- Hierarchical weight: Hierarchical weight
- Number of fragments: Number of fragments
- Mean number of individuals per fragment: Mean number of individuals per fragment
- FirstAuthor: Last name of first author of study
- Pub_Year: Publication year of study
- Habitat3: Flag indicating if classification of fragment habitat (2 categories) is (1) / is not (0) available for effect
- Matrix2: Flag indicating if classification of matrix habitat (3 categories) is (1) / is not (0) available for effect
- Organism_group4: Flag indicating if organism groups (animals, nonwoody-plants, woody-plants) is (1) / is not (0) available for effect
- Habitat2: Flag indicating if classification of fragment habitat (6 categories) is (1) / is not (0) available for effect
- Plants_Lifeform: Flag indicating if plant traits (see Appendix S2: Table S2) is (1) / is not (0) available for effect
- Plants_Sex: Flag indicating if plant traits (see Appendix S2: Table S2) is (1) / is not (0) available for effect
- Plants_Self_compatibility: Flag indicating if plant traits (see Appendix S2: Table S2) is (1) / is not (0) available for effect
- Plants_Mating_system: Flag indicating if plant traits (see Appendix S2: Table S2) is (1) / is not (0) available for effect
- Plants_Pollination_vector: Flag indicating if plant traits (see Appendix S2: Table S2) is (1) / is not (0) available for effect
- Plants_Seed_dispersal_vector: Flag indicating if plant traits (see Appendix S2: Table S2) is (1) / is not (0) available for effect
- Animals_Length_cat: Flag indicating if animal traits (see Appendix S2: Table S3) is (1) / is not (0) available for effect
- Animals_Mass_cat: Flag indicating if animal traits (see Appendix S2: Table S3) is (1) / is not (0) available for effect
- Animals_Dispersal_ability: Flag indicating if animal traits (see Appendix S2: Table S3) is (1) / is not (0) available for effect
- Animals_Trophic_group: Flag indicating if animal traits (see Appendix S2: Table S3) is (1) / is not (0) available for effect
- EffectAgeCat2_ord_yrs: Flag indicating if life span in years is (1) / is not (0) available for effect
- Effect_NGenSinceFrag_ord: Flag indicating if relative age of fragmentation in number of generations since start of fragmentation is (1) / is not (0) available for effect
File: DataS1_TableS1_PublishedDataReferences.csv
Description: References of studies used in meta-analysis
Variables
- ID_article: Unique identifier of study
- Reference: Reference of article
File: MetadataS1_Table_PublishedData_ColumnExplanation.csv
Description: Explanation of columns for Table S2
Variables
- Field: Variable
- Explanation: Explanation of variable
File: MetadataS2_Table_CalculatedEffectSizesPerSpeciesAndResponse_ColumnExplanation.csv
Description: Explanation of columns for Table S3
Variables
- Field: Variable
- Explanation: Explanation of variable
Code/software
The R code utilized for the analysis is available from https://github.com/dschlaep/GeneticEffects_of_Fragmentation [https://doi.org/10.5281/zenodo.1402234]
DataS1
TABLE S1. References of studies used in meta-analysis
TABLE S2. Prepared set of extracted data. Data file is in ‘long-format’, i.e., each row contains data for one combination of fragment, genetic measure (A, He, Sh, PLP, and Fis), species, genetic marker, and study
METADATA S2. Explanation of columns for TABLE S2
TABLE S3. Calculated effect sizes for main analysis.
METADATA S3. Explanation of columns for TABLE S3