DOI: 10.5061/dryad.44k7304
title: Data from: Genetic effects of anthropogenic habitat fragmentation on remnant animal and plant populations: a meta-analysis

description: 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.
description: <strong>DataS1 </strong> 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
description: # Data from: Genetic effects of anthropogenic habitat fragmentation on
 remnant animal and plant populations: a meta-analysis
 [https://doi.org/10.5061/dryad.44k7304](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](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://github.com/dschlaep/GeneticEffects_of_Fragmentation) [[https://doi.org/10.5281/zenodo.1402234](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 file `Step5g_Manuscript_SupplementaryTables.R` with the logical flag `do_Data1_TablesS1and2`. Thus, this table is produced by the variable `dat0_final` as output of the code file `Step1c_Moderators.R` and is loaded in the subsequent steps as `datl`. * 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 the `0_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://github.com/dschlaep/GeneticEffects_of_Fragmentation) [[https://doi.org/10.5281/zenodo.1402234](https://doi.org/10.5281/zenodo.1402234)]