Of islands on islands: Natural habitat fragmentation drives microallopatric differentiation in the context of distinct biological assemblages
Data files
Jun 23, 2025 version files 3.92 MB
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conthil010a.dbf
20.05 KB
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conthil010a.prj
443 B
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conthil010a.shp
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conthil010a.shp.xml
8.03 KB
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conthil010a.shx
3.42 KB
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conthil010a.txt
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conthil010a.xml
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geo_dist.csv
32.38 KB
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inventory.csv
192.24 KB
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Kipuka_extent.dbf
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Kipuka_extent.prj
143 B
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Kipuka_extent.qpj
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Kipuka_extent.shp
292 B
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Kipuka_extent.shx
108 B
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Kona_extent.dbf
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Kona_extent.prj
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Kona_extent.qpj
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Kona_extent.shp
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Kona_extent.shx
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Merged_by_site_2.csv
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nmds3otu.csv
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OTU3_Bray_Order.csv
272.69 KB
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OTU3_Bray.csv
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README.md
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Stainbeck_extent.dbf
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Stainbeck_extent.prj
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Stainbeck_extent.qpj
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Stainbeck_extent.shp
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Stainbeck_extent.shx
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zOTU_Jaccard_Order.csv
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zOTU_jaccard.csv
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Abstract
An important evolutionary hypothesis posits that much of the biodiversity we see today was generated by the interplay of colonization, extinction, adaptation, and speciation during episodes of natural habitat fragmentation. To interrogate the generality of this hypothesis, we leverage the natural experiment provided by arthropod communities in kīpuka—patches of Hawaiian wet forest isolated by lava flows. With DNA metabarcoding, we provide the first simultaneous exploration of ecological and evolutionary characteristics in the kīpuka system. At both species- and haplotype-equivalent scales, we find that diversity scales with kīpuka area, and that kīpuka accelerate the distance decay of similarity relative to continuous forest. Open lava, kīpuka edges, and the centers of the smallest kīpuka host lower inter- and intra-specific richness, are more biologically homogeneous, and have higher proportions of non-native OTUs than kīpuka centers for the order we could test (Araneae). Our work shows how natural habitat fragmentation stimulates, in tandem, ecological shifts in community composition and genetic differentiation. The strong signatures of both ecological and evolutionary processes highlight the importance of studying both processes simultaneously if we are to understand how biological communities respond to change.
https://doi.org/10.5061/dryad.mgqnk996x
Key for abbreviations used below
zOTU- zero-radius operational taxonomic unit
OTU- operational taxonomic unit
NMDS- non-metric multidimensional scaling
MDS- multidimensional scaling
Description of the data and file structure
Data was collected for a study of how natural fragmentation impacts OTU richness and turnover at the zOTU and 3 % radius OTU scales.
Files and variables
File: geo_dist.csv
Description:
A geographic distance matrix between pairs of sampling sites. Site names occur along column names and row names. Distances are in meters.
File: Merged_by_site_2.csv
Description: operational taxonomic unit (OTU) counts per site
Variables
- The blank cells at the top left of the sheet are there on purpose, because each sampling site (rows) and zOTU (columns) is associated with a richer set of data, as described here.
- Site identification codes occur as row names, starting in row 10.
- First 9 rows contain data pertinent to each zOTU, starting in column 14 :
- ZOTU: ID of the zOTU
- INVNAT: Whether OTU is native ("NAT"), non-native ("INV"), or unassigned ("NA").
- 3PercOTU: The 3% OTU pertaining to each zOTU
- Kingdom, Phylum, Class, Order, Family, Genus, Species: Taxonomic information pertaining to each zOTU
- The first 13 columns contain further data pertinent to each sampling site:
- Name: Site name
- Hoehe: elevation in meters above sea level
- MDS1: first axis of MDS
- MDS2: second axis of MDS
- Niederschlag: Annual precipitation in millimeters
- Temp: Average annual temperature in degrees Celcius
- Perimeter/Length: Perimeter in meters of kipuka sites
- Site: Habitat type
- Area: Kipuka area in meters squared
- Area log: Log of kipuka area in meters squared
- Specimens: Count of specimens collected
- Lat: latitude in decimal degrees
- Lon: longitude in decimal degrees
File: nmds3otu.csv
Description: Data required for NMDS of 3% radius OTU.
Variables
- ID: Site name
- Site: Habitat type
- Hoehe: Elevation in meters above sea level
- MDS1zOTU: zOTU MDS axis 1
- MDS2zOTU: zOTU MDS axis 2
- MDS1OTU: 3 % OTU MDS axis 1
- MDS2OTU: 3 % OTU MDS axis 2
- Niederschlag: Average annual precipitation (millimeters)
- Temp: Average annual temperature in degrees Celcius
- Perimeter/Length: Perimeter of kipuka in meters
- Area: Area of kipuka in meters squared
- Arealog: Log area of kipuka
- SRzOTU, SROTU: Ignore these outdated data columns.
- Lat: Latitude in decimal degrees
- Lon: Longitude in decimal degrees
- Columns 24 forward contain count data per each 3% radius OTU named in the column names.
File: OTU3_Bray.csv
Description: Bray-Curtis dissimilarity data for 3% radius OTUs.
Variables
- Var1: First sampling site ID
- Var2: Second sampling site ID
- value: Bray-Curtis dissimilarity values for 3% radius OTUs.
File: OTU3_Bray_Order.csv
Description: Bray-Curtis dissimilarity data for 3% radius OTUs, order-by-order
Variables
- Var1: First sampling site ID
- Var2: Second sampling site ID
- Araneae_value, Hemiptera_value, Psocoptera_value, Coleoptera_value, Lepidoptera_value, Diptera_value: Bray-Curtis dissimilarity value for that site pair for the specified order.
File: zOTU_Jaccard_Order.csv
Description: Jaccard dissimilarities between site pairs based on zOTUs, order-by-order.
Variables
- Var1: First site name
- Var2: Second site name
- Hemiptera_value, Araneae_value, Psocoptera_value, Lepidoptera_value, Coleoptera_value, Diptera_value: Jaccard dissimilarity value between the given pair of sites for the named order.
File: zOTU_jaccard.csv
Description: Jaccard dissimilarities between site pairs based on zOTUs.
Variables
- Var1: First site name
- Var2: Second site name
- value: Jaccard dissimilarity value for given pair of sites.
File: inventory.csv
Description: Phylogenetic information per zOTU
Variables (rows)
- Class, Order, Family, Genus, Species: taxonomic information pertinent to each zOTU
- ID: zOTU ID
- 3PercOTU: 3% radius OTU ID per zOTU
File: Stainbeck_extent, Kona_extent, & Kipuka_extent files (shp, prj, shx, qpj, dbf)
Description: Spatial extent shapefile polygons for each of the sampling areas (a box surrounding the kipuka landscape, Stainback sampling sites, and Kona sampling sites). Shapefiles can be visualized with QGIS, ArcGIS, or your favorite spatial package/module in R/Python.
- shp file: stores the geometry
- prj file: Spatial reference (WGS84)
- shx file: spatial index file
- qpj file: map projection file
- dbf file: No particular attributes associated with this data
- Data source: drawn by authors around study areas
File: conthil010a (shp, prj, dbf, shx, & txt)
Description: Big Island contour shapefile for mapping. As per the description provided in the metadata text file by the US Geological Survey: "This map layer shows elevation contour lines for Hawaii. The map layer was derived from the 100-meter resolution elevation data set which is published by the National Atlas of the United States, and is in the same Albers Equal-area Conic projection as that source data set. Contour intervals match the steps used in the National Atlas Color-Sliced Elevation data sets. Contours were adjusted so that they are in the proper relationship to National Atlas 1:1,000,000-scale lakes, reservoirs, and wide (double-line) streams.". Shapefiles can be visualized with QGIS, ArcGIS, or your favorite spatial package/module in R/Python.
- shp file: stores the geometry
- prj file: Spatial reference (WGS84)
- dbf file: Attribute file associated with shapefile. Attribute definitions are given in the metadata text file.
- shx file: spatial index file
- txt file: Additional metadata associated with the shapefile
- Data source: Published by the National Atlas of the United states at the link provided in the txt metadata file
Code/software
Programs available in the Materials and Methods of the article, and scripts available through the github linked in the Code Availability Statement.
See "Materials and methods" of the manuscript.
