The key role of vicariance for soil animal biogeography in a biodiversity hotspot region
Data files
May 12, 2025 version files 646.06 KB
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all_mantel_rp_20241026.xlsx
13.05 KB
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GeoCoordinates_and_ClimateData_and_SoilData_20241026.xlsx
25.68 KB
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IAA_eleven_region_taxonmoic_list_20241026.xlsx
212.61 KB
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README.md
13.42 KB
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Taxonomic_list_long_format_20241026.xlsx
213.71 KB
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Taxonomic_list_wide_format_20241026.xlsx
167.59 KB
Abstract
Aim: The Indo-Australian Archipelago is known as a biodiversity hotspot with a high level of endemism typically ascribed to vicariance as reflected by the “Wallace’s line”. However, it is unknown how vicariance has affected belowground biodiversity, especially process-based beta diversity. Here, we relate beta diversity of soil oribatid mite (Oribatida, Acari) assemblages to geographic distance as well as climatic and soil factors to explore the factors shaping the diversity of oribatid mites across eleven regions of the Indo-Australian Archipelago.
Location: Indo-Australian Archipelago.
Time Period: Present.
Major taxa studied: Oribatida, Acari.
Methods: We compiled a list of 2,549 oribatid mite species in the Indo-Australian Archipelago and investigated the level of endemism and beta diversity of oribatid mites in the eleven regions at species, genus and family level. We then summarized the biogeographical dissimilarity patterns of oribatid mites using ordination and clustering methods, and compared the patterns with the zoological boundaries based on aboveground taxa such as the Wallace’s, Lydekker’s, Weber’s and Holt’s line. We integrated data on geography, climate and soil to reveal the key drivers of species compositional dissimilarity of oribatid mites among regions using Mantel tests.
Results: Generally, the level of endemism of oribatid mite assemblages in the eleven regions was high; they formed three groups (west of New Guinea, New Guinea and south of New Guinea) with dissimilarity changing from northwest to southeast. The patterns reflect and integrate the lines of Weber, Lydekker and Holt. Species turnover generally correlated with geographic distance reflecting the critical role of vicariance in dispersal-limited oribatid mites.
Main conclusions: Our results, for the first time, demonstrate contrasting patterns in below- and aboveground organisms in the Indo-Australian Archipelago, and elucidate how geographic distance-based vicariance has structured soil animal diversity in this biodiversity hotspot region.
Dataset DOI: 10.5061/dryad.m905qfvbq
Description of the data and file structure
We compiled a list of 2,549 oribatid mite species in the Indo-Australian Archipelago and investigated the level of endemism and beta diversity of oribatid mites in the eleven regions at species, genus and family level. We then summarized the biogeographical dissimilarity patterns of oribatid mites using ordination and clustering methods, and compared the patterns with the zoological boundaries based on aboveground taxa such as the Wallace’s, Lydekker’s, Weber’s and Holt’s line. We integrated data on geography, climate and soil to reveal the key drivers of species compositional dissimilarity of oribatid mites among regions using Mantel tests.
Files and variables
File: all_mantel_rp_20241026.xlsx
Description: It summarized all results from Mantel permutation tests between geographic distance, climate and soil variables (column B) and beta-indexes (column A). Mantel's statistical r and p values are given in columns C and D.
File: GeoCoordinates_and_ClimateData_and_SoilData_20241026.xlsx
Description: It includes three sheets: Note_ClimaticFactors, Note_SoilFactors and allfactors_data. The third sheet is used to conduct analysis in R, and the first and second sheets are descriptions for each climate factor and each soil factor in the third sheet.
File: IAA_eleven_region_taxonmoic_list_20241026.xlsx
Description: This file includes 11 sheet table with each sheet table present the oribatid mite species we used in this paper. Those sheet tables are identical with the Supplementary TableS2–S12. Specifically, for each sheet table, variables from column A to column H are No., Infraorder, Family, Genus, Species.name.in.Subias2022, Species.name.in.paper, Distrbution.in.this.study, Distrbution.in.paper
Variables
| Column | Variables | Units | Description |
|---|---|---|---|
| A | No. | Count | How many oribatid mites were collected from this region |
| B | Infraorder | Categorical | Infomation are given according to Subías (2022) |
| C | Family | Categorical | Infomation are given according to Subías (2022) |
| D | Genus | Categorical | Infomation are given according to Subías (2022) |
| E | Species.name.in.Subias2022 | Categorical | Infomation are given according to Subías (2022) |
| F | Species.name.in.paper | Categorical | Oribatid mite species name in sourced paper |
| G | Distrbution.in.this.study | Categorical | Species distribution information in this study |
| H | Distrbution.in.paper | Categorical | Species distribution information in sourced paper |
Subías, L. S. 2022a. “Listado sistemático, sinonímico y biogeográfico de los ácaros oribátidos (Acariformes, Oribatida) del mundo (excepto fósiles) (17a actualización).”
File: Taxonomic_list_long_format_20241026.xlsx
Description: It includes taxonomic and distribution information at species/genus/family level in a long-data format. Specifically, variables from column A to column L are Species.name.in.Subias2022 (or Genus, and or Family), Australia, Bali, Borneo, Indo-China Peninsula, Java, Lesser Sunda Islands, New Guinea, New Zealand, Philippines, Sulawesi and Sumatra.
Variables
| Column | variables | units | description |
|---|---|---|---|
| A | Species.name.in.Subias2022 (or Genus, and or Family) | Categorical | Infomation are given according to Subías (2022) |
| B | Australia | Present/Absent | Species present/absent infomation in Australia |
| C | Bali | Present/Absent | Species present/absent infomation in Bali |
| D | Borneo | Present/Absent | Species present/absent infomation in Borneo |
| E | Indo-China Peninsula | Present/Absent | Species present/absent infomation in Indo-China Peninsula |
| F | Java | Present/Absent | Species present/absent infomation in Java |
| G | Lesser Sunda Islands | Present/Absent | Species present/absent infomation in Lesser Sunda Islands |
| H | New Guinea | Present/Absent | Species present/absent infomation in New Guinea |
| I | New Zealand | Present/Absent | Species present/absent infomation in New Zealand |
| J | Philippines | Present/Absent | Species present/absent infomation in Philippines |
| K | Sulawesi | Present/Absent | Species present/absent infomation in Sulawesi |
| L | Sumatra | Present/Absent | Species present/absent infomation in Sumatra |
Subías, L. S. 2022a. “Listado sistemático, sinonímico y biogeográfico de los ácaros oribátidos (Acariformes, Oribatida) del mundo (excepto fósiles) (17a actualización).”
File: Taxonomic_list_wide_format_20241026.xlsx
Description: It includes taxonomic and distribution information at species/genus/family level in a wide-data format. Specifically, the first column is distribution (including 11 regions: Australia, Bali, Borneo, Indo-China Peninsula, Java, Lesser Sunda Islands, New Guinea, New Zealand, Philippines, Sulawesi and Sumatra) and columns B–End are species/genus/family names.
Supplementary files (Zenodo)
Supplementary Figure S1-S21.docx ===== Figure captions are given below each figure.
Supplementary TableS1_keywords for the eleven regions.docx ===== Keywords for extracting the species list and their distribution information of the each eleven regions, i.e., Australia, Bali, Borneo, Indo-China Peninsula, Java and Lesser Sunda Islands. The regional classification in this study was basically based on the Lohman et al (2011) and Ali and Heaney (2021). Regions located in Sunda and Sahul shelf are marked in red and blue respectively.
Supplementary TableS2_Australia species list.xlsx ===== Full oribatid mite species list and their distribution in Australia. Specifically, variables from column A to column H are No., Infraorder, Family, Genus, Species.name.in.Subias2022, Species.name.in.paper, Distrbution.in.this.study, Distrbution.in.paper.
Supplementary TableS3_Bali species list.xlsx ===== Full oribatid mite species list and their distribution in Bali. Specifically, variables from column A to column H are No., Infraorder, Family, Genus, Species.name.in.Subias2022, Species.name.in.paper, Distrbution.in.this.study, Distrbution.in.paper.
Supplementary TableS4_Borneo species list.xlsx ===== Full oribatid mite species list and their distribution in Borneo. Specifically, variables from column A to column H are No., Infraorder, Family, Genus, Species.name.in.Subias2022, Species.name.in.paper, Distrbution.in.this.study, Distrbution.in.paper.
Supplementary TableS5_Indo-China Peninsula species list.xlsx ===== Full oribatid mite species list and their distribution in Indo-China Peninsula. Specifically, variables from column A to column H are No., Infraorder, Family, Genus, Species.name.in.Subias2022, Species.name.in.paper, Distrbution.in.this.study, Distrbution.in.paper.
Supplementary TableS6_Java species list.xlsx ===== Full oribatid mite species list and their distribution in Java. Specifically, variables from column A to column H are No., Infraorder, Family, Genus, Species.name.in.Subias2022, Species.name.in.paper, Distrbution.in.this.study, Distrbution.in.paper.
Supplementary TableS7_Lesser Sunda Islands species list.xlsx ===== Full oribatid mite species list and their distribution in Lesser Sunda Islands (excluding Bali). Specifically, variables from column A to column H are No., Infraorder, Family, Genus, Species.name.in.Subias2022, Species.name.in.paper, Distrbution.in.this.study, Distrbution.in.paper.
Supplementary TableS8_New Guinea species list.xlsx ===== Full oribatid mite species list and their distribution in New Guinea. Specifically, variables from column A to column H are No., Infraorder, Family, Genus, Species.name.in.Subias2022, Species.name.in.paper, Distrbution.in.this.study, Distrbution.in.paper.
Supplementary TableS9_New Zealand species list.xlsx ===== Full oribatid mite species list and their distribution in New Zealand. Specifically, variables from column A to column H are No., Infraorder, Family, Genus, Species.name.in.Subias2022, Species.name.in.paper, Distrbution.in.this.study, Distrbution.in.paper.
Supplementary TableS10_Philippines species list.xlsx ===== Full oribatid mite species list and their distribution in Philippines. Specifically, variables from column A to column H are No., Infraorder, Family, Genus, Species.name.in.Subias2022, Species.name.in.paper, Distrbution.in.this.study, Distrbution.in.paper.
Supplementary TableS11_Sulawesi species list.xlsx ===== Full oribatid mite species list and their distribution in Sulawesi. Specifically, variables from column A to column H are No., Infraorder, Family, Genus, Species.name.in.Subias2022, Species.name.in.paper, Distrbution.in.this.study, Distrbution.in.paper.
Supplementary TableS12_Sumatra species list.xlsx ===== Full oribatid mite species list and their distribution in Sumatra. Specifically, variables from column A to column H are No., Infraorder, Family, Genus, Species.name.in.Subias2022, Species.name.in.paper, Distrbution.in.this.study, Distrbution.in.paper.
Supplementary TableS13_Eleven Regions incidence data.xlsx ===== Presence–absence (‘1’–‘0’) matrix of oribatid mites in the eleven regions of the Indo-Australian Archipelago; columns represent regions and rows represent species.
Supplementary TableS14_Coordinates climatic and soil data.xlsx ===== Estimated geographic centroids (longitude and latitude) of polygons for each region and their climate and soil data. See section “Exploring drivers of dissimilarity” in the published paper for explanation of the variables.
Supplementary TableS15_UpSet_plot_info.xlsx ===== Details on oribatid mite species, genera, families and their unique or overlapped distribution based on the UpSet plot in Figures S2-S4.
Supplementary TableS16_Venn_plot_info.xlsx ===== Details on oribatid mite species, genera, families and their unique or overlapped distribution based on the Venn diagrams in Figure 4.
Supplementary TableS17_Mantel R_P-values.docx ===== Results of Mantel tests using Person’s correlations among geographic, climatic and soil variables and oribatid mite dissimilarity at species level for pairs of region of the Indo-Australian Archipelago. Significant effects (P < 0.05) are given in red and bold.
Code/software (Zenodo)
GEB_ordination_Species+Genus+Family levels.R ===== All data were analysed in R (version 4.1.3). The R script is structured by different headers/ annotations/ comments leading through the script. The R script can be used to reproduce results.
GEB_upset plot and intersection info_Species+Genus+Family levels.R ===== All data were analysed in R (version 4.1.3). The R script is structured by different headers/ annotations/ comments leading through the script. The R script can be used to reproduce results.
GEB_Venn Digram_Species+Genus+Family levels.R ===== All data were analysed in R (version 4.1.3). The R script is structured by different headers/ annotations/ comments leading through the script. The R script can be used to reproduce results.
GEB_β-diversity and mantel Pearson test_FamilyLevel.R ===== All data were analysed in R (version 4.1.3). The R script is structured by different headers/ annotations/ comments leading through the script. The R script can be used to reproduce results.
GEB_β-diversity and mantel Pearson test_GenusLevel.R ===== All data were analysed in R (version 4.1.3). The R script is structured by different headers/ annotations/ comments leading through the script. The R script can be used to reproduce results.
GEB_β-diversity and mantel Pearson test_SpeciesLevel.R ===== All data were analysed in R (version 4.1.3). The R script is structured by different headers/ annotations/ comments leading through the script. The R script can be used to reproduce results.
Access information
Other publicly accessible locations of the data:
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Data was derived from the following sources:
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We extracted the list of species of oribatid mites (including genus and family) of the Indo-Australian Archipelago from Colloff (2023), Corpuz-Raros and Ermilov (2019, 2020) and Subías (2022), and grouped the distribution of the species into eleven regions, i.e., Australia, Bali, Borneo, Indo-China Peninsula, Java, Lesser Sunda Islands (excluding Bali), New Guinea, New Zealand, Philippines, Sulawesi and Sumatra (Figure 1, Table S1). Species names of oribatid mites were standardized following Subías (2022) for the following reasons: (a) Subías’ (2022) includes oribatid mites across the world. By contrast, the classification used in other papers such as Corpuz-Raros and Ermilov (2019, 2020) and Niedbała and Liu (2023) only includes certain taxa, with most of the subdivisions of large families and genera also being adopted from Subías but from his 2004 catalogue (Subías, 2004) and not the more recent and updated one from 2022. (b) A recent study based on molecular data of 317 oribatid mite species/taxa revealed that a number of traits used for the taxonomic classification of oribatid mites evolved convergently and therefore the current classification is likely to change substantially in future (Cordes et al., 2024). (c) Subías’ (2022) classification was used in a recent biogeographic study (Lu et al., 2024) allowing to compare our results with this previous publication. Species lists of the eleven regions and distribution data are given in Tables S2–S12. Species occurrences across the eleven regions were transformed into a presence–absence (‘1’–‘0’) matrix (Table S13).