DOI: 10.5061/dryad.m905qfvbq
title: The key role of vicariance for soil animal biogeography in a biodiversity hotspot region

description: 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.
description: 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
 <em>et al.</em>, 2024). (c) Subías’ (2022) classification was
 used in a recent biogeographic study (Lu <em>et al.</em>,
 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).
description: # The key role of vicariance for soil animal biogeography in a
 biodiversity hotspot region Dataset DOI:
 [10.5061/dryad.m905qfvbq](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* &lt; 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: * No Data was derived from the
 following sources: * No