Data from: Microallopatric speciation in southern African dung beetle genus Macroderes driven by Miocene aridification and ancestral flight loss
Data files
Oct 20, 2025 version files 677.61 KB
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16S.fas
18.80 KB
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28S.fas
26.25 KB
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CAD.fas
34.81 KB
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COI.fasta
62.38 KB
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Data_S1.xml
345.11 KB
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Data_S2.xml
180.07 KB
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flight_mode_data.csv
1.27 KB
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habitat_reconstruction_data.csv
469 B
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pruned_tree_2.nwk
1.48 KB
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range.data
1.20 KB
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README.md
3.27 KB
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tip_labels.csv
2.50 KB
Abstract
Southern Africa hosts a highly diverse array of dung beetles (Scarabaeidae: Scarabaeinae), the majority of which are endemic to the region. However, the historical drivers of this diversity remain largely unexplored. While each lineage exhibits a distinct diversification history, many remain poorly understood. To address this gap, we employed molecular phylogenetic analyses to investigate the evolutionary history of the flightless dung beetle genus Macroderes Westwood, which comprises 21 species with highly restricted distributions, collectively covering a relatively small geographic range. Specifically, we tested the hypothesis of monophyly of the genus Macroderes and inferred its hypothesised biogeographical history. Using biogeographical analyses and ancestral character reconstruction, we examined the genus's origins, environmental adaptations (semi-arid vs. moist habitats), and the emergence of flightlessness as an adaptive trait. Additionally, we explored how late Cenozoic aridification in southwestern Africa influenced the microallopatric speciation patterns observed today. Our findings indicate that Macroderes represents a monophyletic lineage, with its most recent common ancestor (MRCA) originating in the late Miocene (~8.44 mya; 95 % CI: 9.74–7.06 mya). The MRCA was flightless and associated with a semi-arid environment resembling the present-day Succulent Karoo biome of South Africa. This was followed by multiple southward colonization events from the Karoo into Fynbos. This repeated southward movement highlights the dynamic evolutionary history of Macroderes and the significant role of environmental transitions in shaping its lineage. Furthermore, our analyses suggest that intensified aridification in southwestern Africa played a pivotal role in the genus's diversification. The emergence of flightlessness appears intrinsically linked to semi-arid conditions, providing a compelling explanation for the genus's short-range endemicity. In summary, both aridification and flightlessness have been key drivers of the microallopatric speciation patterns observed within Macroderes.
The dataset comprises raw molecular data used for phylogenetic inferences. We have also included distribution data used for biogeographical inferences as well as data for ancestral trait reconstruction.
Description of the data and file structure
- The molecular data comprises five gene regions as follows: three ribosomal genes (16S and 28S) and two protein-coding genes (COI - Cytochrome Oxidase subunit I and CAD - carbamoyl-phosphate synthetase-aspartate transcarbamoylase-dihydroorotase). The data are in fasta file format. The same tree was used for biogeographical, diversification analyses and ancestral character reconstruction analyses. These tree files can be viewed in R or Fig tree programs.
- For biogeographical analyses we used two data files: (range. data) contains the distribution ranges of each species. The distribution ranges are represented by letters A, B, C, D and E., as follows: (A) Succulent Karoo, (B) Fynbos, (C) Savanna, (D) Grassland, and (E) Forest
Here are the list of the files and respective details.
a) 16S.fasta - .fasta files can be viewed in a standard text editor, like notepad or notepad ++ .
b) 28S.fasta - .fasta files can be viewed in a standard text editor, like notepad or notepad ++ .
c) CAD.fasta - .fasta files can be viewed in a standard text editor, like notepad or notepad ++ .
d) COI.fasta - .fasta files can be viewed in a standard text editor, like notepad or notepad ++ .
e) pruned_tree_2.nwk - This is a dated molecular tre file used for biogeographical, diversification analyses and ancestral character reconstruction analyses. The .nwk file can be viewed in a standard text editor, like notepad or notepad ++, but to visualize the tree we use FigTree program.
f) flight_mode_data.csv – This file contains data on the presence or absence of hind wings, used to assess whether the ancestral form of Macroderes was flightless or capable of flight. It can be viewed using standard Microsoft Excel.
g) habitat_reconstruction_data.csv – This file includes habitat data (moist vs. semi-arid) used to evaluate whether the ancestral form of Macroderes was associated with semi-arid environments. It can be viewed using standard Microsoft Excel.
h) range.data. This file contains distribution data of the species used in the biogeographical analysis. The .data files queue be opened in a standard text editor, like notepad or notepad ++ .
i) tip_labels.xlsx – This file contains codes and abbreviations used in the molecular dataset. It is compatible with standard Microsoft Excel.
i) tip_labels.csv – This file contains codes and abbreviations used in the molecular dataset. It is compatible with standard Microsoft Excel.
j) Data_S1.xml - Table listing the Macroderes species analysed in this study, along with their respective collection localities and GenBank accession numbers.It is compatible with standard Microsoft Word.
l) Data_S2.xml. Table listing the outgroup taxa included in the phylogeny in this study, along with their respective collection GenBank accession numbers.It is compatible with standard Microsoft Word.