DOI: 10.5061/dryad.j0zpc86v1
title: Data from: Microallopatric speciation in southern African dung beetle genus <em>Macroderes</em> driven by Miocene aridification and ancestral flight loss

description: 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.
description: # README: Data from: Microallopatric speciation in southern African dung
 beetle genus *Macroderes* driven by Miocene aridification and ancestral
 flight loss 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.