DOI: 10.5061/dryad.wm37pvmz2
title: Out of north Africa: Evolution and biogeography of Afro-Arabian dwarf tarantulas (Theraphosidae, Ischnocolinae)

description: Large-scale vicariant events are expected to create congruent
 phylogeographic patterns among unrelated taxa. A continental-wide
 disjunction displayed by unrelated plant taxa across Afro-Arabia (the RAND
 flora pattern) has been traditionally explained as a consequence of late
 Miocene aridification of the region and the formation of the Sahara
 Desert. We implement genomic data (UCE), divergence time estimation and
 biogeographic analyses to uncover the origins of RAND pattern distribution
 in dwarf tarantula genus Ischnocolus Ausserer, 1871. The results suggest
 that the disjunct distribution of Ischnocolus resulted from ecological
 vicariance driven by the Middle Miocene climate cooling, predating the
 timing of the aridification of the region. Our results thus bring evidence
 of phylogeographic discordance of the RAND pattern origins among different
 taxa. Conserved lifestyle and the preference for humid environments among
 the early diverging Ischnocolus lineages also suggest that dispersal
 across Afro-Arabia was likely catalyzed by interspecific competitive
 exclusion. Subsequent lifestyle switches, that enabled the dwarf
 tarantulas to successfully colonize dry environments, evolved repeatedly
 in the group’s evolution. Additionally, we delimit the boundaries of the
 genus Ischnocolus and assess its position within the tarantula phylogeny.
 As a consequence, we revalidate the genus Luphocemus Denis, 1960, which is
 endemic to North Africa.
description: ## **Out of North Africa: Evolution and biogeography of Afro-Arabian dwarf
 tarantulas (Theraphosidae, Ischnocolinae)**
 [https://doi.org/10.5061/dryad.wm37pvmz2](https://doi.org/10.5061/dryad.wm37pvmz2) Jan Korba^1^ and Vera Opatova^1^* *^1^Department of Zoology, Faculty of Sciences, Charles University, Viničná 7, Prague 2, 128 44, Czech Republic* *Corresponding Author: [Vera.Opatova@gmail.com](mailto:Vera.Opatova@gmail.com) Jan Korba: [https://orcid.org/0009-0006-0578-1725](https://orcid.org/0009-0006-0578-1725) Vera Opatova: [https://orcid.org/0000-0002-4324-1344](https://orcid.org/0000-0002-4324-1344) ## Description of the data and file structure Data type: Genomic DNA sequence data, Ultraconserved elemets (UCE) Raw sequence reads were processed using *illumiprocessor* (Faircloth, 2013) and *trimmomatic* (Bolger et al., 2014), both implemented within the *Phyluce v.1.7.3.* pipeline (Faircloth, 2016). Assemblies were conducted de novo using SPAdes 3.14.1 (Prjibelski et al., 2020) and Abyss v.2.1.5 (Simpson et al., 2009). The reads were subsequently matched against the Spider2Kit UCE probe set (Kulkarni et al., 2020). Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina sequence data. *Bioinformatics*, *30*(15), 2114–2120. Faircloth, B. (2013). *Illumiprocessor: A trimmomatic wrapper for parallel adapter and quality trimming*. Faircloth, B. C. (2016). PHYLUCE is a software package for the analysis of conserved genomic loci. *Bioinformatics*, *32*(5), Article 5. Kulkarni, S., Wood, H., Lloyd, M., & Hormiga, G. (2020). Spider‐specific probe set for ultraconserved elements offers new perspectives on the evolutionary history of spiders (Arachnida, Araneae). *Molecular Ecology Resources*, *20*(1), Article 1. Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A., & Korobeynikov, A. (2020). Using SPAdes de novo assembler. *Current Protocols in Bioinformatics*, *70*(1), e102. Simpson, J. T., Wong, K., Jackman, S. D., Schein, J. E., Jones, S. J., & Birol, I. (2009). ABySS: a parallel assembler for short read sequence data. *Genome Research*, *19*(6), 1117–1123. **Data Matrices:** Data format: phylip, missing data "?", gaps "- " Matrix structure: [number of taxa sequence lenght in base pairs (bp)] 70% occupancy matrices: `All_Mygalomorpahe-70.phylip` (Comprises ingroup + outgroup taxa) \[78 taxa 336349 bp] `All_Ischnocolus_70.phylip` (Comprises ingroup taxa) \[37 taxa 683365 bp] 90% occupancy matrices: `All_Mygalomorpahe_90.phylip` (Comprises ingroup + outgroup taxa) \[78 taxa 336349 bp] `All_Ischnocolus_90.phylip` (Comprises ingroup taxa) \[37 taxa 50740 bp] Data matrixes and their corresponding partition files (see below) were used in Maximum likelihood analyses conducted in IQ-TREE v.2 (Minh et al., 2020) Minh, B. Q., Schmidt, H. A., Chernomor, O., Schrempf, D., Woodhams, M. D., Von Haeseler, A., & Lanfear, R. (2020). IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. *Molecular Biology and Evolution*, *37*(5), 1530–1534. **Partition files:** `All_Mygalomorphae_70_partitions_models.txt.nex` \- to be used with "All_Mygalomorpahe-70.phylip" matrix `All_Ischnocolus_70_partitions_models.txt.nex` - to be used with "All_Ischnocolus_70.phylip" matrix `All_Mygalomorphae_90_partitions_models.txt.nex` - to be used with "All_Mygalomorpahe-90.phylip" matrix `All_Ischnocolus_90_partitions_models.txt.nex` - to be used with "All_Ischnocolus_70.phylip" matrix Partition files comprise information about the position position of the linidividual loci in their respective matrixes. Loci are merged into paritions with an assigned nucleotide substitution model selected by MODELFINDER (Kalyaanamoorthy et al. 2017). Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A., & Jermiin, L. S. (2017). ModelFinder: Fast model selection for accurate phylogenetic estimates. *Nature Methods*, *14*(6), 587–589. ## Sharing/Access information Data was derived from the following sources: Source data proceeding from other publications (see "Table Supplemental Table S1") are available from the following Sequence Read Archives: SRR8944274 SRR8944272 SRR8944284 SRR8944286 SRR18936171 SAMN33786863 SRR8944269 SRR8944283 SRR1024075 SRR13605914 SRR8944280 SRR8944287 SRR8944281 SRR8944270 SRR8944285 SRR8944282 SRR8944275 SRR8944262 SRR8944263 ERR2008012 SRR8944260 SRR8944276 SRR1514881 SRR8944261 Source Publications: Foley, S., Krehenwinkel, H., Cheng, D.-Q., & Piel, W. H. (2021). Phylogenomic analyses reveal a Gondwanan origin and repeated out of India colonizations into Asia by tarantulas (Araneae: Theraphosidae). PeerJ, 9, e11162. Ortiz, D. (2023). High utility of Ultraconserved Elements (UCE) for disentangling the elusive relationships of tarantulas. Zoologica Scripta, 52(6), 645–653.