Out of north Africa: Evolution and biogeography of Afro-Arabian dwarf tarantulas (Theraphosidae, Ischnocolinae)
Data files
Jan 15, 2026 version files 58.41 MB
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All_Ischnocolus_70_partitions_models.txt.nex
60.71 KB
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All_Ischnocolus_70.phylip
25.29 MB
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All_Ischnocolus_90_partitions_models.txt.nex
2.54 KB
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All_Ischnocolus_90.phylip
2.84 MB
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All_Mygalomorpahe_90.phylip
3.96 MB
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All_Mygalomorpahe-70.phylip
26.24 MB
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All_Mygalomorphae_70_partitions_models.txt.nex
15.87 KB
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All_Mygalomorphae_90_partitions_models.txt.nex
2.66 KB
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README.md
4.87 KB
Abstract
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.
Out of North Africa: Evolution and biogeography of Afro-Arabian dwarf tarantulas (Theraphosidae, Ischnocolinae)
https://doi.org/10.5061/dryad.wm37pvmz2
Jan Korba1 and Vera Opatova1*
1Department of Zoology, Faculty of Sciences, Charles University, Viničná 7, Prague 2, 128 44, Czech Republic
*Corresponding Author: Vera.Opatova@gmail.com
Jan Korba: https://orcid.org/0009-0006-0578-1725
Vera Opatova: 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.
