Supplementary information of: High utility of Ultraconserved Elements (UCE) to resolve the long-lasting puzzle of tarantula phylogenetics

   Although tarantulas are a widespread, highly diversified, and charismatic spider group, our understanding of their evolution remains limited. A recent transcriptome-based approach, including 16% of the nominal tarantula genera (25), provided the first robust phylogenetic hypothesis of deep tarantula relationships. However, transcriptomics has practical downsides, making it less than ideal for phylogenomic analyses. Ultraconserved Elements (UCE) sequencing, a cost-effective alternative, allows for the simultaneous reading of hundreds of loci and utilizing samples with degraded DNA, including museum material, but its utility for resolving tarantula relationships remains to be tested. In this study, I recovered up to ~850 unique UCE loci from publicly available individual tarantula transcriptomes. Phylogenetic estimation using these loci resulted in topologies identical to those obtained from the published complete transcriptomic datasets, with limited phylogenetic uncertainty restricted to two branches in the tarantula tree of life. I conclude that UCE information has great potential for resolving tarantula relationships and that numerous UCE loci can be harvested from tarantula transcriptomic data. Finally, I provide databases of transcripts and UCE loci for the 27 currently available tarantula genera, facilitating their inclusion in future phylogenomic studies with deeper taxon coverage.</p

Appendix S3. Maximum Likelihood COI tree

Maximum Likelihood COI tre

Appendix S5. Mean intra- and inter-specific p distances of Bonnetina species

Intra and inter-specific p distances of Bonnetina datase

Appendix S2. MaxEnt predicted distribution models

Bonnetina species distribution model

Appendix S4. Species delimitation analyses

Species delimitation result

Appendix S1. Bonnetina-COI-2016 matrix

MSA of Bonnetina-CO

Supplementary information of: Phylogenomics and loci dropout patterns of deeply diverged Zodarion ant-eating spiders suggest a high potential of RAD-seq for genus-level spider phylogenetics

Supplementary information of paper:Phylogenomics and loci dropout patterns of deeply diverged Zodarion ant-eating spiders suggest a high potential of RAD-seq for genus-level spider phylogenetics</div

Two DNA barcodes and morphology for multi-method species delimitation in <i>Bonnetina</i> tarantulas (Araneae: Theraphosidae)

<p>Supplementary data of the paper in the title</p

Supplementary information of: Gene flow assessment helps to distinguish strong genomic structure from speciation in an Iberian ant-eating spider

Although genomic data is boosting our understanding of evolution, we still lack a solid framework to perform reliable genome-based species delineation. This problem is especially critical in the case of phylogeographically structured organisms, with allopatric populations showing similar divergence patterns as species. Here, we assess the species limits and phylogeography of Zodarion alacre, an ant-eating spider widely distributed across the Iberian Peninsula. We first performed species delimitation based on genome-wide data and then validated these results using additional evidence. A commonly employed species delimitation strategy detected four distinct lineages with almost no admixture, which present allopatric distributions. These lineages showed ecological differentiation but no clear morphological differentiation, and evidence of introgression in a mitochondrial barcode. Phylogenomic networks found evidence of substantial gene flow between lineages. Finally, phylogeographic methods highlighted remarkable isolation by distance and detected evidence of range expansion from south-central Portugal to central-north Spain. We conclude that despite their deep genomic differentiation, the lineages of Z. alacre do not show evidence of complete speciation. Our results likely shed light on why Zodarion is among the most diversified spider genera despite its limited distribution and support the use of gene flow evidence to inform species boundaries.</p

Supplementary information: A tangle of forms and phylogeny: extensive morphological homoplasy and molecular clock heterogeneity in Bonnetina and related tarantulas

Supplementary information of paper: <div>A tangle of forms and phylogeny: extensive morphological homoplasy and molecular clock heterogeneity in <i>Bonnetina</i> and related tarantulas<p><b></b></p></div