DOI: 10.5061/dryad.g1jwstqsd
title: Data from: Phylogenomics of paleoendemic lampshade spiders (Araneae, Hypochilidae, Hypochilus), with description of a new species from montane California

description: The spider genus Hypochilus is a relictual lineage of Nearctic species
 distributed disjunctly across the United States in three montane regions
 (California, southern Rocky Mountains, southern Appalachia). Phylogenetic
 resolution of species relationships in Hypochilus has been challenging,
 with different data types recovering sometimes conflicting topologies.
 Furthermore, conserved morphology coupled with extreme genetic divergence
 and paraphyletic topologies at the species level has led to uncertain
 species limits in some complexes. Using a combination of ultraconserved
 elements (UCEs), mitochondrial CO1 by-catch, and studies of morphology, we
 have reconstructed Hypochilus interspecies relationships and have more
 critically evaluated the possibility of cryptic species in California and
 in southern Appalachia. Phylogenomic data from hundreds of nuclear loci
 strongly support the monophyly of regional clades, and furthermore support
 a ((California, Appalachia), southern Rocky Mountains)) topology. We
 hypothesize late Cenozoic age divergences in North America, but
 acknowledge that more research is needed to reliably date divergences in
 this genus. Within the southern Appalachian fauna, five species are
 resolved as four lineages (H. thorelli Marx, 1888 and H. coylei Platnick,
 1987 are clearly sister taxa), but the interrelationships of these four
 lineages remain unresolved despite phylogenomic-scale data. The
 Appalachian species H. pococki Platnick, 1987 is recovered as
 monophyletic, which differs from prior mitochondrial evidence, but is
 clearly highly genetically structured at the nuclear level. Although
 algorithmic analyses of the nuclear data indicate many species (e.g., all
 populations as species), scanning electron microscopy (SEM) surveys of
 male morphology instead reveal striking morphological stasis, clearly
 illustrating the cryptic species problem. Within the California clade,
 nuclear and mitochondrial lineages of H. petrunkevitchi Gertsch, 1958
 correspond directly to drainage basins of the southern Sierra Nevada, with
 H. bernardino Catley, 1994 nested within H. petrunkevitchi and sister to
 the southernmost basin populations. Again, algorithmic analyses of nuclear
 and mitochondrial data suggest many species, but we take a more
 conservative approach, allowing for population genetic structure within
 species. Combining nuclear, mitochondrial, geographic and morphological
 evidence we describe a new species from the Tule River and Cedar Creek
 drainages, Hypochilus xomote sp. nov. We also emphasize the conservation
 issues that face several microendemic, habitat-specialized species in this
 remarkable genus.
description: Sequence capture libraries were prepared using a UCE capture
 protocol for arachnids (Starrett <em>et al.</em> 2017, Hedin
 <em>et al.</em> 2019), with arachnid probes designed by
 Faircloth (2017). Sequencing was done at the Brigham Young University DNA
 Sequencing Center on an Illumina HiSeq 2500 150 cycle paired-end
 sequencing platform. Published data for two <em>H. pococki
 </em>specimens (H595 and H232, from Starrett <em>et
 al.</em> 2017), one <em>H. kastoni</em> Platnick, 1987
 (G2519, Hedin <em>et al.</em> 2019), and
 <em>Ectatosticta </em>(Ramírez <em>et al.</em>
 2021) were used from prior studies. Raw reads were filtered using the
 illumiprocessor wrapper (Faircloth 2013) within PHYLUCE v1.6 (Faircloth
 2016), after which cleaned reads were assembled using Trinity v2.0.6
 (Grabherr <em>et al.</em> 2011) and Velvet v1.0.19 (Zerbino
 and Birney 2008) on the HPC Cluster at UC Riverside. These assemblies were
 combined and resulting contigs were matched to probes with minimum
 identity and minimum coverage values of 80 (--min-identity 80
 --min-coverage 80). UCE loci were aligned and trimmed within phyluce using
 MAFFT (Katoh and Standley 2013) and Gblocks (Castresana 2000; Talavera and
 Castresana 2007) with relatively liberal settings for GBLOCKS (--b1 0.5
 --b2 0.5 --b3 10 --b4 8).