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Abstract <bold>Background</bold>Existing software for comparison of species delimitation models do not provide a (true) metric or distance functions between species delimitation models, nor a way to compare these models in terms of relative clustering differences along a lattice of partitions. <bold>Results</bold>is a Python package for analyzing and visualizing species delimitation models in an information theoretic framework that, in addition to classic measures of information such as the entropy and mutual information [1], provides for the calculation of the Variation of Information (VI) criterion [2], a true metric or distance function for species delimitation models that is aligned with the lattice of partitions. <bold>Conclusions</bold>is available under the MIT license from its public repository (https://github.com/jeetsukumaran/piikun), and can be installed locally using the Python package manager ‘pip‘. 

ABSTRACT Although patterns of population genomic variation are well‐studied in animals, there remains room for studies that focus on non‐model taxa with unique biologies. Here we characterise and attempt to explain such patterns in mygalomorph spiders, which are generally sedentary, often occur as spatially clustered demes and show remarkable longevity. Genome‐wide single nucleotide polymorphism (SNP) data were collected for 500 individuals across a phylogenetically representative sample of taxa. We inferred genetic populations within focal taxa using a phylogenetically informed clustering approach, and characterised patterns of diversity and differentiation within‐ and among these genetic populations, respectively. Using phylogenetic comparative methods we asked whether geographical range sizes and ecomorphological variables (behavioural niche and body size) significantly explain patterns of diversity and differentiation. Specifically, we predicted higher genetic diversity in genetic populations with larger geographical ranges, and in small‐bodied taxa. We also predicted greater genetic differentiation in small‐bodied taxa, and in burrowing taxa. We recovered several significant predictors of genetic diversity, but not genetic differentiation. However, we found generally high differentiation across genetic populations for all focal taxa, and a consistent signal for isolation‐by‐distance irrespective of behavioural niche or body size. We hypothesise that high population genetic structuring, likely reflecting combined dispersal limitation and microhabitat specificity, is a shared trait for all mygalomorphs. Few studies have found ubiquitous genetic structuring for an entire ancient and species‐rich animal clade. 

The systematics of humble-in-appearance brown spiders (“marronoids”), within a larger group of spiders with a modified retrolateral tibial apophysis (the RTA Clade), has long vexed arachnologists. Although not yet fully settled, recent phylogenomics has allowed the delimitation and phylogenetic relationships of families within marronoids to come into focus. Understanding relationships within these families still awaits more comprehensive generic-level sampling, as the majority of described marronoid genera remain unsampled for phylogenomic data. Here we conduct such an analysis in the family Cybaeidae Banks, 1892. We greatly increase generic-level sampling, assembling ultraconserved element (UCE) data for 18 of 22 described cybaeid genera, including all North American genera, and rigorously test family monophyly using a comprehensive outgroup taxon sample. We also conduct analyses of traditional Sanger loci, allowing curation of some previously published data. Our UCE phylogenomic results support the monophyly of recognized cybaeids, with strongly supported internal relationships, and evidence for five primary molecular subclades. We hypothesize potential morphological synapomorphies for most of these subclades, bringing a robust phylogenomic underpinning to cybaeid classification. A new cybaeid genusSiskiyugen. nov.and speciesSiskiyu armillasp. nov.is discovered and described from far northern California and adjacent southern Oregon and a new species in the elusive genusCybaeozyga,C. furtivasp. nov., is described from far northern California. 

The rarely encountered spider genusHexurellaGertsch & Platnick, 1979 includes some of the smallest mygalomorph spiders in the world, with four poorly known taxa from central and southeastern montane Arizona, southern California, and northern Baja California Norte. At time of description the genus was known from fewer than 20 individuals, with sparse natural history information suggesting a vagrant, web-building, litter-dwelling natural history. Here the first published taxonomic and natural history information for this taxon is provided in more than 50 years, working from extensive new geographic sampling, consideration of male and female morphology, and sequence capture-based nuclear phylogenomics and mitogenomics. Several new species are easily diagnosed based on distinctive male morphologies, while a complex of populations from central and northern Arizona required an integrative combination of genomic algorithmic species delimitation analyses and morphological study. Four new species are described, includingH. ephedrasp. nov.,H. uwiiltilsp. nov.,H. xericasp. nov., andH. zassp. nov.Females ofH. encinaGertsch & Platnick, 1979 are also described for the first time. It is predicted that additional new species will ultimately be found in the mountains of central and northwestern Arizona, northern mainland Mexico, and the Mojave Desert of California. 

This revision is based on sampling efforts over the past three decades in the southern Appalachian Mountains which have providedNesticus(Araneae, Nesticidae) collections of approximately 2100 adult specimens from more than 475 unique collecting events. Using a “morphology first” framework we examined recently collected specimens plus museum material to formulate morphology-based species hypotheses for putative new taxa (discovery phase). Using sequence capture of nuclear ultraconserved elements (UCEs) we analyzed 801 nuclear loci to validate new (and prior) morphology-based species hypotheses (validation phase) and reconstructed a robust backbone phylogeny including all described and new species. Sanger sequencing and UCE-bycatch were also used to gather mitochondrial data for more than 240 specimens. Based on our integrative taxonomic framework ten newNesticusspecies are herein described, includingN. binfordaesp. nov.,N. bondisp. nov.,N. caneisp. nov.,N. cherokeensissp. nov.,N. dellingerisp. nov.,N. dykemanaesp. nov.,N. jemisinaesp. nov.,N. lowderisp. nov.,N. roanensissp. nov., andN. templetonisp. nov.Previously unknown males are also described forN. bishopiGertsch, 1984,N. crosbyiGertsch, 1984, andN. silvanusGertsch, 1984, as well as the previously unknown female forN. mimusGertsch, 1984. Based on combined evidenceN. cooperiGertsch, 1984 is placed in synonymy withN. reclususGertsch, 1984. Overall, the montane radiation of AppalachianNesticusreveals a general lack of species sympatry and compelling biogeographic patterns. Several regionalNesticustaxa are rare, microendemic habitat specialists that deserve conservation attention and detailed future monitoring as conservation sentinels. 

Hypochilus is a relictual lineage of Nearctic spiders 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, and conserved morphology coupled with extreme genetic divergence has led to uncertain species limits in some complexes. Here, Hypochilus interspecies relationships have been reconstructed and cryptic speciation more critically evaluated using a combination of ultraconserved elements, mitochondrial CO1 by-catch, and morphology. Phylogenomic data strongly support the monophyly of regional clades and support a ((California, Appalachia), southern Rocky Mountains) topology. In Appalachia, 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. The Appalachian species H. pococki Platnick, 1987 is recovered as monophyletic but is highly genetically structured at the nuclear level. While algorithmic analyses of nuclear data indicate many species (e.g., all H. pococki populations as species), male morphology instead reveals striking stasis. 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. Combining nuclear, mitochondrial, geographical, and morphological evidence a new species from the Tule River and Cedar Creek drainages is described, Hypochilus xomote sp. nov. We also emphasize the conservation issues that face several microendemic, habitat-specialized species in this remarkable genus.