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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. 

Abstract The recognition and delineation of cryptic species remains a perplexing problem in systematics, evolution, and species delimitation. Once recognized as such, cryptic species complexes provide fertile ground for studying genetic divergence within the context of phenotypic and ecological divergence (or lack thereof). Herein we document the discovery of a new cryptic species of trapdoor spider,Promyrmekiaphila korematsuisp. nov. Using subgenomic data obtained via target enrichment, we document the phylogeography of the California endemic genusPromyrmekiaphilaand its constituent species, which also includesP. clathrataandP. winnemem. Based on these data we show a pattern of strong geographic structuring among populations but cannot entirely discount recent gene flow among populations that are parapatric, particularly for deeply diverged lineages withinP. clathrata. The genetic data, in addition to revealing a new undescribed species, also allude to a pattern of potential phenotypic differentiation where species likely come into close contact. Alternatively, phenotypic cohesion among genetically divergentP. clathratalineages suggests that some level of gene flow is ongoing or occurred in the recent past. Despite considerable field collection efforts over many years, additional sampling in potential zones of contact for both species and lineages is needed to completely resolve the dynamics of divergence inPromyrmekiaphilaat the population–species interface. 

Abstract Species delimitation is an imperative first step toward understanding Earth's biodiversity, yet what constitutes a species and the relative importance of the various processes by which new species arise continue to be debatable. Species delimitation in spiders has traditionally used morphological characters; however, certain mygalomorph spiders exhibit morphological homogeneity despite long periods of population‐level isolation, absence of gene flow, and consequent high degrees of molecular divergence. Studies have shown strong geographic structuring and significant genetic divergence among several species complexes within the trapdoor spider genusAptostichus, most of which are restricted to the California Floristic Province (CAFP) biodiversity hotspot. Specifically, theAptostichus icenogleicomplex, which comprises the three sibling species,A. barackobamai,A. isabella, andA. icenoglei, exhibits evidence of cryptic mitochondrial DNA diversity throughout their ranges in Northern, Central, and Southern California. Our study aimed to explicitly test species hypotheses within this assemblage by implementing a cohesion species‐based approach. We used genomic‐scale data (ultraconserved elements, UCEs) to first evaluate genetic exchangeability and then assessed ecological interchangeability of genetic lineages. Biogeographical analysis was used to assess the likelihood of dispersal versus vicariance events that may have influenced speciation pattern and process across the CAFP's complex geologic and topographic landscape. Considering the lack of congruence across data types and analyses, we take a more conservative approach by retaining species boundaries withinA. icenoglei. 

Abstract We report here the discovery of a remarkable new monotypic mygalomorph spider genus, known only from one geographical location along the central coast of California. The single relict species comprising Cryptocteniza kawtakn. gen. n. sp., is morphologically distinct and geographically isolated from other related genera, with its closest phylogenetic relatives found much further to the east in New Mexico and Arizona. Using a phylogenomic approach employing anchored hybrid enrichment, we reconstruct the evolutionary history of the family Euctenizidae Raven, 1985 to explore relationships among genera, affirmatively place previously undescribed taxa, explore rates of diversification, and reconstruct the group’s biogeography. A biogeographic analysis shows that extinction likely played a significant role in shaping the observed disjunct modern-day distribution of Cryptocteniza and its sister taxa. Our extinction hypothesis is further bolstered by a diversification rate analysis identifying considerably higher rates of speciation in other euctenizid lineages like AptostichusSimon, 1891. Consequently, changes in environmental conditions (or other related biotic and/or abiotic factors) may have spurred an adaptive radiation in related genera now widely distributed across the California Floristic Province biodiversity hotspot, with concomitant extinction in Cryptocteniza following the Miocene and establishment of a Mediterranean climate. Owing to its phylogenetic distinctiveness, incredibly narrow distribution and age, we show that Cryptocteniza meets all the criteria of an ‘Endangered Living Fossil’ and is consequently of grave conservation concern. 

Abstract Animals communicate using a diversity of signals produced by a wide array of physical structures. Determining how a signal is produced provides key insights into signal evolution. Here, we examine a complex vibratory mating display produced by maleSchizocosa floridanawolf spiders. This display contains three discrete substrate‐borne acoustic components (known as “thumps”, “taps”, and “chirps”), each of which is anecdotally associated with the movement of a different body part (the pedipalps, legs, and abdomen respectively). In order to determine the method of production, we employ a combination of high‐speed video/audio recordings and SEM imaging of possible sound‐producing structures. Previous work has suggested that the “chirp” component is tonal, a signal trait that would be potentially unique in the genus. We measured signal tonality for all courtship components, as well as for courtship components from sixteen otherSchizocosawolf spiders. Our results suggest thatS. floridanaproduces courtship song using a combination of shared (palpal stridulation and foreleg percussion) and novel (abdominal movement) sound production mechanisms. Of particular interest, the “chirp”, which is produced using a novel abdominal production mechanism, is the only known tonal signal with acoustic properties that are unique within the genus. We argue that the potential evolution of a novel sound production mechanism has opened up a new axis of signaling trait space in this species, with important implications for how this signal is likely to function and evolve. 

Abstract The integration of ecological niche modelling into phylogeographic analyses has allowed for the identification and testing of potential refugia under a hypothesis‐based framework, where the expected patterns of higher genetic diversity in refugial populations and evidence of range expansion of nonrefugial populations are corroborated with empirical data. In this study, we focus on a montane‐restricted cryophilic harvestman,Sclerobunus robustus, distributed throughout the heterogeneous Southern Rocky Mountains and Intermontane Plateau of southwestern North America. We identified hypothetical refugia using ecological niche models (ENMs) across three time periods, corroborated these refugia with population genetic methods using double‐digest RAD‐seq data and conducted population‐level phylogenetic and divergence dating analyses. ENMs identify two large temporally persistent regions in the mid‐latitude highlands. Genetic patterns support these two hypothesized refugia with higher genetic diversity within refugial populations and evidence for range expansion in populations found outside hypothesized refugia. Phylogenetic analyses identify five to six genetically divergent, geographically cohesive clades ofS. robustus. Divergence dating analyses suggest that these separate refugia date to the Pliocene and that divergence between clades pre‐dates the late Pleistocene glacial cycles, while diversification within clades was likely driven by these cycles. Population genetic analyses reveal effects of both isolation by distance (IBD) and isolation by environment (IBE), with IBD more important in the continuous mountainous portion of the distribution, while IBE was stronger in the populations inhabiting the isolated sky islands of the south. Using model‐based coalescent approaches, we find support for postdivergence migration between clades from separate refugia. 

Abstract Next‐generation sequencing technologies now allow researchers of non‐model systems to perform genome‐based studies without the requirement of a (often unavailable) closely related genomic reference. We evaluated the role of restriction endonuclease (RE) selection in double‐digest restriction‐site‐associatedDNAsequencing (ddRADseq) by generating reduced representation genome‐wide data using four differentREcombinations. Our expectation was thatREselections targeting longer, more complex restriction sites would recover fewer loci thanREwith shorter, less complex sites. We sequenced a diverse sample of non‐model arachnids, including five congeneric pairs of harvestmen (Opiliones) and four pairs of spiders (Araneae). Sample pairs consisted of either conspecifics or closely related congeneric taxa, and in total 26 sample pair analyses were tested. Sequence demultiplexing, read clustering and variant calling were performed in thepyRADprogram. The 6‐base pair cutterEcoRIcombined with methylated site‐specific 4‐base pair cutterMspIproduced, on average, the greatest numbers of intra‐individual loci and shared loci per sample pair. As expected, the number of shared loci recovered for a sample pair covaried with the degree of genetic divergence, estimated with cytochrome oxidase I sequences, although this relationship was non‐linear. Our comparative results will prove useful in guiding protocol selection for ddRADseq experiments on many arachnid taxa where reference genomes, even from closely related species, are unavailable.