Although species delimitation can be highly contentious, the development of reliable methods to accurately ascertain species boundaries is an imperative step in cataloguing and describing Earth's quickly disappearing biodiversity. Spider species delimitation remains largely based on morphological characters; however, many mygalomorph spider populations are morphologically indistinguishable from each other yet have considerable molecular divergence. The focus of our study, the Antrodiaetus unicolor species complex containing two sympatric species, exhibits this pattern of relative morphological stasis with considerable genetic divergence across its distribution. A past study using two molecular markers, COI and 28S, revealed that A. unicolor is paraphyletic with respect to A. microunicolor. To better investigate species boundaries in the complex, we implement the cohesion species concept and use multiple lines of evidence for testing genetic exchangeability and ecological interchangeability. Our integrative approach includes extensively sampling homologous loci across the genome using a RADseq approach (3RAD), assessing population structure across their geographic range using multiple genetic clustering analyses that include structure, principal components analysis and a recently developed unsupervised machine learning approach (Variational Autoencoder). We evaluate ecological similarity by using large‐scale ecological data for niche‐based distribution modelling. Based on our analyses, we conclude that this complex has at least one additional species as well as confirm species delimitations based on previous less comprehensive approaches. Our study demonstrates the efficacy of genomic‐scale data for recognizing cryptic species, suggesting that species delimitation with one data type, whether one mitochondrial gene or morphology, may underestimate true species diversity in morphologically homogenous taxa with low vagility.

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Planetary extinction of biodiversity underscores the need for taxonomy. Here, we scrutinize spider taxonomy over the last decade (2008–2018), compiling 2083 published accounts of newly described species. We evaluated what type of data were used to delineate species, whether data were made freely available, whether an explicit species hypothesis was stated, what types of media were used, the sample sizes, and the degree to which species constructs were integrative. The findings we report reveal that taxonomy remains largely descriptive, not integrative, and provides no explicit conceptual framework. Less than 4% of accounts explicitly stated a species concept and over one-third of all new species described were based on 1–2 specimens or only one sex. Only ~5% of studies made data freely available, and only ~14% of all newly described species employed more than one line of evidence, with molecular data used in ~6% of the studies. These same trends have been discovered in other animal groups, and therefore we find it logical that taxonomists face an uphill challenge when justifying the scientific rigor of their field and securing the needed resources. To move taxonomy forward, we make recommendations that, if implemented, will enhance its rigor, repeatability, and scientific standards.

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 genus Aptostichus, most of which are restricted to the California Floristic Province (CAFP) biodiversity hotspot. Specifically, the Aptostichus icenoglei complex, which comprises the three sibling species, A. barackobamai, A. isabella, and A. 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 within A. icenoglei.

The use of gDNAs isolated from museum specimens for high throughput sequencing, especially targeted sequencing in the context of phylogenetics, is a common practice. Yet, little understanding has been focused on comparing the quality of DNA and results of sequencing museum DNAs. Dragonflies and damselflies are ubiquitous in freshwater ecosystems and are commonly collected and preserved insects in museum collections hence their use in this study. However, the history of odonate preservation across time and museums has resulted in wide variability in the success of viable DNA extraction, necessitating an assessment of their usefulness in genetic studies. Using Anchored Hybrid Enrichment probes, we sequenced DNA from samples at 2 museums, 48 from the American Museum of Natural History (AMNH) in NYC, USA and 46 from the Naturalis Biodiversity Center (RMNH) in Leiden, Netherlands ranging from global collection localities and across a 120-year time span. We recovered at least 4 loci out of an >1,000 locus probe set for all samples, with the average capture being ~385 loci (539 loci on average when a clade of ambiguous taxa omitted). Neither specimen age nor size was a good predictor of locus capture, but recapture rates differed significantly between museums. Samples from the AMNH had lower overall locus capture than the RMNH, perhaps due to differences in specimen storage over time.