Few phylogeographical studies exist for taxa inhabiting the Colorado Plateau province. We combined mitochondrial and genomic data with species distribution modeling to test Pleistocene hypotheses for Aphonopelma marxi, a large tarantula endemic to the plateau region. Mitochondrial and genomic analyses revealed that the species comprises at least three main clades that diverged in the Pleistocene. A clade distributed along the Mogollon Rim appears to have persisted in place during the last glacial maximum, whereas the other two clades probably colonized the central and northeastern portion of the species’ range from small refugial areas along river-carved canyons. Climate models support this hypothesis for the Mogollon Rim, but late glacial climate data appear too coarse to detect suitable areas in canyons. Locations of canyon refugia could not be inferred from genomic analyses due to missing data, encouraging us to explore the effect of missing loci in phylogeographical inferences using RADseq. In phylogenetic analyses, node support for major clades decreased with the addition of samples with significant amounts of missing data (more than 30%). Population genomic structure was greatly influenced by missing data, with the group membership of many taxa changing as samples with missing loci were added. Results from DAPC, a distance-based method, did not change as samples with significant amounts missing data were added. We conclude that the specific loci that are missing matters more than the number of missing loci, and that samples with missing data can still add information to RADseq-based analyses as long as results are interpreted cautiously.

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, Antrodiaetus unicolor species complex which contains 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 employ 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, PCA, and a recently developed unsupervised machine learning approach (Variational Autoencoder). We evaluate ecological similarity by using large-scale ecological data for niche-based distribution modeling. 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.

Sampling impediments and paucity of suitable material for molecular analyses have precluded the study of speciation and radiation of deep-sea species in Antarctic ecosystems. This knowledge may serve to establish the framework for evaluating future anthropogenic alterations, particularly in a highly susceptible region like Antarctica. Here, we analyze genome-wide single nucleotide polymorphisms (SNPs) obtained from double digestion restriction site-associated DNA sequencing (ddRADseq) for most species in the family Antarctophilinidae and throughout the geographic distribution and bathymetric ranges of these marine snails. We also reevaluate the fossil record associated with this taxon. In light of the new data provided we discuss relevant diversification processes and biogeographic and bathymetric affinities. Novel approaches in finding genetic distinctive lineages, including unsupervised machine learning variational autoencoder (VAE) plots, are further used to establish species hypothesis frameworks aided by available morphological data. In this sense, two new species and a complex of cryptic species are here identified, suggesting allopatric speciation connected to geographic or bathymetric isolation. We further, observe that the shallow waters around the Scotia Arc and on the continental shelf in the Weddell Sea present high endemism and diversity. In contrast, likely due to the glacial pressure during the Cenozoic, a deep-sea group with fewer species emerged expanding over great areas in the South-Atlantic Antarctic Ridge. Our study exemplifies how diachronic paleoclimatic and current environmental factors shaped Antarctic communities both at the shallow and deep-sea levels, promoting Antarctica as the center of origin for numerous taxa such as gastropod mollusks.