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Abstract Sampling impediments and paucity of suitable material for molecular analyses have precluded the study of speciation and radiation of deep-sea species in Antarctica. We analyzed barcodes together with genome-wide single nucleotide polymorphisms obtained from double digestion restriction site-associated DNA sequencing (ddRADseq) for species in the family Antarctophilinidae. We also reevaluated the fossil record associated with this taxon to provide further insights into the origin of the group. Novel approaches to identify distinctive genetic lineages, including unsupervised machine learning variational autoencoder plots, were used to establish species hypothesis frameworks. In this sense, three undescribed species and a complex of cryptic species were identified, suggesting allopatric speciation connected to geographic or bathymetric isolation. We further observed 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 agrees on 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. 

Abstract AimThe long history of isolation of the Antarctic continent, coupled with the harsh ecological conditions of freezing temperatures, could affect the patterns of genetic diversity in the organisms living there. We aim (a) to test whether such pattern can be seen in a mitochondrial marker of bdelloid rotifers, a group of microscopic aquatic and limno‐terrestrial animals and (b) to speculate on the potential mechanisms driving the pattern. LocationFocus on Antarctica. TaxonRotifera Bdelloidea. MethodsWe analysed different metrics of genetic diversity, also spatially explicit ones, including number of haplotypes, accumulation curves, genetic distances, time to the most recent common ancestor, number of independently evolving units from DNA taxonomy, strength of the correlation between geographical and genetic distances, population genetics neutrality and differentiation indices, potential historical processes, obtained from an extensive sample of cytochrome oxidase subunit I (COI) sequences obtained from bdelloid rotifers. We included 2242 individuals from 23 species in a comparison between Antarctic and non‐Antarctic taxa, correcting for sample size directly in the analyses and then by confirming the results also using only a restricted dataset of nine well‐sampled species. ResultsAntarctic species had consistently lower genetic diversity and potential younger relative age than non‐Antarctic species, even if they were similar in sample size, geographical extent, neutrality and differentiation indices, and correlation between genetic and geographical distances. Main conclusionsThe extensive survey of genetic diversity in one mitochondrial marker in Antarctic bdelloids supports previous suggestions from other organisms that the origin and maintenance of terrestrial Antarctic fauna are different from those of other continents. Such differences could be speculated to be due, in the case of bdelloid rotifers, to the more recent origin of the species living there in comparison to non‐Antarctic species.