An approach using ddRADseq and machine learning for understanding speciation in Antarctic Antarctophilinidae gastropods

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 (SNPs) 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 (VAE) 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.

南极深海物种的物种形成与辐射演化研究长期受限于采样障碍与适用于分子分析的实验材料匮乏。本研究针对南极嗜菲螺科（Antarctophilinidae）物种，分析了其DNA条形码（DNA Barcode）与通过双酶切限制性位点相关DNA测序（double digestion restriction site-associated DNA sequencing, ddRADseq）获得的全基因组单核苷酸多态性（SNPs）；此外，本研究还重新评估了该类群的相关化石记录，以进一步阐明该类群的起源。本研究采用了多种识别独特遗传谱系的新方法，包括无监督机器学习变分自编码器（variational autoencoder, VAE）可视化分析，以此构建物种假说框架。据此，本研究共鉴定出3个未描述物种与1个隐存物种复合群，结果表明该类群的物种形成属于与地理隔离或水深隔离相关的异域物种形成。进一步研究发现，斯科舍海岭（Scotia Arc）周边浅水区及威德尔海（Weddell Sea）大陆架区域拥有极高的特有性与物种多样性；与之相反，受新生代（Cenozoic）冰期压力的影响，一个物种数量较少的深海类群得以兴起，并在南大西洋南极海岭（South-Atlantic Antarctic Ridge）的广阔区域内扩散。本研究证实，历时古气候与当前环境因素共同塑造了南极浅海与深海群落，推动南极洲成为腹足类软体动物（gastropod mollusks）等众多类群的起源中心。