Zhao Zhongning, Conradie Werner, Pietersen Darren W, Jordaan Adriaan, Nicolau Gary, Edwards Shelley, Riekert Stephanus, Heideman Neil
Department of Zoology and Entomology, University of the Free State, Bloemfontein, South Africa; Department of Genetics, University of the Free State, Bloemfontein, South Africa.
Port Elizabeth Museum (Bayworld), P.O. Box 13147, Humewood, Port Elizabeth 6013, South Africa; Department of Nature Conservation Management, Natural Resource Science and Management Cluster, Faculty of Science, George Campus, Nelson Mandela University, George, South Africa.
Mol Phylogenet Evol. 2023 May;182:107747. doi: 10.1016/j.ympev.2023.107747. Epub 2023 Feb 26.
Cladogenic diversification is often explained by referring to climatic oscillations and geomorphic shifts that cause allopatric speciation. In this regard, southern Africa retains a high level of landscape heterogeneity in vegetation, geology, and rainfall patterns. The legless skink subfamily Acontinae occurs broadly across the southern African subcontinent and therefore provides an ideal model group for investigating biogeographic patterns associated with the region. A robust phylogenetic study of the Acontinae with comprehensive coverage and adequate sampling of each taxon has been lacking up until now, resulting in unresolved questions regarding the subfamily's biogeography and evolution. In this study, we used multi-locus genetic markers (three mitochondrial and two nuclear) with comprehensive taxon coverage (all currently recognized Acontinae species) and adequate sampling (multiple specimens for most taxa) of each taxon to infer a phylogeny for the subfamily. The phylogeny retrieved four well-supported clades in Acontias and supported the monophyly of Typhlosaurus. Following the General Lineage Concept (GLC), many long-standing phylogenetic enigmas within Acontias occidentalis and the A. kgalagadi, A. lineatus and A. meleagris species complexes, and within Typhlosaurus were resolved. Our species delimitation analyses suggest the existence of hidden taxa in the A. occidentalis, A. cregoi and A. meleagris species groups, but also suggest that some currently recognized species in the A. lineatus and A. meleagris species groups, and within Typhlosaurus, should be synonymised. We also possibly encountered "ghost introgression" in A. occidentalis. Our inferred species tree revealed a signal of gene flow, which implies possible cross-over in some groups. Fossil evidence calibration dating results showed that the divergence between Typhlosaurus and Acontias was likely influenced by cooling and increasing aridity along the southwest coast in the mid-Oligocene caused by the opening of the Drake Passage. Further cladogenesis observed in Typhlosaurus and Acontias was likely influenced by Miocene cooling, expansion of open habitat, uplifting of the eastern Great Escarpment (GE), and variation in rainfall patterns, together with the effect of the warm Agulhas Current since the early Miocene, the development of the cold Benguela Current since the late Miocene, and their co-effects. The biogeographic pattern of the Acontinae bears close resemblance to that of other herpetofauna (e.g., rain frogs and African vipers) in southern Africa.
分支发生多样化通常通过提及导致异域物种形成的气候振荡和地貌变化来解释。在这方面，南部非洲在植被、地质和降雨模式方面保持着高度的景观异质性。无腿石龙子亚科Acontinae广泛分布于南部非洲次大陆，因此为研究与该地区相关的生物地理模式提供了一个理想的模型类群。到目前为止，一直缺乏对Acontinae进行全面覆盖且对每个分类单元进行充分采样的强有力的系统发育研究，导致关于该亚科生物地理学和进化的问题尚未得到解决。在本研究中，我们使用多基因座遗传标记（三个线粒体和两个核基因座），对所有分类单元进行全面覆盖（涵盖所有目前公认的Acontinae物种）并对每个分类单元进行充分采样（大多数分类单元有多个标本），以推断该亚科的系统发育。该系统发育在Acontias中检索到四个得到充分支持的分支，并支持Typhlosaurus的单系性。遵循通用谱系概念（GLC），解决了西方Acontias以及A. kgalagadi、A. lineatus和A. meleagris物种复合体以及Typhlosaurus内部许多长期存在的系统发育谜团。我们的物种界定分析表明，在西方Acontias、A. cregoi和A. meleagris物种组中存在隐性分类单元，但也表明，目前在A. lineatus和A. meleagris物种组以及Typhlosaurus内部公认的一些物种应予以同义化。我们在西方Acontias中还可能遇到了“幽灵渐渗”。我们推断的物种树显示了基因流动的信号，这意味着在一些群体中可能存在杂交。化石证据校准定年结果表明，Typhlosaurus和Acontias之间的分歧可能受到渐新世中期德雷克海峡打开导致西南海岸变冷和干旱加剧影响。在Typhlosaurus和Acontias中观察到的进一步分支发生可能受到中新世变冷、开阔栖息地扩张、东非大裂谷（GE）隆起、降雨模式变化的影响，以及自中新世早期以来温暖的厄加勒斯洋流、自中新世晚期以来寒冷的本格拉洋流的影响及其共同作用。Acontinae的生物地理模式与南部非洲其他爬行动物区系（如雨蛙和非洲蝰蛇）的模式非常相似。
