09/06/2024
𝗦𝗔𝗟𝗔𝗠𝗔𝗡𝗗𝗥𝗔 𝗦𝗮𝘁𝘂𝗿𝗱𝗮𝘆
𝗧𝗵𝗲 𝗲𝗳𝗳𝗲𝗰𝘁 𝗼𝗳 𝗵𝘆𝗯𝗿𝗶𝗱𝘀 𝗼𝗻 𝗽𝗵𝘆𝗹𝗼𝗴𝗲𝗻𝗼𝗺𝗶𝗰𝘀 𝗮𝗻𝗱 𝘀𝘂𝗯𝘀𝗽𝗲𝗰𝗶𝗲𝘀 𝗱𝗲𝗹𝗶𝗺𝗶𝘁𝗮𝘁𝗶𝗼𝗻 𝗶𝗻 𝙎𝙖𝙡𝙖𝙢𝙖𝙣𝙙𝙧𝙖, 𝗮 𝗵𝗶𝗴𝗵𝗹𝘆 𝗱𝗶𝘃𝗲𝗿𝘀𝗶𝗳𝗶𝗲𝗱 𝗮𝗺𝗽𝗵𝗶𝗯𝗶𝗮𝗻 𝗴𝗲𝗻𝘂𝘀
Traditional methods of phylogenetic reconstruction and species delimitation may be impeded by frequent hybridization among lineages. In this study, we conducted phylogenetic and clustering analyses of ddRAD genomic data on the entire genus 𝘚𝘢𝘭𝘢𝘮𝘢𝘯𝘥𝘳𝘢, which includes six species and over 25 subspecies of terrestrial salamanders. We expanded previous datasets to include missing subspecies and incorporated new samples, with an emphasis on secondary contact zones. Results obtained from a full dataset of 392 individuals (356,874 bp; 24,192 SNPs) were compared with those obtained after excluding substantially admixed individuals (n = 95; 835,467 bp; 51,557 SNPs) to explore the consequences of introgression on phylogenetic inference and taxonomic arrangement of subspecies.
We found conflicting phylogenetic placements for taxa represented by many admixed individuals (identified by clustering ancestries). In contrast, a time-calibrated tree constructed without hybrids largely agrees with previous phylogenetic hypotheses. Within 𝘚. 𝘢𝘵𝘳𝘢 we found paraphyly of 𝘚. 𝘢𝘵𝘳𝘢 𝘢𝘵𝘳𝘢, suggesting an additional candidate subspecies. Within 𝘚. 𝘪𝘯𝘧𝘳𝘢𝘪𝘮𝘮𝘢𝘤𝘶𝘭𝘢𝘵𝘢, two lineages are assignable to known subspecies and we additionally identified a third, deeply diverged lineage sampled near the Turkish/Syrian border. In 𝘚. 𝘢𝘭𝘨𝘪𝘳𝘢, we found limited admixture between the subspecies 𝘚. 𝘢. 𝘵𝘪𝘯𝘨𝘪𝘵𝘢𝘯𝘢 and 𝘚. 𝘢. 𝘴𝘱𝘭𝘦𝘯𝘥𝘦𝘯𝘴 despite their geographic proximity. Finally, within 𝘚. 𝘴𝘢𝘭𝘢𝘮𝘢𝘯𝘥𝘳𝘢, we detected significant levels of hybridization between subspecies, which blurred their phylogenetic relationships, although the removal of admixed samples in subset analyses clarified the situation in most cases.
Monophyly was recovered for subspecies that were previously found paraphyletic, including 𝘚. 𝘴. 𝘴𝘢𝘭𝘢𝘮𝘢𝘯𝘥𝘳𝘢, 𝘚. 𝘴. 𝘨𝘢𝘭𝘭𝘢𝘪𝘤𝘢, and 𝘚. 𝘴. 𝘧𝘢𝘴𝘵𝘶𝘰𝘴𝘢. 𝘚𝘢𝘭𝘢𝘮𝘢𝘯𝘥𝘳𝘢 𝘴. “𝘢𝘭𝘧𝘳𝘦𝘥𝘴𝘤𝘩𝘮𝘪𝘥𝘵𝘪” was confirmed to be a junior synonym of 𝘚. 𝘴. 𝘣𝘦𝘳𝘯𝘢𝘳𝘥𝘦𝘻𝘪. Previously disputed subspecies, like 𝘚. 𝘴. “𝘮𝘰𝘭𝘭𝘦𝘳𝘪” and 𝘚. 𝘴. “𝘩𝘪𝘴𝘱𝘢𝘯𝘪𝘤𝘢”, correspond to separated lineages but are affected by admixture with other lineages. Further newly identified candidate subspecies in 𝘚. 𝘴𝘢𝘭𝘢𝘮𝘢𝘯𝘥𝘳𝘢 included a southern lineage within 𝘚. 𝘴. 𝘸𝘦𝘳𝘯𝘦𝘳𝘪 and a western lineage within 𝘚. 𝘴. 𝘣𝘦𝘳𝘯𝘢𝘳𝘥𝘦𝘻𝘪. Finally, we re-evaluate the status of recognized subspecies in 𝘚𝘢𝘭𝘢𝘮𝘢𝘯𝘥𝘳𝘢, based on evidence from multiple delimitation criteria. Given that the evolutionary history could not be resolved for all subspecies, we highlight taxa within 𝘚𝘢𝘭𝘢𝘮𝘢𝘯𝘥𝘳𝘢 that warrant further molecular examination and taxonomic revision, notably within the 𝘚. 𝘴. 𝘨𝘢𝘭𝘭𝘢𝘪𝘤𝘢/“𝘮𝘰𝘭𝘭𝘦𝘳𝘪”/𝘣𝘦𝘫𝘢𝘳𝘢𝘦 complex. This study illustrates the impact of hybridization in phylogenetic analyses and its downstream effects in the identification of conservation units and their naming in the Lɪɴɴᴇᴀɴ classification.
Gɪᴘᴘɴᴇʀ, S., N. Sᴛʀᴏᴡʙʀɪᴅɢᴇ, E. Šᴜɴᴊᴇ, M. Cᴀᴘsᴛɪᴄᴋ, F. Aᴍᴀᴛ, S. Bᴏɢᴀᴇʀᴛs, K. Mᴇʀᴀʙᴇᴛ, K. Pʀᴇɪssʟᴇʀ, P. Gᴀʟᴀ́ɴ, I. Mᴀʀᴛɪ́ɴᴇᴢ-Sᴏʟᴀɴᴏ, L. Bᴏɴᴀᴛᴏ, S. Sᴛᴇɪɴғᴀʀᴛᴢ, G. Vᴇʟᴏ-Aɴᴛᴏ́ɴ, C. Dᴜғʀᴇsɴᴇs, K. R. Eʟᴍᴇʀ & M. Vᴇɴᴄᴇs (2024): The effect of hybrids on phylogenomics and subspecies delimitation in 𝘚𝘢𝘭𝘢𝘮𝘢𝘯𝘥𝘳𝘢, a highly diversified amphibian genus. – Salamandra 60(2): 105–128 plus supplementary material.
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Tagged 𝘚𝘢𝘭𝘢𝘮𝘢𝘯𝘥𝘳𝘢 𝘴𝘢𝘭𝘢𝘮𝘢𝘯𝘥𝘳𝘢 from Solling, Germany.
Photo: Sven Gippner.