Climate-driven range shifts and demographic events over the history of Kruper's Nuthatch <i>Sitta krueperi</i>

<div><p><b>Capsule</b> This study is the first ever documented evidence of an interglacial refugium during the Last Interglacial for birds in Anatolia and suggests the need of a re-examination of the effects of the Last Interglacial on the geographic distribution and genetic structure of species.</p><p><b>Aims</b> We tested whether, in accordance with the ‘refugia within refugia’ model, multiple refugia existed for Kruper's Nuthatch <i>Sitta krueperi</i> during the Last Glacial Maximum or the species survived along the coastal belt of Anatolia through the Late Quaternary glacial–interglacial cycles.</p><p><b>Methods</b> An ecological niche model was developed to predict the geographic distribution of Kruper's Nuthatch under reconstructed past (the Last Interglacial and the Last Glacial Maximum), present, and projected future bioclimatic conditions. Also, robust coalescent-based analyses were used to assess demographic events over the history of Kruper's Nuthatch.</p><p><b>Results</b> Kruper's Nuthatch survived the Last Glacial Maximum almost along the coastal belt of Anatolia, but not in multiple refugia, and surprisingly, contrary to expectations, it survived the Last Interglacial in southern Anatolia, but not along the coastal belt of Anatolia.</p><p><b>Conclusion</b> A kind of the ‘refugia within refugia’ model (i.e. the ‘refugium within refugium’ model) was supported because range shifts took place within Anatolia (itself also a refugium) for Kruper's Nuthatch.</p></div

Data from: Phylogenetics support an ancient common origin of two scientific icons: Devils Hole and Devils Hole pupfish

The Devils Hole pupfish (Cyprinodon diabolis; DHP) is an icon of conservation biology. Isolated in a 50 m2 pool (Devils Hole), DHP is one of the rarest vertebrate species known and an evolutionary anomaly, having survived in complete isolation for thousands of years. However, recent findings suggest DHP might be younger than commonly thought, potentially introduced to Devils Hole by humans in the past thousand years. As a result, the significance of DHP from an evolutionary and conservation perspective has been questioned. Here we present a high-resolution genomic analysis of DHP and two closely related species, with the goal of thoroughly examining the temporal divergence of DHP. To this end, we inferred the evolutionary history of DHP from multiple random genomic subsets and evaluated four historical scenarios using the multispecies coalescent. Our results provide substantial information regarding the evolutionary history of DHP. Genomic patterns of secondary contact present strong evidence that DHP were isolated in Devils Hole prior to 20–10 ka and the model best supported by geological history and known mutation rates predicts DHP diverged around 60 ka, approximately the same time Devils Hole opened to the surface. We make the novel prediction that DHP colonized and have survived in Devils Hole since the cavern opened, and the two events (colonization and collapse of the cavern's roof) were caused by a common geologic event. Our results emphasize the power of evolutionary theory as a predictive framework and reaffirm DHP as an important evolutionary novelty, worthy of continued conservation and exploration

cramfiles

Individual alignment files in CRAM format

Pupfish_contigs.fa

de-novo partial reference genome for Cyprinodon diabolis containing 793,068 RAD contigs ranging between 300 - 796 bp

BEAST_xml_files

XML files used in *BEAST analysi

Phylogenetic_data_sets

fasta formatted sequence files for 200 random RAD loc