Proteomic Analysis of Species Differentiation in Long-Tailed Finches

<p dir="ltr">Speciation is the process of new species formation and is driven by genetic and molecular divergence, but it remains poorly characterized at the proteomic level. In this study, we investigated quantitative tissue-specific proteomic differences in blood, brain and liver samples across three <i>Poephila </i>finch subspecies: yellow-billed (<i>P. acuticauda acuticauda</i>), red-billed (<i>P. acuticauda hecki</i>), and black- throated (<i>P. cincta atropygialis</i>), and two of their hybrids.</p><p dir="ltr">We optimized volumetric absorptive microsampling (VAMS) for avian blood, achieving robust proteome coverage across all samples analysed. The proteomic profiles indicated lineage-specific protein expression patterns have emerged across tissues. <i>P. a. hecki </i>finches exhibited elevated detoxification markers (ALDH2, ABCB9) in blood, consistent with oxidative stress adaptation. Conversely, <i>P. c. atropygialis </i>finches showed reduced GP1BB (clotting regulation) and elevated immune related proteins in brain tissues (A0A674GJ26, JCHAIN), alongside suppressed stress-resilience markers (CRYAB, GPS1). Liver proteomes of <i>P. a. acuticauda </i>finches revealed metabolic trade-offs, including downregulated detoxifiers (MAT2B, ALDH1A1, SULT1C3) and elevated protease inhibitors (LOC100225789). Hybrids displayed intermediate expression profiles, with fewer differentially expressed proteins, suggesting reduced adaptive specialization.</p><p dir="ltr">These findings highlight tissue-specific molecular adaptations as potential drivers of ecological divergence, and underscores proteomics as a critical tool for unravelling speciation mechanisms.</p>