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PNAS Papers on Philippine Migrations, Snowfinch Adaptation, NAD-RNA Sequencing Method,

An international team takes a look at historical migrations into the present-day Philippines using genotyping and ancient sequence profiles spanning current and past population representatives. Based on genome-wide genotypes for 1,028 individuals from 115 Indigenous populations in the Philippines, along with genome sequence data from two ancient individuals who lived in the Taiwan Strait region roughly 8,000 years ago, the investigators identified five waves of migration into the Philippine islands involving Negrito, Manobo, Sama, Papuan, and Cordilleran-related populations, providing clues to population origins and relationships in the region. "The Cordillerans migrated into the Philippines prior to the arrival of rice agriculture, where some remain as the least admixed East Asians carrying an ancestry shared by all Austronesian-speaking populations, thereby challenging an exclusive out-of-Taiwan model of joint farming-language-people dispersal," the authors note, adding that the current results "portray the Philippines as a crucial gateway, with a multilayered history, that ultimately changed the genetic landscape of the Asia-Pacific region."

Researchers in China, Sweden, and Denmark explore evolutionary features and high-elevation adaptations in snowfinches from the Qinghai-Tibet Plateau region with the help of high-quality genome sequence data for the white-rumped snowfinch, the rufous-necked snowfinch, and the black-winged snowfinch, representing three phylogenetic lineages in the snowfinch species complex. Using comparative genomics, phylogenomics, functional assays, and other data, the team found that genes under positive selection in the passerine snowfinches were largely distinct from those in the birds' shared ancestors, reflecting more recent adaptive evolution. "Our study … shows that ancestral snowfinches had phenotypically evolved larger body size and genetically an accelerated selection on genes related to development and signaling," the authors report. "From this ancestral state of adaptation, three descendants have undergone independent adaptive processes in response to the differences in selective pressures acting on them."

Investigators in the US and China describe a sequencing strategy for profiling messenger RNA transcripts capped by nicotinamide adenine diphosphate (NAD+) at their 5'-ends — an approach that was used to find new NAD-RNAs in the model Arabidopsis plant. The SPAAC-NAD sequencing (SPAAC-NAD-seq) approach is designed to capture and characterize NAD-RNAs using a scheme that avoids a copper catalyzed enzymatic conversion step used in a conventional NAD captureSeq method, the team says, noting that the copper ions can contribute to RNA fragmentation that dials down sensitivity of that approach. "[W]e developed the copper-free SPAAC-NAD-seq, which utilizes the strain-promoted azide-alkyne cycloaddition reaction to capture NAD-RNAs followed by high-throughput sequencing," the authors write. "Compared to NAD captureSeq, SPAAC-NAD-seq is more sensitive and retains full-length sequence information."