https://research-information.bris.ac.uk/files/186876515/Mismatch_MS_STARMethods.pdf

Multiple Deeply Divergent Denisovan Ancestries in Papuans.

Adaptive evolution in new or changing environments can be difficult to predict because the functional connections between genotype, phenotype, and fitness are complex. Here, we make these explicit connections by combining field and laboratory experiments in wild mice. We first directly estimate natural selection on pigmentation traits and an underlying pigment locus, Agouti, by using experimental enclosures of mice on different soil colors. Next, we show how a mutation in Agouti associated with survival causes lighter coat color through changes in its protein binding properties. Together, our findings demonstrate how a sequence variant alters phenotype and then reveal the ensuing ecological consequences that drive changes in population allele frequency, thereby illuminating the process of evolution by natural selection.

https://science.sciencemag.org/content/sci/363/6426/499.full.pdf

Linking a mutation to survival in wild mice.

Understanding the genetic changes underlying phenotypic variation in sheep (Ovis aries) may facilitate our efforts towards further improvement. Here, we report the deep resequencing of 248 sheep including the wild ancestor (O. orientalis), landraces, and improved breeds. We explored the sheep variome and selection signatures. We detected genomic regions harboring genes associated with distinct morphological and agronomic traits, which may be past and potential future targets of domestication, breeding, and selection. Furthermore, we found non-synonymous mutations in a set of plausible candidate genes and significant differences in their allele frequency distributions across breeds. We identified PDGFD as a likely causal gene for fat deposition in the tails of sheep through transcriptome, RT-PCR, qPCR, and Western blot analyses. Our results provide insights into the demographic history of sheep and a valuable genomic resource for future genetic studies and improved genome-assisted breeding of sheep and other domestic animals.

/pdf/whole-genome-resequencing-of-wild-and-domestic-sheep-2ize1jdcg2.pdf

Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits

Convergent adaptation occurs at the genome scale when independently evolving lineages use the same genes to respond to similar selection pressures. These patterns of genetic repeatability provide insights into the factors that facilitate or constrain the diversity of genetic responses that contribute to adaptive evolution. A first step in studying such factors is to quantify the observed amount of repeatability relative to expectations under a null hypothesis. Here, we formulate a novel index to quantify the constraints driving the observed amount of repeated adaptation in pairwise contrasts based on the hypergeometric distribution, and then generalize this for simultaneous analysis of multiple lineages. This index is explicitly based on the probability of observing a given amount of repeatability by chance under a given null hypothesis and is readily compared among different species and types of trait. We also formulate an index to quantify the effective proportion of genes in the genome that have the potential to contribute to adaptation. As an example of how these indices can be used to draw inferences, we assess the amount of repeatability observed in existing datasets on adaptation to stress in yeast and climate in conifers. This approach provides a method to test a wide range of hypotheses about how different kinds of factors can facilitate or constrain the diversity of genetic responses observed during adaptive evolution.

/pdf/quantifying-how-constraints-limit-the-diversity-of-viable-1ckahe6qnh.pdf

Quantifying how constraints limit the diversity of viable routes to adaptation.

Compared to its predecessors, the Telomere-to-Telomere CHM13 genome adds nearly 200 million base pairs of sequence, corrects thousands of structural errors, and unlocks the most complex regions of the human genome for clinical and functional study. We show how this reference universally improves read mapping and variant calling for 3202 and 17 globally diverse samples sequenced with short and long reads, respectively. We identify hundreds of thousands of variants per sample in previously unresolved regions, showcasing the promise of the T2T-CHM13 reference for evolutionary and biomedical discovery. Simultaneously, this reference eliminates tens of thousands of spurious variants per sample, including reduction of false positives in 269 medically relevant genes by up to a factor of 12. Because of these improvements in variant discovery coupled with population and functional genomic resources, T2T-CHM13 is positioned to replace GRCh38 as the prevailing reference for human genetics. 

A complete reference genome improves analysis of human genetic variation

https://backend.orbit.dtu.dk/ws/files/146993375/filestore_5_.pdf

Physiological and Genetic Adaptations to Diving in Sea Nomads

This research aims to describe the ability to solve the problems of students’ mathematics and through direct learners based on SAVI is expected to provide a change in the ability to solve problems of students class VII in Junior High School 6 Bualemo, especially on triangular material. This type of research is descriptive with a qualitative approach. The subjects in this study were two class VII students. The results of this study showed that students' math problem-solving abilities were still in the "low" category. The causes are: 1) difficulty identifying the problem given, 2) difficulty determining the height of the triangle, 3) difficulty in calculating, 4) difficulty puts value into the formula, and 5) difficulty in making a partition of the triangle story problem. So, based on this information, the alternative solution is to apply direct learning based on SAVI. SAVI-based hands-on learning can provide a student's math problem-solving skills change from a "low" category to a "high enough" category. This can be demonstrated by the change in the class's grade point average from 36.78 to 81.05. Keywords: Mathematical Problem Solving Skills, Triangles, SAVI. Abstrak: Penelitian ini bertujuan untuk mendeskripsikan kemampuan pemecahan masalah matematika siswa dan melalui pembelajaran langsung berbasis SAVI diharapkan dapat memberikan perubahan kemampuan pemecahan masalah matematika siswa kelas VII SMP Negeri 6 Bualemo khususnya pada materi segitiga. Jenis penelitian ini adalah deskriptif dengan pendekatan kualitatif. Subjek dalam penelitian ini adalah dua orang siswa kelas VII. Hasil penelitian ini menunjukkan bahwa kemampuan pemecahan masalah matematika siswa masih berada dalam kategori “rendah”. Penyebabnya adalah: 1) kesulitan dalam mengidentifikasi soal yang diberikan, 2) kesulitan menentukan tinggi segitiga, 3) kesulitan dalam perhitungan, 4) kesulitan dalam menempatkan nilai ke dalam rumus yang ada, dan 5) kesulitan dalam membuat pemisalan dari soal cerita segitiga. Sehingga, berdasarkan informasi tersebut alternative penyelesaianya yaitu dengan menerapkan pembelajaran langsung berbasis SAVI. Pembelajaran langsung berbasis SAVI dapat memberikan perubahan kemampuan pemecahan masalah matematika siswa dari kategori “rendah” menjadi kategori “cukup tinggi”. Hal ini dapat ditunjukkan dengan adanya perubahan nilai rata-rata kelas dari 36.78 menjadi 81.05. Kata kunci: Kemampuan Pemecahan Masalah Matematika, Segitiga, SAVI. DOI: http://dx.doi.org/10.23960/jpmipa/v23i3.pp952-967 

Suhartini Salingkat

Papers

Physiological and Genetic Adaptations to Diving in Sea Nomads

Direct Instruction with SAVI Learning Model to Improve Students’ Mathematical Problem-Solving Ability: A Descriptive Study