Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants.

Structural variants (SVs) are widespread in vertebrate genomes, yet their evolutionary dynamics remain poorly understood. Using 45 long-read de novo genome assemblies and pangenome tools, we analyze SVs within three closely related species of North American jays (, scrub-jays) displaying a 60-fold range in effective population size. We find rapid evolution of genome architecture, including ~100 Mb variation in genome size driven by dynamic satellite landscapes with unexpectedly long (> 10 kb) repeat units and widespread variation in gene content, influencing gene expression.

Systematic review and meta-analysis comparative analysis of the safety and efficacy of fenestrated pedicle screw with cement and conventional pedicle screw with cement in the treatment of osteoporotic vertebral fractures: A meta-analysis.

Purpose: Bone cement-reinforced fenestrated pedicle screws (FPSs) have been widely used in the internal fixation and repair of the spine with osteoporosis in recent years and show significant improvement in fixation strength and stability. However, compared with conventional reinforcement methods, the advantages of bone cement-reinforced FPSs remain undetermined. This article compares the effects of fenestrated and conventional pedicle screws (CPSs) combined with bone cement in the treatment of osteoporosis.

Fitness consequences of structural variation inferred from a House Finch pangenome.

Genomic structural variants (SVs) play a crucial role in adaptive evolution, yet their average fitness effects and characterization with pangenome tools are understudied in wild animal populations. We constructed a pangenome for House Finches (), a model for studies of host-pathogen coevolution, using long-read sequence data on 16 individuals (32 de novoassembled haplotypes) and one outgroup. We identified 887,118 SVs larger than 50 base pairs, mostly (60%) involving repetitive elements, with reduced SV diversity in the eastern US as a result of its introduction by humans.

Mitogenomics clarifies the position of the Nearctic magpies ( and ) within the Holarctic magpie radiation.

Partial separation of a peripheral population may lead to its divergence and, potentially, speciation due to genetic drift followed by selection and geographic isolation. This process may cause taxonomic uncertainty because reproductive isolation in allopatry cannot be verified directly. The two Nearctic allopatric species of magpies (Aves, Corvidae: ) serve as a good example of these problems.

The Association Between the Non-essential Metal Mixture and Handgrip Strength in Chinese Community-Dwelling Older Adults.

There is limited research on the effects of non-essential metal (NEM) mixture on handgrip strength in the elderly. This study aimed to assess the associations of single NEMs and their mixture with handgrip strength in Chinese community-dwelling older adults. A total of 3807 elderly people aged 60 years or above were included in this study.

Design and construction of light-regulated gene transcription and protein translation systems in yeast P. Pastoris.

Introduction: P. pastoris is a common host for effective biosynthesis of heterologous proteins as well as small molecules. Accurate regulation of gene transcription and protein synthesis is necessary to coordinate synthetic gene circuits and optimize cellular energy distribution.

Transcription factor binding sites are frequently under accelerated evolution in primates.

Recent comparative genomic studies have identified many human accelerated elements (HARs) with elevated substitution rates in the human lineage. However, it remains unknown to what extent transcription factor binding sites (TFBSs) are under accelerated evolution in humans and other primates. Here, we introduce two pooling-based phylogenetic methods with dramatically enhanced sensitivity to examine accelerated evolution in TFBSs.

Chromosome-level genome assembly of a high-altitude-adapted frog (Rana kukunoris) from the Tibetan plateau provides insight into amphibian genome evolution and adaptation.

Background: The high-altitude-adapted frog Rana kukunoris, occurring on the Tibetan plateau, is an excellent model to study life history evolution and adaptation to harsh high-altitude environments. However, genomic resources for this species are still underdeveloped constraining attempts to investigate the underpinnings of adaptation.

Results: The R.

Allopatric origin of sympatric whitefish morphs with insights on the genetic basis of their reproductive isolation.

The European whitefish (Coregonus lavaretus) species complex is a classic example of recent adaptive radiation. Here, we examine a whitefish population introduced to northern Finnish Lake Tsahkal in the late 1960s, where three divergent morphs (viz. littoral, pelagic, and profundal feeders) were found 10 generations after.

Population Structure Limits Parallel Evolution in Sticklebacks.

Population genetic theory predicts that small effective population sizes (Ne) and restricted gene flow limit the potential for local adaptation. In particular, the probability of evolving similar phenotypes based on shared genetic mechanisms (i.e.

Genetic population structure constrains local adaptation in sticklebacks.

Repeated and independent adaptation to specific environmental conditions from standing genetic variation is common. However, if genetic variation is limited, the evolution of similar locally adapted traits may be restricted to genetically different and potentially less optimal solutions or prevented from happening altogether. Using a quantitative trait locus (QTL) mapping approach, we identified the genomic regions responsible for the repeated pelvic reduction (PR) in three crosses between nine-spined stickleback populations expressing full and reduced pelvic structures.

On the causes of geographically heterogeneous parallel evolution in sticklebacks.

The three-spined stickleback (Gasterosteus aculeatus) is an important model system for the study of parallel evolution in the wild, having repeatedly colonized and adapted to freshwater from the sea throughout the northern hemisphere. Previous studies identified numerous genomic regions showing consistent genetic differentiation between freshwater and marine ecotypes but these had typically limited geographic sampling and mostly focused on the Eastern Pacific region. We analysed population genomic data from global samples of the three-spined stickleback marine and freshwater ecotypes to detect loci involved in parallel evolution at different geographic scales.

Estimating uncertainty in divergence times among three-spined stickleback clades using the multispecies coalescent.

Incomplete lineage sorting (ILS) can lead to biased divergence time estimates. To explore if and how ILS has influenced the results of a recent worldwide phylogeny of three-spined sticklebacks (Gasterosteus aculeatus), we estimated divergence times among major clades by applying both a concatenation approach and the multispecies coalescent (MSC) model to single-nucleotide polymorphisms. To further test the influence of different calibration strategies, we applied different calibrations to the root and to younger nodes in addition to the ones used in the previous study.

A phylogenomic perspective on diversity, hybridization and evolutionary affinities in the stickleback genus Pungitius.

Hybridization and convergent evolution are phenomena of broad interest in evolutionary biology, but their occurrence poses challenges for reconstructing evolutionary affinities among affected taxa. Sticklebacks in the genus Pungitius are a case in point: evolutionary relationships and taxonomic validity of different species and populations in this circumpolarly distributed species complex remain contentious due to convergent evolution of traits regarded as diagnostic in their taxonomy, and possibly also due to frequent hybridization among taxa. To clarify the evolutionary relationships among different Pungitius species and populations globally, as well as to study the prevalence and extent of introgression among recognized species, genomic data sets of both reference genome-anchored single nucleotide polymorphisms and de novo assembled RAD-tag loci were constructed with RAD-seq data.

Worldwide phylogeny of three-spined sticklebacks.

Stickleback fishes in the family Gasterosteidae have become model organisms in ecology and evolutionary biology. However, even in the case of the most widely studied species in this family - the three-spined stickleback (Gasterosteus aculeatus) - the worldwide phylogenetic relationships and colonization history of the different populations and lineages remain poorly resolved. Using a large collection of samples covering most parts of the species distribution range, we subjected thousands of single nucleotide polymorphisms to coalescent analyses in order to reconstruct a robust worldwide phylogeny of extant G.