Estimating population size via line graph reconstruction

Background: We propose a novel graph theoretic method to estimate haplotype population size from genotype data. The method considers only the potential sharing of haplotypes between individuals and is based on transforming the graph of potential haplotype sharing into a line graph using a minimum number of edge and vertex deletions. Results: We show that the resulting line graph deletion problems are NP complete and provide exact integer programming solutions for them. We test our approach using extensive simulations of multiple population evolution and genotypes sampling scenarios. Our results also indicate that the method may be useful in comparing populations and it may be used as a first step in a method for haplotype phasing. Conclusions: Our computational experiments show that when most of the sharings are true sharings the problem can be solved very fast and the estimated size is very close to the true size; when many of the potential sharings do not stem from true haplotype sharing, our method gives reasonable lower bounds on the underlying number of haplotypes. In comparison, a naive approach of phasing the input genotypes provides trivial upper bounds of twice the number of genotypes

Þéttleiki og samfélög fugla á svæðum sem hafa verið grædd upp með framandi eða innlendum plöntutegundum

This paper was prepared as a part of the M.Sc. thesis of the first author at the Agricultural University of Iceland. We are grateful for the contribution of The Icelandic Soil Conservation Service, Náttúrusjóður Pálma Jónssonar and Kvískerjasjóður to this project. We thank the employees of The Icelandic Soil Conservation Service and Icelandic Institute of Natural History who contributed with their help and advice.Degradation of ecosystems and introductions of invasive species pose a threat to global biodiversity. Ecosystem restoration and revegetation actions are important for amending habitat loss and for the protection of species of plants and animals. Iceland has the highest rate of soil erosion and desertification in Northern Europe and counteractions to erosion and revegetation measures have taken place for over a century. We studied the effect of revegetation on the density and composition of birds and invertebrate abundance in 26 survey areas comparing: a) unvegetated eroded areas, b) native heathlands restored on eroded land, and c) revegetation by the introduced and exotic Nootka lupin (Lupinus nootkatensis) on eroded land. Birds were counted on transects and invertebrates sampled with a sweep net. Both revegetation methods greatly increased the abundance of birds. The highest total numbers of invertebrates and birds were recorded on land revegetated with Nootka lupin. On average 31 birds km-2 were recorded on barren land, 337 on heathland and 627 in Nootka lupin. Bird species composition differed between the two revegetation methods. Restored heathland provided habitat for waders of internationally decreasing populations, whereas Nootka lupin stands harboured more common bird species. Golden Plover (Pluvialis apricaria) and Dunlin (Calidris alpina) were most common on restored heathland, while Snipe (Gallinago gallinago) and Meadow Pipit (Anthus pratensis) were most common in Nootka lupine. The abundance of birds was positively correlated with that of invertebrates. The abundance of different bird species differed by successional stage in each habitat. The study showed the generally positive effects of revegetation on animal biodiversity and also how different revegetation methods produce different trajectories of ecosystem development.Hnignun vistkerfa og dreifing ágengra tegunda ógna líffræðilegum fjölbreytileika á heimsvísu. Vistheimt og landgræðsla eru mikilvægar aðgerðir til að endurheimta töpuð vistkerfi. Hvergi í Norður-Evrópu hefur jarðvegseyðing og eyðimerkurmyndun verið hraðari en á Íslandi. Í þessari rannsókn voru könnuð áhrif mismunandi landgræðsluaðgerða á þéttleika og tegundasamsetningu fugla og á fjölda smádýra. Rannsóknirnar voru gerðar á 26 stöðum á landinu. Á hverjum stað voru borin saman; a) óuppgrætt svæði, b) endurheimt mólendi og c) land sem hafði verið grætt upp með alaskalúpínu (Lupinus nootkatensis). Á óuppgræddu landi var að meðaltali 31 fugl á km2, 337 á endurheimtu mólendi og 627 á landi sem hafði verið grætt upp með lúpínu. Þéttleiki fugla hafði jákvæða fylgni við fjölda smádýra. Tegundasamsetning fugla var ólík eftir uppgræðsluaðferðum. Í endurheimtu mólendi var mest um vaðfugla af tegundum sem er að hnigna á heimsvísu, en í lúpínu var meira um algengari tegundir. Heiðlóa og lóuþræll voru algengustu tegundirnar í endurheimtu mólendi, en hrossagaukur og þúfutittlingur í lúpínu. Þéttleiki sumra fuglategunda virtist vera háður framvindustigi landgræðslusvæða. Þessi rannsókn sýnir að landgræðsla eykur líffræðilega fjölbreytni dýrategunda, en mismunandi landgræðsluaðgerðir leiða til mismunandi þróunar vistkerfanna.Náttúrusjóður Pálma Jónssonar; KvískerjasjóðurPeer Reviewe

Feasibility of different harvesting strategies and economies of scale in ranching wild cod (Gadus morhua)

Peer reviewe

popSTR2 enables clinical and population-scale genotyping of microsatellites

Summary: popSTR2 is an update and augmentation of our previous work ‘popSTR: a population-based microsatellite genotyper’. To make genotyping sensitive to inter-sample differences, we supply a kernel to estimate sample-specific slippage rates. For clinical sequencing purposes, a panel of known pathogenic repeat expansions is provided along with a script that scans and flags for manual inspection markers indicative of a pathogenic expansion. Like its predecessor, popSTR2 allows for joint genotyping of samples at a population scale. We now provide a binning method that makes the microsatellite genotypes more amenable to analysis within standard association pipelines and can increase association power. Availability and implementation: https://github.com/DecodeGenetics/popSTR. Contact: [email protected] or [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.Peer Reviewed (ritrýnd grein

Whole genome sequencing identifies structural variants contributing to hematologic traits in the NHLBI TOPMed program

Genome-wide association studies have identified thousands of single nucleotide variants and small indels that contribute to variation in hematologic traits. While structural variants are known to cause rare blood or hematopoietic disorders, the genome-wide contribution of structural variants to quantitative blood cell trait variation is unknown. Here we utilized whole genome sequencing data in ancestrally diverse participants of the NHLBI Trans Omics for Precision Medicine program (N = 50,675) to detect structural variants associated with hematologic traits. Using single variant tests, we assessed the association of common and rare structural variants with red cell-, white cell-, and platelet-related quantitative traits and observed 21 independent signals (12 common and 9 rare) reaching genome-wide significance. The majority of these associations (N = 18) replicated in independent datasets. In genome-editing experiments, we provide evidence that a deletion associated with lower monocyte counts leads to disruption of an S1PR3 monocyte enhancer and decreased S1PR3 expression

DELISHUS: an efficient and exact algorithm for genome-wide detection of deletion polymorphism in autism

Motivation: The understanding of the genetic determinants of complex disease is undergoing a paradigm shift. Genetic heterogeneity of rare mutations with deleterious effects is more commonly being viewed as a major component of disease. Autism is an excellent example where research is active in identifying matches between the phenotypic and genomic heterogeneities. A considerable portion of autism appears to be correlated with copy number variation, which is not directly probed by single nucleotide polymorphism (SNP) array or sequencing technologies. Identifying the genetic heterogeneity of small deletions remains a major unresolved computational problem partly due to the inability of algorithms to detect them

GraphTyper2 enables population-scale genotyping of structural variation using pangenome graphs

Publisher's version (útgefin grein).Analysis of sequence diversity in the human genome is fundamental for genetic studies. Structural variants (SVs) are frequently omitted in sequence analysis studies, although each has a relatively large impact on the genome. Here, we present GraphTyper2, which uses pangenome graphs to genotype SVs and small variants using short-reads. Comparison to the syndip benchmark dataset shows that our SV genotyping is sensitive and variant segregation in families demonstrates the accuracy of our approach. We demonstrate that incorporating public assembly data into our pipeline greatly improves sensitivity, particularly for large insertions. We validate 6,812 SVs on average per genome using long-read data of 41 Icelanders. We show that GraphTyper2 can simultaneously genotype tens of thousands of whole-genomes by characterizing 60 million small variants and half a million SVs in 49,962 Icelanders, including 80 thousand SVs with high-confidence.We are grateful to our colleagues from deCODE genetics / Amgen Inc. for their contributions. We also wish to thank all research participants who provided a biological sample to deCODE genetics.Peer Reviewe

A sequence variant associating with educational attainment also affects childhood cognition

Only a few common variants in the sequence of the genome have been shown to impact cognitive traits. Here we demonstrate that polygenic scores of educational attainment predict specific aspects of childhood cognition, as measured with IQ. Recently, three sequence variants were shown to associate with educational attainment, a confluence phenotype of genetic and environmental factors contributing to academic success. We show that one of these variants associating with educational attainment, rs4851266-T, also associates with Verbal IQ in dyslexic children (P=4.3 x 10(-4), beta=0.16 s.d.). The effect of 0.16 s.d. corresponds to 1.4 IQ points for heterozygotes and 2.8 IQ points for homozygotes. We verified this association in independent samples consisting of adults (P=8.3 x 10(-5), beta=0.12 s.d., combined P=2.2 x 10(-7), beta=0.14 s.d.). Childhood cognition is unlikely to be affected by education attained later in life, and the variant explains a greater fraction of the variance in verbal IQ than in educational attainment (0.7% vs 0.12%,. P=1.0 x 10(-5))

A sequence variant associating with educational attainment also affects childhood cognition

Only a few common variants in the sequence of the genome have been shown to impact cognitive traits. Here we demonstrate that polygenic scores of educational attainment predict specific aspects of childhood cognition, as measured with IQ. Recently, three sequence variants were shown to associate with educational attainment, a confluence phenotype of genetic and environmental factors contributing to academic success. We show that one of these variants associating with educational attainment, rs4851266-T, also associates with Verbal IQ in dyslexic children (P=4.3 x 10(-4), beta=0.16 s.d.). The effect of 0.16 s.d. corresponds to 1.4 IQ points for heterozygotes and 2.8 IQ points for homozygotes. We verified this association in independent samples consisting of adults (P=8.3 x 10(-5), beta=0.12 s.d., combined P=2.2 x 10(-7), beta=0.14 s.d.). Childhood cognition is unlikely to be affected by education attained later in life, and the variant explains a greater fraction of the variance in verbal IQ than in educational attainment (0.7% vs 0.12%,. P=1.0 x 10(-5))