Improving the throughput of the forward population genetic simulation environment simuPOP

Biological populations arise, develop and evolve under a series of well-studied laws and fairly regular mechanisms. Population genetics is a field of science, that aims to study and model these laws and the genetic composition and diversity of populations of various types of species and life. At best, population genetic models can be of use in verifying past events of a population and eventually reconstructing unknown population histories in light of multidisciplinary evidence. An example case of this is the research concerning human population prehistory of Finland. Population simulations are a sub-branch of the rapidly developing field of bioinformatics and can be divided into two pipelines: forward-in-time and backward-in-time (coalescent). The methodologies enable in silico testing of the development of genetic composition of individuals in a well-defined population. This thesis focuses on the forward-in-time approach. Multiple pieces of software exist today for forward population simulations, and simuPOP [http://simupop.sourceforge.net] probably is the single most flexible one of them. Being able to incorporate transmission of genomes and arbitrary individual information between generations, simuPOP has potential applications even beyond population genetics. However, simuPOP tends to use an enormous amount of computer random access memory when simulating large population sizes. This thesis introduces three approaches to improve the throughput of simuPOP. These are i) introducing scripting guidelines, ii) approximating a complex simulation using the inbuilt biallelic mode of simuPOP and iii) changes in the source code of simuPOP that would enable improved throughput. A previous simuPOP script designed to simulate past demographic events of Finnish population history is used as an example. A batch of 100 simulation runs is run on three versions of the previous script: standard, modified and biallelic. As compared to the standard mode, the modified simulation script performs marginally faster. Despite doubling the user time of a single simulation run, the biallelic approximation method proves to consume three times less random access memory still being compatible from the population genetic point of view. This suggests that built-in support for the biallelic approximation could be a valuable supplement to simuPOP. Evidently, simuPOP can be applied to very complex forward population simulations. The use of individual information fields enables the user to set up arbitrary simulation scenarios. Data structure changes at source code level are likely to improve throughput even further. Besides introducing improvements and guidelines to the simulation workflow, this thesis is a standalone case study concerning the use and development of a bioinformatics software. Furthermore, an individual development version of simuPOP called simuPOP-rev is founded with the goal of implementing the source code changes suggested in this thesis. ACM Computing Classification System (CCS): D.1 [Programming techniques], G.1.6 [Optimization], H.3 [Information storage and retrieval

Mobile IPV6 security and return routability

Mobile IPv6 -protokolla (MIPv6) kuvailee ne yhteyskäytännöt, joilla kotiverkkonsa ulkopuolelle vaeltava langaton asiakassolmu kykenee säilyttämään yhteyden mahdollisesti kokonaan eri verkossa sijaitsevaan vastaanottavaan solmuun. Asiakassolmu kommunikoi vastaanottavan solmun kanssa aluksi kotiverkossaan sijaitsevan kotireitittimen välityksellä ja tarvittaessa lopulta ilman kotireitittimen apua. Kotireitittimen tärkein tehtävä on ylläpitää asiakassolmun kotiosoitteen ja tilapäisosoitteen välistä sidontaa. Solmujen välisen yhteyden säilyttämisen lisäksi yhteys on suojattava mahdollisilta palvelunesto-, välimies-, monistus- ja muilta hyökkäyksiltä. Suojautumiskeinona asiakassolmun ja kotireitittimen välille muodostetaan IPsec-turvayhteys IPsec-protokollakokoelman avulla. IPsec-turvayhteyden kuljetusmoodi suojaa asiakassolmun ja vastaanottavan solmun väliset sidonnan päivitykset. IPsecturvayhteys ei kuitenkaan sovellu kotireitittimen ja vastaanottavan solmun välisen tietoliikenneverkon osuuden eikä asiakassolmun ja vastaanottavan solmun välisen suoran linkin suojaamiseen. Suoran linkin muodostamisen suojaamista varten MIPv6:een on kehitetty protokollakohtainen turvaratkaisu, reititystesti. Reititystestin tavoitteena on asiakassolmun ja vastaanottavan solmun välisen tietoliikenneyhteyden todentaminen siten, että vastaanottava solmu voi tallentaa asiakassolmun osoitteiden sidonnan. Näin vältytään kotireitittimen kuormittamiselta, ja tiedonsiirto nopeutuu. IPsec-turvayhteyden tunnelimoodilla suojataan osa reititystestin keskeisistä viesteistä. Tämä tutkielma käsittelee ensin MIPv6:ta yleisellä tasolla. Myöhemmät luvut esittelevät MIPv6:n keskeiset turvallisuusuhat, IPsec-protokollakokoelman ja reititystestin. Aiheet koskevat erityisesti asiakassolmua, kotireititintä ja asiakassolmun kanssa kommunikoivaa vastaanottavaa solmua. Myös tutkielman näkökulma rajoittuu näihin kolmeen solmuun. Pääpaino on MIPv6:n turvallisuusuhkien esittelyssä ja turvaratkaisuissa, joilla vastataan näihin uhkiin. IPsec-protokollakokoelmaan kuuluvan IKE-protokollan yksityiskohtainen käsittely kuten myös reititystestin mahdolliset muunnokset eri verkkoinfrastruktuureissa jäävät tämän tutkielman aihealueiden ulkopuolelle. Tärkeimpänä tuloksenaan tutkielma näyttää reititystestin onnistuneen kulun. Reititystestin avulla asiakassolmun ja vastaanottavan solmun välille muodostetaan riittävän voimakas IPsec:stä riippumaton turvayhteys, jolla siis MIPv6:lle keskeiset sidonnan päivitykset voidaan hyväksyä. Tietoturvan näkökulmasta MIPv6 on käyttövalmis. IPsec:n avulla saadaan suojattua kriittisimmät vaiheet MIPv6-solmujen välisessä tietoliikenteessä. Reititystesti vastaa hyvin langattoman tiedonsiirron haasteisiin niin tietoturvan kuin yhteysnopeudenkin suhteen. Käytön lisääntymisen myötä MIPv6 tulee lähitulevaisuudessa kokemaan laajamittaista käytännon testausta ja ongelmien ratkaisua, mikä asettaa hyvät suuntaviivat MIPv6:n kehitykselle

Sealed in a lake : Biology and conservation of the endangered Saimaa ringed seal

Wildlife species living in proximity with humans often suffer from various anthropogenic factors. Here, we focus on the endangered Saimaa ringed seal (Pusa hispida saimensis), which lives in close connection with humans in Lake Saimaa, Finland. This unique endemic population has remained landlocked since the last glacial period, and it currently consists of only similar to 400 individuals. In this review, we summarize the current knowledge on the Saimaa ringed seal, identify the main risk factors and discuss the efficacy of conservation actions put in place to ensure its long-term survival. The main threats for this rare subspecies are bycatch mortality, habitat destruction and increasingly mild winters. Climate change, together with small population size and an extremely impoverished gene pool, forms a new severe threat. The main conservation actions and priorities for the Saimaa ringed seal are implementation of fishing closures, land-use planning, protected areas, and reduction of pup mortality. Novel innovations, such as provisioning of artificial nest structures, may become increasingly important in the future. Although the Saimaa ringed seal still faces the risk of extinction, the current positive trend in the number of seals shows that endangered wildlife populations can recover even in regions with considerable human inhabitation, when legislative protection is combined with intensive research, engagement of local inhabitants, and innovative conservation actions. Such multifaceted conservation approaches are needed in a world with a growing human population and a rapidly changing climate.Peer reviewe

gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output

Unknown sequences, or gaps, are present in many published genomes across public databases. Gap filling is an important finishing step in de novo genome assembly, especially in large genomes. The gap filling problem is nontrivial and while there are many computational tools partially solving the problem, several have shortcomings as to the reliability and correctness of the output, i.e. the gap filled draft genome. SSPACE-LongRead is a scaffolding tool that utilizes long reads from multiple third-generation sequencing platforms in finding links between contigs and combining them. The long reads potentially contain sequence information to fill the gaps created in the scaffolding, but SSPACE-LongRead currently lacks this functionality. We present an automated pipeline called gapFinisher to process SSPACE-LongRead output to fill gaps after the scaffolding. gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. We compare the performance of gapFinisher against two other published gap filling tools PBJelly and GMcloser. We conclude that gapFinisher can fill gaps in draft genomes quickly and reliably. In addition, the serial design of gapFinisher makes it scale well from prokaryote genomes to larger genomes with no increase in the computational footprint.Peer reviewe

Genomic evidence uncovers inbreeding and supports translocations in rescuing the genetic diversity of a landlocked seal population

Peer reviewe

Complete genome sequence of Propionibacterium freudenreichii DSM 20271T

Abstract Propionibacterium freudenreichii subsp. freudenreichii DSM 20271T is the type strain of species Propionibacterium freudenreichii that has a long history of safe use in the production dairy products and B12 vitamin. P. freudenreichii is the type species of the genus Propionibacterium which contains Gram-positive, non-motile and non-sporeforming bacteria with a high G + C content. We describe the genome of P. freudenreichii subsp. freudenreichii DSM 20271T consisting of a 2,649,166 bp chromosome containing 2320 protein-coding genes and 50 RNA-only encoding genes

Improved chromosome-level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) integrating Pacific Biosciences long reads and a high-density linkage map

Background The Glanville fritillary (Melitaea cinxia) butterfly is a model system for metapopulation dynamics research in fragmented landscapes. Here, we provide a chromosome-level assembly of the butterfly's genome produced from Pacific Biosciences sequencing of a pool of males, combined with a linkage map from population crosses. Results The final assembly size of 484 Mb is an increase of 94 Mb on the previously published genome. Estimation of the completeness of the genome with BUSCO indicates that the genome contains 92-94% of the BUSCO genes in complete and single copies. We predicted 14,810 genes using the MAKER pipeline and manually curated 1,232 of these gene models. Conclusions The genome and its annotated gene models are a valuable resource for future comparative genomics, molecular biology, transcriptome, and genetics studies on this species.Peer reviewe

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.Peer reviewe

Author Correction: Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch.

In the version of this article initially published, there was a mistake in the calculation of the nucleotide mutation rate per site per generation: 1 × 10−9 mutations per site per generation was used, whereas 9.5 × 10−9 was correct. This error affects the interpretation of population-size changes over time and their possible correspondence with known geological events, as shown in the original Fig. 4 and supporting discussion in the text, as well as details in the Supplementary Note. Neither the data themselves nor any other results are affected. Figure 4 has been revised accordingly. Images of the original and corrected figure panels are shown in the correction notice