4 results on '"mitochondrial-DNA"'
Search Results
2. Using in silico predicted ancestral genomes to improve the efficiency of paleogenome reconstruction
- Author
-
M. Thomas P. Gilbert, Filipe G. Vieira, and José Alfredo Samaniego Castruita
- Subjects
0106 biological sciences ,DNA damage ,MITOCHONDRIAL-DNA ,In silico ,Biology ,MISCODING LESIONS ,010603 evolutionary biology ,01 natural sciences ,Genome ,ancestral genome reconstruction ,DNA sequencing ,03 medical and health sciences ,symbols.namesake ,Mapping algorithm ,HISTORY ,ANCIENT DNA ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Nature and Landscape Conservation ,Sanger sequencing ,DAMAGE ,0303 health sciences ,Ecology ,SEQUENCES ,ORIGIN ,Hypotheses ,EVOLUTION ,INSIGHTS ,Ancient DNA ,paleogenomics ,Evolutionary biology ,symbols ,Evolutionary divergence - Abstract
Paleogenomics is the nascent discipline concerned with sequencing and analysis of genome‐scale information from historic, ancient, and even extinct samples. While once inconceivable due to the challenges of DNA damage, contamination, and the technical limitations of PCR‐based Sanger sequencing, following the dawn of the second‐generation sequencing revolution, it has rapidly become a reality. However, a significant challenge facing ancient DNA studies on extinct species is the lack of closely related reference genomes against which to map the sequencing reads from ancient samples. Although bioinformatic efforts to improve the assemblies have focused mainly in mapping algorithms, in this article we explore the potential of an alternative approach, namely using reconstructed ancestral genome as reference for mapping DNA sequences of ancient samples. Specifically, we present a preliminary proof of concept for a general framework and demonstrate how under certain evolutionary divergence thresholds, considerable mapping improvements can be easily obtained., A significant challenge facing ancient DNA studies on extinct species is the lack of closely related reference genomes against which to map the sequencing reads from the ancient samples. Although bioinformatic efforts to improve the assemblies have focused mainly in mapping algorithms, in this article we explore the potential of an alternative approach, namely using reconstructed ancestral genome as reference for mapping DNA sequences of ancient samples.
- Published
- 2020
3. Hybridization selects for prime‐numbered life cycles in Magicicada: An individual‐based simulation model of a structured periodical cicada population
- Author
-
Jaakko Toivonen, Lutz Fromhage, and Department of Computer Science
- Subjects
PRODOXIDAE ,0106 biological sciences ,structured population model ,MITOCHONDRIAL-DNA ,media_common.quotation_subject ,Population ,Biology ,010603 evolutionary biology ,01 natural sciences ,Magicicada ,Prime (order theory) ,Competition (biology) ,Predation ,HOMOPTERA-CICADIDAE ,13-YEAR ,03 medical and health sciences ,Individual based ,populaatiot ,lcsh:QH540-549.5 ,DIVERGENCE ,jälkeläiset ,education ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Nature and Landscape Conservation ,media_common ,Original Research ,suosinta ,0303 health sciences ,education.field_of_study ,Ecology ,kaskaat ,YUCCA MOTH ,alkuluvut ,Prime number ,prime numbers ,elinkaari ,lisääntyminen ,EVOLUTION ,LEPIDOPTERA ,17-YEAR CICADAS ,Evolutionary biology ,1181 Ecology, evolutionary biology ,individual‐based model ,lcsh:Ecology ,individual-based model - Abstract
We investigate competition between separate periodical cicada populations each possessing different life‐cycle lengths. We build an individual‐based model to simulate the cicada life cycle and allow random migrations to occur between patches inhabited by the different populations. We show that if hybridization between different cycle lengths produces offspring that have an intermediate life‐cycle length, then predation acts disproportionately to select against the hybrid offspring. This happens because they emerge in low densities without the safety‐in‐numbers provided by either parent population. Thus, prime‐numbered life cycles that can better avoid hybridization are favored. However, we find that this advantage of prime‐numbered cycles occurs only if there is some mechanism that can occasionally synchronize emergence between local populations in sufficiently many patches., We investigate competition between separate periodical cicada populations each possessing different life‐cycle lengths. We show that prime‐numbered life cycles are selected for when hybridization produces offspring with an intermediate life‐cycle length compared to their parents.
- Published
- 2020
4. Differentiation in neutral genes and a candidate gene in the pied flycatcher
- Author
-
Martin Päckert, Klaus Schwenk, Kerstin Kuhn, Ulf S. Johansson, Till Töpfer, Christiaan Both, Steven van der Mije, David Canal, and Both group
- Subjects
MITOCHONDRIAL-DNA ,Population ,Biology ,MOLECULAR ANALYSIS ,microsatellites ,Candidate genes ,Gene flow ,MUSEUM SPECIMENS ,Control region ,biological archives ,ddc:570 ,Genetic variation ,HISTORICAL BIOGEOGRAPHY ,ddc:550 ,Climate change ,ANCIENT DNA ,POPULATION-STRUCTURE ,Stabilizing selection ,Microsatellites ,education ,Ecology, Evolution, Behavior and Systematics ,Nature and Landscape Conservation ,Local adaptation ,Original Research ,education.field_of_study ,Genetic diversity ,Ecology ,Ficedula ,LATITUDINAL CLINE ,control region ,FICEDULA-HYPOLEUCA ,biology.organism_classification ,EVOLUTION ,Biological archives ,climate change ,candidate genes ,Avian clock gene ,CLOCK GENE ,Genetic marker ,Avian Clock gene - Abstract
Global climate change is one of the major driving forces for adaptive shifts in migration and breeding phenology and possibly impacts demographic changes if a species fails to adapt sufficiently. In Western Europe, pied flycatchers (Ficedula hypoleuca) have insufficiently adapted their breeding phenology to the ongoing advance of food peaks within their breeding area and consequently suffered local population declines. We address the question whether this population decline led to a loss of genetic variation, using two neutral marker sets (mitochondrial control region and microsatellites), and one potentially selectively non-neutral marker (avian Clock gene). We report temporal changes in genetic diversity in extant populations and biological archives over more than a century, using samples from sites differing in the extent of climate change. Comparing genetic differentiation over this period revealed that only the recent Dutch population, which underwent population declines, showed slightly lower genetic variation than the historic Dutch population. As that loss of variation was only moderate and not observed in all markers, current gene flow across Western and Central European populations might have compensated local loss of variation over the last decades. A comparison of genetic differentiation in neutral loci versus the Clock gene locus provided evidence for stabilizing selection. Furthermore, in all genetic markers, we found a greater genetic differentiation in space than in time. This pattern suggests that local adaptation or historic processes might have a stronger effect on the population structure and genetic variation in the pied flycatcher than recent global climate changes
- Published
- 2013
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.