scholarly journals Levels of linkage disequilibrium in a wild bird population

2006 ◽  
Vol 2 (3) ◽  
pp. 435-438 ◽  
Author(s):  
Niclas Backström ◽  
Anna Qvarnström ◽  
Lars Gustafsson ◽  
Hans Ellegren
Keyword(s):  
Linkage Disequilibrium ◽  
Wild Species ◽  
Background Level ◽  
Population Based ◽  
Snp Markers ◽  
Z Chromosome ◽  
Phenotypic Traits ◽  
Limited Information ◽  
Bird Population ◽  
Bird Populations

Population-based mapping approaches are attractive for tracing the genetic background to phenotypic traits in wild species, given that it is often difficult to gather extensive and well-defined pedigrees needed for quantitative trait locus analysis. However, the feasibility of association or hitch-hiking mapping is dependent on the degree of linkage disequilibrium (LD) in the population, on which there is yet limited information for wild species. Here we use single nucleotide polymorphism (SNP) markers from 23 genes in a recently established linkage map of the Z chromosome of the collared flycatcher, to study the extent of LD in a natural bird population. In most but not all cases we find SNPs within the same intron (less than 500 bp) to be in perfect LD. However, LD then decays to background level at a distance 1 cM or 400–500 kb. Although LD seems more extensive than in other species, if the observed pattern is representative for other regions of the genome and turns out to be a general feature of natural bird populations, dense marker maps might be needed for genome scans aimed at identifying association between marker and trait loci.

Assessment of invasive rodent impacts on island avifauna: methods, limitations and the way forward

2015 ◽  
Vol 42 (2) ◽  
pp. 185 ◽  
Author(s):  
Lise Ruffino ◽  
Diane Zarzoso-Lacoste ◽  
Eric Vidal
Keyword(s):  
Population Growth ◽  
Population Level ◽  
Bird Conservation ◽  
Bird Population ◽  
Breeding Parameters ◽  
Population Growth Rates ◽  
Bird Populations ◽  
Field Evidence ◽  
Bird Breeding

Bird conservation is nowadays a strong driving force for prioritising rodent eradications, but robust quantitative estimates of impacts are needed to ensure cost-effectiveness of management operations. Here, we review the published literature to investigate on what methodological basis rodent effects on island bird communities have been evaluated for the past six decades. We then discuss the advantages and limitations of each category of methods for the detection and quantification of impacts, and end with some recommendations on how to strengthen current approaches and extend our knowledge on the mechanisms of impacts. Impact studies (152 studies considered) emphasised seabirds (67%), black rats (63%) and the Pacific Ocean (57%). Among the most commonly used methods to study rodent impacts on birds were the observation of dead eggs or empty nests while monitoring bird breeding success, and the analyses of rodent diets, which can both lead to misleading conclusions if the data are not supported by direct field evidence of rodent predation. Direct observations of rodent–bird interactions (19% of studies) are still poorly considered despite their potential to reveal cryptic behaviours and shed light on the mechanisms of impacts. Rodent effects on birds were most often measured as a change or difference in bird breeding parameters (74% of studies), while estimates of bird population growth rates (4%) are lacking. Based on the outcomes of this literature review, we highlight the need for collecting unbiased population-level estimates of rodent impacts, which are essential prerequisites for predicting bird population growth scenarios and prioritising their conservation needs. This could be achieved by a more systematic integration of long-term monitoring of bird populations into rodent management operations and modelling bird population dynamics. We also strongly recommend including various complementary methods in impact assessment strategies to unravel complex interactions between rodents and birds and avoid faulty evidence. Finally, more research should be devoted to a better understanding of the cases of non-impacts (i.e. long-term coexistence) and those impacts mediated by mechanisms other than predation and ecosystem-level processes.

scholarly journals EVOLUTION OF DNA SEQUENCING METHODS AND PROSPECTS FOR THEIR USE IN FORENSIC DNA EXAMINATION

2020 ◽  
Vol 11 (87) ◽  
Author(s):  
Zhanna Bazyliuk ◽  
Keyword(s):  
Dna Sequencing ◽  
Molecular Genetic ◽  
Genetic Research ◽  
Snp Markers ◽  
Degraded Dna ◽  
Phenotypic Traits ◽  
Nucleotide Polymorphisms ◽  
Biological Origin ◽  
Genetic Traits ◽  
Str Loci

The study of the human genome makes it possible to use genetic information to identify individual traits, diagnosis of diseases and forecasting and prevention of their development, promotes a personal approach when choosing treatment methods; population research, ethnogenesis and evolutionary processes. Introduction of DNA sequencing methods in domestic genetic fingerprinting will contribute to a more informative establishment of human genetic traits. The main purpose of molecular genetic research is to establish the genetic features of missing people, their relatives, to conduct paternity, to identify traces of biological origin and their identification. This article talks about the gradual development of DNA sequencing technology, which is conventionally divided into three types. The first type includes sequencing using capillary electrophoresis and pyrosequencing. The second type is high-throughput pyrosequencing, semiconductor, cyclic ligase, and the use of fluorescently labeled precursors, based on the sequencing of millions of DNA fragments simultaneously. The third stage includes methods that do not require prior sample preparation. These are methods of nanoporous sequencing, sequencing of one molecule, one-molecular sequencing. Today, each of the sequencing methods is aimed at performing different tasks. A number of methods are promising in the field of molecular-genetic examination. In world jurisprudence, sequencing is implemented mainly with the help of devices - Illumina’s, MiSeq FGx, Ion Torrent PGM from ThermoFisher and Ion S5. Research in forensic expertise of single nucleotide polymorphisms (SNP), sequencing of STR-loci and mitochondrial DNA, STR-loci and SNP-markers of the Y chromosome, will provide a high level of information, determination of human phenotypic traits, the possibility of establishing genetic traits from significantly degraded DNA. This article deals with modern problems of identification of human genetic traits and the prospect of introduction of the newest methods of sequencing for their qualitative and complete establishment.

Higher probability of prodromal Parkinson disease is related to lower cognitive performance

Neurology ◽  
2019 ◽  
Vol 92 (19) ◽  
pp. e2261-e2272 ◽  
Author(s):  
Anastasia Bougea ◽  
Maria I. Maraki ◽  
Mary Yannakoulia ◽  
Maria Stamelou ◽  
Georgia Xiromerisiou ◽  
...  
Keyword(s):  
Parkinson Disease ◽  
Cognitive Performance ◽  
Neuropsychological Testing ◽  
Population Based ◽  
Cognitive Outcomes ◽  
Limited Information ◽  
Neuropsychological Battery ◽  
Cognitive Domains ◽  
Clinical Onset ◽  
Z Scores

ObjectiveGiven the limited information on cognitive function before Parkinson disease (PD) clinical onset in the general population, we sought to assess prodromal PD (pPD) probability and relate it to detailed cognitive performance in a community cohort.MethodsIn a population-based cohort of 1,629 dementia-free and PD-free participants ≥65 years of age in Greece, we assessed probability of pPD according to the International Parkinson and Movement Disorder Society's criteria. Clinical cognitive diagnoses (cognitively unimpaired, mild cognitive impairment [MCI], dementia) considering neuropsychological testing and functional status were assigned in consensus conferences. Cognitive performance in 5 cognitive domains was assessed by a detailed neuropsychological battery and summarized in the form of z scores. We investigated associations between pPD probability (and its individual constituents) and cognitive outcomes.ResultsThe median probability of pPD was 1.81% (0.2%–96.7%). Participants with MCI had higher probability of pPD compared to those with normal cognition (p < 0.001). Higher probability of pPD was related to lower performance in all cognitive domains (memory, language, executive, attention, and visuospatial function) (p < 0.001). Lower cognitive performance was further associated with certain nonmotor markers of pPD, such as daytime somnolence, depression, urinary dysfunction, constipation, and subthreshold parkinsonism (p < 0.001).ConclusionsHigher probability of pPD was associated with lower cognitive performance in all domains and higher probability of MCI. This may reflect a widespread pathologic process although future studies are warranted to infer causality. These results suggest to clinicians that they should assess cognition early, and to researchers that they should further look into the possible mechanisms that may underlie this observation.

scholarly journals Population genetic structure of the great star coral, Montastraea cavernosa, across the Cuban archipelago with comparisons between microsatellite and SNP markers

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Alexis B. Sturm ◽  
Ryan J. Eckert ◽  
Juliett González Méndez ◽  
Patricia González-Díaz ◽  
Joshua D. Voss
Keyword(s):  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Snp Markers ◽  
Genetic Connectivity ◽  
Limited Information ◽  
Western Atlantic ◽  
Trade Offs ◽  
Significant Genetic Structure ◽  
Montastraea Cavernosa

Abstract Coral reef habitats surrounding Cuba include relatively healthy, well-developed shallow and mesophotic (30–150 m) scleractinian communities at the cross-currents of the Tropical Western Atlantic (TWA). However, Cuba’s coral communities are not immune to the declines observed throughout the TWA, and there is limited information available regarding genetic connectivity, diversity, and structure among these populations. This represents an immense gap in our understanding of coral ecology and population dynamics at both local and regional scales. To address this gap, we evaluated the population genetic structure of the coral Montastraea cavernosa across eight reef sites surrounding Cuba. Colonies were genotyped using nine microsatellite markers and > 9,000 single nucleotide polymorphism (SNP) markers generated using the 2bRAD approach to assess fine-scale genetic structure across these sites. Both the microsatellite and SNP analyses identified patterns of genetic differentiation among sample populations. While the microsatellite analyses did not identify significant genetic structure across the seven shallow M. cavernosa sampling sites, the SNP analyses revealed significant pairwise population differentiation, suggesting that differentiation is greater between eastern and western sites. This study provides insight into methodological differences between microsatellite and SNP markers including potential trade-offs between marker-specific biases, sample size, sequencing costs, and the ability to resolve subtle patterns of population genetic structure. Furthermore, this study suggests that locations in western Cuba may play important roles in this species’ regional metapopulation dynamics and therefore may merit incorporation into developing international management efforts in addition to the local management the sites receive.

Analysis of Family- and Population-Based Samples Using Multiple Linkage Disequilibrium Mapping

2013 ◽  
Vol 77 (3) ◽  
pp. 251-267 ◽  
Author(s):  
Yen-Feng Chiu ◽  
Chun-Yi Lee ◽  
Hui-Yi Kao ◽  
Wen-Harn Pan ◽  
Fang-Chi Hsu
Keyword(s):  
Linkage Disequilibrium ◽  
Population Based ◽  
Linkage Disequilibrium Mapping

HORDEIN VARIATION IN WILD (HORDEUM SPONTANEUM) AND CULTIVATED (H. VULGARE) BARLEY

1979 ◽  
Vol 21 (3) ◽  
pp. 391-404 ◽  
Author(s):  
Hans Doll ◽  
A. H. D. Brown
Keyword(s):  
Linkage Disequilibrium ◽  
Wild Species ◽  
Storage Protein ◽  
Natural Populations ◽  
Hordeum Spontaneum ◽  
Allele Frequencies ◽  
Evolutionary Processes ◽  
Highly Correlated ◽  
The Individual ◽  
Allozyme Loci

The storage protein hordein contains two major groups of polypeptides which are highly polymorphic in barley, and in its evolutionary progenitor Hordeum spontaneum Koch. Crosses between the two species showed that the complex electrophoretic phenotypes within the two groups of polypeptides are governed by codominant alleles at two corresponding loci, Hor-1 and Hor-2, which are moderately linked (11% ± 2). In natural populations of the wild species, the two complex hordein loci were much more polymorphic than the allozyme loci. Furthermore, the variation at these two loci was highly correlated so that individuals differ from one another at both loci much more frequently than expected from the allele frequencies at the individual loci. Considerable hordein variation was also present in Composite Cross XXI, and there was evidence of reassortment of patterns by the seventeenth generation. Thus the complex hordein loci, with their extreme diversity and linkage disequilibrium, are ideal markers for monitoring evolutionary processes in both natural, or composite cross populations.

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