scholarly journals Genomic Data from an Endangered Amphibian Reveal Unforeseen Consequences of Fragmentation by Roads

2018 ◽  
Author(s):  
Evan McCartney-Melstad ◽  
Jannet K. Vu ◽  
H. Bradley Shaffer
Keyword(s):  
Statistical Power ◽  
Sequence Data ◽  
Molecular Ecology ◽  
Geographic Distance ◽  
Structured Populations ◽  
Anthropogenic Factors ◽  
Ambystoma Tigrinum ◽  
Strong Positive Correlation ◽  
Effective Population ◽  
Road Effects

AbstractRoads fragment landscapes and can cause the loss of metapopulation dynamics in threatened species, but as relatively new landscape features, few studies have had the statistical power to genetically examine road effects. We used DNA sequence data from thousands of nuclear loci to characterize the population structure of New York-endangered Eastern tiger salamanders (Ambystoma tigrinum) on Long Island and quantify the impacts of roads on population fragmentation. We uncovered highly genetically structured populations over an extremely small spatial scale (approximately 40 km2) in an increasingly human-modified landscape. Geographic distance and the presence of roads between ponds are both strong predictors of genetic divergence, suggesting that both natural and anthropogenic factors are responsible for the observed patterns of genetic variation. Our study demonstrates the value of genomic approaches in molecular ecology, as these patterns did not emerge in an earlier study of the same system using microsatellite loci. Ponds supported small effective population sizes, and pond surface area showed a strong positive correlation with salamander population size. When combined with the high degree of structuring in this heavily modified landscape, our study indicates that these endangered amphibians require management at the individual pond, or pond cluster, level. Particular efforts should be made to preserve large vernal pools, which harbor the greatest genetic diversity, and their surrounding upland habitat. Contiguous upland landscapes between ponds that facilitate natural metapopulation connectivity and demographic rescue from future local extirpations should also be protected.

scholarly journals Inferring time-dependent migration and coalescence patterns from genetic sequence and predictor data in structured populations

2018 ◽  
Author(s):  
Nicola F. Müller ◽  
Gytis Dudas ◽  
Tanja Stadler
Keyword(s):  
Population Dynamics ◽  
Phylogenetic Trees ◽  
Ebola Virus ◽  
Sequence Data ◽  
Geographic Distance ◽  
Structured Populations ◽  
Effective Population ◽  
Genetic Sequence ◽  
Migration Rates ◽  
Population Sizes

AbstractPopulation dynamics can be inferred from genetic sequence data using phylodynamic methods. These methods typically quantify the dynamics in unstructured populations or assume the parameters describing the dynamics to be constant through time in structured populations. Inference methods allowing for structured populations and parameters to vary through time involve many parameters which have to be inferred. Each of these parameters might be however only weakly informed by data. Here we introduce an approach that uses so-called predictors, such as geographic distance between locations, within a generalized linear model to inform the population dynamic parameters, namely the time-varying migration rates and effective population sizes under the marginal approximation of the structured coalescent. By using simulations, we show that we are able to reliably infer the parameters from phylogenetic trees. We then apply this framework to a previously described Ebola virus dataset. We infer incidence to be the strongest predictor for effective population size and geographic distance the strongest predictor for migration. This allows us to show not only on simulated data, but also on real data, that we are able to identify reasonable predictors. Overall, we provide a novel method that allows to identify predictors for migration rates and effective population sizes and to use these predictors to quantify migration rates and effective population sizes. Its implementation as part of the BEAST2 software package MASCOT allows to jointly infer population dynamics within structured populations, the phylogenetic tree, and evolutionary parameters.

scholarly journals Inferring time-dependent migration and coalescence patterns from genetic sequence and predictor data in structured populations

2019 ◽  
Vol 5 (2) ◽  
Author(s):  
Nicola F Müller ◽  
Gytis Dudas ◽  
Tanja Stadler
Keyword(s):  
Population Dynamics ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Structured Populations ◽  
Model Parameters ◽  
Effective Population ◽  
Genetic Sequence ◽  
Migration Rates ◽  
Population Sizes ◽  
Structured Coalescent

Abstract Population dynamics can be inferred from genetic sequence data by using phylodynamic methods. These methods typically quantify the dynamics in unstructured populations or assume migration rates and effective population sizes to be constant through time in structured populations. When considering rates to vary through time in structured populations, the number of parameters to infer increases rapidly and the available data might not be sufficient to inform these. Additionally, it is often of interest to know what predicts these parameters rather than knowing the parameters themselves. Here, we introduce a method to  infer the predictors for time-varying migration rates and effective population sizes by using a generalized linear model (GLM) approach under the marginal approximation of the structured coalescent. Using simulations, we show that our approach is able to reliably infer the model parameters and its predictors from phylogenetic trees. Furthermore, when simulating trees under the structured coalescent, we show that our new approach outperforms the discrete trait GLM model. We then apply our framework to a previously described Ebola virus dataset, where we infer the parameters and its predictors from genome sequences while accounting for phylogenetic uncertainty. We infer weekly cases to be the strongest predictor for effective population size and geographic distance the strongest predictor for migration. This approach is implemented as part of the BEAST2 package MASCOT, which allows us to jointly infer population dynamics, i.e. the parameters and predictors, within structured populations, the phylogenetic tree, and evolutionary parameters.

Population genetics, phylogeography, and systematics of the thornyhead rockfishes (Sebastolobus) along the deep continental slopes of the North Pacific Ocean

2000 ◽  
Vol 57 (8) ◽  
pp. 1701-1717 ◽  
Author(s):  
Carol A Stepien ◽  
Alison K Dillon ◽  
Amy K Patterson
Keyword(s):  
Pacific Ocean ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
North Pacific Ocean ◽  
Geographic Distance ◽  
The North ◽  
Continental Slopes ◽  
Genetic Patterns ◽  
Northern Pacific ◽  
Shortspine Thornyhead

Population genetic, phylogeographic, and systematic relationships are elucidated among the three species comprising the thornyhead rockfish genus Sebastolobus (Teleostei: Scorpaenidae). Genetic variation among sampling sites representing their extensive ranges along the deep continental slopes of the northern Pacific Ocean is compared using sequence data from the left domain of the mtDNA control region. Comparisons are made among the shortspine thornyhead (S. alascanus) (from seven locations), the longspine thornyhead (S. altivelis) (from five sites), which are sympatric in the northeast, and the broadbanded thornyhead (S. macrochir) (a single site) from the northwest. Phylogenetic trees rooted to Sebastes show that S. macrochir is the sister taxon of S. alascanus and S. altivelis. Intraspecific genetic variability is appreciable, with most individuals having unique haplotypes. Gene flow is substantial among some locations and others diverged significantly. Genetic divergences among sampling sites for S. alascanus indicate an isolation by geographic distance pattern. Genetic divergences for S. altivelis are unrelated to the hypothesis of isolation by geographic distance and appear to be more consistent with the hypothesis of larval retention in currents and gyres. Differences in geographic genetic patterns between the species are attributed to life history differences in their relative mobilities as juveniles and adults.

scholarly journals The effect of life-history and mode of inheritance on neutral genetic variability

2001 ◽  
Vol 77 (2) ◽  
pp. 153-166 ◽  
Author(s):  
BRIAN CHARLESWORTH
Keyword(s):  
Sequence Variation ◽  
Adult Mortality ◽  
Structured Populations ◽  
Human Populations ◽  
Effective Population ◽  
Transmission Modes ◽  
Population Sizes ◽  
Age Structured ◽  
Infinite Sites Model ◽  
Site Diversity

Formulae for the effective population sizes of autosomal, X-linked, Y-linked and maternally transmitted loci in age-structured populations are developed. The approximations used here predict both asymptotic rates of increase in probabilities of identity, and equilibrium levels of neutral nucleotide site diversity under the infinite-sites model. The applications of the results to the interpretation of data on DNA sequence variation in Drosophila, plant, and human populations are discussed. It is concluded that sex differences in demographic parameters such as adult mortality rates generally have small effects on the relative effective population sizes of loci with different modes of inheritance, whereas differences between the sexes in variance in reproductive success can have major effects, either increasing or reducing the effective population size for X-linked loci relative to autosomal or Y-linked loci. These effects need to be accounted for when trying to understand data on patterns of sequence variation for genes with different transmission modes.

scholarly journals An iterative and automated computational pipeline for untargeted strain-level identification using MS/MS spectra from pathogenic samples

2019 ◽  
Author(s):  
Mathias Kuhring ◽  
Joerg Doellinger ◽  
Andreas Nitsche ◽  
Thilo Muth ◽  
Bernhard Y. Renard
Keyword(s):  
Statistical Power ◽  
Sequence Data ◽  
A Priori ◽  
Search Space ◽  
Strain Level ◽  
Reference Sequence ◽  
Viral Origin ◽  
Identification Of Species ◽  
Taxonomic Assignments

AbstractUntargeted accurate strain-level classification of a priori unidentified organisms using tandem mass spectrometry is a challenging task. Reference databases often lack taxonomic depth, limiting peptide assignments to the species level. However, the extension with detailed strain information increases runtime and decreases statistical power. In addition, larger databases contain a higher number of similar proteomes.We present TaxIt, an iterative workflow to address the increasing search space required for MS/MS-based strain-level classification of samples with unknown taxonomic origin. TaxIt first applies reference sequence data for initial identification of species candidates, followed by automated acquisition of relevant strain sequences for low level classification. Furthermore, proteome similarities resulting in ambiguous taxonomic assignments are addressed with an abundance weighting strategy to improve candidate confidence.We apply our iterative workflow on several samples of bacterial and viral origin. In comparison to non-iterative approaches using unique peptides or advanced abundance correction, TaxIt identifies microbial strains correctly in all examples presented (with one tie), thereby demonstrating the potential for untargeted and deeper taxonomic classification. TaxIt makes extensive use of public, unrestricted and continuously growing sequence resources such as the NCBI databases and is available under open-source license at https://gitlab.com/rki_bioinformatics.

scholarly journals Molecular markers applying in forest trees gene pool conservation

2009 ◽  
pp. 101-113
Author(s):  
Jelena Milovanovic ◽  
Mirjana Sijacic-Nikolic
Keyword(s):  
Population Genetics ◽  
Molecular Markers ◽  
Gene Flow ◽  
Gene Pool ◽  
Statistical Power ◽  
Forest Trees ◽  
Effective Population ◽  
Migration Patterns ◽  
Geographic Diversity ◽  
Marker Loci

Many studies performed during the last years demonstrated the usefulness of neutral molecular markers in the field of conservation and population genetics of forest trees, in particular to understand the importance of migration patterns in shaping current genetic and geographic diversity and to measure important parameters such as effective population size, gene flow and past bottleneck. During the next years, a large amount of data at marker loci or at sequence level is expected to be collected, and to become excellent statistical power for the assessment of biological and evolutionary value.

Phylogenetics and phylogeography of a long-legged harvestman (Arachnida : Opiliones) in the Brazilian Atlantic Rain Forest reveals poor dispersal, low diversity and extensive mitochondrial introgression

2015 ◽  
Vol 29 (4) ◽  
pp. 386 ◽  
Author(s):  
Cibele Bragagnolo ◽  
Ricardo Pinto-da-Rocha ◽  
Manuel Antunes ◽  
Ronald M. Clouse
Keyword(s):  
Rain Forest ◽  
Species Complex ◽  
Sequence Data ◽  
Historical Event ◽  
12S Rrna ◽  
Atlantic Rain Forest ◽  
Effective Population ◽  
Narrow Region ◽  
Low Genetic Diversity ◽  
Mitochondrial Introgression

We used DNA sequence data to test the morphology-based taxonomy and examine the biogeography of the Brazilian Atlantic Rain Forest genus Promitobates. Most species are well differentiated morphologically, and a previous morphological phylogeny recovered the genus as monophyletic. However, some of these species have overlapping geographical distributions and considerable intraspecific variation, perhaps representing a species complex. Mitochondrial (12S rRNA and COI) and nuclear (ITS2 and 28S) genes were sequenced from 132 specimens collected from 27 localities. The results are consistent with significant mitochondrial introgression among the species P. ornatus, P. hatschbachi, P. lager, P. bellus and P. intermedius (the ‘P. ornatus species complex’), with one specimen identified as a hybrid between P. nigripes and this complex. A phylogeographic study of the complex was conducted using mitochondrial haplotypes. This revealed remarkably poor dispersal among populations, with only one case of a shared haplotype, and very low genetic diversity. The phylogeny showed a clear break between populations on either side of a narrow region of forest, suggesting an important historical event separated these lineages in the genus. The analyses also pointed to population breaks that date back several millions of years or extremely small effective population sizes, depending on the mutation rate.

scholarly journals Coalescence theory for a general class of structured populations with fast migration

2011 ◽  
Vol 43 (04) ◽  
pp. 1027-1047 ◽  
Author(s):  
O. Hössjer
Keyword(s):  
Population Size ◽  
General Class ◽  
Population Genetic ◽  
Total Population ◽  
Structured Populations ◽  
Effective Population ◽  
Constant Change ◽  
Skorokhod Topology ◽  
Age Structured ◽  
Dependency Structures

In this paper we study a general class of population genetic models where the total population is divided into a number of subpopulations or types. Migration between subpopulations is fast. Extending the results of Nordborg and Krone (2002) and Sagitov and Jagers (2005), we prove, as the total population sizeNtends to ∞, weak convergence of the joint ancestry of a given sample of haploid individuals in the Skorokhod topology towards Kingman's coalescent with a constant change of time scalec. Our framework includes age-structured models, geographically structured models, and combinations thereof. We also allow each individual to have offspring in several subpopulations, with general dependency structures between the number of offspring of various types. As a byproduct, explicit expressions for the coalescent effective population sizeN/care obtained.

scholarly journals Planktonic foraminifera genomic variations reflect paleoceanographic changes in the Arctic: evidence from sedimentary ancient DNA

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Joanna Pawłowska ◽  
Jutta E. Wollenburg ◽  
Marek Zajączkowski ◽  
Jan Pawlowski
Keyword(s):  
Ancient Dna ◽  
Sequence Data ◽  
Planktonic Foraminifera ◽  
Molecular Ecology ◽  
The Arctic ◽  
Marine Biodiversity ◽  
Neogloboquadrina Pachyderma ◽  
Rna Genes ◽  
The Last Glacial Maximum ◽  
The Last Glacial

Abstract Deciphering the evolution of marine plankton is typically based on the study of microfossil groups. Cryptic speciation is common in these groups, and large intragenomic variations occur in ribosomal RNA genes of many morphospecies. In this study, we correlated the distribution of ribosomal amplicon sequence variants (ASVs) with paleoceanographic changes by analyzing the high-throughput sequence data assigned to Neogloboquadrina pachyderma in a 140,000-year-old sediment core from the Arctic Ocean. The sedimentary ancient DNA demonstrated the occurrence of various N. pachyderma ASVs whose occurrence and dominance varied through time. Most remarkable was the striking appearance of ASV18, which was nearly absent in older sediments but became dominant during the last glacial maximum and continues to persist today. Although the molecular ecology of planktonic foraminifera is still poorly known, the analysis of their intragenomic variations through time has the potential to provide new insight into the evolution of marine biodiversity and may lead to the development of new and important paleoceanographic proxies.

scholarly journals On the estimation of ancestral population sizes of modern humans

1997 ◽  
Vol 69 (2) ◽  
pp. 111-116 ◽  
Author(s):  
ZIHENG YANG
Keyword(s):  
Population Size ◽  
Sequence Data ◽  
Divergence Time ◽  
Ancestral Population ◽  
Rate Variation ◽  
Effective Population ◽  
Modern Humans ◽  
Extant Species ◽  
Population Sizes ◽  
Highly Correlated

The theory developed by Takahata and colleagues for estimating the effective population size of ancestral species using homologous sequences from closely related extant species was extended to take account of variation of evolutionary rates among loci. Nuclear sequence data related to the evolution of modern humans were reanalysed and computer simulations were performed to examine the effect of rate variation on estimation of ancestral population sizes. It is found that the among-locus rate variation does not have a significant effect on estimation of the current population size when sequences from multiple loci are sampled from the same species, but does have a significant effect on estimation of the ancestral population size using sequences from different species. The effects of ancestral population size, species divergence time and among-locus rate variation are found to be highly correlated, and to achieve reliable estimates of the ancestral population size, effects of the other two factors should be estimated independently.

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