scholarly journals From sectors to speckles: The impact of long-range migration on gene surfing

2019 ◽  
Author(s):  
Jayson Paulose ◽  
Oskar Hallatschek
Keyword(s):  
Genetic Variation ◽  
Long Range ◽  
Range Expansion ◽  
Spatial Genetic Structure ◽  
Dispersal Distance ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Species Invasions ◽  
Dispersal Distances ◽  
The Impact

Range expansions lead to distinctive patterns of genetic variation in populations, even in the absence of selection. These patterns and their genetic consequences have been well-studied for populations advancing through successive short-ranged migration events. However, most populations harbor some degree of long-range dispersal, experiencing rare yet consequential migration events over arbitrarily long distances. Although dispersal is known to strongly affect spatial genetic structure during range expansions, the resulting patterns and their impact on neutral diversity remain poorly understood. Here, we systematically study the consequences of long-range dispersal on patterns of neutral variation during range expansion in a class of dispersal models which spans the extremes of local (effectively short-ranged) and global (effectively well-mixed) migration. We find that sufficiently long-ranged dispersal leaves behind a mosaic of monoallelic patches, whose number and size are highly sensitive to the distribution of dispersal distances. We develop a coarse-grained model which connects statistical features of these spatial patterns to the evolution of neutral diversity during the range expansion. We show that growth mechanisms that appear qualitatively similar can engender vastly different outcomes for diversity: depending on the tail of the dispersal distance distribution, diversity can either be preserved (i.e. many variants survive) or lost (i.e. one variant dominates) at long times. Our results highlight the impact of spatial and migratory structure on genetic variation during processes as varied as range expansions, species invasions, epidemics, and the spread of beneficial mutations in established populations.

scholarly journals The impact of long-range dispersal on gene surfing

2020 ◽  
Vol 117 (14) ◽  
pp. 7584-7593 ◽  
Author(s):  
Jayson Paulose ◽  
Oskar Hallatschek
Keyword(s):  
Genetic Variation ◽  
Long Range ◽  
Range Expansion ◽  
Spatial Genetic Structure ◽  
Dispersal Distance ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Species Invasions ◽  
Dispersal Distances ◽  
The Impact

Range expansions lead to distinctive patterns of genetic variation in populations, even in the absence of selection. These patterns and their genetic consequences have been well studied for populations advancing through successive short-ranged migration events. However, most populations harbor some degree of long-range dispersal, experiencing rare yet consequential migration events over arbitrarily long distances. Although dispersal is known to strongly affect spatial genetic structure during range expansions, the resulting patterns and their impact on neutral diversity remain poorly understood. Here, we systematically study the consequences of long-range dispersal on patterns of neutral variation during range expansion in a class of dispersal models which spans the extremes of local (effectively short-ranged) and global (effectively well-mixed) migration. We find that sufficiently long-ranged dispersal leaves behind a mosaic of monoallelic patches, whose number and size are highly sensitive to the distribution of dispersal distances. We develop a coarse-grained model which connects statistical features of these spatial patterns to the evolution of neutral diversity during the range expansion. We show that growth mechanisms that appear qualitatively similar can engender vastly different outcomes for diversity: Depending on the tail of the dispersal distance distribution, diversity can be either preserved (i.e., many variants survive) or lost (i.e., one variant dominates) at long times. Our results highlight the impact of spatial and migratory structure on genetic variation during processes as varied as range expansions, species invasions, epidemics, and the spread of beneficial mutations in established populations.

Staying close: short local dispersal distances on a managed forest of two Patagonian Nothofagus species

2020 ◽  
Vol 93 (5) ◽  
pp. 652-661 ◽  
Author(s):  
Georgina Sola ◽  
Verónica El Mujtar ◽  
Leonardo Gallo ◽  
Giovanni G Vendramin ◽  
Paula Marchelli
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Spatial Genetic Structure ◽  
Pollen Dispersal ◽  
Dispersal Distance ◽  
Restricted Gene Flow ◽  
Fine Scale ◽  
Gene Dispersal ◽  
Mature Trees ◽  
The Impact

Abstract Understanding the impact of management on the dispersal potential of forest tree species is pivotal in the context of global change, given the implications of gene flow on species evolution. We aimed to determine the effect of logging on gene flow distances in two Nothofagus species from temperate Patagonian forests having high ecological relevance and wood quality. Therefore, a total of 778 individuals (mature trees and saplings) of Nothofagus alpina and N. obliqua, from a single plot managed 20 years ago (2.85 hectares), were mapped and genotyped at polymorphic nuclear microsatellite loci. Historical estimates of gene dispersal distance (based on fine-scale spatial genetic structure) and contemporary estimates of seed and pollen dispersal (based on spatially explicit mating models) were obtained. The results indicated restricted gene flow (gene distance ≤ 45 m, both pollen and seed), no selfing and significant seed and pollen immigration from trees located outside the studied plot but in the close surrounding area. The size of trees (diameter at breast height and height) was significantly associated with female and/or male fertility. The significant fine-scale spatial genetic structure was consistent with the restricted seed and pollen dispersal. Moreover, both estimates of gene dispersal (historical and contemporary) gave congruent results. This suggests that the recent history of logging within the study area has not significantly influenced on patterns of gene flow, which can be explained by the silviculture applied to the stand. The residual tree density maintained species composition, and the homogeneous spatial distribution of trees allowed the maintenance of gene dispersal. The short dispersal distance estimated for these two species has several implications both for understanding the evolution of the species and for defining management, conservation and restoration actions. Future replication of this study in other Nothofagus Patagonian forests would be helpful to validate our conclusions.

Modeling no-take marine reserves in regulated fisheries: assessing the role of larval dispersal

2008 ◽  
Vol 65 (11) ◽  
pp. 2509-2523 ◽  
Author(s):  
Carey R. McGilliard ◽  
Ray Hilborn
Keyword(s):  
Larval Dispersal ◽  
Marine Reserves ◽  
Dispersal Distance ◽  
Maximum Sustainable Yield ◽  
Catch Per Unit Effort ◽  
Long Distance ◽  
Total Allowable Catch ◽  
Dispersal Distances ◽  
The Impact

We explored the effects of larval dispersal distance on the impact of no-take marine reserves (NTMRs) implemented in fisheries with catch regulations. NTMRs exist in many fisheries with harvest regulated by annual catch limits. In these fisheries, catch is taken from outside NTMRs, potentially resulting in reduced abundance outside NTMRs and an overall reduction in catch. We used a spatial model with two life stages (larvae and adults) to evaluate the effects of larval dispersal distance for fisheries managed by a total allowable catch (TAC) and an NTMR. We examined effects of the timing of density-dependent mortality in relation to larval movement. Abundance reached similar values for populations with long and short larval dispersal distances. Catch declined substantially for stocks with short larval dispersal distances. When larval dispersal distances were long, catch declined to values below maximum sustainable yield (MSY), but stabilized. Catch per unit effort (CPUE) declined to 9% of CPUE at MSY for stocks with short distance larval dispersal after the implementation of an NTMR; with long distance larval dispersal, CPUE declined to approximately 50% or less of the CPUE at MSY. The CPUE did not reflect trends in abundance after the implementation of an NTMR.

scholarly journals Causal Geometry

Entropy ◽  
2020 ◽  
Vol 23 (1) ◽  
pp. 24
Author(s):  
Pavel Chvykov ◽  
Erik Hoel
Keyword(s):  
Causal Relationship ◽  
Causal Model ◽  
Information Geometry ◽  
Scientific Models ◽  
Coarse Grained ◽  
Model Parameters ◽  
Coarse Grained Model ◽  
Fundamental Part ◽  
The Impact ◽  
Causal Geometry

Information geometry has offered a way to formally study the efficacy of scientific models by quantifying the impact of model parameters on the predicted effects. However, there has been little formal investigation of causation in this framework, despite causal models being a fundamental part of science and explanation. Here, we introduce causal geometry, which formalizes not only how outcomes are impacted by parameters, but also how the parameters of a model can be intervened upon. Therefore, we introduce a geometric version of “effective information”—a known measure of the informativeness of a causal relationship. We show that it is given by the matching between the space of effects and the space of interventions, in the form of their geometric congruence. Therefore, given a fixed intervention capability, an effective causal model is one that is well matched to those interventions. This is a consequence of “causal emergence,” wherein macroscopic causal relationships may carry more information than “fundamental” microscopic ones. We thus argue that a coarse-grained model may, paradoxically, be more informative than the microscopic one, especially when it better matches the scale of accessible interventions—as we illustrate on toy examples.

scholarly journals Water confined in self-assembled ionic surfactant nano-structures

Soft Matter ◽  
2015 ◽  
Vol 11 (12) ◽  
pp. 2469-2478 ◽  
Author(s):  
Samuel Hanot ◽  
Sandrine Lyonnard ◽  
Stefano Mossa
Keyword(s):  
Computer Simulation ◽  
Aqueous Solutions ◽  
Structural Features ◽  
Coarse Grained ◽  
Ionic Surfactants ◽  
Ionic Surfactant ◽  
Coarse Grained Model ◽  
Nano Structures ◽  
Consequent Effect ◽  
The Impact

We present a coarse-grained model for ionic surfactants in explicit aqueous solutions, and study by computer simulation both the impact of water content on the morphology of the system, and the consequent effect of the formed interfaces on the structural features of the absorbed fluid.

scholarly journals Seasonal streamflow forecasting by conditioning climatology with precipitation indices

2017 ◽  
Vol 21 (3) ◽  
pp. 1573-1591 ◽  
Author(s):  
Louise Crochemore ◽  
Maria-Helena Ramos ◽  
Florian Pappenberger ◽  
Charles Perrin
Keyword(s):  
Long Range ◽  
Precipitation Forecast ◽  
Low Flow ◽  
Drought Risk ◽  
Streamflow Forecasting ◽  
Streamflow Forecasts ◽  
Precipitation Indices ◽  
Seasonal Streamflow ◽  
Prediction Approach ◽  
The Impact

Abstract. Many fields, such as drought-risk assessment or reservoir management, can benefit from long-range streamflow forecasts. Climatology has long been used in long-range streamflow forecasting. Conditioning methods have been proposed to select or weight relevant historical time series from climatology. They are often based on general circulation model (GCM) outputs that are specific to the forecast date due to the initialisation of GCMs on current conditions. This study investigates the impact of conditioning methods on the performance of seasonal streamflow forecasts. Four conditioning statistics based on seasonal forecasts of cumulative precipitation and the standardised precipitation index were used to select relevant traces within historical streamflows and precipitation respectively. This resulted in eight conditioned streamflow forecast scenarios. These scenarios were compared to the climatology of historical streamflows, the ensemble streamflow prediction approach and the streamflow forecasts obtained from ECMWF System 4 precipitation forecasts. The impact of conditioning was assessed in terms of forecast sharpness (spread), reliability, overall performance and low-flow event detection. Results showed that conditioning past observations on seasonal precipitation indices generally improves forecast sharpness, but may reduce reliability, with respect to climatology. Conversely, conditioned ensembles were more reliable but less sharp than streamflow forecasts derived from System 4 precipitation. Forecast attributes from conditioned and unconditioned ensembles are illustrated for a case of drought-risk forecasting: the 2003 drought in France. In the case of low-flow forecasting, conditioning results in ensembles that can better assess weekly deficit volumes and durations over a wider range of lead times.

scholarly journals Genomic variation in the American pika: signatures of geographic isolation and implications for conservation

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Kelly B. Klingler ◽  
Joshua P. Jahner ◽  
Thomas L. Parchman ◽  
Chris Ray ◽  
Mary M. Peacock
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Sierra Nevada ◽  
Spatial Genetic Structure ◽  
Spatial Scales ◽  
Thermal Sensitivity ◽  
Genomic Variation ◽  
Genome Wide ◽  
A Genome ◽  
American Pika

Abstract Background Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada. Results Our genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. Populations in Nevada were characterized by low genetic diversity (π = 0.0006–0.0009; θW = 0.0005–0.0007) relative to populations in California (π = 0.0014–0.0019; θW = 0.0011–0.0017) and the Rocky Mountains (π = 0.0025–0.0027; θW = 0.0021–0.0024), indicating substantial genetic drift in these isolated populations. Tajima’s D was positive for all sites (D = 0.240–0.811), consistent with recent contraction in population sizes range-wide. Conclusions Substantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada.

scholarly journals Whole-genome sequencing from the New Zealand Saccharomyces cerevisiae population reveals the genomic impacts of novel microbial range expansion

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Peter Higgins ◽  
Cooper A Grace ◽  
Soon A Lee ◽  
Matthew R Goddard
Keyword(s):  
Saccharomyces Cerevisiae ◽  
New Zealand ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Range Expansion ◽  
Copy Number ◽  
Small Scale ◽  
Whole Genome ◽  
Copy Number Changes ◽  
The Impact

Abstract Saccharomyces cerevisiae is extensively utilized for commercial fermentation, and is also an important biological model; however, its ecology has only recently begun to be understood. Through the use of whole-genome sequencing, the species has been characterized into a number of distinct subpopulations, defined by geographical ranges and industrial uses. Here, the whole-genome sequences of 104 New Zealand (NZ) S. cerevisiae strains, including 52 novel genomes, are analyzed alongside 450 published sequences derived from various global locations. The impact of S. cerevisiae novel range expansion into NZ was investigated and these analyses reveal the positioning of NZ strains as a subgroup to the predominantly European/wine clade. A number of genomic differences with the European group correlate with range expansion into NZ, including 18 highly enriched single-nucleotide polymorphism (SNPs) and novel Ty1/2 insertions. While it is not possible to categorically determine if any genetic differences are due to stochastic process or the operations of natural selection, we suggest that the observation of NZ-specific copy number increases of four sugar transporter genes in the HXT family may reasonably represent an adaptation in the NZ S. cerevisiae subpopulation, and this correlates with the observations of copy number changes during adaptation in small-scale experimental evolution studies.

Sign in / Sign up

Export Citation Format

Share Document