scholarly journals Evolution at two time frames: polymorphisms from an ancient singular divergence event fuel contemporary parallel evolution

2018 ◽  
Author(s):  
Steven M. Van Belleghem ◽  
Carl Vangestel ◽  
Katrien De Wolf ◽  
Zoë De Corte ◽  
Markus Möst ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Large Scale ◽  
Environmental Changes ◽  
Parallel Evolution ◽  
Genomic Variation ◽  
Glacial Cycles ◽  
Short Wing ◽  
Time Frames ◽  
Fast Evolution ◽  
European Coast

AbstractWhen species occur in repeated ecologically distinct habitats across their range, adaptation may proceed surprisingly fast and result in parallel evolution. There is increasing evidence that such cases of rapid parallel evolution are fueled by standing genetic variation, but the origin of this genetic variation remains poorly understood. In Pogonus chalceus beetles, short- and long-winged ecotypes have diverged in response to contrasting hydrological regimes and can be repeatedly found along the Atlantic European coast. By analyzing genomic variation across the beetles’ distribution, we reveal that genomically widespread short-wing selected alleles evolved during a singular divergence event, estimated at ~0.19 Mya. The ancient and differentially selected alleles are currently polymorphic in all populations across the range, allowing for the fast evolution of one ecotype from a small number of random individuals, as low as 5 to 15, of the populations of the other ecotype. Our results suggest that cases of fast parallel ecological divergence might be the result of evolution at two different time frames: divergence in the past, followed by repeated selection on the divergently evolved alleles after admixture. We suggest that this mechanism may be common and potentially further driven by periods of geographic isolation imposed by large-scale environmental changes such as glacial cycles.

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 Impact of the municipal merger on watershed management: a study of Lake Kasumigaura, Japan

2021 ◽  
Author(s):  
Takeshi Mizunoya ◽  
Noriko Nozaki ◽  
Rajeev Kumar Singh
Keyword(s):  
Watershed Management ◽  
Large Scale ◽  
Environmental Changes ◽  
Water Environment ◽  
Reduction Rate ◽  
Oxygen Demand ◽  
Policy Implications ◽  
Pollution Reduction ◽  
Lake Kasumigaura ◽  
The Impact

AbstractIn the early 2000s, Japan instituted the Great Heisei Consolidation, a national strategy to promote large-scale municipal mergers. This study analyzes the impact that this strategy could have on watershed management. We select the Lake Kasumigaura Basin, the second largest lake in Japan, for the case study and construct a dynamic expanded input–output model to simulate the ecological system around the Lake, the socio-environmental changes over the period, and their mutual dependency for the period 2012–2020. In the model, we regulate and control the following water pollutants: total nitrogen, total phosphorus, and chemical oxygen demand. The results show that a trade-off between economic activity and the environment can be avoided within a specific range of pollution reduction, given that the prefectural government implements optimal water environment policies, assuming that other factors constraining economic growth exist. Additionally, municipal mergers are found to significantly reduce the budget required to improve the water environment, but merger budget efficiency varies nonlinearly with the reduction rate. Furthermore, despite the increase in financial efficiency from the merger, the efficiency of installing domestic wastewater treatment systems decreases drastically beyond a certain pollution reduction level and eventually reaches a limit. Further reductions require direct regulatory instruments in addition to economic policies, along with limiting the output of each industry. Most studies on municipal mergers apply a political, administrative, or financial perspective; few evaluate the quantitative impact of municipal mergers on the environment and environmental policy implications. This study addresses these gaps.

scholarly journals Genetic variation in recombination rate in the pig

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Martin Johnsson ◽  
Andrew Whalen ◽  
Roger Ros-Freixedes ◽  
Gregor Gorjanc ◽  
Ching-Yi Chen ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Recombination Rate ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Genetic Material ◽  
A Genome ◽  
Pig Genome ◽  
Genetic Length ◽  
Trait Locus ◽  
Genomic Regions

Abstract Background Meiotic recombination results in the exchange of genetic material between homologous chromosomes. Recombination rate varies between different parts of the genome, between individuals, and is influenced by genetics. In this paper, we assessed the genetic variation in recombination rate along the genome and between individuals in the pig using multilocus iterative peeling on 150,000 individuals across nine genotyped pedigrees. We used these data to estimate the heritability of recombination and perform a genome-wide association study of recombination in the pig. Results Our results confirmed known features of the recombination landscape of the pig genome, including differences in genetic length of chromosomes and marked sex differences. The recombination landscape was repeatable between lines, but at the same time, there were differences in average autosome-wide recombination rate between lines. The heritability of autosome-wide recombination rate was low but not zero (on average 0.07 for females and 0.05 for males). We found six genomic regions that are associated with recombination rate, among which five harbour known candidate genes involved in recombination: RNF212, SHOC1, SYCP2, MSH4 and HFM1. Conclusions Our results on the variation in recombination rate in the pig genome agree with those reported for other vertebrates, with a low but nonzero heritability, and the identification of a major quantitative trait locus for recombination rate that is homologous to that detected in several other species. This work also highlights the utility of using large-scale livestock data to understand biological processes.

scholarly journals Variability in larval gut pH regulation defines sensitivity to ocean acidification in six species of the Ambulacraria superphylum

2017 ◽  
Vol 284 (1864) ◽  
pp. 20171066 ◽  
Author(s):  
Marian Hu ◽  
Yung-Che Tseng ◽  
Yi-Hsien Su ◽  
Etienne Lein ◽  
Hae-Gyeong Lee ◽  
...  
Keyword(s):  
Ocean Acidification ◽  
Large Scale ◽  
Environmental Changes ◽  
Ph Regulation ◽  
Gastric Ph ◽  
Differential Sensitivity ◽  
Larval Stages ◽  
Regulatory Systems ◽  
Alkaline Conditions ◽  
Gut Ph

The unusual rate and extent of environmental changes due to human activities may exceed the capacity of marine organisms to deal with this phenomenon. The identification of physiological systems that set the tolerance limits and their potential for phenotypic buffering in the most vulnerable ontogenetic stages become increasingly important to make large-scale projections. Here, we demonstrate that the differential sensitivity of non-calcifying Ambulacraria (echinoderms and hemichordates) larvae towards simulated ocean acidification is dictated by the physiology of their digestive systems. Gastric pH regulation upon experimental ocean acidification was compared in six species of the superphylum Ambulacraria. We observed a strong correlation between sensitivity to ocean acidification and the ability to regulate gut pH. Surprisingly, species with tightly regulated gastric pH were more sensitive to ocean acidification. This study provides evidence that strict maintenance of highly alkaline conditions in the larval gut of Ambulacraria early life stages may dictate their sensitivity to decreases in seawater pH. These findings highlight the importance of identifying and understanding pH regulatory systems in marine larval stages that may contribute to substantial energetic challenges under near-future ocean acidification scenarios.

scholarly journals Assessing the Vulnerability of Marine Fisheries in China: Towards an Inter-Provincial Perspective

2018 ◽  
Vol 10 (11) ◽  
pp. 4302 ◽  
Author(s):  
Qi Chen ◽  
Weiteng Shen ◽  
Bing Yu
Keyword(s):  
Climate Change ◽  
Adaptive Capacity ◽  
Fisheries Management ◽  
Vocational Training ◽  
Large Scale ◽  
Environmental Changes ◽  
Marine Pollution ◽  
Marine Fisheries ◽  
Intergovernmental Panel ◽  
Adaptation Measures

China’s marine fisheries are undergoing large-scale environmental changes associated with climate change, marine pollution, and overfishing. The assessment of marine fisheries vulnerability has become extremely necessary for fisheries management and sustainable development. However, studies on China’s marine fisheries vulnerability remains sparse. This study aimed to provide an analysis of the inter-provincial level vulnerability of China’s marine fisheries under multiple disturbances. The vulnerability measure was composed of exposure, sensitivity, and adaptive capacity indicators specific to marine fisheries based on the Intergovernmental Panel on Climate Change (IPCC) definitions. Results showed that Liaoning, Hebei, Fujian, and Hainan provinces appeared to be the most vulnerable; Shanghai appeared to be less vulnerable among China’s 11 coastal provinces; and the key sources of vulnerability differed considerably among coastal regions. The high vulnerability regions could be divided into two different patterns according to the combination of exposure, sensitivity, and adaptive capacity, but they all had one thing in common: relatively low adaptive capacity. While some existing coercive measures to reduce dependence on fisheries were found to be helpful in China, the reality showed that appropriate adaptation measures such as improving fishermen’s education level and increasing vocational training may be helpful in enhancing the existing policy effectiveness.

scholarly journals Methods of Landscape Valorization and Possibilities of Its Application in Hunting Area Categorisation

2020 ◽  
Author(s):  
Szewczyk Grzegorz ◽  
Krzysztof Lipka ◽  
Piotr Wężyk ◽  
Karolina Zięba-Kulawik ◽  
Monika Winczek
Keyword(s):  
Natural Environment ◽  
Functional Role ◽  
Large Scale ◽  
Forest Cover ◽  
Agricultural Landscape ◽  
Environmental Changes ◽  
Environmental Values ◽  
Small Game ◽  
Forest Habitats

As a result of environmental changes, assessment indexes for the agricultural landscape have been changing dramatically. Being at the interface of human activity and the natural environment, hunting is particularly sensitive to environmental changes, such as increasing deforestation or large-scale farming. The classical categorisation of hunting grounds takes into account the area, forest cover, number of forest complexes, fertility of forest habitats, lack of continuity of areas potentially favourable to wild animals. Landscape assessment methods used in architecture often better reflect the actual breeding and hunting value of a given area, especially in relation to fields and forests. The forest-field mosaic, large spatial fragmentation as well as interweaving of natural environment elements with buildings do not have to be the factors that limit the numbers of small game. Identification of the constituents of architectural-landscape interiors: content and significance assessment, determination of the functional role or assessment based on the general environmental values being represented take into account factors important for the existence of game, in particular small game.

scholarly journals Intraspecific genomic variation and local adaptation in a young hybrid species

2019 ◽  
Author(s):  
Angélica Cuevas ◽  
Mark Ravinet ◽  
Glenn-Peter Sætre ◽  
Fabrice Eroukhmanoff
Keyword(s):  
Genetic Variation ◽  
Local Adaptation ◽  
Climatic Variation ◽  
Genomic Variation ◽  
Population Divergence ◽  
Parent Species ◽  
Evolutionary Potential ◽  
Variable Environment ◽  
Hybrid Species ◽  
Species Population

ABSTRACTHybridization increases genetic variation, hence hybrid species may have a strong evolutionary potential once their admixed genomes have stabilized and incompatibilities have been purged. Yet, little is known about how such hybrid lineages evolve at the genomic level following their formation, in particular the characteristics of their adaptive potential, i.e. constraints and facilitations of diversification. Here we investigate how the Italian sparrow (Passer italiae), a homoploid hybrid species, has evolved and locally adapted to its variable environment. Using restriction site-associated DNA sequencing (RAD-seq) on several populations across the Italian peninsula, we evaluate how genomic constraints and novel genetic variation have influenced population divergence and adaptation. We show that population divergence within this hybrid species has evolved in response to climatic variation. As in non-hybrid species, climatic differences may even reduce gene flow between populations, suggesting ongoing local adaptation. We report outlier genes associated with adaptation to climatic variation, known to be involved in beak morphology in other species. Most of the strongly divergent loci among Italian sparrow populations seem not to be differentiated between its parent species, the house and Spanish sparrow. Within the parental species, population divergence has occurred mostly in loci where different alleles segregate in the parent species, unlike in the hybrid, suggesting that novel combinations of parental alleles in the hybrid have not necessarily enhanced its evolutionary potential. Rather, our study suggests that constraints linked to incompatibilities may have restricted the evolution of this admixed genome, both during and after hybrid species formation.

scholarly journals The crucial role of genome-wide genetic variation in conservation

2021 ◽  
Vol 118 (48) ◽  
pp. e2104642118
Author(s):  
Marty Kardos ◽  
Ellie E. Armstrong ◽  
Sarah W. Fitzpatrick ◽  
Samantha Hauser ◽  
Philip W. Hedrick ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Environmental Changes ◽  
Population Viability ◽  
Adaptive Potential ◽  
Biodiversity Crisis ◽  
Genome Wide ◽  
Simulation Based ◽  
Functional Genetic Variation

The unprecedented rate of extinction calls for efficient use of genetics to help conserve biodiversity. Several recent genomic and simulation-based studies have argued that the field of conservation biology has placed too much focus on conserving genome-wide genetic variation, and that the field should instead focus on managing the subset of functional genetic variation that is thought to affect fitness. Here, we critically evaluate the feasibility and likely benefits of this approach in conservation. We find that population genetics theory and empirical results show that conserving genome-wide genetic variation is generally the best approach to prevent inbreeding depression and loss of adaptive potential from driving populations toward extinction. Focusing conservation efforts on presumably functional genetic variation will only be feasible occasionally, often misleading, and counterproductive when prioritized over genome-wide genetic variation. Given the increasing rate of habitat loss and other environmental changes, failure to recognize the detrimental effects of lost genome-wide genetic variation on long-term population viability will only worsen the biodiversity crisis.

scholarly journals ABySS 2.0: Resource-Efficient Assembly of Large Genomes using a Bloom Filter

2016 ◽  
Author(s):  
Shaun D Jackman ◽  
Benjamin P Vandervalk ◽  
Hamid Mohamadi ◽  
Justin Chu ◽  
Sarah Yeo ◽  
...  
Keyword(s):  
Human Genome ◽  
Dna Sequences ◽  
Message Passing ◽  
Large Scale ◽  
De Novo ◽  
Bloom Filter ◽  
Genomic Variation ◽  
De Bruijn Graph ◽  
Single Individual ◽  
Probabilistic Data Structure

AbstractThe assembly of DNA sequences de novo is fundamental to genomics research. It is the first of many steps towards elucidating and characterizing whole genomes. Downstream applications, including analysis of genomic variation between species, between or within individuals critically depends on robustly assembled sequences. In the span of a single decade, the sequence throughput of leading DNA sequencing instruments has increased drastically, and coupled with established and planned large-scale, personalized medicine initiatives to sequence genomes in the thousands and even millions, the development of efficient, scalable and accurate bioinformatics tools for producing high-quality reference draft genomes is timely.With ABySS 1.0, we originally showed that assembling the human genome using short 50 bp sequencing reads was possible by aggregating the half terabyte of compute memory needed over several computers using a standardized message-passing system (MPI). We present here its re-design, which departs from MPI and instead implements algorithms that employ a Bloom filter, a probabilistic data structure, to represent a de Bruijn graph and reduce memory requirements.We present assembly benchmarks of human Genome in a Bottle 250 bp Illumina paired-end and 6 kbp mate-pair libraries from a single individual, yielding a NG50 (NGA50) scaffold contiguity of 3.5 (3.0) Mbp using less than 35 GB of RAM, a modest memory requirement by today’s standard that is often available on a single computer. We also investigate the use of BioNano Genomics and 10x Genomics’ Chromium data to further improve the scaffold contiguity of this assembly to 42 (15) Mbp.

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