scholarly journals Vulnerability to Fishing and Life History Traits Correlate with the Load of Deleterious Mutations in Teleosts

2020 ◽  
Vol 37 (8) ◽  
pp. 2192-2196 ◽  
Author(s):  
Jonathan Rolland ◽  
Dolph Schluter ◽  
Jonathan Romiguier
Keyword(s):  
Life History ◽  
Evolutionary Biology ◽  
Life History Traits ◽  
Deleterious Mutation ◽  
Purifying Selection ◽  
Synonymous Substitution ◽  
Deleterious Mutations ◽  
Data Set ◽  
Terrestrial Vertebrates ◽  
Genome Data

Abstract Understanding why some species accumulate more deleterious substitutions than others is an important question relevant in evolutionary biology and conservation sciences. Previous studies conducted in terrestrial taxa suggest that life history traits correlate with the efficiency of purifying selection and accumulation of deleterious mutations. Using a large genome data set of 76 species of teleostean fishes, we show that species with life history traits associated with vulnerability to fishing have an increased rate of deleterious mutation accumulation (measured via dN/dS, i.e., nonsynonymous over synonymous substitution rate). Our results, focusing on a large clade of aquatic species, generalize previous patterns found so far in few clades of terrestrial vertebrates. These results also show that vulnerable species to fishing inherently accumulate more deleterious substitutions than nonthreatened ones, which illustrates the potential links among population genetics, ecology, and fishing policies to prevent species extinction.

scholarly journals Vulnerability and life-history traits correlate with the load of deleterious mutations in fish

2019 ◽  
Author(s):  
Jonathan Rolland ◽  
Jonathan Romiguier
Keyword(s):  
Life History ◽  
Evolutionary Biology ◽  
Life History Traits ◽  
Deleterious Mutation ◽  
Purifying Selection ◽  
Synonymous Substitution ◽  
Life History Strategies ◽  
Deleterious Mutations ◽  
Terrestrial Vertebrates ◽  
Genome Dataset

AbstractUnderstanding why some species accumulate more deleterious substitutions than others is an important question relevant in evolutionary biology and conservation sciences. Previous studies conducted in terrestrial taxa suggest that life history traits correlate with the efficiency of purifying selection and accumulation of deleterious mutations. Using a large genome dataset of 76 species of fishes, we show that the rate of deleterious mutation accumulation (measured via dN/dS, i.e. non-synonymous over synonymous substitution rate) is associated to the vulnerability, the life-history strategies, and the latitude of species. Our results, focusing on a large clade of aquatic species, generalizes previous patterns found so far in few clades of terrestrial vertebrates. These results also suggest that vulnerable species accumulate more deleterious substitutions than non-threatened ones, which give insights in how life-history traits, populations sizes and genetic risk of extinction can be tightly interconnected.

Demographic life history traits of reproductive natterjack toads (Bufo calamita) vary between northern and southern latitudes

2006 ◽  
Vol 27 (3) ◽  
pp. 365-375 ◽  
Author(s):  
Delfi Sanuy ◽  
Christoph Leskovar ◽  
Neus Oromi ◽  
Ulrich Sinsch
Keyword(s):  
Life History ◽  
Life History Traits ◽  
Large Female ◽  
Breeding Period ◽  
Female Size ◽  
Data Set ◽  
Bufo Calamita ◽  
Trade Offs ◽  
Age Variation ◽  
The Cost

AbstractDemographic life history traits were investigated in three Bufo calamita populations in Germany (Rhineland-Palatinate: Urmitz, 50°N; 1998-2000) and Spain (Catalonia: Balaguer, Mas de Melons, 41°N; 2004). We used skeletochronology to estimate the age as number of lines of arrested growth in breeding adults collected during the spring breeding period (all localities) and during the summer breeding period (only Urmitz). A data set including the variables sex, age and size of 185 males and of 87 females was analyzed with respect to seven life history traits (age and size at maturity of the youngest first breeders, age variation in first breeders, longevity, potential reproductive lifespan, median lifespan, age-size relationship). Spring and summer cohorts at the German locality differed with respect to longevity and potential reproductive lifespan by one year in favour of the early breeders. The potential consequences on fitness and stability of cohorts are discussed. Latitudinal variation of life history traits was mainly limited to female natterjacks in which along a south-north gradient longevity and potential reproductive lifespan increased while size decreased. These results and a review of published information on natterjack demography suggest that lifetime number of offspring seem to be optimized by locally different trade-offs: large female size at the cost of longevity in southern populations and increased longevity at the cost of size in northern ones.

scholarly journals Genome size correlates with reproductive fitness in seed beetles

2015 ◽  
Vol 282 (1815) ◽  
pp. 20151421 ◽  
Author(s):  
Göran Arnqvist ◽  
Ahmed Sayadi ◽  
Elina Immonen ◽  
Cosima Hotzy ◽  
Daniel Rankin ◽  
...  
Keyword(s):  
Life History ◽  
Natural Selection ◽  
Genome Size ◽  
Evolutionary Biology ◽  
Large Scale ◽  
Life History Traits ◽  
Single Species ◽  
Reproductive Fitness ◽  
Correlated Evolution ◽  
Seed Beetles

The ultimate cause of genome size (GS) evolution in eukaryotes remains a major and unresolved puzzle in evolutionary biology. Large-scale comparative studies have failed to find consistent correlations between GS and organismal properties, resulting in the ‘ C -value paradox’. Current hypotheses for the evolution of GS are based either on the balance between mutational events and drift or on natural selection acting upon standing genetic variation in GS. It is, however, currently very difficult to evaluate the role of selection because within-species studies that relate variation in life-history traits to variation in GS are very rare. Here, we report phylogenetic comparative analyses of GS evolution in seed beetles at two distinct taxonomic scales, which combines replicated estimation of GS with experimental assays of life-history traits and reproductive fitness. GS showed rapid and bidirectional evolution across species, but did not show correlated evolution with any of several indices of the relative importance of genetic drift. Within a single species, GS varied by 4–5% across populations and showed positive correlated evolution with independent estimates of male and female reproductive fitness. Collectively, the phylogenetic pattern of GS diversification across and within species in conjunction with the pattern of correlated evolution between GS and fitness provide novel support for the tenet that natural selection plays a key role in shaping GS evolution.

scholarly journals The Rate of Spontaneous Mutation for Life-History Traits in Caenorhabditis elegans

Genetics ◽  
1999 ◽  
Vol 151 (1) ◽  
pp. 119-129 ◽  
Author(s):  
Larissa L Vassilieva ◽  
Michael Lynch
Keyword(s):  
Life History ◽  
Caenorhabditis Elegans ◽  
Mutation Rate ◽  
Life History Traits ◽  
Deleterious Mutation ◽  
Spontaneous Mutation ◽  
Spontaneous Mutations ◽  
Homozygous State ◽  
Mutational Effect ◽  
Biological Differences

Abstract Spontaneous mutations were accumulated in 100 replicate lines of Caenorhabditis elegans over a period of ∼50 generations. Periodic assays of these lines and comparison to a frozen control suggest that the deleterious mutation rate for typical life-history characters in this species is at least 0.05 per diploid genome per generation, with the average mutational effect on the order of 14% or less in the homozygous state and the average mutational heritability ∼0.0034. While the average mutation rate per character and the average mutational heritability for this species are somewhat lower than previous estimates for Drosophila, these differences can be reconciled to a large extent when the biological differences between these species are taken into consideration.

scholarly journals Genetic Diversity in the 3′ Terminal 4.7-kb Region of Grapevine leafroll-associated virus 3

2011 ◽  
Vol 101 (4) ◽  
pp. 445-450 ◽  
Author(s):  
Jinbo Wang ◽  
Abhineet M. Sharma ◽  
Siobain Duffy ◽  
Rodrigo P. P. Almeida
Keyword(s):  
Genetic Diversity ◽  
Purifying Selection ◽  
Synonymous Substitution ◽  
Effective Population ◽  
Data Set ◽  
Reading Frame ◽  
Napa Valley ◽  
Synonymous Substitution Rates ◽  
Leafroll Disease

Grapevine leafroll-associated virus 3 (GLRaV-3; Ampelovirus, Closteroviridae), associated with grapevine leafroll disease, is an important pathogen found across all major grape-growing regions of the world. The genetic diversity of GLRaV-3 in Napa Valley, CA, was studied by sequencing 4.7 kb in the 3′ terminal region of 50 isolates obtained from Vitis vinifera ‘Merlot’. GLRaV-3 isolates were subdivided into four distinct phylogenetic clades. No evidence of positive selection was observed in the data set, although neutral selection (ratio of nonsynonymous to synonymous substitution rates = 1.1) was observed in one open reading frame (ORF 11, p4). Additionally, the four clades had variable degrees of overall nucleotide diversity. Moreover, no geographical structure among isolates was observed, and isolates belonging to different phylogenetic clades were found in distinct vineyards, with one exception. Considered with the evidence of purifying selection (i.e., against deleterious mutations), these data indicate that the population of GLRaV-3 in Napa Valley is not expanding and its effective population size is not increasing. Furthermore, research on the biological characterization of GLRaV-3 strains might provide valuable insights on the biology of this species that may have epidemiological relevance.

scholarly journals Deleterious mutation accumulation in Arabidopsis thaliana pollen genes: a role for a recent relaxation of selection

2015 ◽  
Author(s):  
MC Harrison ◽  
EB Mallon ◽  
D Twell ◽  
RL Hammond
Keyword(s):  
Arabidopsis Thaliana ◽  
Life History ◽  
Deleterious Mutation ◽  
Rapid Evolution ◽  
Relative Strength ◽  
Pollen Competition ◽  
Deleterious Mutations ◽  
Deleterious Alleles ◽  
Polymorphism Data ◽  
Plant Pollen

AbstractIn many studies sex related genes have been found to evolve rapidly. We therefore expect plant pollen genes to evolve faster than sporophytic genes. In addition, pollen genes are expressed as haploids which can itself facilitate rapid evolution because recessive advantageous and deleterious alleles are not masked by dominant alleles. However, this mechanism is less straightforward to apply in the model plant species Arabidopsis thaliana. For 1 million years A.thaliana has been self-compatible, a life history switch that has caused: a reduction in pollen competition, increased homozygosity and a dilution of masking in diploid expressed, sporophytic genes. In this study we have investigated the relative strength of selection on pollen genes compared to sporophytic genes in A. thaliana. We present two major findings: 1) before becoming self-compatible positive selection was stronger on pollen genes than sporophytic genes for A. thaliana; 2) current polymorphism data indicate selection is weaker on pollen genes compared to sporophytic genes. These results indicate that since A. thaliana has become self-compatible, selection on pollen genes has become more relaxed. This has led to higher polymorphism levels and a higher build-up of deleterious mutations in pollen genes compared to sporophytic genes.

scholarly journals Reconstruction of body mass evolution in the Cetartiodactyla and mammals using phylogenomic data

2017 ◽  
Author(s):  
E. Figuet ◽  
M. Ballenghien ◽  
N. Lartillot ◽  
N. Galtier
Keyword(s):  
Body Mass ◽  
Substitution Rate ◽  
Evolutionary Biology ◽  
Gc Content ◽  
Evolutionary Process ◽  
Synonymous Substitution ◽  
Molecular Data ◽  
Large Species ◽  
Data Set ◽  
Peer Community

ABSTRACTThis preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100042).Reconstructing ancestral characters on a phylogeny is an arduous task because the observed states at the tips of the tree correspond to a single realization of the underlying evolutionary process. Recently, it was proposed that ancestral traits can be indirectly estimated with the help of molecular data, based on the fact that life history traits influence substitution rates. Here we challenge these new approaches in the Cetartiodactyla, a clade of large mammals which, according to paleontology, derive from small ancestors. Analysing transcriptome data in 41 species, of which 22 were newly sequenced, we provide a dated phylogeny of the Cetartiodactyla and report a significant effect of body mass on the overall substitution rate, the synonymous vs. non-synonymous substitution rate and the dynamics of GC-content. Our molecular comparative analysis points toward relatively small Cetartiodactyla ancestors, in agreement with the fossil record, even though our data set almost exclusively consists of large species. This analysis demonstrates the potential of phylogenomic methods for ancestral trait reconstruction and gives credit to recent suggestions that the ancestor to placental mammals was a relatively large and long-lived animal.

scholarly journals Intra-Species Differences in Population Size shape Life History and Genome Evolution

2019 ◽  
Author(s):  
David Willemsen ◽  
Rongfeng Cui ◽  
Martin Reichard ◽  
Dario Riccardo Valenzano
Keyword(s):  
Life History ◽  
Population Size ◽  
Genetic Drift ◽  
Sex Chromosome ◽  
Purifying Selection ◽  
Life History Trait ◽  
Deleterious Mutations ◽  
Effective Population ◽  
Annual Life Cycle ◽  
Evolutionary Forces

AbstractThe evolutionary forces shaping life history trait divergence within species are largely unknown. Killifish (oviparous Cyprinodontiformes) evolved an annual life cycle as an exceptional adaptation to life in arid savannah environments characterized by seasonal water availability. The turquoise killifish (Nothobranchius furzeri) is the shortest-lived vertebrate known to science and displays differences in lifespan among wild populations, representing an ideal natural experiment in the evolution and diversification of life history. Here, by combining genome sequencing and population genetics, we investigate the evolutionary forces shaping lifespan among turquoise killifish populations. We generate an improved reference assembly for the turquoise killifish genome, trace the evolutionary origin of the sex chromosome, and identify genes under strong positive and purifying selection, as well as those evolving neutrally. We find that the shortest-lived turquoise killifish populations, which dwell in fragmented and isolated habitats at the outer margin of the geographical range of the species, are characterized by small effective population size and accumulate throughout the genome several small to large-effect deleterious mutations due to genetic drift. The genes most affected by drift in the shortest-lived turquoise killifish populations are involved in the WNT signalling pathway, neurodegenerative disorders, cancer and the mTOR pathway. As the populations under stronger genetic drift are the shortest-lived ones, we propose that limited population size due to habitat fragmentation and repeated population bottlenecks, by causing the genome-wide accumulation of deleterious mutations, cumulatively contribute to the short adult lifespan in turquoise killifish populations.

Physiological Adaptations for Breeding in Birds

2012 ◽  
Author(s):  
Tony D. Williams
Keyword(s):  
Life History ◽  
Individual Variation ◽  
Evolutionary Biology ◽  
Life History Traits ◽  
Egg Quality ◽  
Gonadal Development ◽  
Egg Laying ◽  
Reproductive Physiology ◽  
Avian Reproduction ◽  
Trade Offs

This book is an up-to-date and comprehensive account of research on avian reproduction. It develops two unique themes: the consideration of female avian reproductive physiology and ecology, and an emphasis on individual variation in life-history traits. The book investigates the physiological, metabolic, energetic, and hormonal mechanisms that underpin individual variation in the key female-specific reproductive traits and the trade-offs between these traits that determine variation in fitness. The core of the book deals with the avian reproductive cycle, from seasonal gonadal development, through egg laying and incubation, to chick rearing. Reproduction is considered in the context of the annual cycle and through an individual's entire life history. The book focuses on timing of breeding, clutch size, egg size and egg quality, and parental care. It also provides a primer on female reproductive physiology and considers trade-offs and carryover effects between reproduction and other life-history stages. Each chapter describes individual variation in the trait of interest and the evolutionary context for trait variation. The book argues that there is only a rudimentary, and in some cases nonexistent, understanding of the physiological mechanisms that underpin individual variation in the major reproductive life-history traits, and that research efforts should refocus on these key unresolved problems by incorporating detailed physiological studies into existing long-term population studies, generating a new synthesis of physiology, ecology, and evolutionary biology.

Snail–trematode life history interactions: past trends and future directions

Parasitology ◽  
2001 ◽  
Vol 123 (7) ◽  
pp. S3-S18 ◽  
Author(s):  
R. E. SORENSEN ◽  
D. J. MINCHELLA
Keyword(s):  
Life History ◽  
Laboratory Experiments ◽  
Life History Traits ◽  
Trematode Species ◽  
Snail Species ◽  
Experimental Conditions ◽  
Data Set ◽  
Future Directions ◽  
Host Growth ◽  
History Of

Life history traits expressed by organisms vary due to ecological and evolutionary constraints imposed by their current environmental conditions and genetic heritage. Trematodes often alter the life history of their host snails by inducing parasitic castration. Our understanding of the variables that influence the resulting changes in host growth, fecundity and survivorship is insufficient to confidently predict specific outcomes of novel snail–trematode combinations. In a literature review of the last 30 years, we found 41 publications examining various life history characteristics of trematode-infected snails. These publications reported 113 different field and laboratory experiments involving 30 snail species and 39 trematode species and provided a data set for assessing factors that potentially affect life history outcomes. Analysis of the diverse responses across various snail–trematode systems and experimental conditions teased out general patterns for the expression of host growth, fecundity and survival. These were used to address existing hypotheses and develop several new ones relating the response of snail-trematode interactions to environmental and genetic factors. Finally, we propose directions for future experiments that will better assess the ecological and evolutionary factors influencing snail life history responses to trematode parasitism.

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