scholarly journals An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
João PL Castro ◽  
Michelle N Yancoskie ◽  
Marta Marchini ◽  
Stefanie Belohlavy ◽  
Layla Hiramatsu ◽  
...  
Keyword(s):  
Bone Growth ◽  
Rapid Evolution ◽  
Genomic Analysis ◽  
Selection Response ◽  
Major Effect ◽  
Selection Experiment ◽  
Genomic Analyses ◽  
Selection Experiments ◽  
Polygenic Adaptation ◽  
History Of

Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response.

scholarly journals An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice

2018 ◽  
Author(s):  
João P. L. Castro ◽  
Michelle N. Yancoskie ◽  
Marta Marchini ◽  
Stefanie Belohlavy ◽  
Marek Kučka ◽  
...  
Keyword(s):  
Bone Growth ◽  
Rapid Evolution ◽  
Genomic Analysis ◽  
Selection Response ◽  
Major Effect ◽  
Selection Experiment ◽  
Genomic Analyses ◽  
Selection Experiments ◽  
Polygenic Adaptation ◽  
History Of

AbstractEvolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under strong selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicate lines. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci likely to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivation of two limb enhancers of an inhibitor,Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response.

scholarly journals Genomic changes under rapid evolution: selection for parasitoid resistance

2014 ◽  
Vol 281 (1779) ◽  
pp. 20132303 ◽  
Author(s):  
Kirsten M. Jalvingh ◽  
Peter L. Chang ◽  
Sergey V. Nuzhdin ◽  
Bregje Wertheim
Keyword(s):  
High Throughput Sequencing ◽  
Rapid Evolution ◽  
Complex Trait ◽  
Selection Response ◽  
Larval Survival ◽  
Major Effect ◽  
Genomic Changes ◽  
Asobara Tabida ◽  
Signature Of Selection ◽  
Segregating Sites

In this study, we characterize changes in the genome during a swift evolutionary adaptation, by combining experimental selection with high-throughput sequencing. We imposed strong experimental selection on an ecologically relevant trait, parasitoid resistance in Drosophila melanogaster against Asobara tabida. Replicated selection lines rapidly evolved towards enhanced immunity. Larval survival after parasitization increased twofold after just five generations of selection. Whole-genome sequencing revealed that the fast and strong selection response in innate immunity produced multiple, highly localized genomic changes. We identified narrow genomic regions carrying a significant signature of selection, which were present across all chromosomes and covered in total less than 5% of the whole D. melanogaster genome. We identified segregating sites with highly significant changes in frequency between control and selection lines that fell within these narrow ‘selected regions’. These segregating sites were associated with 42 genes that constitute possible targets of selection. A region on chromosome 2R was highly enriched in significant segregating sites and may be of major effect on parasitoid defence. The high genetic variability and small linkage blocks in our base population are likely responsible for allowing this complex trait to evolve without causing widespread erosive effects in the genome, even under such a fast and strong selective regime.

scholarly journals Integrative analysis of histomorphology, transcriptome and whole genome resequencing identified DIO2 gene as a crucial gene for the protuberant knob located on forehead in geese

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yan Deng ◽  
Shenqiang Hu ◽  
Chenglong Luo ◽  
Qingyuan Ouyang ◽  
Li Li ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Protein Secondary Structure ◽  
Genomic Analysis ◽  
Production Performance ◽  
Genetic Mechanism ◽  
Farm Animals ◽  
Practical Significance ◽  
Genome Resequencing ◽  
Genomic Analyses ◽  
Whole Genome Resequencing

Abstract Background During domestication, remarkable changes in behavior, morphology, physiology and production performance have taken place in farm animals. As one of the most economically important poultry, goose owns a unique appearance characteristic called knob, which is located at the base of the upper bill. However, neither the histomorphology nor the genetic mechanism of the knob phenotype has been revealed in geese. Results In the present study, integrated radiographic, histological, transcriptomic and genomic analyses revealed the histomorphological characteristics and genetic mechanism of goose knob. The knob skin was developed, and radiographic results demonstrated that the knob bone was obviously protuberant and pneumatized. Histologically, there were major differences in structures in both the knob skin and bone between geese owing knob (namely knob-geese) and those devoid of knob (namely non-knob geese). Through transcriptome analysis, 592 and 952 genes differentially expressed in knob skin and bone, and significantly enriched in PPAR and Calcium pathways in knob skin and bone, respectively, which revealed the molecular mechanisms of histomorphological differences of the knob between knob- and non-knob geese. Furthermore, integrated transcriptomic and genomic analysis contributed to the identification of 17 and 21 candidate genes associated with the knob formation in the skin and bone, respectively. Of them, DIO2 gene could play a pivotal role in determining the knob phenotype in geese. Because a non-synonymous mutation (c.642,923 G > A, P265L) changed DIO2 protein secondary structure in knob geese, and Sanger sequencing further showed that the AA genotype was identified in the population of knob geese, and was prevalent in a crossing population which was artificially selected for 10 generations. Conclusions This study was the first to uncover the knob histomorphological characteristics and genetic mechanism in geese, and DIO2 was identified as the crucial gene associated with the knob phenotype. These data not only expand and enrich our knowledge on the molecular mechanisms underlying the formation of head appendages in both mammalian and avian species, but also have important theoretical and practical significance for goose breeding.

scholarly journals Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley

2016 ◽  
Vol 48 (9) ◽  
pp. 1089-1093 ◽  
Author(s):  
Martin Mascher ◽  
Verena J Schuenemann ◽  
Uri Davidovich ◽  
Nimrod Marom ◽  
Axel Himmelbach ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
History Of

scholarly journals Rapid evolution and molecular convergence in cryptorchidism-related genes associated with inherently undescended testes in mammals

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Simin Chai ◽  
Ran Tian ◽  
Juanjuan Bi ◽  
Shixia Xu ◽  
Guang Yang ◽  
...  
Keyword(s):  
Muscle Development ◽  
Rapid Evolution ◽  
Genetic Material ◽  
Comparative Genomic ◽  
Testicular Descent ◽  
Ancestral State ◽  
Undescended Testes ◽  
Genomic Analyses ◽  
Genetic Mechanisms ◽  
Molecular Convergence

Abstract Background The mammalian testis is an important male exocrine gland and spermatozoa-producing organ that usually lies in extra-abdominal scrotums to provide a cooler environment for spermatogenesis and sperm storage. Testicles sometimes fail to descend, leading to cryptorchidism. However, certain groups of mammals possess inherently ascrotal testes (i.e. testes that do not descend completely or at all) that have the same physiological functions as completely descended scrotal testes. Although several anatomical and hormonal factors involved in testicular descent have been studied, there is still a paucity of comprehensive research on the genetic mechanisms underlying the evolution of testicular descent in mammals and how mammals with ascrotal testes maintain their reproductive health. Results We performed integrative phenotypic and comparative genomic analyses of 380 cryptorchidism-related genes and found that the mammalian ascrotal testes trait is derived from an ancestral scrotal state. Rapidly evolving genes in ascrotal mammals were enriched in the Hedgehog pathway—which regulates Leydig cell differentiation and testosterone secretion—and muscle development. Moreover, some cryptorchidism-related genes in ascrotal mammals had undergone positive selection and contained specific mutations and indels. Genes harboring convergent/parallel amino acid substitutions between ascrotal mammals were enriched in GTPase functions. Conclusions Our results suggest that the scrotal testis is an ancestral state in mammals, and the ascrotal phenotype was derived multiple times in independent lineages. In addition, the adaptive evolution of genes involved in testicular descent and the development of the gubernaculum contributed to the evolution of ascrotal testes. Accurate DNA replication, the proper segregation of genetic material, and appropriate autophagy are the potential mechanisms for maintaining physiological normality during spermatogenesis in ascrotal mammals. Furthermore, the molecular convergence of GTPases is probably a mechanism in the ascrotal testes of different mammals. This study provides novel insights into the evolution of the testis and scrotum in mammals and contributes to a better understanding of the pathogenesis of cryptorchidism in humans.

scholarly journals Author response: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice

2019 ◽  
Author(s):  
João PL Castro ◽  
Michelle N Yancoskie ◽  
Marta Marchini ◽  
Stefanie Belohlavy ◽  
Layla Hiramatsu ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Author Response ◽  
Selection Experiment

scholarly journals A SIMULATION STUDY OF TRUNCATION SELECTION FOR A QUANTITATIVE TRAIT OPPOSED BY NATURAL SELECTION

Genetics ◽  
1980 ◽  
Vol 94 (4) ◽  
pp. 989-1000
Author(s):  
Francis Minvielle
Keyword(s):  
Natural Selection ◽  
Artificial Selection ◽  
Random Mating ◽  
Selection Response ◽  
Quantitative Character ◽  
Mass Selection ◽  
Frequency Selection ◽  
Selection Experiments ◽  
Selection For ◽  
Selective Process

ABSTRACT A quantitative character controlled at one locus with two alleles was submitted to artificial (mass) selection and to three modes of opposing natural selection (directional selection, overdominance and underdominance) in a large random-mating population. The selection response and the limits of the selective process were studied by deterministic simulation. The lifetime of the process was generally between 20 and 100 generations and did not appear to depend on the mode of natural selection. However, depending on the values of the parameters (initial gene frequency, selection intensity, ratio of the effect of the gene to the environmental standard deviation, fitness values) the following outcomes of selection were observed: fixation of the allele favored by artificial selection, stable nontrivial equilibrium, unstable equilibrium and loss of the allele favored by artificial selection. Finally, the results of the simulation were compared to the results of selection experiments.

Surface and Subsurface Quality Evaluation of Engineered Wood Products by Ultrasonic Means

2014 ◽  
pp. 182-220
Author(s):  
Frank C. Beall ◽  
Henrique Reis
Keyword(s):  
Product Development ◽  
Material Properties ◽  
Rapid Evolution ◽  
Solid Wood ◽  
Wood Products ◽  
Assessment And Evaluation ◽  
Engineered Wood Products ◽  
Engineered Wood ◽  
History Of ◽  
Ultrasonic Techniques

The use of ultrasonic techniques to evaluate the properties of engineered wood-based materials is discussed with respect to research to date and the use of more advanced techniques. The latter is critical because of the rapid evolution from solid wood to reconstituted structural materials. In addition, although considerable research has been done, there have been few introductions into manufacturing. This chapter traces the history of the use and latest developments of ultrasonics in several key areas, particularly the measurement of adhesive curing and quality in composites and laminates, and detection of flaws in solid wood materials. The techniques reviewed apply to product development, material properties, process control, product quality assessment, and evaluation of products in service.

scholarly journals Selection Response in a Divergent Selection Experiment for Birth Weight Variability in Mice Compared with a Control Line

Animals ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 920
Author(s):  
Nora Formoso-Rafferty ◽  
Katherine Natalia Chavez ◽  
Candela Ojeda ◽  
Isabel Cervantes ◽  
Juan Pablo Gutiérrez
Keyword(s):  
Birth Weight ◽  
Litter Size ◽  
Laboratory Mouse ◽  
Selection Response ◽  
Divergent Selection ◽  
Suitable Model ◽  
Control Line ◽  
Selection Experiment ◽  
High Line ◽  
Third Line

Birth weight (BW) in animal production is an economically important trait in prolific species. The laboratory mouse (Mus musculus) is used as an experimental animal because it is considered a suitable model for prolific species such as rabbits and pigs. Two mouse lines were divergently selected for birth weight variability with a third line of non-selected control population of the same origin as the animals starting the experiment. The objective of this study was, therefore, to compare and evaluate the differential response of each line. The animals were from the 17th generation of both low and high BW variability lines of the divergent selection experiment, including in addition animals from the control line. The dataset contained 389 records from 48 litters of the high line, 734 records from 73 litters of the low line, and 574 records from 71 litters of the control line. The studied traits were as follows: the BW, the BW variance, the BW standard deviation, the BW coefficient of variation within-litter, the weaning weight (WW), the litter size at birth and at weaning, the weight gain, and the preweaning survival. The model included the line effect jointly with the parturition number and its interaction, the linear and quadratic LS as covariates except for the LS trait itself when analyzing litter traits, as well as the pup sex when analyzing individual traits. The low line had a lower BW and WW, but a higher litter size, and greater robustness owing to a higher survival at weaning. As a model of livestock animals, the findings from this experiment led to a proposal of selection for pig production that would combine an increase in litter size with higher survival and welfare. Compared with the control line, a much higher response was observed in the low variability line than in the high line, making it extremely satisfactory given that homogeneity provides advantages in terms of animal welfare and robustness.

The Triassic U–Pb age for the aquatic long-necked protorosaur of Guizhou, China

2014 ◽  
Vol 151 (4) ◽  
pp. 749-754 ◽  
Author(s):  
YANBIN WANG ◽  
DETING YANG ◽  
JUAN HAN ◽  
LITING WANG ◽  
JIANXIN YAO ◽  
...  
Keyword(s):  
Middle Triassic ◽  
Rapid Evolution ◽  
Guizhou Province ◽  
Ion Microprobe ◽  
Isotopic Age ◽  
Zircon Age ◽  
Marine Reptiles ◽  
Wide Range ◽  
History Of ◽  
Permian Mass Extinction

AbstractThe ancient marine limestone beds of the upper part of the Guanling Formation, Panxian County, Guizhou Province, SW China, yielded a wide range of high-diversity well-preserved marine reptiles such as the fully aquatic protorosaur with an extremely long neckDinocephalosaurus orientalis, the oldest mixosaurid ichthyosaurs and lariosaurs. However, there is no precise isotopic age to study the intriguing origin, evolution and emigration history of the important fauna. We report a sensitive high-resolution ion microprobe (SHRIMP) U–Pb zircon age for a volcanic tuff bed within the upper part of the Guanling Formation. The result indicates that the age of the fossil horizon is 244.0±1.3 Ma, 14 Ma earlier than the previously estimated age based on conodont evidence. We consider that the marine reptiles had a relatively rapid evolution during Middle Triassic time, some 8 Ma after the end-Permian mass extinction.

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