Global functional variation in alpine vegetation

This book examines the connections between the formal and functional (semantic and syntactic) properties of indefinite pronouns. It considers the main theoretical debates surrounding the semantic and syntactic properties of indefinite pronouns as well as the diachronic sources of the markers of indefinite pronouns. It describes the new generalizations that emerge from the typological and diachronic research and provides explanations. It also outlines the goals and methods of the typological approach, focusing on the important preconditions for typology such as the availability of data from a variety of languages. Other topics covered by the book include the space of formal and functional variation found in indefinite pronouns, implicational universals, theoretical approaches to the functions of indefinite pronouns such as the tradition of structuralist semantics, the grammaticalization of indefinite pronouns, further sources of indefinite pronouns that cannot be easily subsumed under grammaticalization, and the cross-linguistic patterning of negative indefinite pronouns.

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Evolutionary Transitions in Mode of Development

10.1093/oso/9780198786962.003.0004 ◽

2018 ◽

Cited By ~ 1

Keyword(s):

Analytical Approach ◽

Large Body ◽

Functional Variation ◽

Evolutionary Mechanisms ◽

Evolutionary Transitions ◽

Comparative Phylogenetics ◽

Mode Of Development ◽

Larval Traits ◽

Complex Characters

In the large body of literature on ecological and evolutionary mechanisms underlying transitions between planktotrophy and lecithotrophy, the focus has typically covered long evolutionary timescales; that is, evolution of complex larval traits is generally discussed in the context of phylogenetic patterns detectable at the level of families, classes, or phyla. An analytical approach incorporating comparative phylogenetics is increasingly used to address these long-view questions. Here, we discuss what has been learned from taking a comparative phylogenetic approach and the limitations of this approach. We propose that approaches based on a closer view—that is, analyses that focus on genetic, morphological, and functional variation among individuals, populations, or closely related congeners—have greater potential to answer questions about mechanisms underlying the loss and regain of major complex characters such as feeding larvae.

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Interactions Between Natural Selection, Recombination and Gene Density in the Genes of Drosophila

Genetics ◽

10.1093/genetics/160.2.595 ◽

2002 ◽

Vol 160 (2) ◽

pp. 595-608 ◽

Cited By ~ 17

Author(s):

Jody Hey ◽

Richard M Kliman

Keyword(s):

Gene Expression ◽

Natural Selection ◽

Recombination Rate ◽

Codon Bias ◽

Gene Density ◽

Drosophila Genome ◽

Functional Variation ◽

Subtle Effect ◽

Efficiency Of Selection ◽

The Impact

AbstractIn Drosophila, as in many organisms, natural selection leads to high levels of codon bias in genes that are highly expressed. Thus codon bias is an indicator of the intensity of one kind of selection that is experienced by genes and can be used to assess the impact of other genomic factors on natural selection. Among 13,000 genes in the Drosophila genome, codon bias has a slight positive, and strongly significant, association with recombination—as expected if recombination allows natural selection to act more efficiently when multiple linked sites segregate functional variation. The same reasoning leads to the expectation that the efficiency of selection, and thus average codon bias, should decline with gene density. However, this prediction is not confirmed. Levels of codon bias and gene expression are highest for those genes in an intermediate range of gene density, a pattern that may be the result of a tradeoff between the advantages for gene expression of close gene spacing and disadvantages arising from regulatory conflicts among tightly packed genes. These factors appear to overlay the more subtle effect of linkage among selected sites that gives rise to the association between recombination rate and codon bias.

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A comprehensive annotation dataset of intact LTR retrotransposons of 300 plant genomes

Scientific Data ◽

10.1038/s41597-021-00968-x ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Shan-Shan Zhou ◽

Xue-Mei Yan ◽

Kai-Fu Zhang ◽

Hui Liu ◽

Jie Xu ◽

...

Keyword(s):

Evolutionary Dynamics ◽

Age Determination ◽

Genome Plasticity ◽

Ltr Retrotransposons ◽

Functional Variation ◽

Plant Genomes ◽

Sequencing Technologies ◽

Plant Groups ◽

Functional Implications ◽

Classification Information

AbstractLTR retrotransposons (LTR-RTs) are ubiquitous and represent the dominant repeat element in plant genomes, playing important roles in functional variation, genome plasticity and evolution. With the advent of new sequencing technologies, a growing number of whole-genome sequences have been made publicly available, making it possible to carry out systematic analyses of LTR-RTs. However, a comprehensive and unified annotation of LTR-RTs in plant groups is still lacking. Here, we constructed a plant intact LTR-RTs dataset, which is designed to classify and annotate intact LTR-RTs with a standardized procedure. The dataset currently comprises a total of 2,593,685 intact LTR-RTs from genomes of 300 plant species representing 93 families of 46 orders. The dataset is accompanied by sequence, diverse structural and functional annotation, age determination and classification information associated with the LTR-RTs. This dataset will contribute valuable resources for investigating the evolutionary dynamics and functional implications of LTR-RTs in plant genomes.

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A SNP assay for assessing diversity in immune genes in the honey bee (Apis mellifera L.)

Scientific Reports ◽

10.1038/s41598-021-94833-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Dora Henriques ◽

Ana R. Lopes ◽

Nor Chejanovsky ◽

Anne Dalmon ◽

Mariano Higes ◽

...

Keyword(s):

Apis Mellifera ◽

Honey Bee ◽

Large Scale ◽

Medium Density ◽

Nucleotide Polymorphisms ◽

Functional Variation ◽

Immune Genes ◽

Wide Range ◽

Scale Range ◽

Innate Immune Genes

AbstractWith a growing number of parasites and pathogens experiencing large-scale range expansions, monitoring diversity in immune genes of host populations has never been so important because it can inform on the adaptive potential to resist the invaders. Population surveys of immune genes are becoming common in many organisms, yet they are missing in the honey bee (Apis mellifera L.), a key managed pollinator species that has been severely affected by biological invasions. To fill the gap, here we identified single nucleotide polymorphisms (SNPs) in a wide range of honey bee immune genes and developed a medium-density assay targeting a subset of these genes. Using a discovery panel of 123 whole-genomes, representing seven A. mellifera subspecies and three evolutionary lineages, 180 immune genes were scanned for SNPs in exons, introns (< 4 bp from exons), 3’ and 5´UTR, and < 1 kb upstream of the transcription start site. After application of multiple filtering criteria and validation, the final medium-density assay combines 91 quality-proved functional SNPs marking 89 innate immune genes and these can be readily typed using the high-sample-throughput iPLEX MassARRAY system. This medium-density-SNP assay was applied to 156 samples from four countries and the admixture analysis clustered the samples according to their lineage and subspecies, suggesting that honey bee ancestry can be delineated from functional variation. In addition to allowing analysis of immunogenetic variation, this newly-developed SNP assay can be used for inferring genetic structure and admixture in the honey bee.

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Assessing Climate Change Trends and Their Relationships with Alpine Vegetation and Surface Water Dynamics in the Everest Region, Nepal

Atmosphere ◽

10.3390/atmos12080987 ◽

2021 ◽

Vol 12 (8) ◽

pp. 987

Author(s):

Mana Raj Rai ◽

Amnat Chidthaisong ◽

Chaiwat Ekkawatpanit ◽

Pariwate Varnakovida

Keyword(s):

Climate Change ◽

Surface Water ◽

River Basin ◽

Climate Impacts ◽

Glacial Lake ◽

Annual Precipitation ◽

Series Data ◽

Lake Area ◽

Alpine Vegetation ◽

Koshi River Basin

The Himalayas, especially the Everest region, are highly sensitive to climate change. Although there are research works on this region related to cryospheric work, the ecological understandings of the alpine zone and climate impacts are limited. This study aimed to assess the changes in surface water including glacier lake and streamflow and the spatial and temporal changes in alpine vegetation and examine their relationships with climatic factors (temperature and precipitation) during 1995–2019 in the Everest region and the Dudh Koshi river basin. In this study, Landsat time-series data, European Commission’s Joint Research Center (JRC) surface water data, ECMWF Reanalysis 5th Generation (ERA5) reanalysis temperature data, and meteorological station data were used. It was found that the glacial lake area and volume are expanding at the rates of 0.0676 and 0.0198 km3/year, respectively; the average annual streamflow is decreasing at the rate of 2.73 m3/s/year. Similarly, the alpine vegetation greening as indicated by normalized difference vegetation index (NDVI) is increasing at the rate of 0.00352 units/year. On the other hand, the annual mean temperature shows an increasing trend of 0.0329 °C/year, and the annual precipitation also shows a significant negative monotonic trend. It was also found that annual NDVI is significantly correlated with annual temperature. Likewise, the glacial lake area expansion is strongly correlated with annual minimum temperature and annual precipitation. Overall, we found a significant alteration in the alpine ecosystem of the Everest region that could impact on the water–energy–food nexus of the Dudh Koshi river basin.

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