scholarly journals Plastome Structural Evolution and Homoplastic Inversions in Neo-Astragalus (Fabaceae)

2021 ◽  
Vol 13 (10) ◽  
Author(s):  
Joseph L M Charboneau ◽  
Richard C Cronn ◽  
Aaron Liston ◽  
Martin F Wojciechowski ◽  
Michael J Sanderson
Keyword(s):  
Large Scale ◽  
New World ◽  
Phylogenetic Signal ◽  
Structural Evolution ◽  
Inverted Repeats ◽  
Structural Rearrangements ◽  
Repeat Structure ◽  
Plastid Genomes ◽  
Large Genus ◽  
Conserved Gene

Abstract The plastid genomes of photosynthetic green plants have largely maintained conserved gene content and order as well as structure over hundreds of millions of years of evolution. Several plant lineages, however, have departed from this conservation and contain many plastome structural rearrangements, which have been associated with an abundance of repeated sequences both overall and near rearrangement endpoints. We sequenced the plastomes of 25 taxa of Astragalus L. (Fabaceae), a large genus in the inverted repeat-lacking clade of legumes, to gain a greater understanding of the connection between repeats and plastome inversions. We found plastome repeat structure has a strong phylogenetic signal among these closely related taxa mostly in the New World clade of Astragalus called Neo-Astragalus. Taxa without inversions also do not differ substantially in their overall repeat structure from four taxa each with one large-scale inversion. For two taxa with inversion endpoints between the same pairs of genes, differences in their exact endpoints indicate the inversions occurred independently. Our proposed mechanism for inversion formation suggests the short inverted repeats now found near the endpoints of the four inversions may be there as a result of these inversions rather than their cause. The longer inverted repeats now near endpoints may have allowed the inversions first mediated by shorter microhomologous sequences to propagate, something that should be considered in explaining how any plastome rearrangement becomes fixed regardless of the mechanism of initial formation.

scholarly journals Structural rearrangements in plastid genomes of Apiaceae as phylogenetic markers

2021 ◽  
Vol 38 ◽  
pp. 00107
Author(s):  
Tahir Samigullin ◽  
Carmen Vallejo-Roman ◽  
Galina Degtjareva ◽  
Elena Terentieva
Keyword(s):  
Single Copy ◽  
Sampling Scheme ◽  
Taxon Sampling ◽  
Inverted Repeats ◽  
Structural Rearrangements ◽  
Large Single Copy ◽  
Plastid Genomes ◽  
Dense Sampling ◽  
Large Single Copy Region

Apiaceae belong to angiosperm families with frequent plastome structural rearrangements, some of which are generally regarded as synapomorphic for large clades, although typically with limited taxon sampling. Our study aims to improve understanding of the structural rearrangements in plastome within the Tordylieae tribe (ApiaceaeApioideae) with a dense sampling scheme of its species. We showed that presence of psbA pseudogene in inverted repeats near the border with a large single-copy region, which is found in the Tordylieae tribe, may be a clade-specific synapomorphy.

scholarly journals Conserved Gene Order and Expanded Inverted Repeats Characterize Plastid Genomes of Thalassiosirales

PLoS ONE ◽  
2014 ◽  
Vol 9 (9) ◽  
pp. e107854 ◽  
Author(s):  
Jamal S. M. Sabir ◽  
Mengjie Yu ◽  
Matt P. Ashworth ◽  
Nabih A. Baeshen ◽  
Mohammad N. Baeshen ◽  
...  
Keyword(s):  
Gene Order ◽  
Inverted Repeats ◽  
Plastid Genomes ◽  
Conserved Gene

scholarly journals Systematic Detection of Large-Scale Multi-Gene Horizontal Transfer in Prokaryotes

2021 ◽  
Author(s):  
Lina Kloub ◽  
Sean Gosselin ◽  
Matthew Fullmer ◽  
Joerg Graf ◽  
J Peter Gogarten ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Large Scale ◽  
Single Gene ◽  
Gene Families ◽  
Microbial Evolution ◽  
Phylogenetic Distance ◽  
Secretion Systems ◽  
Type Iii Secretion Systems ◽  
A Genome ◽  
Conserved Gene

Abstract Horizontal gene transfer (HGT) is central to prokaryotic evolution. However, little is known about the “scale” of individual HGT events. In this work, we introduce the first computational framework to help answer the following fundamental question: How often does more than one gene get horizontally transferred in a single HGT event? Our method, called HoMer, uses phylogenetic reconciliation to infer single-gene HGT events across a given set of species/strains, employs several techniques to account for inference error and uncertainty, combines that information with gene order information from extant genomes, and uses statistical analysis to identify candidate horizontal multi-gene transfers (HMGTs) in both extant and ancestral species/strains. HoMer is highly scalable and can be easily used to infer HMGTs across hundreds of genomes. We apply HoMer to a genome-scale dataset of over 22000 gene families from 103 Aeromonas genomes and identify a large number of plausible HMGTs of various scales at both small and large phylogenetic distances. Analysis of these HMGTs reveals interesting relationships between gene function, phylogenetic distance, and frequency of multi-gene transfer. Among other insights, we find that (i) the observed relative frequency of HMGT increases as divergence between genomes increases, (ii) HMGTs often have conserved gene functions, and (iii) rare genes are frequently acquired through HMGT. We also analyze in detail HMGTs involving the zonula occludens toxin and type III secretion systems. By enabling the systematic inference of HMGTs on a large scale, HoMer will facilitate a more accurate and more complete understanding of HGT and microbial evolution.

scholarly journals Relationship between the Track and Structural Evolution of Hurricane Sandy (2012) Using a Regional Ensemble

2018 ◽  
Vol 146 (12) ◽  
pp. 4279-4302 ◽  
Author(s):  
Alex M. Kowaleski ◽  
Jenni L. Evans
Keyword(s):  
Large Scale ◽  
Wrf Model ◽  
Structural Evolution ◽  
Hurricane Sandy ◽  
Weather Research And Forecasting ◽  
Extratropical Transition ◽  
Ensemble Forecasts ◽  
High Predictability ◽  
Regression Mixture ◽  
The Relationship

Abstract An ensemble of 72 Weather Research and Forecasting (WRF) Model simulations is evaluated to examine the relationship between the track of Hurricane Sandy (2012) and its structural evolution. Initial and boundary conditions are obtained from ECMWF and GEFS ensemble forecasts initialized at 0000 UTC 25 October. The 5-day WRF simulations are initialized at 0000 UTC 27 October, 48 h into the global model forecasts. Tracks and cyclone phase space (CPS) paths from the 72 simulations are partitioned into 6 clusters using regression mixture models; results from the 4 most populous track clusters are examined. The four analyzed clusters vary in mean landfall location from southern New Jersey to Maine. Extratropical transition timing is the clearest difference among clusters; more eastward clusters show later Sandy–midlatitude trough interaction, warm seclusion formation, and extratropical transition completion. However, the intercluster variability is much smaller when examined relative to the landfall time of each simulation. In each cluster, a short-lived warm seclusion forms and contracts through landfall while lower-tropospheric potential vorticity concentrates at small radii. Despite the large-scale similarity among the clusters, relevant intercluster differences in landfall-relative extratropical transition are observed. In the easternmost cluster the Sandy–trough interaction is least intense and the warm seclusion decays the most by landfall. In the second most eastward cluster Sandy retains the most intact warm seclusion at landfall because of a slightly later (relative to landfall) and weaker trough interaction compared to the two most westward clusters. Nevertheless, the remarkably similar large-scale evolution of Sandy among the four clusters indicates the high predictability of Sandy’s warm seclusion extratropical transition before landfall.

scholarly journals A new world natural vegetation map for global change studies

2008 ◽  
Vol 80 (2) ◽  
pp. 397-408 ◽  
Author(s):  
David M. Lapola ◽  
Marcos D. Oyama ◽  
Carlos A. Nobre ◽  
Gilvan Sampaio
Keyword(s):  
Large Scale ◽  
New World ◽  
Climate Models ◽  
Global Climate ◽  
Horizontal Resolution ◽  
Vegetation Classification ◽  
Natural Vegetation ◽  
Global Climate Models ◽  
Vegetation Map ◽  
Vegetation Maps

We developed a new world natural vegetation map at 1 degree horizontal resolution for use in global climate models. We used the Dorman and Sellers vegetation classification with inclusion of a new biome: tropical seasonal forest, which refers to both deciduous and semi-deciduous tropical forests. SSiB biogeophysical parameters values for this new biome type are presented. Under this new vegetation classification we obtained a consensus map between two global natural vegetation maps widely used in climate studies. We found that these two maps assign different biomes in ca. 1/3 of the continental grid points. To obtain a new global natural vegetation map, non-consensus areas were filled according to regional consensus based on more than 100 regional maps available on the internet. To minimize the risk of using poor quality information, the regional maps were obtained from reliable internet sources, and the filling procedure was based on the consensus among several regional maps obtained from independent sources. The new map was designed to reproduce accurately both the large-scale distribution of the main vegetation types (as it builds on two reliable global natural vegetation maps) and the regional details (as it is based on the consensus of regional maps).

scholarly journals Dynamic evolution of inverted repeats in Euglenophyta plastid genomes

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Anna Karnkowska ◽  
Matthew S. Bennett ◽  
Richard E. Triemer
Keyword(s):  
Dynamic Evolution ◽  
Inverted Repeats ◽  
Plastid Genomes

scholarly journals Comparative Cladistics: Fossils, Morphological Data Partitions and Lost Branches in the Fossil Tree of Life

2017 ◽  
Author(s):  
Ross Mounce
Keyword(s):  
Large Scale ◽  
Phylogenetic Signal ◽  
Scientific Progress ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Sets ◽  
Phylogenetic Groups ◽  
Use Of Data ◽  
Wide Range ◽  
Cladistic Analyses

In this thesis I attempt to gather together a wide range of cladistic analyses of fossil and extant taxa representing a diverse array of phylogenetic groups. I use this data to quantitatively compare the effect of fossil taxa relative to extant taxa in terms of support for relationships, number of most parsimonious trees (MPTs) and leaf stability. In line with previous studies I find that the effects of fossil taxa are seldom different to extant taxa – although I highlight some interesting exceptions. I also use this data to compare the phylogenetic signal within vertebrate morphological data sets, by choosing to compare cranial data to postcranial data. Comparisons between molecular data and morphological data have been previously well explored, as have signals between different molecular loci. But comparative signal within morphological data sets is much less commonly characterized and certainly not across a wide array of clades. With this analysis I show that there are many studies in which the evidence provided by cranial data appears to be be significantly incongruent with the postcranial data – more than one would expect to see just by the effect of chance and noise alone. I devise and implement a modification to a rarely used measure of homoplasy that will hopefully encourage its wider usage. Previously it had some undesirable bias associated with the distribution of missing data in a dataset, but my modification controls for this. I also take an in-depth and extensive review of the ILD test, noting it is often misused or reported poorly, even in recent studies. Finally, in attempting to collect data and metadata on a large scale, I uncovered inefficiencies in the research publication system that obstruct re-use of data and scientific progress. I highlight the importance of replication and reproducibility – even simple reanalysis of high profile papers can turn up some very different results. Data is highly valuable and thus it must be retained and made available for further re-use to maximize the overall return on research investment.

Hunting Indians

Manhunts ◽  
2012 ◽  
Author(s):  
Grégoire Chamayou ◽  
Steven Rendall
Keyword(s):  
Economic Activity ◽  
Large Scale ◽  
New World ◽  
Social Phenomenon ◽  
Way Of Life

This chapter discusses how the conquest of the New World gave rise to vast manhunts that continued for almost four centuries and took place all over the Americas. This was a massive phenomenon with its specially trained dogs, professional hunters, weapons, and culture. As a social phenomenon, Indian hunting was indissolubly a large-scale economic activity, a way of life, and a cruel pleasure, a macabre form of sport—and this was so from the beginning of the conquests. Acquisition hunts were intended to take future slaves. Extermination hunts were entirely different; their main goal was the eradication of the population in order to conquer the territory. These hunts of conquest had to be provided with legitimations, with theories. How could the hunts for Indians be justified? That is where, very early on, philosophers made their entrance.

scholarly journals Rampant Nuclear Transfer and Substitutions of Plastid Genes in Passiflora

2020 ◽  
Vol 12 (8) ◽  
pp. 1313-1329 ◽  
Author(s):  
Bikash Shrestha ◽  
Lawrence E Gilbert ◽  
Tracey A Ruhlman ◽  
Robert K Jansen
Keyword(s):  
Nuclear Transfer ◽  
Protein Complexes ◽  
Nuclear Gene ◽  
Transit Peptide ◽  
Purifying Selection ◽  
Rna Recognition Motif ◽  
Rna Recognition ◽  
Plastid Genomes ◽  
Type Gene ◽  
Conserved Gene

Abstract Gene losses in plastid genomes (plastomes) are often accompanied by functional transfer to the nucleus or substitution of an alternative nuclear-encoded gene. Despite the highly conserved gene content in plastomes of photosynthetic land plants, recent gene loss events have been documented in several disparate angiosperm clades. Among these lineages, Passiflora lacks several essential ribosomal genes, rps7, rps16, rpl20, rpl22, and rpl32, the two largest plastid genes, ycf1 and ycf2, and has a highly divergent rpoA. Comparative transcriptome analyses were performed to determine the fate of the missing genes in Passiflora. Putative functional transfers of rps7, rpl22, and rpl32 to nucleus were detected, with the nuclear transfer of rps7, representing a novel event in angiosperms. Plastid-encoded rps7 was transferred into the intron of a nuclear-encoded plastid-targeted thioredoxin m-type gene, acquiring its plastid transit peptide (TP). Plastid rpl20 likely experienced a novel substitution by a duplicated, nuclear-encoded mitochondrial-targeted rpl20 that has a similar gene structure. Additionally, among rosids, evidence for a third independent transfer of rpl22 in Passiflora was detected that gained a TP from a nuclear gene containing an organelle RNA recognition motif. Nuclear transcripts representing rpoA, ycf1, and ycf2 were not detected. Further analyses suggest that the divergent rpoA remains functional and that the gene is under positive or purifying selection in different clades. Comparative analyses indicate that alternative translocon and motor protein complexes may have substituted for the loss of ycf1 and ycf2 in Passiflora.

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