scholarly journals A Spatially Explicit Model of Stabilizing Selection for Improving Phylogenetic Inference

2020 ◽  
Author(s):  
Jeremy M Beaulieu ◽  
Brian C O’Meara ◽  
Michael A Gilchrist
Keyword(s):  
Gaussian Function ◽  
Phylogenetic Position ◽  
Stabilizing Selection ◽  
Rate Heterogeneity ◽  
Data Set ◽  
Variable Regions ◽  
Selective Forces ◽  
Selection For ◽  
Spatially Varying ◽  
Flanking Regions

Abstract Ultraconserved elements (UCEs) are stretches of hundreds of nucleotides with highly conserved cores flanked by variable regions. Although the selective forces responsible for the preservation of UCEs are unknown, they are nonetheless believed to contain phylogenetically meaningful information from deep to shallow divergence events. Phylogenetic applications of UCEs assume the same degree of rate heterogeneity applies across the entire locus, including variable flanking regions. We present a Wright–Fisher model of selection on nucleotides (SelON) which includes the effects of mutation, drift, and spatially varying, stabilizing selection for an optimal nucleotide sequence. The SelON model assumes the strength of stabilizing selection follows a position-dependent Gaussian function whose exact shape can vary between UCEs. We evaluate SelON by comparing its performance to a simpler and spatially invariant GTR+Γ model using an empirical data set of 400 vertebrate UCEs used to determine the phylogenetic position of turtles. We observe much improvement in model fit of SelON over the GTR+Γ model, and support for turtles as sister to lepidosaurs. Overall, the UCE-specific parameters SelON estimates provide a compact way of quantifying the strength and variation in selection within and across UCEs. SelON can also be extended to include more realistic mapping functions between sequence and stabilizing selection as well as allow for greater levels of rate heterogeneity. By more explicitly modeling the nature of selection on UCEs, SelON and similar approaches can be used to better understand the biological mechanisms responsible for their preservation across highly divergent taxa and long evolutionary time scales.

scholarly journals A spatially-explicit model of stabilizing selection for improving phylogenetic inference

2020 ◽  
Author(s):  
Jeremy M. Beaulieu ◽  
Brian C. O’Meara ◽  
Michael A. Gilchrist
Keyword(s):  
Gaussian Function ◽  
Phylogenetic Position ◽  
Stabilizing Selection ◽  
Rate Heterogeneity ◽  
Variable Regions ◽  
Selective Forces ◽  
Exact Shape ◽  
Selection For ◽  
Spatially Varying ◽  
Flanking Regions

AbstractUltraconserved elements (UCEs) are stretches of hundreds of nucleotides with highly conserved cores flanked by variable regions. Although the selective forces responsible for the preservation of UCEs are unknown, they are nonetheless believed to contain phylogenetically meaningful information from deep to shallow divergence events. Phylogenetic applications of UCEs assume the same degree of rate heterogeneity applies across the entire locus, including variable flanking regions. We present a Wright-Fisher model of selection on nucleotides (SelON) which includes the effects of mutation, drift, and spatially varying, stabilizing selection for an optimal nucleotide sequence. The SelON model assumes the strength of stabilizing selection follows a position dependent Gaussian function whose exact shape can vary between UCEs. We evaluate SelON by comparing its performance to a simpler and spatially invariant GTR+Γ model using an empirical dataset of 400 vertebrate UCEs used to determine the phylogenetic position of turtles. We observe much improvement in model fit of SelON over the GTR+Γ model, and support for turtles as sister to lepidosaurs. Overall, the UCE specific parameters SelON estimates provide a compact way of quantifying the strength and variation in selection within and across UCEs. SelON can also be extended to include more realistic mapping functions between sequence and stabilizing selection as well as allow for greater levels of rate heterogeneity. By more explicitly modeling the nature of selection on UCEs, SelON and similar approaches can be used to better understand the biological mechanisms responsible for their preservation across highly divergent taxa and long evolutionary time scales.

scholarly journals The Complete DNA Sequence of the Mitochondrial Genome of a “Living Fossil,” the Coelacanth (Latimeria chalumnae)

Genetics ◽  
1997 ◽  
Vol 146 (3) ◽  
pp. 995-1010 ◽  
Author(s):  
Rafael Zardoya ◽  
Axel Meyer
Keyword(s):  
Mitochondrial Genome ◽  
Tandem Repeats ◽  
Phylogenetic Analyses ◽  
Large Data ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Data Set ◽  
Living Fossil ◽  
Latimeria Chalumnae ◽  
Relationship Of

The complete nucleotide sequence of the 16,407-bp mitochondrial genome of the coelacanth (Latimeria chalumnae) was determined. The coelacanth mitochondrial genome order is identical to the consensus vertebrate gene order which is also found in all ray-finned fishes, the lungfish, and most tetrapods. Base composition and codon usage also conform to typical vertebrate patterns. The entire mitochondrial genome was PCR-amplified with 24 sets of primers that are expected to amplify homologous regions in other related vertebrate species. Analyses of the control region of the coelacanth mitochondrial genome revealed the existence of four 22-bp tandem repeats close to its 3′ end. The phylogenetic analyses of a large data set combining genes coding for rRNAs, tRNA, and proteins (16,140 characters) confirmed the phylogenetic position of the coelacanth as a lobe-finned fish; it is more closely related to tetrapods than to ray-finned fishes. However, different phylogenetic methods applied to this largest available molecular data set were unable to resolve unambiguously the relationship of the coelacanth to the two other groups of extant lobe-finned fishes, the lungfishes and the tetrapods. Maximum parsimony favored a lungfish/coelacanth or a lungfish/tetrapod sistergroup relationship depending on which transversion:transition weighting is assumed. Neighbor-joining and maximum likelihood supported a lungfish/tetrapod sistergroup relationship.

scholarly journals Mapping the Spatial-Temporal Dynamics of Vegetation Response Lag to Drought in a Semi-Arid Region

2019 ◽  
Vol 11 (16) ◽  
pp. 1873 ◽  
Author(s):  
Li Hua ◽  
Huidong Wang ◽  
Haigang Sui ◽  
Brian Wardlow ◽  
Michael J. Hayes ◽  
...  
Keyword(s):  
Vegetation Index ◽  
Temporal Dynamics ◽  
Risk Mitigation ◽  
Scientific Information ◽  
Gaussian Function ◽  
Drought Risk ◽  
Severe Drought ◽  
Similar Response ◽  
Vegetation Types ◽  
Data Set

Drought, as an extreme climate event, affects the ecological environment for vegetation and agricultural production. Studies of the vegetative response to drought are paramount to providing scientific information for drought risk mitigation. In this paper, the spatial-temporal pattern of drought and the response lag of vegetation in Nebraska were analyzed from 2000 to 2015. Based on the long-term Daymet data set, the standard precipitation index (SPI) was computed to identify precipitation anomalies, and the Gaussian function was applied to obtain temperature anomalies. Vegetation anomaly was identified by dynamic time warping technique using a remote sensing Normalized Difference Vegetation Index (NDVI) time series. Finally, multilayer correlation analysis was applied to obtain the response lag of different vegetation types. The results show that Nebraska suffered severe drought events in 2002 and 2012. The response lag of vegetation to drought typically ranged from 30 to 45 days varying for different vegetation types and human activities (water use and management). Grasslands had the shortest response lag (~35 days), while forests had the longest lag period (~48 days). For specific crop types, the response lag of winter wheat varied among different regions of Nebraska (35–45 days), while soybeans, corn and alfalfa had similar response lag times of approximately 40 days.

scholarly journals Intergeneric Relationships within the Early-Diverging Angiosperm Family Nymphaeaceae Based on Chloroplast Phylogenomics

2018 ◽  
Vol 19 (12) ◽  
pp. 3780 ◽  
Author(s):  
Dingxuan He ◽  
Andrew Gichira ◽  
Zhizhong Li ◽  
John Nzei ◽  
Youhao Guo ◽  
...  
Keyword(s):  
Genome Structure ◽  
Morphological Data ◽  
Basal Angiosperm ◽  
Phylogenetic Position ◽  
Data Set ◽  
Protein Coding ◽  
Plastid Genomes ◽  
Chloroplast Genomes ◽  
Gene Data ◽  
High Degree

The order Nymphaeales, consisting of three families with a record of eight genera, has gained significant interest from botanists, probably due to its position as a basal angiosperm. The phylogenetic relationships within the order have been well studied; however, a few controversial nodes still remain in the Nymphaeaceae. The position of the Nuphar genus and the monophyly of the Nymphaeaceae family remain uncertain. This study adds to the increasing number of the completely sequenced plastid genomes of the Nymphaeales and applies a large chloroplast gene data set in reconstructing the intergeneric relationships within the Nymphaeaceae. Five complete chloroplast genomes were newly generated, including a first for the monotypic Euryale genus. Using a set of 66 protein-coding genes from the chloroplast genomes of 17 taxa, the phylogenetic position of Nuphar was determined and a monophyletic Nymphaeaceae family was obtained with convincing statistical support from both partitioned and unpartitioned data schemes. Although genomic comparative analyses revealed a high degree of synteny among the chloroplast genomes of the ancient angiosperms, key minor variations were evident, particularly in the contraction/expansion of the inverted-repeat regions and in RNA-editing events. Genome structure, and gene content and arrangement were highly conserved among the chloroplast genomes. The intergeneric relationships defined in this study are congruent with those inferred using morphological data.

scholarly journals Random Sequencing of Paramecium Somatic DNA

2002 ◽  
Vol 1 (3) ◽  
pp. 341-352 ◽  
Author(s):  
Linda Sperling ◽  
Philippe Dessen ◽  
Marek Zagulski ◽  
Ron E. Pearlman ◽  
Andrzey Migdalski ◽  
...  
Keyword(s):  
Germ Line ◽  
Gene Discovery ◽  
Strong Support ◽  
Distance Matrix ◽  
Sexual Cycle ◽  
Phylogenetic Position ◽  
Paramecium Tetraurelia ◽  
Data Set ◽  
Somatic Genome ◽  
Random Survey

ABSTRACT We report a random survey of 1 to 2% of the somatic genome of the free-living ciliate Paramecium tetraurelia by single-run sequencing of the ends of plasmid inserts. As in all ciliates, the germ line genome of Paramecium (100 to 200 Mb) is reproducibly rearranged at each sexual cycle to produce a somatic genome of expressed or potentially expressed genes, stripped of repeated sequences, transposons, and AT-rich unique sequence elements limited to the germ line. We found the somatic genome to be compact (>68% coding, estimated from the sequence of several complete library inserts) and to feature uniformly small introns (18 to 35 nucleotides). This facilitated gene discovery: 722 open reading frames (ORFs) were identified by similarity with known proteins, and 119 novel ORFs were tentatively identified by internal comparison of the data set. We determined the phylogenetic position of Paramecium with respect to eukaryotes whose genomes have been sequenced by the distance matrix neighbor-joining method by using random combined protein data from the project. The unrooted tree obtained is very robust and in excellent agreement with accepted topology, providing strong support for the quality and consistency of the data set. Our study demonstrates that a random survey of the somatic genome of Paramecium is a good strategy for gene discovery in this organism.

scholarly journals Stabilizing selection on individual pattern elements of aposematic signals

2017 ◽  
Vol 284 (1861) ◽  
pp. 20170926 ◽  
Author(s):  
Anne E. Winters ◽  
Naomi F. Green ◽  
Nerida G. Wilson ◽  
Martin J. How ◽  
Mary J. Garson ◽  
...  
Keyword(s):  
Pattern Analysis ◽  
Marine Organism ◽  
Warning Signal ◽  
Colour Pattern ◽  
Stabilizing Selection ◽  
Warning Signals ◽  
Fish Predator ◽  
Selection For ◽  
Aposematic Signals ◽  
Behavioural Experiments

Warning signal variation is ubiquitous but paradoxical: low variability should aid recognition and learning by predators. However, spatial variability in the direction and strength of selection for individual elements of the warning signal may allow phenotypic variation for some components, but not others. Variation in selection may occur if predators only learn particular colour pattern components rather than the entire signal. Here, we used a nudibranch mollusc, Goniobranchus splendidus , which exhibits a conspicuous red spot/white body/yellow rim colour pattern, to test this hypothesis. We first demonstrated that secondary metabolites stored within the nudibranch were unpalatable to a marine organism. Using pattern analysis, we demonstrated that the yellow rim remained invariable within and between populations; however, red spots varied significantly in both colour and pattern. In behavioural experiments, a potential fish predator, Rhinecanthus aculeatus , used the presence of the yellow rims to recognize and avoid warning signals. Yellow rims remained stable in the presence of high genetic divergence among populations. We therefore suggest that how predators learn warning signals may cause stabilizing selection on individual colour pattern elements, and will thus have important implications on the evolution of warning signals.

scholarly journals Phylogenetic Position of the New World Quail (Odontophoridae): Eight Nuclear Loci and Three Mitochondrial Regions Contradict Morphology and the Sibley-Ahlquist Tapestry

The Auk ◽  
2007 ◽  
Vol 124 (1) ◽  
pp. 71-84 ◽  
Author(s):  
W. Andrew Cox ◽  
Rebecca T. Kimball ◽  
Edward L. Braun
Keyword(s):  
New World ◽  
Sequence Data ◽  
Evolutionary Relationship ◽  
Strong Support ◽  
Nuclear Data ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Data Set ◽  
Mitochondrial Data ◽  
Nuclear Loci

Abstract The evolutionary relationship between the New World quail (Odontophoridae) and other groups of Galliformes has been an area of debate. In particular, the relationship between the New World quail and guineafowl (Numidinae) has been difficult to resolve. We analyzed >8 kb of DNA sequence data from 16 taxa that represent all major lineages of Galliformes to resolve the phylogenetic position of New World quail. A combined data set of eight nuclear loci and three mitochondrial regions analyzed with maximum parsimony, maximum likelihood, and Bayesian methods provide congruent and strong support for New World quail being basal members of a phasianid clade that excludes guineafowl. By contrast, the three mitochondrial regions exhibit modest incongruence with each other. This is reflected in the combined mitochondrial analyses that weakly support the Sibley-Ahlquist topology that placed the New World quail basal in relation to guineafowl and led to the placement of New World quail in its own family, sister to the Phasianidae. However, simulation-based topology tests using the mitochondrial data were unable to reject the topology suggested by our combined (mitochondrial and nuclear) data set. By contrast, similar tests using our most likely topology and our combined nuclear and mitochondrial data allow us to strongly reject the Sibley-Ahlquist topology and a topology based on morphological data that unites Old and New World quail. Posición Filogenética de las Codornices del Nuevo Mundo (Odontophoridae): Ocho Loci Nucleares y Tres Regiones Mitocondriales Contradicen la Morfología y la Filogenia de Sibley y Ahlquist

scholarly journals Substitution Rates Under Stabilizing Selection

Genetics ◽  
1987 ◽  
Vol 116 (3) ◽  
pp. 479-486
Author(s):  
Alan Hastings
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Simulations ◽  
Quantitative Traits ◽  
Strong Dependence ◽  
Phenotypic Selection ◽  
Analytical Models ◽  
Stabilizing Selection ◽  
Substitution Rates ◽  
Quantitative Characters ◽  
Selection For

ABSTRACT Allelic substitutions under stabilizing phenotypic selection on quantitative traits are studied in Monte Carlo simulations of 8 and 16 loci. The results are compared and contrasted to analytical models based on work of M. Kimura for two and "infinite" loci. Selection strengths of S = 4Nes approximately four (which correspond to reasonable strengths of selection for quantitative characters) can retard substitution rates tenfold relative to rates under neutrality. An important finding is a strong dependence of per locus substitution rates on the number of loci.

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