scholarly journals Variable Rates of Simple Satellite Gains across the Drosophila Phylogeny

2018 ◽  
Vol 35 (4) ◽  
pp. 925-941 ◽  
Author(s):  
Kevin H -C Wei ◽  
Sarah E Lower ◽  
Ian V Caldas ◽  
Trevor J S Sless ◽  
Daniel A Barbash ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Rapid Evolution ◽  
Single Mutation ◽  
Closely Related Species ◽  
Interspecific Differences ◽  
Limited Sampling ◽  
Drosophila Phylogeny ◽  
Males And Females ◽  
Species Specific ◽  
Turn Over

Abstract Simple satellites are tandemly repeating short DNA motifs that can span megabases in eukaryotic genomes. Because they can cause genomic instability through nonallelic homologous exchange, they are primarily found in the repressive heterochromatin near centromeres and telomeres where recombination is minimal, and on the Y chromosome, where they accumulate as the chromosome degenerates. Interestingly, the types and abundances of simple satellites often vary dramatically between closely related species, suggesting that they turn over rapidly. However, limited sampling has prevented detailed understanding of their evolutionary dynamics. Here, we characterize simple satellites from whole-genome sequences generated from males and females of nine Drosophila species, spanning 40 Ma of evolution. We show that PCR-free library preparation and postsequencing GC-correction better capture satellite quantities than conventional methods. We find that over half of the 207 simple satellites identified are species-specific, consistent with previous descriptions of their rapid evolution. Based on a maximum parsimony framework, we determined that most interspecific differences are due to lineage-specific gains. Simple satellites gained within a species are typically a single mutation away from abundant existing satellites, suggesting that they likely emerge from existing satellites, especially in the genomes of satellite-rich species. Interestingly, unlike most of the other lineages which experience various degrees of gains, the lineage leading up to the satellite-poor D. pseudoobscura and D. persimilis appears to be recalcitrant to gains, providing a counterpoint to the notion that simple satellites are universally rapidly evolving.

scholarly journals Transposable element dynamics are consistent across the Drosophila phylogeny, despite drastically differing content

2019 ◽  
Author(s):  
Tom Hill
Keyword(s):  
Drosophila Melanogaster ◽  
Related Species ◽  
Evolutionary Dynamics ◽  
Common Ancestor ◽  
Low Frequency ◽  
Fitness Costs ◽  
Closely Related Species ◽  
Drosophila Phylogeny ◽  
Turn Over ◽  
Insertion Frequency

AbstractBackgroundThe evolutionary dynamics of transposable elements (TEs) vary across the tree of life and even between closely related species with similar ecologies. In Drosophila, most of the focus on TE dynamics has been completed in Drosophila melanogaster and the overall pattern indicates that TEs show an excess of low frequency insertions, consistent with their frequent turn over and high fitness cost in the genome. Outside of D. melanogaster, insertions in the species Drosophila algonquin, suggests that this situation may not be universal, even within Drosophila. Here we test whether the pattern observed in D. melanogaster is similar across five Drosophila species that share a common ancestor more than fifty million years ago.ResultsFor the most part, TE family and order insertion frequency patterns are broadly conserved between species, supporting the idea that TEs have invaded species recently, are mostly costly and dynamics are conserved in orthologous regions of the host genomeConclusionsMost TEs retain similar activities and fitness costs across the Drosophila phylogeny, suggesting little evidence of drift in the dynamics of TEs across the phylogeny, and that most TEs have invaded species recently.

scholarly journals Heterospecific aggression differs predominately by species, rather than sex, in Lake Malawi cichlid fish

2019 ◽  
Author(s):  
Emily C. Moore ◽  
Reade B. Roberts
Keyword(s):  
Community Structure ◽  
Rapid Evolution ◽  
Cichlid Fish ◽  
Lake Malawi ◽  
Male Aggression ◽  
Males And Females ◽  
Potential Impact ◽  
Cortisol Levels ◽  
Species Specific ◽  
Heterospecific Aggression

ABSTRACTBecause of their striking diversity, Lake Malawi cichlid fish have been well studied for male aggression, particularly among dominant males of closely related sister species within the framework of mate-choice and speciation. However, aggression in females has been largely ignored, and variation in aggressive behaviors between more distantly-related taxa is not well understood despite its potential impact in a complex community structure. To better understand variation in patterns of aggression between species, we presented males and females from five species of Lake Malawi cichlid with a non-predator intruder and recorded all movement and aggressive acts. Additionally, we measured excreted cortisol levels the day after the intruder assay to evaluate one physiological aspect of stress response. We identified species-specific patterns in both specific aggressive acts, and overall level of aggression. Additionally, we found that sexual dimorphism in aggressive acts varies by species and act, where the species with the most aggressive males also has aggressive females. Additionally, cortisol levels vary by taxa, and are associated with restless behavior in the intruder assay, but not levels of aggression. These findings have bearing on understanding sex differences in aggression and their impact on community structure in this important model of rapid evolution.

scholarly journals From plant populations to communities: using hierarchical trait environment relationships to reveal within ecosystem filtering

2019 ◽  
Author(s):  
Lucas Deschamps ◽  
Raphaël Proulx ◽  
Nicolas Gross ◽  
Guillaume Rheault ◽  
Vincent Maire
Keyword(s):  
Evolutionary Dynamics ◽  
Functional Trait ◽  
Population Characteristics ◽  
Diversity Gradient ◽  
Species Specific ◽  
Turn Over ◽  
Favorable Conditions ◽  
Nutrient Conservation ◽  
Space Occupation ◽  
Demographic Responses

AbstractExplaining the existence of highly diverse plant communities under strong abiotic filtering is a long-standing challenge in ecology. Hierarchical aspects of abiotic and biotic filters are rarely taken into account and studies focus mainly on community-level aggregated patterns. Because variations in biotic conditions might take place in short abiotic gradient and within the tolerance of species in regional pool, it is likely that biotic filtering will select individuals within species and adjust population characteristics. To challenge this idea, we replicated a diversity gradient in four highly contrasted wetlands with an almost complete species turn-over, sampling individuals in communities irrespective of their taxonomic identities or status. Using hierarchical distributional modelling, we analyzed the variation of the mean and dispersion of functional trait space at the ecosystem, community and species level. We found that the abiotic differences between ecosystems filtered species contrasted in their growth/nutrient conservation trade-off, while within ecosystems community variation were mainly due to the partitioning of canopy and leaf adaptations to light conditions. We found strong species-specific functional and demographic responses of dominant species along the diversity gradient, especially for traits linked to biomass and space occupation. Two contrasted strategies emerged, with species using plasticity to maintain equally dense populations, while others used plasticity to become overwhelmingly abundant when in favorable conditions. Our results demonstrate that within ecosystems, variation in biotic conditions selects individuals within populations, revealing the importance of phenotypic variation for a species to be maintained in more or less diverse communities. Because phenotypic variations are related to demographic responses, it offers a way to link the study of species diversity and eco-evolutionary dynamics.

scholarly journals Evolutionary dynamics of circular RNAs in primates

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Gabriela Santos-Rodriguez ◽  
Irina Voineagu ◽  
Robert James Weatheritt
Keyword(s):  
Related Species ◽  
Evolutionary Dynamics ◽  
Expression Profiles ◽  
Primate Evolution ◽  
Circular Rnas ◽  
Species Identity ◽  
Closely Related Species ◽  
Tissue Specific ◽  
Organ Type ◽  
Species Specific

Many primate genes produce circular RNAs (circRNAs). However, the extent of circRNA conservation between closely related species remains unclear. By comparing tissue-specific transcriptomes across over 70 million years of primate evolution, we identify that within 3 million years circRNA expression profiles diverged such that they are more related to species identity than organ type. However, our analysis also revealed a subset of circRNAs with conserved neural expression across tens of millions of years of evolution. By comparing to species-specific circRNAs, we identified that the downstream intron of the conserved circRNAs display a dramatic lengthening during evolution due to the insertion of novel retrotransposons. Our work provides comparative analyses of the mechanisms promoting circRNAs to generate increased transcriptomic complexity in primates.

scholarly journals High rates of evolution preceded shifts to sex-biased gene expression in Leucadendron, the most sexually dimorphic angiosperms

2021 ◽  
Author(s):  
Mathias Scharmann ◽  
Anthony G Rebelo ◽  
John R Pannell
Keyword(s):  
Gene Expression ◽  
Sexual Dimorphism ◽  
Rapid Evolution ◽  
Sex Bias ◽  
Sexually Dimorphic ◽  
Expression Levels ◽  
Rates Of Evolution ◽  
Expression Evolution ◽  
Males And Females ◽  
Species Specific

AbstractThe males and females of many dioecious plants differ in morphological (Dawson and Geber 1999; Barrett and Hough 2013; Tonnabel et al. 2017), physiological (Juvany and Munné-Bosch 2015), life-history (Delph 1999), and defence traits (Cornelissen and Stiling 2005). Ultimately, such sexual dimorphism must largely be due to differential gene expression between the sexes (Ellegren and Parsch 2007), but little is known about how sex-biased genes are recruited and how their expression evolves over time. We measured gene expression in leaves of males and females of ten species sampled across the South African Cape genus Leucadendron, which shows repeated changes in sexual dimorphism and includes the most extreme differences between males and females in flowering plants (Midgley 2010; Barrett and Hough 2013; Tonnabel et al. 2014). Even in the most dimorphic species in our sample, fewer than 2% of genes showed sex-biased gene expression (SBGE) in vegetative tissue, with surprisingly little correspondence between SBGE and vegetative dimorphism across species. The identity of sex-biased genes in Leucadendron was highly species-specific, with a rapid turnover among species. In animals, sex-biased genes often evolve more quickly than unbiased genes in their sequences and expression levels (Ranz et al. 2003; Khaitovich et al. 2005; Ellegren and Parsch 2007; Voolstra et al. 2007; Harrison et al. 2015; Naqvi et al. 2019), consistent with hypotheses invoking rapid evolution due to sexual selection. Our phylogenetic analysis in Leucadendron, however, clearly indicates that sex-biased genes are recruited from a class of genes with ancestrally rapid rates of expression evolution, perhaps due to low evolutionary or pleiotropic constraints. Nevertheless, we also find evidence for adaptive evolution of expression levels once sex bias evolves. Thus, although the expression of sex-biased genes is ultimately responsive to selection, high rates of expression evolution might usually predate the evolution of sex bias.

scholarly journals Bark traits, decomposition and flammability of Australian forest trees

2017 ◽  
Vol 65 (4) ◽  
pp. 327 ◽  
Author(s):  
Saskia Grootemaat ◽  
Ian J. Wright ◽  
Peter M. van Bodegom ◽  
Johannes H. C. Cornelissen ◽  
Veronica Shaw
Keyword(s):  
Forest Tree ◽  
Remarkable Feature ◽  
Interspecific Differences ◽  
Eucalypt Plantations ◽  
Physical Traits ◽  
Key Driver ◽  
Multiple Species ◽  
Species Specific ◽  
First Time ◽  
Different Tissues

Bark shedding is a remarkable feature of Australian trees, yet relatively little is known about interspecific differences in bark decomposability and flammability, or what chemical or physical traits drive variation in these properties. We measured the decomposition rate and flammability (ignitibility, sustainability and combustibility) of bark from 10 common forest tree species, and quantified correlations with potentially important traits. We compared our findings to those for leaf litter, asking whether the same traits drive flammability and decomposition in different tissues, and whether process rates are correlated across tissue types. Considerable variation in bark decomposability and flammability was found both within and across species. Bark decomposed more slowly than leaves, but in both tissues lignin concentration was a key driver. Bark took longer to ignite than leaves, and had longer mass-specific flame durations. Variation in flammability parameters was driven by different traits in the different tissues. Decomposability and flammability were each unrelated, when comparing between the different tissue types. For example, species with fast-decomposing leaves did not necessarily have fast-decomposing bark. For the first time, we show how patterns of variation in decomposability and flammability of bark diverge across multiple species. By taking species-specific bark traits into consideration there is potential to make better estimates of wildfire risks and carbon loss dynamics. This can lead to better informed management decisions for Australian forests, and eucalypt plantations, worldwide.

scholarly journals The Tomato Interspecific NB-LRR Gene Arsenal and Its Impact on Breeding Strategies

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 184
Author(s):  
Giuseppe Andolfo ◽  
Nunzio D’Agostino ◽  
Luigi Frusciante ◽  
Maria Raffaella Ercolano
Keyword(s):  
Evolutionary Dynamics ◽  
Special Focus ◽  
Breeding Strategies ◽  
Adaptive Diversification ◽  
Solanum Lycopersicum L ◽  
Solanaceae Species ◽  
Specific Pathogen ◽  
Adaptive Processes ◽  
Species Specific ◽  
R Loci

Tomato (Solanum lycopersicum L.) is a model system for studying the molecular basis of resistance in plants. The investigation of evolutionary dynamics of tomato resistance (R)-loci provides unique opportunities for identifying factors that promote or constrain genome evolution. Nucleotide-binding domain and leucine-rich repeat (NB-LRR) receptors belong to one of the most plastic and diversified families. The vast amount of genomic data available for Solanaceae and wild tomato relatives provides unprecedented insights into the patterns and mechanisms of evolution of NB-LRR genes. Comparative analysis remarked a reshuffling of R-islands on chromosomes and a high degree of adaptive diversification in key R-loci induced by species-specific pathogen pressure. Unveiling NB-LRR natural variation in tomato and in other Solanaceae species offers the opportunity to effectively exploit genetic diversity in genomic-driven breeding programs with the aim of identifying and introducing new resistances in tomato cultivars. Within this motivating context, we reviewed the repertoire of NB-LRR genes available for tomato improvement with a special focus on signatures of adaptive processes. This issue is still relevant and not thoroughly investigated. We believe that the discovery of mechanisms involved in the generation of a gene with new resistance functions will bring great benefits to future breeding strategies.

scholarly journals A Comparative Study of 5S rDNA Non-Transcribed Spacers in Elaeagnaceae Species

Plants ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 4
Author(s):  
Oleg S. Alexandrov ◽  
Olga V. Razumova ◽  
Gennady I. Karlov
Keyword(s):  
Polymerase Chain Reaction ◽  
Molecular Markers ◽  
Dna Markers ◽  
5S Rdna ◽  
Chain Reaction ◽  
Closely Related Species ◽  
Pcr Products ◽  
Polymerase Chain ◽  
Species Specific ◽  
Shepherdia Canadensis

5S rDNA is organized as a cluster of tandemly repeated monomers that consist of the conservative 120 bp coding part and non-transcribed spacers (NTSs) with different lengths and sequences among different species. The polymorphism in the 5S rDNA NTSs of closely related species is interesting for phylogenetic and evolutional investigations, as well as for the development of molecular markers. In this study, the 5S rDNA NTSs were amplified with universal 5S1/5S2 primers in some species of the Elaeagnaceae Adans. family. The polymerase chain reaction (PCR) products of five Elaeagnus species had similar lengths near 310 bp and were different from Shepherdia canadensis (L.) Nutt. and Sh. argentea (Pusch.) Nutt. samples (260 bp and 215 bp, respectively). The PCR products were cloned and sequenced. An analysis of the sequences revealed that intraspecific levels of NTS identity are high (approximately 95–96%) and similar in the Elaeagnus L. species. In Sh. argentea, this level was slightly lower due to the differences in the poly-T region. Moreover, the intergeneric and intervarietal NTS identity levels were studied and compared. Significant differences between species (except E. multiflora Thunb. and E. umbellata Thunb.) and genera were found. Herein, a range of the NTS features is discussed. This study is another step in the investigation of the molecular evolution of Elaeagnaceae and may be useful for the development of species-specific DNA markers in this family.

scholarly journals Environmental correlates and energetics of winter flight by bats in southern Alberta, Canada

2016 ◽  
Vol 94 (12) ◽  
pp. 829-836 ◽  
Author(s):  
B.J. Klüg-Baerwald ◽  
L.E. Gower ◽  
C.L. Lausen ◽  
R.M. Brigham
Keyword(s):  
Heat Loss ◽  
Barometric Pressure ◽  
Myotis Lucifugus ◽  
Energetic Cost ◽  
Cold Temperatures ◽  
Bat Activity ◽  
Environmental Correlates ◽  
Interspecific Differences ◽  
Winter Activity ◽  
Species Specific

Winter activity of bats is common, yet poorly understood. Other studies suggest a relationship between winter activity and ambient temperature, particularly temperature at sunset. We recorded echolocation calls to determine correlates of hourly bat activity in Dinosaur Provincial Park, Alberta, Canada. We documented bat activity in temperatures as low as −10.4 °C. We observed big brown bats (Eptesicus fuscus (Palisot de Beauvois, 1796)) flying at colder temperatures than species of Myotis bats (genus Myotis Kaup, 1829). We show that temperature and wind are important predictors of winter activity by E. fuscus and Myotis, and that Myotis may also use changes in barometric pressure to cue activity. In the absence of foraging opportunity, we suggest these environmental factors relate to heat loss and thus the energetic cost of flight. To understand the energetic consequences of bat flight in cold temperatures, we estimated energy expenditure during winter flights of E. fuscus and little brown myotis (Myotis lucifugus (Le Conte, 1831)) using species-specific parameters. We estimated that winter flight uses considerable fat stores and that flight thermogenesis could mitigate energetic costs by 20% or more. We also show that temperature-dependent interspecific differences in winter activity likely stem from differences between species in heat loss and potential for activity–thermoregulatory heat substitution.

scholarly journals How Can Satellite DNA Divergence Cause Reproductive Isolation? Let Us Count the Chromosomal Ways

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Patrick M. Ferree ◽  
Satyaki Prasad
Keyword(s):  
Reproductive Isolation ◽  
Developmental Stages ◽  
Rapid Evolution ◽  
Model Organisms ◽  
Cellular Mechanisms ◽  
Closely Related Species ◽  
Heterochromatin Formation ◽  
Interspecies Hybrids ◽  
Postzygotic Reproductive Isolation ◽  
And Function

Satellites are one of the most enigmatic parts of the eukaryotic genome. These highly repetitive, noncoding sequences make up as much as half or more of the genomic content and are known to play essential roles in chromosome segregation during meiosis and mitosis, yet they evolve rapidly between closely related species. Research over the last several decades has revealed that satellite divergence can serve as a formidable reproductive barrier between sibling species. Here we highlight several key studies on Drosophila and other model organisms demonstrating deleterious effects of satellites and their rapid evolution on the structure and function of chromosomes in interspecies hybrids. These studies demonstrate that satellites can impact chromosomes at a number of different developmental stages and through distinct cellular mechanisms, including heterochromatin formation. These findings have important implications for how loci that cause postzygotic reproductive isolation are viewed.

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