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 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 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 Demographic responses underlying eco‐evolutionary dynamics as revealed with inverse modelling

2019 ◽  
Vol 88 (5) ◽  
pp. 768-779
Author(s):  
Marjolein Bruijning ◽  
Eelke Jongejans ◽  
Martin M. Turcotte
Keyword(s):  
Evolutionary Dynamics ◽  
Inverse Modelling ◽  
Demographic Responses

scholarly journals Divergent and convergent evolution of housekeeping genes in human–pig lineage

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4840 ◽  
Author(s):  
Kai Wei ◽  
Tingting Zhang ◽  
Lei Ma
Keyword(s):  
Active Sites ◽  
Evolutionary Dynamics ◽  
Purifying Selection ◽  
Housekeeping Genes ◽  
Neutral Evolution ◽  
Structure Evolution ◽  
Tissue Cell ◽  
Sequencing Data ◽  
Cellular Functions ◽  
Species Specific

Housekeeping genes are ubiquitously expressed and maintain basic cellular functions across tissue/cell type conditions. The present study aimed to develop a set of pig housekeeping genes and compare the structure, evolution and function of housekeeping genes in the human–pig lineage. By using RNA sequencing data, we identified 3,136 pig housekeeping genes. Compared with human housekeeping genes, we found that pig housekeeping genes were longer and subjected to slightly weaker purifying selection pressure and faster neutral evolution. Common housekeeping genes, shared by the two species, achieve stronger purifying selection than species-specific genes. However, pig- and human-specific housekeeping genes have similar functions. Some species-specific housekeeping genes have evolved independently to form similar protein active sites or structure, such as the classical catalytic serine–histidine–aspartate triad, implying that they have converged for maintaining the basic cellular function, which allows them to adapt to the environment. Human and pig housekeeping genes have varied structures and gene lists, but they have converged to maintain basic cellular functions essential for the existence of a cell, regardless of its specific role in the species. The results of our study shed light on the evolutionary dynamics of housekeeping genes.

scholarly journals Dynamical analysis of the global elevational diversity gradient in passerine birds reveals a prominent role for highlands as species pumps

2020 ◽  
Author(s):  
Paul van Els ◽  
Leonel Herrera-Alsina ◽  
Alex L. Pigot ◽  
Rampal Etienne
Keyword(s):  
Evolutionary Dynamics ◽  
Strong Support ◽  
High Elevation ◽  
Dynamical Analysis ◽  
Reverse Direction ◽  
Passerine Birds ◽  
Diversification Rates ◽  
Diversity Gradient ◽  
As Species ◽  
Almost All

Abstract Low elevation regions harbor the majority of the world’s species diversity compared to high elevation areas. This global elevational diversity gradient, suggests that lowland species have had more time to diversify, or that net diversification rates have been higher in the lowlands (either due to higher ecological limits or intrinsically higher diversification rates). However, highlands seem to be cradles of diversity as they contain many young endemics, suggesting that their rates of speciation are exceptionally fast. Here, we use a phylogenetic diversification model that accounts for the dispersal of species between different elevations to examine the evolutionary dynamics of the elevational diversity gradient in passerine birds, a group that has radiated globally to occupy almost all elevations and latitudes. We find strong support for a model where passerines diversify at the same rate in the highlands and the lowlands but where the rate of dispersal from high to low elevations is more than twice as fast as in the reverse direction. This suggests that while there is no consistent trend in diversification across elevations, highland regions act as species pumps because the diversity they generate migrates into the lowlands, thus setting up the observed gradient in passerine diversity. This species pump is particularly strong in the tropics, where the inferred rate of speciation is 1.4 times faster than in the temperate zone. We conclude that despite their lower diversity, highland regions are disproportionally important for maintaining diversity in the adjacent lowlands. The extinction of species in the tropical highlands due to rapid climate change this century could thus have major and long-lasting impacts on global passerine diversity.

scholarly journals Microbial control of host gene regulation and the evolution of host–microbiome interactions in primates

2020 ◽  
Vol 375 (1808) ◽  
pp. 20190598 ◽  
Author(s):  
Laura Grieneisen ◽  
Amanda L. Muehlbauer ◽  
Ran Blekhman
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Host Species ◽  
Evolutionary Dynamics ◽  
Microbial Control ◽  
Host Gene ◽  
Primate Species ◽  
Microbiome Composition ◽  
Wide Range ◽  
Species Specific

Recent comparative studies have found evidence consistent with the action of natural selection on gene regulation across primate species. Other recent work has shown that the microbiome can regulate host gene expression in a wide range of relevant tissues, leading to downstream effects on immunity, metabolism and other biological systems in the host. In primates, even closely related host species can have large differences in microbiome composition. One potential consequence of these differences is that host species-specific microbial traits could lead to differences in gene expression that influence primate physiology and adaptation to local environments. Here, we will discuss and integrate recent findings from primate comparative genomics and microbiome research, and explore the notion that the microbiome can influence host evolutionary dynamics by affecting gene regulation across primate host species. This article is part of the theme issue ‘The role of the microbiome in host evolution’.

scholarly journals Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Elissavet Kentepozidou ◽  
Sarah J. Aitken ◽  
Christine Feig ◽  
Klara Stefflova ◽  
Ximena Ibarra-Soria ◽  
...  
Keyword(s):  
Large Scale ◽  
Evolutionary Dynamics ◽  
Computational Study ◽  
Genome Structure ◽  
Higher Order ◽  
Ctcf Binding ◽  
Natural Genetic Variation ◽  
Transcription Start Sites ◽  
Topologically Associating Domains ◽  
Species Specific

Abstract Background CTCF binding contributes to the establishment of a higher-order genome structure by demarcating the boundaries of large-scale topologically associating domains (TADs). However, despite the importance and conservation of TADs, the role of CTCF binding in their evolution and stability remains elusive. Results We carry out an experimental and computational study that exploits the natural genetic variation across five closely related species to assess how CTCF binding patterns stably fixed by evolution in each species contribute to the establishment and evolutionary dynamics of TAD boundaries. We perform CTCF ChIP-seq in multiple mouse species to create genome-wide binding profiles and associate them with TAD boundaries. Our analyses reveal that CTCF binding is maintained at TAD boundaries by a balance of selective constraints and dynamic evolutionary processes. Regardless of their conservation across species, CTCF binding sites at TAD boundaries are subject to stronger sequence and functional constraints compared to other CTCF sites. TAD boundaries frequently harbor dynamically evolving clusters containing both evolutionarily old and young CTCF sites as a result of the repeated acquisition of new species-specific sites close to conserved ones. The overwhelming majority of clustered CTCF sites colocalize with cohesin and are significantly closer to gene transcription start sites than nonclustered CTCF sites, suggesting that CTCF clusters particularly contribute to cohesin stabilization and transcriptional regulation. Conclusions Dynamic conservation of CTCF site clusters is an apparently important feature of CTCF binding evolution that is critical to the functional stability of a higher-order chromatin structure.

scholarly journals Functional trait space and the latitudinal diversity gradient

2014 ◽  
Vol 111 (38) ◽  
pp. 13745-13750 ◽  
Author(s):  
C. Lamanna ◽  
B. Blonder ◽  
C. Violle ◽  
N. J. B. Kraft ◽  
B. Sandel ◽  
...  
Keyword(s):  
Functional Trait ◽  
Latitudinal Diversity Gradient ◽  
Diversity Gradient ◽  
Trait Space

scholarly journals Why are There so Many Bee-Orchid Species? Adaptive Radiation by Intraspecific Competition for Mnemonic Pollinators

2019 ◽  
Author(s):  
Michel Baguette ◽  
Joris Bertrand ◽  
Virginie M. Stevens ◽  
Bertrand Schatz
Keyword(s):  
Adaptive Radiation ◽  
Evolutionary Dynamics ◽  
Evolutionary Relationship ◽  
Ecological Niches ◽  
Local Diversity ◽  
Pollinator Species ◽  
Main Driver ◽  
Adaptive Radiations ◽  
Suitable Habitats ◽  
Species Specific

Adaptive radiations occur mostly in response to environmental variation through the evolution of key eco-morphological innovations that allow emerging species to occupy new ecological niches. However, rapid phenotypic evolution and the evolution of key novelties are likely to also occur when a couple or few species are engaged into narrow ecological interactions. To demonstrate coevolution is a difficult task; only elusive evidences confirm that coevolution is a driver of speciation and diversification. Here we propose that the adaptive radiation of the Mediterranean orchid genus Ophrys, which gave rise to ca. 350 species since the apparition of the genus is due to the particular co-evolutionary dynamics between these plants and their pollinators. We suggest that the pollination by sexual swindle used by Ophrys orchids is the main driver of this coevolution. Flowers of each Ophrys species mimic sexually receptive females of one particular insect species, mainly bees. Male bees are attracted by pseudo-pheromones emitted by Ophrys flowers that are similar to the sexual pheromones of their females. Males lured by the flower shape, color and hairiness attempt to copulate with the flower, which glues pollen on their bodies. Pollen is eventually transferred to the stigma of another flower of the same Ophrys species during similar copulation attempts. Three observations led us to propose the scenario of an asymmetric co-evolutionary relationship between Ophrys and their pollinators. Firstly, there is a strong intra-specific competition among Ophrys individuals for the attraction of their species-specific pollinators, which is due to the high learning and memorization abilities of bees that record the pheromone signatures of kin or of previously courted partner to avoid (further) copulation attempts. Mnemonic pollinators induce thus a strong selective pressure for variation in the pseudo-pheromones emitted by individual flowers, which will potentially generate shifts in pollinator species, and hence Ophrys speciation. These pollinator shifts are adaptive for new Ophrys species because they may benefit from a competitor-free space. Secondly, such shifts in pollinator species are due to the random crossing of peaks in the olfactory landscape of the pollinator guild that is syntopic to each particular Ophrys population. This selective process on individual, random variation in pseudo-pheromone bouquets is followed by directional selection on flower phenotypes that will reinforce the attraction of the new pollinator. Thirdly, pollinators use the pseudo-pheromones emitted by Ophrys to locate suitable habitats from a distance within complex landscapes. Pollinators stay fixed for a while in these habitats by the local diversity of pseudo-pheromones, which increases their probability of encounter with a receptive female and hence the reproduction probability of both sexes. Conversely, pollinators disperse out of small suitable habitats once they have memorized the local diversity of sexual pseudo-pheromone bouquet or if fecundated Ophrys flowers repel pollinators, which decreases the probability of geitonogamy (plant advantage) but limit pollinator mating with locally emergent insect females, thus limiting inbreeding and favoring gene flow (pollinator advantage). Finally, we propose several research avenues that emerged according to this scenario of adaptive radiation by assymetric coevolution between Ophrys species and their pollinators.

scholarly journals Identification of multiple TAR DNA Binding Protein retropseudogene lineages during the evolution of primates

2021 ◽  
Author(s):  
Juan Opazo ◽  
Kattina Zavala ◽  
Luis Vargas-Chacoff ◽  
Francisco Morera ◽  
Gonzalo Mardones
Keyword(s):  
Dna Binding ◽  
Evolutionary History ◽  
Evolutionary Dynamics ◽  
Binding Protein ◽  
Genetic Material ◽  
Dna Binding Protein ◽  
Functional Protein ◽  
Species Specific ◽  
Regulatory Functions ◽  
Rule Out

The TAR DNA Binding Protein (TARDBP) gene has gained attention in biomedicine after the discovery of several pathogenic mutations. The lack of knowledge about its evolutionary history contrasts with a large number of studies in the biomedical area. This study aimed to investigate the retrotransposition evolutionary dynamics associated with this gene in primates. We identified retropseudogenes that originated in the ancestors of anthropoids, catarrhines, and lemuriformes, i.e. the strepsirrhine clade that inhabit Madagascar. We also found species-specific retropseudogenes in the philippine tarsier, Bolivian squirrel monkey, capuchin monkey and vervet. Although retropseudogenes are not able to produce a functional protein, we can not rule out that they may represent genetic material upon which evolution acts on, especially with regulatory functions.

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