Evolutionary Causes Research Articles

A complex mechanism translating variation of a simple genetic architecture into alternative life histories

Understanding the processes that link genotype to phenotype is a central challenge in biology. Despite progress in discovering genes associated with ecologically relevant traits, a poor understanding of the processes and functions via which molecules mediate evolutionary differences leaves us critically far from linking proximate and ultimate causes of evolution. This knowledge gap is particularly large in multifaceted phenotypes of ecological relevance such as life histories where multiple traits covary and influence fitness. In Atlantic salmon (Salmo salar), variation in a key life-history trait, maturation age, is largely linked to the transcription cofactor vestigial-like 3 (vgll3). Here, we show that despite this simple genetic architecture, vgll3 genotype influences maturation age through a complex regulatory mechanism whereby it controls the expression of diverse pubertal signaling pathways. Using a multiomic approach in salmon testes, we show that the vgll3 genotype conferring early maturity up-regulates key genes controlling androgen production, cellular energy and adiposity, and TGF-β signaling, thereby increasing the likelihood of earlier pubertal initiation. By mapping VGLL3 regulatory elements we further show its interaction with distinct transcription factors in a genotype-dependent manner, thus coordinating differential activation of regulatory pathways. This study reveals the proximate mechanisms through which a genetically simple association leads to functionally complex molecular differences in a spectrum of cellular traits, thus explaining the molecular basis of pleiotropy in a large-effect gene. Our results indicate that evolution in correlated phenotypes, as exemplified by alternative life history strategies, can be dictated by the function of major life-history genes.

Global patterns and determinants of phylogenetic beta diversity among liverwort floras

AbstractAimInvestigating phylogenetic beta diversity, and its turnover and nestedness components, can shed light on the evolutionary causes shaping the similarity (or dissimilarity) in composition between biological assemblages. Liverworts are important constituents of most terrestrial ecosystems worldwide but studies on phylogenetic beta diversity in liverworts are scarce. Here, we explore geographic patterns of phylogenetic beta diversity and its two components in liverworts across the world and evaluate the relative importance of dispersal limitation and environmental filtering processes in shaping beta diversity patterns at different spatial extents by relating phylogenetic beta diversity or phylogenetic turnover to geographic and climatic distances.LocationGlobal.TaxonLiverworts.MethodsWe conducted correlation and regression analyses to relate phylogenetic beta diversity and its two components (turnover and nestedness) to six variables representing current climate conditions and two variables representing historical (Quaternary) climate change, and to geographic and climatic distances at different spatial extents (global, continental, and regional).ResultsWe found that of the eight variables of current and historical climates considered, precipitation seasonality was the strongest determinant of phylogenetic beta diversity in liverworts. At the global extent, geographic and climatic distances explained similar amounts of the variation in phylogenetic turnover, whereas at the continental extent, climatic distance explained more variation than geographic distance in five of the seven continents, and at a regional extent (roughly a circle of 4000 km in diameter), geographic distances generally had a greater effect than climatic distance on phylogenetic turnover.Main ConclusionsWe conclude that both dispersal limitation and environmental filtering played an important role in shaping phylogenetic structure of liverwort floras, but their relative importance varies at different spatial scales and among geographic regions.

Research on the Reversal Phenomenon of Online Public Opinion in the Post-Truth Era

"Post-truth" is full of negative effects of the current network public opinion - ignoring the truth, disregarding the facts, dissolving the authority, position first, coupled with the frequent occurrence of global emergencies and hotspot events, the netizens wrapped up in group emotions have to join the public opinion of the network world carnival, this phenomenon also provides an environment for rumors to grow secretly, seriously undermining the harmony and stability of the Internet ecosystem. This phenomenon also provides an environment for network rumors to grow secretly, which seriously undermines the harmony and stability of the Internet ecology. In this paper, we take the "fat cat" incident as the starting point to analyze the impact, evolutionary causes and countermeasures of the popular public opinion events.

Evolutionary causes of global patterns of species richness in regional fern floras across the world

AbstractAimGlobally, biodiversity is unevenly distributed, as a result of varying environmental conditions and regionally different historical processes. The influence of the latter on current diversity patterns is poorly understood. We explore geographic patterns of matches and mismatches between phylogenetic relatedness metrics measuring different depths of evolutionary history and investigate the effects of evolutionary legacy at different evolutionary depths on species density of ferns.MethodsWe divided the globe into 392 geographic regions on land, and collated species lists of ferns for each geographic region. We related species richness to phylogenetic metrics reflecting different depths of evolutionary history (standardized effect sizes of mean nearest taxon distance and mean pairwise distance, MNTDses and MPDses, respectively) for ferns in regional floras across the world.LocationGlobal.Time PeriodCurrent.TaxonFerns.ResultsWe show that different centers of fern diversity have strikingly different phylogenetic composition. We find that overall fern species diversity is negatively correlated with both MNTDses and MPDses, so that regions with high species diversity tend to have clustered species assemblages, whereas species‐poor regions tend to have overdispersed species assemblages. At the global extent, MNTDses and MPDses together explained 62.2%, 19.3%, and 65.7% of the variation in species diversity for all ferns as a whole, non‐polypod ferns, and polypods, respectively.Main ConclusionsOur study suggests that current geographic patterns of fern species richness are driven, at least in part, by evolutionary history of ferns, which varies among biogeographic regions.

Insights into adaptive behavioural plasticity from the guppy model system.

Behavioural plasticity allows organisms to respond to environmental challenges on short time scales. But what are the ecological and evolutionary processes that underlie behavioural plasticity? The answer to this question is complex and requires experimental dissection of the physiological, neural and molecular mechanisms contributing to behavioural plasticity as well as an understanding of the ecological and evolutionary contexts under which behavioural plasticity is adaptive. Here, we discuss key insights that research with Trinidadian guppies has provided on the underpinnings of adaptive behavioural plasticity. First, we present evidence that guppies exhibit contextual, developmental and transgenerational behavioural plasticity. Next, we review work on behavioural plasticity in guppies spanning three ecological contexts (predation, parasitism and turbidity) and three underlying mechanisms (endocrinological, neurobiological and genetic). Finally, we provide three outstanding questions that could leverage guppies further as a study system and give suggestions for how this research could be done. Research on behavioural plasticity in guppies has provided, and will continue to provide, a valuable opportunity to improve understanding of the ecological and evolutionary causes and consequences of behavioural plasticity.

Overcoming Dormancy in Prunus Species under Conditions of Insufficient Winter Chilling in Israel.

The phenomenon of dormancy and the evolutionary causes for its development are presented together with the effects of the climatic factors: temperature and light. Shade and darkness have been found to enhance bud breaking in peach. The effects of various temperatures on chilling accumulation, chilling negation and chilling enhancement are described. The way these are computed in the face of global warming is explained, using the dynamic model. When natural chilling is less than that required, there are ways of compensation, up to a certain level. Various horticultural, physical and chemical means to achieve this are described, including bending branches, reducing vegetative vigor, shading the orchard, sprinkling to reduce daytime temperature and the application of various chemicals to break dormancy. When winter chilling is markedly reduced and temperatures increase considerably, the use of dormancy avoidance is suggested in frost-free places. This technique can induce a new growing cycle by avoiding dormancy altogether. However, the best approach is to breed high-quality cultivars requiring much less chilling. Another aspect discussed in this work, independent of the chilling requirement, is the negative effect of heat spells in winter and spring on the abnormal development of flower buds, leading to a low level of the stone fruit set and a reduced yield.

Woody plant taxonomic, functional, and phylogenetic diversity decrease along elevational gradients in Andean tropical montane forests: Environmental filtering and arrival of temperate taxa

Mountains are paramount for exploring biodiversity patterns due to the mosaic of topographies and climates encompassed over short distances. Biodiversity research has traditionally focused on taxonomic diversity when investigating changes along elevational gradients, but other facets should be considered. For first time, we simultaneously assessed elevational trends in taxonomic, functional, and phylogenetic diversity of woody plants in Andean tropical montane forests and explored their underlying ecological and evolutionary causes. This investigation covered four transects (traversing ca. 2200 m a.s.l.) encompassing 114 plots of 0.1 ha across a broad latitudinal range (ca. 10°). Using Hill numbers to quantify abundance-based diversity among 37,869 individuals we observed a consistent decrease in taxonomic, functional, and phylogenetic diversity as elevation increased, although the decrease was less pronounced for higher Hill orders. The exception was a slight increase in phylogenetic diversity when dominant species were over-weighted. The decrease in taxonomic and functional diversity might be attributed to an environmental filtering process towards highlands, where the increasingly harsher conditions exclude species and functional strategies. Besides, the differences in steepness decrease between Hill orders suggest that rare species disproportionately contribute to functional diversity. For phylogenetic diversity the shifting elevational trend between Hill orders indicates a greater than previously considered influence in central Andean highlands of tropical lowlands originated species with strong niche conservatism relative to distantly related temperate lineages. This could be explained by a decreasing presence and abundance of temperate, extratropical taxa towards the central Andes relative to northern or southern Andes, where they are more prevalent.

Multiple Transitions between Y Chromosome and Autosome in Tago's Brown Frog Species Complex.

Sex chromosome turnover is the transition between sex chromosomes and autosomes. Although many cases have been reported in poikilothermic vertebrates, their evolutionary causes and genetic mechanisms remain unclear. In this study, we report multiple transitions between the Y chromosome and autosome in the Japanese Tago's brown frog complex. Using chromosome banding and molecular analyses (sex-linked and autosomal single nucleotide polymorphisms, SNPs, from the nuclear genome), we investigated the frogs of geographic populations ranging from northern to southern Japan of two species, Rana tagoi and Rana sakuraii (2n = 26). Particularly, the Chiba populations of East Japan and Akita populations of North Japan in R. tagoi have been, for the first time, investigated here. As a result, we identified three different sex chromosomes, namely chromosomes 3, 7, and 13, in the populations of the two species. Furthermore, we found that the transition between the Y chromosome (chromosome 7) and autosome was repeated through hybridization between two or three different populations belonging to the two species, followed by restricted chromosome introgression. These dynamic sex chromosome turnovers represent the first such findings in vertebrates and imply that speciation associated with inter- or intraspecific hybridization plays an important role in sex chromosome turnover in frogs.

Neural mechanisms involved in female mate choice in invertebrates.

Mate choice is a critical decision with direct implications for fitness. Although it has been recognized for over 150 years, our understanding of its underlying mechanisms is still limited. Most studies on mate choice focus on the evolutionary causes of behavior, with less attention given to the physiological and molecular mechanisms involved. This is especially true for invertebrates, where research on mate choice has largely focused on male behavior. This review summarizes the current state of knowledge on the neural, molecular and neurohormonal mechanisms of female choice in invertebrates, including behaviors before, during, and after copulation. We identify areas of research that have not been extensively explored in invertebrates, suggesting potential directions for future investigation. We hope that this review will stimulate further research in this area.

Sharks Violate Rensch's Rule for Sexual Size Dimorphism.

Systematic trends in body size variation exist in a multitude of vertebrate radiations, however their underlying ecological and evolutionary causes remain poorly understood. Rensch's rule describes one such trend-in which the scaling of sexual size dimorphism (SSD) depends on which sex is larger. Where SSD is male-biased, SSD should scale hyperallometrically, as opposed to hypoallometrically where SSD is female-biased. The evidence for Rensch's rule is mixed, and comes from a small subset of total vertebrate diversity. We conducted the first empirical test of Rensch's rule in sharks, seeking to confirm or refute a long-hypothesied trend. We find that sharks violate Rensch's rule, as the magnitude of SSD increases with body size despite sharks predominantly exhibiting female-biased SSD. This adds to a growing literature of vertebrate clades that appear not to follow Rensch's rule, suggesting the absence of a single, conserved scaling trend for SSD amongst vertebrates. It is likely that selection associated with fecundity results in the "inverse Rensch's rule" observed in sharks, although additional studies will be required to fully reveal the factors underlying SSD variation in this clade.

Genome size variation and evolution during invasive range expansion in an introduced plant.

Plants demonstrate exceptional variation in genome size across species, and their genome sizes can also vary dramatically across individuals and populations within species. This aspect of genetic variation can have consequences for traits and fitness, but few studies attributed genome size differentiation to ecological and evolutionary processes. Biological invasions present particularly useful natural laboratories to infer selective agents that might drive genome size shifts across environments and population histories. Here, we test hypotheses for the evolutionary causes of genome size variation across 14 invading populations of yellow starthistle, Centaurea solstitialis, in California, United States. We use a survey of genome sizes and trait variation to ask: (1) Is variation in genome size associated with developmental trait variation? (2) Are genome sizes smaller toward the leading edge of the expansion, consistent with selection for "colonizer" traits? Or alternatively, does genome size increase toward the leading edge of the expansion, consistent with predicted consequences of founder effects and drift? (3) Finally, are genome sizes smaller at higher elevations, consistent with selection for shorter development times? We found that 2C DNA content varied 1.21-fold among all samples, and was associated with flowering time variation, such that plants with larger genomes reproduced later, with lower lifetime capitula production. Genome sizes increased toward the leading edge of the invasion, but tended to decrease at higher elevations, consistent with genetic drift during range expansion but potentially strong selection for smaller genomes and faster development time at higher elevations. These results demonstrate how genome size variation can contribute to traits directly tied to reproductive success, and how selection and drift can shape that variation. We highlight the influence of genome size on dynamics underlying a rapid range expansion in a highly problematic invasive plant.

Morphology of gustatory organs of a crocodile newt (genus Tylototriton)

The evolutionary causes behind the development of taste discs (TDs), recognized as the only gustatory organs in metamorphosed Batrachia (Caudata and Anura), have yet to be determined. Taste buds (TBs) serve as the gustatory organs in aquatic batrachian larvae, as well as in both larval and adult caecilians (Gymnophiona) inhabiting either aquatic environments or moist terrestrial habitats. We describe the morphology of gustatory organs of adult crocodile newts (Tylototriton cf. verrucosus, Salamandridae, Caudata). Crocodile newts are semi-aquatic and exhibit increased specialization towards an aquatic feeding, distinguishing it from most members of the subfamily Pleurodelinae. Our findings confirm that TDs serve as the gustatory organs in adult T. cf. verrucosus, similarly to many batrachians. We also determined the density and sizes of TDs’ sensory zones on the tongue and palate of T. cf. verrucosus, which differs from Batrachia. In terms of micro-morphology, two types of gustatory cells (GCs) were identified in the gustatory epithelium of T. cf. verrucosus. Our literature analysis suggests that TDs were larger in anurans compared to caudate amphibians, but were also larger in aquatic/semi-aquatic than in terrestrial anurans.

The mechanistic, genetic and evolutionary causes of bird eye colour variation

Birds display a rainbow of eye colours, but this trait has been little studied compared with plumage coloration. Avian eye colour variation occurs at all phylogenetic scales: it can be conserved throughout whole families or vary within one species, yet the evolutionary importance of this eye colour variation is under‐studied. Here, we summarize knowledge of the causes of eye colour variation at three primary levels: mechanistic, genetic and evolutionary. Mechanistically, we show that avian iris pigments include melanin and carotenoids, which also play major roles in plumage colour, as well as purines and pteridines, which are often found as pigments in non‐avian taxa. Genetically, we survey classical breeding studies and recent genomic work on domestic birds that have identified potential ‘eye colour genes’, including one associated with pteridine pigmentation in pigeons. Finally, from an evolutionary standpoint, we present and discuss several hypotheses explaining the adaptive significance of eye colour variation. Many of these hypotheses suggest that bird eye colour plays an important role in intraspecific signalling, particularly as an indicator of age or mate quality, although the importance of eye colour may differ between species and few evolutionary hypotheses have been directly tested. We suggest that future studies of avian eye colour should consider all three levels, including broad‐scale iris pigment analyses across bird species, genome sequencing studies to identify loci associated with eye colour variation, and behavioural experiments and comparative phylogenetic analyses to test adaptive hypotheses. By examining these proximate and ultimate causes of eye colour variation in birds, we hope that our review will encourage future research to understand the ecological and evolutionary significance of this striking avian trait.

Life-History and Ecological Correlates of Egg and Clutch Mass Variation in Sympatric Bird Species at High Altitude.

The variation in egg and clutch mass in sympatric species at high altitudes is poorly understood, and the potential causes of variation are rarely investigated. This study aimed to describe the interspecific variation in avian egg and clutch mass among 22 sympatric bird species at an altitude of 3430 m. Our objective was to reduce potential confounding effects of biotic/abiotic factors and investigated hypotheses concerning allometry, clutch size, parental care, nest predation, and lifespan as possible correlates and explanations for the observed variation. Our findings indicated that both egg and clutch mass evolve with body mass across species. We found that egg mass variation was not explained by clutch size when controlling for allometric effects, which contrasts the "egg mass vs. clutch size trade-off" hypothesis. Additionally, we found that clutch mass was positively associated with parental care (reflected by development period) but negatively associated with predation rate. By substituting egg mass and clutch size into the models, we found that clutch size was significantly correlated with parental care, predation rate, and lifespan, while egg mass was only significantly associated with development period. Overall, these findings support life-history theories suggesting that reduced clutch size or mass is associated with a higher risk of predation, reduced parental care, but longer adult lifespan. Interestingly, our results indicate that clutch size has a greater influence on these factors compared to egg mass. This could be attributed to the fact that smaller clutch sizes result in a more notable decrease in energetic allocation, as they require a reduced effort in terms of offspring production, incubation, and feeding, as opposed to solely reducing egg size. These findings contribute to the growing evidence that life-history and ecological traits correlate with egg and clutch mass variation in sympatric species. However, further research is needed to explore the potential evolutionary causes underlying these patterns.

Piaget’s Paradox: Adaptation, Evolution, and Agency

Piaget’s Behaviour and Evolution (1976) sought to reconcile the view that organismal adaptiveness – in the form of equilibration – could contribute to human behavioural, cognitive, and epistemic evolution with the prevailing evolutionary orthodoxy of the time. He was particularly concerned to demonstrate that human behaviour, cognition, and knowledge acquisition could be drivers of human evolution. Piaget hypothesised constructive role for organisms in evolution was significantly at variance with the prevailing modern synthesis orthodoxy of his time (and ours). He looked to Conrad Hal Waddington’s genetic assimilation as a model for how equilibration could generate evolutionary novelties which become fixed by subsequent evolution. I make two claims. Firstly, that Piaget’s appeal to Waddington fails to reconcile his views of human evolution with the modern synthesis. Secondly, the newly emerging agential conception of evolution, in which the purposive activities of organisms are the principal causes of evolution, offers strong support to Piaget’s model of “organisational” evolution.

The role of conflict in shaping plant biodiversity.

Although intrinsic postzygotic reproductive barriers can play a fundamental role in speciation, their underlying evolutionary causes are widely debated. One hypothesis is that incompatibilities result from genomic conflicts. Here, I synthesize the evidence that conflict generates incompatibilities in plants, thus playing a creative role in plant biodiversity. While much evidence supports a role for conflict in several classes of incompatibility, integrating knowledge of incompatibility alleles with natural history can provide further essential tests. Moreover, comparative work can shed light on the relative importance of conflict in causing incompatibilities, including the extent to which their evolution is repeatable. Together, these approaches can provide independent lines of evidence that conflict causes incompatibilities, cementing its role in plant speciation.

Uterine leiomyomata and keloids fibrosis origins: a mini-review of fibroproliferative diseases.

Diseases such as uterine leiomyomata (fibroids and benign tumors of the uterus) and keloids (raised scars) may share common etiology. Fibroids and keloids can co-occur in individuals, and both are highly heritable, suggesting they may share common genetic risk factors. Fibroproliferative diseases are common and characterized by scarring and overgrowth of connective tissue, impacting multiple organ systems. These conditions both have racial disparities in prevalence, with the highest prevalence observed among individuals of African ancestry. Several fibroproliferative diseases are more severe and common in populations of sub-Saharan Africa. This mini-review aims to provide a broad overview of the current knowledge of the evolutionary origins and causes of fibroproliferative diseases. We also discuss current hypotheses proposing that the increased prevalence of these diseases in African-derived populations is due to the selection for profibrotic alleles that are protective against helminth infections and provide examples from knowledge of uterine fibroid and keloid research.

Long-read genome assemblies for the study of chromosome expansion: Drosophila kikkawai, Drosophila takahashii, Drosophila bipectinata, and Drosophila ananassae.

Flow cytometry estimates of genome sizes among species of Drosophila show a 3-fold variation, ranging from ∼127 Mb in Drosophila mercatorum to ∼400 Mb in Drosophila cyrtoloma. However, the assembled portion of the Muller F element (orthologous to the fourth chromosome in Drosophila melanogaster) shows a nearly 14-fold variation in size, ranging from ∼1.3 Mb to >18 Mb. Here, we present chromosome-level long-read genome assemblies for 4 Drosophila species with expanded F elements ranging in size from 2.3 to 20.5 Mb. Each Muller element is present as a single scaffold in each assembly. These assemblies will enable new insights into the evolutionary causes and consequences of chromosome size expansion.

Comparative genomics reveals insights into anuran genome size evolution

BackgroundAmphibians, particularly anurans, display an enormous variation in genome size. Due to the unavailability of whole genome datasets in the past, the genomic elements and evolutionary causes of anuran genome size variation are poorly understood. To address this, we analyzed whole-genome sequences of 14 anuran species ranging in size from 1.1 to 6.8 Gb. By annotating multiple genomic elements, we investigated the genomic correlates of anuran genome size variation and further examined whether the genome size relates to habitat types.ResultsOur results showed that intron expansions or contraction and Transposable Elements (TEs) diversity do not contribute significantly to genome size variation. However, the recent accumulation of transposable elements (TEs) and the lack of deletion of ancient TEs primarily accounted for the evolution of anuran genome sizes. Our study showed that the abundance and density of simple repeat sequences positively correlate with genome size. Ancestral state reconstruction revealed that genome size exhibits a taxon-specific pattern of evolution, with families Bufonidae and Pipidae experiencing extreme genome expansion and contraction events, respectively. Our result showed no relationship between genome size and habitat types, although large genome-sized species are predominantly found in humid habitats.ConclusionsOverall, our study identified the genomic element and their evolutionary dynamics accounting for anuran genome size variation, thus paving a path to a greater understanding of the size evolution of the genome in amphibians.

Neuroethology in The Age of Gene Editing: New Tools And Novel Insights into The Molecular And Neural Basis of Behavior

Synopsis Fifty years ago, animal models studied in the lab were highly diverse, and biological insights were derived from experiments in many species. However, the pursuit of mechanistic explanations in organismal biology led to a shift in the species most commonly studied. The advent of genetic manipulations and economies of scale promoted the consolidation of research into fewer species (eg, Drosophila melanogaster, Mus musculus, Danio rerio, Caenorhabditis elegans). As a result, the tremendous variety of evolutionary adaptations across species provided insights into ultimate causes of evolution, but their proximate mechanisms have been understudied in recent decades. Within the last decade, developments in genome modifications have enabled functional genetic studies in a wide variety of species. This special issue combines papers derived from a symposium organized at the Society for Integrative and Comparative Biology conference in January 2023 in Austin, Texas. The symposium entitled “Neuroethology in the age of gene editing: New tools and novel insights into the molecular and neural basis of behavior” was convened to catalyze the transfer of knowledge and skills from researchers who have applied genome modification technologies in new model organisms to scientists who would like to bring these approaches to their own research programs. We highlight this work here, and suggest how the future of biological knowledge will be informed by these powerful experiments.