Phenotypic Disparity Research Articles

Convergent evolution in shape in European lineages of gobies.

During their radiation, certain groups of animals evolved significant phenotypic disparity (morphological diversity), enabling them to thrive in diverse environments. Adaptations to the same type of environment can lead to convergent evolution in function and morphology. However, well-documented examples in repeated adaptations of teleost fishes to different habitats, which are not primarily related to trophic specialization, are still scarce. Gobies are a remarkable fish group, exhibiting a great species diversity, morphological variability, and extraordinary ability to colonize very different environments. A variety of lifestyles and body forms evolved also in European lineages of gobies. We conducted two-dimensional geometric morphometric and phylomorphospace analyses in European lineages of gobies and evaluated the extent of convergent evolution in shape associated with adaptation to various habitats. Our analyses revealed the change in shape along the nektonic-cryptobenthic axis, from very slender head and body to stout body and wide head. We showed convergent evolution related to mode of locomotion in the given habitat in four ecological groups: nektonic, hyperbenthic, cryptobenthic and freshwater gobies. Gobies, therefore, emerge as a highly diversified lineage with unique lifestyle variations, offering invaluable insights into filling of ecomorphological space and mechanisms of adaptation to various aquatic environments with distinct locomotion requirements.

Understanding species limits through the formation of phylogeographic lineages.

The outcomes of speciation across organismal dimensions (e.g., ecological, genetic, phenotypic) are often assessed using phylogeographic methods. At one extreme, reproductively isolated lineages represent easily delimitable species differing in many or all dimensions, and at the other, geographically distinct genetic segments introgress across broad environmental gradients with limited phenotypic disparity. In the ambiguous gray zone of speciation, where lineages are genetically delimitable but still interacting ecologically, it is expected that these lineages represent species in the context of ontology and the evolutionary species concept when they are maintained over time with geographically well-defined hybrid zones, particularly at the intersection of distinct environments. As a result, genetic structure is correlated with environmental differences and not space alone, and a subset of genes fail to introgress across these zones as underlying genomic differences accumulate. We present a set of tests that synthesize species delimitation with the speciation process. We can thereby assess historical demographics and diversification processes while understanding how lineages are maintained through space and time by exploring spatial and genome clines, genotype-environment interactions, and genome scans for selected loci. Employing these tests in eight lineage-pairs of snakes in North America, we show that six pairs represent 12 "good" species and that two pairs represent local adaptation and regional population structure. The distinct species pairs all have the signature of divergence before or near the mid-Pleistocene, often with low migration, stable hybrid zones of varying size, and a subset of loci showing selection on alleles at the hybrid zone corresponding to transitions between distinct ecoregions. Locally adapted populations are younger, exhibit higher migration, and less ecological differentiation. Our results demonstrate that interacting lineages can be delimited using phylogeographic and population genetic methods that properly integrate spatial, temporal, and environmental data.

Does Phenotypic Integration Promote Convergent Evolution?

Phenotypic integration is often perceived as being able to produce convergent evolution in the absence of selection, but specific mechanisms for this process are lacking and a connection has never been empirically demonstrated. A new model of the effect of integration on convergence provides such a mechanism, along with other predictions about the influence of integration on evolutionary patterns. I use simulations and data from three empirical systems-turtle shells, characiform fishes, and squirrel mandibles-to investigate the degree to which evolutionary integration is associated with high levels of convergent evolution. Levels of integration were varied in Brownian motion simulations and the resulting amounts of stochastic convergent evolution were quantified. Each empirical system was divided into modules, and the strength of integration, average amount of convergence, phenotypic disparity, and rate of evolution in each module was measured. Results from the simulations and from all three empirical systems converge on a common result: higher levels of phenotypic integration are indeed associated with higher levels of convergence. This is despite a lack of consistent association between the strength of phenotypic integration and evolutionary rate or disparity. The results here are only correlational. Further studies which more closely examine the influence of within-population drivers of evolutionary integration-for example, genetic or developmental integration-on convergence are required before it is possible to definitively establish when phenotypic integration can cause evolutionary convergence. Until then, however, the results of this study strongly suggest that phenotypic integration will often promote convergent evolution.

Unveiling the Mainland vs. Insular Variability of the Eumerus barbarus Species Group (Diptera: Syrphidae) in the Western Mediterranean Basin.

Comprising nearly 300 described species, Eumerus Meigen, 1822, is one of the most speciose syrphid genera worldwide, and its taxonomic diversity is remarkable in the Mediterranean basin. The Eumerus barbarus (Coquebert, 1804) group consists of four species in the western Mediterranean. Although the phenotypic variability of this species group has been commented on in previous studies, it has never been contrasted with molecular data. In the present work, the morphological variation found in 300+ specimens of this species group from the western Mediterranean is explored and tested against the COI mitochondrial DNA (mtDNA). The highest phenotypic disparity was found in E. barbarus and Eumerus sulcitibius Rondani 1868. The integrative approach has not revealed cryptic diversity within the species E. barbarus but in E. sulcitibius. As a result, a new species close to E. sulcitibius was discovered, Eumerus sardus Aguado-Aranda, Ricarte & Hauser sp. n., from Sardinia, Italy. The new insular species is here described, illustrated, and discussed. A total of twenty-three haplotypes of COI mtDNA were identified amongst the analyzed Mediterranean specimens of E. barbarus, whereas two and five haplotypes were distinguished in the Iberian specimens of E. sulcitibius and Eumerus gibbosus van Steenis, Hauser & van Zuijen, 2017, respectively. Moreover, the first known barcodes of E. gibbosus and Eumerus schmideggeri van Steenis, Hauser & van Zuijen, 2017 were obtained, and the distribution ranges of all species are mapped. An updated dichotomous key to the males of the E. barbarus group from the western Mediterranean is provided.

Considering Decoupled Phenotypic Diversification Between Ontogenetic Phases in Macroevolution: An Example Using Triggerfishes (Balistidae).

Across the Tree of Life, most studies of phenotypic disparity and diversification have been restricted to adult organisms. However, many lineages have distinct ontogenetic phases that differ from their adult forms in morphology and ecology. Focusing disproportionately on the evolution of adult forms unnecessarily hinders our understanding of the pressures shaping evolution over time. Non-adult disparity patterns are particularly important to consider for coastal ray-finned fishes, which can have juvenile phases with distinct phenotypes. These juvenile forms are often associated with sheltered nursery environments, with phenotypic shifts between adults and juvenile stages that are readily apparent in locomotor morphology. Whether this ontogenetic variation in locomotor morphology reflects a decoupling of diversification dynamics between life stages remains unknown. Here we investigate the evolutionary dynamics of locomotor morphology between adult and juvenile triggerfishes. We integrate a time-calibrated phylogenetic framework with geometric morphometric approaches and measurement data of fin aspect ratio and incidence, and reveal a mismatch between morphospace occupancy, the evolution of morphological disparity, and the tempo of trait evolution between life stages. Collectively, our results illuminate how the heterogeneity of morpho-functional adaptations can decouple the mode and tempo of morphological diversification between ontogenetic stages.

Phylogenetic, morphological and niche differentiation unveil new species limits for the big brown bat (Eptesicus fuscus).

Phylogeographic accounts of mammals across fragmented landscapes show high levels of genetic, morphological and ecological variation. The big brown bat (Eptesicus fuscus) widely spans mainland landmasses from Canada to Ecuador and Colombia, and the insular Caribbean through The Bahamas and Greater and Lesser Antilles. Given the distribution of E. fuscus, we hypothesized that insular lineages could represent a different species aided by isolation. We assessed species limits by capitalizing on available mitochondrial and genomic data. Novel morphological and spatial datasets were produced to examine limits phenotypically and whether ecological niches could be associated with differences between groups. Phylogenetics strongly supported the Caribbean as unique compared to the mainland. Genomic data indicated high levels of genetic structure within the Caribbean and no detectable admixture of the Caribbean with continental lineages. Similarly, the Caribbean group shows high phenotypic disparity, and niche models revealed differences in habitat suitability between groups, concordant with the phylogenetic results. This study uncovered signals of divergence supporting the Caribbean clade of E. fuscus as unique through an integrative framework. We endorse re-evaluating the taxonomic status of Caribbean big brown bats as Eptesicus dutertreus. This recognition can help promote local conservation plans for insular lineages of big brown bats.

Evolution of phenotypic disparity in the plant kingdom.

The plant kingdom exhibits diverse bodyplans, from single-celled algae to complex multicellular land plants, but it is unclear how this phenotypic disparity was achieved. Here we show that the living divisions comprise discrete clusters within morphospace, separated largely by reproductive innovations, the extinction of evolutionary intermediates and lineage-specific evolution. Phenotypic complexity correlates not with disparity but with ploidy history, reflecting the role of genome duplication in plant macroevolution. Overall, the plant kingdom exhibits a pattern of episodically increasing disparity throughout its evolutionary history that mirrors the evolutionary floras and reflects ecological expansion facilitated by reproductive innovations. This pattern also parallels that seen in the animal and fungal kingdoms, suggesting a general pattern for the evolution of multicellular bodyplans.

Untangling the evolution of soldier beetles (Coleoptera: Cantharidae) and the evaluation of the morphological phylogenetic signal in a soft-bodied elateroid lineage.

This study addresses the long-standing uncertainty about the internal classification of soldier beetles (Elateroidea: Cantharidae). Four datasets were compiled and analysed: 66 genes for 14 terminals, 15 mtDNA genes for 79 terminals, one mtDNA and two rRNA genes for 217 terminals, and barcodes for 576 terminals. Based on congruent topologies, Chauliognathinae is proposed as a sister to the remaining Cantharidae, followed by the redefined Malthininae (including Tytthonyxini), the paraphyletic "dysmorphocerine" lineages (Dysmorphocerinae sensu stricto and Heteromastiginae subfam. nov.), and Silinae + Cantharinae as a terminal clade. The present phylogeny supersedes earlier morphology and short-fragment molecular hypotheses that have not converged on a consensus. Few morphological characters corroborate the DNA-based relationships (see the adults and larval keys). However, morphology-based hypotheses have relied on a few informative characters, and no evidence strongly rejects the preferred molecular topology. The interpretation of morphological characters and uncertain polarity resulting from the high phenotypic disparity of Elateroidea are discussed in detail. The dated phylogeny hypothesizes the earliest split within the Cantharidae in the Berriasian stage (Early Cretaceous, ~141 Myr) and the diversification of most extant subfamilies and tribes already in the Late Cretaceous. The most diverse subfamily, Cantharinae, represents a delayed radiation that started during the Eocene climatic optimum, 55.5 Myr. The late origin of Cantharinae questions the classification of Cretaceous Cantharidae as members of Cantharinae. Instead, the results suggest their deeper rooting after separating from dysmorphocerine lineages and before the node between Cantharinae and Silinae.

The environment: A vector of phenotypic disparity during the settlement phase of coral reef fishes

In coral reef fish, the transition from pelagic larvae to reef-associated juveniles is a complete metamorphosis in which coordinated physiological, morphological, and behavioural changes occur, enabling the fish to settle and grow in coastal habitats and then recruit into the adult population. Environmental factors can modulate different aspects of metamorphosis such as the timing of its initiation, its duration, and the coordination of the morphological changes. Here, we raised the coral-reef-dwelling convict surgeonfish, Acanthurus triostegus, in different types of habitats during the post-settlement period. The selected habitats, whether natural (beach rock, mangrove, and sand beach habitats where A. triostegus settle naturally), or experimental (pelagic ocean and oxygen depleted ‘dead’ zone) were characterized by their substrate type, fish community composition, and physico-chemical profile. By using landmark-based geometric morphometric methods, we compared growth, body shape changes, and quantified phenotypic disparity levels among and within the different habitats. The results showed that fish raised in mangrove grew faster than in the other habitats and, most importantly that different habitats lead to variations in the rate and the nature of shape transformation. The ontogenetic trajectories defined in the shape space differed across habitats in terms of length and direction. A peak of shape disparity was observed for the natural habitats at three days post settlement when compared to fish reared in dead zone or oceanic environment. Overall, these results suggest that environmental diversity could generate developmental plasticity, ultimately producing phenotypic disparity that may allow the acclimation of fish to their local environment.

Fossilization can mislead analyses of phenotypic disparity.

Analyses of morphological disparity can incorporate living and fossil taxa to facilitate the exploration of how phenotypic variation changes through time. However, taphonomic processes introduce non-random patterns of data loss in fossil data and their impact on perceptions of disparity is unclear. To address this, we characterize how measures of disparity change when simulated and empirical data are degraded through random and structured data loss. We demonstrate that both types of data loss can distort the disparity of clades, and that the magnitude and direction of these changes varies between the most commonly employed distance metrics and disparity indices. The inclusion of extant taxa and exceptionally preserved fossils mitigates these distortions and clarifies the full extent of the data lost, most of which would otherwise go uncharacterized. This facilitates the use of ancestral state estimation and evolutionary simulations to further control for the effects of data loss. Where the addition of such reference taxa is not possible, we urge caution in the extrapolation of general patterns in disparity from datasets that characterize subsets of phenotype, which may represent no more than the traits that they sample.

Disentangling Mechanical and Sensory Modules in the Radiation of Noctilionoid Bats.

AbstractWith diverse mechanical and sensory functions, the vertebrate cranium is a complex anatomical structure whose shifts between modularity and integration, especially in mechanical function, have been implicated in adaptive diversification. Yet how mechanical and sensory systems and their functions coevolve, as well as how their interrelationship contributes to phenotypic disparity, remain largely unexplored. To examine the modularity, integration, and evolutionary rates of sensory and mechanical structures within the head, we analyzed hard and soft tissue scans from ecologically diverse bats in the superfamily Noctilionoidea, a clade that ranges from insectivores and carnivores to frugivores and nectarivores. We identified eight regions that evolved in a coordinated fashion, thus recognizable as evolutionary modules: five associated with bite force and three linked to olfactory, visual, and auditory systems. Interrelationships among these modules differ between Neotropical leaf-nosed bats (family Phyllostomidae) and other noctilionoids. Consistent with the hypothesis that dietary transitions begin with changes in the capacity to detect novel food items followed by adaptations to process them, peak rates of sensory module evolution predate those of some mechanical modules. We propose that the coevolution of structures influencing bite force, olfaction, vision, and hearing constituted a structural opportunity that allowed the phyllostomid ancestor to take advantage of existing ecological opportunities and contributed to the clade's remarkable radiation.

Hydraulic tradeoffs underlie enhanced performance of polyploid trees under soil water deficit.

The relationships between aerial organ morpho-anatomy of woody polyploid plants with their functional hydraulics under water stress remain largely understudied. We evaluated growth-associated traits, aerial organ xylem anatomy, and physiological parameters of diploid, triploid, and tetraploid genotypes of atemoyas (Annona cherimola × Annona squamosa), which belong to the woody perennial genus Annona (Annonaceae), testing their performance under long-term soil water reduction. The contrasting phenotypes of vigorous triploids and dwarf tetraploids consistently showed stomatal size-density tradeoff. The vessel elements in aerial organs were ∼1.5 times wider in polyploids compared with diploids, and triploids displayed the lowest vessel density. Plant hydraulic conductance was higher in well-irrigated diploids while their tolerance to drought was lower. The phenotypic disparity of atemoya polyploids associated with contrasting leaf and stem xylem porosity traits that coordinate to regulate water balances between the trees and the belowground and aboveground environments. Polyploid trees displayed better performance under soil water scarcity, and consequently, could present more sustainable agricultural and forestry genotypes to cope with water stress.

Intratumor heterogeneity is associated with less CD8+ T cell infiltration and worse survival in patients with small cell lung cancer.

Small cell lung cancer (SCLC) is a heterogeneous malignancy with genetic and phenotypic disparity. However, the association between intratumor heterogeneity (ITH) and immunological features as well as the impact of ITH on prognosis has never been explored in SCLC. Hence, we investigated the relationship between ITH and their immunological features and explored the effect of ITH on overall survival (OS) in patients with SCLC. Programmed cell death-ligand 1 (PD-L1), CD8+ cell infiltration was calculated through immunohistochemical staining and tumor mutational burden (TMB), tumor neoantigen burden (TNB), and ITH levels via whole-exome sequencing (WES). Significant correlation was not found in ITH versus TMB, ITH versus TNB (P = 0.1821, P = 0.0612). No significant variation in ITH was found between negative PD-L1 SCLC patients and positive PD-L1 ones (P = 0.0610 for TPS, P = 0.6347 for CPS). Interestingly, we demonstrated the negative correlation between CD8+ T cell infiltration and ITH (P = 0.0220). More importantly, significant OS benefit was detected in ITH-low SCLC patients in comparison with ITH-high ones (P = 0.0049). ITH was an independent prognostic factor on OS with clinicopathological variables adjusted (HR, 2.044; 95% CI 1.190-3.512; P = 0.010). We also demonstrated significantly different driver genes and CNV between ITH-low and ITH-high SCLC. Our work pointed the negative association of ITH with CD8+ T cell infiltration and suggested ITH as a potential predictor of OS in SCLC, putting forward a direction for more precise and individualized therapeutic strategies for SCLC.

Genome-wide screening for genetic variants in polyadenylation signal (PAS) sites in mouse selection lines for fatness and leanness

Alternative polyadenylation (APA) determines mRNA stability, localisation, translation and protein function. Several diseases, including obesity, have been linked to APA. Studies have shown that single nucleotide polymorphisms in polyadenylation signals (PAS-SNPs) can influence APA and affect phenotype and disease susceptibility. However, these studies focussed on associations between single PAS-SNP alleles with very large effects and phenotype. Therefore, we performed a genome-wide screening for PAS-SNPs in the polygenic mouse selection lines for fatness and leanness by whole-genome sequencing. The genetic variants identified in the two lines were overlapped with locations of PAS sites obtained from the PolyASite 2.0 database. Expression data for selected genes were extracted from the microarray expression experiment performed on multiple tissue samples. In total, 682 PAS-SNPs were identified within 583 genes involved in various biological processes, including transport, protein modifications and degradation, cell adhesion and immune response. Moreover, 63 of the 583 orthologous genes in human have been previously associated with human diseases, such as nervous system and physical disorders, and immune, endocrine, and metabolic diseases. In both lines, PAS-SNPs have also been identified in genes broadly involved in APA, such as Polr2c, Eif3e and Ints11. Five PAS-SNPs within 5 genes (Car, Col4a1, Itga7, Lat, Nmnat1) were prioritised as potential functional variants and could contribute to the phenotypic disparity between the two selection lines. The developed PAS-SNPs catalogue presents a key resource for planning functional studies to uncover the role of PAS-SNPs in APA, disease susceptibility and fat deposition.

A comprehensive review on phytochemistry, molecular pharmacology, clinical and translational outfit of Ocimum sanctum L.

Ocimum sanctum L. a benevolent herb has been integrated into the traditional medicine practice from ancient times. The phytochemical analysis signifies the presence of polyphenols, flavonoids, terpenoids, amino acids, unsaturated fatty acids, and essential elements (vitamins and minerals). Polyphenols and flavonoids are the major essential components present in the various form of tulsi extract and responsible for different pharmacological activities such as anticancer, antioxidant, antimicrobial, anti-inflammation, etc. These activities were mediated through altering the functionality associated with the nF-κβ, ERK, p38, and MPK pathways. Further, the antimicrobial activity is amplified by the presence of unsaturated fatty acids such as linolic acid and linoleic acid which manipulate the membrane integrity of microbial. The molecular mechanism for such activity is mediated through destabilization of the microbial membrane by interfering with the electron transport chain and oxidative phosphorylation process. An extensive literature survey was carried out through various scientific search engine such as PubMed, Google scholar, science Direct, Medline, Embase, Cochrane library, and Indian medical databases. Diversified phenolic and flavonoid phytoconstituents of tulsi are responsible for anti-oxidant, antimicrobial, hypolipidemic, immunomodulatory, hepatoprotective, neuroprotective, antistress, antidiabetic, antiulcer, anticancer, anti-inflamatory, etc. Further, therapeutic potency of tulsi reflects in clinical trail reports provide satisfactory results with negligible adverse effects, which might be emerge as a green medicine to lessen the global burden of microbial, inflammation, metabolic associated disorders, etc. However, alteration in the composition and variation in the percentage yield of secondary metabolites due to phenotypic and genotypic disparity are the critical challenges that need to address in future. • From ancient times, Ocimum sanctum L . commonly known as holy basil or tulsi is considered one of the core pillars of the traditional practice of herbal medicine. • Presences of therapeutically active polyphenols and flavonoid enriched phytoconstituents are responsible for potent antioxidant, anticancer, anti-inflammatory, antimicrobial activity, etc. • Encouraging preclinical results brings 11 clinical trials on exploring the antimicrobial activity in the maintenance of oral hygiene, metabolic associated, inflammatory mediated disorders, neuroprotection, antistress activity, etc. • Translationally major portions of the osmium-based formulations are intended for the treatment of cold and cough (29.1%) and food supplement/functional food (14.5%) which remains the witness for its strong antimicrobial, antimicrobial, and anti-inflammatory activity and balance composition of macro and micronutrient.

Convergence without divergence in North American red-flowering Silene.

Combinations of correlated floral traits have arisen repeatedly across angiosperms through convergent evolution in response to pollinator selection to optimize reproduction. While some plant groups exhibit very distinct combinations of traits adapted to specific pollinators (so-called pollination syndromes), others do not. Determining how floral traits diverge across clades and whether floral traits show predictable correlations in diverse groups of flowering plants is key to determining the extent to which pollinator-mediated selection drives diversification. The North American Silene section Physolychnis is an ideal group to investigate patterns of floral evolution because it is characterized by the evolution of novel red floral color, extensive floral morphological variation, polyploidy, and exposure to a novel group of pollinators (hummingbirds). We test for correlated patterns of trait evolution that would be consistent with convergent responses to selection in the key floral traits of color and morphology. We also consider both the role of phylogenic distance and geographic overlap in explaining patterns of floral trait variation. Inconsistent with phenotypically divergent pollination syndromes, we find very little clustering of North American Silene into distinct floral morphospace. We also find little evidence that phylogenetic history or geographic overlap explains patterns of floral diversity in this group. White- and pink-flowering species show extensive phenotypic diversity but are entirely overlapping in morphological variation. However, red-flowering species have much less phenotypic disparity and cluster tightly in floral morphospace. We find that red-flowering species have evolved floral traits that align with a traditional hummingbird syndrome, but that these trait values overlap with several white and pink species as well. Our findings support the hypothesis that convergent evolution does not always proceed through comparative phenotypic divergence, but possibly through sorting of standing ancestral variation.

Evolution of fungal phenotypic disparity.

Organismal-grade multicellularity has been achieved only in animals, plants and fungi. All three kingdoms manifest phenotypically disparate body plans but their evolution has only been considered in detail for animals. Here we tested the general relevance of hypotheses on the evolutionary assembly of animal body plans by characterizing the evolution of fungal phenotypic variety (disparity). The distribution of living fungal form is defined by four distinct morphotypes: flagellated; zygomycetous; sac-bearing; and club-bearing. The discontinuity between morphotypes is a consequence of extinction, indicating that a complete record of fungal disparity would present a more homogeneous distribution of form. Fungal disparity expands episodically through time, punctuated by a sharp increase associated with the emergence of multicellular body plans. Simulations show these temporal trends to be non-random and at least partially shaped by hierarchical contingency. These trends are decoupled from changes in gene number, genome size and taxonomic diversity. Only differences in organismal complexity, characterized as the number of traits that constitute an organism, exhibit a meaningful relationship with fungal disparity. Both animals and fungi exhibit episodic increases in disparity through time, resulting in distributions of form made discontinuous by extinction. These congruences suggest a common mode of multicellular body plan evolution.

Characterizing phenotypic diversity of trehalose biosynthesis mutants in multiple wild strains of Saccharomyces cerevisiae.

In the yeast Saccharomyces cerevisiae, trehalose-6-phospahte synthase (Tps1) and trehalose-6-phosphate phosphatase (Tps2) are the main proteins catalyzing intracellular trehalose production. In addition to Tps1 and Tps2, 2 putative regulatory proteins with less clearly defined roles also appear to be involved with trehalose production, Tps3 and Tsl1. While this pathway has been extensively studied in laboratory strains of S. cerevisiae, we sought to examine the phenotypic consequences of disrupting these genes in wild strains. Here we deleted the TPS1, TPS2, TPS3, and TSL1 genes in 4 wild strains and 1 laboratory strain for comparison. Although some tested phenotypes were not shared between all strains, deletion of TPS1 abolished intracellular trehalose, caused inability to grow on fermentable carbon sources and resulted in severe sporulation deficiency for all 5 strains. After examining tps1 mutant strains expressing catalytically inactive variants of Tps1, our results indicate that Tps1, independent of trehalose production, is a key component for yeast survival in response to heat stress, for regulating sporulation, and growth on fermentable sugars. All tps2Δ mutants exhibited growth impairment on nonfermentable carbon sources, whereas variations were observed in trehalose synthesis, thermosensitivity and sporulation efficiency. tps3Δ and tsl1Δ mutants exhibited mild or no phenotypic disparity from their isogenic wild type although double mutants tps3Δ tsl1Δ decreased the amount of intracellular trehalose production in all 5 strains by 17-45%. Altogether, we evaluated, confirmed, and expanded the phenotypic characteristics associated trehalose biosynthesis mutants. We also identified natural phenotypic variants in multiple strains that could be used to genetically dissect the basis of these traits and then develop mechanistic models connecting trehalose metabolism to diverse cellular processes.

Bridging macroecology and macroevolution in the radiation of sigmodontine rodents.

Investigations of phenotypic disparity across geography often ignore macroevolutionary processes. As a corollary, the random null expectations to which disparity is compared and interpreted may be unrealistic. We tackle this issue by representing, in geographical space, distinct processes of phenotypic evolution underlying ecological disparity. Under divergent natural selection, assemblages in a given region should have empirical disparity higher than expected under an evolutionarily oriented null model, whereas the opposite may indicate constraints on phenotypic evolution. We gathered phylogenies, biogeographic distributions, and data on the skull morphology of sigmodontine rodents to discover which regions of the Neotropics were more influenced by divergent, neutral, or constrained phenotypic evolution. We found that regions with higher disparity than expected by the evolutionary-oriented null model, in terms of both size and shape, were concentrated in the Atlantic Forest, suggesting a larger role for divergent natural selection there. Phenotypic disparity in the rest of South America, mainly the Amazon basin, northeastern Brazil, and Southern Andes, was constrained-lower than predicted by the evolutionary model. We also demonstrated equivalence between the disparity produced by randomization-based null models and constrained-evolution null models. Therefore, including evolutionary simulations into the null modeling framework used in ecophylogenetics can strengthen inferences on the processes underlying phenotypic evolution.

Fast Likelihood Calculations for Automatic Identification of Macroevolutionary Rate Heterogeneity in Continuous and Discrete Traits.

Understanding phenotypic disparity across the tree of life requires identifying where and when evolutionary rates change on phylogeny. A primary methodological challenge in macroevolution is therefore to develop methods for accurate inference of among-lineage variation in rates of phenotypic evolution. Here, we describe a method for inferring among-lineage evolutionary rate heterogeneity in both continuous and discrete traits. The method assumes that the present-day distribution of a trait is shaped by a variable-rate process arising from a mixture of constant-rate processes and uses a single-pass tree traversal algorithm to estimate branch-specific evolutionary rates. By employing dynamic programming optimization techniques and approximate maximum likelihood estimators where appropriate, our method permits rapid exploration of the tempo and mode of phenotypic evolution. Simulations indicate that the method reconstructs rates of trait evolution with high accuracy. Application of the method to data sets on squamate reptile reproduction and turtle body size recovers patterns of rate heterogeneity identified by previous studies but with computational costs reduced by many orders of magnitude. Our results expand the set of tools available for detecting macroevolutionary rate heterogeneity and point to the utility of fast, approximate methods for studying large-scale biodiversity dynamics. [Brownian motion; continuous characters; discrete characters; macroevolution; Markov process; rate heterogeneity.].