Development Of Control Research Articles

Functional packaging of seeds.

SummaryThe encapsulation of seeds in hard coats and fruit walls (pericarp layers) fulfils protective and dispersal functions in many plant families. In angiosperms, packaging structures possess a remarkable range of different morphologies and functionalities, as illustrated by thermo and hygro‐responsive seed pods and appendages, as well as mechanically strong and water‐impermeable shells. Key to these different functionalities are characteristic structural arrangements and chemical modifications of the underlying sclerenchymatous tissues. Although many ecological aspects of hard seed encapsulation have been well documented, a detailed understanding of the relationship between tissue structure and function only recently started to emerge, especially in the context of environmentally driven fruit opening and seed dispersal (responsive encapsulations) and the outstanding durability of some seed coats and indehiscent fruits (static encapsulations). In this review, we focus on the tissue properties of these two systems, with particular consideration of water interactions, mechanical resistance, and force generation. Common principles, as well as unique adaptations, are discussed in different plant species. Understanding how plants integrate a broad range of functions and properties for seed protection during storage and dispersal plays a central role for seed conservation, population dynamics, and plant‐based material developments.

Non-specific phospholipases C2 and C6 redundantly function in pollen tube growth via triacylglycerol production in Arabidopsis.

Non-specific phospholipase Cs (NPCs) are responsible for membrane lipid remodeling that involves hydrolysis of the polar head group of membrane phospholipids. Arabidopsis NPC2 and NPC6 are essential in gametogenesis, but their underlying role in the lipid remodeling remains elusive. Here, we show that these NPCs are required for triacylglycerol (TAG) production in pollen tube growth. NPC2 and NPC6 are highly expressed in developing pollen tubes and are localized at the endoplasmic reticulum. Mutants of NPC2 and NPC6 showed reduced rate of pollen germination, length of pollen tube and amount of lipid droplets (LDs). Overexpression of NPC2 or NPC6 induced LD accumulation, which suggests that these NPCs are involved in LD production. Furthermore, mutants defective in the biosynthesis of TAG, a major component of LDs, showed defective pollen tube growth. These results suggest that NPC2 and NPC6 are essential in gametogenesis for a role in hydrolyzing phospholipids and producing TAG required for pollen tube growth. Thus, lipid remodeling from phospholipids to TAG during pollen tube growth represents an emerging role for the NPC family in plant developmental control.

Carnivoran intraspecific tooth-size variation shows heterogeneity along the tooth row and among species

Abstract Developing morphological diagnoses for fossil mammals requires an understanding of intraspecific variation in the anatomical elements under study. Dental traits along with tooth size can be informative of taxonomic identify for extinct species. However, it is unclear what selective or developmental processes are responsible for documented patterns in tooth-size variation making application to the fossil record difficult. We assessed combined species tooth-type variation and intraspecific tooth-size variation for 19 species to evaluate whether developmental controls or occlusion-driven functional demands influence carnivoran tooth-size variation. We also estimated phylogenetic signal for the coefficient of variation (CV). Combined species tooth-size variation separated by tooth type shows that canines are more variable than molars and lower premolars. We found intraspecific tooth-size variation patterns differ between species. However, comparisons of the CVs did not support the hypotheses that developmental controls or functional demands of occlusion constrain size variation in mammal teeth. Our results suggest that a combination of factors influence carnivoran tooth-size variation, such as differences in ontogeny, diet, sexual dimorphism, and evolutionary history. Patterns of carnivoran intraspecific tooth-size variation suggest a better understanding of dental size variation in extant species is essential for accurate morphological studies of fossil taxa.

Sequential changes in the regulatory mechanism of carbohydrate digestion in larvae of the silkworm, Bombyx mori.

Nutritional signals strictly control post-embryonic development in insects. Dietary carbohydrates are hydrolyzed to monosaccharides in the gut and then transported into the hemolymph. These monosaccharides in hemolymph are rapidly taken up by tissues and utilized in glycolysis, the pentose phosphate shunt, and glycogen or trehalose synthesis. These metabolic pathways are essential for nutrient metabolism; therefore, the control of carbohydrate digestion is indispensable for maintaining energy supply during development. Carbohydrate digestion was believed to be controlled by dietary mechanisms. We previously reported that hormonal and developmental controls participate in the regulation of carbohydrate digestion during larval-pupal metamorphosis. However, it is unclear whether this regulatory mechanism also works during larval-larval molting and inter-molt feeding period. Here, we show that control mechanisms of the carbohydrate digestion show sequential changes that are controlled by different mechanisms. In the penultimate larval instar, carbohydrate hydrolysis activity changed depending on developmental progress and dietary state. Maltose- and sucrose-hydrolysis activity were suppressed by ecdysteroid, an insect steroid hormone. During the inter-molt feeding period, carbohydrate hydrolysis activities were grouped as either nutrient-sensitive or nutrient-insensitive. Although the activity in both groups was suppressed by ecdysteroid, this hormonal regulatory machinery remains in an "off-state" because ecdysteroid is scarce during the feeding period, suggesting that the carbohydrate digestion system is exclusively regulated by the dietary state during inter-molt feeding period.

The skin microbiome of Xenopus laevis and the effects of husbandry conditions

BackgroundHistorically the main source of laboratory Xenopus laevis was the environment. The increase in genetically altered animals and evolving governmental constraints around using wild-caught animals for research has led to the establishment of resource centres that supply animals and reagents worldwide, such as the European Xenopus Resource Centre. In the last decade, centres were encouraged to keep animals in a “low microbial load” or “clean” state, where embryos are surface sterilized before entering the housing system; instead of the conventional, “standard” conditions where frogs and embryos are kept without prior surface treatment. Despite Xenopus laevis having been kept in captivity for almost a century, surprisingly little is known about the frogs as a holobiont and how changing the microbiome may affect resistance to disease. This study examines how the different treatment conditions, “clean” and “standard” husbandry in recirculating housing, affects the skin microbiome of tadpoles and female adults. This is particularly important when considering the potential for poor welfare caused by a change in husbandry method as animals move from resource centres to smaller research colonies.ResultsWe found strong evidence for developmental control of the surface microbiome on Xenopus laevis; adults had extremely similar microbial communities independent of their housing, while both tadpole and environmental microbiome communities were less resilient and showed greater diversity.ConclusionsOur findings suggest that the adult Xenopus laevis microbiome is controlled and selected by the host. This indicates that the surface microbiome of adult Xenopus laevis is stable and defined independently of the environment in which it is housed, suggesting that the use of clean husbandry conditions poses little risk to the skin microbiome when transferring adult frogs to research laboratories. This will have important implications for frog health applicable to Xenopus laevis research centres throughout the world.

Genome-Wide Characterization of HSP90 Gene Family in Cucumber and Their Potential Roles in Response to Abiotic and Biotic Stresses.

Heat shock protein 90 (HSP90) possesses critical functions in plant developmental control and defense reactions. The HSP90 gene family has been studied in various plant species. However, the HSP90 gene family in cucumber has not been characterized in detail. In this study, a total of six HSP90 genes were identified from the cucumber genome, which were distributed to five chromosomes. Phylogenetic analysis divided the cucumber HSP90 genes into two groups. The structural characteristics of cucumber HSP90 members in the same group were similar but varied among different groups. Synteny analysis showed that only one cucumber HSP90 gene, Csa1G569290, was conservative, which was not collinear with any HSP90 gene in Arabidopsis and rice. The other five cucumber HSP90 genes were collinear with five Arabidopsis HSP90 genes and six rice HSP90 genes. Only one pair of paralogous genes in the cucumber HSP90 gene family, namely one pair of tandem duplication genes (Csa1G569270/Csa1G569290), was detected. The promoter analysis showed that the promoters of cucumber HSP90 genes contained hormone, stress, and development-related cis-elements. Tissue-specific expression analysis revealed that only one cucumber HSP90 gene Csa3G183950 was highly expressed in tendril but low or not expressed in other tissues, while the other five HSP90 genes were expressed in all tissues. Furthermore, the expression levels of cucumber HSP90 genes were differentially induced by temperature and photoperiod, gibberellin (GA), downy mildew, and powdery mildew stimuli. Two cucumber HSP90 genes, Csa1G569270 and Csa1G569290, were both differentially expressed in response to abiotic and biotic stresses, which means that these two HSP90 genes play important roles in the process of cucumber growth and development. These findings improve our understanding of cucumber HSP90 family genes and provide preliminary information for further studies of cucumber HSP90 gene functions in plant growth and development.

From environmental sensing to developmental control: cognitive evolution in dictyostelid social amoebas.

Dictyostelid social amoebas respond to starvation by self-organizing into multicellular slugs that migrate towards light to construct spore-bearing structures. These behaviours depend on excitable networks that enable amoebas to produce propagating waves of the chemoattractant cAMP, and to respond by directional movement. cAMP additionally regulates cell differentiation throughout development, with differentiation and cell movement being coordinated by interaction of the stalk inducer c-di-GMP with the adenylate cyclase that generates cAMP oscillations. Evolutionary studies indicate how the manifold roles of cAMP in multicellular development evolved from a role as intermediate for starvation-induced encystation in the unicellular ancestor. A merger of this stress response with the chemotaxis excitable networks yielded the developmental complexity and cognitive capabilities of extant Dictyostelia.This article is part of the theme issue ‘Basal cognition: conceptual tools and the view from the single cell’.

Application of hydrodynamic models for designing structural measures for river flood mitigation: the case of Kulfo River in southern Ethiopia

Flood is one of life-threatening events in different parts of Ethiopia. The causes of flood might vary from place to place, for instance, rates of deforestation, agricultural expansion, urbanization, wetland drainage, climate change, siltation of river bed, and several other types of land use change might be the cause for flood in different rivers banks. This study aims to assess, investigate, and design suitable river training works on lower Kulfo river reach. The study reach has been seriously affected by extreme floods due to the above reasons. For minimizing the loss due to flood, and to use the advantage of flood for different developmental activities various flood control measures should be adopted. The flood control measures which should more correctly be termed as “flood management” can be planed either through structural engineering measures or non-structural measures. Structural measures comprise retarding structures which store flood water, channel improvements which increase flood-carrying capacity of the river, embankments, and levees which keep the waterway from flood-prone area, detention basin which retards and absorbs most of the floodwater. Within the identified 6 km reach, field investigation including secondary data collection has been done to predict the flood extent using 1D hydrodynamic model, HECRAS and HEC Geo RAS. Estimated flood depth and extent helped us in fixing the dimension of different river training structures selected. The modelling result indicates a maximum channel bed flood depth of 4.3 m and flood plain flood depth 2.3 m obtained using a 100-year return flow. Analysis of soil samples indicates that the lower reach of Kulfo river is gravel and sand dominated meandering river, with estimated scour depth up to 3.41 m along the river course. Levees have been designed in conjunction with Groynes to protect the Upstream farm located at the prison and upper part of the Limat households. Frequent floods happening near both bridges shall be reduced by using Guide banks without influencing the bridges and diversion structures. Consideration is given for the ecosystem to stay in equilibrium, by providing suitable outer slopes so that plantation is possible on the top and side slope of the levees and guide banks.

\u2018CTRL\u2019: an online, Dynamic Consent and participant engagement platform working towards solving the complexities of consent in genomic research

The complexities of the informed consent process for participating in research in genomic medicine are well-documented. Inspired by the potential for Dynamic Consent to increase participant choice and autonomy in decision-making, as well as the opportunities for ongoing participant engagement it affords, we wanted to trial Dynamic Consent and to do so developed our own web-based application (web app) called CTRL (control). This paper documents the design and development of CTRL, for use in the Australian Genomics study: a health services research project building evidence to inform the integration of genomic medicine into mainstream healthcare. Australian Genomics brought together a multi-disciplinary team to develop CTRL. The design and development process considered user experience; security and privacy; the application of international standards in data sharing; IT, operational and ethical issues. The CTRL tool is now being offered to participants in the study, who can use CTRL to keep personal and contact details up to date; make consent choices (including indicate preferences for return of results and future research use of biological samples, genomic and health data); follow their progress through the study; complete surveys, contact the researchers and access study news and information. While there are remaining challenges to implementing Dynamic Consent in genomic research, this study demonstrates the feasibility of building such a tool, and its ongoing use will provide evidence about the value of Dynamic Consent in large-scale genomic research programs.

Stable Transformation of Arabidopsis thaliana Cell Suspension Cultures: A Case Study for The Overexpression of the COI1 Receptor.

Cell suspension cultures have been studied for decades to produce natural molecules. However, the difficulty in generating stably transformed cell lines has limited their use to produce high value chemicals reproducibly and in elevated quantities. In this protocol, a method to stably transform and maintain Arabidopsis cell suspension cultures is devised and presented in detail. Arabidopsis cell cultures were directly transformed with A. tumefaciens for the overexpression of the CORONATINE INSENSITIVE 1 (COI1) jasmonate receptor. Cell cultures were established after transformation and continuously maintained and tested for the overexpression of COI1. The protocol was also previously used to silence Arabidopsis peroxidases and allows for long term maintenance of transformed cells. Details on culture maintenance, both in liquid and solid media are provided, alongside with evidence of protein expression to confirm transformation. The system described provides a powerful tool for synthetic biology to study signaling independent of developmental control and to obtain metabolites of interest for the biotechnological and medical sectors.

Control of the Internal and External Staggered Distance of Coal Mining Face to the Water‐Conducting Fissures in the Overlying Strata of the Near Coal

In Northwest China, rainfall is low, water resources are scarce, and the ecological environment is fragile. For shallow‐buried and close‐spaced coal seams with a thickness of upper coal bed >60∼70 m, the water‐conducting fissures of the overlying rock will not penetrate the water‐isolating layer after the upper coal seam is mined; the internal and external gap angles of the water‐conducting fissures are not generated from the water‐isolating layer. We set out to explore the critical internal and external dislocations for the second significant development of water‐conducting fissures in the overlying rock after coal mining under control. A calculation model for the critical internal and external staggered distances of coal mining face in shallow‐buried and close‐spaced coal seams is established, the calculation formula is given, and the calculation formula for the critical seam mining ratio under the condition of internal staggered mining mode is given. Numerical simulation performed by UDEC methods: taking the overburden strata in the shallow‐buried and close‐spaced coal seam mining area of Shigetai Coal Mine as a prototype, it was verified that the critical internal and external offsets of the coal mining face in shallow‐buried and close‐spaced coal seams have a significant effect on the overlying water flow cracks in the mining of the lower coal seam. For the feasibility of developmental control, according to the engineering geological conditions of Shigetai, through the calculation method of external staggered distance, it is concluded that the distance of the open cut of the lower coal face and the upper coal face is only 21∼27 m, which is much smaller than the water barrier. It does not produce the critical distance of the water‐conducting cracks. Therefore, in the process of mining the lower coal seam, the water‐proof layer will produce water‐conducting cracks, lose its water‐proof performance, and cause water loss. This is also the cause of the water inrush accident in Shigetai Coal Mine.

Diaphragm neuromuscular transmission failure in a mouse model of an early-onset neuromotor disorder.

The spa transgenic mouse displays spasticity and hypertonia that develops during the early postnatal period, with motor impairments that are remarkably similar to symptoms of human cerebral palsy. Previously, we observed that spa mice have fewer phrenic motor neurons innervating the diaphragm muscle (DIAm). We hypothesize that spa mice exhibit increased susceptibility to neuromuscular transmission failure (NMTF) due to an expanded innervation ratio. We retrogradely labeled phrenic motor neurons with rhodamine and imaged them in horizontal sections (70 µm) using confocal microscopy. Phrenic nerve-DIAm strip preparations from wild type and spa mice were stretched to optimal length, and force was evoked by phrenic nerve stimulation at 10, 40, or 75 Hz in 330-ms duration trains repeated each second (33% duty cycle) across a 120-s period. To assess NMTF, force evoked by phrenic nerve stimulation was compared to force evoked by direct DIAm stimulation superimposed every 15 s. Total DIAm fiber number was estimated in hematoxylin and eosin-stained strips. Compared to wild type, spa mice had over twofold greater NMTF during the first stimulus train that persisted throughout the 120 s period of repetitive activation. In both wild type and spa mice, NMTF was stimulation-frequency dependent. There was no difference in neuromuscular junction morphology or the total number of DIAm fibers between wild type and spa mice, however, there was an increase innervation ratio (39%) in spa mice. We conclude that early-onset developmental neuromotor disorders impair the efficacy of DIAm neuromuscular transmission, likely to contribute to respiratory complications.NEW & NOTEWORTHY Individuals with motor control deficits, including cerebral palsy (CP) often have respiratory impairments. Glycine-receptor mutant spa mice have early-onset hypertonia, and limb motor impairments, similar to individuals with CP. We hypothesized that in the diaphragm of spa mice, disruption of glycinergic inputs to MNs would result in increased phrenic-DIAm neuromuscular transmission failure. Pathophysiologic abnormalities in neuromuscular transmission may contribute to respiratory dysfunction in conditions where early developmental MN loss or motor control deficits are apparent.

Molecular analysis of structural genes involved in flavonoids biosynthesis in naturally colored cotton

AbstractIn order to facilitate the development of cotton (Gossypium hirsutum L.) strains with colored fiber, the genetic and developmental control of flavonoids in fibers must be understood. The major goal of this study was to determine whether anthocyanidins accumulate in three different natural colored cotton fibers during their development, and to document the expression levels of flavonoid genes necessary for the production of anthocyanidins to determine if differences in expression levels reflect differences in anthocyanidin production. Most flavonoid structural genes were more highly expressed during fiber elongation than before the beginning of secondary cell wall formation. High performance liquid chromatography (HPLC) analyses showed that the abundance of anthocyanidins was higher in brown fibers than in green or white fibers. Anthocyanidins were present at high levels in fibers, starting at 20 d post‐anthesis of fiber development, which is almost at the end of the fiber elongation stage. Brown cotton contains higher delphinidin levels than of green and white cotton. This pattern is consistent with greater expression of anthocyanin pathway genes in brown fibers. In naturally colored cotton, the enzyme Lar (leucoanthocyanidin reductase) converted leucoanthocyanidins to catechin, which are proanthocyanins (PAs) precursor subunits. It is suggested that failure to produce anthocyanins is likely due to a combination of insufficient expression of Ufgt (UDP‐glucose: flavonoid 3‐O‐glucosyltransferase) and high expression of Lar and Anr (anthocyanidin reductase).

Smoothelin-like 2 Inhibits Coronin-1B to Stabilize the Apical Actin Cortex during Epithelial Morphogenesis

The actin cortex is involved in many biological processes and needs to be significantly remodeled during cell differentiation. Developing epithelial cells construct a dense apical actin cortex to carry out their barrier and exchange functions. The apical cortex assembles in response to three-dimensional (3D) extracellular cues, but the regulation of this process during epithelial morphogenesis remains unknown. Here, we describe the function of Smoothelin-like 2 (SMTNL2), a member of the smooth-muscle-related Smoothelin protein family, in apical cortex maturation. SMTNL2 is induced during development in multiple epithelial tissues and localizes to the apical and junctional actin cortex in intestinal and kidney epithelial cells. SMTNL2 deficiency leads to membrane herniations in the apical domain of epithelial cells, indicative of cortex abnormalities. We find that SMTNL2 binds to actin filaments and is required to slow down the turnover of apical actin. We also characterize the SMTNL2 proximal interactome and find that SMTNL2 executes its functions partly through inhibition of coronin-1B. Although coronin-1B-mediated actin dynamics are required for early morphogenesis, its sustained activity is detrimental for the mature apical shape. SMTNL2 binds to coronin-1B through its N-terminal coiled-coil region and negates its function to stabilize the apical cortex. In sum, our results unveil a mechanism for regulating actin dynamics during epithelial morphogenesis, providing critical insights on the developmental control of the cellular cortex.

Expression profiling of MADS-box gene family revealed its role in vegetative development and stem ripening in S. spontaneum

Sugarcane is the most important sugar and biofuel crop. MADS-box genes encode transcription factors that are involved in developmental control and signal transduction in plants. Systematic analyses of MADS-box genes have been reported in many plant species, but its identification and characterization were not possible until a reference genome of autotetraploid wild type sugarcane specie, Saccharum spontaneum is available recently. We identified 182 MADS-box sequences in the S. spontaneum genome, which were annotated into 63 genes, including 6 (9.5%) genes with four alleles, 21 (33.3%) with three, 29 (46%) with two, 7 (11.1%) with one allele. Paralogs (tandem duplication and disperse duplicated) were also identified and characterized. These MADS-box genes were divided into two groups; Type-I (21 Mα, 4 Mβ, 4 Mγ) and Type-II (32 MIKCc, 2 MIKC*) through phylogenetic analysis with orthologs in Arabidopsis and sorghum. Structural diversity and distribution of motifs were studied in detail. Chromosomal localizations revealed that S. spontaneum MADS-box genes were randomly distributed across eight homologous chromosome groups. The expression profiles of these MADS-box genes were analyzed in leaves, roots, stem sections and after hormones treatment. Important alleles based on promoter analysis and expression variations were dissected. qRT-PCR analysis was performed to verify the expression pattern of pivotal S. spontaneum MADS-box genes and suggested that flower timing genes (SOC1 and SVP) may regulate vegetative development.

Maternal Vitamin D Levels During Pregnancy in Association With Autism Spectrum Disorders (ASD) or Intellectual Disability (ID) in Offspring; Exploring Non-linear Patterns and Demographic Sub-groups.

Increasing vitamin D deficiency and evidence for vitamin D's role in brain and immune function have recently led to studies of neurodevelopment; however, few are specific to autism spectrum disorder (ASD) and vitamin D in pregnancy, a likely susceptibility period. We examined this in a case-control study of 2000-2003 Southern Californian births; ASD and intellectual disability (ID) were identified through the Department of Developmental Services and controls from birth certificates (N = 534, 181, and 421, respectively, in this analysis). Total 25-Hydroxyvitamin D (25(OH)D) was measured in mid-pregnancy serum, categorized as deficient (<50 nmol/L), insufficient (50-74 nmol/L), or sufficient (≥75 nmol/L, referent category), and examined continuously (per 25 nmol/L). Crude and adjusted odds ratios (AORs) and 95% confidence intervals (95% CI) were calculated. Non-linearity was examined with cubic splines. AORs (95% CI) for ASD were 0.79 (0.49-1.3) for maternal deficiency (9.5%), 0.93 (0.68-1.3) for insufficiency (25.6%), and 0.95 (0.86, 1.05) for linear continuous 25(OH)D. Results were similarly null for ASD with or without ID, and ID only. Interactions were observed; non-Hispanic whites (NHW) (AOR = 0.82, 95% CI = 0.69-0.98) and males (AOR = 0.89, 95% CI = 0.80-0.99) had protective associations for ASD with continuous 25(OH)D. A positive association with ASD was observed in females (AOR = 1.40, 95% CI = 1.06-1.85). With splines, a non-linear inverted j-shaped pattern was seen overall (P = 0.009 for non-linearity), with the peak around 100 nmol/L; a non-linear pattern was not observed among NHW, females, nor for ID. Our findings from a large study of ASD and prenatal vitamin D levels indicate that further research is needed to investigate non-linear patterns and potentially vulnerable sub-groups. LAY SUMMARY: We studied whether mothers' vitamin D levels during pregnancy were related to their children having autism (or low IQ) later. Low vitamin D levels were not related to greater risk of autism or low IQ in children overall. With higher levels of mothers' vitamin D, risk of autism went down in boys, but went up in girls. Risk of autism also went down in children of non-Hispanic white mothers with higher vitamin D levels, but we did not find a relation in other race/ethnic groups.

Evolved Differences in cis and trans Regulation Between the Maternal and Zygotic mRNA Complements in the Drosophila Embryo.

How gene expression can evolve depends on the mechanisms driving gene expression. Gene expression is controlled in different ways in different developmental stages; here we ask whether different developmental stages show different patterns of regulatory evolution. To explore the mode of regulatory evolution, we used the early stages of embryonic development controlled by two different genomes, that of the mother and that of the zygote. During embryogenesis in all animals, initial developmental processes are driven entirely by maternally provided gene products deposited into the oocyte. The zygotic genome is activated later, when developmental control is handed off from maternal gene products to the zygote during the maternal-to-zygotic transition. Using hybrid crosses between sister species of Drosophila (Dsimulans, D.sechellia, and D.mauritiana) and transcriptomics, we find that the regulation of maternal transcript deposition and zygotic transcription evolve through different mechanisms. We find that patterns of transcript level inheritance in hybrids, relative to parental species, differ between maternal and zygotic transcripts, and maternal transcript levels are more likely to be conserved. Changes in transcript levels occur predominantly through differences in trans regulation for maternal genes, while changes in zygotic transcription occur through a combination of both cis and trans regulatory changes. Differences in the underlying regulatory landscape in the mother and the zygote are likely the primary determinants for how maternal and zygotic transcripts evolve.

Do Meristic Characters Used in Phylogenetic Analysis Evolve in an Ordered Manner?

The use of ordered characters in phylogenetic analysis has been inconsistent throughout the history of phylogenetic inference. It has become more widespread in recent years, and some have advocated that all characters representing continuous or meristic traits should be ordered as a matter of course. Here, using the example of dental evolution, we examine two factors that may impact on whether meristic characters actually evolve in an ordered manner: the regulatory hierarchy governing the development of teeth that allows large sections of the entire tooth row to be suppressed in a single transition and regionalization of the tooth row where different modules have a degree of independence in their evolution. These are studied using both empirical and simulated data. Models of evolution of such characters are examined over molecular phylogenies to see if ordered or unordered models fit best. Simulations of tooth-row evolution are designed to incorporate changes in region size and multiple levels of developmental control to suppress individual regions or the entire row. The empirical analyses show that in a clade with largely homodont dentition the characters evolve in an ordered manner, but if dentition is heterodont with distinct regionalization their evolution better fits an unordered model. In the simulations, even if teeth are added and removed from the tooth row in an ordered manner, dividing the row into independently evolving modules can lead to characters covering multiple modules better fitting an unordered model of evolution. Adding the ability to suppress regions or the entire tooth row has a variable effect depending on the rates of suppression relative to the rates of addition and subtraction of individual teeth. We therefore advise not following a single policy when deciding whether to order meristic traits but to base the decision on a priori knowledge of the focal clade's evolution and developmental biology. [Discrete characters; ordered characters; phylogeny; teeth.].

A release from developmental bias accelerates morphological diversification in butterfly eyespots

Development can bias the independent evolution of traits sharing ontogenetic pathways, making certain evolutionary changes less likely. The eyespots commonly found on butterfly wings each have concentric rings of differing colors, and these serially repeated pattern elements have been a focus for evo-devo research. In the butterfly family Nymphalidae, eyespots have been shown to function in startling or deflecting predators and to be involved in sexual selection. Previous work on a model species of Mycalesina butterfly, Bicyclus anynana, has provided insights into the developmental control of the size and color composition of individual eyespots. Experimental evolution has also shown that the relative size of a pair of eyespots on the same wing surface is highly flexible, whereas they are resistant to diverging in color composition, presumably due to the underlying shared developmental process. This fixed color composition has been considered as a prime example of developmental bias with significant consequences for wing pattern evolution. Here, we test this proposal by surveying eyespots across the whole subtribe of Mycalesina butterflies and demonstrate that developmental bias shapes evolutionary diversification except in the genus Heteropsis which has gained independent control of eyespot color composition. Experimental manipulations of pupal wings reveal that the bias has been released through a novel regional response of the wing tissue to a conserved patterning signal. Our study demonstrates that development can bias the evolutionary independence of traits, but it also shows how bias can be released through developmental innovations, thus, allowing rapid morphological change, facilitating evolutionary diversification.

Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster (Magallana hongkongensis) genome

BackgroundHomeobox-containing genes encode crucial transcription factors involved in animal, plant and fungal development, and changes to homeobox genes have been linked to the evolution of novel body plans and morphologies. In animals, some homeobox genes are clustered together in the genome, either as remnants from ancestral genomic arrangements, or due to coordinated gene regulation. Consequently, analyses of homeobox gene organization across animal phylogeny provide important insights into the evolution of genome organization and developmental gene control, and their interaction. However, homeobox gene organization remains to be fully elucidated in several key animal ancestors, including those of molluscs, lophotrochozoans and bilaterians.ResultsHere, we present a high-quality chromosome-level genome assembly of the Hong Kong oyster, Magallana hongkongensis (2n = 20), for which 93.2% of the genomic sequences are contained on 10 pseudomolecules (~ 758 Mb, scaffold N50 = 72.3 Mb). Our genome assembly was scaffolded using Hi-C reads, facilitating a larger scaffold size compared to the recently published M. hongkongensis genome of Peng et al. (Mol Ecol Resources, 2020), which was scaffolded using the Crassostrea gigas assembly. A total of 46,963 predicted gene models (45,308 protein coding genes) were incorporated in our genome, and genome completeness estimated by BUSCO was 94.6%. Homeobox gene linkages were analysed in detail relative to available data for other mollusc lineages.ConclusionsThe analyses performed in this study and the accompanying genome sequence provide important genetic resources for this economically and culturally valuable oyster species, and offer a platform to improve understanding of animal biology and evolution more generally. Transposable element content is comparable to that found in other mollusc species, contrary to the conclusion of another recent analysis. Also, our chromosome-level assembly allows the inference of ancient gene linkages (synteny) for the homeobox-containing genes, even though a number of the homeobox gene clusters, like the Hox/ParaHox clusters, are undergoing dispersal in molluscs such as this oyster.