The Genetics of Canine Skull Shape Variation

A dog’s craniofacial diversity is the result of continual human intervention in natural selection, a process that began tens of thousands of years ago. To date, we know little of the genetic underpinnings and developmental mechanisms that make dog skulls so morphologically plastic. In this Perspectives, we discuss the origins of dog skull shapes in terms of history and biology and highlight recent advances in understanding the genetics of canine skull shapes. Of particular interest are those molecular genetic changes that are associated with the development of distinct breeds.     

现代中国人眼眶的形态变异

研究证实人类骨性[眶形态具有明显的]化变化,在现代人群之间的表现也有一定程度的差别,因而[眶形态是研究人类]化及现代人群关系的重要特征之一。但是,学术界对与眼眶形态有关的许多问题还不是很清楚,或有争议。基于这一情况,本文对3项代表眼眶形态的性状在五组全新世近代—现代人群中的表现情况进行了观测,并结合对比了部分更新世晚期人类化石标本。本文研究发现:在中国地区,人类[眶的高低变异在]化过程中具有明显的时代变化,从新石器时代起出现了区域性的差异,并一直延续到现代;方形眼眶应该是中国人群较稳定的连续性特征,其高出现率从更新世一直延续到现代;在中国人群中,眼眶外下侧缘圆钝这一特征应该也是从更新世一直延续到现代的,但是其高出现率则只维持到新石器时代为止。     

Sources of Variation in Leaf Shape among Two Populations of Achillea Lanulosa

Achillea lanulosa has complex, highly dissected leaves that vary in shape and size along an altitudinal gradient. Plants from a high and an intermediate altitude population were clonally replicated and grown in a controlled environment at warm and cool conditions under bright light. There were genetic differences among populations and among individuals within populations in leaf size and shape. Heritabilities for leaf size and shape characters were moderate. Leaves of the lower altitude population were larger and differed from the higher altitude plants in both coarse and fine shape. Plastic response to temperature of the growth environment paralleled the genetic differentiation between low and high altitude populations. There was no apparent trade-off between genetic control over morphology and the capacity for directional plastic response to the environment. Differences in leaf dissection and size at contrasting altitudes in this species are the result of both genetic divergence among populations and of acclimative responses to local environments.     

A Genetic Framework for Grain Size and Shape Variation in Wheat

Grain morphology in wheat (Triticum aestivum) has been selected and manipulated even in very early agrarian societies and remains a major breeding target. We undertook a large-scale quantitative analysis to determine the genetic basis of the phenotypic diversity in wheat grain morphology. A high-throughput method was used to capture grain size and shape variation in multiple mapping populations, elite varieties, and a broad collection of ancestral wheat species. This analysis reveals that grain size and shape are largely independent traits in both primitive wheat and in modern varieties. This phenotypic structure was retained across the mapping populations studied, suggesting that these traits are under the control of a limited number of discrete genetic components. We identified the underlying genes as quantitative trait loci that are distinct for grain size and shape and are largely shared between the different mapping populations. Moreover, our results show a significant reduction of phenotypic variation in grain shape in the modern germplasm pool compared with the ancestral wheat species, probably as a result of a relatively recent bottleneck. Therefore, this study provides the genetic underpinnings of an emerging phenotypic model where wheat domestication has transformed a long thin primitive grain to a wider and shorter modern grain.     

Assessing Local Influence in Measurement Error Models

We consider the assessment of local influence for generalized linear models when the covariates are measured with errors. We show how to evaluate the effect that perturbations to the data, case weights, and model assumptions may have on the parameter estimates. Based on the likelihood displacement functions, some useful influence diagnostics are derived. Two examples illustrate application of the proposed diagnostics and assessment of the measurement error assumptions.     

Variation in Body Shape across Species and Populations in a Radiation of Diaptomid Copepods

Inter and intra-population variation in morphological traits, such as body size and shape, provides important insights into the ecological importance of individual natural populations. The radiation of Diaptomid species (~400 species) has apparently produced little morphological differentiation other than those in secondary sexual characteristics, suggesting sexual, rather than ecological, selection has driven speciation. This evolutionary history suggests that species, and conspecific populations, would be ecologically redundant but recent work found contrasting ecosystem effects among both species and populations. This study provides the first quantification of shape variation among species, populations, and/or sexes (beyond taxonomic illustrations and body size measurements) to gain insight into the ecological differentiation of Diaptomids. Here we quantify the shape of five Diaptomid species (family Diaptomidae) from four populations each, using morphometric landmarks on the prosome, urosome, and antennae. We partition morphological variation among species, populations, and sexes, and test for phenotype-by-environment correlations to reveal possible functional consequences of shape variation. We found that intraspecific variation was 18-35% as large as interspecific variation across all measured traits. Interspecific variation in body size and relative antennae length, the two traits showing significant sexual dimorphism, were correlated with lake size and geographic location suggesting some niche differentiation between species. Observed relationships between intraspecific morphological variation and the environment suggest that divergent selection in contrasting lakes might contribute to shape differences among local populations, but confirming this requires further analyses. Our results show that although Diaptomid species differ in their reproductive traits, they also differ in other morphological traits that might indicate ecological differences among species and populations.     

非平衡群体基因变异测量的Shannon信息量方法

在Shannon信息量的基础上,对非平衡群体建立了群体基因型相对信息量S′（G）,纯合体相对信息量S′J（G）、杂合体相对信息量S′H（G）的概念,并赋予它们以遗传学意义,与基因一致度J和基因多样度D进行了理论比较,结果表明,二者在数量规律上有很好的一致性,但又是相对独立的指标体系,且各相对信息量还有新的内涵。S′（G）既能表征基因变异,又能反映基因型水平上的遗传变异,S′J（G）主要反映纯合体的遗传变异,S′H（G）主要反映杂合体的遗传变异,各相对信息量既可反映群体的遗传变异程度,又能比较不同位点间的遗传变异程度。     

Local Increases in Mechanical Tension Shape Compartment Boundaries by Biasing Cell Intercalations

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Daily Variation in Global and Local DNA Methylation in Mouse Livers

DNA methylation is one of the best-characterized epigenetic modifications and has an important biological relevance. Here we showed that global DNA methylation level in mouse livers displayed a daily variation where the peak phases occurred during the end of the day and the lowest level at the beginning of the day in the light-dark or dark-dark cycles. Typical repeat sequence long interspersed nucleotide element-1 (LINE-1) had a similar methylation rhythm to global DNA. DNA methyltransferase 3A (DNMT3A) and ratio of S-adenosylmethionine (SAM) to S-adenosylhomocysteine (SAH) brought a relative forward daily variation to global DNA methylation, and the temporary change in ratio of SAM to SAH had no influence on the DNA methylation level. The rhythm of global DNA methylation was lost and DNA methylation level was increased in Per1^-/-Per2^-/- double knockout mice, which were in accordance with changes of Dnmt3a mRNA levels and its rhythm. Our results suggest that the daily variation in global DNA methylation was associated with the change of Dnmt3a expression rather than ratio of SAM to SAH.     

Immune Subversion and Quorum-Sensing Shape the Variation in Infectious Dose among Bacterial Pathogens

Many studies have been devoted to understand the mechanisms used by pathogenic bacteria to exploit human hosts. These mechanisms are very diverse in the detail, but share commonalities whose quantification should enlighten the evolution of virulence from both a molecular and an ecological perspective. We mined the literature for experimental data on infectious dose of bacterial pathogens in humans (ID50) and also for traits with which ID50 might be associated. These compilations were checked and complemented with genome analyses. We observed that ID50 varies in a continuous way by over 10 orders of magnitude. Low ID50 values are very strongly associated with the capacity of the bacteria to kill professional phagocytes or to survive in the intracellular milieu of these cells. Inversely, high ID50 values are associated with motile and fast-growing bacteria that use quorum-sensing based regulation of virulence factors expression. Infectious dose is not associated with genome size and shows insignificant phylogenetic inertia, in line with frequent virulence shifts associated with the horizontal gene transfer of a small number of virulence factors. Contrary to previous proposals, infectious dose shows little dependence on contact-dependent secretion systems and on the natural route of exposure. When all variables are combined, immune subversion and quorum-sensing are sufficient to explain two thirds of the variance in infectious dose. Our results show the key role of immune subversion in effective human infection by small bacterial populations. They also suggest that cooperative processes might be important for successful infection by bacteria with high ID50. Our results suggest that trade-offs between selection for population growth-related traits and selection for the ability to subvert the immune system shape bacterial infectiousness. Understanding these trade-offs provides guidelines to study the evolution of virulence and in particular the micro-evolutionary paths of emerging pathogens.     

Impact of Hybridization on Shape,Variation and Covariation of the Mouse Molar

Hybridization can generate phenotypes departing from the parental range through many processes: increased variance due to increased heterozygosity, decreased phenotypic integration and altered covariation structure due to changes in the expression of (co)variation generating developmental processes, and transgression that may arise from epistasis and compensatory genes. Morphometric assessment of shape differentiation, variance and covariance may shed light on these processes, especially for complex characters for which the genetic basis has not yet been assessed. The shape of the first upper molar was thus quantified in a cross between inbred strains of the two European subspecies of the house mouse (Mus musculus domesticus and M. m. musculus). Hybrids appeared as moderately transgressive. Morphological variance was increased in F2s, back to levels observed in wild populations. The pattern of variance–covariance was different between the two parental strains, but restored to a wild-type structure in F2s. Finally, F2s displayed a degree of morphological integration comparable to wild populations but lower than observed in the parental strains. This is interpreted as the result of the reshuffling of the standing genetic variation in hybrids that should have restored the expression of (co)variance generating processes made ineffective in parents due to random allele fixation of some loci. Inter-parental differentiation was more important in regions of the tooth developing early during embryogenesis, whereas transgression was more pronounced in late developing regions. Mutations may more easily generate important geometric differences early during tooth development, occurring as a cascade of signalization from the first cusp to initiate onward. Epistasis and constraints of neighboring parts may be more important later, promoting transgression and impeding differentiation.     

LeafJ: An ImageJ Plugin for Semi-automated Leaf Shape Measurement

High throughput phenotyping (phenomics) is a powerful tool for linking genes to their functions (see review¹ and recent examples^2-4). Leaves are the primary photosynthetic organ, and their size and shape vary developmentally and environmentally within a plant. For these reasons studies on leaf morphology require measurement of multiple parameters from numerous leaves, which is best done by semi-automated phenomics tools^5,6. Canopy shade is an important environmental cue that affects plant architecture and life history; the suite of responses is collectively called the shade avoidance syndrome (SAS)⁷. Among SAS responses, shade induced leaf petiole elongation and changes in blade area are particularly useful as indices⁸. To date, leaf shape programs (e.g. SHAPE⁹, LAMINA¹⁰, LeafAnalyzer¹¹, LEAFPROCESSOR¹²) can measure leaf outlines and categorize leaf shapes, but can not output petiole length. Lack of large-scale measurement systems of leaf petioles has inhibited phenomics approaches to SAS research. In this paper, we describe a newly developed ImageJ plugin, called LeafJ, which can rapidly measure petiole length and leaf blade parameters of the model plant Arabidopsis thaliana. For the occasional leaf that required manual correction of the petiole/leaf blade boundary we used a touch-screen tablet. Further, leaf cell shape and leaf cell numbers are important determinants of leaf size¹³. Separate from LeafJ we also present a protocol for using a touch-screen tablet for measuring cell shape, area, and size. Our leaf trait measurement system is not limited to shade-avoidance research and will accelerate leaf phenotyping of many mutants and screening plants by leaf phenotyping.     

Evolutionary History and Ecological Processes Shape a Local Multilevel Antagonistic Network

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Local Variation in Shredder Distribution can Explain their Oversight in Tropical Streams

Stream shredders play an important role in the breakdown of allochthonous leaf litter—a well-known, key process in temperate headwater streams. In contrast, it has been suggested that litter breakdown in tropical streams is driven by microorganisms, shredders being scarce or absent. We propose that shredders have been overlooked in some tropical streams for two reasons: (1) assuming that tropical shredders belong to the same taxa as temperate ones, without determining the diet of tropical litter fauna; and (2) the small spatial scale of most tropical stream studies, which do not account for intra- and inter-site comparisons. We explored shredder abundance and species richness in six streams in each of two tropical regions, the Australian wet tropics (AWT) and Panama (PAN), finding 734 individuals of 12 shredder species in AWT and 391 individuals of 16 species in PAN. Shredder species richness was positively related to altitude in AWT, but not in PAN. Shredder contribution to total leaf breakdown in the field was 24±3 SE percent in AWT and negligible in PAN, but this was probably due to the unsuccessful colonization of experimental cages by PAN shredders. In the laboratory, shredder contribution to total leaf breakdown was higher than in the field (35%±2 SE in AWT and 64%±3 SE in PAN) and varied with leaf decomposability. Our results support earlier indications that shredders are not scarce or functionally unimportant in the tropics, and suggest that their contribution to litter processing should be determined along altitudinal gradients.
     

Does Optimal Packing of Flowers in Syconia Shape Style Length Variation in Monoecious Figs?1

Style length variation in female flowers of monoecious figs has been shown to play an important role in regulating the proportion of flowers that develop into seeds and those that become infested by the pollinator wasp. In this study, we tested the suggestion that style length variation in figs is a consequence of optimal packing of the flowers. We show that optimal packing of flowers in fig syconia will result in a highly skewed distribution of style lengths and a positive skewness of pedicel lengths. These predictions were qualitatively tested in eight species of figs and the results indicate that observed style length distributions did not conform to those expected. We argue that while the pedicel lengths are likely to be a spinoff of optimal packing of the flowers, style lengths are probably shaped by independent selective fotces. The pedicel lengths also are subjected to compensatory growth so as to place the stigmas at a common height in the central cavity for effective pollination of the flowers. This was substantiated by the response (dependence) of pedicels to (on) the length of the style, neck, and other floral features. In all species the coefficient of variation of styles was very consistent (ca 30 %). This is in accordance with expectations if style lengths are shaped to regulate the proportion of flowers for wasp and seed production.