Recombination systems and plant domestication

Speculations on the role of recombination systems in plant domestication are presented. It is suggested that those colonizing species which had more open, or at least more flexible, recombination systems were, in a sense, pre-adapted to domestication. Such systems allow the rapid switching of variability between the potential and free states, an ability which is argued to have been of great importance during the domestication process. Species which were never domesticated, or were abandoned later, are suggested to have had inappropriate recombination systems which did not allow the storage and/or release of sufficient variability. A review of the ecology of recombination systems in disturbed habitats and a comparison of some aspects of the recombination systems in crop progenitors with those in non-cultivated colonizing species provides some evidence both for and against the hypothesis.     

The ecology of sex explains patterns of helping in arthropod societies

Across arthropod societies, sib‐rearing (e.g. nursing or nest defence) may be provided by females, by males or by both sexes. According to Hamilton's ‘haplodiploidy hypothesis’, this diversity reflects the relatedness consequences of diploid vs. haplodiploid inheritance. However, an alternative ‘preadaptation hypothesis’ instead emphasises an interplay of ecology and the co‐option of ancestral, sexually dimorphic traits for sib‐rearing. The preadaptation hypothesis has recently received empirical support, but remains to be formalised. Here, we mathematically model the coevolution of sex‐specific helping and sex allocation, contrasting these hypotheses. We find that ploidy per se has little effect. Rather, the ecology of sex shapes patterns of helping: sex‐specific preadaptation strongly influences who helps; a freely adjustable sex ratio magnifies sex biases and promotes helping; and sib‐mating, promiscuity, and reproductive autonomy also modulate the sex and abundance of helpers. An empirical survey reveals that patterns of sex‐specific helping in arthropod taxa are consistent with the preadaptation hypothesis.     

Evaluating the self‐domestication hypothesis of human evolution

“Self‐domestication” has been invoked to understand important aspects of human evolution, integrating physiological, behavioral, and morphological information in a novel way. It proposes that selection for reduced aggression on animals undergoing domestication provides a model for selection favoring prosocial behaviors in humans and for a set of seemingly independent features, which arose as a result of developmental correlation. We review the history of the idea and examine patterns of domestication. A lack of empirical studies on evolutionary rates and variation thwarts meaningful comparison with domestication. The neural crest hypothesis for domestication has great explanatory power but it is difficult to test. We suggest a scenario in which the morphological byproducts of domestication can act as an honest signal of reduced xenophobia. Future studies should test if alternative explanations for the features deemed to result from self‐domestication are mutually exclusive and generate data to test predictions of these hypotheses.     

Domestication of maize, sorghum, and sugarcane did not drive the divergence of their smut pathogens

We investigated two alternative hypotheses for the origin of crop pathogen species: that human-mediated agricultural practices drove the divergence of many crop plant pathogen species or that coevolutionary processes in natural populations of the crops' ancestors drove divergence of pathogen species. We distinguished between these two hypotheses by constructing a robust multigene phylogeny and estimating the dates of divergence among four, monophyletic species of smut fungi (Ustilago maydis, U. scitaminea, Sporisorium reilianum, S. sorghi) known to specifically infect maize, sorghum, sugarcane, and their wild ancestors. Without a fossil record for smut fungi, we calibrated the pathogen species' divergence times to their plant host divergence times. Specifically, a calibration date of 10,000 years was employed to test the hypothesis that the fungal species originated at the time of domestication of their current hosts and a calibration date of 50 million years was employed to test the hypothesis that the fungal species originated on wild ancestors of their domesticated hosts. Substitution rates at five protein coding genes were calculated and rates obtained for the 10,000 year calibration date were orders of magnitude faster than those commonly reported for eukaryotes, thus rejecting the hypothesis that these smut pathogen species diverged at the time of domestication. In contrast, substitution rates obtained for the 50 million year calibration were comparable to eukaryotic substitution rates. We used the 50 million year calibration to estimate divergence times of taxa in two datasets, one comprised solely the focal species and one comprised the focal species and additional related taxa. Both datasets indicate that all taxa diverged millions of years ago, strongly supporting the hypothesis that smut species diverged before the time of domestication and modern agriculture. Thus, smut species diverged in the ecological context of natural host plant and fungal populations.     

Biogeographic bases for a shift in crop C : N : P stoichiometries during domestication

We lack both a theoretical framework and solid empirical data to understand domestication impacts on plant chemistry. We hypothesised that domestication increased leaf N and P to support high plant production rates, but biogeographic and climate patterns further influenced the magnitude and direction of changes in specific aspects of chemistry and stoichiometry. To test these hypotheses, we used a data set of leaf C, N and P from 21 herbaceous crops and their wild progenitors. Domestication increased leaf N and/or P for 57% of the crops. Moreover, the latitude of the domestication sites (negatively related to temperature) modulated the domestication effects on P (+), C (?), N : P (?) and C : P (?) ratios. Further results from a litter decomposition assay showed that domestication effects on litter chemistry affected the availability of soil N and P. Our findings draw attention to evolutionary effects of domestication legacies on plant and soil stoichiometry and related ecosystem services (e.g. plant yield and soil fertility).     

A weak effect of background selection on trinucleotide microsatellites in maize

Artificial selection during the domestication of maize is thought to have been predominantly positive and to have had little effect on the surrounding neutral diversity because linkage disequilibrium breaks down rapidly when physical distance increases. However, the degree to which indirect selection has shaped neutral diversity in the maize genome during domestication remains unclear. In this study, we investigate the relationship between local recombination rate and neutral polymorphism in maize and in teosinte using both sequence and microsatellite data. To quantify diversity, we estimate 3 parameters expected to differentially reflect the effects of indirect selection and mutation. We find no general correlation between diversity and recombination, indicating that indirect selection has had no genome-wide impact on maize diversity. However, we detect a weak correlation between heterozygosity and recombination for trinucleotide microsatellites deviating from the stepwise mutation model and located within genes (rho = 0.32, P < 0.03). This result can be explained by a background selection hypothesis. The fact that the same correlation is not confirmed for nucleotide diversity suggests that the strength of purifying selection at or near this class of microsatellites is higher than for nucleotide mutations.     

Out of the quagmire of plant defense hypotheses

Several hypotheses, mainly Optimal Defense (OD), Carbon: Nutrient Balance (CNB), Growth Rate (GR), and Growth-Differentiation Balance (GDB), have individually served as frameworks for investigating the patterns of plant defense against herbivores, in particular the pattern of constitutive defense. The predictions and tests of these hypotheses have been problematic for a variety of reasons and have led to considerable confusion about the state of the "theory of plant defense." The primary contribution of the OD hypothesis is that it has served as the main framework for investigation of genotypic expression of plant defense, with the emphasis on allocation cost of defense. The primary contribution of the CNB hypothesis is that it has served as the main framework for investigation of how resources affect phenotypic expression of plant defense, often with studies concerned about allocation cost of defense. The primary contribution of the GR hypothesis is that it explains how intrinsic growth rate of plants shaped evolutionarily by resource availability affects defensive patterns. The primary contribution of the expanded GDB hypothesis is that it recognizes the constant physiological tradeoff between growth and differentiation at the cellular and tissue levels relative to the selective pressures of resource availability, including explicitly taking into account plant tolerance of damage by enemies. A clearer understanding of these hypotheses and what we have learned from investigations that use them can facilitate development of well-designed experiments that address the gaps in our knowledge of plant defense.     

Domestication of the neotropical tree Chrysophyllum cainito from a geographically limited yet genetically diverse gene pool in Panama

Species in the early stages of domestication, in which wild and cultivated forms co‐occur, provide important opportunities to develop and test hypotheses about the origins of crop species. Chrysophyllum cainito (Sapotaceae), the star apple or caimito, is a semidomesticated tree widely cultivated for its edible fruits; it is known to be native to the neotropics, but its precise geographic origins have not been firmly established. Here, we report results of microsatellite marker analyses supporting the hypothesis that the center of domestication for caimito was the Isthmus of Panama, a region in which few crop species are believed to have originated, despite its importance as a crossroads for the dispersal of domesticated plants between North and South America. Our data suggest that caimito was domesticated in a geographically restricted area while incorporating a diverse gene pool. These results refute the generally accepted Antillean origin of caimito, as well as alternative hypotheses that the species was domesticated independently in the two areas or over a broad geographic range including both. Human‐mediated dispersal from Panama to the north and east was accompanied by strong reductions in both genotypic and phenotypic diversity. Within Panama, cultivated and wild trees show little neutral genetic divergence, in contrast to striking phenotypic differentiation in fruit and seed traits. In addition to providing a rare example of data that support the hypothesis of a narrow geographic origin on the Isthmus of Panama for a now widespread cultivated plant species, this study is one of the first investigations of the origins of an edible species of the large pantropical family Sapotaceae.     

Choosing benefits or partners: a review of the evidence for the evolution of myrmecochory

Myrmecochory, or seed dispersal by ants, is a dispersal syndrome found among several thousand plant species occupying different ecosystems and geographical regions. Typically, ants benefit from consuming a lipid-rich appendage on the seed and in return provide seed dispersal service to the plant. Several hypotheses have been proposed to explain the selective advantage for plants resulting from myrmecochory, including directed dispersal, dispersal for distance and escape from seed predators. I contrast the evidence available in the literature for these hypotheses and distinguish the studies on the basis of ecosystem and plant growth forms. The predator-avoidance and the distance dispersal hypotheses were supported in most studies that addressed them, and the directed dispersal hypothesis was supported in about half of the studies that tested it. Multiple hypotheses were supported in most studies that tested more than one hypothesis, suggesting that the various selective advantages conferred from myrmecochory are seldom exclusive. I also review evidence for the hypothesis that plants have evolved adaptations both for selecting seed dispersers and for manipulating the behavior of those dispersers. Based on this evidence, I argue that focusing future research on the evolution of partner choice by myrmecochores and its effects on the overall plant fitness will be more fruitful than putting an emphasis on classifying the selective advantage to plants into distinct categories and test for their existence separately.     

Comparative analyses between lolium/festuca introgression lines and rice reveal the major fraction of functionally annotated gene models is located in recombination-poor/very recombination-poor regions of the genome

Publication of the rice genome sequence has allowed an in-depth analysis of genome organization in a model monocot plant species. This has provided a powerful tool for genome analysis in large-genome unsequenced agriculturally important monocot species such as wheat, barley, rye, Lolium, etc. Previous data have indicated that the majority of genes in large-genome monocots are located toward the ends of chromosomes in gene-rich regions that undergo high frequencies of recombination. Here we demonstrate that a substantial component of the coding sequences in monocots is localized proximally in regions of very low and even negligible recombination frequencies. The implications of our findings are that during domestication of monocot plant species selection has concentrated on genes located in the terminal regions of chromosomes within areas of high recombination frequency. Thus a large proportion of the genetic variation available for selection of superior plant genotypes has not been exploited. In addition our findings raise the possibility of the evolutionary development of large supergene complexes that confer a selective advantage to the individual.     

Estimated plant richness pattern across northwest South America provides similar support for the species-energy and spatial heterogeneity hypotheses

Explaining geographic variation in plant species richness at broad spatial scales has long been a major challenge. Many hypotheses have been proposed during the last 200 yr, but recent work has focused on a few major alternatives. Among these, two hypotheses contend that plant species richness reflects 1) variation in energy and water availability among sampling units (the species-energy hypothesis) and 2) habitat and topographic heterogeneity within sampling units (the spatial heterogeneity hypothesis). We used a large botanical database and regression models to simultaneously confront the predictions from both hypotheses against an estimate of vascular plant richness across northwest South America. This estimate provided similar support for both hypotheses, a result that may be seen as contrasting with the notion that variation in energy and water availability among sampling units is the main determinant of plant species richness. We discuss potential explanations for this apparent discrepancy. Regression models that incorporated the relative contributions of both hypotheses predicted that the highest plant species richness in northwest South America is found in topographically complex areas. In contrast to several of the most recent mapping efforts, lowland Amazonia was predicted to be a plant richness trough in the study region. We suggest that diverging portrayals of plant richness across northwest South America result from differences in estimates of the relative importance of the species-energy and the spatial heterogeneity hypotheses.     

Evidence suggesting preadaptation to domestication throughout the small Felidae

One obstacle in the development of a coherent theoretical framework for the process of animal domestication is the rarity of domestication events in human history. It is unclear whether: (1) many species are suitable for domestication, the limiting factor being the requirement of people for new domestic animals; or (2) very few species are preadapted for domestication. Comparisons between 16 species and subspecies of small cats (Felidae) kept in zoos indicated that affiliative behaviour towards people, an important preadaptation to domestication, is widely, if patchily, distributed throughout this taxon, and is not concentrated in species closely related to the domestic cat, Felis silvestris catus . The highest proportion of individuals showing affiliative behaviour was found in the ocelot lineage, which is estimated to have diverged from the rest of the Felidae between 5 and 13 Mya. The domestication of F. silvestris alone among felids is therefore likely to have been the result of a specific set of human cultural events and requirements in the Egyptian New Kingdom, rather than the consequence of a unique tendency to tame-ness in this subspecies.© 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 75 , 2002, 361–366.     

Effects of life history, domestication and agronomic selection on plant defence against insects: Evidence from maizes and wild relatives

Plant domestication and agronomic selection for increased yield may have an associated effect of reducing plant defence against herbivorous insects. This hypothesis is based on evidence for a metabolic cost associated with defence, and on evidence that increases in yield generally come from the re-partitioning of photoassimilates rather than from fundamental increases in photosynthetic rates. We propose that for plants in which domestication and crop development constitute strong selection for increased growth and reproduction, reallocation of resources may result in lower defence against insects. We examine this hypothesis by means of comparative studies of growth, reproduction and resistance in a complex of maizes and closely related wild taxa, the teosintes. The results of these studies are consistent with assumptions of differential investment in growth and reproduction between wild and domesticated plants. A wild perennial grew slowest and had lowest grain production, while a modern cultivar grew fastest and had the highest grain yield. A wild annual and a land-race cultivar were intermediate. Damage from a diverse assemblage of folivorous insects, and from a specialist stemboring lepidopteran larva, fit the defence predictions closely. A gradient of attack levels suggests that the wild perennial is most defended, followed in descending order by the wild annual, the land-race cultivar and the modern high-yielding variety. Alternative hypotheses for this pattern are consistent with some, but not all, of our data.     

中国栽培稻的起源与演化

中国栽培稻起源地主要有4种假说:华南起源说、云南起源说、长江中下游说和长江中游-淮河上游说。对其进行了简要概括,并进行评述:目前没有一种假说能完全符合水稻起源的4个条件,此外有些学者提出水稻的多起源中心;从分子生物学角度综述了栽培稻籼粳分化研究进展,主要有两个起源说:一源论和二次(或多次)起源论,大量研究支持籼稻和粳稻多起源论;从古DNA、水稻落粒性与驯化、植硅石等方面探讨栽培稻起源演化的研究方法。旨在能为水稻的起源演化研究提供有价值的参考。     

Contrasting consequences of plant domestication for the chemical defenses of leaves and seeds in lima bean plants

Plant domestication is assumed to result in reduced levels of defensive compounds in crops, because this makes the plants more suitable for consumption by humans and livestock. We argue that this should mainly be reflected in the concentrations of defense compounds in the plant parts that are used for consumption and not necessarily for other parts of crop plants. We tested this hypothesis for domesticated lima bean (Phaseolus lunatus), by comparing its chemical defenses against a leaf herbivore, the beet armyworm (Spodoptera exigua), and a seed predator, the beetle Zabrotes subfasciatus. For seeds and leaves we determined the concentrations of cyanogenic glycosides (CNGs) in cultivated varieties and wild populations and evaluated the preference and performance of the herbivores when exposed to leaves and seeds from wild and cultivated plants. Concentrations of CNGs were significantly different between wild and cultivated plants. In the leaves the concentration of CNGs in the cultivated varieties were more than double that of the wild leaves. In contrast, seeds from cultivated plants had up to 20 times lower CNG concentration compared to seeds from the wild populations. Insect preference and performance do not parallel the chemical data. Larvae of S. exigua preferred wild leaves but had higher survival on cultivated leaves. The beetles, however, strongly preferred seeds from cultivated plants and females developed more quickly on these seeds. We conclude that domestication of P. lunatus has altered the concentration of CNGs in both the seeds and the leaves in opposite directions. This results in differential effects on the herbivores that attack these two plant structures. The contrasting effect of domestication on different plant tissues can be explained by the fact that bean plants have been specifically selected for human consumption of the seeds. Tissue-specific effects of plant domestication on plant defenses can be expected for other crops as well.     

Changes in the Cell Volume of Didinium nasutum During Population Increase*

SYNOPSIS. In 3 species of carnivorous protozoa, the rate of individual food intake per generation declines with an increase in the density of the population. In all, the rate of division remains constant. Three hypotheses may be proposed to explain these phenomena: the individual size decreases, thus bringing about a decline in food need; the individuals in the earlier stages of population growth consume excess food which is passed on to later generations to supplement their food intake; an increase in density within the carnivore population decreases the activity rate, thus reducing the food requirement. Experiments using Didinium nasutum as the carnivore and Paramecium aurelia, syngen 4, as the food source were conducted to test these 3 hypotheses. The results contradicted the 1st hypothesis and part of the 2nd. A new working hypothesis based on the remaining hypotheses is proposed.     

Natural selection on synonymous sites is correlated with gene length and recombination in Drosophila.

Evolutionary analysis of codon bias in Drosophila indicates that synonymous mutations are not neutral, but rather are subject to weak selection at the translation level. Here we show that the effectiveness of natural selection on synonymous sites is strongly correlated with the rate of recombination, in accord with the nearly neutral hypothesis. This correlation, however, is apparent only in genes encoding short proteins. Long coding regions have both a lower codon bias and higher synonymous substitution rates, suggesting that they are affected less efficiently by selection. Therefore, both the length of the coding region and the recombination rate modulate codon bias. In addition, the data indicate that selection coefficients for synonymous mutations must vary by a minimum of one or two orders of magnitude. Two hypotheses are proposed to explain the relationship among the coding region length, the codon bias, and the synonymous divergence and polymorphism levels across the range of recombination rates in Drosophila. The first hypothesis is that selection coefficients on synonymous mutations are inversely related to the total length of the coding region. The second hypothesis proposes that interference among synonymous mutations reduces the efficacy of selection on these mutations. We investigated this second hypothesis by carrying out forward simulations of weakly selected mutations in model populations. These simulations show that even with realistic recombination rates, this interference, which we call the "small-scale" Hill-Robertson effect, can have a moderately strong influence on codon bias.     

Wolves Are Better Imitators of Conspecifics than Dogs

Domestication is thought to have influenced the cognitive abilities of dogs underlying their communication with humans, but little is known about its effect on their interactions with conspecifics. Since domestication hypotheses offer limited predictions in regard to wolf-wolf compared to dog-dog interactions, we extend the cooperative breeding hypothesis suggesting that the dependency of wolves on close cooperation with conspecifics, including breeding but also territory defense and hunting, has created selection pressures on motivational and cognitive processes enhancing their propensity to pay close attention to conspecifics’ actions. During domestication, dogs’ dependency on conspecifics has been relaxed, leading to reduced motivational and cognitive abilities to interact with conspecifics. Here we show that 6-month-old wolves outperform same aged dogs in a two-action-imitation task following a conspecific demonstration. While the wolves readily opened the apparatus after a demonstration, the dogs failed to solve the problem. This difference could not be explained by differential motivation, better physical insight of wolves, differential developmental pathways of wolves and dogs or a higher dependency of dogs from humans. Our results are best explained by the hypothesis that higher cooperativeness may come together with a higher propensity to pay close attention to detailed actions of others and offer an alternative perspective to domestication by emphasizing the cooperativeness of wolves as a potential source of dog-human cooperation.     

Integrative response of plant mitochondrial electron transport chain to nitrogen source

Nitrogen (N) availability is widely known as a determinant of plant growth and respiration rate. However, less attention has been paid to the effect of the type of N source (nitrate, nitrite or ammonium) on the respiratory system. This review summarizes the latest findings on this topic, with an emphasis on the effect of ammonium and nitric oxide (NO) on the respiratory system, and the physiological role of alternative oxidase (AOX). First, concentrated ammonium has been found to increase plant respiration rate (ammonium-dependent respiratory increase, ARI). We will introduce two hypotheses to explain ARI, futile ammonium cycling and excess reducing equivalents, and verify the validity of each hypothesis. We suggest that these two hypotheses are not necessarily mutually exclusive. Second, gene expression of AOX is suppressed when N is predominately available as nitrate instead of ammonium. We will discuss possible signaling pathways leading to this expression pattern. Third, while AOX expression is induced by NO, AOX activity itself is insensitive to NO. In contrast, activity of cytochrome c oxidase (COX) is sensitive to NO. We outline the NO production pathway, focusing on nitrite-dependent NO production, and discuss the physiological significance of the fact that AOX activity is insensitive to NO. Finally, this review aims to build an integrated scheme of the respiratory response to the type of N source, considering leaves in high light conditions or hypoxic roots.