Chromosome number, karyotype, and taxonomic considerations on the enigmatic Sellocharis paradoxa Taubert (Leguminosae, Papilionoideae, Genisteae)

Until recently, Sellocharis paradoxa Taubert, the only species of this Genisteae genus, was known solely by the isotypes. Recent new collections in Rio Grande do Sul, southern Brazil, have enabled data on chromosome number and karyotype morphology to be obtained for the first time. S. paradoxa has 2 n  = 20 chromosomes, and a bimodal asymmetrical karyotype, composed of one pair of long ( c . 6.3 µm) metacentric, five pairs of shorter acrocentric, and four pairs of shorter telocentric chromosomes ranging from c . 3.7 to 2.7 µm. The chromosome number and karyotype morphology of S. paradoxa do not fit into the Genisteae pattern. Existing information is so far insufficient to answer evolutionary questions about its origin and phylogenetic relationships, but the uniqueness of this taxon, first indicated by its peculiar leaf arrangement, and now supported by its uncommon karyological constitution, strongly suggests that the suprageneric taxonomic position of S. paradoxa should be re-evaluated.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 155 , 223–226.     

Homology versus analogy: possible evolutionary relationship of immunoglobulins, cupredoxins, and Cu,Zn-superoxide dismutase

The 'immunoglobulin-like' fold is one of most common structural motifs observed in proteins. This topology is found in more than 80 superfamilies of proteins, including Cu,Zn-superoxide dismutase (SOD) and cupredoxin. Evolutionary relationships have not been identified, but may exist. The challenge remains, therefore, of resolving the issue of whether the diverse distribution of the fold is accounted for by divergent evolution of function or convergent evolution of structure following multiple independent origins of function. Since the early studies that revealed conformational similarity of immunoglobulins and other proteins, the number of primary structures available for comparison has dramatically increased and new computational approaches for analysis of sequences have been developed. It now appears that a hypothesis of a common evolutionary origin for cupredoxins, Cu,Zn-SOD, and immunoglobulins may be credible. The distinction between protein homology and protein analogy is fundamental. The immunoglobulin-like fold may represent a robust system within which to examine again the issue of protein homology versus analogy.     

小麦的分类、起源与进化

小麦是世界历史上最古老的作物之一,约在一万年以前,在西南亚,人类首先成功地将小麦进行栽培生产粮食,因此小麦栽培历史和人类开化有着密切的相互关系。在现代世界农业中,小麦也是最重要的作物之一。它分布面积很广,从北纬67°的挪威、芬兰和苏联到南纬45°的阿根庭都有栽培。世界生产小麦的地区有苏联南部、美国中部平     

Unconstrained 3D-kinematics of prehension in five primates: Lemur,capuchin, gorilla,chimpanzee, human

Primates are known for their use of the hand in many activities including food grasping. Yet, most studies concentrate on the type of grip used. Moreover, kinematic studies remain limited to a few investigations of the distal elements in constrained conditions in humans and macaques. In order to improve our understanding of the prehension movement in primates, we analyse here the behavioural strategies (e.g., types of grip, body postures) as well as the 3D kinematics of the whole forelimb and the trunk during the prehension of small static food items in five primate species in unconstrained conditions. All species preferred the quadrupedal posture except lemurs, which used a typical crouched posture. Grasp type differed among species, with smaller animals (capuchins and lemurs) using a whole-hand grip and larger animals (humans, gorillas, chimpanzees) using predominantly a precision grip. Larger animals had lower relative wrist velocities and spent a larger proportion of the movement decelerating. Humans grasped food items with planar motions involving small joint rotations, more similar to the smaller animals than to gorillas and chimpanzees, which used greater rotations of both the shoulder and forearm. In conclusion, the features characterising human food prehension are present in other primates, yet differences exist in joint motions. These results provide a good basis to suggest hypotheses concerning the factors involved in driving the evolution of grasping abilities in primates.     

Population structure, levels of selection, and the evolution of intracellular symbionts

Many obligately intracellular symbionts exhibit a characteristic set of genetic changes that include an increase in substitution rates, loss of many genes, and apparent destabilization of many proteins and structural RNAs. Authors have suggested that these changes are due to increased mutation rates, or, more commonly, decreased effective population size due to population bottlenecks at the symbiont or, perhaps, host level. I propose that the increase in substitution rates and accumulation of deleterious mutations is a consequence of the population structure imposed on the endosymbionts by strict host association, loss of horizontal transmission and potentially conflicting levels of selection. I analyze a population genetic model of endosymbiont evolution, and demonstrate that substitution rates will increase, and the effect of those substitutions on endosymbiont fitness will become more deleterious as horizontal transmission among hosts decreases. Additionally, I find that there is a critical level of horizontal transmission below which natural selection cannot effectively purge deleterious mutations, leading to an expected loss of fitness over time. This critical level varies across loci with the degree of correlation between host and endosymbiont fitness, and may help explain differential retention and loss of certain genes.     

Vicariance, climate change, anatomy and phylogeny of Restionaceae

Cutler suggested almost 30 years ago that there was convergent evolution between African and Australian Restionaceae in the distinctive culm anatomical features of Restionaceae. This was based on his interpretation of the homologies of the anatomical features, and these are here tested against a 'supertrec' phylogeny, based on three separate phvlogenies. The first is based on morphology and includes all genera; the other two are based on molecular sequences from the chloroplast genome-, one covers the African genera, and the other tin-Australian genera. This analysis corroborates Cutler's interpretation of convergent evolution between African and Australian Restionaceae. However, it indicates that for the Australian genera, the evolutionary pathway of the culm anatomy is much more complex than originally thought. In the most likely scenario, the ancestral Restionaceae have protective cells derived from the chlorenchyma. These persist in African Restionaceae, but are soon lost in Australian Restionaceae. Pillar cells and sclerenchyma ribs evolve early in the diversification of Australian Restionaceae, but are secondarily lost numerous times. In some of the reduction cases, the result is a very simple culm anatomy, which Cutler had interpreted as a primitively simple culm type, while in other cases it appears as if the functions of the ribs and pillars may have been taken over by a new structure, protective cells developed from epidermal, rather than chlorenchyma, cells. Cutler suggested that this convergent evolution might have been in response to Tertiary climatic deterioration, but this study finds no strong corroborating evidence for this.     

Glycogen phosphorylase sequences from the amitochondriate protists, Trichomonas vaginalis, Mastigamoeba balamuthi, Entamoeba histolytica and Giardia intestinalis

Glycogen phosphorylase genes or messages from four amitochondriate eukaryotes, Trichomonas vaginalis, Mastigamoeba balamuthi, Entamoeba histolytica (two genes) and Giardia intestinalis, have been isolated and sequenced. The sequences of the amitochondriate protist enzymes appear to share a most recent common ancestor. The clade containing these sequences is closest to that of another protist, the slime mold (Dictyostelium discoideum), and is more closely related to fungal and plant phosphorylases than to mammalian and eubacterial homologs. Structure-based amino acid alignment shows conservation of the residues and domains involved in catalysis and allosteric regulation by glucose 6-phosphate but high divergence at domains involved in phosphorylation-dependent regulation and AMP binding in fungi and animals. Protist phosphorylases, as their prokaryotic and plant counterparts, are probably not regulated by phosphorylation.     

小麦的分类、起源与进化

小麦是世界历史上最古老的作物之一,约在一万年以前,在西南亚,人类首先成功地将小麦进行栽培生产粮食,因此小麦栽培历史和人类开化有着密切的相互关系。在现代世界农业中,小麦也是最重要的作物之一。它分布面积很广,从北纬67°的挪威、芬兰和苏联到南纬45°的阿根庭都有栽培。世界生产小麦的地区有苏联南部、美国中部平原和加拿大相邻地区、地中海地区、中国、印度、阿根廷北部和澳大利亚的西南部。这类作物在比较宽的环境 范围内都能获得高产。据统计,全世界有1/3的人口以小麦为主要粮食.消费的小麦食物卡值占全世界的20%以上。     

Enhancers,development, and evolution

A single-celled fertilized egg develops into a complex, multicellular animal through a series of selection processes of developmental pathways. During these processes, regulatory genes exhibit spatiotemporally restricted expression under the control of the species-specific genetic program, and dictate developmental processes from germ layer formation to cellular differentiation. Elucidation of molecular mechanisms underlying developmental processes and also of mechanistic bases for morphological diversification during evolution is one of the central issues in contemporary developmental biology. Progress has been made due to recent technological innovations, such as high-throughput nucleotide sequencing, live-cell imaging, efficient genetic manipulation, and establishment of the organoid system, opening new avenues to the above issues.     

Robustness, evolvability, and neutrality

Biological systems, from macromolecules to whole organisms, are robust if they continue to function, survive, or reproduce when faced with mutations, environmental change, and internal noise. I focus here on biological systems that are robust to mutations and ask whether such systems are more or less evolvable, in the sense that they can acquire novel properties. The more robust a system is, the more mutations in it are neutral, that is, without phenotypic effect. I argue here that such neutral change--and thus robustness--can be a key to future evolutionary innovation, if one accepts that neutrality is not an essential feature of a mutation. That is, a once neutral mutation may cause phenotypic effects in a changed environment or genetic background. I argue that most, if not all, neutral mutations are of this sort, and that the essentialist notion of neutrality should be abandoned. This perspective reconciles two opposing views on the forces dominating organismal evolution, natural selection and random drift: neutral mutations occur and are especially abundant in robust systems, but they do not remain neutral indefinitely, and eventually become visible to natural selection, where some of them lead to evolutionary innovations.     

LIMITED DISPERSAL, BUDDING DISPERSAL, AND COOPERATION: AN EXPERIMENTAL STUDY

Numerous theoretical studies have investigated how limited dispersal may provide an explanation for the evolution of cooperation, by leading to interactions between relatives. However, despite considerable theoretical attention, there has been a lack of empirical tests. In this article, we test how patterns of dispersal influence the evolution of cooperation, using iron-scavenging in the bacterium Pseudomonas aeruginosa as our cooperative trait. We found that relatively limited dispersal does not favor cooperation. The reason for this is that although limited dispersal increases the relatedness between interacting individuals, it also leads to increased local competition for resources between relatives. This result supports Taylor's prediction that in the simplest possible scenario, the effects of increased relatedness and local competition exactly cancel out. In contrast, we show that one way for cooperation to be favored is if individuals disperse in groups (budding dispersal), because this maintains high relatedness while reducing local competition between relatives (relatively global competition).     

Ectoderm,endoderm, and the evolution of heterodont dentitions

Mammalian dentitions consist of different shapes/types of teeth that are positioned in different regions of the jaw (heterodont) whereas in many fish and reptiles all teeth are of similar type (homodont). The process by which heterodont dentitions have evolved in mammals is not understood. In many teleosts teeth develop in the pharynx from endoderm (endodermal teeth), whereas mammalian teeth develop from the oral ectoderm indicating that teeth can develop (and thus possibly evolve) via different mechanisms. In this article, we compare the molecular characteristics of pharyngeal/foregut endoderm with the molecular characteristics of oral ectoderm during mouse development. The expression domains of Claudin6, Hnf3β, α‐fetoprotein, Rbm35a, and Sox2 in the embryonic endoderm have boundaries overlapping the molar tooth‐forming region, but not the incisor region in the oral ectoderm. These results suggest that molar teeth (but not incisors) develop from epithelium that shares molecular characteristics with pharyngeal endoderm. This opens the possibility that the two different theories proposed for the evolution of teeth may both be correct. Multicuspid (eg. molars) having evolved from the externalization of endodermal teeth into the oral cavity and monocuspid (eg. incisors) having evolved from internalization of ectodermal armour odontodes of ancient fishes. The two different mechanisms of tooth development may have provided the developmental and genetic diversity on which evolution has acted to produce heterodont dentitions in mammals. genesis 48:382–389, 2010. © 2010 Wiley‐Liss, Inc.     

The crown joules: energetics,ecology, and evolution in humans and other primates

Biological diversity is metabolic diversity: Differences in anatomy, physiology, life history, and activity reflect differences in energy allocation and expenditure among traits and tasks. Traditional frameworks in primatology, human ecology, public health, and paleoanthropology view daily energy expenditure as being more variable within than between species, changing with activity level but essentially fixed for a given body size. Growing evidence turns this view on its head. Total energy expenditure (kcal/d), varies relatively little within species, despite variation in physical activity; it varies considerably among species even after controlling for the effect of body size. Embracing this emerging paradigm requires rethinking potential trade‐offs in energy allocation within and between species, assessing evidence of metabolic acceleration within lineages, and abandoning activity‐based estimates of total energy expenditure. Difficult and exciting work lies ahead in the effort to untangle the ecological and evolutionary pressures shaping primate metabolic diversity.     

The tree, the network, and the species

To enrich the Hennigian internodal conception of species, a new formalization of the definition of the species concept is proposed. This rigorous definition allows for considerable unification of the various, and sometimes conflicting, techniques of species delimitation used in practice. First, the domain of such a definition is set out, namely, the set of all organisms on Earth, past, present, and future. Next, the focus is on the genealogical relationship among organisms, which provides the key to analysing the giant or global genealogical network (GGN) connecting all these organisms. This leads to the construction of an algorithm revealing the topological structure of the GGN, from families to lineages, ending up with a definition of species as equivalence classes of organisms corresponding to branches of the 'tree of life'. Such a theoretical definition of the species concept must be accompanied by various recognition criteria to be operational. These criteria are, for example, the ill-named 'biological species concepts', 'phylogenetic species concepts', etc., usually, but wrongly, presented as definitions of the species concept. Besides clarifying this disputed point, the definition in the present study displays the huge diversity of the scales (time-scale and population size) involved in actual species, thus explaining away the classical problems raised by previous attempts at defining the species concept (uniparental reproduction, temporal depth of species, and hybridization).  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 509–521.     

Evolutionary Epistemology, Social Epistemology, and the Demic Structure of Science

One of the principal difficulties in assessing Science as aProcess (Hull 1988) is determining the relationship between the various elements of Hull's theory. In particular, it is hard to understand precisely how conceptual selection is related to Hull's account of the social dynamics of science. This essay aims to clarify the relation between these aspects of his theory by examining his discussion of the``demic structure' of science. I conclude that the social account cando significant explanatory work independently of the selectionistaccount. Further, I maintain that Hull's treatment of the demicstructure of science points us toward an important set of issues insocial epistemology. If my reading of Science as a Process iscorrect, then most of Hull's critics (e.g., those who focus solelyon his account of conceptual selection) have ignored promisingaspects of his theory.     

Warfare,terrain, and political expansion

Very little explicit attention has been paid to the determinants of political borders and why they form at one location rather than another. With a statistically significant frequency, the political borders on the island of Tahiti at contact coincided with ridge formations that radiated from the island's interior and crossed the coastal plain to meet the sea in steep cliffs or bluffs. Since warfare had become the primary means of political expansion by contact, the determinants of this striking correlation appear to have been the strategic problems these features posed to the extension of armed might. These same processes were at work on many other Polynesian islands with the result that contactera variations in the degree of political unification and even sociopolitical development can be traced in considerable part to variations in island topography.     

鹿科麂属动物基因组演化研究进展

鹿科麂属(Muntiacus, Cervidae)在近两三百万年内经历了快速物种辐射, 但其物种间核型差异巨大. 5个现生种核型数据显示, 该类群染色体数目范围从小麂(Muntiacus reevesi)的46条到赤麂(M. muntjak vaginalis)的6条. 该类群的基因组在较短时间内发生了快速演化, 使其成为进化生物学研究的理想材料. 40多年来, 技术的革新使该领域的研究不断深入, 染色体重排的类型、推动重排的分子机制及物种间的核型演化历程逐渐被阐释. 而且, 研究中发现, 雄性黑麂(M. crinifrons)1p+4染色体的演化途径与哺乳动物Y染色体的演化历程相似, 可成为哺乳动物性染色体演化研究的珍贵模型. 有关麂属动物基因组演化依然有许多问题等待更加全面、深入的探讨. 本文总结了该领域研究进展, 并对未来研究热点进行了展望.     

Rapid,nonparallel genomic evolution of Brassica rapa (field mustard) under experimental drought

While we know that climate change can potentially cause rapid phenotypic evolution, our understanding of the genetic basis and degree of genetic parallelism of rapid evolutionary responses to climate change is limited. In this study, we combined the resurrection approach with an evolve-and-resequence design to examine genome-wide evolutionary changes following drought. We exposed genetically similar replicate populations of the annual plant Brassica rapa derived from a field population in southern California to four generations of experimental drought or watered conditions in a greenhouse. Genome-wide sequencing of ancestral and descendant population pools identified hundreds of SNPs that showed evidence of rapidly evolving in response to drought. Several of these were in stress response genes, and two were identified in a prior study of drought response in this species. However, almost all genetic changes were unique among experimental populations, indicating that the evolutionary changes were largely nonparallel, despite the fact that genetically similar replicates of the same founder population had experienced controlled and consistent selection regimes. This nonparallelism of evolution at the genetic level is potentially because of polygenetic adaptation allowing for multiple different genetic routes to similar phenotypic outcomes. Our findings help to elucidate the relationship between rapid phenotypic and genomic evolution and shed light on the degree of parallelism and predictability of genomic evolution to environmental change.     

Phenotypic variation of life‐history traits in native,invasive, and landrace populations of Brassica tournefortii

Varying environments can result in different patterns of adaptive phenotypes. By performing a common greenhouse experiment, we identified phenotypic differentiation on phenology, leaf morphology, branch architecture, size, and reproduction, among native, invasive, and landrace ranges of Brassica tournefortii. We first compared trait means and fitness functions among ranges, then we analyzed how trait means and selection strength of populations respond to varying aridity. Most traits varied such that landrace > invasive > native. Excluding reproduction, which was positively selected, most trait PCs experienced nonlinear selection in the native range but frequently shifted to directional selection in invasive and/or landrace ranges. The absence of strong clines for trait means in landrace and invasive populations suggest that agricultural practices and novel environments in source locations affected adaptive potential. Selection strength on faster reproductive phenology (negative directional) and leaf margin trait (disruptive) PCs coincided with increasing moisture. In native populations, higher aridity was associated with more days to reproduction, but landrace and invasive populations show stable mean time to reproduction with increasing moisture. A stable adaptive trait can increase range expansion in the invasive range, but stability can be beneficial for future harvest of B. tournefortii seed crops in the face of climate change.