Estimators of the human effective sex ratio detect sex biases on different timescales

Determining historical sex ratios throughout human evolution can provide insight into patterns of genomic variation, the structure and composition of ancient populations, and the cultural factors that influence the sex ratio (e.g., sex-specific migration rates). Although numerous studies have suggested that unequal sex ratios have existed in human evolutionary history, a coherent picture of sex-biased processes has yet to emerge. For example, two recent studies compared human X chromosome to autosomal variation to make inferences about historical sex ratios but reached seemingly contradictory conclusions, with one study finding evidence for a male bias and the other study identifying a female bias. Here, we show that a large part of this discrepancy can be explained by methodological differences. Specifically, through reanalysis of empirical data, derivation of explicit analytical formulae, and extensive simulations we demonstrate that two estimators of the effective sex ratio based on population structure and nucleotide diversity preferentially detect biases that have occurred on different timescales. Our results clarify apparently contradictory evidence on the role of sex-biased processes in human evolutionary history and show that extant patterns of human genomic variation are consistent with both a recent male bias and an earlier, persistent female bias.     

Experimental evolution

Experimental evolution is the study of evolutionary processes occurring in experimental populations in response to conditions imposed by the experimenter. This research approach is increasingly used to study adaptation, estimate evolutionary parameters, and test diverse evolutionary hypotheses. Long applied in vaccine development, experimental evolution also finds new applications in biotechnology. Recent technological developments provide a path towards detailed understanding of the genomic and molecular basis of experimental evolutionary change, while new findings raise new questions that can be addressed with this approach. However, experimental evolution has important limitations, and the interpretation of results is subject to caveats resulting from small population sizes, limited timescales, the simplified nature of laboratory environments, and, in some cases, the potential to misinterpret the selective forces and other processes at work.     

Conflict theory of genomic imprinting in mammals

In mammals, some embryonic genes are expressed differently depending on whether they are inherited from the sperm or egg, a phenomenon known as genomic imprinting. The information on the parental origin is transmitted by an epigenetic mark. Both the molecular mechanisms and evolutionary processes of genomic imprinting have been studied extensively. Here, I illustrate the simplest evolutionary dynamics of imprinting evolution based on the “conflict theory,” by considering the evolution of a gene encoding an embryonic growth factor controlling the maternal resource supply. It demonstrates that (a) the autosomal genes controlling placenta development to modify maternal resource acquisition may evolve a strong asymmetry of gene expression, provided the mother has some chance of accepting multiple males. (b) The genomic imprinting may not evolve if there is a small fraction of recessive deleterious mutations on the gene. (c) The growth-enhancing genes should evolve to paternally expressed, while the growth-suppressing genes should evolve to maternally expressed. (d) The X-linked genes also evolve genomic imprinting, but the main evolutionary force is the sex difference in the optimal embryonic size. I discuss other aberrations that can be explained by the modified versions of the basic model.     

Understanding Neutral Genomic Molecular Clocks

The molecular clock hypothesis is a central concept in molecular evolution and has inspired much research into why evolutionary rates vary between and within genomes. In the age of modern comparative genomics, understanding the neutral genomic molecular clock occupies a critical place. It has been demonstrated that molecular clocks run differently between closely related species, and generation time is an important determinant of lineage specific molecular clocks. Moreover, it has been repeatedly shown that regional molecular clocks vary even within a genome, which should be taken into account when measuring evolutionary constraint of specific genomic regions. With the availability of a large amount of genomic sequence data, new insights into the patterns and causes of variation in molecular clocks are emerging. In particular, factors such as nucleotide composition, molecular origins of mutations, weak selection and recombination rates are important determinants of neutral genomic molecular clocks.     

Primate CpG islands are maintained by heterogeneous evolutionary regimes involving minimal selection

Mammalian CpG islands are key epigenomic elements that were first characterized experimentally as genomic fractions with low levels of DNA methylation. Currently, CpG islands are defined based on their genomic sequences alone. Here, we develop evolutionary models to show that several distinct evolutionary processes generate and maintain CpG islands. One central evolutionary regime resulting in enriched CpG content is driven by low levels of DNA methylation and consequentially low rates of CpG deamination. Another major force forming CpG islands is biased gene conversion that stabilizes constitutively methylated CpG islands by balancing rapid deamination with CpG fixation. Importantly, evolutionary analysis and population genetics data suggest that selection for high CpG content is not?a significant factor contributing to conservation of CpGs in differentially methylated regions. The heterogeneous, but not selective, origins of CpG islands have direct implications for the understanding of DNA methylation patterns in healthy and diseased cells.     

物种形成过程中的分化基因组岛及其形成机制

理解物种形成机制是生态和进化领域的重要任务。得益于测序技术的快速发展, 越来越多研究发现分化种群(亚种、物种)间的基因组常呈现异质性分化景观, 存在分化基因组岛, 这被认为是基因流存在下的歧化选择引起的, 支持基因流存在下的成种假说。然而, 基因渐渗、祖先多态性的差异分选、连锁选择等其他进化过程也可导致分化基因组岛的形成。现有实证研究在解析分化基因组岛的形成机制时, 往往忽略了上述其他进化过程的作用。为此, 本文在辨析分化基因组岛相关概念的基础上, 总结了利用种群基因组数据鉴定分化基因组岛的方法, 对比了不同进化过程形成分化基因组岛的特征, 指出在区分不同机制时联用基因渐渗程度、绝对分化指数(d_XY)、相对节点深度(RND)、重组率等多个指标的必要性, 归纳了物种形成过程中分化基因组岛形成机制解析的研究思路, 并对未来在生殖隔离机制上的深入探索以及实证研究的整合分析等方面进行了展望。     

Coupled Genomic Evolutionary Histories as Signatures of Organismal Innovations in Cephalopods

How genomic innovation translates into organismal organization remains largely unanswered. Possessing the largest invertebrate nervous system, in conjunction with many species‐specific organs, coleoid cephalopods (octopuses, squids, cuttlefishes) provide exciting model systems to investigate how organismal novelties evolve. However, dissecting these processes requires novel approaches that enable deeper interrogation of genome evolution. Here, the existence of specific sets of genomic co‐evolutionary signatures between expanded gene families, genome reorganization, and novel genes is posited. It is reasoned that their co‐evolution has contributed to the complex organization of cephalopod nervous systems and the emergence of ecologically unique organs. In the course of reviewing this field, how the first cephalopod genomic studies have begun to shed light on the molecular underpinnings of morphological novelty is illustrated and their impact on directing future research is described. It is argued that the application and evolutionary profiling of evolutionary signatures from these studies will help identify and dissect the organismal principles of cephalopod innovations. By providing specific examples, the implications of this approach both within and beyond cephalopod biology are discussed.     

Adaptation genomics: next generation sequencing reveals a shared haplotype for rapid early development in geographically and genetically distant populations of rainbow trout

Local adaptation occurs when a population evolves a phenotype that confers a selective advantage in its local environment, but which may not be advantageous in other habitats. Restricted gene flow and strong selection pressures are prerequisites for local adaptation. Fishes in the family Salmonidae are predicted to provide numerous examples of local adaptation because of the high fidelity of returning to spawn in their natal streams, which results in highly structured populations, and the wide diversity of environments that salmonids have colonized. These conditions are ideally suited for producing a set of specialist phenotypes, whose fitness is maximized for one specific habitat, rather than a generalist phenotype similarly viable in several environments. Understanding patterns and processes leading to local adaptations has long been a goal of evolutionary biology, but it is only recently that identifying the molecular basis for local adaptation has become feasible because of advances in genomic technologies. The study of shared adaptive phenotypes in populations that are both geographically distant and genetically distinct should reveal some of the fundamental molecular mechanisms associated with local adaptation. In this issue of Molecular Ecology, Miller et al. (2012) make a significant contribution to the development of adaptation genomics. This study suggests that salmonids use standing genetic variation to select beneficial alleles for local adaptations rather than de novo mutations in the same gene or alternative physiological pathways. Identifying the genetic basis for local adaptation has major implications for the management, conservation and potential restoration of salmonid populations.     

Molecular evolutionary signatures reveal the role of host ecological dynamics in viral disease emergence and spread

RNA viruses account for numerous emerging and perennial infectious diseases, and are characterized by rapid rates of molecular evolution. The ecological dynamics of most emerging RNA viruses are still poorly understood and difficult to ascertain. The availability of genome sequence data for many RNA viruses, in principle, could be used to infer ecological dynamics if changes in population numbers produced a lasting signature within the pattern of genome evolution. As a result, the rapidly emerging phylogeographic structure of a pathogen, shaped by the rise and fall in the number of infections and their spatial distribution, could be used as a surrogate for direct ecological assessments. Based on rabies virus as our example, we use a model combining ecological and evolutionary processes to test whether variation in the rate of host movement results in predictive diagnostic patterns of pathogen genetic structure. We identify several linearizable relationships between host dispersal rate and measures of phylogenetic structure suggesting genetic information can be used to directly infer ecological process. We also find phylogenetic structure may be more revealing than demography for certain ecological processes. Our approach extends the reach of current analytic frameworks for infectious disease dynamics by linking phylogeography back to underlying ecological processes.     

Zebrafish as a model organism for nutrition and growth: towards comparative studies of nutritional genomics applied to aquacultured fishes

Zebrafish (Danio rerio) is a common research model in fish studies of toxicology, developmental biology, neurobiology and molecular genetics; it has been proposed as a possible model organism for nutrition and growth studies in fish. The advantages of working with zebrafish in these areas are their small size, short generation time (12–14 weeks) and their capacity to produce numerous eggs (100–200 eggs/clutch). Since a wide variety of molecular tools and information are available for genomic analysis, zebrafish has also been proposed as a model for nutritional genomic studies in fish. The detailed study of every species employed as a model organism is important because these species are used to generalize how several biological processes occur in related organisms, and contribute considerably toward improving our understanding of the mechanisms involved in nutrition and growth. The objective of this review is to show the relevant aspects of the nutrition and growth in zebrafish that support its utility as a model organism for nutritional genomics studies. We made a particular emphasis that gene expression and genetic variants in response to zebrafish nutrition will shed light on similar processes in aquacultured fish.     

An out-of-body experience: the extracellular dimension for the transmission of mutualistic bacteria in insects

Across animals and plants, numerous metabolic and defensive adaptations are a direct consequence of symbiotic associations with beneficial microbes. Explaining how these partnerships are maintained through evolutionary time remains one of the central challenges within the field of symbiosis research. While genome erosion and co-cladogenesis with the host are well-established features of symbionts exhibiting intracellular localization and transmission, the ecological and evolutionary consequences of an extracellular lifestyle have received little attention, despite a demonstrated prevalence and functional importance across many host taxa. Using insect–bacteria symbioses as a model, we highlight the diverse routes of extracellular symbiont transfer. Extracellular transmission routes are unified by the common ability of the bacterial partners to survive outside their hosts, thereby imposing different genomic, metabolic and morphological constraints than would be expected from a strictly intracellular lifestyle. We emphasize that the evolutionary implications of symbiont transmission routes (intracellular versus extracellular) do not necessarily correspond to those of the transmission mode (vertical versus horizontal), a distinction of vital significance when addressing the genomic and physiological consequences for both host and symbiont.     

Mitochondrial gene rearrangements: new paradigm in the evolutionary biology and systematics

Mitochondrial (mt) genomic study may reveal significant insight into the molecular evolution and several other aspects of genome evolution such as gene rearrangements evolution, gene regulation, and replication mechanisms. Other questions such as patterns of gene expression mechanism evolution, genomic variation and its correlation with physiology, and other molecular and biochemical mechanisms can be addressed by the mt genomics. Rare genomic changes have attracted evolutionary biology community for providing homoplasy free evidence of phylogenetic relationships. Gene rearrangements are considered to be rare evolutionary events and are being used to reconstruct the phylogeny of diverse group of organisms. Mt gene rearrangements have been established as a hotspot for the phylogenetic and evolutionary analysis of closely as well as distantly related organisms.     

Tightly Constrained Genome Reduction and Relaxation of Purifying Selection during Secondary Plastid Endosymbiosis

Endosymbiosis, the establishment of a former free-living prokaryotic or eukaryotic cell as an organelle inside a host cell, can dramatically alter the genomic architecture of the endosymbiont. Plastids or chloroplasts, the light-harvesting organelle of photosynthetic eukaryotes, are excellent models to study this phenomenon because plastid origin has occurred multiple times in evolution. Here, we investigate the genomic signature of molecular processes acting through secondary plastid endosymbiosis—the origination of a new plastid from a free-living eukaryotic alga. We used phylogenetic comparative methods to study gene loss and changes in selective regimes on plastid genomes, focusing on green algae that have given rise to three independent lineages with secondary plastids (euglenophytes, chlorarachniophytes, and Lepidodinium). Our results show an overall increase in gene loss associated with secondary endosymbiosis, but this loss is tightly constrained by the retention of genes essential for plastid function. The data show that secondary plastids have experienced temporary relaxation of purifying selection during secondary endosymbiosis. However, this process is tightly constrained, with selection relaxed only relative to the background in primary plastids. Purifying selection remains strong in absolute terms even during the endosymbiosis events. Selection intensity rebounds to pre-endosymbiosis levels following endosymbiosis events, demonstrating the changes in selection efficiency during different origin phases of secondary plastids. Independent endosymbiosis events in the euglenophytes, chlorarachniophytes, and Lepidodinium differ in their degree of relaxation of selection, highlighting the different evolutionary contexts of these events. This study reveals the selection–drift interplay during secondary endosymbiosis and evolutionary parallels during organellogenesis.     

对我国分子生态学研究近期发展战略的一些思考

分子生态学是多学科交叉的整合性研究领域, 是运用进化生物学理论解决宏观生物学问题的科学。经过半个多世纪的发展, 本学科已日趋成熟, 它不仅已经广泛渗透到宏观生物学的众多学科领域, 而且已经成为连接和融合很多不同学科的桥梁, 是目前最具活力的研究领域之一。其研究的范畴, 从最基础的理论和方法技术, 到格局和模式的发现和描述, 到对过程和机制的深入探讨, 再到付诸于实践的行动和规划指导等各个层次。分子生态学的兴起给宏观生物学带来了若干飞跃性的变化, 使宏观生物学由传统的以观察、测量和推理为主的描述性研究转变为以从生物和种群的遗传构成的变化和历史演化背景上检验、证明科学假设及揭示机制和规律为主的机制性/解释性研究, 因而使得对具有普遍意义的科学规律、生态和进化过程及机制的探索成为可能。分子生态学已经进入组学研究时代, 这使得阐明复杂生态过程、生物地理过程和适应性演化过程的机制性研究由原来难以企及的梦想变成完全可以实现的探求; 它也带来了全新的挑战, 其中最有深远影响的将是对分子生态学研究至关重要的进化生物学基础理论方面的突破, 例如遗传变异理论、种群分化理论、表观遗传因素的作用, 乃至进化生物学的基本知识构架等等。这些方面的进展必将使宏观生物学迎来一场空前的革命, 并对生态学的所有分支学科产生重大影响, 甚至催生诸如生态表观组学这样的新分支学科。对于中国科学家来说, 分子生态学组学时代的开启, 更是一个千载难逢的机遇, 为提出和建立生命科学的新方法、新假说、新思想和新理论提供了莫大的探索空间——此前我们对宏观生物学方法、理论和思想的发展贡献很小。然而, 限制组学时代重大突破的关键因素是理论、概念、理念、实验方法或分析方法方面的创新和突破, 这正是我国分子生态学研究最薄弱的环节。我国教育部门应尽快调整生命科学本科生培养的理念和方法, 以培养具备突出创新潜力的年轻一代后备人才; 同时, 科研项目资助部门和研究人员不仅应清醒地认识本学科领域的发展态势, 更要及时调整思路, 树立新的项目管理理念和治学 理念。     

Genomic consequences of multiple speciation processes in a stick insect

Diverse geographical modes and mechanisms of speciation are known, and individual speciation genes have now been identified. Despite this progress, genome-wide outcomes of different evolutionary processes during speciation are less understood. Here, we integrate ecological and spatial information, mating trials, transplantation data and analysis of 86 130 single nucleotide polymorphisms (SNPs) in eight populations (28 pairwise comparisons) of Timema cristinae stick insects to test the effects of different factors on genomic divergence in a system undergoing ecological speciation. We find patterns consistent with effects of numerous factors, including geographical distance, gene flow, divergence in host plant use and climate, and selection against maladaptive hybridization (i.e. reinforcement). For example, the number of highly differentiated ‘outlier loci’, allele-frequency clines and the overall distribution of genomic differentiation were recognizably affected by these factors. Although host use has strong effects on phenotypic divergence and reproductive isolation, its effects on genomic divergence were subtler and other factors had pronounced effects. The results demonstrate how genomic data can provide new insights into speciation and how genomic divergence can be complex, yet predictable. Future work could adopt experimental, mapping and functional approaches to directly test which genetic regions are affected by selection and determine their physical location in the genome.     

The origins of polypeptide domains

Three decades ago Gilbert posited that novel proteins arise by re-shuffling genomic sequences encoding polypeptide domains. Today, with numerous genomes and countless genes sequenced, it is well established that recombination of sequences encoding polypeptide domains plays a major role in protein evolution. There is, however, less evidence to suggest how the novel polypeptide domains, themselves, arise. Recent comparisons of genomes from closely related species have revealed numerous species-specific exons, supporting models of domain origin based on "exonization" of intron sequences. Also, a mechanism for the origin of novel polypeptide domains has been proposed based on analyses of insertion-based polymorphisms between orthologous genes across broad phylogenetic spectra and between allelic variants of genes within species. This review discusses these processes and how each might participate in the evolutionary emergence of novel polypeptide domains.     

Genomic insights into adaptation to high-altitude environments

Elucidating the molecular genetic basis of adaptive traits is a central goal of evolutionary genetics. The cold, hypoxic conditions of high-altitude habitats impose severe metabolic demands on endothermic vertebrates, and understanding how high-altitude endotherms cope with the combined effects of hypoxia and cold can provide important insights into the process of adaptive evolution. The physiological responses to high-altitude stress have been the subject of over a century of research, and recent advances in genomic technologies have opened up exciting opportunities to explore the molecular genetic basis of adaptive physiological traits. Here, we review recent literature on the use of genomic approaches to study adaptation to high-altitude hypoxia in terrestrial vertebrates, and explore opportunities provided by newly developed technologies to address unanswered questions in high-altitude adaptation at a genomic scale.