From Genome to Diversity
The genus Oryza is composed of approximately 24 species. Wild species of Oryza contain a largely untapped resource of agronomically important genes. As an increasing number of genomes of wild rice species have been or will be sequenced, Oryza is becoming a model system for plant comparative, functional and evolutionary genomics studies. Comparative analyses of large genomic regions and whole-genome sequences have revealed molecular mechanisms involved in genome size variation, gene movement, genome evolution of polyploids, transition of euchromatin to heterochromatin and centromere evolution in the genus Oryza. Transposon activity and removal of transposable elements by unequal recombination or illegitimate recombination are two important factors contributing to expansion or contraction of Oryza genomes. Double-strand break repair mediated gene movement, especially non-homologous end joining, is an important source of non-colinear genes. Transition of euchromatin to heterochromatin is accompanied by transposable element amplification, segmental and tandem duplication of genic segments, and acquisition of heterochromatic genes from other genomic locations. Comparative analyses of multiple genomes dramatically improve the precision and sensitivity of evolutionary inference than single-genome analyses can provide. Further investigations on the impact of structural variation, lineage-specific genes and evolution of agriculturally important genes on phenotype diversity and adaptation in the genus Oryza should facilitate molecular breeding and genetic improvement of rice.
The term “Tree of Life” was first used by Charles Darwin in 1859 as a metaphor for describing phylogenetic relationships among organisms. Over the past three decades, the recognized tree of life has improved considerably in overall size and reliability due to an increase in diversity of character resources, a dramatic growth in useable data, and the development of tree-reconstruction methods. As a bridge connecting phylogeny, evolution and related disciplines, such as molecular biology, ecology, genomics, bioinformatics and computer science, the tree of life is increasingly widely used. In this paper, we review the history and progress of tree of life studies and focus on its application in the following fields: (1) the reconstruction of phylogenetic trees at different taxonomic hierarchies to understand phylogenetic relationships among taxa; (2) investigation of the origins of taxa and biogeographic patterns based on dating estimation and biogeographic reconstruction; (3) examination of species’ diversification and its causes by integrating dated trees, ecological factors, environmental variation and key innovations; (4) the study of the origin and patterns of biodiversity, predating biodiversity dynamics, and development of conservation strategies. Finally, we evaluate the difficulties from matrix alignment, gene tree incongruence and “rogue taxa” distraction in tree reconstruction due to massive increases of useable data and in the context consider “supertree” building in the future.
Modes of pollen dispersal are important for plant ecology, conservation, and evolutionary biology as pollen-mediated gene flow connects one generation of sexually-reproducing plants to the next. With the development of DNA molecular techniques, molecular markers (especially microsatellite markers) have replaced traditional physical markers for pollen flow analysis. Methods of paternity assignment with maximum likelihood and Bayesian inference have greatly improved the estimation of pollen flow characteristics with regard to direction, distance, and strength. Pollen dispersal curves have been characterized by single parameter, two-parameter, multi-parameter, and two-component composite models to better evaluate the shape of dispersal distributions. These innovative techniques and methods have been successfully applied to assess pollination patterns in studies of plant sexual polymorphism, population connectivity, and natural hybridization, which, in turn, have provided important insights into basic theories of evolution, ecology, and conservation. In the coming years, high-throughput sequencing technologies are expected to accelerate the application of molecular marker-based pollen flow analysis across a wide range of plant taxa.
The sea surrounding the Antarctic continent is one of the coldest regions in the world. It provides an environmentally unique and isolated “hotbed” for evolution to take place. In the past 30 million years, species of Perciform suborder Notothenioidei evolved and diversified from a benthic and temperate-water ancestor, and now dominate the fish fauna of the coldest ocean. Because of their distribution across temperature zones both inside and outside the Antarctic Polar Front, notothenioid fishes are regarded as excellent model organisms for exploring mechanisms of adaptive evolution, particularly cold adaptation. We first summarize research progress on the biodiversity of Antarctic fish and then review current findings on the peculiar biological characteristics of Antarctic notothenioids that evolved in response to a freezing environment. Research has revealed that extensive gene duplication and transcriptomic changes occurred during the adaptive radiation of notothenioid fish. Examples of highly duplicated genes in the Antarctic lineages include genes encoding hepcidin, and zona pellucida proteins, in addition to various retrotransposable elements. A few genes from Antarctic notothenioid fishes have been used as transgenes and demonstrated to be effective in making transgenic plants cold-hardy. In the coming years, the genomes of some Antarctic notothenioid species will be fully sequenced and the adaptive functions of duplicated genes will be further elucidated. Such studies will deepen our understanding of how genomes evolve in freezing environments, and provide an improved knowledge of molecular mechanisms of cold adaptation.
An important task in evolutionary biology is to understand the reason for and mechanisms of morphological diversification. Studies in evolutionary developmental biology have revealed that, rather than being invented repeatedly from scratch, many complex morphological structures have evolved by modification of ancient regulatory networks. In other words, morphological diversity is not always produced by changes in the protein-coding region of regulatory genes; rather, it largely depends on the evolution of gene regulation. As the main components of the regulatory regions of a gene, cis regulatory elements bind to specific trans factors and determine the precise expression of the gene in time, place and amount. As a result, gain, loss, change or modification of cis regulatory elements may lead to shifts in gene expression, which, in turn, generate morphological diversity. Here, by reviewing recent progress in this and related fields, we summarize the basic features of gene regulation in eukaryotes, elucidating its fundamental evolutionary pattern and revealing its importance in generating morphological diversity.
Angiosperm phylogenetics investigates the evolutionary history and relationships of angiosperms based on the construction of phylogenetic trees. Since the 1990s, nucleotide or amino acid sequences have been widely used for this and angiosperm phylogenetic analysis has advanced from using single or a combination of a few organellar genes to whole plastid genome sequences, resulting in the widely accepted modern molecular systematics of angiosperms. The current framework of the angiosperm phylogeny includes highly supported basal angiosperm relationships, five major clades (eudicots, monocots, magnoliids, Chloranthales, and Ceratophyllales), orders grouped within these clades, and core groups in the monocots or eudicots. However, organellar genes have some limitations; these involve uniparental inheritance in most instances and a relatively low percentage of phylogenetic informative sites. Thus, they are unable to resolve some relationships even when whole plastid genome sequences are used. Therefore, the utility of biparentally inherited nuclear genes with more information about evolutionary history, has gradually received more attention. Nevertheless, there are still some plant groups that are difficult to place in the angiosperm phylogeny, such as those involving the relative positions of the five major groups as well as those of several orders of eudicots. In this review, we discuss the applications, advantages and disadvantages of marker genes, the deep relationships that have been resolved in angiosperm phylogeny, groups with uncertain positions, and the challenges that remain in resolving an accurate phylogeny for angiosperms.
Speciation has long been a core issue in evolutionary biology and is of fundamental importance to the formation of biodiversity. The traditional view of allopatric speciation holds that geographic isolation is a major driver of speciation and that species divergence only occurs in circumstances where there is geographic isolation between populations. In recent years, with the development of population genomics and the advance of coalescent-based analytical methods, speciation with gene flow has become a topic of major interest in the field of evolutionary biology research. Does gene flow occur during the process of speciation? How does it affect species divergence? What are the reproductive isolation underlying the speciation in the presence of gene flow? All these questions are foci of attention in current speciation research. In this paper, we review the distribution patterns of temporal and spatial gene flow, and elucidate the effects of gene flow on speciation and the evolution of reproductive isolation. We conclude that speciation with gene flow could be common in nature.
Southeast (SE) Asia refers to the region east to the Philippine islands, west to the Indian subcontinent, north to central China and south to the Sunda islands. This region includes six of the world’s 25 biodiversity hotspots and is of strategic significance in global biodiversity conservation. The complicated geological and climatological history of this region has resulted in extremely high species diversity and endemism. Two classic biogeographic boundaries, the Wallace Line and the Isthmus of Kra, divide SE Asia into the Indochinese province to the north and Sundaic province to the south. Because the Indochinese and Sundaic provinces are connected today through the Malay Peninsula and the Sunda shelf was exposed for the majority of time during the Quaternary glaciation, previous biogeographic studies have proposed that gene flow occurred between mainland and different island populations causing low divergence in the region. However, recent molecular genetic studies have reported that migration of terrestrial mammal populations was not as great as previously thought due to ecological restrictions. Thus, deep vicariant divergence was present in several mammals as early as two million years ago and appeared not to have been affected by gene flow following the formation of land bridges during later glacial periods. Furthermore, the super eruption of the Toba volcano in Sumatra about 73,000 years ago may have intensified divergence. A literature review has indicated three hierarchical levels present in the formation of mammalian diversity in SE Asia. These include populations between the Indochinese and Sundaic provinces which diverged millions of years ago, populations among the Sunda Islands which diverged hundreds of thousands of years ago, and Late Pleistocene biogeographic events causing demographic changes. Most of the previous population genetic studies on SE Asia mammals were based on analyses of mitochondrial or nuclear DNA data. Recent advances in population genomics provide new opportunities to obtain a comprehensive understanding of the demographic history and speciation processes of SE Asian mammals during the Quaternary glaciation.
Adult individuals of multicellular organisms are derived from single cells, the zygote. If the phenotype of a mature organism is regarded as a pattern of existence, then the process that generates the pattern can be called developmental patterning. Consequently, modification or alteration of the original developmental trajectory to generate novel phenotype(s) is the process of developmental repatterning. Accumulated data in recent years suggest that developmental repatterning is not only widespread, but is also very important during the evolution of multicellular organisms. According to the type and consequence of mutation, developmental repatterning can be divided into four main types: heterochrony, heterotopy, heterometry, and heterotypy. Heterochrony, heterotopy and heterometry refer to changes of gene expression over time, space and in amount/concentration, respectively, while heterotypy is the replacement of gene product. Here, by introducing examples of developmental repatterning, we explain the relationship between developmental repatterning and phenotypic evolution, and discuss its contribution to biodiversity.
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