Polyploidy, hybridization and reticulate evolution: lessons from the Brassicaceae

The family Brassicaceae is well known for its large variation in chromosome numbers, common occurrence of polyploids and many reports of interspecific gene flow. The present review summarizes studies from the past decades on polyploidization and hybridization events, recognizing them as important evolutionary forces in the family. Attention is drawn to the issue of the reconstruction of reticulated pattern of evolution resulting from allopolyploid and homoploid hybrid speciation. The research of various authors on several Brassicaceae genera is presented and discussed in the context of our current understanding of polyploid and hybrid evolution. Model species, Arabidopsis thaliana and Brassica taxa, are referred to only marginally, major focus is on a comprehensive survey of studies on about a dozen best explored non-model genera (e.g. Cardamine, Draba, Rorippa, Thlaspi). The increasing amount of genetic and genomic resources available for Brassicaceae model species provides excellent opportunities for comparative genetic and genomic studies. Future research directions and challenges are thus outlined, in order to obtain more detailed insights into the evolution of polyploid and hybrid genomes.     

A current perspective on apomixis in ferns

This review provides a synopsis of apogamous reproduction in ferns and highlights important progress made in recent studies of fern apomixis. First, a summary of the apomictic fern life cycle is provided, distinguishing between two pathways to diploid spore production that have been documented in apomictic ferns (premeiotic endomitosis and meiotic first division restitution) and briefly discussing the evolutionary implications of each. Next, recent trends in fern apomixis research are discussed, exposing a shift in focus from the observation and characterization of apomixis in ferns to more integrated studies of the evolutionary and ecological implications of this reproductive mode. Peer-reviewed contributions from the past decade are then summarized, spanning the identification of new apomictic lineages through to the developmental, phylogenetic, and population genetic insights that have been made in studies of fern apomixis during that time. Gaps in our understanding are also discussed, including the extent and implications of recombinant apomixis in ferns, the possible reversibility of reproductive mode (from apomictic to sexual) in ferns, and the genomic causes and consequences of apomixis in seed free vascular plants. To conclude, future directions for fern apomixis research are proposed in the context of modern technological advances and recent insights from studies of apomixis in other groups.     

Detection of F1 Hybrids from Single-genome Data Reveals Frequent Hybridization in Hymenoptera and Particularly Ants

Hybridization occupies a central role in many fundamental evolutionary processes, such as speciation or adaptation. Yet, despite its pivotal importance in evolution, little is known about the actual prevalence and distribution of current hybridization across the tree of life. Here we develop and implement a new statistical method enabling the detection of F1 hybrids from single-individual genome sequencing data. Using simulations and sequencing data from known hybrid systems, we first demonstrate the specificity of the method, and identify its statistical limits. Next, we showcase the method by applying it to available sequencing data from more than 1,500 species of Arthropods, including Hymenoptera, Hemiptera, Coleoptera, Diptera, and Archnida. Among these taxa, we find Hymenoptera, and especially ants, to display the highest number of candidate F1 hybrids, suggesting higher rates of recent hybridization between previously isolated gene pools in these groups. The prevalence of F1 hybrids was heterogeneously distributed across ants, with taxa including many candidates tending to harbor specific ecological and life-history traits. This work shows how large-scale genomic comparative studies of recent hybridization can be implemented, uncovering the determinants of first-generation hybridization across whole taxa.     

Recurrent genome duplication events likely contributed to both the ancient and recent rise of ferns

Ferns, the second largest group of vascular plants, originated ～400 mil ion years ago(Mya). They became dominant in the ancient Earth landscape before the angiosperms and are stil important in current ecosystems.Many ferns have exceptional y high chromosome numbers,possibly resulting from whole-genome duplications(WGDs).However, WGDs have not been investigated molecularly across fern diversity. Here we detected and dated fern WGDs using a phylogenomic approach and by calculating synonymous substitution rates(Ks). We also investigated a possible correlation between proposed WGDs and shifts in species diversification rates. We identified 19 WGDs: three ancient events along the fern phylogenetic backbone that are shared by 66%–97% of extant ferns, with additional lineage-specific WGDs for eight orders, providing strongevidence for recurring genome duplications across fern evolutionary history. We also observed similar Ks peak values for more than half of these WGDs, with multiple WGDs occurring close to the Cretaceous(～145–66 Mya). Despite the repeated WGD events, the biodiversity of ferns declined during the Cretaceous, implying that other factors probably contributed to the floristic turnover from ferns to angiosperms. This study provides molecular evidence for recurring WGDs in ferns and offers important clues to the genomic evolutionary history of ferns.     

Elevational diversity patterns as an example for evolutionary and ecological dynamics in ferns and lycophytes

Evolutionary processes such as adaptation, ecological filtering, and niche conservatism involve the interaction of organisms with their environment and are thus commonly studied along environmental gradients. Elevational gradients have become among the most studied environmental gradients to understand large-scale patterns of species richness and composition because they are highly replicated with different combinations of geographical, environmental and historical factors. We here review the literature on using elevational gradients to understand evolutionary processes in ferns. Some phylogenetic studies of individual fern clades have considered elevation in the analysis or interpretation and postulated that fern diversification is linked to the colonization of mountain habitats. Other studies that have linked elevational community composition and hence ecological filtering with phylogenetic community composition and morphological traits, usually only found limited phylogenetic signal. However, these studies are ultimately only correlational, and there are few actual tests of the evolutionary mechanisms leading to these patterns. We identify a number of challenges for improving our understanding of how evolutionary and ecological processes are linked to elevational richness patterns in ferns: i) limited information on traits and their ecological relevance, ii) uncertainties on the dispersal kernels of ferns and hence the delimitation of regional species pools from which local assemblages are recruited, iii) limited genomic data to identify candidate genes under selection and hence actually document adaptation and selection, and iv) conceptual challenges in developing clear and testable hypotheses to how specific evolutionary processes can be linked to patterns in community composition and species richness.     

Research advances in animal distant hybridization

Distant hybridization refers to crosses between two different species or higher-ranking taxa that enables interspecific genome transfer and leads to changes in phenotypes and genotypes of the resulting progeny. If progeny derived from distant hybridization are bisexual and fertile, they can form a hybrid lineage through self-mating, with major implications for evolutionary biology, genetics, and breeding. Here, we review and summarize the published literature, and present our results on fish distant hybridization. Relevant problems involving distant hybridization between orders, families, subfamilies, genera, and species of animals are introduced and discussed, with an additional focus on fish distant hybrid lineages, genetic variation, patterns, and applications. Our review serves as a useful reference for evolutionary biology research and animal genetic breeding.     

What do we know about Hawaiian ferns and lycophytes?

The Hawaiian Islands are home to one of the most distinctive fern and lycophyte floras in the world. Of the 144 native fern species, 76% are endemic and, including subspecies and varieties, 84% of the 167 native fern taxa are endemic. There are 15 native lycophyte species, 47% of which are endemic, and 16 taxa, 50% of which are endemic. I review here most of the available literature on Hawaiian ferns and lycophytes. Few species of ferns or lycophytes have been studied in any kind of detail and, for most, we only know basic classification and general ecological information. Although the total number of studies reviewed here is not large, research has been conducted on a wide range of topics including systematics, floristics, dispersal, phylogeny, biogeography, ecology, form and function, population genetics, microevolution, fern-animal and fern-fungi associations, reproductive biology, demography, ethnobotany, and conservation.     

The evolution of chloroplast genes and genomes in ferns

Most of the publicly available data on chloroplast (plastid) genes and genomes come from seed plants, with relatively little information from their sister group, the ferns. Here we describe several broad evolutionary patterns and processes in fern plastid genomes (plastomes), and we include some new plastome sequence data. We review what we know about the evolutionary history of plastome structure across the fern phylogeny and we compare plastome organization and patterns of evolution in ferns to those in seed plants. A large clade of ferns is characterized by a plastome that has been reorganized with respect to the ancestral gene order (a similar order that is ancestral in seed plants). We review the sequence of inversions that gave rise to this organization. We also explore global nucleotide substitution patterns in ferns versus those found in seed plants across plastid genes, and we review the high levels of RNA editing observed in fern plastomes.     

Mammalian hybrid zones: a review

相似文献   

Incongruence between primary sequence data and the distribution of a mitochondrial atp1 group II intron among ferns and horsetails

Using DNA sequence data from multiple genes (often from more than one genome compartment) to reconstruct phylogenetic relationships has become routine. Augmenting this approach with genomic structural characters (e.g., intron gain and loss, changes in gene order) as these data become available from comparative studies already has provided critical insight into some long-standing questions about the evolution of land plants. Here we report on the presence of a group II intron located in the mitochondrial atp1 gene of leptosporangiate and marattioid ferns. Primary sequence data for the atp1 gene are newly reported for 27 taxa, and results are presented from maximum likelihood-based phylogenetic analyses using Bayesian inference for 34 land plants in three data sets: (1) single-gene mitochondrial atp1 (exon+intron sequences); (2) five combined genes (mitochondrial atp1 [exon only]; plastid rbcL, atpB, rps4; nuclear SSU rDNA); and (3) same five combined genes plus morphology. All our phylogenetic analyses corroborate results from previous fern studies that used plastid and nuclear sequence data: the monophyly of euphyllophytes, as well as of monilophytes; whisk ferns (Psilotidae) sister to ophioglossoid ferns (Ophioglossidae); horsetails (Equisetopsida) sister to marattioid ferns (Marattiidae), which together are sister to the monophyletic leptosporangiate ferns. In contrast to the results from the primary sequence data, the genomic structural data (atp1 intron distribution pattern) would seem to suggest that leptosporangiate and marattioid ferns are monophyletic, and together they are the sister group to horsetails--a topology that is rarely reconstructed using primary sequence data.     

附生蕨类植物的克隆性研究进展

石松类及蕨类植物在高等植物中处于比较特殊的进化与系统发育地位, 同时具有孢子植物(孢子)与种子植物(维管束)的双重特征。附生蕨类植物是蕨类植物中占据独特生境的一个大类群, 其生活史策略及进化历史与其附生生长的森林生态系统紧密相关。大部分附生蕨类植物的克隆生长习性及克隆生活史性状在其生态适应中具有重要作用, 但这方面未引起广泛关注。本文主要综述了中国山地森林中附生蕨类植物的根状茎克隆生长、克隆性与生态适应性、不同克隆生长方式与进化等方面, 并展望了蕨类植物克隆性在森林生态系统过程与功能中的作用, 以及今后如何将蕨类植物生态学研究与气候变化、植被恢复、土地利用变化等全球变化的主流方向进行结合。     

Evidence for natural selection in a fern hybrid zone

Morphological characters, chloroplast DNA, and allozymes were used to analyze the distribution of individuals within a hybrid population of the ferns Polystichum munitum and P. imbricans in northwestern California. Microsites within the population were characterized according to soil moisture and light levels reaching the plants. In sites with low soil moisture and high light levels, all of the ferns were genetically and morphologically like P. imbricans. In contrast, ferns with the genetic and morphological identity of P. munitum predominated in moist shady sites. Intermediate sites supported very few P.munitum, a wide variety of hybrid recombinants, and a majority of ferns with P. imbricans characteristics. The pattern of variation within the population is noteworthy because of the close proximity of the habitat extremes and the long-range dispersal of fern spores. We conclude that natural selection along environmental gradients must be a major factor in determining the ecological and genetic associations within the hybrid zone. The results of this study are evaluated in the context of the fern life cycle and compared to the assumptions of models explaining the establishment and maintenance of hybrid zones, which vary in the role attributed to environmentally mediated natural selection.     

Genomic markers reveal introgressive hybridization in the Indo-West Pacific mangroves: a case study

Biodiversity of mangrove ecosystems is difficult to assess, at least partly due to lack of genetic verification of morphology-based documentation of species. Natural hybridization, on the one hand, plays an important role in evolution as a source of novel gene combinations and a mechanism of speciation. However, on the other hand, recurrent introgression allows gene flow between species and could reverse the process of genetic differentiation among populations required for speciation. To understand the dynamic evolutionary consequences of hybridization, this study examines genomic structure of hybrids and parental species at the population level. In the Indo-West Pacific, Bruguiera is one of the dominant mangrove genera and species ranges overlap extensively with one another. Morphological intermediates between sympatric Bruguiera gymnorrhiza and Bruguiera sexangula have been reported as a variety of B. sexangula or a new hybrid species, B. × rhynchopetala. However, the direction of hybridization and extent of introgression are unclear. A large number of species-specific inter-simple sequence repeat (ISSR) markers were found in B. gymnorrhiza and B. sexangula, and the additive ISSR profiling of B. × rhynchopetala ascertained its hybrid status and identified its parental origin. The varying degree of scatterness among hybrid individuals in Principal Coordinate Analysis and results from NewHybrids analysis indicate that B. × rhynchopetala comprises different generations of introgressants in addition to F(1)s. High genetic relatedness between B. × rhynchopetala and B. gymnorrhiza based on nuclear and chloroplast sequences suggests preferential hybrid backcrosses to B. gymnorrhiza. We conclude that B. × rhynchopetala has not evolved into an incipient hybrid species, and its persistence can be explained by recurrent hybridization and introgression. Genomic data provide insights into the hybridization dynamics of mangrove plants. Such information can assist in biodiversity assessment by helping detect novel taxa and/or define species boundaries.     

蕨类植物配子体发育及其性器官分化的研究进展

作者概述了蕨类植物生活周期中不同发育阶段的特点,并着重介绍了光、植物生长调节物质、水和温度等因素对蕨类植物配子体发育的影响以及成精子囊素、光、钙离子和其它植物生长调节物质在性器官形成和分化过程中的作用。同时作者对蕨类植物性器官分化的不稳定性进行了探讨、并结合目前蕨类植物性器官分化的遗传学和分子生物学研究的最新进展,说明蕨类植物作为研究系统在植物生物学研究领域中的优势。     

Deciphering the origins of apomictic polyploids in the Cheilanthes yavapensis complex (Pteridaceae)

Deciphering species relationships and hybrid origins in polyploid agamic species complexes is notoriously difficult. In this study of cheilanthoid ferns, we demonstrate increased resolving power for clarifying the origins of polyploid lineages by integrating evidence from a diverse selection of biosystematic methods. The prevalence of polyploidy, hybridization, and apomixis in ferns suggests that these processes play a significant role in their evolution and diversification. Using a combination of systematic approaches, we investigated the origins of apomictic polyploids belonging to the Cheilanthes yavapensis complex. Spore studies allowed us to assess ploidy levels; plastid and nuclear DNA sequencing revealed evolutionary relationships and confirmed the putative progenitors (both maternal and paternal) of taxa of hybrid origin; enzyme electrophoretic evidence provided information on genome dosage in allopolyploids. We find here that the widespread apomictic triploid, Cheilanthes lindheimeri, is an autopolyploid derived from a rare, previously undetected sexual diploid. The apomictic triploid Cheilanthes wootonii is shown to be an interspecific hybrid between C. fendleri and C. lindheimeri, whereas the apomictic tetraploid C. yavapensis is comprised of two cryptic and geographically distinct lineages. We show that earlier morphology-based hypotheses of species relationships, while not altogether incorrect, only partially explain the complicated evolutionary history of these ferns.     

蕨类植物配子体育及其性器官分化的研究进展

作者概述了蕨类植物生活周期中不同发育阶段的特点,并着重介绍了不,植物生长调节物质,水和温度等因素对蕨类植物配子体发育的影响以及精子囊素,光,钙离子和其它植物生长调节物质在性器官形成和分化过程中的作用,同时作者对蕨类植物性器官分化的不稳定性进行了探讨,并结合目前蕨类植物性器官分化的遗传学和分子生物学研究的最新进展,说明蕨类植物作为研究系统在植物生物学研究领域中的优势。     

A systematic overview of fossil osmundalean ferns in China: Diversity variation,distribution pattern,and evolutionary implications

The order Osmundales is a unique fern taxon with extensive fossil records in geological past. Diverse osmundalean fossils have been reported from China, ranging in age from the Late Palaeozoic to the Cenozoic. Most of them are based on leaf impressions/compressions, but permineralized rhizomes are also well documented. In this study, we provide a systematic overview on fossil osmundalean ferns in China with special references on diversity variations, distribution patterns, and evolutionary implications. Fossil evidence indicates that this fern lineage first appeared in the Late Palaeozoic in China. The Late Triassic to Middle Jurassic interval was the radiation stage. From the Late Jurassic onward, fossil diversity declined rapidly. Cenozoic osmundalean taxa are represented by the relict species of Osmunda. Geographically, osmundalean fossils are found from both the Northern and Southern phytoprovinces of China, though variations are documented for geographical ranges. The Chinese fossil records cover almost all important stages for the macroevolution of the Osmundales, and contribute to further understanding of evolutionary processes of this peculiar fern lineage.     

Hybridization involving independent gametophytes in the Vandenboschia radicans complex (Hymenophyllaceae): a new perspective on the distribution of fern hybrids

To test our hypothesis of hybrid formation involving the ‘independent gametophyte’ phenomenon in ferns, we identified the genomic formulae and ploidy level of gametophytes of the Vandenboschia radicans complex at the periphery of a sporophyte population. We identified haploid gametophytes of V. kalamocarpa (one of the two putative parents of V.×stenosiphon) in a hybrid sporophyte population in Japan that lacks fertile non‐hybrid individuals. Furthermore, diploid sporophytes of the species were not found within a 50‐km radius. This finding supports a hypothesis of hybridization involving the ‘independent gametophyte’ phenomenon and provides a new perspective on the geographical distribution of fern hybrids.     

Incomplete reproductive isolation between Rhododendron taxa enables hybrid formation and persistence

The evolutionary consequences of hybridization ultimately depend on the magnitude of reproductive isolation between hybrids and their parents. We evaluated the relative contributions of pre-and post-zygotic barriers to reproduction for hybrid formation, hybrid persistence and potential for reproductive isolation of hybrids formed between two Rhododendron species,R. spiciferum and R. spinuliferum. Our study established that incomplete reproductive isolation promotes hybrid formation and persistence and delays hybrid speciation.All pre-zygotic barriers to reproduction leading to hybrid formation are incomplete: parental species have overlapping flowering; they share the same pollinators;reciprocal assessments of pollen tube germination and growth do not differ among parents. The absence of post-zygotic barriers between parental taxa indicates that the persistence of hybrids is likely. Reproductive isolation was incomplete between hybrids and parents in all cases studied, although asymmetric differences in reproductive fitness were prevalent and possibly explain the genetic structure of natural hybrid swarms where hybridization is known to be bidirectional but asymmetric. Introgression, rather than speciation, is a probable evolutionary outcome of hybridization between the two Rhododendron taxa. Our study provides insights into understanding the evolutionary implications of natural hybridization in woody plants.     

Hybridization during altitudinal range shifts: nuclear introgression leads to extensive cyto‐nuclear discordance in the fire salamander

Ecological models predict that, in the face of climate change, taxa occupying steep altitudinal gradients will shift their distributions, leading to the contraction or extinction of the high‐elevation (cold‐adapted) taxa. However, hybridization between ecomorphologically divergent taxa commonly occurs in nature and may lead to alternative evolutionary outcomes, such as genetic merger or gene flow at specific genes. We evaluate this hypothesis by studying patterns of divergence and gene flow across three replicate contact zones between high‐ and low‐elevation ecomorphs of the fire salamander (Salamandra salamandra) that have experienced altitudinal range shifts over the current postglacial period. Strong population structure with high genetic divergence in mitochondrial DNA suggests that vicariant evolution has occurred over several glacial–interglacial cycles and that it has led to cryptic differentiation within ecomorphs. In current parapatric boundaries, we do not find evidence for local extinction and replacement upon postglacial expansion. Instead, parapatric taxa recurrently show discordance between mitochondrial and nuclear markers, suggesting nuclear‐mediated gene flow across contact zones. Isolation with migration models support this hypothesis by showing significant gene flow across all five parapatric boundaries. Together, our results suggest that, while some genomic regions, such as the mitochondria, may follow morphologic species traits and retreat to isolated mountain tops, other genomic regions, such as nuclear markers, may flow across parapatric boundaries, sometimes leading to a complete genetic merger. We show that despite high ecologic and morphologic divergence over prolonged periods of time, hybridization allows for evolutionary outcomes alternative to extinction and replacement of taxa in response to climate change.