The role of chromosome changes in the diversification of Passiflora L. (Passifloraceae)

Passiflora L. has more than 575 species distributed especially in the Neotropics. The chromosome number variation in the genus is highly congruent with its main subgenera, but its basic chromosome number (x) and the underlying events responsible for this variation have remained controversial. Here, we provide a robust and well-resolved time-calibrated phylogeny that includes 102 taxa, and by means of phylogenetic comparative methods (PCM) we tested the relative importance of polyploidy and dysploidy events to Passiflora karyotype evolution and diversification. Passiflora arose 42.9 Mya, with subgenus diversification at the end of the Palaeogene (Eocene-Oligocene). The basic chromosome number of the genus is proposed as x?=?6, and a strong recent diversification found in the Passiflora subgenus (Miocene) correlated to genome size increase and a chromosome change from n?=?6 to n?=?9 by ascending dysploidy. Polyploidy, conversely, appeared restricted to few lineages, such as Astrophea and Deidamioides subgenera, and did not lead to diversification increases. Our findings suggest that ascending dysploidy provided a great advantage for generating long-term persistent lineages and promoting species diversification. Thus, chromosome numbers/genome size changes may have contributed to morphological/ecological traits that explain the pattern of diversification observed in the genus Passiflora.     

Polyploidy and angiosperm diversification

Polyploidy has long been recognized as a major force in angiosperm evolution. Recent genomic investigations not only indicate that polyploidy is ubiquitous among angiosperms, but also suggest several ancient genome-doubling events. These include ancient whole genome duplication (WGD) events in basal angiosperm lineages, as well as a proposed paleohexaploid event that may have occurred close to the eudicot divergence. However, there is currently no evidence for WGD in Amborella, the putative sister species to other extant angiosperms. The question is no longer "What proportion of angiosperms are polyploid?", but "How many episodes of polyploidy characterize any given lineage?" New algorithms provide promise that ancestral genomes can be reconstructed for deep divergences (e.g., it may be possible to reconstruct the ancestral eudicot or even the ancestral angiosperm genome). Comparisons of diversification rates suggest that genome doubling may have led to a dramatic increase in species richness in several angiosperm lineages, including Poaceae, Solanaceae, Fabaceae, and Brassicaceae. However, additional genomic studies are needed to pinpoint the exact phylogenetic placement of the ancient polyploidy events within these lineages and to determine when novel genes resulting from polyploidy have enabled adaptive radiations.     

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV

Advances in recent years have revolutionized our understanding of both the context and occurrence of polyploidy in plants. Molecular phylogenetics has vastly improved our understanding of plant relationships, enabling us to better understand trait and character evolution, including chromosome number changes. This, in turn, has allowed us to appreciate better the frequent occurrence and extent of polyploidy throughout the history of angiosperms, despite the occurrence of low chromosome numbers in some groups, such as in Arabidopsis (A. thaliana was the first plant genome to be sequenced and assembled). In tandem with an enhanced appreciation of phylogenetic relationships, the accumulation of genomic data has led to the conclusion that all angiosperms are palaeopolyploids, together with better estimates of the frequency and type of polyploidy in different angiosperm lineages. The focus therefore becomes when a lineage last underwent polyploidization, rather than simply whether a plant is ‘diploid’ or ‘polyploid’. This legacy of past polyploidization in plants is masked by large‐scale genome reorganization involving repetitive DNA loss, chromosome rearrangements (including fusions and fissions) and complex patterns of gene loss, a set of processes that are collectively termed ‘diploidization’. We argue here that it is the diploidization process that is responsible for the ‘lag phase’ between polyploidization events and lineage diversification. If so, diploidization is important in determining chromosome structure and gene content, and has therefore made a significant contribution to the evolutionary success of flowering plants. © 2015 The Authors. Botanical Journal of the Linnean Society published by John Wiley & Sons Ltd on behalf of Linnean Society of London, 2016, 180 , 1–5.     

Evolutionary trends in Iridaceae: new cytogenetic findings from the New World

With the present work, we aim to provide a better understanding of chromosome evolutionary trends among southern Brazilian species of Iridoideae. Chromosome numbers and genome sizes were determined for 21 and 22 species belonging to eight genera of Tigridieae and two genera of Trimezieae, respectively. The chromosome numbers of nine species belonging to five genera are reported here for the first time. Analyses of meiotic behaviour, tetrad normality and pollen viability in 14 species revealed regular meiosis and high meiotic indexes and pollen viability (> 90%). The chromosome data obtained here and compiled from the literature were plotted onto a phylogenetic framework to identify major events of chromosome rearrangements across the phylogenetic tree of Iridoideae. Following this approach, we propose that the ancestral base chromosome number for Iridoideae is x = 8 and that polyploidy and dysploidy events have occurred throughout evolution. Despite the variation in chromosome numbers observed in Tigridieae and Trimezieae, for these two tribes our data provide support for an ancestral base number of x = 7, largely conserved in Tigridieae, but a polyploidy event may have occurred prior to the diversification of Trimezieae, giving rise to a base number of x₂ = 14 (detected by maximum‐parsimony using haploid number and maximum likelihood). In Tigridieae, polyploid cytotypes were commonly observed (2x, 4x, 6x and 8x), whereas in Trimezieae, dysploidy seems to have been the most important event. This feature is reflected in the genome size, which varied greatly among species of Iridoideae, 4.2‐fold in Tigridieae and 1.5‐fold in Trimezieae. Although no clear difference was observed among the genome sizes of Tigridieae and Trimezieae, an important distinction was observed between these two tribes and Sisyrinchieae, with the latter possessing the smallest genome sizes in Iridoideae. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 177 , 27–49.     

Karyotype diversity and genome size variation in Neotropical Maxillariinae orchids

• Orchidaceae is a widely distributed plant family with very diverse vegetative and floral morphology, and such variability is also reflected in their karyotypes. However, since only a low proportion of Orchidaceae has been analysed for chromosome data, greater diversity may await to be unveiled. Here we analyse both genome size (GS) and karyotype in two subtribes recently included in the broadened Maxillariinea to detect how much chromosome and GS variation there is in these groups and to evaluate which genome rearrangements are involved in the species evolution.
• To do so, the GS (14 species), the karyotype – based on chromosome number, heterochromatic banding and 5S and 45S rDNA localisation (18 species) – was characterised and analysed along with published data using phylogenetic approaches.
• The GS presented a high phylogenetic correlation and it was related to morphological groups in Bifrenaria (larger plants – higher GS). The two largest GS found among genera were caused by different mechanisms: polyploidy in Bifrenaria tyrianthina and accumulation of repetitive DNA in Scuticaria hadwenii. The chromosome number variability was caused mainly through descending dysploidy, and x=20 was estimated as the base chromosome number.
• Combining GS and karyotype data with molecular phylogeny, our data provide a more complete scenario of the karyotype evolution in Maxillariinae orchids, allowing us to suggest, besides dysploidy, that inversions and transposable elements as two mechanisms involved in the karyotype evolution. Such karyotype modifications could be associated with niche changes that occurred during species evolution.

     

葱属Amerallium亚属（石蒜科）的系统发生与性状进化

运用贝叶斯和简约法对葱属（Allium）Amerallium亚属的核糖体DNA内转录间隔区（ITS）进行了分析,对该亚属的系统发生进行了推测。系统分析证实 Amerallium是单系的,并表明该亚属由三个隔离的地理群组成：北美Ameralliums,地中海区Ameralliums和东亚Ameralliums。性状进化的重建表明鳞茎是原始或祖先状态,根状茎和肉质增粗的根是衍生状态且在Amerallium这个亚属的类群中独立进化发生了几次。重建也表明该亚属的原始染色体基数x=7,其它染色体基数（x=8, 9, 10, 11）是由它转化而来的。在北美类群中,异基数性相当罕见,而多倍性似乎是一个相对频繁的进化事件。在地中海区类群和东亚类群中,异基数性和多倍性是染色体进化的两个主要驱动力。     

葱属Amerallium亚属 (石蒜科) 的系统发生与性状进化

运用贝叶斯和简约法对葱属（Allium）Amerallium亚属的核糖体DNA内转录间隔区（ITS）进行了分析,对该亚属的系统发生进行了推测。系统分析证实 Amerallium是单系的,并表明该亚属由三个隔离的地理群组成：北美Ameralliums,地中海区Ameralliums和东亚Ameralliums。性状进化的重建表明鳞茎是原始或祖先状态,根状茎和肉质增粗的根是衍生状态且在Amerallium这个亚属的类群中独立进化发生了几次。重建也表明该亚属的原始染色体基数x=7,其它染色体基数（x=8, 9, 10, 11）是由它转化而来的。在北美类群中,异基数性相当罕见,而多倍性似乎是一个相对频繁的进化事件。在地中海区类群和东亚类群中,异基数性和多倍性是染色体进化的两个主要驱动力。     

Size is not everything: rates of genome size evolution,not C-value,correlate with speciation in angiosperms

Angiosperms represent one of the key examples of evolutionary success, and their diversity dwarfs other land plants; this success has been linked, in part, to genome size and phenomena such as whole genome duplication events. However, while angiosperms exhibit a remarkable breadth of genome size, evidence linking overall genome size to diversity is equivocal, at best. Here, we show that the rates of speciation and genome size evolution are tightly correlated across land plants, and angiosperms show the highest rates for both, whereas very slow rates are seen in their comparatively species-poor sister group, the gymnosperms. No evidence is found linking overall genome size and rates of speciation. Within angiosperms, both the monocots and eudicots show the highest rates of speciation and genome size evolution, and these data suggest a potential explanation for the megadiversity of angiosperms. It is difficult to associate high rates of diversification with different types of polyploidy, but it is likely that high rates of evolution correlate with a smaller genome size after genome duplications. The diversity of angiosperms may, in part, be due to an ability to increase evolvability by benefiting from whole genome duplications, transposable elements and general genome plasticity.     

新分类系统下长蒴苣苔亚科(苦苣苔科)细胞学研究概述

在最新分类系统框架下对长蒴苣苔亚科(Didymocarpoideae)的染色体资料进行了详细的整理和分析,结果表明,长蒴苣苔亚科的细胞学研究仍存在不足,尤其在种级水平上的研究不足25%,且存在一些属的染色体数据空白的现象。在新的分类系统下,一些修订后的属染色体数目表现出一致性或更加具有合理性,但也存在一些属的染色体数目变异仍十分复杂,如汉克苣苔属(Henckelia)和长蒴苣苔属(Didymocarpus)。基于已有的染色体数据,对长蒴苣苔亚科内一些重要属的染色体进化模式及其对物种分化的影响进行了探讨,推测染色体数目的多倍化及非整倍化进化可能对各类群的物种分化具有重要作用,但需要今后利用基于DNA探针的荧光原位杂交技术并结合分子系统学和基因组学研究才能深入地解析染色体的进化模式及其对物种分化的影响。     

Contribution to the genome size knowledge of New World species from the Heliantheae alliance (Asteraceae)

This article contributes first genome size assessments by flow cytometry for 16 species, 12 genera, and 3 tribes from family Asteraceae, mostly belonging to the Heliantheae alliance, an assembly of 13 tribes from subfamily Asteroideae with a large majority of its species in the New World. Most genome sizes are accompanied by their own chromosome counts, confirming in most cases, although not all, previous counts for the species, and revealing possible cases of unknown dysploidy or polyploidy for certain taxa. The data contribute to the pool of knowledge on genome size and chromosome numbers in the family Asteraceae and will further allow deeper studies and a better understanding on the role of dysploidy in the evolution of the Heliantheae alliance. However, we still lack data for tribes Chaenactideae, Neurolaeneae, Polymnieae, and Feddeeae (the latter, monospecific) to complete the alliance representation.     

Molecular phylogenetic analyses of nuclear and plastid DNA sequences support dysploid and polyploid chromosome number changes and reticulate evolution in the diversification of Melampodium (Millerieae, Asteraceae)

Chromosome evolution (including polyploidy, dysploidy, and structural changes) as well as hybridization and introgression are recognized as important aspects in plant speciation. A suitable group for investigating the evolutionary role of chromosome number changes and reticulation is the medium-sized genus Melampodium (Millerieae, Asteraceae), which contains several chromosome base numbers (x = 9, 10, 11, 12, 14) and a number of polyploid species, including putative allopolyploids. A molecular phylogenetic analysis employing both nuclear (ITS) and plastid (matK) DNA sequences, and including all species of the genus, suggests that chromosome base numbers are predictive of evolutionary lineages within Melampodium. Dysploidy, therefore, has clearly been important during evolution of the group. Reticulate evolution is evident with allopolyploids, which prevail over autopolyploids and several of which are confirmed here for the first time, and also (but less often) on the diploid level. Within sect. Melampodium, the complex pattern of bifurcating phylogenetic structure among diploid taxa overlain by reticulate relationships from allopolyploids has non-trivial implications for intrasectional classification.     

Polyploidy does not control all: Lineage‐specific average chromosome length constrains genome size evolution in ferns

Recent studies investigating the evolution of genome size diversity in ferns have shown that they have a distinctive genome profile compared with other land plants. Ferns are typically characterized by possessing medium‐sized genomes, although a few lineages have evolved very large genomes. Ferns are different from other vascular plant lineages as they are the only group to show evidence for a correlation between genome size and chromosome number. In this study, we aim to explore whether the evolution of fern genome sizes is not only shaped by chromosome number changes arising from polyploidy but also by constraints on the average amount of DNA per chromosome. We selected the genus Asplenium L. as a model genus to study the question because of the unique combination of a highly conserved base chromosome number and a high frequency of polyploidy. New genome size data for Asplenium taxa were combined with existing data and analyzed within a phylogenetic framework. Genome size varied substantially between diploid species, resulting in overlapping genome sizes among diploid and tetraploid spleenworts. The observed additive pattern indicates the absence of genome downsizing following polyploidy. The genome size of diploids varied non‐randomly and we found evidence for clade‐specific trends towards larger or smaller genomes. The 578‐fold range of fern genome sizes have arisen not only from repeated cycles of polyploidy but also through clade‐specific constraints governing accumulation and/or elimination of DNA.     

Macroevolutionary insights into sedges (Carex: Cyperaceae): The effects of rapid chromosome number evolution on lineage diversification

Changes in holocentric chromosome number due to fission and fusion have direct and immediate effects on genome structure and recombination rates. These, in turn, may influence ecology and evolutionary trajectories profoundly. Sedges of the genus Carex (Cyperaceae) comprise ca. 2000 species with holocentric chromosomes. The genus exhibits a phenomenal range in the chromosome number (2n = 10 − 132) with almost not polyploidy. In this study, we integrated the most comprehensive cytogenetic and phylogenetic data for sedges with associated climatic and morphological data to investigate the hypothesis that high recombination rates are selected when evolutionary innovation is required, using chromosome number evolution as a proxy for recombination rate. We evaluated Ornstein–Uhlenbeck models to infer shifts in chromosome number equilibrium and selective regime. We also tested the relationship between chromosome number and diversification rates. Our analyses demonstrate significant correlations between morphology and climatic niche and chromosome number in Carex. Nevertheless, the amount of chromosomal variation that we are able to explain is very small. We recognized a large number of shifts in mean chromosome number, but a significantly lower number in climatic niche and morphology. We also detected a peak in diversification rates near intermediate recombination rates. In combination, these analyses point toward the importance of chromosome evolution to the evolutionary history of Carex. Our work suggests that the effect of chromosome evolution on recombination rates, not just on reproductive isolation, may be central to the evolutionary history of sedges.     

Diversification rates and chromosome evolution in the most diverse angiosperm genus of the temperate zone (Carex, Cyperaceae)

The sedge family (Cyperaceae: Poales; ca. 5600 spp.) is a hyperdiverse cosmopolitan group with centres of species diversity in Africa, Australia, eastern Asia, North America, and the Neotropics. Carex, with ca. 40% of the species in the family, is one of the most species-rich angiosperm genera and the most diverse in temperate regions of the Northern Hemisphere, making it atypical among plants in that it inverts the latitudinal gradient of species richness. Moreover, Carex exhibits high rates of chromosome rearrangement via fission, fusion, and translocation, which distinguishes it from the rest of the Cyperaceae. Here, we use a phylogenetic framework to examine how the onset of contemporary temperate climates and the processes of chromosome evolution have influenced the diversification dynamics of Carex. We provide estimates of diversification rates and map chromosome transitions across the evolutionary history of the main four clades of Carex. We demonstrate that Carex underwent a shift in diversification rates sometime between the Late Eocene and the Oligocene, during a global cooling period, which fits with a transition in diploid chromosome number. We suggest that adaptive radiation to novel temperate climates, aided by a shift in the mode of chromosome evolution, may explain the large-scale radiation of Carex and its latitudinal pattern of species richness.     

On the abundance of polyploids in flowering plants

The wide distribution of polyploidy among plants has led to a variety of theories for the evolutionary advantages of polyploidy. Here we claim that the abundance of polyploidy may be the result of a simple ratcheting process that does not require evolutionary advantages due to the biological properties of organisms. The evolution of polyploidy is a one-way process in which chromosome number can increase but not decrease. Using a simple mathematical model, we show that average ploidal level within a plant lineage can continually increase to the levels observed today, even if there are ecological or physiological disadvantages to higher ploidy. The model allowed us to estimate the average net speciation and polyploidy rates for ten angiosperm genera. Based on these estimates, the model predicts distributions of ploidal levels statistically similar to those observed in nine of the 10 genera.     

Nonuniform processes of chromosome evolution in sedges (Carex: Cyperaceae)

Holocentric chromosomes-chromosomes that lack localized centromeres-occur in numerous unrelated clades of insects, flatworms, and angiosperms. Chromosome number changes in such organisms often result from fission and fusion events rather than polyploidy. In this study, I test the hypothesis that chromosome number evolves according to a uniform process in Carex section Ovales (Cyperaceae), the largest New World section of an angiosperm genus renowned for its chromosomal variability and species richness. I evaluate alternative models of chromosome evolution that allow for shifts in both stochastic and deterministic evolutionary processes and that quantify the rate of evolution and heritability/phylogenetic dependence of chromosome number. Estimates of Ornstein-Uhlenbeck model parameters and tree-scaling parameters in a generalized least squares framework demonstrate that (1) chromosome numbers evolve rapidly toward clade-specific stationary distributions that cannot be explained by constant variance (Brownian motion) evolutionary models, (2) chromosome evolution in the section is rapid and exhibits little phylogenetic inertia, and (3) explaining the phylogenetic pattern of chromosome numbers in the section entails inferring a shift in evolutionary dynamics at the root of a derived clade. The finding that chromosome evolution is not a uniform process in sedges provides a novel example of karyotypic orthoselection in an organism with holocentric chromosomes.     

Comparative analysis reveals that polyploidy does not decelerate diversification in fish

While the proliferation of the species‐rich teleost fish has been ascribed to an ancient genome duplication event at the base of this group, the broader impact of polyploidy on fish evolution and diversification remains poorly understood. Here, we investigate the association between polyploidy and diversification in several fish lineages: the sturgeons (Acipenseridae: Acipenseriformes), the botiid loaches (Botiidae: Cypriniformes), Cyprininae fishes (Cyprinidae: Cypriniformes) and the salmonids (Salmonidae: Salmoniformes). Using likelihood‐based evolutionary methodologies, we co‐estimate speciation and extinction rates associated with polyploid vs. diploid fish lineages. Family‐level analysis of Acipenseridae and Botiidae revealed no significant difference in diversification rates between polyploid and diploid relatives, while analysis of the subfamily Cyprininae revealed higher polyploid diversification. Additionally, order‐level analysis of the polyploid Salmoniformes and its diploid sister clade, the Esociformes, did not support a significantly different net diversification rate between the two groups. Taken together, our results suggest that polyploidy is generally not associated with decreased diversification in fish – a pattern that stands in contrast to that previously observed in plants. While there are notable differences in the time frame examined in the two studies, our results suggest that polyploidy is associated with different diversification patterns in these two major branches of the eukaryote tree of life.     

Is genome downsizing associated with diversification in polyploid lineages of Veronica?

The study of genome size evolution in a phylogenetic context in related polyploid and diploid lineages can help us to understand the advantages and disadvantages of genome size changes and their effect on diversification. Here, we contribute 199 new DNA sequences and a nearly threefold increase in genome size estimates in polyploid and diploid Veronica (Plantaginaceae) (to 128 species, c. 30% of the genus) to provide a comprehensive baseline to explore the effect of genome size changes. We reconstructed internal transcribed spacer (ITS) and trnL‐trnL‐trnF phylogenetic trees and performed phylogenetic generalized least squares (PGLS), ancestral character state reconstruction, molecular dating and diversification analyses. Veronica 1C‐values range from 0.26 to 3.19 pg. Life history is significantly correlated with 1C‐value, whereas ploidy and chromosome number are strongly correlated with both 1C‐ and 1Cx‐values. The estimated ancestral Veronica 1Cx‐value is 0.65 pg, with significant genome downsizing in the polyploid Southern Hemisphere subgenus Pseudoveronica and two Northern Hemisphere subgenera, and significant genome upsizing in two diploid subgenera. These genomic downsizing events are accompanied by increased diversification rates, but a ‘core shift’ was only detected in the rate of subgenus Pseudoveronica. Polyploidy is important in the evolution of the genus, and a link between genome downsizing and polyploid diversification and species radiations is hypothesized. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178 , 243–266.     

中国西南地区鹿药属4种15居群核型研究

对产于中国西南部的鹿药属（Maianthemum）4种植物进行了细胞学研究,包括染色体数目,多倍化,非整倍性和随体染色体,以及核型不对称性和核型进化。结果表明：1）除了在云南丽江采集的Maianthemum tatsienensis染色体数目为2n=72之外,其余的居群全为2n=36;2）核型在居群间存在变异,特别是在具中部染色体和近中部染色体的数目以及随体染色体的数目和位置上。此外,M．nanchuanense和M．szechuanicum的核型是首次报道,B染色体也是首次在该属中发现。我们推测鹿药属的进化方式包括频繁的染色体畸变以及不同水平上的多倍化,而中国西南部是该属的分化中心。