Maximum likelihood inference implies a high, not a low, ancestral haploid chromosome number in Araceae, with a critique of the bias introduced by 'x'

Background and Aims

For 84 years, botanists have relied on calculating the highest common factor for series of haploid chromosome numbers to arrive at a so-called basic number, x. This was done without consistent (reproducible) reference to species relationships and frequencies of different numbers in a clade. Likelihood models that treat polyploidy, chromosome fusion and fission as events with particular probabilities now allow reconstruction of ancestral chromosome numbers in an explicit framework. We have used a modelling approach to reconstruct chromosome number change in the large monocot family Araceae and to test earlier hypotheses about basic numbers in the family.

Methods

Using a maximum likelihood approach and chromosome counts for 26 % of the 3300 species of Araceae and representative numbers for each of the other 13 families of Alismatales, polyploidization events and single chromosome changes were inferred on a genus-level phylogenetic tree for 113 of the 117 genera of Araceae.

Key Results

The previously inferred basic numbers x = 14 and x = 7 are rejected. Instead, maximum likelihood optimization revealed an ancestral haploid chromosome number of n = 16, Bayesian inference of n = 18. Chromosome fusion (loss) is the predominant inferred event, whereas polyploidization events occurred less frequently and mainly towards the tips of the tree.

Conclusions

The bias towards low basic numbers (x) introduced by the algebraic approach to inferring chromosome number changes, prevalent among botanists, may have contributed to an unrealistic picture of ancestral chromosome numbers in many plant clades. The availability of robust quantitative methods for reconstructing ancestral chromosome numbers on molecular phylogenetic trees (with or without branch length information), with confidence statistics, makes the calculation of x an obsolete approach, at least when applied to large clades.     

Cytology and systematica of Araceae

The chromosome numbers of 75 species belonging to the family Araceae have been determined. The numbers for 53 species are reported for the first time. One number differs from previous reports ( Aglaodorum ), and one number is corrected (Phymatarum). Within 15 genera ( Gymnostachys, Pothoidium, Alloschemone, Heteropsis, Holochlamys, Anaphyllopsis, Dracontioides, Pseudohydrosme, Montrichardia, Bucephalandra, Taccarum, Asterostigma, Gorgonidium, Spathantheum and Ulearum ) the chromosome numbers have not previously been determined. The total number of genera cytologically investigated is now 99 (c. 94%).
A great diversity in chromosome numbers as well as in chromosome size and constitution is found. The results are discussed in relation to the phylogeny and the previously published classifications of the family.
A total list of chromosome numbers counted (>700 species) in the Araceae is presented (Appendix).     

Karyological Differentiation in Sapindaceae with Special Reference to Serjania and Cardiospermum

New chromosome counts for 9 species and 2 genera of Sapindaceae are presented and compared with a review of all available chromosome numbers of the family. In 4 species diploid numbers differing from previous reports are found. In 4 species of the tribe Paullinieae (S. diversiflora, S. subdentata, C. grandiflorum and C. halicacabum) detailed studies on interphase nucleus structure, condensing behaviour and chromosome banding patterns are presented. The karyological differentiation of Paullinieae is generally characterized by dysploid reduction of chromosome numbers and the increase of chromosome size. Sequential staining of nuclei with CMA/DAPI and Giemsa-C-banding demonstrates diversification of constitutive heterochromatin (= hc) and different types of chromatin organization in Serjania and Cardiospermum. The obvious lack of polyploid series and the karyological evolution within the family is discussed. The outstanding small genome size found in Cardiospermum halicacabum is considered to be due to a secondary loss of DNA in the course of the change to herbaceous growth.     

Cytotaxonomy of Commelinaceae: chromosome numbers of some African and Asiatic species

Chromosome counts are reported for 32 taxa (31 species and 1 subspecies) belonging to 10 genera of Commelinaceae from seven African and Asiatic countries. Counts for 13 species and 1 subspecies are recorded for the first time. Published chromosome numbers for Anhicopsis and Polyspatha are confirmed. It is suggested that Pdisota, Pollia and Stanfieldidla each has a single basic number (x = 20, 16 and 11, respectively). The known cytological diversity in Floscopa is extended. The third continental African species of Coleolrype is found to have the same chromosome number (2n = 36) as the other two. The preponderance of the basic number x = 15 in Commelina is supported. The uncommon basic number x = 13 is reported in four taxa of Cyanotis together with karyotypic differences. The basic number x = 6 is found in a second species of Murdannia . Karyotypic data in addition to chromosome numbers are presented for 24 of the 32 taxa investigated. Karyotypes are found to be useful in assessing relationships in the family, and evolutionary trends in the karyotype are noted.     

Cytogenetic analysis of three sea catfish species (Teleostei, Siluriformes, Ariidae) with the first report of Ag-NOR in this fish family

Despite their ecological and economical importance, fishes of the family Ariidae are still genetically and cytogenetically poorly studied. Among the 133 known species of ariids, only eight have been karyotyped. Cytogenetic analyses performed on Genidens barbus and Sciades herzbergii revealed that both species have 2n = 56 chromosomes and Cathorops aff. mapale has 2n = 52 chromosomes: Genidens barbus has 10 Metacentrics (M), 14 Submetacentrics (SM), 26 Subtelocentrics (ST), and 6 Acrocentrics (A), Sciades herzbergii has 14M, 20SM, 18ST and 4A, whereas Cathorops aff. mapale has 14M, 20SM, and 18ST. The nucleolus organizer regions (NORs) were found in a single chromosome pair on the short arm of a large-sized ST pair in Genidens barbus and on the short arm of a middle-size SM pair in Cathorops aff. mapale. Multiple NORs on the short arms of two large-sized ST pairs were found in Sciades herzbergii. The occurrence of diploid numbers ranging from 2n = 52 through 56 chromosomes and the presence of different karyotypic compositions, besides the number and position of NORs suggest that several numeric and structural chromosome rearrangements were fixed during the evolutionary history of this fish family.     

Phylogenetic conservation of chromosome numbers in Actinopterygiian fishes

The genomes of ray-finned fishes (Actinopterygii) are well known for their evolutionary dynamism as reflected by drastic alterations in DNA content often via regional and whole-genome duplications, differential patterns of gene silencing or loss, shifts in the insertion-to-deletion ratios of genomic segments, and major re-patternings of chromosomes via non-homologous recombination. In sharp contrast, chromosome numbers in somatic karyotypes have been highly conserved over vast evolutionary timescales – a histogram of available counts is strongly leptokurtic with more than 50% of surveyed species displaying either 48 or 50 chromosomes. Here we employ comparative phylogenetic analyses to examine the evolutionary history of alterations in fish chromosome numbers. The most parsimonious ancestral state for major actinopterygiian clades is 48 chromosomes. When interpreted in a phylogenetic context, chromosome numbers evidence many recent instances of polyploidization in various lineages but there is no clear indication of a singular polyploidization event that has been hypothesized to have immediately preceded the teleost radiation. After factoring out evident polyploidizations, a correlation between chromosome numbers and genome sizes across the Actinopterygii is marginally statistically significant (p = 0.012) but exceedingly weak (R ² = 0.0096). Overall, our phylogenetic analysis indicates a mosaic evolutionary pattern in which the forces that govern labile features of fish genomes must operate largely independently of those that operate to conserve chromosome numbers.     

甘蔗组织培养中染色体数目变异的初步研究

本文通过甘蔗桂糖11号组培腋芽苗与其原种的染色体数目的比较,研究了腋芽苗染色体数目的变化情况。发现腋芽苗82％的细胞的染色体数目仍在其原种染色体数目变异的高峰之内。     

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.     

Chromosome diversity of South American Oxalis (Oxalidaceae)

Mitotic or meiotic chromosome studies are reported for 39 species or subspecies of Oxalis from South America belonging to 14 sections. Chromosome numbers of 34 of these taxa are reported for the first time. Diploids and polyploids with six different basic chromosome numbers x=5, 6, 7, 8, 9 and 11 are described. Thirteen species of subgenus lhamnoxys were analysed and two new basic chromosome numbers were observed in diploid entities of this subgenus, x = 6 and x=9. The underground stem-bearing entities of Oxalis subgenus Oxalis studied (in sections Articulatae, Jonoxalis and Palmatifoliae) are mostly diploids and polyploids with a basic chromosome number x=7. Five species of section Carnosa are diploids with x = 9. In species of sections Rosea, Ortgieseae, Clematodes and Laxae the basic chromosome numbers x = 6, 7, 8 and 9 were observed. Groups of related species sharing the same chromosome number are discussed with the aim of improving the infrageneric delimitation of the genus. The basic chromosome number x=6 seems to be primitive in the genus and other basic chromosome numbers probably appeared several times in the course of chromosome evolution of Oxalis .     

十二种沫蝉的染色体研究 (同翅目： 沫蝉总科)

观察了同翅目头喙亚目12种沫蝉雄性的染色体数目和减数分裂行为。通过对沫蝉总科现有核型资料的分析,认为沫蝉总科的核型特点是：①染色体较小,数目较多,总科内染色体数目变化范围较大,众数为2n=26（24+XO）;②染色体的易位现象极为普遍,因此可以推测,通过染色体的易位导致染色体数目增加是核型进化的主要机制;③减数分裂前期Ⅰ具有典型的花束期,但没有弥散期。因此从精子发生来看沫蝉总科与叶蝉总科、角蝉总科和蝉总科的关系更为密切,而与蜡蝉总科的关系较远。头喙亚目的亲缘关系可能是：蜡蝉总科+{蝉总科+［沫蝉总科+（叶蝉总科+角蝉总科）］}。     

Alignment of the PiGMaP and USDA linkage maps of porcine chromosomes 3 and 9

The European Pig Gene Mapping Project (PiGMaP) and United States Department of Agriculture (USDA) porcine linkage maps for chromosomes 3 and 9 have been aligned by typing three USDA microsatellites from chromosome 3 and five from chromosome 9 on the PiGMaP reference families. Using the crimap linkage analysis package, revised multipoint linkage maps were constructed for chromosome 3 and 9. Inclusion of these USDA markers in the multipoint analysis resulted in an increase in length of 47% and 33% respectively for these two PiGMaP linkage groups. This increase in size is mainly the result of extension of the ends of both linkage groups.     

Chromosome variation in dividing protoplasts and cell suspensions of wheat

Summary The cytology of bread wheat (Triticum aestivum) suspension lines, recycled lines (selected for high division frequency) and their dividing protoplasts, have been examined. Extensive numerical and structural chromosome variation was present in all the lines. The most frequently observed chromosome numbers were around 2n=32, indicating that considerable chromosome loss from the normal wheat complement (2n=6x=42) had occurred during selection of the lines. Chromosome aberrations also indicated loss of chromosome arms and chromosome segments. The implications of this variation for studies on transformation and for the potential regeneration of whole plants from protoplasts of bread wheat are discussed.     

Combining FISH and model-based predictions to understand chromosome evolution in Typhonium (Araceae)

Background and Aims

Since the advent of molecular phylogenetics, numerous attempts have been made to infer the evolutionary trajectories of chromosome numbers on DNA phylogenies. Ideally, such inferences should be evaluated against cytogenetic data. Towards this goal, we carried out phylogenetic modelling of chromosome number change and fluorescence in situ hybridization (FISH) in a medium sized genus of Araceae to elucidate if data from chromosomal markers would support maximum likelihood-inferred changes in chromosome numbers among close relatives. Typhonium, the focal genus, includes species with 2n = 65 and 2n = 8, the lowest known count in the family.

Methods

A phylogeny from nuclear and plastid sequences (96 taxa, 4252 nucleotides) and counts for all included species (15 of them first reported here) were used to model chromosome number evolution, assuming discrete events, such as polyploidization and descending or ascending dysploidy, occurring at different rates. FISH with three probes (5S rDNA, 45S rDNA and Arabidopsis-like telomeres) was performed on ten species with 2n = 8 to 2n = 24.

Key Results

The best-fitting models assume numerous past chromosome number reductions. Of the species analysed with FISH, the two with the lowest chromosome numbers contained interstitial telomeric signals (Its), which together with the phylogeny and modelling indicates decreasing dysploidy as an explanation for the low numbers. A model-inferred polyploidization in another species is matched by an increase in rDNA sites.

Conclusions

The combination of a densely sampled phylogeny, ancestral state modelling and FISH revealed that the species with n = 4 is highly derived, with the FISH data pointing to a Robertsonian fusion-like chromosome rearrangement in the ancestor of this species.     

Nuclear DNA variation, chromosome numbers and polyploidy in the endemic and indigenous grass flora of New Zealand

BACKGROUND AND AIMS: Little information is available on DNA C-values for the New Zealand flora. Nearly 85 % of the named species of the native vascular flora are endemic, including 157 species of Poaceae, the second most species-rich plant family in New Zealand. Few C-values have been published for New Zealand native grasses, and chromosome numbers have previously been reported for fewer than half of the species. The aim of this research was to determine C-values and chromosome numbers for most of the endemic and indigenous Poaceae from New Zealand. SCOPE: To analyse DNA C-values from 155 species and chromosome numbers from 55 species of the endemic and indigenous grass flora of New Zealand. KEY RESULTS: The new C-values increase significantly the number of such measurements for Poaceae worldwide. New chromosome numbers were determined from 55 species. Variation in C-value and percentage polyploidy were analysed in relation to plant distribution. No clear relationship could be demonstrated between these variables. CONCLUSIONS: A wide range of C-values was found in the New Zealand endemic and indigenous grasses. This variation can be related to the phylogenetic position of the genera, plants in the BOP (Bambusoideae, Oryzoideae, Pooideae) clade in general having higher C-values than those in the PACC (Panicoideae, Arundinoideae, Chloridoideae + Centothecoideae) clade. Within genera, polyploids typically have smaller genome sizes (C-value divided by ploidy level) than diploids and there is commonly a progressive decrease with increasing ploidy level. The high frequency of polyploidy in the New Zealand grasses was confirmed by our additional counts, with only approximately 10 % being diploid. No clear relationship between C-value, polyploidy and rarity was evident.     

Karyological and taxonomic notes on Genista L. (Papilionoideae, Leguminosae) from the Iberian Peninsula

Karyological information about Iberian Genista species is limited because of their wide geographical distribution. It is a major factor in the understanding of a genus whose genetic evolution is mostly related to aneuploidy and euploidy. The chromosome numbers of the following taxa have been counted: G. carpetana subsp. carpetana (n = 20), G. cinerascens (n = 12), G. micrantha (n = 18), G. mugronensis subsp. rigidissima (n = 18), G. ramosissima (2n = 48) and G. tinctoria (n = 24). The previously-assumed uniformity of chromosome number (n = 24) for all the subspecies of G. cinerea is supported here by data from subspp. murcica and speciosa. In G. florida, a new chromosome number, n = 23, has been found for both subspecies (florida and polygaliphylla). A discussion of the discrepancies between these data and previous ones is included. A new level of ploidy has been found in G. tuurnefortii subsp. tournefortii (n = 32). The data stress the necessity of obtaining chromosomal information from a number of plants of a taxon before its characteristic number is clear, and indicate that more chromosomal data will help the understanding of the cytological diversity within taxa in Genista.     

Targeting of marker loci to chicken chromosome 16 by representational difference analysis

Representational difference analysis (RDA) was initially used to identify differences between two inbred lines of chickens, line N and line 15I, on which the Compton mapping reference population is based. RDA was subsequently used to identify marker loci targeted specifically to chicken chromosome 16. Chromosome 16 contains the major histocompatibility complex (MHC), nucleolar organiser region (NOR) and Rfp-Y complex. To generate markers specific for this chromosome a bird was selected from the Compton mapping reference population which had inherited N line alleles for the MHC, NOR and Rfp-Y regions on this chromosome. DNA from this bird was compared with pooled DNA from 16 of its siblings, all of which had inherited line 15I alleles for the MHC, NOR and Rfp-Y regions. Initially amplicons were derived from Bam HI digested samples, RDA products were cloned after the first round of hybridisation and 113 clones were investigated: 45 of these identified Bam HI polymorphisms in this population. Of the 45 polymorphic clones, 17 have been mapped in the reference population so far, and these have identified seven new loci on chromosome 16. Interestingly a group of 16 other loci were linked on chromosome 4. The same birds were also compared by RDA following digestion with Taq I. Again large numbers of clones were generated of which 65 were investigated. Of these 17 clones were polymorphic and of five clones mapped so far three lie on chromosome 16. Two of the loci mapped to chromosome 16 have been used to identify yeast artificial chromosome (YAC) clones (GenBank accession numbers: AF057302, AF057303, AF057304, AF063218, AF06347, AF06348, AF06349, AF06350, AF063#51, AF06353, AF06354, AF06355, AF06356).     

青藏高原东北部植物染色体数目和多倍性研究

对青藏高原东北高山冰缘地区和相邻低海拔地区５９种多年生草本被子植物进行了染色体计数。其中,４５个种的染色体记数为首次报道,并确定其倍性。对分布于高山冰缘地区和冰缘以下不同海拔地区植物染色体的多倍性进行分析研究。     

基于染色体计数和ITS序列初步探讨横断山区柴胡属植物(伞形科)的系统发育

横断山区是中国柴胡属Bupleurum植物的分布中心。本文对横断山区6个种2变种进行了染色体记数报道,其中4个种2变种是首次报道。对横断山区的10个种4个变种、中国北方（河北和黑龙江）的3个种的nrDNA ITS进行测序,同时从GenBank里面下载同属的来自非洲和地中海西部的16个nrDNA ITS序列数据,结合染色体数目变化结果,初步探讨了横断山区柴胡属植物的系统发育。结果表明横断山区可能是现代柴胡属植物的频度中心和多样分布中心之一。它们的祖先种可能是非洲北部的木本柴胡属植物B.fruticosum,或者是地中海西部的柴胡属植物,推测是通过中东和高加索扩散而形成的,其中与非洲南部特有种B.mundtii的亲缘关系也较近;染色体基数演化趋势是：8是较原始基数,6和7是次生基数,其染色体异基数变异和多倍化可能是物种形成、进化以及向外扩散的主要方式;在ITS系统发育树中,中国柴胡属植物染色体基数为8的种类聚为一支,染色体基数为6和7的种类聚为了一支,不支持舒璞等（1998）关于中国柴胡属的属下分类系统。结合已有的形态学、细胞学、孢粉学证据和ITS系统发育树,建议窄竹叶柴胡B.marginatum var.stenophyllum独立成种。     

Karyological and taxonomic notes on Cytisus Desf. Sect. Spartopsis Dumort. and Sect. Alburnoides DC. (Genisteae, Leguminosae) from the Iberian Peninsula and Morocco

Karyological information on Cytisus species indicates at least two chromosome numbers for most of the taxa. This instability is, a striking karyological feature of Cytisus . Chromosome numbers of taxa in Sect. Spartopsis and Sect. Alburnoides, both well represented in Morocco and the Iberian Peninsula, are presented here. We provide the first data on chromosome numbers for the Moroccan taxa: C. grandiflorus subsp. barbarus , and subsp. haplophyllus (n = 23, 2 n = 46) , C. maurus (2 n = 48), C. megalanthus ( n = 23), C. arboreus subsp. arboreus , subsp. baeticus , and subsp. catalaunicus (2 n = 50), C. valdesii ( n = 23 ). New populations from the Iberian Peninsula have been counted: C. grandiflorus subsp. grandiflorus (2 n = 46), C. scoparius subsp. scoparius ( n = 23) , C. striatus subsp. eriocarpus ( n = 23, 2 n = 46), C. multiflorus (n = 23), C. oromediterraneus ( n = 23, 24). Our data confirm the instability of the chromosome number in Cytisus . The presence of B chromosomes in C. valdesii and C. megalanthus , as well in other species, is discussed in relation to this instability and previous data. We suggest that instability of the chromosome number within a taxon, and even in the same population, may be related to the breakage of A chromosomes and the appearance of B chromosomes.     

Chromosomal evolution in the South American Riodinidae (Lepidoptera: Papilionoidea)

We give the haploid chromosome numbers of 173 species or subspecies of Riodinidae as well as of 17 species or subspecies of neotropical Lycaenidae for comparison. The chromosome numbers of riodinids have thus far been very poorly known. We find that their range of variation extends from n =?9 to n =?110 but numbers above n =?31 are rare. While lepidopterans in general have stable chromosome numbers, or variation is limited at most a subfamily or genus, the entire family Riodinidae shows variation within genera, tribes and subfamilies with no single modal number. In particular, a stepwise pattern with chromosome numbers that are about even multiples is seen in several unrelated genera. We propose that this variation is attributable to the small population sizes, fragmented populations with little migration, and the behavior of these butterflies. Small and isolated riodinid populations would allow for inbreeding to take place. Newly arisen chromosomal variants could become fixed and contribute to reproductive isolation and speciation. In contrast to the riodinids, the neotropical Lycaenidae (Theclinae and Polyommatinae) conform to the modal n =?24 that characterizes the family.