Species coherence in the face of karyotype diversification in holocentric organisms: the case of a cytogenetically variable sedge (Carex scoparia,Cyperaceae)

Background and Aims

The sedge genus Carex, the most diversified angiosperm genus of the northern temperate zone, is renowned for its holocentric chromosomes and karyotype variability. The genus exhibits high variation in chromosome numbers both among and within species. Despite the possibility that this chromosome evolution may play a role in the high species diversity of Carex, population-level patterns of molecular and cytogenetic differentiation in the genus have not been extensively studied.

Methods

Microsatellite variation (11 loci, 461 individuals) and chromosomal diversity (82 individuals) were investigated in 22 Midwestern populations of the North American sedge Carex scoparia and two Northeastern populations.

Key Results

Among Midwestern populations, geographic distance is the most important predictor of genetic differentiation. Within populations, inbreeding is high and chromosome variation explains a significant component of genetic differentiation. Infrequent dispersal among populations separated by >100 km explains an important component of molecular genetic and cytogenetic diversity within populations. However, karyotype variation and correlation between genetic and chromosomal variation persist within populations even when putative migrants based on genetic data are excluded.

Conclusions

These findings demonstrate dispersal and genetic connectivity among widespread populations that differ in chromosome numbers, explaining the phenomenon of genetic coherence in this karyotypically diverse sedge species. More generally, the study suggests that traditional sedge taxonomic boundaries demarcate good species even when those species encompass a high range of chromosomal diversity. This finding is important evidence as we work to document the limits and drivers of biodiversity in one of the world''s largest angiosperm genera.     

Unlocking Holocentric Chromosomes: New Perspectives from Comparative and Functional Genomics?

The presence of chromosomes with diffuse centromeres (holocentric chromosomes) has been reported in several taxa since more than fifty years, but a full understanding of their origin is still lacking. Comparative and functional genomics are nowadays furnishing new data to better understand holocentric chromosome evolution thus opening new perspectives to analyse karyotype rearrangements in species with holocentric chromosomes in particular evidencing unusual common features, such as the uniform GC content and gene distribution along chromosomes.     

Major structural genomic alterations can be associated with hybrid speciation in Aegilops markgrafii (Triticeae)

During evolutionary history many grasses from the tribe Triticeae have undergone interspecific hybridization, resulting in allopolyploidy; whereas homoploid hybrid speciation was found only in rye. Homoeologous chromosomes within the Triticeae preserved cross‐species macrocolinearity, except for a few species with rearranged genomes. Aegilops markgrafii, a diploid wild relative of wheat (2n = 2x = 14), has a highly asymmetrical karyotype that is indicative of chromosome rearrangements. Molecular cytogenetics and next‐generation sequencing were used to explore the genome organization. Fluorescence in situ hybridization with a set of wheat cDNAs allowed the macrostructure and cross‐genome homoeology of the Ae. markgrafii chromosomes to be established. Two chromosomes maintained colinearity, whereas the remaining were highly rearranged as a result of inversions and inter‐ and intrachromosomal translocations. We used sets of barley and wheat orthologous gene sequences to compare discrete parts of the Ae. markgrafii genome involved in the rearrangements. Analysis of sequence identity profiles and phylogenic relationships grouped chromosome blocks into two distinct clusters. Chromosome painting revealed the distribution of transposable elements and differentiated chromosome blocks into two groups consistent with the sequence analyses. These data suggest that introgressive hybridization accompanied by gross chromosome rearrangements might have had an impact on karyotype evolution and homoploid speciation in Ae. markgrafii.     

Allozyme differentiation of populations of the dogwhelk Nucella lapillus, (L.): the relative effects of geographic distance and variation in chromosome number

Geographic patterns of genie differentiation were compared with differentiation between karyotypes in the intertidal snail Nucella lapillus. Samples from 24 sites covering the species range in Europe and North America were analysed for allozyme variation at 16 soluble enzyme loci. Two homokaryotypes have been identified with diploid numbers 2n = 26 and 2n= 36 (variation is Robertsonian and hybrids have intermediate chromosome numbers) and samples were classified (on the basis of published data) according to karyotype. Group 1 consisted of samples from three English Channel populations of higher chromosome number (on average 2n > 32) and Group 2 consisted of the remaining 21 samples (presumed to be 2n= 26). Karyotype variation accounts for roughly the same amount of the absolute allozyme variance as geographic variation (46.3 °, and 53.7°, respectively). Yet the patterns of differentiation seen between karyotypes and with geographic separation are very different. In samples classified as 2n= 26 (Group 2), while there is a significant amount of heterogeneity (F_ST per locus averaged 0.128 for 10 polymorphic loci), allozyme variation occurs independently at different loci so mean genetic identity (Nei) is high: 0.972. There is only a slight decline in genetic identity with distance (genetic identity averaged 0.965 for amphi-atlantic comparisons) indicating that passive transport of juveniles or adults may contribute significantly to gene flow. Conversely, allozyme variation between karyotypes was concordant. High chromosome number populations possessed a suite of alleles at four allozyme loci (Esl-3, Lap-2, Mdh-1 and Pep-2) which were absent or rare in Group 2 samples resulting in high F_ST values for these loci (from 0.294 to 0.472) when karyotypic classes were combined. Consequently the mean genetic identity between these Robertsonian races is low, 0.856, and falls within the range more usually associated with congeneric comparisons than with con-specific comparisons. The mechanisms maintaining this genie difference are unclear. However the distribution of the karyotypes and physiological and morphological differences (in shell shape) between them strongly suggest that karyotypic variation in Nucella is adaptive.     

High-resolution chromosome banding studies in Cebus apella,Cebus albifrons,and Lagothrix lagothricha: Comparison with the human karyotype

Karyotypes of three species of South American primates (Cebus apella, Cebus albifrons, and Lagothrix lagothricha) were studied using high-resolution banding techniques, and were compared to the human karyotype. The number of homologies was very high for the three species. Some of the breakpoints implicated in chromosome rearrangements corresponded with human fragile sites. The fragile sites in human chromosomes often correspond with the localization of latent centromeres in the platyrrhines or with large heterochromatic regions that may have been lost or newly added during evolution.     

An extraordinarily stable karyotype of the woody Populus species revealed by chromosome painting

The karyotype represents the basic genetic make‐up of a eukaryotic species. Comparative cytogenetic analysis of related species based on individually identified chromosomes has been conducted in only a few plant groups and not yet in woody plants. We have developed a complete set of 19 chromosome painting probes based on the reference genome of the model woody plant Populus trichocarpa. Using sequential fluorescence in situ hybridization we were able to identify all poplar chromosomes in the same metaphase cells, which led to the development of poplar karyotypes based on individually identified chromosomes. We demonstrate that five Populus species, belonging to five different sections within Populus, have maintained a remarkably conserved karyotype. No inter‐chromosomal structural rearrangements were observed on any of the 19 chromosomes among the five species. Thus, the chromosomal synteny in Populus has been remarkably maintained after nearly 14 million years of divergence. We propose that the karyotypes of woody species are more stable than those of herbaceous plants since it may take a longer period of time for woody plants to fix chromosome number or structural variants in natural populations.     

Karyotype variation in 11 species of the Vernonieae Cass. tribe (Asteraceae Bercht. & J. Presl)

The Vernonieae tribe presents strong taxonomic delimitation problems as it is considered one of the most complex groups of the Asteraceae family, comprising approximately 1100 species distributed across 129 genera. In this study, a comparative analysis of the Vernonieae species was performed to understand the events involved in the chromosome evolution of these species and to further deduce their taxonomy. The representatives were cytogenetically characterized via analyses of morphology, karyotype asymmetry and differential staining with fluorochromes CMA and DAPI as well as FISH. According to morphometric data, all species showed symmetrical karyotypes with prevailing metacentric chromosomes, even in species belonging to different genera. Variability in diploid chromosome number was detected (2n = 18 to 2n = 60), and chromosome sizes were observed to be between 1.00 and 4.09 μm. Additionally, variation in the pattern of heterochromatin was observed mainly in relation to CMA⁺ bands, in which the number varied from 4 to 16 heterochromatic regions. Only one species, Vernonia scorpioides, presented positive DAPI bands, which were located in the terminal position in most of the chromosomes. The differences in the sizes and quantities of heterochromatic bands may be related to small structural rearrangements during karyotype evolution of the Vernonieae tribe.     

Chromosome painting in<Emphasis Type="Italic"> Callicebus lugens</Emphasis>, the species with the lowest diploid number (2<Emphasis Type="Italic">n</Emphasis>=16) known in primates

Cytogenetic studies have shown that New World primates are karyologically diverse and highly derived. The genus Callicebus is the best example of this karyological diversity, with diploid numbers ranging from 2n=50 to 2n=16. We report on Callicebus lugens, which has the lowest diploid number (2n=16) yet found in the primate order and represents a striking example of extreme karyotypic shuffling. To better understand the genomic rearrangements that have resulted in this extremely low diploid number, we mapped chromosome homologies between C. lugens and humans by in situ hybridization. The total number of hybridization signals was 42, excluding the Y chromosome, with a total of 34 syntenic associations not found in humans. This species has one of the most derived karyotypes among the Platyrrhini. Fusion has been the predominant mode of karyological evolution, although fissions and inversions have also transformed the C. lugens karyotype. Remarkably in such a highly rearranged karyotype, the synteny of 11 human chromosomes (4, 5, 9, 12, 13, 14, 17, 18, 20, 21, and X) was maintained intact, even if most of these human-homologous gene clusters were translocated. Other human syntenies, such as homologues to human chromosomes 10 and 16, were highly fragmented. Comparisons of the C. lugens-human homology map with those of other New World primates have not yet helped establish a phylogenic arrangement between congeneric species or link Callicebus with any other genus.Communicated by S. Henikoff     

Fast chromosomal evolution and karyotype instability: recurrent chromosomal rearrangements in the peach potato aphid Myzus persicae (Hemiptera: Aphididae)

The occurrence of karyotype variations with respect to both chromosome number and structure has been frequently reported in aphids. Here, we review recent data attesting to the presence of recurrent chromosomal changes in the karyotype of the peach potato aphid Myzus persicae, where clones presenting metaphases with different chromosome number (from 12 to 17) have been observed, also comparing plates obtained within the same embryo. According to the available data, M. persicae autosomes 3 and 1 are the chromosomes mostly involved in changes compared to other autosomes, suggesting that they could have sites more susceptible to fragmentation. Chromosomal fissions involving the X chromosomes have also been observed, suggesting that they may have fragile sites located at the termini opposite to the nucleolar organizer regions‐bearing telomere. The presence of holocentric chromosomes and reproduction by apomictic parthenogenesis, together with a constitutive expression of telomerase, could explain the inheritance of the observed chromosomal instability in aphids. Considering that chromosomal changes may affect the host choice and could also favour speciation, it would be intriguing to confirm whether the observed karyotype variants have effects over short temporal and spatial scales.     

Trends of karyotypical evolution in the pearl cichlid,Geophagus brasiliensis,from southern Brazil

Chromosomal rearrangements such as inversions can facilitate speciation even in the presence of gene flow. The present study aims to analyze the karyotypic variation in six populations of Geophagus brasiliensis from southern Brazil. All specimens showed 2n = 48 chromosomes, but three karyotypes were found to have one, two or three pairs of submetacentric chromosomes. Although G. brasiliensis did not exhibit variation in the diploid number, it presented a wide interpopulational variation mainly regarding the karyotype formula and specific chromosomal markers. Differences in the location of the major and minor rDNA loci were observed among the populations. Moreover, different patterns were observed in the distribution of the constitutive heterochromatin, presenting intra- and interpopulational variation. This supports the hypothesis that this taxon represents a complex species or that cryptic species are included in this group, indicating a possibleprocess of sympatric speciation. By potentially restricting gene flow between heterokaryotypes, the segregating chromosome rearrangements we describe for G. brasiliensis may play a role in diversification in this species complex.     

Comparative Chromosome Painting in Mammals: Human and the Indian Muntjac (Muntiacus muntjak vaginalis)

We have used human chromosome-specific painting probes forin situhybridization on Indian muntjac (Muntiacus muntjak vaginalis,2n= 6, 7) metaphase chromosomes to identify the homologous chromosome regions of the entire human chromosome set. Chromosome rearrangements that have been involved in the karyotype evolution of these two species belonging to different mammalian orders were reconstructed based on hybridization patterns. Although, compared to human chromosomes, the karyotype of the Indian muntjac seems to be highly rearranged, we could identify a limited number of highly conserved homologous chromosome regions for each of the human chromosome-specific probes. We identified 48 homologous autosomal chromosome segments, which is in the range of the numbers found in other artiodactyls and carnivores recently analyzed by chromosome painting. The results demonstrate that the reshuffling of the muntjac karyotype is mostly due to fusions of huge blocks of entire chromosomes. This is in accordance with previous chromosome painting analyses between various Muntjac species and contrasts the findings for some other mammals (e.g., gibbons, mice) that show exceptional chromosome reshuffling due to multiple reciprocal translocation events.     

RAD‐seq linkage mapping and patterns of segregation distortion in sedges: meiosis as a driver of karyotypic evolution in organisms with holocentric chromosomes

Meiotic drive, the class of meiotic mechanisms that drive unequal segregation of alleles among gametes, may be an important force in karyotype evolution. Its role in holocentric organisms, whose chromosomes lack localized centromeres, is poorly understood. We crossed two individuals of Carex scoparia (Cyperaceae) with different chromosome numbers (2n = 33^II = 66 × 2n = 32^II = 64) to obtain F1 individuals, which we then self‐pollinated to obtain second‐generation (F2) crosses. RAD‐seq was performed for 191 individuals (including the parents, five F1 individuals and 184 F2 individuals). Our F2 linkage map based on stringent editing of the RAD‐seq data set yielded 32 linkage groups. In the final map, 865 loci were located on a linkage map of 3966.99 cM (linkage groups ranged from 24.39 to 193.31 cM in length and contained 5–51 loci each). Three linkage groups exhibit more loci under segregation distortion than expected by chance; within linkage groups, loci exhibiting segregation distortion are clustered. This finding implicates meiotic drive in the segregation of chromosome variants, suggesting that selection of chromosome variants in meiosis may contribute to the establishment and fixation of chromosome variants in Carex, which is renowned for high chromosomal and species diversity. This is an important finding as previous studies demonstrate that chromosome divergence may play a key role in differentiation and speciation in Carex.     

The vanishing clone: karyotypic evidence for extensive intraclonal genetic variation in the peach potato aphid,Myzus persicae (Hemiptera: Aphididae)

Analysis of holocentric mitotic metaphase chromosomes of the peach‐potato aphid Myzus persicae (Sulzer) clone 33H revealed different chromosome numbers, ranging from 12 to 17 within each embryo, in contrast to the standard karyotype of this species (2n = 12). Chromosome length measurements revealed that the observed chromosomal mosaicism is the result of recurrent fragmentations of chromosomes X, 1 and 3 because of fragile sites or hot spots of recombination. Fluorescent in situ hybridization experiments showed that X chromosomes were frequently involved in recurrent fragmentations, in particular their telomeric end opposite to the nucleolar organizer region. Experiments to induce males showed that M. persicae clone 33H is obligately parthenogenetic. The reproduction by apomictic parthenogenesis, together with a high telomerase expression that stabilized the chromosomes involved in the fragmentations observed in the M. persicae clone 33H, appears to favour the stabilization of the observed chromosome instability. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 350–358.     

Ricerche Citotassonomiche in Artemisia Vulgaris L. Ed Artemisia Verlotorum Lamotte

Abstract

Cytotaxonomical studies in Artemisia vulgaris L. and Artemisia verlotorum Lamotte. — Karyotype analysis of A. vulgaris and A. verlotorum has shown in the first species, in agreement with previous data, a chromosome number of 2n=16 and in the second the chromosome number of 2n=48 which does not agree with previous data. This seems to be the first case of polyploidy observed in Artemisia with basic number eight. A few specimens of A. verlotorum had shown 2n=48 + 2B chromosomes. The comparison of karyotypes has shown that, while the two species have, in some respect, the same degree of symmetry (ΣL%=57; ΣC9% = 43), the quality of their chromosomes is different (see karyotype formulas). We see no explanation for such an unlikely phenomenon.     

Fissions,fusions, and translocations shaped the karyotype and multiple sex chromosome constitution of the northeast‐Asian wood white butterfly,Leptidea amurensis

Previous studies have shown a dynamic karyotype evolution and the presence of complex sex chromosome systems in three cryptic Leptidea species from the Western Palearctic. To further explore the chromosomal particularities of Leptidea butterflies, we examined the karyotype of an Eastern Palearctic species, Leptidea amurensis. We found a high number of chromosomes that differed between the sexes and slightly varied in females (i.e. 2n = 118–119 in females and 2n = 122 in males). The analysis of female meiotic chromosomes revealed multiple sex chromosomes with three W and six Z chromosomes. The curious sex chromosome constitution [i.e. W_1–3/Z_1–6 (females) and Z_1–6/Z_1–6 (males)] and the observed heterozygotes for a chromosomal fusion are together responsible for the sex‐specific and intraspecific variability in chromosome numbers. However, in contrast to the Western Palearctic Leptidea species, the single chromosomal fusion and static distribution of cytogenetic markers (18S rDNA and H3 histone genes) suggest that the karyotype of L. amurensis is stable. The data obtained for four Leptidea species suggest that the multiple sex chromosome system, although different among species, is a common feature of the genus Leptidea. Furthermore, inter‐ and intraspecific variations in chromosome numbers and the complex meiotic pairing of these multiple sex chromosomes indicate the role of chromosomal fissions, fusions, and translocations in the karyotype evolution of Leptidea butterflies.     

A monophyletic origin of the B chromosomes ofBrachycome dichromosomatica (Asteraceae)

The A and B chromosomes of different karyotype variants (cytodemes A1, A2, A3 and A4) ofBrachycome dichromosomatica were analysed by computer-aided chromosome image analysis and fluorescencein situ hybridisation (FISH). Ribosomal DNA and the B chromosome-specific sequence Bd49 were detected on all B chromosomes. In addition to minor size variation of the Bs, polymorphism of the rDNA and Bd49 position and copy number revealed two major types of B chromosomes. The B chromosomes of all the cytodemes were indistinguishable from each other in length, but that of A3 showed evidence of rearrangements consistent with its long-term geographic isolation. The results presented suggest a monophyletic origin of the B chromosomes ofB. dichromosomatica.     

Mechanisms of chromosomal evolution and its possible relation to natural history characteristics in Ancistrus catfishes (Siluriformes: Loricariidae)

Ancistrus is the most speciose genus of the tribe Ancistrini, with 58 valid species and many yet to be described. Cytogenetic studies were conducted on five apparently undescribed species from the Amazon basin, which showed different diploid numbers: Ancistrus sp. Purus (2n = 34); Ancistrus sp. Macoari (2n = 46); Ancistrus sp. Dimona (2n = 52); Ancistrus sp. Vermelho (2n = 42) and Ancistrus sp. Trombetas (2n = 38). All species possessed only one pair of NOR‐carrying chromosomes, but with extensive variation in both the location on the chromosome as well as in the position of the ribosomal sites on the karyotype. The karyotypic evolution of Ancistrus species seems to be based on chromosomal rearrangements, with a tendency to a reduction of the diploid number. Two new instances of XX/XY sex chromosomes for Ancistrus species, based on the heteromorphism in the male karyotype, were also recorded. The large karyotypic diversity among Ancistrus species may be related to biological and behavioural characteristics of these fish that include microhabitat preferences, territoriality and specialized reproductive tactics. These characteristics may lead to a fast rate of fixation of chromosomal mutations and eventually speciation across the basin.     

Extreme degree of chromosome number variability in species of the spider genus Scytodes (Araneae, Haplogynae, Scytodidae)

Genus Scytodes includes most species of the spider family Scytodidae. Until now, 187 species of the genus have been described. In spite of this great diversity, only three Scytodes species were karyotyped so far. The present paper provides for the first time karyotype analysis of two synanthropic species, Scytodes fusca and Scytodes itapevi. Furthermore, new data on karyotype of Scytodes globula are also provided using conventional and differential cytogenetical procedures. The diploid number in the genus Scytodes varied considerably, namely from 2n = 13 to 2n = 31. The diploid number found in S. globula (2n♂ = 13) is the lowest in haplogyne spiders with monocentric chromosomes. Except S. globula, this number has been found only in one haplogyne spider with monocentric chromosomes, namely Ochyrocera sp. (Ochyroceratidae). On the contrary, the diploid number of S. fusca (2n♂ = 31) is one of the highest diploid numbers recorded in haplogyne spiders. The degree of intrageneric variation found in the genus Scytodes is the highest recorded in araneomorph spiders with monocentric chromosomes so far. Some karyotype characteristics (diploid number, chromosome morphology, total chromosome length, and distribution of constitutive heterochromatin) allowed us to postulate a close relationship between S. globula and S. itapevi. According to the karyotype data, S. fusca is not closely related to these two species. This conclusion corroborates a recent taxonomic work that grouped S. globula, S. itapevi, and other four Scytodes species in the ‘globula group’.