Karyotype of Hynobiusfucus Lai et Lue, 2008, a salamander endemic to Taiwan with comments in memory of June-Shian Lai, a pioneer in studies of mountainous salamanders (Urodela, Hynobiidae)

Karyotype, including the chromosome and arm numbers, is a fundamental genetic characteristic of all organisms and has long been used as a species-diagnostic character. Additionally, karyotype evolution plays an important role in divergent adaptation and speciation. Centric fusion and fission change chromosome numbers, whereas the intra-chromosomal movement of the centromere, such as pericentric inversion, changes arm numbers. A probabilistic model simultaneously incorporating both chromosome and arm numbers has not been established. Here, we built a probabilistic model of karyotype evolution based on the “karyograph”, which treats karyotype evolution as a walk on the two-dimensional space representing the chromosome and arm numbers. This model enables analysis of the stationary distribution with a stable karyotype for any given parameter. After evaluating their performance using simulated data, we applied our model to two large taxonomic groups of fish, Eurypterygii and series Otophysi, to perform maximum likelihood estimation of the transition rates and reconstruct the evolutionary history of karyotypes. The two taxa significantly differed in the evolution of arm number. The inclusion of speciation and extinction rates demonstrated possibly high extinction rates in species with karyotypes other than the most typical karyotype in both groups. Finally, we made a model including polyploidization rates and applied it to a small plant group. Thus, the use of this probabilistic model can contribute to a better understanding of tempo and mode in karyotype evolution and its possible role in speciation and extinction.

Karyotype, including the chromosome and arm numbers, is a fundamental genetic characteristic of all organisms and has long been used as a species-diagnostic character. Additionally, karyotype evolution plays an important role in divergent adaptation and speciation. Centric fusion and fission change chromosome numbers, whereas the intra-chromosomal movement of the centromere, such as pericentric inversion, changes arm numbers. A probabilistic model simultaneously incorporating both chromosome and arm numbers has not been established. Here, we built a probabilistic model of karyotype evolution based on the "karyograph", which treats karyotype evolution as a walk on the two-dimensional space representing the chromosome and arm numbers. This model enables analysis of the stationary distribution with a stable karyotype for any given parameter. After evaluating their performance using simulated data, we applied our model to two large taxonomic groups of fish, Eurypterygii and series Otophysi, to perform maximum likelihood estimation of the transition rates and reconstruct the evolutionary history of karyotypes. The two taxa significantly differed in the evolution of arm number. The inclusion of speciation and extinction rates demonstrated possibly high extinction rates in species with karyotypes other than the most typical karyotype in both groups. Finally, we made a model including polyploidization rates and applied it to a small plant group. Thus, the use of this probabilistic model can contribute to a better understanding of tempo and mode in karyotype evolution and its possible role in speciation and extinction.

Aspects of chromosomal mutation and karyotype evolution in ants are discussed with reference to recently accumulated karyological data, and to detailed karyotype analyses of several species or species complexes with low chromosome number and unusual chromosomal mutations (the complexes of Myrmecia pilosula (Smith) (n = 1, 5 or 9 to 16); M. piliventris Smith (n = 2, 3-4, 17 or 32), and Ponera scabra Wheeler (n = 3 or 4, 2n = 7 or 8). Translocations and Robertsonian polymorphisms are confirmed to be non-randomly distributed among ants -the former are found at high frequencies in species with low chromosome numbers (n less than or equal to 12), while the latter predominate in those with high numbers (n greater than 12). This situation is consistent with the minimum interaction hypothesis of Imai et al. (1986), under which translocations are expected to occur most frequently in low-numbered karyotypes, and that the resulting genetic risks are minimized by increases in chromosome and/or arm numbers through centric fission and pericentric inversion. Centric fusion is considered to be a transient event in karyotype evolution, resulting from telomere instability in acrocentric chromosomes.

The karyotype, which is the number and shape of chromosomes, is a fundamental characteristic of all eukaryotes. Karyotypic changes play an important role in many aspects of evolutionary processes, including speciation. In organisms with monocentric chromosomes, it was previously thought that chromosome number changes were mainly caused by centric fusions and fissions, whereas chromosome shape changes, that is, changes in arm numbers, were mainly due to pericentric inversions. However, recent genomic and cytogenetic studies have revealed examples of alternative cases, such as tandem fusions and centromere repositioning, found in the karyotypic changes within and between species. Here, we employed comparative genomic approaches to investigate whether centromere repositioning occurred during karyotype evolution in medaka fishes. In the medaka family (Adrianichthyidae), the three phylogenetic groups differed substantially in their karyotypes. The Oryzias latipes species group has larger numbers of chromosome arms than the other groups, with most chromosomes being metacentric. The O. javanicus species group has similar numbers of chromosomes to the O. latipes species group, but smaller arm numbers, with most chromosomes being acrocentric. The O. celebensis species group has fewer chromosomes than the other two groups and several large metacentric chromosomes that were likely formed by chromosomal fusions. By comparing the genome assemblies of O. latipes, O. javanicus, and O. celebensis, we found that repositioning of centromere-associated repeats might be more common than simple pericentric inversion. Our results demonstrated that centromere repositioning may play a more important role in karyotype evolution than previously appreciated.

The bug family Nabidae (Heteroptera) includes taxa showing either a low chromosome number 2n = 16 + XY or high chromosome numbers 2n = 26 or 32 + XY. In order to reveal the direction of karyotype evolution in the family, a molecular phy- logeny of the family was created to reveal the taxon closest to the ancestral type and hence the ancestral karyotype. The phylogeny was based on a partial sequence of the 18S rDNA gene of both high and low chromosome number species belonging to the subfami- lies Prostemmatinae and Nabinae. Phylogeny created by the Neighbour Joining method separated the subfamilies, Prostemmatinae and Nabinae, which form sister groups at the base of this phylogenetic tree, as well as within the Nabinae, tribes Nabini and Arach- nocorini. Combining karyosystematic data with the phylogeny of the family indicated that the ancestral karyotype was a high chro- mosome number, consisting of 2n = 32 + XY. During the course of evolution changes have occurred both in meiotic behaviour of the sex chromosomes and in the number of autosomes. The direction of karyotype evolution was from a high to low autosome number. Abrupt decreases in the number of autosomes have occurred twice; firstly when the tribe Arachnocorini differentiated from the main stem in the subfamily Nabinae and secondly within the tribe Nabini, when within the genus Nabis 2n = 16 + XY species diverged from the 2n = 32 + XY species. A scheme of the sequence of events in karyotype evolution during the evolution of the Nabidae is presented.

Chromosome numbers vary greatly in Orgyiu, from low numbers, like n = 11 in O.thyellina and n = 14 in O.antiqua, to a high number, n = 30, as in O.recens and O. ericue. Meiotic synapsis was regular in O. thyellina and O.antiqua; 11 and 14 normal bivalents, respectively, were found in meiosis. The paired homologues displayed homologous chromomere patterns. In the species hybrid between antiqua and thyellina, many synapsed chromosome segments were found in meiosis. This indicates sufficient segmental homology between chromosomes of the two species although the paired pachytene chromosome segments rarely displayed similar chromomere patterns. Chromosomes switched pairing partners, thus forming multivalents, linked by chiasmata in males, and long synaptic chains in the achiasmatic females. Multivalent formation is understood as the consequence of a separate evolution of the two species from a species with a high chromosome number. Multiple chromosome fusions resulted in similarly low chromosome numbers but different segmental compositions of the chromosomes in the two species.

Karyotype evolution in species with non-localised centromeres (holocentric chromosomes) is usually very dynamic and associated with recurrent fission and fusion (also termed agmatoploidy/symploidy) events. In Rhynchospora (Cyperaceae), one of the most species-rich sedge genera, all analysed species have holocentric chromosomes and their numbers range from 2n=4 to 2n=84. Agmatoploidy/symploidy and polyploidy were suggested as the main processes in the reshuffling of Rhynchospora karyotypes, although testing different scenarios of chromosome number evolution in a phylogenetic framework has not been attempted until now. Here, we used maximum likelihood and model-based analyses, in combination with genome size estimation and ribosomal DNA distribution, to understand chromosome evolution in Rhynchospora. Overall, chromosome number variation showed a significant phylogenetic signal and the majority of the lineages maintained a karyotype of 2n=10 (~48% of the species), the most likely candidate for the ancestral number of the genus. Higher and lower chromosome numbers were restricted to specific clades, whilst polyploidy and/or fusion/fission events were present in specific branches. Variation in genome size and ribosomal DNA site number showed no correlation with ploidy level or chromosome number. Although different mechanisms of karyotype evolution (polyploidy, fusion and fission) seem to be acting in distinct lineages, the degree of chromosome variation and the main mechanisms involved are comparable to those found in some monocentric genera and lower than expected for a holocentric genus.

The gymnosperms are the modern representatives of the most ancient group of seed-bearing plants. Their chromosomes have been studied extensively and chromosome numbers are known for representatives of all but three genera. A unique feature of the gymnosperms is the relative uniformity of their chromosome numbers both between species within genera and between genera in families. Polyploidy is very rare. Gymnosperm chromosomes are characteristically large and within most genera karyotypes also show uniformity, the exceptions being amongst some cycads. Despite this overall uniformity of shape and number differential banding patterns with Giemsa and base-specific fluorochromes reveal considerable variation in the number, size, location and base-composition of bands. Similarly, fluorescence in situ hybridization also demonstrates significant variation in number and location of many repetitive DNA elements within and between genera and families. Karyotype evolution does not appear to involve extensive structural rearrangements as meiotic pairing in F1 hybrids is usually regular and where available genetic maps suggest the conservation of large syntenic groups of genes.

SUMMARYThe chromosome number of nine species belonging to the genus Amara varies between 2n = 37 and 2n = 20, whereas six species of Zabrus have 2n = 57 —59. These genera show different patterns in karyotypic evolution: 37 or lower chromosome numbers, mediocentric chromosomes, and alternation of XO—XY systems are found in Amara, whereas in Zabrus the chromosome numbers are higher than 46, there are small subtelocentric pairs, and XO sex chromosomes predominate.

Despite the variation observed in the diploid chromosome number of storks (Ciconiiformes, Ciconiidae), from 2n = 52 to 2n = 78, most reports have relied solely on analyses by conventional staining. As most species have similar macrochromosomes, some authors propose that karyotype evolution involves mainly fusions between microchromosomes, which are highly variable in species with different diploid numbers. In order to verify this hypothesis, in this study, the karyotypes of 2 species of storks from South America with different diploid numbers, the jabiru (Jabiru mycteria, 2n = 56) and the maguary stork (Ciconia maguary, 2n = 72), were analyzed by chromosome painting using whole chromosome probes from the macrochromosomes of Gallus gallus (GGA) and Leucopternis albicollis (LAL). The results revealed that J. mycteria and C. maguary share synteny within chromosome pairs 1-9 and Z. The syntenies to the macrochromosomes of G. gallus are conserved, except for GGA4, which is homologous to 2 different pairs, as in most species of birds. A fusion of GGA8 and GGA9 was observed in both species. Additionally, chromosomes corresponding to GGA4p and GGA6 are fused to other segments that did not hybridize to any of the macrochromosome probes used, suggesting that these segments correspond to microchromosomes. Hence, our data corroborate the proposed hypothesis that karyotype evolution is based on fusions involving microchromosomes. In view of the morphological constancy of the macrochromosome pairs in most Ciconiidae, we propose a putative ancestral karyotype for the family, including the GGA8/GGA9 fusion, and a diploid number of 2n = 78. The use of probes for microchromosome pairs should be the next step in identifying other synapomorphies that may help to clarify the phylogeny of this family.

Rhinolophus (Rhinolophidae) is the second most speciose genus in Chiroptera and has extensively diversified diploid chromosome numbers (from 2n = 28 to 62). In spite of many attempts to explore the karyotypic evolution of this genus, most studies have been based on conventional Giemsa staining rather than G-banding. Here we have made a whole set of chromosome-specific painting probes from flow-sorted chromosomes of Aselliscus stoliczkanus (Hipposideridae). These probes have been utilized to establish the first genome-wide homology maps among six Rhinolophus species with four different diploid chromosome numbers (2n = 36, 44, 58, and 62) and three species from other families: Rousettus leschenaulti (2n = 36, Pteropodidae), Hipposideros larvatus (2n = 32, Hipposideridae), and Myotis altarium (2n = 44, Vespertilionidae) by fluorescence in situ hybridization. To facilitate integration with published maps, human paints were also hybridized to A. stoliczkanus chromosomes. Our painting results substantiate the wide occurrence of whole-chromosome arm conservation in Rhinolophus bats and suggest that Robertsonian translocations of different combinations account for their karyotype differences. Parsimony analysis using chromosomal characters has provided some new insights into the Rhinolophus ancestral karyotype and phylogenetic relationships among these Rhinolophus species so far studied. In addition to Robertsonian translocations, our results suggest that whole-arm (reciprocal) translocations involving multiple non-homologous chromosomes as well could have been involved in the karyotypic evolution within Rhinolophus, in particular those bats with low and medium diploid numbers.

SUMMARYSpontaneous intercellular chromatin migration (cytomixis) occurred in PMCs of Lilium davidii at synizesis stage of meiosis, and less frequent in later stages. This process has led to the formation of up to 9.44% to 13.6% of PMCs, microspores, and generative cells with chromosome numbers deviating from the normal haploid chromosome complement, n= 12. The abnormal cells contained chromosome numbers ranging from 8 to 15. The patterns of intercellular chromatin migration may be divided into two types: (a) The chromatin substance may migrate from one nucleus into one adjacent cell, and (b) from one nucleus into two or more cells or from two or more nuclei into one cell. According to the chi-square test, it has been shown that the differences between the patterns of intercellular chromatin migration and the variation of chromosome number in the PMCs, microspores or generative cells are not significant. Because of cytomixis, about 10% cells proved to be aneuploids, with hypoploids predominating. It shows that the descending basic number is greater than that of the ascending. This is in accordance with the principle of the trend in karyotype evolution—the progressive reduction of the basic chromosome number. If these newly established karyotypes are survived by rigorous selection, they may be expected to accomplish fertilization and thus give rise to aneuploid progeny in a population. It is these selected chromosome mutations which may be of considerable evolutionary significance.

-The relationship between genic and chromosomal distance was examined for 11 sets of mammalian taxa using a matrix regression procedure. Nine of the 11 comparisons were statistically significant, indicating a lack of independence between genic and chromosomal evolution, but not necessarily a causal relationship. The covariation of genic and chromosomal distance may be related to population structure. Genic and chromosomal evolution would be affected in a similar way by a population structure that is sensitive to the influence of genetic drift and inbreeding. [Chromosomal evolution; genic evolution; population structure; genetic drift; divergence time.] Genetic differentiation is the basis of evolutionary change. Even closely related species usually differ in karyotype and have differences in structural genes as shown by electrophoresis. Numerous studies have documented genic and karyotypic differences between taxa; however, the concordance between genic and chromosomal change during and subsequent to speciation is poorly understood. For example, fish species of the speciose family Centrarchidae show considerable genic divergence, but almost all of the species in the family have the same diploid and fundamental number of chromosomes (Avise et al., 1977; Avise and Gold, 1977). On the other hand, Baccus et al. (1983) reported fairly high associations between measures of genic and chromosomal divergence within a group of artiodactylid species and within populations of a pocket gopher, Thomomys talpoides. Schnell and Selander (1981) summarized recent data of electrophoretic and karyotypic patterns of variation in mammals and concluded that karyotypic and genic evolution proceed more or less independently. However, their support for the independence of genic and chromosomal evolution is based upon only a few examples, and to date a more detailed study comparing genic and chromosomal divergence of a variety of taxa has not been undertaken. The purpose of our study was to examine statistically the relationship between measures of genic and chromosomal differentiation in a number of mammalian taxa in order to test more rigorously the relationship between genic and karyotypic evolution.

A new mechanism for changing chromosome numbers (preserving the fundamental number of long chromosome arms) during karyotype evolution is suggested. It includes: 1) Occurrence of individuals heterozygous for two interchanges between different arms of three chromosomes (a metacentric and two acrocentric ones). 2) Formation in heterokaryotypes of multivalents during meiosis between the chromosomes involved in the interchanges and their unchanged homologues. 3) Mis-segregation of chromosomes from these multivalents resulting in hypoploid (n-1) and hyperploid (n+1) simultaneously instead of euhaploid gametes. 4) Fusion of n-1 or n+1 gametes which gives rise to (zygotes and) individuals representing homokaryotypes with changed number of chromosomes (2n+2 or 2n-2), but preserves (as compared to the parental karyotypes) the number of long chromosome arms. Under definite conditions, chromosome numbers of the progeny may be changed by this process in both directions (upwards and downwards). The mechanism is free of the difficulties associated with the explanation for such changes by direct Robertsonian interchanges (see "Discussion"), which are usually considered to be responsible for such alterations in chromosome number. The above-mentioned process has been experimentally documented in Vicia faba and it probably also occurred naturally within the Vicia sativa group.

Chromosomes and karyotypes are important aspects of plant phylogeny and evolution. The chromosome numbers and karyotypes of Lycoris radiata display great variability among and within different populations. By studying different populations of L. radiata we acquired some basic data on karyotype evolution and evolutionary mechanisms in L. radiata and the genus Lycoris. Six populations of L. radiata from Anhui and Zhejiang provinces in China were investigated cytologically. The chromosome numbers and karyotype formulae are as follows: Huoshan populations, 2n=44=28st+8t+8T, 2n=22=6st+12t+4T; Huangshan populations, 2n=22=22t, 2n=22=18st+4t, 2n=21=12st+7t+2T; Chuzhou population, 2n=33=33t; Ma'anshan populations, 2n=33=18st+15T, 2n=25=1m+20st+2t+2T; Xuancheng populations, 2n=22=20st+2T, 2n=21=1m+20st; and Hangzhou populations 2n=22=12st+4t+6T, 2n=21=18st+3t. The chromosome numbers and karyotypes of some populations are reported here for the first time and the wild tetraploid population of L. radiata was found for the first time. In addition, karyotype evolution among populations and the origin of polyploids are discussed.