Karyotypic conservatism in the suborder Feliformia (Order Carnivora)

Multidirectional comparative chromosome painting was used to investigate the karyotypic relationships among representative species from three Feliformia families of the order Carnivora ( Viverridae, Hyaenidae and Felidae). Complete sets of painting probes derived from flow-sorted chromosomes of the domestic dog, American mink, and human were hybridized onto metaphases of the spotted hyena (Crocuta crocuta, 2n = 40) and masked palm civet (Paguma larvata, 2n = 44). Extensive chromosomal conservation is evident in these two species when compared with the cat karyotype, and only a few events of chromosome fusion, fission and inversion differentiate the karyotypes of these Feliformia species. The comparative chromosome painting data have enabled the integration of the hyena and palm civet chromosomes into the previously established comparative map among the domestic cat, domestic dog, American mink and human and improved our understanding on the karyotype phylogeny of Feliformia species. Copyright (C) 2005 S. Karger AG, Basel.

Karyotypic evolution of the family Sciuridae: inferences from the genome organizations of ground squirrels

Cross- species chromosome painting has made a great contribution to our understanding of the evolution of karyotypes and genome organizations of mammals. Several recent papers of comparative painting between tree and flying squirrels have shed some light

New insights into the karyotypic relationships of Chinese muntjac (Muntiacus reevesi), forest musk deer (Moschus berezovskii) and gayal (Bos frontalis)

To investigate the karyotypic relationships between Chinese muntjac (Muntiacus reevesi), forest musk deer (Moschus berezovskii) and gayal (Bos frontalis), a complete set of Chinese muntjac chromosome-specific painting probes has been assigned to G-banded chromosomes of these three species. Sixteen autosomal probes (i.e. 6-10, 12-22) of the Chinese muntjac each delineated one pair of conserved segments in the forest musk deer and gayal, respectively. The remaining six autosomal probes (1-5, and 11) each delineated two to five pairs of conserved segments. In total, the 22 autosomal painting probes of Chinese muntjac delineated 33 and 34 conserved chromosomal segments in the genomes of forest musk deer and gayal, respectively. The combined analysis of comparative chromosome painting and G-band comparison reveals that most interspecific homologous segments show a high degree of conservation in G-banding patterns. Eleven chromosome fissions and five chromosome fusions differentiate the karyotypes of Chinese muntjac and forest musk deer; twelve chromosome fissions and six fusions are required to convert the Chinese muntjac karyotype to that of gayal; one chromosome fission and one fusion separate the forest musk deer and gayal. The musk deer has retained a highly conserved karyotype that closely resembles the proposed ancestral pecoran karyotype but shares none of the rearrangements characteristic for the Cervidae and Bovidae. Our results substantiate that chromosomes 1-5 and 11 of Chinese muntjac originated through exclusive centromere-to-telomere fusions of ancestral acrocentric chromosomes. Copyright (C) 2005 S. Karger AG, Basel.

Flying lemurs – The 'flying tree shrews'? Molecular cytogenetic evidence for a Scandentia-Dermoptera sister clade

Background: Flying lemurs or Colugos (order Dermoptera) represent an ancient mammalian lineage that contains only two extant species. Although molecular evidence strongly supports that the orders Dermoptera, Scandentia, Lagomorpha, Rodentia and Primates form a superordinal clade called Supraprimates (or Euarchontoglires), the phylogenetic placement of Dermoptera within Supraprimates remains ambiguous. Results: To search for cytogenetic signatures that could help to clarify the evolutionary affinities within this superordinal group, we have established a genome-wide comparative map between human and the Malayan flying lemur (Galeopterus variegatus) by reciprocal chromosome painting using both human and G. variegatus chromosome-specific probes. The 22 human autosomal paints and the X chromosome paint defined 44 homologous segments in the G. variegatus genome. A putative inversion on GVA 11 was revealed by the hybridization patterns of human chromosome probes 16 and 19. Fifteen associations of human chromosome segments (HSA) were detected in the G. variegatus genome: HSA1/3, 1/10, 2/21, 3/ 21, 4/8, 4/18, 7/15, 7/16, 7/19, 10/16, 12/22 (twice), 14/15, 16/19 (twice). Reverse painting of G. variegatus chromosome-specific paints onto human chromosomes confirmed the above results, and defined the origin of the homologous human chromosomal segments in these associations. In total, G. variegatus paints revealed 49 homologous chromosomal segments in the HSA genome. Conclusion: Comparative analysis of our map with published maps from representative species of other placental orders, including Scandentia, Primates, Lagomorpha and Rodentia, suggests a signature rearrangement (HSA2q/21 association) that links Scandentia and Dermoptera to one sister clade. Our results thus provide new evidence for the hypothesis that Scandentia and Dermoptera have a closer phylogenetic relationship to each other than either of them has to Primates.

蹄蝠科的核型进化：比较染色体涂色、G带和C带分析

：与其姐妹科(菊头蝠科)相比，蹄蝠科的细胞遗传学研究较少。迄今为止，仅少数蹄蝠科几个物种有高分辨率的G带核型报道，且有关该科核型进化的大多数结论都是基于常规Giemsa染色研究而得。该研究利用三叶小蹄蝠的染色体特异探针，通过比较染色体涂色、G和C显带，建立了5种蹄蝠的染色体同源性图谱，并探讨了它们同源染色体间的G和C带异同。结果表明：罗伯逊易位、臂内倒位以及异染色质的扩增可能是蹄蝠科物种核型进化的主要机制。通过对这5种蹄蝠物种及其外群物种之间的同源染色体片段的比较分析，作者推测蹄蝠科的祖先核型并不像先前认为的全由端着丝粒染色体组成, 而应该含有中着丝粒染色体。

Comparative cytogenetics of bats (Chiroptera): The prevalence of Robertsonian translocations limits the power of chromosomal characters in resolving interfamily phylogenetic relationships

Although the monophyly of Chiroptera is well supported by many independent studies, higher-level systematics, e.g. the monophyly of microbats, remains disputed by morphological and molecular studies. Chromosomal rearrangements, as one type of rare genomic changes, have become increasingly popular in phylogenetic studies as alternatives to molecular and other morphological characters. Here, the representatives of families Megadermatidae and Emballonuridae are studied by comparative chromosome painting for the first time. The results have been integrated into published comparative maps, providing an opportunity to assess genome-wide chromosomal homologies between the representatives of eight bat families. Our results further substantiate the wide occurrence of Robertsonian translocations in bats, with the possible involvement of whole-arm reciprocal translocations (WARTs). In order to search for valid cytogenetic signature(s) for each family and superfamily, evolutionary chromosomal rearrangements identified by chromosomal painting and/or banding comparison are subjected to two independent analyses: (1) a cladistic analysis using parsimony and (2) the mapping of these chromosomal changes onto the molecularly defined phylogenetic tree available fromthe literature. Both analyses clearly indicate the prevalence of homoplasic events that reduce the reliability of chromosomal characters for resolving interfamily relationships in bats.

食虫目核心类群的比较分子细胞遗传学研究

食虫目（Order Insectivora）是理解哺乳动物系统进化关系的一个关键类群。然 而, 对于其分类以及系统发育的关系，300 多年的研究都没有得出一致的结论。染色 体在进化过程中所发生的重组可以作为生物分类和系统发育关系的一个指标。通过 比较染色体涂色技术（Chromosome Painting）可以从全基因组水平揭示染色体同源 关系，并且可以鉴定物种进化过程中所发生的染色体重组。 本论文旨在对分布在我国的猬科、鼹科与鼩鼱科的代表物种的基因组结构进行 研究。通过比较染色体涂色的方法，建立了它们与人的基因组同源性。通过人与食 虫目主要代表类群的比较染色体涂色研究，我们从全基因组水平揭示了食虫目几个 代表类群之间的核型系统发育关系。研究结果表明： 猬科动物具有高度重组的基因组结构。人染色体片段联合HAS 4/8/5 和11/15 可 能是猬科动物的细胞遗传学鉴定特征。 与猬科动物具有高度重组的核型相比，鼹科动物的基因组结构相对保守。染色 体臂间的倒位是鼹科核型进化的主要方式。 鼩鼱科中的麝鼩亚科动物具有保守的核型。 以染色体重排作为系统发育指标，鼩鼱科与鼹科相对于猬科，具有比较近的亲 缘关系。 食虫目核心类群（猬科，鼹科与鼩鼱科）的基因组结构与现划入Afrotheria 超目 的象鼩科、无尾猬科和金鼹科的基因组结构有很大的差异。 此外，本研究所构建的比较染色体图谱，有助于已经测序的人的基因组序列信 息向其他没有基因定位数据的食虫目动物转移

三株肺癌细胞株的分子细胞遗传学研究

本课题采用流式细胞分选和双向及多色的染色体涂色等技术，详细地分析了三株非小细胞肺癌细胞系（YTMLC-90、GLC-82和A549）核型的异同，以揭示其核型特点，并希望能够找到三株细胞系共有的染色体断裂位点和可能发生的基因重组。染色体涂色技术揭示了三株细胞复杂的染色体数目和结构畸变。引人注目的是YTMLC-90和GLC-82具有相似且保守的核型，其中GLC-82的核型与其刚建立时的核型相比几乎没有发生改变。这与A549 的核型特点差别迥异。YTMLC-90 和GLC-82都有23 条异常染色体，除了i (5p) 有3个拷贝外，其余均为单拷贝；A549 有13条衍生染色体。在这三株细胞中，含有两个共有的断裂位点：HSA12q13 和 8q24.1。通过对NCBI的CancerChromosome数据库进行数据挖掘，发现8个可能的肿瘤相关基因位于这两个位点，其中3个已经被证实是肿瘤相关基因，其它5个基因可能是潜在的肿瘤抑制基因，需要进一步的实验来验证。

利用比较染色体涂色和BAC定位技术探讨麂属动物染色体的起源和演化

比较细胞遗传学研究发现物种的形成过程往往伴随着核型结构的变化，各种鹿属动物染色体的巨大差异正是很好的例证'赤魔的染色体被证明是由具有端着丝粒的祖先染色体经过多次的串联融合进化而来的。根据祖先染色体的形态和连接方式，可以将染色体串联融合主要分为三类：着丝粒一着丝粒融合，着丝粒一端粒融合和端粒一端粒融合。经典细胞遗传学，比较染色体涂色，卫星DNA序列和部分融合位点序列比较研究都支持串联融合假说。但串联融合的类型和分子机制迄今没有完全弄清楚。本论文旨在对魔属动物的串联融合类型和分子机制进行研究，分为两个部分：一、通过比较染色体涂色的方法，建立小鹿一林察一大额牛的比较染色体图谱，结合以前发表的结果来阐明鹿科（小魔）与牛科（大额牛），寮科（林磨）之间的核型关系；二、建立赤鹿的全基因组BAc文库，通过克隆定位的方法确立在赤魔的染色体进化过程中所发生的串联融合类型，并对其机制进行探讨。主要结果如下：利用小鹿的染色体特异探针与林寮，大额牛的染色体进行杂交，首次建立了小鹿一大额牛，小魔一林察的核型对比关系。结果显示小鹿的1-5、11号染色体均与林集和大额牛的多段染色体同源。结合高分辨的G带比较，发现小魔1-5和11号染色体上的与林爵和大额牛对应的所有同源片断在小鹿染色体上呈着丝粒一端粒连接排列。从而进一步证明小鹿的1-5和11号染色体是由2n=70的祖先核型通过染色体的着丝粒一端粒串联融合方式进化而来的。建立了我国第一个赤魔全基因组BAC文库，该文库由124800个克隆组成。大部分插入片段的大小在100-145kb之间，片段的平均大小为12＜0kb。克隆定位显示克隆的分布与小鹿染色体大小成正比关系，说明整个文库没有染色体的偏倚，文库为整个基因组的6倍，覆盖率几乎为100％。通过赤鹿BAC克隆在小魔和赤鹿染色体上的精确定位，使我们得以准确判断小鹿染色体在赤鹿染色体同源片段上的连接方式，并确定串联融合的类型。结果进一步支持赤鹿的核型是由一个2n=70祖先核型通过着丝粒一端粒的融合方式进化而来的。

Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor.

BACKGROUND: The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype and relied almost exclusively on comparative molecular cytogenetics of only the largest chromosomes. Here, novel whole genome sequence information from 21 avian genome sequences (most newly assembled) made available on an interactive browser (Evolution Highway) was analyzed. RESULTS: Focusing on the six best-assembled genomes allowed us to assemble a putative karyotype of the dinosaur ancestor for each chromosome. Reconstructing evolutionary events that led to each species' genome organization, we determined that the fastest rate of change occurred in the zebra finch and budgerigar, consistent with rapid speciation events in the Passeriformes and Psittaciformes. Intra- and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace. Analyzing chicken and zebra finch, we found little evidence to support the hypothesis of an association of evolutionary breakpoint regions with recombination hotspots but some evidence to support the hypothesis that microchromosomes largely represent conserved blocks of synteny in the majority of the 21 species analyzed. All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count. Ostrich, however, appeared to retain an overall karyotype structure of 2n=80 despite undergoing a large number (26) of hitherto un-described interchromosomal changes. CONCLUSIONS: Results suggest that mechanisms exist to preserve a static overall avian karyotype/genomic structure, including the microchromosomes, with widespread interchromosomal change occurring rarely (e.g., in ostrich and budgerigar lineages). Of the species analyzed, the chicken lineage appeared to have undergone the fewest changes compared to the dinosaur ancestor.

Crops and cultures in the Pacific: new data and new techniques for the investigation of old questions

Fifty years ago Carl Sauer suggested, controversially and on the basis of theory rather than evidence, that Southeast Asia was the source area for agriculture throughout the Old World, including the Pacific. Since then, the archaeobotanical record (macroscopic and microscopic) from the Pacific islands has increased, leading to suggestions, also still controversial, that Melanesia was a center of origin of agriculture independent of South-east Asia, based on tree fruits and nuts and vegetatively propagated starchy staples. Such crops generally lack morphological markers of domestication, so exploitation, cultivation and domestication cannot easily be distinguished in the archaeological record. Molecular studies involving techniques such as chromosome painting, DNA fingerprinting and DNA sequencing, can potentially complement the archaeological record by suggesting where species which were spread through the Pacific by man originated and by what routes they attained their present distributions. A combination of archaeobotanical and molecular studies should therefore eventually enable the rival claims of Melanesia versus South-east Asia as independent centers of invention of agriculture to be assessed.

Independent fusions and recent origins of sex chromosomes in the evolution and diversification of glass knife fishes (Eigenmannia)

The genus Eigenmannia comprises several species groups that display a surprising variety of diploid chromosome numbers and sex-determining systems. In this study, hypotheses regarding phylogenetic relationships and karyotype evolution were investigated using a combination of molecular and cytogenetic methods. Phylogenetic relationships were analyzed for 11 cytotypes based on sequences from five mitochondrial DNA regions. Parsimony-based character mapping of sex chromosomes confirms previous suggestions of multiple origins of sex chromosomes. Molecular cytogenetic analyses involved chromosome painting using probes derived from whole sex chromosomes from two taxa that were hybridized to metaphases of their respective sister cytotypes. These analyses showed that a multiple XY system evolved recently (<7 mya) by fusion. Furthermore, one of the chromosomes that fused to form the neo-Y chromosome is fused independently to another chromosome in the sister cytotype. This may constitute an efficient post-mating barrier and might imply a direct function of sex chromosomes in the speciation processes in Eigenmannia. The other chromosomal sex-determination system investigated is shown to have differentiated by an accumulation of heterochromatin on the X chromosome. This has occurred in the past 0.6 my, and is the most recent chromosomal sex-determining system described to date. These results show that the evolution of sex-determining systems can proceed very rapidly. Heredity (2011) 106, 391-400; doi:10.1038/hdy.2010.82; published online 23 June 2010

Intrachromosomal distribution of telomeric repeats in Eumops glaucinus and eumops perotis (Molossidae, Chiroptera)

The location of chromosomal telomeric repeats (TTAGGG)(n) was investigated in two species of the Molossidae family, Eumops glaucinus and Eumops perotis. The diploid chromosome number (2n) is 40 in E. glaucinus and 48 in E. perotis and the fundamental numbers (FN) are 64 and 58, respectively. It has been suggested that the E. glaucinus karyotype has evolved from the E. perotis karyotype through Robertsonian fusion events. In the present study, the telomeric sequences were detected at the termini of chromosomes in both species. In addition, E. glaucinus also displayed telomeric repeats in centromeric and pericentromeric regions in almost all biarmed chromosomes. Conversely, in E. perotis pericentromeric signals were only observed in two biarmed chromosomes. In both E. glaucinus and E. perotis, such telomeric sequences were observed as part of the heterochromatin. The interstitial sites of telomeric sequences suggest that they are remnants of telomeres of ancestral chromosomes that participated in the fusion event.

Comparação cariotípica entre Mazama gouazoubira e Mazama nemorivaga (Artiodactyla; Cervidae) por meio de marcadores citogenéticos clássicos, fish telomérica e pintura cromossômica

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Evolução cromossômica no veado-mateiro – Mazama americana (Mammalia; Cervidae)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)