Dissection of the nuclear genome of barley by chromosome flow sorting

Isolation of mitotic chromosomes using flow cytometry is an attractive way to dissect nuclear genomes into their individual chromosomal components or portions of them. This approach is especially useful in plants with complex genomes, where it offers a targeted and hence economical approach to genome analysis and gene cloning. In several plant species, DNA of flow-sorted chromosomes has been used for isolation of molecular markers from specific genome regions, for physical mapping using polymerase chain reaction (PCR) and fluorescence in situ hybridization (FISH), for integration of genetic and physical maps and for construction of chromosome-specific DNA libraries, including those cloned in bacterial artificial chromosome vectors. Until now, chromosome analysis and sorting using flow cytometry (flow cytogenetics) has found little application in barley (2n = 14, 1C ∼ 5,100 Mbp) because of the impossibility of discriminating and sorting individual chromosomes, except for the smallest chromosome 1H and some translocation chromosomes with DNA content significantly different from the remaining chromosomes. In this work, we demonstrate that wheat–barley ditelosomic addition lines can be used to sort any arm of barley chromosomes 2H–7H. Thus, the barley genome can be dissected into fractions representing only about 6–12% of the total genome. This advance makes the flow cytogenetics an attractive tool, which may greatly facilitate genome analysis and gene cloning in barley.     

A Look at Academic Anthropology: Through a Graph Darkly

An "external," nomothetic perspective that has been formulated by some historians of science (e.g., Kuhn 1968) is used to examine the history of anthropology in the United States. Regularities that characterize the growth of the physical sciences and the production and use of literature associated with them are shown to be characteristic of anthropology as well. Implications for the way anthropology will be done in the future are discussed . [anthropology, future of, growth of, history of]     

Obscurantist Holism Versus Clear-Cut Analysis: Will Anthropology Obviate the Biology-Culture Divide?

Although holism has long been a central theme in anthropology, current perception is that anthropological discourse is being pulled apart along its biology-culture seams. Despite reservations among sociocultural theorists, Darwinism remains the only body of theory that purports to link sub-disciplines of anthropology. The importance of holism in anthropology is reconciled here with disciplinary fragmentation and evolutionary theory. While Darwinism appears to provide interdisciplinary theoretical ties, it cannot successfully relate sub-disciplines of anthropology because this theory itself relies on a preformationist divide between inherited and acquired characteristics. Increasingly subtle language of genetic information and constraints does not ameliorate this problem. Research potential for the ecological constraints model in biological anthropology is discussed. Developmental systems theory (DST) is advocated as a tool for working toward a holistic anthropology [Susan Oyama, Paul Griffiths, and Russell Gray, ``Introduction: What is Developmental Systems Theory?,'' in Susan Oyama, Paul Griffiths, and Russell Gray, eds., Cycles of Contingency: Developmental Systems and Evolution (Cambridge, MA: MIT Press, 2001), 1–11].     

Chromosomal variants with normal phenotype in Man

The origin of human cytogenetics was very intimately associated with medicine, and therefore there was a primary interest in pathogenic effects of chromosomal aberrations only. However, chromosomal aberrations and variants exist which do not change the phenotype of the carrier. Similar aberrations and variants played a prominent role during the evolution of Man (centric fusions, inversions and possibly also translocations; variants in heterochromatic components of chromosomes). The principles of chromosomal evolution are still at work in Man; however the probability of a new and different human karyotype coming into existence, is negligible.New methods in cytogenetics (fluorescence, banding methods) which were used in human cytogenetics for the first time about two years ago, now allow analysis of chromosomes in very fine detail; they started a new era in cytogenetics. It is, therefore, a suitable time to summarize the results of the past era regarding chromosomal variants in Man, which were detected by classical staining methods in the first 15 years of human cytogenetics. The future review based on new methods, will be, of course, more extensive than this one, but it will be available only after years of chromosomal research.This review will be divided in the following way: (1) source of information on variants with normal phenotype, (2) variants with normal phenotype, (3) survival of variants in the population, (4) homozygous variants, (5) evolutionary consequences of chromosomal variants.     

History in the Gene: Negotiations Between Molecular and Organismal Anthropology

In the advertising discourse of human genetic database projects, of genetic ancestry tracing companies, and in popular books on anthropological genetics, what I refer to as the anthropological gene and genome appear as documents of human history, by far surpassing the written record and oral history in scope and accuracy as archives of our past. How did macromolecules become “documents of human evolutionary history”? Historically, molecular anthropology, a term introduced by Emile Zuckerkandl in 1962 to characterize the study of primate phylogeny and human evolution on the molecular level, asserted its claim to the privilege of interpretation regarding hominoid, hominid, and human phylogeny and evolution vis-à-vis other historical sciences such as evolutionary biology, physical anthropology, and paleoanthropology. This process will be discussed on the basis of three key conferences on primate classification and evolution that brought together exponents of the respective fields and that were held in approximately ten-years intervals between the early 1960s and the 1980s. I show how the anthropological gene and genome gained their status as the most fundamental, clean, and direct records of historical information, and how the prioritizing of these epistemic objects was part of a complex involving the objectivity of numbers, logic, and mathematics, the objectivity of machines and instruments, and the objectivity seen to reside in the epistemic objects themselves.     

Statistical methods for classification of human chromosomes.

The basic technical facts of human cytogenetics and the laboratory methods employed in chromosome research are explained in simple terms. The main variables used to describe chromosome images are defined and discussed. Three discriminant analysis models for chromosome classification are developed: one in which each chromosome is classified in isolation, a modification in which the cell, if normal, contains 2 chromosomes of each of the 23 kinds, and a final one in which the cell is the unit of analysis instead of the chromosome. Suggestions are made to reduce the calculations involved and to take into account missing chromosomes. The problem of detection and classification of aberrative chromosomes is studied, also in relation to multiple cell analysis. Finally four relevant problems are briefly discussed: selection of metaphase spreads, selection of variables, uncertain reference classification and measurement of performance.     

Teaching and the Life History of Cultural Transmission in Fijian Villages

Much existing literature in anthropology suggests that teaching is rare in non-Western societies, and that cultural transmission is mostly vertical (parent-to-offspring). However, applications of evolutionary theory to humans predict both teaching and non-vertical transmission of culturally learned skills, behaviors, and knowledge should be common cross-culturally. Here, we review this body of theory to derive predictions about when teaching and non-vertical transmission should be adaptive, and thus more likely to be observed empirically. Using three interviews conducted with rural Fijian populations, we find that parents are more likely to teach than are other kin types, high-skill and highly valued domains are more likely to be taught, and oblique transmission is associated with high-skill domains, which are learned later in life. Finally, we conclude that the apparent conflict between theory and empirical evidence is due to a mismatch of theoretical hypotheses and empirical claims across disciplines, and we reconcile theory with the existing literature in light of our results.     

Construction of a bacterial artificial chromosome (BAC) library for potato molecular cytogenetics research.

Lack of reliable techniques for chromosome identification is the major obstacle for cytogenetics research in plant species with large numbers of small chromosomes. To promote molecular cytogenetics research of potato (Solanum tuberosum, 2n = 4x = 48) we developed a bacterial artificial chromosome (BAC) library of a diploid potato species S. bulbocastanum. The library consists of 23,808 clones with an average insert size of 155 kb, and represents approximately 3.7 equivalents to the potato genome. The majority of the clones in the BAC library generated distinct signals on specific potato chromosomes using fluorescence in situ hybridization (FISH). The hybridization signals provide excellent cytological markers to tag individual potato chromosomes. We also demonstrated that the BAC clones can be mapped to specific positions on meiotic pachytene chromosomes. The excellent resolution of pachytene FISH can be used to construct a physical map of potato by mapping molecular marker-targeted BAC clones on pachytene chromosomes.     

Evolutionary Contributions to Solving the ��Matrilineal Puzzle��

Matriliny has long been debated by anthropologists positing either its primitive or its puzzling nature. More recently, evolutionary anthropologists have attempted to recast matriliny as an adaptive solution to modern social and ecological environments, tying together much of what was known to be associated with matriliny. This paper briefly reviews the major anthropological currents in studies of matriliny and discusses the contribution of evolutionary anthropology to this body of literature. It discusses the utility of an evolutionary framework in the context of the first independent test of Holden et al.'s 2003 model of matriliny as daughter-biased investment. It finds that historical daughter-biased transmission of land among the Mosuo is consistent with the model, whereas current income transmission is not. In both cases, resources had equivalent impacts on male and female reproduction, a result which predicts daughter-biased resource transmission given any nonzero level of paternity uncertainty. However, whereas land was transmitted traditionally to daughters, income today is invested in both sexes. Possible reasons for this discrepancy are discussed.     

Morris Goodman’s hominoid rate slowdown: The importance of being neutral

Half a century ago, when the field of molecular evolution did not even exist, Morris Goodman analyzed profiles of immunological interactions between species and reached the following two remarkable conclusions: first, protein evolution slowed down in the human lineage compared to other primate lineages; second, this slowdown was more pronounced for proteins whose functions were likely to be neutral. It took several decades of research to fully grasp these ideas and document the pattern of hominoid rate slowdown. Along the way, studies of hominoid rate slowdown led to major progresses in understanding determinants of neutral molecular evolution, which in turn is used to calibrate rates of adaptive evolution. Furthermore, the growing knowledge on the origin of mutations provides a basis for understanding differential evolutionary rates between sex chromosomes and autosomes, which has deep implications for inferring human evolutionary histories, and other aspects of molecular evolution. Primate genomics in particular stand to provide critical information in these pursuits, due to the abundance of genomic data, relatively rich documentation of life history traits, and several model systems, including our own species.     

小麦染色体的显微激光分离

探讨了应用氩离子激光进行植物染色体显微激光切割,分离的可行性,应用该技术对普通小麦的体细胞及特定染色体（１Ｂ染色体）实施切割,分离,并且以分离到的单细胞核或单条染色体为模板进行了ＰＣＲ ＤＮＡ扩增。该技术比玻璃针切割分离染色体技术,具有操作方便,容易掌握,且可对整个细胞核进行分离等优点,有利于促进染色体显微操作技术的普及应用。同时,探讨了染色体显微操作技术在细胞遗传学及分子生物学研究领域的应用前景     

It's Not All Sex and Violence: Integrated Anthropology and the Role of Cooperation and Social Complexity in Human Evolution

Social scientists, especially anthropologists, have long endeavored to understand the evolution of "human nature." This investigation frequently focuses on the relative importance of competition versus cooperation in human evolutionary trajectories and usually results in a primary emphasis on competition, aggression, and even war in attempting to understand humanity. This perspective conflicts with long-standing perspectives in anthropology and some emerging trends and theory in evolutionary biology and ecology. Cooperation and competition are not mutually exclusive in an evolutionary context. As anthropologists, we have demonstrated that humans can–and usually do–get along. Evolution is complex with multiple processes and patterns, not all of which involve competition and conflict. In this article, I summarize elements of modern ecological and evolutionary theory in the context of human cooperative patterns in an attempt to illustrate the valuable role of evolutionary theory and cooperative patterns in integrative anthropological approaches to the human condition.     

The development of chromosome microdissection and microcloning technique and its applications in genomic research

The technique of chromosome microdissection and microcloning has been developed for more than 20 years. As a bridge between cytogenetics and molecular genetics, it leads to a number of applications: chromosome painting probe isolation, genetic linkage map and physical map construction, and expressed sequence tags generation. During those 20 years, this technique has not only been benefited from other technological advances but also cross-fertilized with other techniques. Today, it becomes a practicality with extensive uses. The purpose of this article is to review the development of this technique and its application in the field of genomic research. Moreover, a new method of generating ESTs of specific chromosomes developed by our lab is introduced. By using this method, the technique of chromosome microdissection and microcloning would be more valuable in the advancement of genomic research.     

Parent-offspring conflict and the cultural ecology of breast-feeding

Lactation constitutes a major focus for research in international health because of its dramatic impact on child survival; evolutionary biology has investigated lactation as an important aspect of parenting strategy, with implications for understanding parent-offspring conflict. These perspectives are brought together in an attempt to develop integrated models for an issue of key international health concern: the duration of exclusive breast-feeding and the timing of weaning. This analysis highlights the relevance of evolutionary theory for practical problems in public health, and it suggests the utility of public health outcomes for addressing evolutionary questions. Thomas McDade received his Ph.D. degree in anthropology from Emory University in 1999 and is currently an assistant professor in the anthropology department at Northwestern University. His research interests include biocultural perspectives on issues related to health and human development, with current attention focused on the cultural and evolutionary ecology of human immune function.     

Flow karyotyping and chromosome sorting in bread wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.)

Previously, we reported on the development of procedures for chromosome analysis and sorting using flow cytometry (flow cytogenetics) in bread wheat. That study indicated the possibility of sorting large quantities of intact chromosomes, and their suitability for analysis at the molecular level. However, due to the lack of sufficient differences in size between individual chromosomes, only chromosome 3B could be sorted into a high-purity fraction. The present study aimed to identify wheat stocks that could be used to sort other chromosomes. An analysis of 58 varieties and landraces demonstrated a remarkable reproducibility and sensitivity of flow cytometry for the detection of numerical and structural chromosome changes. Changes in flow karyotype, diagnostic for the presence of the 1BL·1RS translocation, have been found and lines from which translocation chromosomes 5BL·7BL and 4AL·4AS-5BL could be sorted have been identified. Furthermore, wheat lines have been identified which can be used for sorting chromosomes 4B, 4D, 5D and 6D. The ability to sort any single arm of the hexaploid wheat karyotype, either in the form of a ditelosome or a isochromosome, has also been demonstrated. Thus, although originally considered recalcitrant, wheat seems to be suitable for the development of flow cytogenetics and the technology can be applied to the physical mapping of DNA sequences, the targeted isolation of molecular makers and the construction of chromosome- and arm-specific DNA libraries. These approaches should facilitate the analysis of the complex genome of hexaploid bread wheat.     

Centromere repositioning in mammals

The evolutionary history of chromosomes can be tracked by the comparative hybridization of large panels of bacterial artificial chromosome clones. This approach has disclosed an unprecedented phenomenon: 'centromere repositioning', that is, the movement of the centromere along the chromosome without marker order variation. The occurrence of evolutionary new centromeres (ENCs) is relatively frequent. In macaque, for instance, 9 out of 20 autosomal centromeres are evolutionarily new; in donkey at least 5 such neocentromeres originated after divergence from the zebra, in less than 1 million years. Recently, orangutan chromosome 9, considered to be heterozygous for a complex rearrangement, was discovered to be an ENC. In humans, in addition to neocentromeres that arise in acentric fragments and result in clinical phenotypes, 8 centromere-repositioning events have been reported. These 'real-time' repositioned centromere-seeding events provide clues to ENC birth and progression. In the present paper, we provide a review of the centromere repositioning. We add new data on the population genetics of the ENC of the orangutan, and describe for the first time an ENC on the X chromosome of squirrel monkeys. Next-generation sequencing technologies have started an unprecedented, flourishing period of rapid whole-genome sequencing. In this context, it is worth noting that these technologies, uncoupled from cytogenetics, would miss all the biological data on evolutionary centromere repositioning. Therefore, we can anticipate that classical and molecular cytogenetics will continue to have a crucial role in the identification of centromere movements. Indeed, all ENCs and human neocentromeres were found following classical and molecular cytogenetic investigations.     

Localization of tandemly repeated DMA sequences in Arabidopsis thaliana

In-situ hybridization to interphase nuclei and chromosomes of Arabidopsis thaliana (2n= 10) shows that there are four sites of rDNA in a diploid nucleus. The sites are located on chromosomes 2 and 4, and the strength of hybridization indicates that copy number is similar at both pairs of sites. Hybridization to trisomic line 4 revealed five hybridization sites. Silver staining of nucleoli demonstrates that all four loci can be active in diploid interphase nuclei. The tandemly repeated probe pAL1 hybridizes near to the centromeres of all five chromosome pairs. In diploid interphase nuclei, 10 sites of hybridization are detected, while 15 are seen in triploid nuclei. The sites of hybridization co-localize with the centromeric heterochromatin visualized by staining DNA with the fluorochrome DAPI. The results demonstrate that molecular cytogenetics can be applied to A. thaliana and high resolution physical chromosome maps can be generated. Both probes may be useful for interphase cytogenetics, where they enable chromosome number and aneuploidy to be examined in tissues without divisions. The physical localization of these hybridization sites provides a starting point for linking RFLP and physical chromosome maps.     

Resolving the Anti-Antievolutionism Dilemma: A Brief for Relational Evolutionary Thinking in Anthropology

ABSTRACT   Anthropologists often disagree about whether, or in what ways, anthropology is "evolutionary." Anthropologists defending accounts of primate or human biological development and evolution that conflict with mainstream "neo-Darwinian" thinking have sometimes been called "creationists" or have been accused of being "antiscience." As a result, many cultural anthropologists struggle with an "anti-antievolutionism" dilemma: they are more comfortable opposing the critics of evolutionary biology, broadly conceived, than they are defending mainstream evolutionary views with which they disagree. Evolutionary theory, however, comes in many forms. Relational evolutionary approaches such as Developmental Systems Theory, niche construction, and autopoiesis–natural drift augment mainstream evolutionary thinking in ways that should prove attractive to many anthropologists who wish to affirm evolution but are dissatisfied with current "neo-Darwinian" hegemony. Relational evolutionary thinking moves evolutionary discussion away from reductionism and sterile nature–nurture debates and promises to enable fresh approaches to a range of problems across the subfields of anthropology. [Keywords: evolutionary anthropology, Developmental Systems Theory, niche construction, autopoeisis, natural drift]     

Trends in chromosome evolution in the genus Hypostomus Lacépède, 1803 (Osteichthyes, Loricariidae): a new perspective about the correlation between diploid number and chromosomes types

Phylogenetic relationships and identification of species of the genus Hypostomus is still unclear. Considering this, cytogenetics may prove itself as an important tool in understanding the systematic of this genus. Reviews in Hypostomus indicate that the diploid number ranges from 54 to 84 chromosomes, and the increase in diploid number has been associated to higher percentages of subtelocentric and acrocentric chromosomes. Although there is a high number of species in the genus, there are relatively few papers concerning Hypostomus cytogenetics, and most of the data is published as grey literature. With the aim to understand the chromosomal evolution in the genus (correlation between diploid number x chromosomes types), H. ancistroides and H. topavae from the Piquiri River, Upper Paraná River basin, were cytogenetically analyzed, and the diploid number observed was 68 and 80 chromosomes, respectively. Additional data on the diploid number and chromosome formulae was compiled from papers (27 analyses) and abstracts from grey literature (77 analyses). Our analysis shows no correlation between chromosome numbers and percentages of subtelocentric and acrocentric chromosomes for most of the species, since there is considerable variation between these percentages even between species with the same diploid number, indicating that the proportion of chromosome types is not always associated to diploid numbers.     

Using a pericentromeric interspersed repeat to recapitulate the phylogeny and expansion of human centromeric segmental duplications

Despite considerable advances in sequencing of the human genome over the past few years, the organization and evolution of human pericentromeric regions have been difficult to resolve. This is due, in part, to the presence of large, complex blocks of duplicated genomic sequence at the boundary between centromeric satellite and unique euchromatic DNA. Here, we report the identification and characterization of an approximately 49-kb repeat sequence that exists in more than 40 copies within the human genome. This repeat is specific to highly duplicated pericentromeric regions with multiple copies distributed in an interspersed fashion among a subset of human chromosomes. Using this interspersed repeat (termed PIR4) as a marker of pericentromeric DNA, we recovered and sequence-tagged 3 Mb of pericentromeric DNA from a variety of human chromosomes as well as nonhuman primate genomes. A global evolutionary reconstruction of the dispersal of PIR4 sequence and analysis of flanking sequence supports a model in which pericentromeric duplications initiated before the separation of the great ape species (>12 MYA). Further, analyses of this duplication and associated flanking duplications narrow the major burst of pericentromeric duplication activity to a time just before the divergence of the African great ape and human species (5 to 7 MYA). These recent duplication exchange events substantially restructured the pericentromeric regions of hominoid chromosomes and created an architecture where large blocks of sequence are shared among nonhomologous chromosomes. This report provides the first global view of the series of historical events that have reshaped human pericentromeric regions over recent evolutionary time.