From genetics of intraspecific differences to genetics of intraspecific similarity

Based on the Mendelian approach to heredity, modern genetics describes inheritance of characters belonging to the category of intraspecific difference. The other large category of characters, intraspecific similarity, stays out of investigation. In this review, the genome part responsible for intraspecific similarity is considered as invariant and regulatory. An approach to studying the invariant part of the Drosophila melanogaster genome is formulated and the results of examining this genome part are presented. The expression of mutations at genes in the invariant genome part is different from that of Mendelian genes. We conclude that these genes are present in the genome in multiple copies and they are functionally haploid in the diploid genome. Severe abnormalities of development appearing in the progeny of mutant parents suggest that the mutant genes are genes regulating ontogeny. A hypothesis on an elementary ontogenetic event is advanced and the general scheme of ontogeny is presented. A concept on two types of gene allelism (cis- and trans-allelism) is formulated. This approach opens a possibility for studying genetic material responsible for the formation of intraspecific similarity characters at different taxonomic levels on the basis of crossing individuals of the same species.     

Patterns of intraspecific variation through ontogeny: a case study of the Cretaceous nautilid Eutrephoceras dekayi and modern Nautilus pompilius

The magnitude and ontogenetic patterns of intraspecific variation can provide important insights into the evolution and development of organisms. Understanding the intraspecific variation of organisms is also a key to correctly pursuing studies in major fields of palaeontology. However, intraspecific variation has been largely overlooked in ectocochleate cephalopods, particularly nautilids. Furthermore, little is known regarding the evolutionary pattern. Here, we present morphological data for the Cretaceous nautilid Eutrephoceras dekayi (Morton) and the modern nautilid Nautilus pompilius Linnaeus through ontogeny. The data are used to describe conch morphology and to elucidate the evolutionary patterns of intraspecific variation. We discovered a similar overall pattern of growth trajectories and the presence of morphological changes at hatching and maturity in both taxa. We also found that intraspecific variation is higher in earlier ontogeny than in later ontogeny in both taxa. The high variation in earlier ontogeny may imply increased flexibility in changing the timing of developmental events, which probably played an important role in nautilid evolution. We assume that the decrease in variation in later ontogeny reflects developmental constraints. Lastly, we compared the similarity/dissimilarity of ontogenetic patterns of variation between taxa. Results reveal that the similarity/dissimilarity of the ontogenetic pattern differs between E. dekayi and N. pompilius. We conclude that this shift in the ontogenetic pattern of variation may be rooted in changes in the developmental programme of nautilids through time. We propose that studying ontogenetic patterns of intraspecific variation can provide new insights into the evolution and development of organisms.     

Genetics of susceptibility to Theiler's virus infection

Theiler's virus is a picornavirus of mouse which causes an acute encephalomyelitis followed by a persistent infection of the white matter resulting in chronic inflammation and demyelination. This disease has been studied as a model for multiple sclerosis. Inbred strains of mice are either resistant--they clear the infection after the acute encephalomyelitis--or susceptible to persistent infection and demyelination. Susceptibility is a polygenic trait which has been analyzed using methods of association with “candidate” genes, and linkage analysis after a complete genome scan. The H-2D^b gene is responsible for an efficient CTL response which makes some strains resistant. Non H-2 genes responsible for the susceptibility of other strains have been mapped by linkage analysis to the Ifng and, possibly, the Mbp loci. The analysis of a set of congenic mice ruled out the possiblity that the relevant gene codes for interferon gamma, and showed that the region around Ifngprobably contains two susceptibility genes. The analysis of mutant mice showed further that the Mbp gene, which codes for the myelin basic protein, has a major effect on viral persistence. BioEssays 20 :627–633, 1998. © 1998 John Wiley & Sons Inc.     

Intraspecific variation in the skull morphology of the black caiman Melanosuchus niger (Alligatoridae,Caimaninae)

Melanosuchus niger is a caimanine alligatorid widely distributed in the northern region of South America. This species has been the focus of several ecological, genetic and morphological studies. However, morphological studies have generally been limited to examination of interspecific variation among extant species of South American crocodylians. Here, we present the first study of intraspecific variation in the skull of M. niger using a two‐dimensional geometric morphometric approach. The crania of 52 sexed individuals varying in size were analysed to quantify shape variation and to assign observed shape changes to different types of intraspecific variation, that is, ontogenetic variation and sexual dimorphism. Most of the variation in this species is ontogenetic variation in snout length, skull depth, orbit size and the width of the postorbital region. These changes are correlated with bite force performance and probably dietary changes. However, a comparison with previous functional studies reveals that functional adaptations during ontogeny seem to be primarily restricted to the postrostral region, whereas rostral shape changes are more related to dietary shifts. Furthermore, the skulls of M. niger exhibit a sexual dimorphism, which is primarily size‐related. The presence of non‐size‐related sexual dimorphism has to be tested in future examinations.     

Nuclear and cytoplasmic chloroplast mutants induced by chemical mutagens in Mimulus cardinalis: Genetics and ultrastructure

Summary The modes of inheritance of chemically induced chlorophyll-deficient phenotypes in Mimulus cardinalis reveal that the chloroplast is controlled by the genome and the plastome. Three of the chlorophyll-deficient mutants in M. cardinalis are inherited through nuclear recessive genes and two are inherited through plastome genes. One chlorophyll-deficient mutant was sterile and could not be analyzed genetically. Ultrastructural analysis of the six mutant types reveals that each possesses a unique defective chloroplast type(s) in comparison to the genotypically and phenotypically normal chloroplasts. Based on plastid ultrastructure it seems reasonable to assume that the mutations, genome and plastome, are non-allelic or at least significantly different forms of the same allele. The isolation of these types of mutants provide suitable material needed to study the effects of specific biochemical blocks and the elucidation of developmental pathways leading to chloroplast biogenesis. The mutants also provide valuable information concerning the interrelationship between the nucleic acid of the genome and the plastome.This study is in part based on a dissertation submitted by the first author in partial fulfillment of the requirements for a Doctor of Philosophy degree in the Department of Botany, Miami University, Oxford, Ohio.     

Ecological wood anatomy of NepaleseRhododendron (Ericaceae). 2. Intraspecific variation

The intraspecific relationship of selected wood anatomical characters with stem diameter, plant height, and altitude was investigated in four NepaleseRhododendron species:R. anthopogon, R. lepidotum, R. campanulatum, andR. arboreum, i.e., two shrubs, one subtree, and one tree. We studied 23 to 27 specimens for each species.R. anthopogon grew from 3,380 to 4,950 m,R. lepidotum from 2,060 to 4,720 m,R. campanulatum from 2,790 to 4,140 m, andR. arboreum from 1,430 to 3,460 m. Multiple regression analysis and actual distribution of character values show that the wood anatomical characters having a significant correlation with non-anatomical factors differ between species. The number of significant characters are two inR. anthopogon andR. campanulatum, five inR. lepidotum, and nine inR. arboreum and tends to be small in species having smaller altitudinal ranges. Average pore area, most strongly correlated with non-anatomical factors in interspecific variation, is significantly correlated only inR. lepidotum andR. arboreum. The general trends in intraspecific variation among four NepaleseRhododendron species differ from the trends found in interspecific variation within the genus and are characteristic of each species.     

Whole-Genome Sequencing of a Single Proband Together with Linkage Analysis Identifies a Mendelian Disease Gene

Although more than 2,400 genes have been shown to contain variants that cause Mendelian disease, there are still several thousand such diseases yet to be molecularly defined. The ability of new whole-genome sequencing technologies to rapidly indentify most of the genetic variants in any given genome opens an exciting opportunity to identify these disease genes. Here we sequenced the whole genome of a single patient with the dominant Mendelian disease, metachondromatosis (OMIM 156250), and used partial linkage data from her small family to focus our search for the responsible variant. In the proband, we identified an 11 bp deletion in exon four of PTPN11, which alters frame, results in premature translation termination, and co-segregates with the phenotype. In a second metachondromatosis family, we confirmed our result by identifying a nonsense mutation in exon 4 of PTPN11 that also co-segregates with the phenotype. Sequencing PTPN11 exon 4 in 469 controls showed no such protein truncating variants, supporting the pathogenicity of these two mutations. This combination of a new technology and a classical genetic approach provides a powerful strategy to discover the genes responsible for unexplained Mendelian disorders.     

Genetics of mosquitoes

Beginning in the mid-1950s, much progress has been made in studying various aspects of the genetics of mosquitoes, particularly involving several species of three principal genera,Aedes, Culex andAnopheles, that transmit important human diseases. Here I discuss selected areas of research involving formal genetics; genome structure, organization and evolution at the interspecific and intraspecific level; and evolutionary genetics of theAedes scutellaris group. Information and insights gained from in-depth analyses of these areas, particularly transmission genetics, cytogenetics and genetics of chromosomal rearrangements, and of mutagen-induced sexual sterility, have proved invaluable for the development of the theory and evaluation of feasibility of genetic control of natural populations. As a result, mosquitoes represent some of the best studied taxa at various levels of genetic organization. Recent developments in molecular genetics offer exciting possibilities for extension of these concepts.     

Genetic analysis of leaf form mutants from the Arabidopsis Information Service collection.

Although a vast inventory of morphological mutants of Arabidopsis thaliana is available, only some have been used for genetic studies of leaf development. Such is the case with the Arabidopsis Information Service (AIS) Form Mutants collection, assembled by A. R. Kranz and currently stored at the Nottingham Arabidopsis Stock Centre, which includes a large number of mutant lines, most of which have been little studied. With the aim of contributing to the genetic dissection of leaf ontogeny, we have subjected 57 mutant lines isolated by others to genetic analysis; 47 of which were from the AIS collection. These are characterized by vegetative leaves of abnormal shape or size, and were chosen as candidates for mutations in genes required for leaf morphogenesis. The mutant phenotypes studied were shown to be inherited as single recessive Mendelian traits and were classified into 10 phenotypic classes. These mutant strains were found to fall into 37 complementation groups, 7 of which corresponded to known genes. Results of the phenotypic analysis and data on the genetic interactions of these mutants are presented, and their possible developmental defects discussed. Received: 28 October 1998 / Accepted: 21 February 1999     

珍稀濒危飘带兜兰叶绿体全基因组种内变异研究(附录)

飘带兜兰(Paphiopedilum parishii)分布范围狭窄,仅在中国、缅甸、泰国以及老挝有少量分布。近年来,因生境破坏和人为滥采而导致飘带兜兰野生种群极度缩减。为开发种内多态性的分子标记用于保护生物学研究,该研究对飘带兜兰4个野生个体经测序、组装、注释获得的叶绿体基因组序列,与已公布的飘带兜兰2个个体的叶绿体全基因组序列进行比对,分析飘带兜兰叶绿体基因组的种内差异。结果表明:(1)飘带兜兰叶绿体基因组具有典型被子植物叶绿体基因组环状四分体结构,基因组长度为154 403～154 809 bp,共编码129个基因,包括78个蛋白质编码基因、39个tRNA基因、8个rRNA基因,以及4个假基因。(2)在飘带兜兰6个个体叶绿体基因组中检测到103～107个SSRs(simple sequence repeats)位点,其中21个SSR位点具有多态性。此外,在6个个体叶绿体基因组中还检测到60个长序列重复,包括17～21个正向重复、18～29个反向重复、9～16个回文重复、4～9个互补重复。(3)通过比较6个个体叶绿体基因组序列的核苷酸多样性,共发现70处变异,包括10个SNPs(single nucleotide polymorphism)、60个插入缺失(InDels)。其中,有3个SNP位点发生了非同义替换,导致编码功能基因的氨基酸发生改变; 19个插入缺失多态性较高,具有开发为分子标记的潜力。(4)通过计算核苷酸多样性值(P_i)共发现8个有变异的区域,P_i值为0～0.006 32,其中变异度较大的是rps3-rpl22、trnL-UAC-rpl32、rpoB-trnC-GCA以及ycf4,这些高变区可开发为分子标记用于评估飘带兜兰遗传多样性。(5)系统发生分析结果表明,飘带兜兰6个个体叶绿体基因组序列聚在一起,与长瓣兜兰互为姐妹群。综上表明,飘带兜兰叶绿体基因组的SSRs、长序列重复、SNPs、InDels以及核苷酸序列呈现了足够的种内多样性,可开发成分子标记用于该种的系统演化及保护生物学研究。     

Intraspecific Variation of Ribosomal Gene Redundancy in ZEA MAYS

Ribosomal genes in eukaryotes are highly redundant. Considerable variation in the level of redundancy among species, especially in higher plants, has been reported; but except for deletion and duplication mutants, it is generally accepted that intraspecific variability in redundancy level is small. We have examined the level of redundancy in several lines of maize by DNA-rRNA saturation hybridization. The amount of nuclear DNA which hybridizes with rRNA in the ten lines examined varied from 0.24% to 0.50%. The number of rRNA genes per diploid genome thus ranges from 1.12 x 10⁴ to 2.32 x 10⁴. Results also indicate that the level of redundancy is genetically transmitted.     

The caudal skeleton of ostariophysan fishes (Teleostei): Intraspecific variation in trichomycteridae (Siluriformes)

The different elements of the caudal skeleton of the South American catfish genera Nematogenys (Nematogenyinae) and Trichomycterus, Hatcheria, and Bullockia (Pygidiinae) (Siluriformes, Trichomycteridae) show Ontogenetic transformation of the second ural centrum in Trichomycteridae separates the subfamilies Nematogenyinae and Pygidiinae. In the former, the second ural centrum is aligned with the first ural centrum in early stages of ontogeny; it is not fused with the bases of hypurals 3 and 4 in any stage of development. In the Pygidiinae, in contrast, the second ural centrum is connected with the base of hypural 3 from an early stage of development on. One of the most noteworthy features of the Pygidiinae is the epural, a polymorphic element with three or four morphotypes that are species specific. The primitive catfish Nematogenys shows intraspecific variation in the ural centra, segmentation of procurrent caudal rays, and principal caudal ray formulae. Species of Trichomycterus, Hatcheria, and Bullockia are characterized by great intraspecific variability that involves ural centra, the epural, hypurapophyses, and the neural arches of the compound centrum. There is intraspecific variation in the fusion of the hypurals in some species of Trichomycterus. Intraspecific variation of the caudal skeleton of fishes of the family Trichomycteridae involves the presence and frequency of different morphotypes of the epural, neural arch of the compound centrum, fusion of hypurals, and principal caudal ray formulae. Ontogenetic changes of the first and second ural centra, hypurapophyses (with the exception of Nematogenys), and segmentation of procurrent caudal rays (in Nematogenys) are involved also.     

Molecules and Morphology,Phylogenetics and Genetics

Various explanations can be offered for the incongruence between phylogenetic hypotheses resulting from morphological and molecular data sets. Of these, the possibility that incongruence may result from the mutation of major morphogenetic genes leading to dramatic morphological divergence unaccompanied by equivalent change of the phylogenetic marker molecule(s) used is discussed in detail. As evidence for this hypothesis, several examples for such incongruence are surveyed. It seems possible that in many cases the genetic basis of the morphological characters responsible for the incongruence found may be simple, and that the genes involved may be homologous to genes known from mutant systems. It is suggested that: 1. the systematic documentation of incongruence between molecular and morphological phylogenies may help to assess the frequency of evolutionary change through the mutation of major morphogenetic genes, and that 2. the identification of major morphological characters distinguishing closely related taxa with mutant phenotypes known from mutant systems eventually may allow an experimental approach to the problem of evolutionary change resulting from major genes. Natural taxa suspected to be the result of such processes could be changed morphologically through transformation with the relevant genes.     

Consistent and variable leaf anatomical characters in Carex (Cyperaceae)

The anatomy and morphology of leaves in Carex have the potential to be taxonomically useful. However, studies on the variability of leaf characteristics in the genus are sparse. Researchers therefore risk using leaf anatomical characters without the knowledge of whether they are consistent in a species. We examined 22 qualitative and seven quantitative leaf anatomy characters from transverse leaf sections to test their consistency across 11 Carex spp. The characters were clearly described and primarily microscopic. Some characters were found to exhibit high levels of intraspecific variation, whereas other characters exhibited high levels of consistency in a species, including the shape of the leaf section, the density of papillae and the size of epidermal cells. Caution must be applied when choosing leaf anatomy to delimit taxa because of the intraspecific variability found in some characters, but sufficient numbers of invariant characters exist to provide useful taxonomic separation. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 371–384.     

Insight on segregation distortions in two intraspecific crosses between annual species of Medicago (Leguminosae)

 About 40% (α=0.05) of the PCR-derived markers scored in a Medicago truncatula and M. tornata intraspecific cross departed from Mendelian expectations at α=0.05. This proportion is among the highest ever documented in the literature, notably for intraspecific crosses. Estimations of DNA amount were also implemented for the parental genotypes or parental lines, and significant variations were observed. Our results suggest that the parental genotypes have diverged for quite a while, and we propose that the level of distortion we documented is correlated with the genome size difference we measured. Received: 11 April 1996 / Accepted: 27 September 1996     

Identification and characterization of lineage-specific genes in Populus trichocarpa

Species- or lineage-specific genes can facilitate studying the unique characteristics of biological processes. Updated genome sequences in Populus trichocarpa were screened against thirty newly sequenced or resequenced plant genomes to identify a set of species-specific genes (PtSS). Forty PtSS genes have been isolated with no similarity to any sequence outside the P. trichocarpa genome, therefore have no annotated functions. Protein motif, intron/exon features, subcellular localization and gene expression were analyzed in these PtSS genes. Results reflect their basic genic characters, expression analysis and primary function exploration might provide insight to their possible involvements in lineage specific biological process in woody plants.     

Intraspecific variability and sexual dimorphism in the skulls ofPan troglodytes verus

A collection of skulls ofPan troglodytes verus from Liberia was analysed according to specific characters of morphology and sexual dimorphism based on osteological data. Morphologic characters of both sexes are described somewhat in detail. Measurements were taken. Morphometric data show a high range of intraspecific variability within our collection. It shows that the mean metric divergence between both sexes is rather slight, skulls of males in our sample are on the average 3.7% larger than those of females.