Brief repot: Interactions with infants by full siblings,paternal half-siblings,and nonrelatives in a captive group of rhesus macaques (Macaca mulatta)

Six mother-infant pairs in a group of captive rhesus monkeys (Macaca mulatta) were observed for six months. “Infant grabs” by others and mothers' resistance to grabs were scored. More full siblings grabbed infants than either paternal half-siblings or nonrelatives. Mothers resisted grabbing by more nonrelatives than by paternal half-siblings. Although the maternal effect suggested by full sib-infant interactions is expected, the paternal effect revealed by mothers' tolerance of paternal half-sibs, but not full siblings, over nonrelatives is unexpected.     

Consequences of group fission for the patterns of relatedness among rhesus macaques

When mammalian social groups exceed their optimal size, they often tend to split. In view of the potential evolutionary benefits, it should be more advantageous for animals to stay with kin, rather than nonkin, during such fission events. In the present study, the spontaneous fission of two social groups, R and S, of rhesus macaques living on Cayo Santiago, Puerto Rico, provided the opportunity to compare the kinship structure of the corresponding parent and daughter groups, using information on both maternal and paternal relatedness. In both instances, maternal half-siblings and pairs of animals from the same family were significantly more prevalent in the fission products than in the parent group. During the split of group R, significantly more paternal half-siblings stayed in the remnants of the parent group than joined the seceding group. Our findings are compatible with previous behavioural studies demonstrating that female primates bias their social behaviour more to maternal than to paternal kin, but that both types of half-siblings prefer each other more than unrelated animals. It remains to be clarified by future research, however, whether the observed co-segregation of paternal half-sibs in our study reflects active choice or is a by-product of the group-specific kin structures, prior to fission.     

Kin recognition by tadpoles and froglets of the wood frog Rana sylvatica

Summary We investigated kin recognition by the wood frog Rana sylvatica in blind laboratory experiments using spatial proximity as a recognition assay. Tadpoles were tested for the ability to discriminate between: 1) familiar full-sibs and unfamiliar non-kin, 2) unfamiliar paternal half-sibs and unfamiliar non-kin, and 3) familiar and unfamiliar full-sibs. Tadpoles discriminated full- and paternal half-sibs from unrelated conspecifics, but did not discriminate between familiar and unfamiliar full-sibs. Froglets from the same laboratory population were tested for the ability to discriminate between 1) familiar full-sibs and unfamiliar non-kin, and 2) unfamiliar paternal half-sibs and unfamiliar non-kin. Froglets preferentially associated with full- and half-sibs over unrelated conspecifics. Our results show that familiarity, i.e., prior association, is not necessary for kin recognition in tadpoles and froglets. The ability of tadpoles and froglets to recognize unfamiliar paternal half-sibs demonstrates that a common maternal factor is not necessary for kin recognition, and indicates that the recognition cue has a genetic component. Our results add to the increasing evidence that a variety of vertebrate and invertebrate animals have the ability to recognize unfamiliar kin by using genetically specified recognition cues.     

Genetic and environmental factors in the longitudinal growth of rats: II. Ventrodorsal craniofacial size

By means of roentgenographic cephalometry and quantitative genetic analysis, the relative contribution of the genetic and environmental components to the ontogenic change of the ventrodorsal view of the craniofacial complex was shown to vary with age. The genetic component of variance significantly increased until the 80th day. Inversely, the maternal component of variance showed a large value during the early stage of postnatal growth and gradually decreased thereafter to a very small amount by the 80th day. In general, it appeared that the genetic effect became larger with the age of the rat and the maternal effects tended to diminish. The environmental component of variance did not change much over the course of the experiment. We thus concluded that the genetic effect contributed to the change of the ontogenic variation of the craniofacial complex through all experimental periods and the maternal effect contributed to the change at the early growth stage of the craniofacial complex.     

Genetic and environmental factors in the longitudinal growth of rats: I. Body weight and overall craniofacial size

By means of roentgenographic cephalometry and quantitative genetic analysis, the relative contribution of the genetic and environmental components to total variance of body weight and overall craniofacial size was shown to vary with age. The genetic component of variance significantly increased until 80 days of age. Inversely, the maternal component of variance showed a high value during the early stage of postnatal growth and gradually decreased thereafter to a very small amount by day 80. Thus it appeared that the genetic effect became larger with age of the rat and the maternal effects diminished. The environmental component of variance did not change much over the course of the experiment. We thus conclude that genetic effect contributed the change of ontogenetic variation of craniofacial complex through all experimental periods and that maternal effect contributed to it at early growth stage of the craniofacial complex.     

Insight into post-mating interactions between the sexes: relatedness suppresses productivity of singly mated female Drosophila melanogaster

Post-mating, prefertilization inbreeding avoidance (PPIA) is well established in plants but not in animals. Support for animal PPIA comes from sperm competition studies showing success of a male's gametes declining with his relatedness to the multiply mated female; however, such studies confound female-male and male-male interaction. To avoid this problem, we investigated offspring productivity of singly mated Drosophila melanogaster females using flies from four different genetic backgrounds. Our experiments established that intrapopulation crosses using highly related parents (within-strain) were significantly less productive than intrapopulation crosses using unrelated individuals from the same population (between-strain). Furthermore, we showed that these effects were not due to inbreeding depression. The average decrease in offspring productivity of within-strain crosses relative to between-strain crosses was 18.3% [nonlaboratory populations: Zimbabwe 20.3%, Riverside 11.4%, neither of which showed inbreeding depression; and temperature-adapted laboratory populations, uncorrected (corrected) for nonsignificant inbreeding depression: 18 degrees C, 26.5% (24.2%) and 29 degrees C, 20.1% (9.5%)]. The significant reduction of within-cross productivity demonstrates PPIA in the absence of multiple mating.     

Finite element scaling analysis of human craniofacial growth

The study of form change is central to traditional cephalometric research. Unfortunately, traditional cephalometric studies operate within systems of measurement that are based on registration and orientation. Measurements produced in registered systems are insufficient for the craniofacial biologist who is interested in locating morphological differences between forms. In this article we apply a registration-free method called finite element scaling analysis in a study of the form change occurring during growth of the normal human craniofacial complex. The method provides form change data that can be summarized at various morphological levels. Twenty normal male individuals are used to analyze the form change that occurs from age 4 to ages 5, 7, 8, 9, 10, 12, 13, and 15 years. The magnitude and direction of growth expressed as shape and size change specific to craniofacial landmarks are presented. Although exceptions occur, our analysis shows that localized size change is, on the average, greater than localized shape change. The relation between size and shape change during growth shows allometry (shape change increasing during growth along with size change) but at a lesser magnitude and slower rate. We conclude that although shape change occurs throughout ontogeny, the magnitude and rate of shape change in relation to size change diminishes as age increases. This analysis represents new insights into the understanding of human craniofacial growth at various levels of morphological integration.     

Maternal and paternal chromosomes 7 show differential methylation of many genes in lymphoblast DNA

Genomic imprinting, the differential expression of paternal and maternal alleles, involves many chromosomal regions and plays a role in development and growth. Differential methylation of maternal and paternal alleles is a hallmark of imprinted genes, and thus methylation assays are widely used to support the identification of novel imprinted genes. Either blood or lymphoblast DNAs are most often used in these assays, even though methylation levels may change in cell culture. We undertook a systematic survey of parent-of-origin-specific methylation of chromosome 7 genes and ESTs by comparing DNA samples from cases of maternal and paternal uniparental disomy for chromosome 7 using DNA from fresh blood and lymphoblast cell lines. Our results revealed that up to 41% of genes and ESTs show parent-of-origin-specific methylation differences in lymphoblast DNA after only a short time in culture, whereas methylation differences were not seen in blood DNA. The methylation changes occurred most commonly on paternal chromosome 7, whereas alterations on maternal chromosome 7 were more infrequent and weaker. These findings indicate that methylation patterns may change significantly during cell culture in a parent-of-origin-dependent manner and suggest that methylation is maintained differently on maternal and paternal chromosomes 7.     

Craniofacial pattern profile (CFPP) evaluation of facial dysmorphology in a familial syndrome with corneal anesthesia and multiple congenital anomalies

Roentgencephalometric findings are presented for a family with an unusual facial morphology. Twenty measurements defining the size and shape of major anatomic areas of the head and face were taken. The measurements were transformed into Z-scores. Using the sigma z (i.e., standard deviation of the Z-scores) value, an estimate of craniofacial pattern deviation from the norms was made for each family member. All members of this family have highly aberrant, i.e., dysmorphic, craniofacial pattern profiles. Familial as well as syndromic craniofacial similarities vs. dissimilarities between Z-score values of pairs of family members were assessed by the Pearson's correlation coefficient rz. Results of correlation coefficients demonstrate a high level (far in excess of the expected value of rz 0.50) of craniofacial pattern profile (CFPP) similarity between sibs and between sibs and their mother. This strongly suggests that the two sibs and their mothers are the carrier of the same genetic syndrome.     

Microsatellite analysis of seed dispersal and parentage of saplings in bur oak, Quercus macrocarpa

Microsatellite analysis was used to examine parentage and spatial distributions of 62 adult bur oaks Quercus macrocarpa, and 100 saplings in a single stand. Using genotypes scored by PCR products at four microsatellite loci, we determined that 94 saplings matched at least one parent in the stand. Saplings often occur as dense clusters of half-sibs around the presumed maternal parent, and only four adults were seed parents to a large proportion of the saplings sampled. A stump apparently was the seed parent of the largest cluster of half-sibs, which occupied a sizeable light gap opened up by the death of their maternal tree. Approximately half of the saplings appeared to have grown from seeds that had not been removed after falling from the tree, and half from seeds that were dispersed beyond the crown of their maternal parent. Long-distance seed dispersal may be more common than has been previously reported. Extremely high levels of long-distance pollination were indicated, and pollen donors within the stand were generally distributed randomly around maternal trees. More than half of the saplings had paternal parents outside of the stand. This study demonstrates the utility of microsatellite analysis for studying mating systems, seed dispersal and seedling establishment in natural plant populations.     

THE GENETICS AND EVOLUTION OF CANNIBALISM IN FLOUR BEETLES (GENUS TRIBOLIUM)

Cannibalism plays a major role in population regulation in Tribolium confusum, accounting for up to tenfold differences in population size between different genetic strains. I characterized the within- and between-strain genetic variation for cannibalism using standard quantitative-genetic methods. The four laboratory strains studied have similar birth and death rates but differ in their strain-specific cannibalistic tendencies. The cannibalism rates of the strains were stable for more than 60 generations of laboratory husbandry. I found considerable genetic variation for cannibalism within each strain. A genetic analysis of the between-strain differences in each of three types of cannibalism (larvae eating eggs, adults eating eggs, and adults eating pupae) showed that all three cannibalism pathways are autosomally inherited and exhibit minor degrees of dominance. Adult cannibalism of eggs and larval cannibalism of eggs appear to be genetically correlated. The differences between the “high” and “low” cannibalism strains appear to be polygenic for two kinds of cannibalism, larvae eating eggs and adults eating pupae. However, strain differences in adult cannibalism of eggs may be due to only two loci. The stability of the between-strain differences for more than 60 generations, the additive nature of inheritance, and the demonstration of considerable within-strain genetic variation suggest that cannibalism may be selectively neutral or under stabilizing selection with many adaptive peaks.     

Comparison of the size of paternal and maternal homologous chromosomes during the first 2 cleavage divisions in mouse embryos

The mouse metaphase chromosomes of the 1st and 2nd cleavage divisions were prepared without colchicine and stained with trypsin-Giemsa. Both the homologues had the same pattern of differential staining (position and number of bands and interbands) in all pairs of chromosomes. The measurements of homologues of the 1st, 2nd, 3rd, 4th and 5th pairs of autosomes have shown that at the first cleavage division metaphase the paternal chromosomes are 1.2 times, on the average longer than the maternal ones, whereas at the second division metaphase no reliable differences in the length of homologues were found. In mice, thus, the heterocyclic pattern of the paternal and maternal sets of chromosomes manifested itself during the 1st cleavage division only and disappeared fully beginning from the 2nd division. This appears to be due to the early functional activity of chromosomes, i.e. to the fact that already in the 2-cell embryos both the maternal and paternal genes are expressed.     

Inbreeding, coancestry, and covariance between relatives for X-chromosomal loci

Knowledge about the relationships between relatives for X-chromosomal loci is necessary to compute genetic variances and covariances for the genetic evaluation of individuals for economically important traits in livestock and poultry. Using a unified approach, we derived explicitly the coefficient of inbreeding for individuals and the coefficient of coancestry between collateral and lineal relatives of the same or different sex, assuming that the male is heterogametic and the female is homogametic. Collateral relatives include full sibs, paternal and maternal half-sibs, paternal and maternal single first cousins, and double first cousins. Lineal relatives include parent-offspring, paternal and maternal grandparent-grandoffspring, and aunt- or uncle-niece or -nephew. We also defined additive and dominance relationships to compute genetic covariance between relatives, assuming random mating equilibrium, and clarified misinterpretations and corrected errors in the literature. Our results are also applicable to organisms that have few autosomal loci, such as Drosophila, in which X-chromosomal loci can account for a large amount of genetic variance, and to haplodiploid organisms, such as the honeybee, in which the entire genome is equivalent to being X-chromosomal.     

Evidence for cytoplasmic inheritance of a developmental organizer affecting growth habit and leaf shape in Antirrhinum majus

A cross between two distinct, true-breeding plants of Antirrhinum majus L. showed an unexpected pattern of inheritance of growth habit in the F2, which was extended to both growth habit and leaf shape in the F3 generation of all the plants traced further. All the F3 families, offspring of individual F2 plants, were very uniform for both growth habit and leaf shape traits but differed distinctly from each other in these respects. The backcrosses of selected F3 and F4 families to the original parents in the cross did not segregate for the distinctive family phenotypes. This led to the postulate that a cytoplasmic factor was involved in the regulation and/or integration of genetic information concerned with growth habit/leaf shape. The similarity of the reciprocal backcrosses of the F3 and F4 families led to the further postulate that the proposed cytoplasmic factor was specified by both the maternal and paternal parents to a similar degree. That the gene component was segregating normally was shown by the inheritance of four marker genes for flower colour, colour pattern and flower shape.     

Higher aggression towards closer relatives by soldier larvae in a polyembryonic wasp

In the polyembryonic wasp Copidosoma floridanum, females commonly lay one male and one female egg in a lepidopteran host. Both sexes proliferate clonally within the growing host larva. Distinct larval castes develop from each wasp egg, the majority being ‘reproductives’ plus some ‘soldiers’ which sacrifice reproduction and attack competitors. Maturing mixed sex broods are usually female biased, as expected when intra-brood mating is common. Pre-mating dispersal followed by outbreeding is expected to increase sexual conflict over brood sex ratios and result in greater soldier attack rates. Owing to sexually asymmetric relatedness, intra-brood conflicts are expected to be resolved primarily via female soldier attack. We observed soldier behaviour in vitro to test whether lower intra-brood relatedness (siblings from either within-strain or between-strain crosses were presented) increased inter-sexual aggression by female as well as male soldiers. As found in prior studies, females were more aggressive than males but, contrary to expectations and previous empirical observations, soldiers of both sexes showed more aggression towards more closely related embryos. We speculate that lower intra-brood relatedness indicates maternal outbreeding and may suggest a rarity of mating opportunities for reproductives maturing from the current brood, which may enhance the value of opposite sex brood-mates, or that higher aggression towards relatives may be a side-effect of mechanisms to discriminate heterospecific competitors.     

Detection of recombination events,haplotype reconstruction and imputation of sires using half-sib SNP genotypes

Background

Identifying recombination events and the chromosomal segments that constitute a gamete is useful for a number of applications in genomic analyses. In livestock, genotypic data are commonly available for half-sib families. We propose a straightforward but computationally efficient method to use single nucleotide polymorphism marker genotypes on half-sibs to reconstruct the recombination and segregation events that occurred during meiosis in a sire to form the haplotypes observed in its offspring. These meiosis events determine a block structure in paternal haplotypes of the progeny and this can be used to phase the genotypes of individuals in single half-sib families, to impute haplotypes of the sire if they are not genotyped or to impute the paternal strand of the offspring’s sequence based on sequence data of the sire.

Methods

The hsphase algorithm exploits information from opposing homozygotes among half-sibs to identify recombination events, and the chromosomal regions from the paternal and maternal strands of the sire (blocks) that were inherited by its progeny. This information is then used to impute the sire’s genotype, which, in turn, is used to phase the half-sib family. Accuracy (defined as R²) and performance of this approach were evaluated by using simulated and real datasets. Phasing results for the half-sibs were benchmarked to other commonly used phasing programs – AlphaPhase, BEAGLE and PedPhase 3.

Results

Using a simulated dataset with 20 markers per cM, and for a half-sib family size of 4 and 40, the accuracy of block detection, was 0.58 and 0.96, respectively. The accuracy of inferring sire genotypes was 0.75 and 1.00 and the accuracy of phasing was around 0.97, respectively. hsphase was more robust to genotyping errors than PedPhase 3, AlphaPhase and BEAGLE. Computationally, hsphase was much faster than AlphaPhase and BEAGLE.

Conclusions

In half-sib families of size 8 and above, hsphase can accurately detect block structure of paternal haplotypes, impute genotypes of ungenotyped sires and reconstruct haplotypes in progeny. The method is much faster and more accurate than other widely used population-based phasing programs. A program implementing the method is freely available as an R package (hsphase).     

异源四倍体鲫鲤及其原始亲本遗传变异的微卫星标记分析

采用从鲤中分离出来的32对微卫星DNA标记,对异源四倍体鲫鲤、红鲫和野鲤的基因组DNA进行了研究。在筛选出的15对微卫星引物中,随引物不同,各等位基因数为1～8个,大小在100～420bp之间。从3个不同群体内部的遗传相似系数来看,异源四倍体鲫鲤个体之间的遗传相似系数最大,说明异源四倍体鲫鲤群体内部的遗传变异程度最低,已经形成了一个遗传性状稳定的群体。从3个不同群体之间的遗传相似系数来看,异源四倍体鲫鲤和红鲫遗传相似系数为0．5625,和野鲤的遗传相似系数为0．5125,说明异源四倍体鲫鲤接受原始母本的遗传物质比原始父本野鲤要多一些。微卫星标记与以前报道的RAPD标记的检测结果是相似的,然而由微卫星标记获得的种群内和种群间的遗传距离均大于RAPD,说明微卫星标记比RAPD标记显示出更高的个体多态性。     

The Developmental Basis of Quantitative Craniofacial Variation in Humans and Mice

The human skull is a complex and highly integrated structure that has long held the fascination of anthropologists and evolutionary biologists. Recent studies of the genetics of craniofacial variation reveal a very complex and multifactorial picture. These findings contrast with older ideas that posit much simpler developmental bases for variation in cranial morphology such as the growth of the brain or the growth of the chondrocranium relative to the dermatocranium. Such processes have been shown to have major effects on cranial morphology in mice. It is not known, however, whether they are relevant to explaining normal phenotypic variation in humans. To answer this question, we obtained vectors of shape change from mutant mouse models in which the developmental basis for the craniofacial phenotype is known to varying degrees, and compared these to a homologous dataset constructed from human crania obtained from a single population with a known genealogy. Our results show that the shape vectors associated with perturbations to chondrocranial growth, brain growth, and body size in mice do largely correspond to axes of covariation in humans. This finding supports the view that the developmental basis for craniofacial variation funnels down to a relatively small number of key developmental processes that are similar across mice and humans. Understanding these processes and how they influence craniofacial shape provides fundamental insights into the developmental basis for evolutionary change in the human skull as well as the developmental-genetic basis for normal phenotypic variation in craniofacial form.     

Evaluating the use of pairwise dissimilarity metrics in paleoanthropology

Questions of alpha taxonomy are best addressed by comparing unknown specimens to samples of the taxa to which they might belong. However, analysis of the hominin fossil record is riddled with methods that claim to evaluate whether pairs of individual fossils belong to the same species. Two such methods, log se_m and the related STET method, have been introduced and used in studies of fossil hominins. Both methods attempt to quantify morphological dissimilarity for a pair of fossils and then evaluate a null hypothesis of conspecificity using the assumption that pairs of fossils that fall beneath a predefined dissimilarity threshold are likely to belong to the same species, whereas pairs of fossils above that threshold are likely to belong to different species. In this contribution, we address (1) whether these particular methods do what they claim to do, and (2) whether such approaches can ever reliably address the question of conspecificity. We show that log se_m and STET do not reliably measure deviations from shape similarity, and that values of these measures for any pair of fossils are highly dependent upon the number of variables compared. To address these issues we develop a measure of shape dissimilarity, the Standard Deviation of Logged Ratios (s_LR). We suggest that while pairwise dissimilarity metrics that accurately measure deviations from isometry (e.g., s_LR) may be useful for addressing some questions that relate to morphological variation, no pairwise method can reliably answer the question of whether two fossils are conspecific.