Genetic signatures of coancestry within surnames

Surnames are cultural markers of shared ancestry within human populations. The Y chromosome, like many surnames, is paternally inherited, so men sharing surnames might be expected to share similar Y chromosomes as a signature of coancestry. Such a relationship could be used to connect branches of family trees, to validate population genetic studies based on isonymy, and to predict surname from crime-scene samples in forensics. However, the link may be weak or absent due to multiple independent founders for many names, adoptions, name changes and nonpaternities, and mutation of Y haplotypes. Here, rather than focusing on a single name, we take a general approach by seeking evidence for a link in a sample of 150 randomly ascertained pairs of males who each share a British surname. We show that sharing a surname significantly elevates the probability of sharing a Y-chromosomal haplotype and that this probability increases as surname frequency decreases. Within our sample, we estimate that up to 24% of pairs share recent ancestry and that a large surname-based forensic database might contribute to the intelligence-led investigation of up to approximately 70 rapes and murders per year in the UK. This approach would be applicable to any society that uses patrilineal surnames of reasonable time-depth.     

Structure, function and evolution of plant disease resistance genes

Gene-for-gene plant disease resistance involves two basic processes: perception of pathogen attack, followed by responses to limit disease. Perception involves receptors with high degrees of specificity for pathogen strains, which are encoded by disease resistance genes. Large repertoires of distantly related resistance (R) genes with diverse recognitional specificities are found within a single plant species. The generation of R-gene polymorphism involves gene duplication, followed by DNA-sequence divergence by point mutation, and by deletion and duplication of intragenic DNA repeats encoding blocks of leucine-rich elements. Recombination between related genes reassorts this variation to further diversify gene sequences. Pathogen pressure selects functional resistance specificities and results in the maintenance of R-gene diversity. Recent genome-sequence data reveal that the NBS-LRR (i.e. nucleotide-binding site-leucine-rich repeat) class of R genes represents as much as 1% of the Arabidopsis genome. Experimental data have shown that the LRR has a role in determination of specificity. Mutation experiments, in which R-gene signaling has been dissociated from specificity in constitutive signal mutants, have provided the potential for non-specific resistance to be expressed from pathogen-infection-induced promoters in transgenic plants.     

Correlations between measures of thermal stress resistance within and between species

Resistance to an environmental stress such as elevated temperature can almost always be measured in several different ways. A number of recent studies in Drosophila show that lethal and non-lethal measures of resistance to heat stress are genetically independent. In contrast, data reported here suggest that there are interspecific correlations between measures of thermal stress resistance. Together, these results show that studies of intraspecific variation in stress resistance must demonstrate the ecological relevance of the measures of stress resistance chosen for study. In contrast, interspecific comparisons could be based on any of several measures of resistance. It would be interesting to determine if this pattern holds for resistance to other major environmental stresses.     

Restricted gene flow within and between rapidly diverging Neotropical plant species

Speciation involves the evolution of traits and genetic differences that contribute to reproductive isolation and the cessation of gene flow, and studying closely related species and divergent populations gives insight into how these phenomena proceed. Here, we document patterns of gene flow within and between two members of a rapid Neotropical species radiation, Costus pulverulentus and Costus scaber (Costaceae). These species co‐occur in the tropical rainforest and share pollinators, but are reproductively isolated by a series of prezygotic barriers, some of which show evidence of reinforcement at sympatric sites. Here, we genotype microsatellite markers in plants from eight sites that span the geographical range of both species, including four sympatric sites. We also genotype putative hybrids found at two sympatric sites. We find high levels of genetic isolation among populations within each species and low but detectable levels of introgression between species at sympatric sites. Putative hybrids identified by morphology are consistent with F1 or more advanced hybrids. Our results highlight the effectiveness of prezygotic isolating mechanisms at maintaining species boundaries in young radiations and provide empirical data on levels of gene flow consistent with reinforcement.     

Variability in diapause propensity within populations of a temperate insect species: interactions between insecticide resistance genes and photoperiodism

Temperate insects generally use day length as a reliable cue for long-term seasonal changes in their environment. Significant variation in photoperiodism between and within populations is thought to be associated with genetic variation resulting from local adaptation. In this study, we investigated whether genetic variation associated with selection for insecticide resistance may be a source of divergence in the photoperiodic timing of diapause through pleiotropic interactions. Critical photoperiods for diapause induction were estimated in one susceptible and two insecticide-resistant homozygous strains of the codling moth Cydia pomonella , as well as in their reciprocal F₁ progeny. Diapause responses to naturally decreasing day length were subsequently followed in the laboratory strains and in two field populations of C. pomonella in south-eastern France. We found higher critical photoperiods for diapause induction in homozygous resistant individuals than in both homozygous susceptible and heterozygous ones. This partly explained the significantly earlier timings of diapause found in homozygous resistant individuals of both laboratory and field populations of C. pomonella under natural photoperiods, relative to those found in both homozygous susceptible and heterozygous ones. We assume that adaptive genetic changes associated with selection for insecticide resistance may generate substantial variation in the seasonal timing of diapause, an essential ecological feature of the fitness of insecticide resistance genes in this species.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 341–351.     

Genetic diversity within and genetic differentiation between blooms of a microalgal species

The field of genetic diversity in protists, particularly phytoplankton, is under expansion. However, little is known regarding variation in genetic diversity within populations over time. The aim of our study was to investigate intrapopulation genetic diversity and genetic differentiation in the freshwater bloom-forming microalga Gonyostomum semen (Raphidophyceae). The study covered a 2-year period including all phases of the bloom. Amplified fragment length polymorphism (AFLP) was used to determine the genetic structure and diversity of the population. Our results showed a significant differentiation between samples collected during the two blooms from consecutive years. Also, an increase of gene diversity and a loss of differentiation among sampling dates were observed over time within a single bloom. The latter observations may reflect the continuous germination of cysts from the sediment. The life cycle characteristics of G.?semen, particularly reproduction and recruitment, most likely explain a high proportion of the observed variation. This study highlights the importance of the life cycle for the intraspecific genetic diversity of microbial species, which alternates between sexual and asexual reproduction.     

Towards a working list of all known plant species

A complete listing of the world's known plant species has long been considered desirable but has remained an elusive target for generations of botanists. The adoption of the Global Strategy for Plant Conservation has reinforced the urgent need for a global plant checklist to support, facilitate and monitor the conservation and sustainable use of plant diversity worldwide. The increasing availability of large databases of biological information over the Internet has demonstrated that many of the obstacles to the collation and dissemination of vast, shared datasets can be overcome. We examine the challenges that still remain to be addressed if the botanical community is to achieve its ambitious objective of delivering a working list of all known plant species by 2010.     

Genetic covariances within and between species: indirect selection for hybrid inviability

Genotype-environment interactions and natural selection can result in local specialization when different genotypes are favored in different environments. Restricted gene flow or genetic subdivision enhances local genetic diversification across a species when natural selection acts on such variation. The indirect evolution of reproductive isolation and the restriction of gene flow between species in statu nascendi may provide a central role for genotype-environment interactions in speciation genetics. We derive the expected genetic covariance between heterospecific and conspecific viability fitness under several different models of selection, dominance, and breeding structure. Standard quantitative genetic methods can be used to estimate these covariances in experimental studies. These genetic covariances permit us to evaluate in a formal way the indirect effects of selection within a species on the evolution of hybrid inviability between species. We find that, for autosomal loci and random mating, the genetic covariance across species is equal to the product of three quantities: (1) the viability of the best hybrid genotype; (2) the viability effect of an allele in hybrids; and, (3) the change in allele frequency due to selection in the conspecific population. Inbreeding within the conspecific population, expressed as Wright's coefficient, F, increases the genetic covariance by a factor (1 + F). In all cases, a negative genetic covariance across species is evidence for hybrid inviability evolving as an indirect effect of selection within species for adaptive (as opposed to neutral) genetic change. “It is an irony of evolutionary genetics, that although it is a fusion of Mendelism and Darwinism, it has made no direct contribution to what Darwin obviously saw as the fundamental problem: the origin of species…. While it is a question of elementary population genetics to state how many generations will be required for the frequency of an allele to change from q₁ to q₂, we do not know how to incorporate such a statement into speciation theory, in large part because we know virtually nothing about the genetic changes that occur in species formation.” (Lewontin 1974, p. 159)     

Genetic diversity and the evolutionary history of plant immunity genes in two species of Zea

Plant pathogenesis-related genes (PR genes) code for enzymes, enzyme inhibitors, and other peptides that confer resistance to pathogens and herbivores. Although several PR genes have been the subject of molecular population genetic analyses, a general understanding of their long-term evolutionary dynamics remains incomplete. Here we analyze sequence data from 17 PR genes from two closely related teosinte species of central Mexico. In addition to testing whether patterns of diversity at individual loci depart from expectations under a neutral model, we compared patterns of diversity at defense genes, as a class, to nondefense genes. In Zea diploperennis, the majority of defense genes have patterns of diversity consistent with neutral expectations while at least two genes showed evidence of recent positive selection consistent with arms-race models of antagonistic coevolution. In Zea mays ssp. parviglumis, by contrast, analyses of both defense and nondefense genes revealed strong and consistent departures from the neutral model, suggestive of nonequilibrium population dynamics or population structure. Nevertheless, we found a significant excess of replacement polymorphism in defense genes compared to nondefense genes. Although we cannot exclude relaxed selective constraint as an explanation, our results are consistent with temporally variable (transient or episodic) selection or geographically variable selection acting on parviglumis defense genes. The different patterns of diversity found in the two Zea species may be explained by parviglumis' greater distribution and population structure together with geographic variation in selection.     

Partial sequencing of the hrpB and endoglucanase genes confirms and expands the known diversity within the Ralstonia solanacearum species complex

We determined partial hrpB and endoglucanase genes sequences for 30 strains of Ralstonia solanacearum and one strain of the blood disease bacterium (BDB), a close relative of Ralstonia solanacearum. Sequence comparisons showed high levels of variability within these two regions of the genome involved in pathogenicity. Phylogenetic analysis based upon sequence comparisons of these two regions revealed three major clusters comprising all Ralstonia solanacearum isolates, the BDB strain constituted a phylogenetically distinct entity. Cluster 1 and cluster 2 corresponded to the previously defined divisions 1 and 2 of Ralstonia solanacearum. Moreover, two subclusters could be identified within cluster 2. The last cluster, designated cluster 3 in this study, included biovar 1 and N2 strains originating from Africa. This recently described group of strains was confirmed to be clearly different from the other strains suggesting a separate evolution from those of both divisions 1 and 2.     

Genetic variability within theAspergillus viridinutans species

The intraspecific variability of theAspergillus viridinutans species was examined using various techniques including morphological examinations, carbon-source-utilization tests, restriction-enzyme analysis of the mitochondrial and nuclear DNA, and sequence analysis of part of the β-tubulin gene. Although the genetic distances between the isolates were higher than between,e.g., A. fumigatus andNeosartorya fischeri, mostA. viridinutans isolates, together withN. aureola andN. udagawae strains, were found to belong to a single cluster based on sequence data. Strain FRR 1266, which was earlier classified as a highly divergentA. fumigatus isolate, was found to belong to theA. viridinutans species. The ochratoxin A producingA. viridinutans strain IMI 306 135 was most closely related to an asexual isolate. These two latter strains were more closely related toA. fumigatus andN. fischeri than to anyA. viridinutans strains, and possibly represent a new species in theAspergillus sectionFumigati. The dendrogram based on carbon source utilization data and results of restriction analysis of the mitochondrial and nuclear DNA of the strains supported most of the evolutionary relationships observed on the basis of sequence data. The results indicate that the presence or absence of nodding conidial heads is not an unequivocal morphological character for the identification of species within theAspergillus sectionFumigati.     

Foraging dynamics of bumble bees: correlates of movements within and between plant species

What rules determine whether bumble bees continue exploitingplants of the species just visited or switch to another species?To tackle this question, we recorded handling times and flighttimes from bees foraging in a natural meadow containing fiveplant species. Inter- and intra-specific plant distances werequantified. The bee-subjective colors of the five species weredetermined; two of these species had similar colors and structures,while three species were distinct from all others. The followingrules were identified: (1) The decision to switch species wascorrelated with previous flower handling time, which we assumeis a function of the reward amount received at the flower. Aftershort handling times, the probability of switching to anotherspecies increased, whereas it decreased after long handlingtimes. This difference became even greater if the bee had hada run of several short or several long handling times. (2) Constantflights (those between flowers of the same species) and transitionflights (those between flowers of different species) followedstereotyped temporal patterns independent of the distances betweenflowers. Constant flights within five plant species consistentlyhad median durations of about 2 seconds, whereas median transitiontimes between species took 3–6 seconds. (3) This temporalrule broke down, however, if the flowers of two species hadsimilar colors, in which case transition flights had equal dynamicsas constant flights. (4) Bees switched more frequently fromrare than from common species but even more frequently betweensimilar species. We conclude that the bees' choices were determinedby a set of rules that guided them to stay with the currentplant species as long as flowers were rewarding and availablewithin close distance but to switch to another species if flowersoffered low rewards or were not encountered at close range     

Convergence in plant traits between species within grassland communities simplifies their monitoring

Plant trait measurement is a very powerful and promising method for assessing the effects of land use change on ecosystem behavior in grasslands, but it is very time-consuming. Hence we pose the following questions for simplifying diagnosis and monitoring: (i) are plant traits (PTs) similar between plant life forms (PLF: grasses, rosettes, upright forbs, legumes) within a plant community? (ii) is it possible to define the main plant community characteristics by measuring traits on one PLF or a limited number of dominant species?Six PTs known for their ability to characterize the capacity of species to exploit resource-rich or -poor environments and for their competitive dominance in response to disturbance (specific leaf area (SLA), leaf dry matter content (LDMC), plant height (H), C and N contents, flowering time) were measured on the species of 18 plant communities located in Central Pyrenees. The experiment combined 2 fertility levels and 3 defoliation regimes (cutting, grazing). Comparisons were made between the weighted values at community, PLF and two dominant species levels. Regression analysis shows that there were significant correlations between grasses and rosettes for 4 PTs. For H, N and C:N ratio, data for both grass and rosette PLFs were close to the bisecting line. The largest difference in the intercept was observed for LDMC. On the basis of plant traits weighted for all the species, plant communities were ranked in similar ways for SLA and H (Spearman r > 0.93; p < 0.001) and to a lesser extent for LDMC (r = 0.72; p < 0.001). Convergence in weighted plant traits for different PLFs within a plant community mean that in the studied grasslands, defoliation regime and nutrient availability act as strong filters that impose, at least at PLF level, very similar PFTs. This determines a specific local community structure and composition. An application of this result in managed grasslands is the possibility of focusing on one PLF or a limited number of species for vegetation diagnosis and monitoring.     

Annotating genes of known and unknown function by large-scale coexpression analysis

About 40% of the proteins encoded in eukaryotic genomes are proteins of unknown function (PUFs). Their functional characterization remains one of the main challenges in modern biology. In this study we identified the PUF encoding genes from Arabidopsis (Arabidopsis thaliana) using a combination of sequence similarity, domain-based, and empirical approaches. Large-scale gene expression analyses of 1,310 publicly available Affymetrix chips were performed to associate the identified PUF genes with regulatory networks and biological processes of known function. To generate quality results, the study was restricted to expression sets with replicated samples. First, genome-wide clustering and gene function enrichment analysis of clusters allowed us to associate 1,541 PUF genes with tightly coexpressed genes for proteins of known function (PKFs). Over 70% of them could be assigned to more specific biological process annotations than the ones available in the current Gene Ontology release. The most highly overrepresented functional categories in the obtained clusters were ribosome assembly, photosynthesis, and cell wall pathways. Interestingly, the majority of the PUF genes appeared to be controlled by the same regulatory networks as most PKF genes, because clusters enriched in PUF genes were extremely rare. Second, large-scale analysis of differentially expressed genes was applied to identify a comprehensive set of abiotic stress-response genes. This analysis resulted in the identification of 269 PKF and 104 PUF genes that responded to a wide variety of abiotic stresses, whereas 608 PKF and 206 PUF genes responded predominantly to specific stress treatments. The provided coexpression and differentially expressed gene data represent an important resource for guiding future functional characterization experiments of PUF and PKF genes. Finally, the public Plant Gene Expression Database (http://bioweb.ucr.edu/PED) was developed as part of this project to provide efficient access and mining tools for the vast gene expression data of this study.     

Structure and evolution of plant disease resistance genes

This article reviews recent advances that shed light on plant disease resistance genes, beginning with a brief overview of their structure, followed by their genomic organization and evolution. Plant disease resistance genes have been exhaustively investigated in terms of their structural organization, sequence evolution and genome distribution. There are probably hundreds of NBS-LRR sequences and other types of R-gene-like sequences within a typical plant genome. Recent studies revealed positive selection and selective maintenance of variation in plant resistance and defence-related genes. Plant resistance genes are highly polymorphic and have diverse recognition specificities. R-genes occur as members of clustered gene families that have evolved through duplication and diversification. These genes appear to evolve more rapidly than other regions of the genome, and domains such as the leucine-rich repeat, are subject to adaptive selection     

Relationships between leaf morphological traits, nutrient concentrations and isotopic signatures for Mediterranean woody plant species and communities

Background and aims

Soil factors are driving forces that influence spatial distribution and functional traits of plant species. We test whether two anchor morphological traits—leaf mass per area (LMA) and leaf dry matter content (LDMC)—are significantly related to a broad range of leaf nutrient concentrations in Mediterranean woody plant species. We also explore the main environmental filters (light availability, soil moisture and soil nutrients) that determine the patterns of these functional traits in a forest stand.

Methods

Four morphological and 19 chemical leaf traits (macronutrients and trace elements and δ¹³C and δ¹⁵N signatures) were analysed in 17 woody plant species. Community-weighted leaf traits were calculated for 57 plots within the forest. Links between LMA, LDMC and other leaf traits were analysed at the species and the community level using standardised major axis (SMA) regressions

Results

LMA and LDMC were significantly related to many leaf nutrient concentrations, but only when using abundance-weighted values at community level. Among-traits links were much weaker for the cross-species analysis. Nitrogen isotopic signatures were useful to understand different resource-use strategies. Community-weighted LMA and LDMC were negatively related to light availability, contrary to what was expected.

Conclusion

Community leaf traits have parallel shifts along the environmental factors that determine the community assembly, even though they are weakly related across individual taxa. Light availability is the main environmental factor determining this convergence of the community leaf traits.     

Genetic relationships within avocado (Persea americana Mill) cultivars and between Persea species

The origin of avocado (Persea americana Mill) cultivars, as well as the genetic relationships between Persea species, are not well defined and are based mainly on morphological parameters. Minisatellite DNA markers were used to analyze 24 P. americana cultivars in an attempt to define their racial allocation. DNA mixes representing the three races were evaluated and used for analysis. The allocation of 19 of the above cultivars was substantiated by the DNA markers, while new suggestions were offered regarding the remaining five. Eight cultivars, of unknown racial origin, were also examined, and a phylogenetic tree suggesting their origin is offered. Selfing progeny of five cultivars were analyzed for six morphological traits which differentiate the three races, and were compared to their parents in order to assess their origin. Eleven Persea species were analyzed, using DNA fingerprint patterns and SSR (simple sequence repeat) alleles, in order to identify the genetic relationships among the Persea species, and between them and the three P. americana races. The phylogenetic tree obtained is presented. The high value of variation between the avocado cultivars and Persea species observed in this work, suggests that the validity of race and species definition within Persea be treated with caution. Received: 3 August 1996 / Accepted: 23 August 1996     

Protein evolution within and between species

Protein evolution can be seen as the successive replacement of amino acids by other amino acids. In general, it is a very slow process which is triggered by point mutations in the nucleotide sequence. These mutations can transform into single nucleotide polymorphisms (SNPs) within populations and diverging proteins between species. It is well known that in many cases amino acids can be replaced by others without impeding the functioning of the protein, even if these are of quite different physico-chemical character. In some cases, however, almost any replacement would result in a functionally deficient protein. Based upon comprehensive published SNP data and applying correlation analysis we quantified the two antagonist factors controlling the process of amino acid replacement and thus protein evolution: First, the degenerate structure of the genetic code which facilitates the exchange of certain amino acids and, second, the physico-chemical forces which limit the range of possible exchanges to maintain a functional protein. We found that the observed frequencies of amino acid exchanges within species are best explained by the genetic code and that the conservation of physico-chemical properties plays a subordinate role, but has nevertheless to be considered as a key factor. Between moderately diverged species genetic code and physico-chemical properties exert comparable influence on amino acid exchanges. We furthermore studied amino acid exchanges in more detail for six species (four mammals, one bird, and one insect) and found that the profiles are highly correlated across all examined species despite their large evolutionary divergence of up to 800 million years. The species specific exchange profiles are also correlated to the exchange profile observed between different species. The currently available huge body of SNP data allows to characterize the role of two major shaping forces of protein evolution more quantitatively than before.