Intraspecific flavonoid variation

This review is concerned with variation of flavonoid patterns within species. Many examples of species with invariant flavonoid patterns are known; there are at least as many examples where complex arrays of pigments are known. Eight categories of variation are discussed: 1) qualitatively invariant pigment profiles, 2) quantitative variation, 3) flavonoid races that do not correspond to recognized taxonomic groups, 4) flavonoid races that do correspond to recognized taxonomic groups, 5) flavonoid profile differences between different ploidy levels, 6) differences between organs or between tissues, 7) differences between developmental stages, and 8) environmentally influenced flavonoid profiles. These types of variation seem to occur randomly in the plant kingdom. Members of the same family, or in some cases, the same genus, can display different types of variation. Careful attention to these sources of variation is necessary before flavonoid characters can be used in taxonomic studies.     

Intraspecific variation,sex-biased dispersal and phylogeography of the eastern grey kangaroo (Macropus giganteus)

Genetic information has played an important role in the development of management units by focusing attention on the evolutionary properties and genetics of populations. Wildlife authorities cannot hope to manage species effectively without knowledge of geographical boundaries and demic structure. The present investigation provides an analysis of mitochondrial DNA and microsatellite data, which is used to infer both historical and contemporary patterns of population structuring and dispersal in the eastern grey kangaroo (Macropus giganteus) in Australia. The average level of genetic variation across sample locations was one of the highest observed for marsupials (h=0.95, HE=0.82). Contrary to ecological studies, both genic and genotypic analyses reveal weak genetic structure of populations, where high levels of dispersal may be inferred up to 230 km. The movement of individuals was predominantly male-biased (average Nem=22.61, average Nfm=2.73). However, neither sex showed significant isolation by distance. On a continental scale, there was strong genetic differentiation and phylogeographic distinction between southern (TAS, VIC and NSW) and northern (QLD) populations, indicating a current and/or historical restriction of gene flow. In addition, it is evident that northern populations are historically more recent, and were derived from a small number of southern founders. Phylogenetic comparisons between M. g. giganteus and M. g. tasmaniensis indicated that the current taxonomic status of these subspecies should be revised as there was a lack of genetic differentiation between the populations sampled.     

Intraspecific interference influences the use of prey hotspots

Resource clumping (prey hotspots) and intraspecific competition may interact to influence predator foraging behaviour. Optimal foraging theory suggests that predators should concentrate most of their foraging activity on prey hotspots, but this prediction has received limited empirical support. On the other hand, if prey concentration at hotspots is high enough to allow its use by several individuals, increased competition may impose constraints on foraging decisions of conspecifics, resulting in a temporal segregation in the use of shared resources. We investigated how artificial prey hotspots influence foraging behaviour in the Iberian lynx Lynx pardinus, and examined variations in the use of prey hotspots by individuals with different competitive abilities. All lynx, irrespective of their position in the competitive hierarchy, focused their activity on prey hotspots. Supplemented lynx concentrated higher proportions of active time on 100 m circular areas around hotspots than non‐supplemented lynx did on any area of the same size. However, we found evidence for a dynamic temporal segregation, where inferior competitors may actively avoid the use of prey hotspots when dominants were present. Dynamic temporal segregation may operate in solitary and territorial predators as a mechanism to facilitate coexistence of conspecifics in the absence of opportunities for spatial segregation when they use extremely clumped resources.     

Intraspecific nuclear DNA variation in Drosophila

We have summarized and analyzed all available nuclear DNA sequence polymorphism studies for three species of Drosophila, D. melanogaster (24 loci), D. simulans (12 loci), and D. pseudoobscura (5 loci). Our major findings are: (1) The average nucleotide heterozygosity ranges from about 0.4% to 2% depending upon species and function of the region, i.e., coding or noncoding. (2) Compared to D. simulans and D. pseudoobscura (which are about equally variable), D. melanogaster displays a low degree of DNA polymorphism. (3) Noncoding introns and 3' and 5' flanking DNA shows less polymorphism than silent sites within coding DNA. (4) X-linked genes are less variable than autosomal genes. (5) Transition (Ts) and transversion (Tv) polymorphisms are about equally frequent in non-coding DNA and at fourfold degenerate sites in coding DNA while Ts polymorphisms outnumber Tv polymorphisms by about 2:1 in total coding DNA. The increased Ts polymorphism in coding regions is likely due to the structure of the genetic code: silent changes are more often Ts's than are replacement substitutions. (6) The proportion of replacement polymorphisms is significantly higher in D. melanogaster than in D. simulans. (7) The level of variation in coding DNA and the adjacent noncoding DNA is significantly correlated indicating regional effects, most notably recombination. (8) Surprisingly, the level of polymorphism at silent coding sites in D. melanogaster is positively correlated with degree of codon usage bias. (9) Three proposed tests of the neutral theory of DNA polymorphisms have been performed on the data: Tajima's test, the HKA test, and the McDonald-Kreitman test. About half of the loci fail to conform to the expectations of neutral theory by one of the tests. We conclude that many variables are affecting levels of DNA polymorphism in Drosophila, from properties of nucleotides to population history and, perhaps, mating structure. No simple, all encompassing explanation satisfactorily accounts for the data.      

Intraspecific variation of recombination rate in maize

Background

In sexually reproducing organisms, meiotic crossovers ensure the proper segregation of chromosomes and contribute to genetic diversity by shuffling allelic combinations. Such genetic reassortment is exploited in breeding to combine favorable alleles, and in genetic research to identify genetic factors underlying traits of interest via linkage or association-based approaches. Crossover numbers and distributions along chromosomes vary between species, but little is known about their intraspecies variation.

Results

Here, we report on the variation of recombination rates between 22 European maize inbred lines that belong to the Dent and Flint gene pools. We genotype 23 doubled-haploid populations derived from crosses between these lines with a 50 k-SNP array and construct high-density genetic maps, showing good correspondence with the maize B73 genome sequence assembly. By aligning each genetic map to the B73 sequence, we obtain the recombination rates along chromosomes specific to each population. We identify significant differences in recombination rates at the genome-wide, chromosome, and intrachromosomal levels between populations, as well as significant variation for genome-wide recombination rates among maize lines. Crossover interference analysis using a two-pathway modeling framework reveals a negative association between recombination rate and interference strength.

Conclusions

To our knowledge, the present work provides the most comprehensive study on intraspecific variation of recombination rates and crossover interference strength in eukaryotes. Differences found in recombination rates will allow for selection of high or low recombining lines in crossing programs. Our methodology should pave the way for precise identification of genes controlling recombination rates in maize and other organisms.     

Intraspecific and interspecific genetic variation in Drosophila

Utilizing the technique of DNA-DNA hybridization, we have characterized the degree of genetic variability in single-copy DNA both within and between several species of Drosophila. The results of intraspecific variation studies indicate considerable variation both for levels of nucleotide heterozygosity (estimated to be over 2%) as well as for insertions-deletions. Interspecific studies confirm this great deal of variability and further establish an extreme heterogeneity within Drosophila genomes for rates of divergence. This heterogeneity is much more extreme than that seen between exons and introns. The degree of single-copy DNA divergence generally supports phylogenetic affinities deduced from more traditional methods. However, exceptions occur where single-copy DNA divergence is not correlated with other properties such as degree of chromosomal differentiation, morphology, or ability to form interspecific hybrids. We argue that single-copy DNA divergence as measured by DNA-DNA hybridization is an accurate indicator of phylogenetic relationships and therefore sheds light on the evolution of other biological properties. Many, if not most, evolutionary tests require an accurate phylogeny of the group being studied and DNA, because of the high information content inherent within the molecule, offers the best hope of deriving true phylogenies.     

Intraspecific variation for resource use in Drosophila

Individuals within natural populations of Drosophila tripunctata and D. falleni varied significantly in their responses to alternative types of food baits; no such variation was detected in D. putrida. The food type at which laboratory-reared D. melanogaster tended to settle in the field was influenced by the type of food on which they had been kept prior to release. Although flies apparently forgot their previous experience within hours, its effect on their behaviour can be manifested for at least 1 day in the field. Mark -recapture experiments on wild flies are shown to be very inefficient at detecting individual variation in behaviour.     

Intraspecific shape variation in horseshoe crabs: The importance of sexual and natural selection for local adaptation

A morphometric analysis of the body shape of three species of horseshoe crabs was undertaken in order to infer the importance of natural and sexual selection. It was expected that natural selection would be most intense, leading to highest regional differentiation, in the American species Limulus polyphemus, which has the largest climatic differences between different populations. Local adaptation driven by sexual selection was expected in males but not females because horseshoe crab mating behaviour leads to competition between males, but not between females. Three hundred fifty-nine horseshoe crabs from nine populations, representing three species, were analyzed using a digitizer to position sixty morphometric landmarks in a three-dimensional space. Discriminant analysis revealed strong regional structuring within a species, which suggests strong philopatry, and showed the existence of geographically-based intraspecific variation. An admixture analysis showed regional intraspecific differentiation for males and females of L. polyphemus and males of the Asian horseshoe crab Carcinoscorpius rotundicauda, but not for females of C. rotundicauda and another Asian horseshoe crab, Tachypleus gigas. Differences in shape variation between sexes were tested with F-tests, which showed lower intrapopulation morphometric variation in males than females. These results indicate a lower degree of local adaptation on body shape in C. rotundicauda and T. gigas than in L. polyphemus and a lower degree of local adaptation in females than in males.     

Intraspecific variation in reproductive traits of burrowing owls

Reviews of hatching asynchrony in birds recommended more studies on intraspecific variation in the extent of hatching asynchrony. We examined intraspecific variation in clutch size, laying chronology, onset of incubation, incubation period, and hatching asynchrony in burrowing owls (Athene cunicularia) in the Imperial Valley of California. Mean clutch size was 7.4 eggs and owls averaged 0.5 eggs laid per day. Females varied considerably in laying interval and onset of incubation (range?=?1st to 9th egg in the clutch). The mean incubation period was 21.9?days. Hatching interval also varied greatly among females ( $ \overline{x} $ ?=?0.8, range 0.1–2.0?days between successively hatched eggs). Past burrowing owl studies have largely overlooked the substantial intraspecific variation in these traits or have reported estimates that differ from ours. Future studies designed to identify the environmental factors that explain the large intraspecific variation in these traits will likely provide insights into the constraints on local abundance.     

Intraspecific variation in Triassic Ophthalmidiid Foraminifera from Timor

Four ophthalmidiid species are described as free specimens extracted from mudstones and wackestones of Triassic age: Atsabella bandeiraensis nov. gen. nov. sp., Karaburunia atsabensis nov. sp., Ophthalmidium sp. cf. O. primitivum Ho and Spirophthalmidium grunaui nov. sp. Analysis of morphological variation found in large suites of specimens suggests that, as in modern miliolids, apertural characteristics, chamber shape and adult test size are features that vary within narrow limits and may be used to define species. In genera with milioline coiling in the post-embryonic stage, chamber arrangement may be highly variable. Post-embryonic coiling in K. atsabensis varies from quinqueloculine to almost spiroloculine and encompasses morphotypes that, in thin-section studies, have been attributed to a number of other genera. In Timor Leste, A. bandeiraensis, K. atsabensis and S. grunaui have been found with conodonts indicative of the Carnian, but the full local stratigraphic range of these species is uncertain. K. atsabensis occurs at another locality with conodonts suggestive of the Middle Triassic or less likely Carnian. Ophthalmidium sp. cf. O. primitivum has been found at one locality associated with A. bandeiraensis and K. atsabensis in a stratigraphic succession that suggests a correlation to the Carnian or Norian. The ophthalmidiids are found commonly associated with organic-cemented agglutinated and hyaline foraminifera and at some localities common to abundant ostracods and mollusc debris. They were most common in organic-rich carbonate mud of shallow-marine environments.     

Intraspecific floral colour variation in three Pedicularis speciesOA

Flower constancy describes the phenomenon that pollinators tend to successively visit flowers of a single species during foraging, reducing reproductive interference in natural communities. The extent of flower constancy is largely determined by the floral traits of co-flowering species. Both higher inter-specific and lower intraspecific differences of floral traits should contribute to a higher level of flower constancy.However, previous studies mainly focused on interspecific difference, and t...     

Intraspecific variation in a predator drives cascading variation in primary producer community composition

Predation has important cascading impacts on primary producer biomass and community composition in many ecosystems. While most studies have focused on the consequences of interspecific or density differences in predators, it is recognized that phenotypic variation within species can have strong and cascading community and ecosystem consequences at lower trophic levels. In coastal New England lakes, both the presence and life history form of the zooplanktivorous fish alewife, Alosa pseudoharengus, have strong influence on the biomass, size structure and community composition of crustacean zooplankton communities. Here we test the hypothesis that alewife presence and life history will have cascading impacts on phytoplankton biomass and community composition in a mesocosm experiment that previously reported strong biomass and compositional differences of crustacean zooplankton communities among alewife treatments. We show that alewife life history led to small but statistically significant differences in phytoplankton community composition among treatments. This compositional difference was driven primarily by an increase in the density of two edible phytoplankton genera associated with lower zooplankton biomass in the anadromous alewife treatment. Our results show that intraspecific variation in a predator can have cascading effects on primary producer communities. However we did not observe significant differences in total algal biomass.     

Intraspecific and interspecific variation in floral volatiles over time

Plant Ecology - Floral volatile organic compounds (VOCs) are traits that influence plant interactions with pollinators and other species. Interspecific and intraspecific variation in traits can...     

Intraspecific variation in resistance of frog eggs to fungal infection

Documenting sources of variation in host viability at pathogen exposure within and among populations is an important task in order to predict host-pathogen evolutionary dynamics. In the present study, we investigated family and population variation in the degree of embryonic infection of the pathogenic fungus Saprolegnia spp., by infecting moor frog (Rana arvalis) eggs from six populations and exposing them to two different temperatures. We found a significant family effect on the degree of Saprolegnia-infection of eggs and embryos, suggesting that there is genetic variation in resistance among embryos, or variation among females in some aspect of maternally induced resistance. Furthermore, infection level differed significantly between temperatures, with most families having more infected eggs in the relatively colder temperature. However, eggs and embryos from the different populations showed different degrees of Saprolegnia-infection in the two temperatures, i.e., there was a significant population × temperature interaction on the proportion of infected eggs. Thus, the degree of Saprolegnia-infection is sensitive to variation at the level of the family, population and environmental conditions, suggesting that responses to fungal outbreaks will vary geographically and will be difficult to predict.     

Intraspecific variation of chloroplast DNA in Dioscorea bulbifera L.

Summary Restriction fragment length polymorphism (RFLP) analysis of chloroplast (ct) DNAs from 15 accessions of Dioscorea bulbifera collected from Africa and Asia was carried out using the Southern hybridization technique. Eight cloned ctDNA fragments of D. bulbifera and D. opposita, which cover 80% of the total chloroplast genome, were used as the probes to detect variation in ctDNA digested with nine restriction endonucleases. Ten variable sites, located in the large and small single-copy regions, were disclosed among the 15 accessions, of which six showed base substitution and four carried length mutation. Positions of the latter mutations were determined on the physical map of ctDNA. Based on these results, chloroplast genomes of the 15 accessions could be classified into nine types. Their phylogenetic relationships are assumed to be as follows: (1) African and Asian chloroplast genomes diverged from each other at the earliest point in time; (2) E-type chloroplast genome, occurring in the south-east edge of the Asian continent, appears to be the most ancient among all the Asian chloroplast genomes; and (3) four chloroplast genomes, found in Asian insular regions, are probably derived independently from the E-type genome. The discrepancy between the taxonomic relationship and the proposed chloroplast genome phylogeny of the present materials is noted.     

Genetic structure and effective population size of Sydney rock oysters in eastern Australia

Oyster reef habitats are critical to coastal biodiversity and their decline has prompted restoration efforts in Australia. Knowledge gaps exist regarding the population structure and diversity of key species in these habitats. This may be critical information for the design of effective restoration programs. Sydney rock oysters (Saccostrea glomerata) are the dominant reef-forming bivalve in eastern Australia. Wild populations of S. glomerata have declined due to overharvesting, disease outbreaks, coastal development and reduced water quality. Here, we use genetic markers identified by genome-wide sequencing to investigate the genetic structure and diversity of wild Sydney rock oysters throughout their distribution in eastern Australia. We examine evidence for past population bottlenecks and spatial genetic structure associated with the East Australian Current. Analysis of 3, 400 neutral single-nucleotide polymorphisms (SNPs) revealed a single population, and an overlap with two other Saccostrea sp. at the northernmost boundary of the distribution. We detected signals of asymmetric gene flow consistent with the direction of the East Australian Current, and spatial structure patterns of limited genetic isolation by distance and spatial autocorrelation in the northern region (which experiences stronger effects of the East Australian Current) but not in the southern region of the distribution. We found no evidence of significant recent bottlenecks, with high effective population size throughout the species’ range. This information will provide a baseline against which to assess the impact of restoration projects, and guide strategies for sourcing stock for the enhancement of wild oyster populations. Our results provide a positive outlook for the resilience and adaptive capacity of Sydney rock oysters, and highlight wild populations as valuable resources for aquaculture and restoration initiatives.

     

Skin color variation in eastern Nepal

The purpose of this paper is to provide skin color data on several endogamous groups of eastern Nepal and to demonstrate genetic microdifferentiation in skin color. Skin reflectance measures were taken at the upper inner arm and forehead sites, using the British DSL Model 99 Reflectance Spectrophotometer fitted with blue, green, and red filters. Measurements on 484 males representing six endogamous groups (Jirel, Sunwar, Sherpa, Tamang, Brahman, Chetri) were utilized. After adjusting for group-specific age effects, multivariate likelihood ratio permutation tests were used to assess ethnic differences in skin reflectance means and covariance matrices. Ethnic group membership had a highly significant effect on skin color at the upper inner arm site and at the forehead site. Differential tanning responses among groups were also detected and may represent the influence of genotype-environment interaction on reflectance traits. Mahalanobis distance analysis revealed patterns of microdifferentiation that are inconsistent with oral historical accounts. Little support was found for the ethnohistorical belief that Jirels are a hybrid group descended from Sunwars and Sherpas, even though this scenario is supported by linguistic, anthropometric, and dermatoglyphic data. We suggest that while reflectometric studies of skin pigmentation may be useful in assessing the macrodifferentiation of human populations, the use of skin color in differentiation studies at the local population level needs to be carefully evaluated.