Genetic relatedness does not retain spatial pattern across multiple spatial scales: dispersal and colonization in the coral,Pocillopora damicornis

Patterns of isolation by distance are uncommon in coral populations. Here, we depart from historical trends of large‐scale, geographical genetic analyses by scaling down to a single patch reef in Kāne‘ohe Bay, Hawai‘i, USA, and map and genotype all colonies of the coral, Pocillopora damicornis. Six polymorphic microsatellite loci were used to assess population genetic and clonal structure and to calculate individual colony pairwise relatedness values. Our results point to an inbred, highly clonal reef (between 53 and 116 clonal lineages of 2352 genotyped colonies) with a much skewed genet frequency distribution (over 70% of the reef was composed of just seven genotypes). Spatial autocorrelation analyses revealed that corals found close together on the reef were more genetically related than corals further apart. Spatial genetic structure disappears, however, as spatial scale increases and then becomes negative at the largest distances. Stratified, random sampling of three neighbouring reefs confirms that reefs are demographically open and inter‐reef genetic structuring was not detected. Attributing process to pattern in corals is complicated by their mixed reproductive strategies. Separate autocorrelation analyses, however, show that the spatial distribution of both clones and nonclones contributes to spatial genetic structure. Overall, we demonstrate genetic structure on an intrareef scale and genetic panmixia on an inter‐reef scale indicating that, for P. damicornis, the effect of small‐ and large‐scale dispersal processes on genetic diversity are not the same. By starting from an interindividual, intrareef level before scaling up to an inter‐reef level, this study demonstrates that isolation‐by‐distance patterns for the coral P. damicornis are limited to small scales and highlights the importance of investigating genetic patterns and ecological processes at multiple scales.     

Analyses of genetic ancestry enable key insights for molecular ecology

Gene flow and recombination in admixed populations produce genomes that are mosaic combinations of chromosome segments inherited from different source populations, that is, chromosome segments with different genetic ancestries. The statistical problem of estimating genetic ancestry from DNA sequence data has been widely studied, and analyses of genetic ancestry have facilitated research in molecular ecology and ecological genetics. In this review, we describe and compare different model‐based statistical methods used to infer genetic ancestry. We describe the conceptual and mathematical structure of these models and highlight some of their key differences and shared features. We then discuss recent empirical studies that use estimates of genetic ancestry to analyse population histories, the nature and genetic basis of species boundaries, and the genetic architecture of traits. These diverse studies demonstrate the breadth of applications that rely on genetic ancestry estimates and typify the genomics‐enabled research that is becoming increasingly common in molecular ecology. We conclude by identifying key research areas where future studies might further advance this field.     

Science of breeding and heredity from ancient Persia to modern Iran

About 1700 years BC, the prophet Zoroaster declared equal right for women and men to choose their "own ways." There is much evidence that ancient Persians believed in the equal contribution of women and men toward producing a child, and all its hereditary characteristics.Even more surprising are the phrases in Vandidad book, which were gathered by Mobedans in the Mad dynasty about egg extraction (gametes) from animal reproductive organs (gonads) and their storage for future conception.Centuries later, Western philosopher beliefs in regard to reproduction were contrary to Persian knowledge. The Greek philosophers believed that man's water (semen) contains all human characteristics, and the female uterus is only responsible for nurturing and development of fetus. After detection of the ovum (de Graaf 2(nd) half 17 century) Malpigy proposed the preformation theory (ovist) which means there is a miniature human inside ovum, that grows after Semen has entered the uterus and grow into a well-developed fetus. This hypothesis was later delegated to spermatozoa. These contradictory and inappropriate beliefs were subject to discussions and dispute, until C.E. Wolf demonstrated that the embryo is a product of the fertilization of ovum by spermatozoa.800 years prior this the sage Ferdowsi "The Great Iranian Poet" explains nicely the equal participation of man and woman in the production of the fetus and transmission of characters.After the renaissance and especially in recent years, tremendous achievements have been made in unraveling biological secrets of reproduction. There was no work o n genetics in Iran until 1936, when a genetic course was added to the biology curriculum in related colleges and universities; Iranian Genetics Society was founded in 1966, initiating a steady movement in this field.Although there was an inevitable gap during the revolution and war in our country, now there is great effort by researchers to eliminate the gap and bring us into the mainstream of world science, and development in biomedical sciences in the third millennium.     

Independent axes of genetic variation and parallel evolutionary divergence of opercle bone shape in threespine stickleback

Evolution of similar phenotypes in independent populations is often taken as evidence of adaptation to the same fitness optimum. However, the genetic architecture of traits might cause evolution to proceed more often toward particular phenotypes, and less often toward others, independently of the adaptive value of the traits. Freshwater populations of Alaskan threespine stickleback have repeatedly evolved the same distinctive opercle shape after divergence from an oceanic ancestor. Here we demonstrate that this pattern of parallel evolution is widespread, distinguishing oceanic and freshwater populations across the Pacific Coast of North America and Iceland. We test whether this parallel evolution reflects genetic bias by estimating the additive genetic variance-covariance matrix (G) of opercle shape in an Alaskan oceanic (putative ancestral) population. We find significant additive genetic variance for opercle shape and that G has the potential to be biasing, because of the existence of regions of phenotypic space with low additive genetic variation. However, evolution did not occur along major eigenvectors of G, rather it occurred repeatedly in the same directions of high evolvability. We conclude that the parallel opercle evolution is most likely due to selection during adaptation to freshwater habitats, rather than due to biasing effects of opercle genetic architecture.     

Increased totipotency of protoplasts from Brassica oleracea plants previously regenerated in tissue culture

Factors affecting the division of cells derived from leaf and cotyledon protoplasts from Brassica oleracea L. var. italica (Green Comet hybrid broccoli) were examined to optimize conditions for plant regeneration and to determine whether there was a genetic basis for improved regeneration from protoplasts derived from plants previously regenerated from tissue cultures [15]. When leaf protoplasts from different plants grown from hybrid seed were isolated and cultured simultaneously, division efficiencies of 1–95% were obtained. Cells from some plants showed high division efficiencies in consecutive experiments while cells from other plants had consistently low division rates. More plants from hybrid seed gave high division efficiencies when cotyledon protoplasts were used. However, cotyledon or leaf protoplasts from selfed progeny of regenerated plants produced more vigorous calli and more shoots than protoplasts from hybrid seed. These results suggest that there may be a genetic component to the increased totipotency of Brassica oleracea protoplasts.     

The impact of endogenous content,replicates and pooling on genome capture from faecal samples

Target‐capture approach has improved over the past years, proving to be very efficient tool for selectively sequencing genetic regions of interest. These methods have also allowed the use of noninvasive samples such as faeces (characterized by their low quantity and quality of endogenous DNA) to be used in conservation genomic, evolution and population genetic studies. Here we aim to test different protocols and strategies for exome capture using the Roche SeqCap EZ Developer kit (57.5 Mb). First, we captured a complex pool of DNA libraries. Second, we assessed the influence of using more than one faecal sample, extract and/or library from the same individual, to evaluate its effect on the molecular complexity of the experiment. We validated our experiments with 18 chimpanzee faecal samples collected from two field sites as a part of the Pan African Programme: The Cultured Chimpanzee. Those two field sites are in Kibale National Park, Uganda (N = 9) and Loango National Park, Gabon (N = 9). We demonstrate that at least 16 libraries can be pooled, target enriched through hybridization, and sequenced allowing for the genotyping of 951,949 exome markers for population genetic analyses. Further, we observe that molecule richness, and thus, data acquisition, increase when using multiple libraries from the same extract or multiple extracts from the same sample. Finally, repeated captures significantly decrease the proportion of off‐target reads from 34.15% after one capture round to 7.83% after two capture rounds, supporting our conclusion that two rounds of target enrichment are advisable when using complex faecal samples.     

QUANTITATIVE GENETIC ANALYSIS OF MORPHOLOGICAL VARIATION IN AN ANTARCTIC DIATOM GROWN AT TWO LIGHT INTENSITIES1

Ten clonal isolates of Thalassiosira tumida (Janisch) Hasle were grown in duplicate semi-continuous batch cultures at 116 and 11.6 μE.m⁻².s⁻¹; acclimated cells were harvested during exponential growth and cleaned for examination by light microscopy (LM) and scanning electron microscopy (SEM). Number of strutted processes surrounding the central annulus (SP) and average number of satellite pores per process (AVSAT) were counted using SEM on 20 valves from each culture grown in high light, for a total of 400 valves examined; number of marginal labiate processes (LP) and overall diameter (DIAM) were measured using LM on 20 valves from each culture grown in both high and low light for a total of 800 valves examined. Univariate analysis of variance showed that bottle effects resulting from microenvironmental differences between replicates were a small but significant source of variation in DIAM, LP, and SP but not AVSAT. Significant differences among clones were observed for all characters. Decreased irradiance resulted in a significant decrease in valve diameter but no significant effect on LP; no light x clone interaction was obsered. Significant covariance between characters among clones was also observed; since valve diameter is known to decrease during asexual growth, the correlation coefficients for SP, AVSAT, and LP with DIAM were used to correct the data for this source of nongenetic differences between clones. Analysis of the size-corrected data showed that the proportion of total phenotypic variance in SP, LP, and AVSAT caused by genetic differences among clones was 0.14, 0.14, and 0.30, respectively. This indicates that the majority of total phenotypic variance was due to environmental or developmental causes, but that sufficient genetic variability exists to support rapid phenotypic evolution in SP, LP, and AVSAT under continued directional selection. Finally, the results of the genetic analysis revealed a high (0.82) genetic correlation between SP and LP.     

Genetic structure of coastal and inland populations of the annual halophyte Suaeda maritima (L.) dumort. in Central Europe, inferred from amplified fragment length polymorphism markers

Naturally occurring inland salt habitats are highly threatened due to increasing fragmentation and area reduction, while the surroundings of former potash mining dumps have experienced a massive invasion by halophytes over the last 20 years. We reconstructed colonisation patterns of these purely anthropogenic inland salt sites using molecular markers in the obligate halophyte Suaeda maritima (L.) dumort. (Chenopodiaceae), a typical plant in such areas. In the present study, 120 individual plants from 40 coastal and inland populations in Central Europe were subjected to AFLP analysis with nine primer combinations. A total of 243 AFLP band positions were scored as presence/absence characters. Genetic diversity values were not significantly different in populations from natural and anthropogenic inland salt sites as compared to coastal habitats. Results from principal coordinate analysis, neighbour-joining analysis and analysis of molecular variance ( amova ) all indicated that most of the genetic variation is preserved within populations, while genetic differentiation among populations is comparatively low. We conclude that S. maritima has repeatedly and independently colonised the surroundings of former potash mining dumps in Central Germany. However, the absence of founder effects and the lack of phylogeographic structure prevented us from identifying putative donor populations.     

Landscape genetic structure of coastal tailed frogs (Ascaphus truei) in protected vs. managed forests

Habitat loss and fragmentation are the leading causes of species’ declines and extinctions. A key component of studying population response to habitat alteration is to understand how fragmentation affects population connectivity in disturbed landscapes. We used landscape genetic analyses to determine how habitat fragmentation due to timber harvest affects genetic population connectivity of the coastal tailed frog (Ascaphus truei), a forest-dwelling, stream-breeding amphibian. We compared rates of gene flow across old-growth (Olympic National Park) and logged landscapes (Olympic National Forest) and used spatial autoregression to estimate the effect of landscape variables on genetic structure. We detected higher overall genetic connectivity across the managed forest, although this was likely a historical signature of continuous forest before timber harvest began. Gene flow also occurred terrestrially, as connectivity was high across unconnected river basins. Autoregressive models demonstrated that closed forest and low solar radiation were correlated with increased gene flow. In addition, there was evidence for a temporal lag in the correlation of decreased gene flow with harvest, suggesting that the full genetic impact may not appear for several generations. Furthermore, we detected genetic evidence of population bottlenecks across the Olympic National Forest, including at sites that were within old-growth forest but surrounded by harvested patches. Collectively, this research suggests that absence of forest (whether due to natural or anthropogenic changes) is a key restrictor of genetic connectivity and that intact forested patches in the surrounding environment are necessary for continued gene flow and population connectivity.