Population genetics of Blanding’s turtle (Emys blandingii) in the midwestern United States

Blanding’s turtle (Emys blandingii) has declined substantially in North America due to anthropogenic activities, leaving populations smaller and increasingly fragmented spatially. We sampled 212 turtles to evaluate variation at eight microsatellite loci within and among 18 populations of E. blandingii across its primary range in the midwestern United States (Illinois, Iowa, Minnesota, and Nebraska). All loci and populations were highly polymorphic. Our analyses also detected considerable genetic structure within and among the sampled localities, and revealed ancestral gene flow of E. blandingii in this region north and east from an ancient refugium in the central Great Plains, concordant with post-glacial recolonization timescales. The data further implied unexpected ‘links’ between geographically disparate populations in Nebraska and Illinois. Our study encourages conservation decisions to be mindful of the genetic uniqueness of populations of E. blandingii across its primary range.     

Population genetics and relatedness in a critically endangered island raptor, Ridgway’s Hawk Buteo ridgwayi

Many island avian populations are of conservation interest because they have a higher risk of extinction than mainland populations. Susceptibility of island birds to extinction is primarily related to human induced change through habitat loss, persecution, and introduction of exotic species, in combination with genetic factors. We used microsatellite profiles from 11 loci to assess genetic diversity and relatedness in the critically endangered hawk Buteo ridgwayi endemic to the island of Hispaniola in the Caribbean. Using samples collected between 2005 and 2009, our results revealed a relatively high level of heterozygosity, evidence of a recent genetic bottleneck, and the occurrence of inbreeding within the population. Pair relatedness analysis found 4 of 7 sampled breeding pairs to be related similar to that of first cousin or greater. Pedigree estimates indicated that up to 18 % of potential pairings would be between individuals with relatedness values similar to that of half-sibling. We discuss our findings in the context of conservation genetic management suggesting both carefully managed translocations and the initiation of a captive population as a safeguard of the remaining genetic diversity.     

Population genetics of wild Hizikia fusiformis (Sargassaceae, Phaeophyta) along China’s coast

Hizikia fusiformis is one of the important commercially cultivated seaweeds in China. Inter-simple sequence repeats (ISSR) and sequence-related amplified polymorphism (SRAP) markers were used to assess genetic structure of nine wild H. fusiformis populations collected along the coast of China. Of the 255 bands generated by 21 ISSR primers, 99.61% were polymorphic and 99.71% of 344 bands amplified by 30 SRAP primers were polymorphic. The tested high genetic diversities show that the average Nei’s genetic diversity (H) were 0.1519 and 0.1624, and average Shannon’s information index (I) were 0.2248 and 0.2400 in ISSR and SRAP analyses, respectively. Unweighted pair group method with arithmetic mean (UPGMA) dendrograms of the nine populations were divided into two main groups. The ISSR and SRAP analyses values of gene differentiation (G _ST, 0.5955, 0.5486, respectively) indicate that high variation exists among the nine populations, likely due to external interferences and limitation of gene flow (N _m?=?0.3397, 0.4114). Our study indicated that human activities and herbivore overgrazing had influenced the natural Hizikia populations and that the understanding of population genetics would be helpful in sustainable utilization and biomass conservation of Sargassaceae resources.     

Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history?

Background  

Phylogenies reconstructed with only one or a few independently inherited loci may be unresolved or incongruent due to taxon and gene sampling, horizontal gene transfer, or differential selection and lineage sorting at individual loci. In an effort to remedy this situation, we examined the utility of conserved orthologous set (COSII) nuclear loci to elucidate the phylogenetic relationships among 29 diploid Solanum species in the sister clades that include tomato and potato, and in Datura inoxia as a far outgroup. We screened 40 COSII markers with intron content over 60% that are mapped in different chromosomes; selected a subset of 19 by the presence of single band amplification of size mostly between 600 and 1200 bp; sequenced these 19 COSII markers, and performed phylogenetic analyses with individual and concatenated datasets. The present study attempts to provide a fully resolved phylogeny among the main clades in potato and tomato that can help to identify the appropriate markers for future studies using additional species.     

Mitochondrial phylogeography and demographic history of the vicuña: implications for conservation

The vicu?a (Vicugna vicugna; Miller, 1924) is a conservation success story, having recovered from near extinction in the 1960s to current population levels estimated at 275,000. However, lack of information about its demographic history and genetic diversity has limited both our understanding of its recovery and the development of science-based conservation measures. To examine the evolution and recent demographic history of the vicu?a across its current range and to assess its genetic variation and population structure, we sequenced mitochondrial DNA from the control region (CR) for 261 individuals from 29 populations across Peru, Chile and Argentina. Our results suggest that populations currently designated as Vicugna vicugna vicugna and Vicugna vicugna mensalis comprise separate mitochondrial lineages. The current population distribution appears to be the result of a recent demographic expansion associated with the last major glacial event of the Pleistocene in the northern (18 to 22 degrees S) dry Andes 14-12,000 years ago and the establishment of an extremely arid belt known as the 'Dry Diagonal' to 29 degrees S. Within the Dry Diagonal, small populations of V. v. vicugna appear to have survived showing the genetic signature of demographic isolation, whereas to the north V. v. mensalis populations underwent a rapid demographic expansion before recent anthropogenic impacts.     

Scute’s polymorphism as a source of evolutionary development of the turtle shell

The scute mosaic (pholidosis) of the turtle shell is a complex correlated system of the modular type. Horny scutes are separate morphological elements partially closely connected with each other and partially relatively autonomous in development. The last feature causes high variability of scutes in the shape, size, rate and direction of growth, and provides the basis of transformation of the entire mosaic. In the evolution of turtles, the horny shell changed towards a decrease in the number of elements composing it. The process of oligomerization developed through reduction and fusion of scutes or their anlages. The traces of these transformations are observed in the ontogeny of living turtles. The scutes undergoing reduction display the following developmental deviations: (1) a decrease in size of the scute anlage, (2) the temporal shift in initiation to later embryonic stages, (3) absence of an anlage of a own furrow (the boundaries of the scute are formed by the furrows of neighboring scutes), and (4) a decrease in size of the zone and rate of the scute growth. The fusion of horny scutes follows two patterns: (1) fusion of scute anlages and (2) reduction of horny furrows separating scutes before. Secondary polymerization of the scute mosaic by the appearance of additional elements usually results from abnormal development and is infrequently fixed in evolution. The main mechanism of evolutionary changes in turtle pholidosis was heterochrony, i.e., the time shift in initiation and developmental rate of scutes. The heterotopies, i.e., changes in the position of scute anlages, played a minor role in the evolution of turtles; they usually caused only scute abnormalities, which was frequently asymmetrical.     

Population structure of pioneer specialist solitary bee Andrena vaga (Hymenoptera: Andrenidae) in central Europe: the effect of habitat fragmentation or evolutionary history?

Because patchiness of food sources or nesting opportunities frequently limits gene flow, specialists often exhibit distinct population structures in fragmented habitats. We studied the influence of habitat fragmentation on population structure in the solitary bee Andrena vaga, an early spring species that nests exclusively in sandy soil and feeds strictly on willows (Salix spp.). Because the homogenous habitat of the German floodplains, where the species was studied previously, resulted in the species’ weak population structure, we expected more structured populations in central Europe, where the sandy soils essential for nesting are highly fragmented. We analysed 387 females from 21 localities in the Czech Republic and Slovakia using nine microsatellite loci, and we inferred population structure using landscape genetics and Bayesian clustering methods. Contrary to our expectations, habitat fragmentation did not result in increased genetic isolation at the localities; however, two differentiated groups of localities, separated by a wide clinal zone of admixture, were detected within the study area. The observed pattern suggests that dispersive ability of A. vaga compensates the species dependence on unstable fragmented habitats. We propose that the population structure may mirror a secondary contact formed by the expansion of two populations that had been separated in the past. We emphasise the necessity of knowing the studied species’ population history before making conclusions concerning correlations between habitat and population structure, especially in areas of known suture zones created by the secondary contact of populations expanding from separate refugia.     

It’s the song,not the singer: an exploration of holobiosis and evolutionary theory

That holobionts (microbial communities and their animal or plant hosts) are units of selection squares poorly with the observation that microbes are often recruited (horizontally acquired) from the environment, not passed down vertically from parent to offspring, as required for collective reproduction. The taxonomic makeup of a holobiont’s microbial community may vary over its lifetime and differ from that of conspecifics. In contrast, biochemical functions of the microbiota and contributions to host biology are more conserved, with taxonomically variable but functionally similar microbes recurring across generations and hosts. To save what is of interest in holobiont thinking, we propose casting metabolic and developmental interaction patterns, rather than the taxa responsible for them, as units of selection. Such units need not directly reproduce or form parent-offspring lineages: their prior existence has created the conditions under which taxa with the genes necessary to carry out their steps have evolved in large numbers. These taxa or genes will reconstruct the original interaction patterns when favorable conditions occur. Interaction patterns will vary (for instance by the alteration or addition of intermediates) in ways that affect the likelihood of and circumstances under which such reconstruction occurs. Thus, they vary in fitness, and evolution by natural selection will occur at this level. It is on the persistence, reconstruction, and spread of such interaction patterns that students of holobiosis should concentrate, we suggest. This model also addresses other multi-species collectively beneficial interactions, such as biofilms or biogeochemical cycles maintaining all life.     

Does past evolutionary history under different mating regimes influence the demographic dynamics of interspecific competition?

Interspecific interactions are contingent upon organism phenotypes, and thus phenotypic evolution can modify interspecific interactions and affect ecological dynamics. Recent studies have suggested that male–male competition within a species selects for capability to reproductively interfere with a closely related species. Here, we examine the effect of past evolutionary history under different mating regimes on the demographic dynamics of interspecific competition in Callosobruchus seed beetles. We used previously established experimental evolution lines of Callosobruchus chinensis that evolved under either forced lifelong monogamy or polygamy for 17 generations, and examined the demographic dynamics of competition between these C. chinensis lines and a congener, Callosobruchus maculatus. Callosobruchus chinensis was competitively excluded by C. maculatus in all trials. Time series data analyses suggested that reproductive interference from C. chinensis was relatively more important in the trials involving polygamous C. chinensis than those involving monogamous C. chinensis, in accordance with the potentially higher reproductive interference capability of polygamous C. chinensis. However, the estimated signs and magnitudes of interspecific interactions were not fully consistent with this explanation, implying the evolution of not only reproductive interference but also other interaction mechanisms. Our study thus suggests multifaceted effects of sexually selected traits on interspecific competitive dynamics.     

Determination of Mercury and Methylmercury in Hair of the Czech Children’s Population

The developed method for mercury speciation analysis has been validated and used for the biomonitoring study of mercury species in human hair. Statistical evaluation proved the reliability of simplified determination of inorganic mercury (difference between total mercury and methylmercury). The results of the validation showed that the method is very well suitable for the determination of both species of mercury in hair for biomonitoring purposes. Non-exposed schoolchildren from three areas in the western and central part of the Czech Republic were chosen as the target group. Tenth of a microgram per gram of the total mercury were generally found in the analyzed hair; values higher than 1 μg g⁻¹ were detected only exceptionally. Comparable results were obtained for two western areas and differed significantly from those for the third area located in the central part of the Czech Republic. In the areas examined, the mean methylmercury contents amounted to 23–46% of the total mercury in the hair. The results confirm an assumption that exposure to mercury does not pose a significant risk to the population in the Czech Republic.     

Classification and evolutionary history of the single-strand annealing proteins,RecT, Redβ, ERF and RAD52

Background  

The DNA single-strand annealing proteins (SSAPs), such as RecT, Redβ, ERF and Rad52, function in RecA-dependent and RecA-independent DNA recombination pathways. Recently, they have been shown to form similar helical quaternary superstructures. However, despite the functional similarities between these diverse SSAPs, their actual evolutionary affinities are poorly understood.     

Going with the flow: a brief history of the study of the honeybee’s navigational ‘odometer’

Honeybees navigate to a food source using a sky-based compass to determine their travel direction, and an odometer to register how far they have travelled. The past 20 years have seen a renewed interest in understanding the nature of the odometer. Early work, pioneered by von Frisch and colleagues, hypothesized that travel distance is measured in terms of the energy that is consumed during the journey. More recent studies suggest that visual cues play a role as well. Specifically, bees appear to gauge travel distance by sensing the extent to which the image of the environment moves in the eye during the journey from the hive to the food source. Most of the evidence indicates that travel distance is measured during the outbound journey. Accumulation of odometric errors is restricted by resetting the odometer every time a prominent landmark is passed. When making detours around large obstacles, the odometer registers the total distance of the path that is flown to the destination, and not the “bee-line” distance. Finally, recent studies are revealing that bees can perform odometry in three dimensions.     

Population and formal genetics of the human C81(α-γ) polymorphism

Summary One hundred and ninety-six unrelated healthy individuals and 30 families with 75 offspring have been studied for the C81(-) polymorphism. The following allele frequencies were calculated: C81^*A=0.5536; C81^*B=0.4286; C81^*A1=0.0178. Observed and expected phenotype frequencies were in a good agreement according to the Hardy Weinberg law. No exceptions from the mode of inheritance were found. In family W the segregation of the rare allele C81^*A1 could be followed. Comparing the results of this study with previous data from Boston and Oslo, a combined technology including C8-dependent lysis and C8 structural variation is suggested for future investigations.     

Rattus exulans and the catastrophic disappearance of Hawai’i’s native lowland forest

Paleoenvironmental and archaeological investigations from the ’Ewa Plain of O’ahu provide insight into the problem of understanding lowland native forest loss in Hawai’i. Data from pollen analysis of a pond core record, avian paleontology, and archeology, document a precipitous decline of the native forest starting before Polynesian settlement on the ’Ewa Plain but after Polynesian colonization of O’ahu. It is hypothesized that rats, introduced by Polynesian colonizers, increased exponentially in the absence of significant predators or competitors, feeding on a largely endemic vegetation that had evolved in the absence of mammalian predators. Rats radiated ahead of human colonizers on O’ahu, eating their way through the vegetation, perhaps before the colonizers had encountered much of the pristine lowland forest into which the rats had radiated. This hypothesis is supported by several observations, including the almost complete absence of extinct or extirpated avian faunal remains in archaeological deposits, the present distribution of endemic vegetation in Hawai’i, rat ecology, population biology, and other evidence.

Distribution of actinomycetes,their antagonistic behaviour and the physico-chemical characteristics of the world’s largest tidal mangrove forest

We examined the relationship between distribution of actinomycetes and antagonistic behaviour with the physico-chemical characteristics of the Sundarbans, off the Bay of Bengal, India. Soil/sediment samples were collected from three regions: near to the sea, intertidal regions and mangrove forests. For the enumeration of actinomycetes, four treatments combining dilution with distilled or sea water with or without heating followed by plating onto starch-casein, glycerol-arginine and starch-nitrate media were done. Dilution with seawater, heating and plating onto starch-casein yielded maximum number of actinomycetes. The highest number of actinomycetes was isolated from an intertidal region having alluvial soil and the lowest from a site containing sandy sediments. Antimicrobial activity was dependent upon seawater. Antimicrobial score of an actinomycetes strain was calculated allotting maximum points to the isolate showing activity against all the test bacteria, next lower point to the isolate showing activity against one less the total and so on. The antagonistic potential (AP) of a sampling site was the ratio of total antimicrobial score of the isolates and their number. The high AP sites were influenced by tides, while the low AP sites were not. Pearson's correlation between soil chemical parameters and microbiological parameters revealed soil nitrogen as the key factor determining the antagonistic activity.