Auxotrophy and intrapopulation complementary in the ‘interactome’ of a cultivated freshwater model community

Microorganisms are usually studied either in highly complex natural communities or in isolation as monoclonal model populations that we manage to grow in the laboratory. Here, we uncover the biology of some of the most common and yet‐uncultured bacteria in freshwater environments using a mixed culture from Lake Grosse Fuchskuhle. From a single shotgun metagenome of a freshwater mixed culture of low complexity, we recovered four high‐quality metagenome‐assembled genomes (MAGs) for metabolic reconstruction. This analysis revealed the metabolic interconnectedness and niche partitioning of these naturally dominant bacteria. In particular, vitamin‐ and amino acid biosynthetic pathways were distributed unequally with a member of Crenarchaeota most likely being the sole producer of vitamin B12 in the mixed culture. Using coverage‐based partitioning of the genes recovered from a single MAG intrapopulation metabolic complementarity was revealed pointing to ‘social’ interactions for the common good of populations dominating freshwater plankton. As such, our MAGs highlight the power of mixed cultures to extract naturally occurring ‘interactomes’ and to overcome our inability to isolate and grow the microbes dominating in nature.     

Efficiently Tracking Selection in a Multiparental Population: The Case of Earliness in Wheat

Multiparental populations are innovative tools for fine mapping large numbers of loci. Here we explored the application of a wheat Multiparent Advanced Generation Inter-Cross (MAGIC) population for QTL mapping. This population was created by 12 generations of free recombination among 60 founder lines, following modification of the mating system from strict selfing to strict outcrossing using the ms1b nuclear male sterility gene. Available parents and a subset of 380 SSD lines of the resulting MAGIC population were phenotyped for earliness and genotyped with the 9K i-Select SNP array and additional markers in candidate genes controlling heading date. We demonstrated that 12 generations of strict outcrossing rapidly and drastically reduced linkage disequilibrium to very low levels even at short map distances and also greatly reduced the population structure exhibited among the parents. We developed a Bayesian method, based on allelic frequency, to estimate the contribution of each parent in the evolved population. To detect loci under selection and estimate selective pressure, we also developed a new method comparing shifts in allelic frequency between the initial and the evolved populations due to both selection and genetic drift with expectations under drift only. This evolutionary approach allowed us to identify 26 genomic areas under selection. Using association tests between flowering time and polymorphisms, 6 of these genomic areas appeared to carry flowering time QTL, 1 of which corresponds to Ppd-D1, a major gene involved in the photoperiod sensitivity. Frequency shifts at 4 of 6 areas were consistent with earlier flowering of the evolved population relative to the initial population. The use of this new outcrossing wheat population, mixing numerous initial parental lines through multiple generations of panmixia, is discussed in terms of power to detect genes under selection and association mapping. Furthermore we provide new statistical methods for use in future analyses of multiparental populations.     

Predicting fine‐scale distributions of peripheral aquatic species in headwater streams

Headwater species and peripheral populations that occupy habitat at the edge of a species range may hold an increased conservation value to managers due to their potential to maximize intraspecies diversity and species' adaptive capabilities in the context of rapid environmental change. The southern Appalachian Mountains are the southern extent of the geographic range of native Salvelinus fontinalis and naturalized Oncorhynchus mykiss and Salmo trutta in eastern North America. We predicted distributions of these peripheral, headwater wild trout populations at a fine scale to serve as a planning and management tool for resource managers to maximize resistance and resilience of these populations in the face of anthropogenic stressors. We developed correlative logistic regression models to predict occurrence of brook trout, rainbow trout, and brown trout for every interconfluence stream reach in the study area. A stream network was generated to capture a more consistent representation of headwater streams. Each of the final models had four significant metrics in common: stream order, fragmentation, precipitation, and land cover. Strahler stream order was found to be the most influential variable in two of the three final models and the second most influential variable in the other model. Greater than 70% presence accuracy was achieved for all three models. The underrepresentation of headwater streams in commonly used hydrography datasets is an important consideration that warrants close examination when forecasting headwater species distributions and range estimates. Additionally, it appears that a relative watershed position metric (e.g., stream order) is an important surrogate variable (even when elevation is included) for biotic interactions across the landscape in areas where headwater species distributions are influenced by topographical gradients.     

PHENOTYPIC DIFFERENTIATION AT SOUTHERN LIMIT BORDERS: THE CASE STUDY OF TWO FUCOID MACROALGAL SPECIES WITH DIFFERENT LIFE‐HISTORY TRAITS1

Marginal populations are often geographically isolated, smaller, and more fragmented than central populations and may frequently have to face suboptimal local environmental conditions. Persistence of these populations frequently involves the development of adaptive traits at phenotypic and genetic levels. We compared population structure and demographic variables in two fucoid macroalgal species contrasting in patterns of genetic diversity and phenotypic plasticity at their southern distribution limit with a more central location. Models were Ascophyllum nodosum (L.) Le Jol. (whose extreme longevity and generation overlap may buffer genetic loss by drift) and Fucus serratus L. (with low genetic diversity at southern margins). At edge locations, both species exhibited trends in life‐history traits compatible with population persistence but by using different mechanisms. Marginal populations of A. nodosum had higher reproductive output in spite of similar mortality rates at all life stages, making edge populations denser and with smaller individuals. In F. serratus, rather than demographic changes, marginal populations differed in habitat, occurring restricted to a narrower vertical habitat range. We conclude that persistence of both A. nodosum and F. serratus at the southern‐edge locations depends on different strategies. Marginal population persistence in A. nodosum relies on a differentiation in life‐history traits, whereas F. serratus, putatively poorer in evolvability potential, is restricted to a narrower vertical range at border locations. These results contribute to the general understanding of mechanisms that lead to population persistence at distributional limits and to predict population resilience under a scenario of environmental change.     

Variation in life history and demography of the American black bear

Variation in life history and demography across a species' range informs researchers about regional adaptations and affects whether managers can borrow information from other populations in decision-making. The American black bear (Ursus americanus) is a long-lived game species whose continued persistence depends on management of harvest and removal of habituated bears that come into conflict with humans. Understanding the demography of black bears guides efforts at management and conservation, yet detailed knowledge of many populations is typically lacking. I performed a hierarchical Bayesian meta-analysis of black bear demographic studies across the geographic range of the species to explore how vital rates vary across the range, what information they give us about population growth, and whether managers can justify borrowing information from other studies to inform management decisions. Cub, yearling, and adult survival and fecundity varied between eastern and western North America, whereas subadult survival did not show geographic structuring. Adult survival and fecundity appeared to trade off, with higher survival in the western portions of bears' range and higher fecundity in the east. Although adult survival had the highest elasticity, differences in reproduction drove differences in population growth rate. Mean population growth rate was higher in the east (0.99; 95% credible interval [CrI]: 0.96, 1.03) than the west (0.97; 95%CrI: 0.93, 1.01). Despite declining trends in the west, 34% of the distribution of population growth rate was >1, compared to 55% in the east. Further work needs to be done to address the cause of the apparent trade-off between adult survival and fecundity and explore how the estimated growth rates are likely to affect population status of black bears. Because population growth rates are close to 1 and small deviations could impact whether a population is considered increasing or decreasing, managers need to employ caution in borrowing vital rates from other populations. © 2011 The Wildlife Society.     

Dynamics of isolated <Emphasis Type="Italic">Saponaria bellidifolia</Emphasis> Sm. populations at northern range periphery

Four populations of Saponaria bellidifolia situated at the species’ northern range periphery (Apuseni Mountains, southeastern Carpathians) were monitored over a period of 5 years. They were chosen to represent different habitat types (rocky, fixed screes, open screes and grassy), disturbance regime (fire), and population sizes (categorized as large and small). The reproductive effort was quantified, and matrix models were used to describe the population dynamics and to assess population viability. Saponaria bellidifolia had very stable population dynamics in the harsh and stable abiotic conditions of the outcrops where populations occur. Habitat conditions exerted a notable influence on the species’ population reproductive performance, growth rate, and vital rates, whereas population size and climate did not have a clear-cut effect on the dynamics of the species. Saponaria bellidifolia maintains viable populations in the southeastern Carpathians, at its northern range periphery.     

Connections Between Benthic Populations and Local Strandings of the Southern Bull Kelp Durvillaea Antarctica Along the Continental Coast of Chile1

Floating seaweeds are important dispersal vectors in marine ecosystems. However, the relationship between benthic populations and stranded seaweeds has received little attention. After detachment, a fraction of floating specimens returns to the shore, resulting in strandings that fluctuate in space and time. It has been hypothesized that the availability of stranded seaweeds is related to their benthic abundance on adjacent coasts. Using the large fucoid Durvillaea antarctica, we tested whether stranded biomasses are higher at sites with dense adjacent benthic populations. Benthic abundance of D. antarctica along the continental coast of Chile was estimated using three approximations: (i) availability of potentially suitable habitat (PSH), (ii) categorical visual abundance estimates in the field, and (iii) abundance measurements in the intertidal zone. Higher PSH for D. antarctica was observed between 31° S–32° S and 40° S–42° S than between 33° S and 39° S. Lowest benthic biomasses were estimated for the northern latitudes (31° S–32° S). Regression models showed that the association between stranded biomass and PSH was highest when only the extent of rocky shore 10 km to the south of each beach was included, suggesting relatively short-distance dispersal and asymmetrical transport of floating kelps, which is further supported by low proportions of rafts with Lepas spp. (indicator of rafting). The results indicate that stranded biomasses are mostly subsidized by nearby benthic populations, which can partly explain the low genetic connectivity among populations in the study region. Future studies should also incorporate other local factors (e.g., winds, currents, wave-exposure) that influence stranding dynamics.     

Habitat preferences of the noisy miner (Manorina melanocephala) – a propensity for prime real estate?

This study investigated habitat characteristics that have been postulated to influence the occurrence of noisy miners (Manorina melanocephala Family Meliphagidae). It builds on an earlier study that identified corners along remnant edges as important predictors of the presence of noisy miners in large blocks of remnant vegetation (>300 ha). Six habitat characteristics were recorded at 39 corner sites within the box‐ironbark region of Victoria. We failed to detect any significant effect of the density of understorey vegetation on the likelihood of noisy miners occupying a site, but this might have been an artefact of prolonged drought conditions. The most powerful predictors of the presence of noisy miners at remnant corners were found to be soil type and the proportion of canopy trees at a site that were yellow gum (Eucalyptus leucoxylon), with noisy miners being associated with deeper, more fertile soils and higher proportions of yellow gums present. As yellow gum is a prolific and reliable nectar producer, the inherent productivity of a site might be more important in determining the attractiveness of a site to noisy miners than structural attributes like the presence or absence of an understorey. Noisy miners are sedentary colonial birds that occupy year‐round territories, often at high densities. Sites capable of supporting such high density occupation year‐round might be limited to the most productive sites within the landscape. This productivity hypothesis has potentially profound implications for other woodland avifauna, as noisy miners might be excluding other woodland birds from some of the most fertile components of the landscape; components that are already rare in the box‐ironbark region due preferential clearing for agriculture at the time of settlement.     

Distribution and coexistence of shrews in patchy landscapes: A field test of multiple hypotheses

Despite the important role of shrews (Soricomorpha: Soricidae) in the functioning of ecosystems, as predators and prey, the effects of habitat loss and fragmentation on this guild of mammals are still unclear. We studied the distribution of 5 species (the greater white toothed shrew Crocidura leucodon; the lesser white toothed shrew Crocidura suaveolens; the pigmy shrew Sorex minutus; the Appennine shrew Sorex samniticus and the Etruscan shrew Suncus etruscus) in a fragmented landscape in central Italy.Shrews were trapped with pitfall traps made from plastic water bottles, the number of traps increased with patch size. A total of 170 individuals, of 5 species of shrews were captured. Shrews were widely distributed in our study area, however patch occupancy was determined mainly by vegetation and geometrical characteristics of the patches. Our data supports the hypotheses that patterns of habitat selection and the dynamics of seasonal abundance (habitat and temporal partitioning between similarly sized species) reduce competitive pressure, thus allowing coexistence of shrews in relatively species-rich assemblages, for such small amounts of habitat. The most important outcome of our results is the crucial role played by vegetation structure in determining distribution patterns. These results strongly suggest that measurements of the vegetation structure of habitat patches should always be included as explanatory variables when studying the distribution of shrews in fragmented landscapes.     

Demography of Reintroduced Eastern Bluebirds and Brown-Headed Nuthatches

ABSTRACT Species reintroductions are used commonly as a tool for conservation, but rigorous, quantitative assessments of their outcome rarely occur. Such assessments are critical for determining success of the reintroduction and for identifying management actions needed to ensure persistence of reintroduced populations. We collected 9 years of demographic data on populations of brown-headed nuthatches (Sitta pusilla) and Eastern bluebirds (Sialia sialis) reintroduced via translocation into Long Pine Key, Everglades National Park, Florida, USA. Realized population growth of brown-headed nuthatches was positive in the first 3 years after cessation of translocations (λ₂₀₀₂ = 1.15, SE = 0.13; λ₂₀₀₃ = 1.28, SE = 0.12; λ₂₀₀₅ = 1.32, SE = 0.20) but became negative thereafter (λ₂₀₀₆ = 0.67, SE = 0.10; λ₂₀₀₇ = 0.77, SE = 0.13). Realized growth rate for the Eastern bluebird population did not vary among years and indicated either a stable or a slowly declining population (λ = 0.92, SE = 0.04). Reintroductions were a qualified success; they resulted in the re-establishment of populations of both species, but neither population grew to the extent expected and both remained at risk of extinction.