Effects of urbanization and urban stream restoration on the physical and biological structure of stream ecosystems

Streams, as low-lying points in the landscape, are strongly influenced by the stormwaters, pollutants, and warming that characterize catchment urbanization. River restoration projects are an increasingly popular method for mitigating urban insults. Despite the growing frequency and high expense of urban stream restoration projects, very few projects have been evaluated to determine whether they can successfully enhance habitat structure or support the stream biota characteristic of reference sites. We compared the physical and biological structure of four urban degraded, four urban restored, and four forested streams in the Piedmont region of North Carolina to quantify the ability of reach-scale stream restoration to restore physical and biological structure to urban streams and to examine the assumption that providing habitat is sufficient for biological recovery. To be successful at mitigating urban impacts, the habitat structure and biological communities found in restored streams should be more similar to forested reference sites than to their urban degraded counterparts. For every measured reach- and patch-scale attribute, we found that restored streams were indistinguishable from their degraded urban stream counterparts. Forested streams were shallower, had greater habitat complexity and median sediment size, and contained less-tolerant communities with higher sensitive taxa richness than streams in either urban category. Because heavy machinery is used to regrade and reconfigure restored channels, restored streams had less canopy cover than either forested or urban streams. Channel habitat complexity and watershed impervious surface cover (ISC) were the best predictors of sensitive taxa richness and biotic index at the reach and catchment scale, respectively. Macroinvertebrate communities in restored channels were compositionally similar to the communities in urban degraded channels, and both were dissimilar to communities in forested streams. The macroinvertebrate communities of both restored and urban degraded streams were correlated with environmental variables characteristic of degraded urban systems. Our study suggests that reach-scale restoration is not successfully mitigating for the factors causing physical and biological degradation.     

Provenance, life span, and phylogeny do not affect grass species' responses to nitrogen and phosphorus

Successful conservation management requires an understanding of how species respond to intervention. Native and exotic species may respond differently to management interventions due to differences arising directly from their origin (i.e., provenance) or indirectly due to biased representations of different life history types (e.g., annual vs. perennial life span) or phylogenetic lineages among provenance (i.e., native or exotic origin) groups. Thus, selection of a successful management regime requires knowledge of the life history and provenance-bias in the local flora and an understanding of the interplay between species characteristics across existing environmental gradients in the landscape. Here we tested whether provenance, phylogeny, and life span interact to determine species distributions along natural gradients of soil chemistry (e.g., soil nitrogen and phosphorus) in 10 upland prairie sites along a 600-km latitudinal transect running from southern Vancouver Island in British Columbia, Canada, to the Willamette Valley in Oregon, USA. We found that soil nitrate, phosphorus, and pH exerted strong control over community composition. However, species distributions along environmental gradients were unrelated to provenance, life span, or phylogenetic groupings. We then used a greenhouse experiment to more precisely measure the response of common grass species to nitrogen and phosphorus supply. As with the field data, species responses to nutrient additions did not vary as a function of provenance, life span, or phylogeny. Native and exotic species differed strongly in the relationship between greenhouse-measured tolerance of low nutrients and field abundance. Native species with the greatest ability to maintain biomass production at low nutrient supply rates were most abundant in field surveys, as predicted by resource competition theory. In contrast, there was no relationship between exotic-species biomass at low nutrient levels and field abundance. The implications of these findings for management of invasive species are substantial in that they overturn a general belief that reduction of nutrient supplies favors native species. The idiosyncratic nature of species response to nutrients in this study suggests that manipulation of nutrient supplies is unlikely to alter the overall balance between native and exotic species, although it may well be useful to control specific exotic species.     

Prenatal diagnosis of bilateral anophthalmia: Identifying de novo SOX2 variant

A 26 year old nulligravida presented at 24 weeks gestation for the second opinion of abnormal fetal profile and mid-face views on ultrasound at another institution. A detailed fetal anatomic ultrasound at our facility revealed the absence of fetal lens and globes bilaterally consistent with bilateral anophthalmia (HP: 0000528) without other anomalies. Karyotype and chromosomal microarray analysis were completed from amniocentesis sample. After these results, duo exome testing with paternal sequencing was completed from proband amniotic fluid sample and parental blood samples. A pathogenic variant in SOX2 (NM_003106.3: c.513C>G p.(Tyr171*Ter)) with heterozygous autosomal dominant inheritance resulted. On duo exome testing with paternal segregation analysis, the variant was found to be consistent with likely sporadic de novo inheritance. The SOX2 variant reported is consistent with the fetal phenotype in this case. While germline mosaicism could exist, this identified variant provided the family with a likely explanation for this proband's finding. This ultrasound and genetic testing allowed the family to make decisions related to planning in current and future pregnancies.     

Fetal hydrops caused by a novel pathogenic MECOM variant

We report a fetus with hydrops, congenital heart disease and bilateral radioulnar synostosis caused by a novel pathogenic MECOM variant. The female fetus was referred for post-mortem examination after fetal hydrops and intrauterine death was diagnosed at 20 weeks gestation. Post-mortem examination confirmed fetal hydrops, pallor, truncus arteriosus and bilateral radioulnar synostosis. Trio whole genome sequencing analysis detected a novel de novo heterozygous pathogenic loss-of-function variant in MECOM (NM_004991), associated with a diagnosis of Radioulnar Synostosis with Amegakaryocytic Thrombocytopenia 2 (RUSAT-2). RUSAT-2 is a variable condition associated postnatally with bone marrow failure, radioulnar synostosis and congenital anomalies. RUSAT-2 is not currently associated with a prenatal phenotype or fetal demise, and was not present on diagnostic NHS prenatal gene panels at time of diagnosis. This case highlights the diagnostic value of detailed phenotyping with post-mortem examination, and of using a broad sequencing approach.     

Tree recruitment in an empty forest

To assess how the decimation of large vertebrates by hunting alters recruitment processes in a tropical forest, we compared the sapling cohorts of two structurally and compositionally similar forests in the Rio Manu floodplain in southeastern Peru. Large vertebrates were severely depleted at one site, Boca Manu (BM), whereas the other, Cocha Cashu Biological Station (CC), supported an intact fauna. At both sites we sampled small (> or =1 m tall, <1 cm dbh) and large (> or =1 cm and <10 cm dbh) saplings in the central portion of 4-ha plots within which all trees > or =10 cm dbh were mapped and identified. This design ensured that all conspecific adults within at least 50 m (BM) or 55 m (CC) of any sapling would have known locations. We used the Janzen-Connell model to make five predictions about the sapling cohorts at BM with respect to CC: (1) reduced overall sapling recruitment, (2) increased recruitment of species dispersed by abiotic means, (3) altered relative abundances of species, (4) prominence of large-seeded species among those showing depressed recruitment, and (5) little or no tendency for saplings to cluster closer to adults at BM. Our results affirmed each of these predictions. Interpreted at face value, the evidence suggests that few species are demographically stable at BM and that up to 28% are increasing and 72% decreasing. Loss of dispersal function allows species dispersed abiotically and by small birds and mammals to substitute for those dispersed by large birds and mammals. Although we regard these conclusions as preliminary, over the long run, the observed type of directional change in tree composition is likely to result in biodiversity loss and negative feedbacks on both the animal and plant communities. Our results suggest that the best, and perhaps only, way to prevent compositional change and probable loss of diversity in tropical tree communities is to prohibit hunting.     

Terrestrial habitat selection and strong density-dependent mortality in recently metamorphosed amphibians

To predict the effects of terrestrial habitat change on amphibian populations, we need to know how amphibians respond to habitat heterogeneity, and whether habitat choice remains consistent throughout the life-history cycle. We conducted four experiments to evaluate how the spatial distribution of juvenile wood frogs, Rana sylvatica (including both overall abundance and localized density), was influenced by habitat choice and habitat structure, and how this relationship changed with spatial scale and behavioral phase. The four experiments included (1) habitat manipulation on replicated 10-ha landscapes surrounding breeding pools; (2) short-term experiments with individual frogs emigrating through a manipulated landscape of 1 m wide hexagonal patches; and habitat manipulations in (3) small (4-m2); and (4) large (100-m2) enclosures with multiple individuals to compare behavior both during and following emigration. The spatial distribution of juvenile wood frogs following emigration resulted from differences in the scale at which juvenile amphibians responded to habitat heterogeneity during active vs. settled behavioral phases. During emigration, juvenile wood frogs responded to coarse-scale variation in habitat (selection between 2.2-ha forest treatments) but not to fine-scale variation. After settling, however, animals showed habitat selection at much smaller scales (2-4 m2). This resulted in high densities of animals in small patches of suitable habitat where they experienced rapid mortality. No evidence of density-dependent habitat selection was seen, with juveniles typically choosing to remain at extremely high densities in high-quality habitat, rather than occupying low-quality habitat. These experiments demonstrate how prediction of the terrestrial distribution of juvenile amphibians requires understanding of the complex behavioral responses to habitat heterogeneity. Understanding these patterns is important, given that human alterations to amphibian habitats may generate extremely high densities of animals, resulting in high density-dependent mortality.     

Determine the most influencing stressors and the most susceptible resources for environmental integrated assessment

The paper presents a method to determine the most influencing stressors and the most susceptible resources for complex assessment problems involving multiple stressors impacting multiple resources over a region. The method is based on the concept of limiting priorities in a square matrix which capture the transmission of influence along all paths between stressors and resources in the matrix. The proposed method allows the relationship between stressors and resources to be looked at in both univariate and multivariate fashion, taking into account the interactions among the variables. Hypothetical and case study examples are given for illustration purpose. It shows that the proposed method is suitable for the determination of the most important stressors and the most susceptible resources, a common (but often uneasy) task in integrated environmental assessment.     

How experienced individuals contribute to an improvement in collective performance in ants

Certain groups of organisms are capable of improving their collective performance with experience. In a recent study, we demonstrated that, over successive emigrations, colonies of the ant Temnothorax albipennis are able to improve their collective performance by reducing the time taken to complete an emigration (Langridge et al., Behav Ecol Sociobiol 56:523–529, 2004). In this paper, by recording the performance of individually marked workers during repeated emigrations, we were able to analyse some of the ways in which time gains are achieved. We found that: (1) those transporters that also transported in the preceding emigration began to transport earlier in the current emigration and, in the majority of emigrations, transported more items than those transporters that had not transported in the preceding emigration; (2) the time that elapsed before the first item was transported into the new nest reduced over successive emigrations, and this first item was, in the majority of emigrations, carried by a transporter that had also transported in the preceding emigration; (3) the number of adults that were transported reduced over successive emigrations. Our results strongly suggest that the behaviour of transporters that also transported in a preceding emigration may be modified as a result of their experience and that, consequently, their efforts in the next emigration make a major contribution to the improved performance of the colony as a whole.     

Effects of timber harvesting on pond-breeding amphibian persistence: testing the evacuation hypothesis.

Numerous studies have documented the decline of amphibians following timber harvest. However, direct evidence concerning the mechanisms of population decline is lacking and hinders attempts to develop conservation or recovery plans and solutions for forest species. We summarized the mechanisms by which abundance of amphibians may initially decline following timber harvest into three testable hypotheses: (1) mortality, (2) retreat, and (3) evacuation. Here, we tested the evacuation hypothesis within a large-scale, replicated experiment. We used drift fences with pitfall traps to capture pond-breeding amphibians moving out of experimental clearcut quadrants and into control quadrants at four replicate arrays located within the Daniel Boone Conservation Area on the upper Ozark Plateau in Warren County, Missouri, USA. During the preharvest year of 2004, only 51.6% of the 312 individuals captured were moving out of pre-clearcut quadrants, and movement did not differ from random. In contrast, during both postharvest years of 2005 and 2006, the number of captures along the quadrant edge increased, and a higher proportion of individuals (59.9% and 56.6%, respectively, by year) were moving out of clearcut quadrants than entering. Salamanders moved out of clearcuts in large percentages (Ambystoma annulatum, 78.2% in 2005, 78.2% in 2006; A. maculatum, 64.0% in 2005, 57.1% in 2006). Frogs and toads also moved out of clearcut quadrants, but in lower percentages (Bufo americanus, 59.6% in 2005, 53.3% in 2006; Rana clamitans, 52.7% in 2006). Salamanders moved out of clearcuts with low-wood treatments more than out of clearcuts with high-wood treatments. Movement of salamanders out of clearcuts was independent of sex. Estimated movement out of clearcuts represented between 8.7% and 35.0% of the total breeding adults captured for two species of salamanders. Although we recognize that some portion of the amphibian population may retreat underground for short periods and others may not survive the effects of timber harvest, these data are the first direct evidence showing that individuals are capable of leaving clearcuts and shifting habitat use.