The hydrogeomorphic approach to functional assessment of riparian wetlands: evaluating impacts and mitigation on river floodplains in the U.S.A.

1. The ’hydrogeomorphic‘ approach to functional assessment of wetlands (HGM) was developed as a synthetic mechanism for compensatory mitigation of wetlands lost or damaged by human activities. The HGM approach is based on: (a) classification of wetlands by geomorphic origin and hydrographic regime (b) assessment models that associate variables as indicators of function, and (c) comparison to reference wetlands that represent the range of conditions that may be expected in a particular region. In this paper, we apply HGM to riparian wetlands of alluvial rivers. 2. In the HGM classification, riverine wetlands are characterized by formative fluvial processes that occur mainly on flood plains. The dominant water sources are overbank flooding from the channel or subsurface hyporheic flows. Examples of riverine wetlands in the U.S.A. are: bottomland hardwood forests that typify the low gradient, fine texture substratum of the south-eastern coastal plain and the alluvial flood plains that typify the high gradient, coarse texture substratum of western montane rivers. 3. Assessment (logic) models for each of fourteen alluvial wetland functions are described. Each model is a composite of two to seven wetland variables that are independently scored in relation to a reference data set developed for alluvial rivers in the western U.S.A. Scores are summarized by a ’functional capacity index‘ (FCI), which is multiplied by the area of the project site to produce a dimensionless ’functional capacity unit‘ (FCU). When HGM is properly used, compensatory mitigation is based on the FCUs lost that must be returned to the riverine landscape under statutory authority. 4. The HGM approach also provides a framework for long-term monitoring of mitigation success or failure and, if failing, a focus on topical remediation. 5. We conclude that HGM is a robust and easy method for protecting riparian wetlands, which are critically important components of alluvial river landscapes.     

Responses of litter arthropods to major natural or artificial ecological disturbances in mountain ash forest

Pitfall trapping was used in commercial Mountain Ash (Eucalyptus regnans) regrowth forest to study the effects on epigeal arthropods of high-intensity wildfire plus salvage logging, and of harvesting by clearfelling plus slash burning, followed by fire-induced natural or artificially established regeneration respectively. The study, the first of its kind in the Victorian Central Highlands, 60 km east of Melbourne, was based on 146 922 specimens of 30 ordinal or lower level taxa collected over a 3-year period. The abrupt replacement of the ecologically complex regrowth forest by ecologically much simpler even-aged regeneration caused appreciable instability among the litter-frequenting arthropods. An immediate decline in diversity occurred due to short-term boosts in activity of some common ‘major’ taxa (notably a species of seed-harvesting ant) and the suppression of other taxa. A broad mix of functionally diverse taxa reappeared within two years of regeneration, and all but three rarely trapped ‘minor’ taxa present in undisturbed 43–46 year old regrowth (‘control’) forest had returned within 5 years. Epigeal arthropods therefore appeared to be affected only over a short period relative to the nominal 80–150 year rotation of the E. regnans ecosystem. Research is needed at the species level to achieve a more precise assessment of arthropod responses to major ecological disturbances.     

Dietary constraints of phytosaurian reptiles revealed by dental microwear textural analysis

Phytosaurs are a group of large, semi‐aquatic archosaurian reptiles from the Middle–Late Triassic. They have often been interpreted as carnivorous or piscivorous due to their large size, morphological similarity to extant crocodilians and preservation in fluvial, lacustrine and coastal deposits. However, these dietary hypotheses are difficult to test, meaning that phytosaur ecologies and their roles in Triassic food webs remain incompletely constrained. Here, we apply dental microwear textural analysis to the three‐dimensional sub‐micrometre scale tooth surface textures that form during food consumption to provide the first quantitative dietary constraints for five species of phytosaur. We furthermore explore the impacts of tooth position and cranial robustness on phytosaur microwear textures. We find subtle systematic texture differences between teeth from different positions along phytosaur tooth rows, which we interpret to be the result of different loading pressures experienced during food consumption, rather than functional partitioning of food processing along tooth rows. We find rougher microwear textures in morphologically robust taxa. This may be the result of seizing and processing larger prey items compared to those captured by gracile taxa, rather than dietary differences per se. We reveal relatively low dietary diversity between our study phytosaurs and that individual species show a lack of dietary specialization. Species are predominantly carnivorous and/or piscivorous, with two taxa exhibiting slight preferences for ‘harder’ invertebrates. Our results provide strong evidence for higher degrees of ecological convergence between phytosaurs and extant crocodilians than previously appreciated, furthering our understanding of the functioning and evolution of Triassic ecosystems.     

To speciate,or not to speciate? Resource heterogeneity,the subjectivity of similarity,and the macroevolutionary consequences of niche‐width shifts in plant‐feeding insects

Coevolutionary studies on plants and plant‐feeding insects have significantly improved our understanding of the role of niche shifts in the generation of new species. Evolving plant lineages essentially constitute moving islands and archipelagoes in resource space, and host shifts by insects are usually preceded by colonizations of novel resources. Critical to hypotheses concerning ecological speciation is what happens immediately before and after colonization attempts: if an available plant is too similar to the current host(s), it simply will be incorporated into the existing diet, but if it is too different, it will not be colonized in the first place. It thus seems that the probability of speciation is maximized when alternative hosts are at an ‘intermediate’ distance in resource space. In this review, I wish to highlight the possibility that resource similarity and, thus, the definition of ‘intermediate’, are subjective concepts that depend on the herbivore lineage's tolerance to dietary variation. This subjectivity of similarity means that changes in tolerance can either decrease or increase speciation probabilities depending on the distribution of plants in resource space: insect lineages with narrow tolerances are likely to speciate by ‘island‐hopping’ on young, species‐rich plant groups, whereas more generalized lineages could speciate by shifting among resource archipelagoes formed by higher plant taxa. Repeated and convergent origins of traits known to broaden or to restrict host‐plant use in multiple different insect groups provide opportunities for studying how tolerance and resource heterogeneity may interact to determine speciation rates.     

Ericaceous plant–fungus network in a harsh alpine–subalpine environment

In terrestrial ecosystems, plant species and diverse root‐associated fungi form complex networks of host–symbiont associations. Recent studies have revealed that structures of those below‐ground plant–fungus networks differ between arbuscular mycorrhizal and ectomycorrhizal symbioses. Nonetheless, we still remain ignorant of how ericaceous plant species, which dominate arctic and alpine tundra, constitute networks with their root‐associated fungi. Based on a high‐throughput DNA sequencing data set, we characterized the statistical properties of a network involving 16 ericaceous plant species and more than 500 fungal taxa in the alpine–subalpine region of Mt. Tateyama, central Japan. While all the 16 ericaceous species were associated mainly with fungi in the order Helotiales, they varied remarkably in association with fungi in other orders such as Sebacinales, Atheliales, Agaricales, Russulales and Thelephorales. The ericaceous plant–fungus network was characterized by high symbiont/host preferences. Moreover, the network had a characteristic structure called ‘anti‐nestedness’, which has been previously reported in ectomycorrhizal plant–fungus networks. The results lead to the hypothesis that ericaceous plants in harsh environments can host unexpectedly diverse root‐associated fungal taxa, constituting networks whose structures are similar to those of previously reported ectomycorrhizal networks but not to those of arbuscular mycorrhizal ones.     

Effects of iodine deficiency on mental and psychomotor abilities

The allometric relationships between canine base area, first molar and summed molar crown area, and the glabella–opisthocranion distance, and the direct allometric relationships between canine and molar size have been established in five primate taxa. Separate sex and combined sex ‘intraspecific’, and ‘interspecific’ regression and ‘best fit’ allometry coefficients were computed. This analysis showed that for any increase in glabella–opisthocranion length, the rate of increase in canine size exceeds the rate of increase in molar area, and ‘best fit’ solutions indicate that canine base area is positively allometric when related directly to molar crown area. These results were compared with data available for the ‘gracile’ australopithecine, A. africanus, and two ‘robust’ australopithecine taxa, A. boisei and A. robustus. The differences in canine and molar size which occur between the ‘gracile’ taxon and the two ‘robust’ taxa do not correspond to any of the trends in the comparative allometric models. Data on glabella–opisthocranion length for the fossils, meagre though they are, show that while the proportional increase in molar crown area between the taxa corresponds to comparative allometry models, the reduced canine size in the ‘robust’ taxa is against comparative allometric trends. These results indicate that, at least in terms of canine/molar proportions, the differences between the ‘gracile’ and ‘robust’ australopithecines are not merely allometric and may indicate significant dietary or behavioural differences.     

Dominant network interactions are not correlated with resource availability: a case study using mistletoe host interactions

Network theory in ecology has been central to understanding species co‐occurrence patterns, specialization and community stability. However, network theory has traditionally focused on the ‘higher’ trophic level where exploitation of network ‘partners’ (i.e. individual interactions in response to resource availability) have remained underappreciated. In this study we tested how clumping and host availability influenced mistletoe–host interactions in a semi‐arid woodland, central Australia. We used a hierarchical approach that evaluated individual interactions by modifying the traditional randomization technique to simulate clumping and host exploitation. Using published literature we then compared our results with mistletoes from other genera. We found that mistletoes clump on fewer trees than predicted, even though interaction strength was no different from random expectations, and we found no evidence that common trees were heavily infected as predicted by the host availability hypothesis. The rate of host exploitation (measured as the proportion of trees infected) in semi‐arid Australia is similar to that for mistletoe genera in other parts of the world. We hypothesize that specific host trees act as a focal point for infection that facilitates the spread and overall population size of mistletoes. Overall our results indicate that resources, such as the number of trees in a mistletoe network, are less important than clumping of individual plants. We suggest that exploitation of available resources may play a similar role in other networks that extend beyond antagonistic relationships such as parasite or herbivore interactions.     

Minority species influences microbiota formation: the role of Bifidobacterium with extracellular glycosidases in bifidus flora formation in breastfed infant guts

The human body houses a variety of microbial ecosystems, such as the microbiotas on the skin, in the oral cavity and in the digestive tract. The gut microbiota is one such ecosystem that contains trillions of bacteria, and it is well established that it can significantly influence host health and diseases. With the advancement in bioinformatics tools, numerous comparative studies based on 16S ribosomal RNA (rRNA) gene sequences, metabolomics, pathological and epidemical analyses have revealed the correlative relationship between the abundance of certain taxa and disease states or amount of certain causative bioactive compounds. However, the 16S rRNA-based taxonomic analyses using next-generation sequencing (NGS) technology essentially detect only the majority species. Although the entire gut microbiome consists of 10¹³ microbial cells, NGS read counts are given in multiples of 10⁶, making it difficult to determine the diversity of the entire microbiota. Some recent studies have reported instances where certain minority species play a critical role in creating locally stable conditions for other species by stabilizing the fundamental microbiota, despite their low abundance. These minority species act as ‘keystone species’, which is a species whose effect on the community is disproportionately large compared to its relative abundance. One of the attributes of keystone species within the gut microbiota is its extensive enzymatic capacity for substrates that are rare or difficult to degrade for other species, such as dietary fibres or host-derived complex glycans, like human milk oligosaccharides (HMOs). In this paper, we propose that more emphasis should be placed on minority taxa and their possible role as keystone species in gut microbiota studies by referring to our recent studies on HMO-mediated microbiota formation in the infant gut.     

The influence of host and non‐host companion plants on the behaviour of pest insects in field crops

Companion plants grown as ‘trap crops’ or ‘intercrops’ can be used to reduce insect infestations in field crops. The ways in which such reductions are achieved are being described currently using either a chemical approach, based on the ‘push‐pull strategy’, or a biological approach, based on the ‘appropriate/inappropriate landing theory’. The chemical approach suggests that insect numbers are reduced by chemicals from the intercrop ‘repelling’ insects from the main crop, and by chemicals from the trap‐crop ‘attracting’ insects away from the main crop. This approach is based on the assumptions that (1) plants release detectable amounts of volatile chemicals, and (2) insects ‘respond’ while still some distance away from the emitting plant. We discuss whether the above assumptions can be justified using the ‘appropriate/inappropriate landing theory’. Our tenet is that specialist insects respond only to the volatile chemicals released by their host plants and that these are released in such small quantities that, even with a heightened response to such chemicals, specialist insects can only detect them when a few metres from the emitting plant. We can find no robust evidence in the literature that plant chemicals ‘attract’ insects from more than 5 m and believe that ‘trap crops’ function simply as ‘interception barriers’. We can also find no evidence that insects are ‘repelled’ from landing on non‐host plants. Instead, we believe that ‘intercrops’ disrupt host‐plant finding by providing insects with a choice of host (appropriate) and non‐host (inappropriate) plant leaves on which to land, as our research has shown that, for intercropping to be effective, insects must land on the non‐host plants. Work is needed to determine whether non‐host plants are repellent (chemical approach) or ‘non‐stimulating’ (biological approach) to insects.     

The effect of differences in methodology among some recent applications of shearing quotients

A shearing quotient (SQ) is a way of quantitatively representing the Phase I shearing edges on a molar tooth. Ordinary or phylogenetic least squares regression is fit to data on log molar length (independent variable) and log sum of measured shearing crests (dependent variable). The derived linear equation is used to generate an ‘expected’ shearing crest length from molar length of included individuals or taxa. Following conversion of all variables to real space, the expected value is subtracted from the observed value for each individual or taxon. The result is then divided by the expected value and multiplied by 100. SQs have long been the metric of choice for assessing dietary adaptations in fossil primates. Not all studies using SQ have used the same tooth position or crests, nor have all computed regression equations using the same approach. Here we focus on re‐analyzing the data of one recent study to investigate the magnitude of effects of variation in 1) shearing crest inclusion, and 2) details of the regression setup. We assess the significance of these effects by the degree to which they improve or degrade the association between computed SQs and diet categories. Though altering regression parameters for SQ calculation has a visible effect on plots, numerous iterations of statistical analyses vary surprisingly little in the success of the resulting variables for assigning taxa to dietary preference. This is promising for the comparability of patterns (if not casewise values) in SQ between studies. We suggest that differences in apparent dietary fidelity of recent studies are attributable principally to tooth position examined. Am J Phys Anthropol 156:166–178, 2015 © 2014 Wiley Periodicals, Inc.     

Cryptic diversity and patterns of host specificity in trematode flatworms

The widespread utilization of molecular markers has revealed that a broad spectrum of taxa contain sets of morphologically cryptic, but genetically distinct lineages ( Bickford et al. 2007 ). The identification of cryptic taxa is important as an accurate appreciation of diversity is crucial for a proper understanding of evolutionary and ecological processes. An example is the study of host specificity in parasitic taxa, where an apparent generalist may be found to contain a complex of several more specific species ( Smith et al. 2006 ). Host specificity is a key life history trait that varies greatly among parasites ( Poulin & Keeney 2007 ). While some can exploit a wide range of hosts, others are confined to just a single species. Access to additional hosts increases the resources available to a parasite. However, physiological or ecological constraints can restrict the extension of host range. Furthermore, there may be a trade‐off between relaxed specificity and performance: generalism can decrease a parasites ability to adapt to each individual host species, and increase exposure to competition from other parasites ( Poulin 1998 ). Despite the central role that host specificity plays in parasite life history, relatively little is known about how host range is determined in natural systems, and data from field studies are required to evaluate among competing ideas. In this issue, an exciting paper by Locke et al. (2010) makes a valuable contribution toward the understanding of host specificity in an important group of trematode flatworms. Using molecular methods, Locke et al. reveal an almost four‐fold increase in the appreciated diversity of their focal group. In combination with a large and elegant sampling design this allows them to accurately assess host specificity for each taxon, and thus draw key insights into the factors that control host range in a dominant parasite group.     

Rewilding the tropics,and other conservation translocations strategies in the tropical Asia‐Pacific region

Alarm over the prospects for survival of species in a rapidly changing world has encouraged discussion of translocation conservation strategies that move beyond the focus of ‘at‐risk’ species. These approaches consider larger spatial and temporal scales than customary, with the aim of recreating functioning ecosystems through a combination of large‐scale ecological restoration and species introductions. The term ‘rewilding’ has come to apply to this large‐scale ecosystem restoration program. While reintroductions of species within their historical ranges have become standard conservation tools, introductions within known paleontological ranges—but outside historical ranges—are more controversial, as is the use of taxon substitutions for extinct species. Here, we consider possible conservation translocations for nine large‐bodied taxa in tropical Asia‐Pacific. We consider the entire spectrum of conservation translocation strategies as defined by the IUCN in addition to rewilding. The taxa considered are spread across diverse taxonomic and ecological spectra and all are listed as ‘endangered’ or ‘critically endangered’ by the IUCN in our region of study. They all have a written and fossil record that is sufficient to assess past changes in range, as well as ecological and environmental preferences, and the reasons for their decline, and they have all suffered massive range restrictions since the late Pleistocene. General principles, problems, and benefits of translocation strategies are reviewed as case studies. These allowed us to develop a conservation translocation matrix, with taxa scored for risk, benefit, and feasibility. Comparisons between taxa across this matrix indicated that orangutans, tapirs, Tasmanian devils, and perhaps tortoises are the most viable taxa for translocations. However, overall the case studies revealed a need for more data and research for all taxa, and their ecological and environmental needs. Rewilding the Asian‐Pacific tropics remains a controversial conservation strategy, and would be difficult in what is largely a highly fragmented area geographically.     

Endophyte microbiome diversity in micropropagated Atriplex canescens and Atriplex torreyi var griffithsii

Microbial diversity associated with micropropagated Atriplex species was assessed using microscopy, isolate culturing, and sequencing. Light, electron, and confocal microscopy revealed microbial cells in aseptically regenerated leaves and roots. Clone libraries and tag-encoded FLX amplicon pyrosequencing (TEFAP) analysis amplified sequences from callus homologous to diverse fungal and bacterial taxa. Culturing isolated some seed borne endophyte taxa which could be readily propagated apart from the host. Microbial cells were observed within biofilm-like residues associated with plant cell surfaces and intercellular spaces. Various universal primers amplified both plant and microbial sequences, with different primers revealing different patterns of fungal diversity. Bacterial and fungal TEFAP followed by alignment with sequences from curated databases revealed 7 bacterial and 17 ascomycete taxa in A. canescens, and 5 bacterial taxa in A. torreyi. Additional diversity was observed among isolates and clone libraries. Micropropagated Atriplex retains a complex, intimately associated microbiome which includes diverse strains well poised to interact in manners that influence host physiology. Microbiome analysis was facilitated by high throughput sequencing methods, but primer biases continue to limit recovery of diverse sequences from even moderately complex communities.     

High resource overlap and small dietary differences are widespread in food-limited warbler (Parulidae) communities

Although both interspecific competition and coexistence mechanisms are central to ecological and evolutionary theory, past empirical studies have generally focused on simple (two-species) communities over short time periods. Experimental tests of these species interactions are challenging in complex study systems. Moreover, several studies of ‘imperfect generalists’, consistent with Liem's Paradox, raise questions about the ability of evolved species differences to partition niche space effectively when resources vary considerably across the annual cycle. Here we used a recently developed theoretical framework to combine past research on population-level processes with observational data on resource use to test for ongoing interspecific competition and understand the nature of resource overlap. We compared species diet overlaps and differences in several distinctive communities centred on a focal species, the American Redstart Setophaga ruticilla replicated both spatially and seasonally, in combination with documentation of population regulation to assess the ability of similar species to partition dietary niche space and limit interspecific competition. Our results document high dietary overlap in most of the communities studied, with only subtle differentiation consistent with known species differences in foraging behaviour and morphology. These findings are largely consistent with species foraging as imperfect generalists. However, in contrast to past studies, the high diet overlaps observed here during times of inferred resource scarcity were driven by low-value prey taxa (e.g. small ants) and did not involve truly ‘private’ resources. All of these factors increase the potential negative impacts of interspecific competition, and limit the ability of these birds to avoid competition if food availability deteriorates further than observed in our study, either seasonally or at longer intervals.     

Dietary classification of extant kangaroos and their relatives (Marsupialia: Macropodoidea)

Kangaroos and kin (superfamily Macropodoidea) are the principal endemic herbivores of Australia and the most diverse radiation of marsupial herbivores ever to have evolved. As is typical of other herbivore groups (e.g. bovids), dietary niches span fruit, fungi, dicot leaves and monocot grasses in both specialists and generalists, but to date dietary classification has been largely ad hoc and poorly tied to actual dietary ecological data. Here we provide a simple dietary classification of the Macropodoidea based on an extensive literature survey. Intake of four major dietary items – grasses, dicot leaves, fruits and seeds, and fungi – was assessed using proportional intake for 19 species and categorical (ranked intake) data for 37 species. Statistical comparisons with cluster and principal components analyses aligned species into four dietary groups. Members of the first group have diets that primarily consist of fungi and fruits. Relative proportions of grasses to dicot leaves separate the remaining species into browser (more than 70% dicots), grazer (more than 70% grasses) and mixed feeder groups. Comparison of our diet‐based classification with a prevailing scheme based on dental morphology suggests that most species with what has traditionally been viewed as a ‘browser‐grade dentition’ are actually mixed feeders. This suggests that either morphology and diet are not tightly linked or that morphological differences between the dentitions of browsers and mixed feeders are subtle and have been overlooked. A positive correlation was found between body mass and average proportional intake of grass in the diet of macropodoids. This parallels the situation found in bovids, as well as the percentage cut‐off between dietary groups. These trends suggest that some underlying ecophysiological constraints may influence food choice in mammalian herbivores providing useful pointers to the diets of extinct taxa.