Macroecology and people

A macroecological perspective has become recognised as an important component of ecological studies, serving particularly to crystallise the notion that processes operating at large spatial (geographic) and temporal scales often play important roles in shaping species assemblages and communities at more local scales. However, within the field, consideration has been surprisingly lacking of the influence of humans in shaping macroecological patterns, the determinants of those patterns, or their consequences for local assemblages and communities. Here I briefly review the reasons why this might be so, and the possible interactions between macroecology and people, and suggest some simple steps for exploring this issue.     

Insect biodiversity meets ecosystem function: differential effects of habitat and insects on carrion decomposition

1. Ecological processes are maintained in different environments by different species performing similar functional roles. Yet, little is known about the role of the environment in shaping insect biodiversity associated with a process that is ephemeral and patchy. 2. In this study, the mass loss of carrion in response to contrasting habitat types (grassland or tree) was quantified experimentally, as well as the presence, diversity and composition of insect assemblages. Differences in insect assemblages between these two habitats were also examined. 3. It was found that the presence of insects led to a doubling in mass loss, but that grassland or tree habitat type had no effect on this process. By contrast, habitat type had a significant effect on the composition of generalist ant and beetle assemblages, but not on specialist fly assemblages. Given the colonisation of insects, carrion mass loss was negatively associated with increasing evenness of fly assemblages and increasing ant abundance. Variation in fly assemblage composition was also found to correlate with variation in carrion mass loss. 4. This study highlights the major role of habitat type in shaping the composition of generalist insects at carrion, but the minor role in affecting specialist and highly vagile insects. This complements the authors' findings that insect colonisation of carrion was critical to accelerated mass loss, and that fly assemblages were responsible for variation in this process, regardless of habitat. The present study sheds new light on the contribution of insect biodiversity to decomposition in variable environments, with consequences for carrion food webs and nutrient cycling.     

Ecomorphological diversity of freshwater fishes as a tool for conservation priority setting: a case study from a Balkan hotspot

Biodiversity studies commonly focus on taxonomic diversity measures such as species richness and abundance. However, alternative measures based on ecomorphological traits are also critical for unveiling the processes shaping biodiversity and community assembly along environmental gradients. Our study presents the first analysis of habitat-trait-community structure in a Balkan biodiversity hotspot (Louros river, NW Greece), through the investigation of the relationships among freshwater fish assemblages’ composition, morphological traits and habitat features. In order to provide a hierarchical classification of species’ priority to protection measures, we highlight the most ecomorphologically distinct species using originality analysis. Our results suggest that the longitudinal changes of habitat variables (water temperature, depth, substrate, altitude) drive the local fish assemblages’ structure highlighting the upstream-downstream gradient. We also present evidence for environmental filtering, establishing fish assemblages according to their ecomorphological traits. The calculation of the seven available indices of ecomorphological originality indicates that Valencia letourneuxi and Cobitis hellenica, which are endemic to Louros and threatened with extinction, exhibited the highest distinctiveness; thus their protection is of great importance. The methodological approach followed and the patterns described herein can contribute further to the application of community ecology theory to conservation, highlighting the need to use ecomorphological traits as a useful ‘tool’.     

Host identity and phylogeny shape the foliar endophytic fungal assemblages of Ficus

Foliar endophytic fungi (FEF) are diverse and ubiquitously associated with photosynthetic land plants. However, processes shaping FEF assemblages remain poorly understood. Previous studies have indicated that host identity and host habitat are contributing factors, but these factors are often difficult to disentangle. In this study, we studied FEF assemblages from plants grown in a botanical garden, enabling us to minimize the variation in abiotic environmental conditions and fungal dispersal capacity. FEF assemblages from 46 Ficus species were sequenced using next‐generation methods, and the results indicated that closely related host species had clearly differentiated FEF assemblages. Furthermore, host phylogenetic proximity was significantly correlated with the similarity of their FEF assemblages. In the canonical correspondence analysis, eleven leaf traits explained 32.9% of the total variation in FEF assemblages, whereas six traits (specific leaf area, leaf N content, leaf pH, toughness, latex alkaloid content, and latex volume per leaf area) were significant in the first two dimensions of ordination space. In the multiple regression on distance matrix analysis, 21.0% of the total variance in FEF assemblage was explained by both host phylogeny and leaf traits while phylogeny alone explained 7.9% of the variance. Thus, our findings suggest that both evolutionary and ecological processes are involved in shaping FEF assemblages.     

Evidence of variability in the structure and recruitment of rhizospheric and endophytic bacterial communities associated with arable sweet sorghum (Sorghum bicolor (L) Moench)

Background and aims

Sorghum is the second most cultivated crop in Africa and is a staple food source in many African communities. Exploiting the associated plant growth-promoting bacteria (PGPB) has potential as an agricultural biotechnology strategy to enhance sorghum growth, yield and nutritional properties. Therefore this study aimed to evaluate factors that shape bacterial communities associated with sorghum farmed in South Africa, and to detect bacteria consistently associated with sorghum which may impart PGP activities.

Methods

Terminal-Restriction Fragment Length Polymorphism (T-RFLP) was used to assess factors that potentially shape rhizospheric (rhizosphere and rhizoplane) and endophytic (root, shoot, stem) bacterial communities associated with South African sorghum, and together with Denaturing Gradient Gel Electrophoresis (DGGE) to identify consistently sorghum-associated bacterial taxa.

Results

The sorghum rhizospheric communities were less variable than the endophytic ones. Geographical location was the main driver in describing bacterial community assemblages found in rhizospheric sorghum-linked niches, with total NO₃-N, NH₄-N, nitrogen, carbon, pH and, to a lesser extent, clay content identified as the main abiotic factors shaping sorghum-associated soil communities. Endophytic communities presented rather stochastic assemblages, with pH being the main variable explaining their structures. Despite community variations, specific bacterial taxa were consistently detected in sorghum-created rhizospheric and endophytic environments, irrespective of environmental factor effects.

Conclusions

Soil structure and composition, which are influenced by agricultural practices, played major roles in shaping sorghum-associated edaphic bacterial communities. In contrast, endophytic bacterial communities displayed more variation. Nevertheless, potentially agronomically relevant (cyano)bacterial taxa constantly associated with sorghum were identified which is suggestive of their deterministic recruitment.     

Endophytic fungal community succession in reproductive organs of two olive tree cultivars with contrasting anthracnose susceptibilities

The factors shaping endophytic fungal assemblages in reproductive organs have been less evaluated than in vegetative organs. Here, the temporal dynamics of fungal endophytes in inflorescences and fruits of olive tree cultivars with contrasting anthracnose susceptibilities was assessed, starting before flowers open until fruit ripening. Fungal diversity assessed by rRNA sequencing of cultivable isolates revealed a higher richness and abundance of endophytes in inflorescences than in fruits. Endophytes from Sordariomycetes were dominant in inflorescences, while in fruits they were from Dothideomycetes. The overall assemblages of inflorescences and fruits were shaped mainly by the plant organ, followed by the phenological stage and lastly, by the plant cultivar. The importance of cultivar as a shaping factor varied according to the plant organ, being only significant in inflorescence-associated endophytes. A set of fungal taxa were positively associated with a particular cultivar and phenological stage, likely contributing to the plant anthracnose resistance.     

"The City Is My Mother": Narratives of Schizophrenia and Homelessness

Recent narrative analysis in medical anthropology provides keys to both the personal meaning of illness and the historical, cultural, and institutional shaping of that experience. Yet Western psychiatric thinking and practice continue to view schizophrenic discourse as closed to interpretation. Caught in this "closed text," the self would seem obliterated. But using narratives of schizophrenia and homelessness, this essay proposes a different understanding of schizophrenic alterity. The openness of the text-as-experience is re-created collectively, from outside the subject's narration: the subject's "self is construction through the added perspectives of his or her interlocutors in the role of storymakers.     

Unravelling the evolutionary origins of biogeographic assemblages

Aim

Floristic and faunal diversity fall within species assemblages that can be grouped into distinct biomes or ecoregions. Understanding the origins of such biogeographic assemblages helps illuminate the processes shaping present‐day diversity patterns and identifies regions with unique or distinct histories. While the fossil record is often sparse, dated phylogenies can provide a window into the evolutionary past of these regions. Here, we present a novel phylogenetic approach to investigate the evolutionary origins of present‐day biogeographic assemblages and highlight their conservation value.

Location

Southern Africa.

Methods

We evaluate the evolutionary turnover separating species clusters in space at different time slices to determine the phylogenetic depth at which the signal for their present‐day structure emerges. We suggest present‐day assemblages with distinct evolutionary histories might represent important units for conservation. We apply our method to the vegetation of southern Africa using a dated phylogeny of the woody flora of the region and explore how the evolutionary history of vegetation types compares to common conservation currencies, including species richness, endemism and threat.

Results

We show the differentiation of most present‐day vegetation types can be traced back to evolutionary splits in the Miocene. The woody flora of the Fynbos is the most evolutionarily distinct, and thus has deeper evolutionary roots, whereas the Savanna and Miombo Woodland show close phylogenetic affinities and likely represent a more recent separation. However, evolutionarily distinct phyloregions do not necessarily capture the most unique phylogenetic diversity, nor are they the most species‐rich or threatened.

Main conclusions

Our approach complements analyses of the fossil record and serves as a link to the history of diversification, migration and extinction of lineages within biogeographic assemblages that is separate from patterns of species richness and endemism. Our analysis reveals how phyloregions capture conservation value not represented by traditional biodiversity metrics.

     

"Decisions and Dispositions": Socializing Spatial Archaeology

Concerns with spatial dimensions and social inference have long histories in archaeology. However, the two histories are not always conjoined. This article considers changing understandings of space in archaeology in the last half century, and the variable nature of what "social" has denoted and connoted during that same span. The review highlights recurring calls for a social archaeology, and the degree to which, in such instances, social inference has been expressed in spatial terms, especially as these have recognized people's "decisions and dispositions" as shaping the archaeological record. Life histories of place receive special attention as ways of discerning the existence and social impact of such decisions and dispositions. These life histories constitute an arena in which archaeologists from diverse theoretical perspectives can offer complementary insights. Moreover, they exemplify ways in which social and spatial inferences in archaeology contribute to wider understanding of human experience. [Keywords: archaeology, social, space, place, life history]     

Impacts of fine sediment input on river macroinvertebrates: the role of the abiotic characteristics at mesohabitat scale

Hydrobiologia - Instream hydraulics and riverbed substrate allow for the identification of mesohabitats, and contribute in shaping benthic macroinvertebrate assemblages. However, the role of...     

Drivers of reef fish assemblages in an upwelling region from the Eastern Tropical Pacific Ocean

Reef fish assemblages are exposed to a wide range of anthropogenic threats as well as chronic natural disturbances. In upwelling regions, for example, there is a seasonal influx of cool nutrient-rich waters that may shape the structure and composition of reef fish assemblages. Given that climate change may disrupt the natural oceanographic processes by altering the frequency and strength of natural disturbances, understanding how fish assemblages respond to upwelling events is essential to effectively manage reef ecosystems under changing ocean conditions. This study used the baited remote underwater video stations (BRUVS) and the traditional underwater visual census (UVC) to investigate the spatiotemporal patterns of reef fish assemblages in an upwelling region in the North Pacific of Costa Rica. A total of 183 reef fish species from 60 families were recorded, of which 166 species were detected using BRUVS and 122 using UVC. Only 66% of all species were detected using both methods. This study showed that the upwelling had an important role in shaping reef fish assemblages in this region, but there was also a significant interaction between upwelling and location. In addition, other drivers such as habitat complexity and habitat composition had an effect on reef fish abundances and species. To authors’ knowledge, this is the first study in the Eastern Tropical Pacific that combines BRUVS and UVC to monitor reef fish assemblages in an upwelling region, which provides more detailed information to assess the state of reef ecosystems in response to multiple threats and changing ocean conditions.     

Spatial variability in intertidal macroalgal assemblages on the North Portuguese coast: consistence between species and functional group approaches

Natural assemblages are variable in space and time; therefore, quantification of their variability is imperative to identify relevant scales for investigating natural or anthropogenic processes shaping these assemblages. We studied the variability of intertidal macroalgal assemblages on the North Portuguese coast, considering three spatial scales (from metres to 10 s of kilometres) following a hierarchical design. We tested the hypotheses that (1) spatial pattern will be invariant at all the studied scales and (2) spatial variability of macroalgal assemblages obtained by using species will be consistent with that obtained using functional groups. This was done considering as univariate variables: total biomass and number of taxa as well as biomass of the most important species and functional groups and as multivariate variables the structure of macroalgal assemblages, both considering species and functional groups. Most of the univariate results confirmed the first hypothesis except for the total number of taxa and foliose macroalgae that showed significant variability at the scale of site and area, respectively. In contrast, when multivariate patterns were examined, the first hypothesis was rejected except at the scale of 10 s of kilometres. Both uni- and multivariate results indicated that variation was larger at the smallest scale, and thus, small-scale processes seem to have more effect on spatial variability patterns. Macroalgal assemblages, both considering species and functional groups as surrogate, showed consistent spatial patterns, and therefore, the second hypothesis was confirmed. Consequently, functional groups may be considered a reliable biological surrogate to study changes on macroalgal assemblages at least along the investigated Portuguese coastline.     

Historical processes explain fish diversity in the upper Amazon River basin

Hydrobiologia - Despite decades of investigation, there are few ecological studies on the Amazonian fish fauna that have looked both at the main factors shaping the fish assemblages at a regional...     

Stone artifacts and hominins in island Southeast Asia: new insights from Flores, eastern Indonesia

This study reexamines the current understanding of Pleistocene stone-artifact assemblages in island Southeast Asia. A differentiation has long been made between assemblages of large-sized "core tools" and assemblages of small-sized "flake tools." "Core tool" assemblages are often argued to be the handiwork of early hominin species such as Homo erectus, while small-sized "flake tool" assemblages have been attributed to Homo sapiens. We argue that this traditional Southeast Asian perspective on stone tools assumes that the artifacts recovered from a site reflect a complete technological sequence. Our analyses of Pleistocene-age artifact assemblages from Flores, Indonesia, demonstrate that large pebble-based cores and small flake-based cores are aspects of one reduction sequence. We propose that the Flores pattern applies across island Southeast Asia: large-sized "core tool" assemblages are in fact a missing element of the small-sized flake-based reduction sequences found in many Pleistocene caves and rock-shelters. We conclude by discussing the implications of this for associating stone-artifact assemblages with hominin species in island Southeast Asia.     

Genome-wide analysis of codon usage bias patterns in an enterotoxigenic <Emphasis Type="Italic">Escherichia coli</Emphasis> F18 strain

Enterogenic Escherichia coli (ETEC) F18 strains are the main pathogenic bacteria causing severe diarrhea in humans and domestic animals. However, the information about synonymous codon usage pattern of ETEC F18 genome remains unclear. We conducted a genome-wide analysis of synonymous codon usage patterns in the ETEC F18 strain SRA: SAMN02471895. After filtering of the complete genome sequence, 4327 coding sequences were analyzed using multivariate statistical methods to calculate synonymous codon usage patterns and to evaluate the influence of various factors in shaping the codon usage. The mean GC content was 51.38%, with a slight preference for G/C-ending codons. Twenty-two codons were determined as ‘‘optimal codons”. ENC plots showed some of the genes were on or close to the expected curve, while only points with low-ENC values were below the curve. PR2 analysis showed that GC and AT were not used proportionally, suggesting major roles for mutational pressure and natural selection in shaping usage. Neutrality plots showed a significant correlation between GC12 and GC3, suggesting that mutational pressure is responsible for nucleotide composition in shaping the strength of codon usage. Translational selection was the main factor shaping the codon usage pattern of ETEC F18 genome, while other factors such as protein length, GRAVY and ARO values also influenced codon usage to some extent. We analyzed the codon usage pattern systematically and identified the factors shaping codon usage bias in the ETEC F18 genome. Such information further elucidates the mechanisms of synonymous codon usage bias and provides the basis of molecular genetic engineering and evolutionary studies.     

Biogeography and lake morphometry drive diatom and chironomid assemblages’ composition in lacustrine surface sediments of oceanic islands

Subfossil biotic assemblages in lakes’ surface sediments have been used to infer ecological conditions across environmental gradients. Local variables are usually the major drivers of assemblage composition, but in remote oceanic islands biogeographic filters may play a significant role. To assess the contribution of local and regional filters in the composition of subfossil diatom and chironomid assemblages in surface sediments, 41 lakes in Azores archipelago were studied and related to environmental variables. Ordination techniques were used to identify the forcing factors that best explain the composition of these assemblages. Both assemblages are influenced by multiple limnological variables (conductivity, pH and nutrients). However, diatom assemblages differed mainly in the proportion of planktonic versus benthic species along lakes’ depth gradient while chironomids differed significantly among islands but not among lake depths. Thus, biogeographic filters play an important role in shaping islands’ freshwater communities, particularly insect ones, more influenced by geographic variables. Results demonstrate the accuracy and potential of biotic remains in sediments for applied studies of lake ecology, trophic status, climatic trends and ecological reconstruction and evolution of lakes. In the Azores, the application of this information for the development of inference models is envisaged as a further step to accomplish these goals.     

Seasonal rather than spatial variability drives planktonic and benthic bacterial diversity in a microtidal lagoon and the adjacent open sea

Coastal lagoons are highly productive ecosystems, which are experiencing a variety of human disturbances at increasing frequency. Bacteria are key ecological players within lagoons, yet little is known about the magnitude, patterns and drivers of diversity in these transitional environments. We carried out a seasonal study in the Venice Lagoon (Italy) and the adjacent sea, to simultaneously explore diversity patterns in different domains (pelagic, benthic) and their spatio‐temporal variability, and test the role of environmental gradients in structuring assemblages. Community composition differed between lagoon and open sea, and between domains. The dominant phyla varied temporally, with varying trends for the two domains, suggesting different environmental constraints on the assemblages. The percentage of freshwater taxa within the lagoon increased during higher river run‐off, pointing at the lagoon as a dynamic mosaic of microbial taxa that generate the metacommunity across the whole hydrological continuum. Seasonality was more important than spatial variability in shaping assemblages. Network analyses indicated more interactions between several genera and environmental variables in the open sea than the lagoon. Our study provides evidences for a temporally dynamic nature of bacterial assemblages in lagoons and suggests that an interplay of seasonally influenced environmental drivers shape assemblages in these vulnerable ecosystems.     

Geographical expansion and increased prevalence of common species in avian assemblages: implications for large-scale patterns of species richness

Aim The assumption that ecological patterns at large spatial scales originate exclusively from non‐anthropogenic processes is growing more questionable with the increasing domination of the biosphere by humans. Because common and rare species are known to respond differently to anthropogenic activities at local scales these differential responses could, over time, be reflected in distributional patterns of species richness at larger spatial scales. This work tests the hypothesis that modern processes have played a role in shaping these patterns, by examining recent changes in the structure and composition of assemblages of breeding avifauna over a large geographical extent. Location The portion of North America containing the contiguous United States and southern Canada. Methods Changes in the geographical range structure of breeding avifauna in North America from 1968 to 2003 were analysed in regions containing historically moderate levels of anthropogenic activities. Two geographical measures, extent of occurrence and area of occupancy, were used to identify the level of rarity or commonality of individual species and to estimate, based on a vector analysis, patterns of change in geographical range structure for individual species and avian assemblages. Results More species experienced patterns of geographical range expansion (51%) than contraction (28%). The majority of avian assemblages (43%) displayed patterns of geographical range expansion: common species increased in number and proportion (6%) in association with reciprocal losses in rare and moderately rare species, resulting in a constant level of species richness. The minority of avian assemblages (21%) displayed patterns of geographical range contraction: gains occurred for common species as well as for rare and moderately rare species, resulting in substantial increases in species richness and a decline in the proportion of common species (4%). The remaining avian assemblages presented equivocal patterns characterized by gains in the number and proportion (2%) of common species and gains in species richness. Main conclusions Modern processes have played a role in shaping the distribution patterns of species richness at large spatial scales based on the composition of common and rare species. This suggests that anthropogenic activities cannot be ignored as a possible causal factor when considering ecological patterns at large spatial scales.     

Effects of macroalgal identity on epifaunal assemblages: native species versus the invasive species Sargassum muticum

Seaweeds are a refuge from stressful conditions associated with life on rocky intertidal shores, and there is evidence that different macrophytes support different assemblages of mobile epifauna. Introduction of non-indigenous macroalgae may have a great impact on associated epifaunal assemblages and ecosystem processes in coastal areas. Previous studies have reported conflicting evidences for the ability of epifauna to colonize non-indigenous species. Here, we analyzed epifaunal assemblages associated with three species of macroalgae that are very abundant on intertidal shores along the Galician coast: the two native species Bifurcaria bifurcata and Saccorhiza polyschides and the invasive species Sargassum muticum. We collected samples of each species from three different sites at three different times to test whether variability of epifaunal assemblages was consistent over space and time. Epifaunal assemblages differed between the three macroalgae. Results suggested that stability and morphology of habitat played an important role in shaping the structure of epifaunal assemblages. This study also showed that the invasive S. muticum offered a suitable habitat for many invertebrates.     

Testis-specific ATP synthase peripheral stalk subunits required for tissue-specific mitochondrial morphogenesis in <Emphasis Type="Italic">Drosophila</Emphasis>

Background

In Drosophila early post-meiotic spermatids, mitochondria undergo dramatic shaping into the Nebenkern, a spherical body with complex internal structure that contains two interwrapped giant mitochondrial derivatives. The purpose of this study was to elucidate genetic and molecular mechanisms underlying the shaping of this structure.

Results

The knotted onions (knon) gene encodes an unconventionally large testis-specific paralog of ATP synthase subunit d and is required for internal structure of the Nebenkern as well as its subsequent disassembly and elongation. Knon localizes to spermatid mitochondria and, when exogenously expressed in flight muscle, alters the ratio of ATP synthase complex dimers to monomers. By RNAi knockdown we uncovered mitochondrial shaping roles for other testis-expressed ATP synthase subunits.

Conclusions

We demonstrate the first known instance of a tissue-specific ATP synthase subunit affecting tissue-specific mitochondrial morphogenesis. Since ATP synthase dimerization is known to affect the degree of inner mitochondrial membrane curvature in other systems, the effect of Knon and other testis-specific paralogs of ATP synthase subunits may be to mediate differential membrane curvature within the Nebenkern.