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Coralligenous habitat is one of the most important and sensitive habitats of the Mediterranean Sea and several different sampling procedures are currently used in the ecological investigations of coralligenous assemblages. This study aimed to assess the efficacy of different methods in detecting anthropogenic impacts on coralligenous habitat. In particular, the choice of sampling methods, the level of taxonomic resolution, the sampling area, the number of replicates and the spatial scales for detecting possible impacts were evaluated. Results showed that photographic samples larger than 1800 cm2, numbers of replicates larger than 10, the use of taxa and morphological groups as assemblage descriptors, and sampling designs with a high replication at small spatial scales are a valid methodological procedure in impact evaluation studies based on coralligenous assemblages. El hábitat coralígeno es uno de los más importantes y sensibles del mar Mediterráneo y actualmente se pueden aplicar varios métodos de muestreo en las investigaciones ecológicas de las comunidades macroalgales coralígenas. El objetivo del presente estudio es evaluar la efectividad de los diferentes procedimientos para detectar el impacto antrópico sobre el hábitat de coralígeno. Se evaluaron en particular la elección de los métodos de muestreo, el nivel de resolución a la que los taxones tienen que ser identificados, la superficie de muestreo, el número de repeticiones y las escalas espaciales adecuadas para la investigación de los posibles impactos. Los resultados indican que muestras fotográficas de 1800 cm2, un número de repeticiones mayor que 10, el uso de taxones y grupos morfológicos como descriptores y diseños de muestreo con una alta replicación asociada a pequeñas escalas espaciales pueden representar elementos metodológicos válidos en los estudios de evaluación de impacto basados en las comunidades coralígenas.

National and international obligations to protect vulnerable species, communities, habitats, and ecosystems (VSCHEs) require greater attention as human uses extend to deeper water. These obligations increase the need for improved understanding of the distribution and abundance of VSCHEs to develop management actions. Data from low-speed vehicles that operate at the seafloor (e.g., remotely operated vehicles, camera sleds) predominate. These “low and slow” approaches, while providing high-resolution data, do not operate at the scale required for management. We suggest autonomous underwater vehicles (AUVs) flown at relatively high altitude and high speed over the seafloor as a “high and fast” approach to survey areas at the scale fisheries and other activities operate. We used REMUS 6000 AUVs to collect presence data for VSCHEs in a rapid assessment on Physalia Seamount. AUVs were programmed to collect digital images, side-scan sonar (120/410 kHz), and environmental parameters and could navigate a 40° slope. Our preliminary results of this approach, predicated on the assumption that coarse taxonomic resolution is adequate for management needs, indicates AUVs can be effective tools for large area surveys in short time periods.

Summary Antibiotics alter microbiota composition and increase infection susceptibility. However, the generalizable effects of antibiotics on and the contribution of environmental variables to gut commensals remain unclear. To address this, we tracked microbiota dynamics with high temporal and taxonomic resolution during antibiotic treatment in a controlled murine system by isolating variables such as diet, treatment history, and housing co-inhabitants. Human microbiotas were remarkably resilient and recovered during antibiotic treatment, with transient dominance of resistant Bacteroides and taxa-asymmetric diversity reduction. In certain cases, in vitro sensitivities were not predictive of in vivo responses, underscoring the significance of host and community context. A fiber-deficient diet exacerbated microbiota collapse and delayed recovery. Species replacement through cross housing after ciprofloxacin treatment established resilience to a second treatment. Single housing drastically disrupted recovery, highlighting the importance of environmental reservoirs. Our findings highlight deterministic microbiota adaptations to perturbations and the translational potential for modulating diet, sanitation, and microbiota composition during antibiotics.

Due to an unfortunate turn of events, the statistical results for TS1 (F- and p-values) in Table 4 were displayed in reversed order. The correct representation of Table 4 is published here and should be treated as definitive.

Additive diversity partitioning (α, β, and γ) is commonly used to study the distribution of species-level diversity across spatial scales. Here, we first investigate whether published studies of additive diversity partitioning show signs of difficulty attaining species-level resolution due to inherent limitations with morphological identifications. Second, we present a DNA barcoding approach to delineate specimens of stream caddisfly larvae (order Trichoptera) and consider the importance of taxonomic resolution on classical (additive) measures of beta (β) diversity. Caddisfly larvae were sampled using a hierarchical spatial design in two regions (subarctic Churchill, Manitoba, Canada; temperate Pennsylvania, USA) and then additively partitioned according to Barcode Index Numbers (molecular clusters that serve as a proxy for species), genus, and family levels; diversity components were expressed as proportional species turnover. We screened 114 articles of additive diversity partitioning and found that a third reported difficulties with achieving species-level identifications, with a clear taxonomic tendency towards challenges identifying invertebrate taxa. Regarding our own study, caddisfly BINs appeared to show greater subregional turnover (e.g., proportional additive β) compared to genus or family levels. Diversity component studies failing to achieve species resolution due to morphological identifications may therefore be underestimating diversity turnover at larger spatial scales.

Premise of the study: To study pollination networks in a changing environment, we need accurate, high-throughput methods. Previous studies have shown that more highly resolved networks can be constructed by studying pollen loads taken from bees, relative to field observations. DNA metabarcoding potentially allows for faster and finer-scale taxonomic resolution of pollen compared to traditional approaches (e.g., light microscopy), but has not been applied to pollination networks. Methods: We sampled pollen from 38 bee species collected in Florida from sites differing in forest management. We isolated DNA from pollen mixtures and sequenced rbcL and ITS2 gene regions from all mixtures in a single run on the Illumina MiSeq platform. We identified species from sequence data using comprehensive rbcL and ITS2 databases. Results: We successfully built a proof-of-concept quantitative pollination network using pollen metabarcoding. Discussion: Our work underscores that pollen metabarcoding is not quantitative but that quantitative networks can be constructed based on the number of interacting individuals. Due to the frequency of contamination and false positive reads, isolation and PCR negative controls should be used in every reaction. DNA metabarcoding has advantages in efficiency and resolution over microscopic identification of pollen, and we expect that it will have broad utility for future studies of plant–pollinator interactions.

Identification of the species origin of pollen has many applications, including assessment of plant–pollinator networks, reconstruction of ancient plant communities, product authentication, allergen monitoring, and forensics. Such applications, however, have previously been limited by microscopy-based identification of pollen, which is slow, has low taxonomic resolution, and has few expert practitioners. One alternative is pollen DNA barcoding, which could overcome these issues. Recent studies demonstrate that both chloroplast and nuclear barcoding markers can be amplified from pollen. These recent validations of pollen metabarcoding indicate that now is the time for researchers in various fields to consider applying these methods to their research programs. In this paper, we review the nascent field of pollen DNA barcoding and discuss potential new applications of this technology, highlighting existing limitations and future research developments that will improve its utility in a wide range of applications.

Metabarcoding is becoming an increasingly valuable alternative approach to biodiversity assessment, due to the combination of extreme sensitivity and potential for the highest taxonomic resolution in a cost- and time-effective methodology. To evaluate the capacity of metabarcoding for estuarine plankton monitoring, a comparison between the results obtained with this approach were compared with those based on traditional taxonomic analysis (microscopy). Database incompleteness, one of the main limitations of metabarcoding, was somewhat overcome by the addition of DNA sequences for local species, which increased the taxonomic assignment success from 23.7 to 50.5 %. When the communities were studied along with environmental variables, similar spatial and temporal trends of taxonomic diversity were observed for metabarcoding and microscopic studies of zooplankton, but not for phytoplankton. This is most likely attributable to the lack of representative sequences for phytoplankton species in current databases. In addition, there was high correspondence in community composition when comparing abundances estimated from metabarcoding and microscopy, suggesting semiquantitative potential for metabarcoding. Furthermore, metabarcoding allowed the detection and identification of two non-indigenous species (NIS) found in the study area at abundances hardly detectable by microscopy. Overall, our results indicate that metabarcoding is a powerful approach with excellent possibilities for use in plankton monitoring, early detection of NIS and plankton biodiversity shifts.

SummaryDeep microbiome profiling has sparked a revolution in biology, recontextualizing mechanisms such as macroorganismal adaptation and evolution. Amplicon sequencing has been critical for characterization of highly diverse microbiomes, but several challenges still hinder their investigation: (1) Poor coverage of the full diversity, (2) Read depth losses and (3) Erroneous diversity inflation/distortion.We developed a modular approach to quickly profile at least 8 interchangeable loci in a single sequencing run, including a simple and cost-effective way to block amplification of non-targets (like host DNA). We further correct observed distortion in amplified diversity by phylogenetically grouping erroneous OTUs, creating a phylogeny-based unit we call OPUs.Our approach achieves full, accurate characterization of a mixed-kingdom mock community of bacteria, fungi and oomycetes at high depth even in non-target contaminated systems. The OPU concept enables much more accurate estimations of alpha and beta diversity trends than OTUs and overcomes disagreements between studies caused by methodology. Leveraging the approach in theArabidopsis thalianaphyllosphere, we generated to our knowledge the most complete microbiome survey to date.Microbiomes are extremely diverse, extending well beyond bacteria and fungi. Our method makes new questions in a variety of fields tractable with accurate, systems-based overviews of microbial community structures.

Environmental sequencing regularly recovers fungi that cannot be classified to any meaningful taxonomic level beyond "Fungi". There are several examples where evidence of such lineages has been sitting in public sequence databases for up to ten years before receiving scientific attention and formal recognition. In order to highlight these unidentified lineages for taxonomic scrutiny, a search function is presented that produces updated lists of approximately genus-level clusters of fungal ITS sequences that remain unidentified at the phylum, class, and order levels, respectively. The search function (https://unite.ut.ee/top50.php) is implemented in the UNITE database for molecular identification of fungi, such that the underlying sequences and fungal lineages are open to third-party annotation. We invite researchers to examine these enigmatic fungal lineages in the hope that their taxonomic resolution will not have to wait another ten years or more. Copyright R. Henrik Nilsson et al.

O Cerrado é o segundo maior bioma do Brasil e é considerado um dos maiores hotspots de biodiversidade do mundo. Nesta savana brasileira, existe uma grande diversidade e abundância de cupins (Isoptera) que são considerados espécies-chave para manutenção de muitos serviços ecossistêmicos. Mesmo com a importância exercida dos cupins no ecossistema, pouco se sabe sobre como a composição de espécies de cupins pode variar em função dos diferentes tipos de vegetação presentes no Cerrado. Além disso, ainda existem grupos de cupins com a taxonomia confusa e para muitos gêneros a identificação de espécies é extremamente difícil. Com isso, no presente estudo foram elaborados dois manuscritos com o intuito de tentar avaliar as problemáticas expostas acima. O primeiro trabalho objetivou verificar a possibilidade de substituição de identificações de cupins a nível de espécie por outros níveis superiores, por meio de uma análise de suficiência taxonômica. Neste estudo correlacionamos a riqueza de espécies com a riqueza de gêneros (r = 0,98903), subfamílias (r = 0,7422) e grupos tróficos (r = 0,77808), e vimos que houve uma alta correlação entre riqueza dos diferentes níveis. Foi avaliada também a concordância entre a composição de espécies e os demais níveis analisados, e vimos que, tanto pelo teste de Mantel: espécies x gênero (r = 0,5323), x subfamília (r = 0,2718) x grupo trófico (r = 0,2847), quanto pelo Procrustes: espécies x gênero (m²:0,6344), x subfamília (m²:0,8989) x grupo trófico (m²:0,8043), os valores obtidos indicaram baixas correlações. Neste artigo, concluímos que ao se trabalhar com a composição de espécies, a substituição das identificações por outros níveis seria inviabilizada pelos baixos valores de sobreposição encontrados. Porém com relação à riqueza, a alta correlação encontrada entre espécies e gêneros sugere a possibilidade de substituição das identificações do nível de espécies por gênero. No segundo artigo, utilizamos amostras de cupins coletadas em 15 municípios da região Centro-Oeste do Cerrado e as correlacionamos com as variáveis ambientais de altitude, distribuição geográfica, índice de cobertura vegetal, perímetro e área do fragmento coletado e tipo de vegetação. Fizemos também uma análise discriminante e uma partição da diversidade. Nessas análises, buscamos observar se as espécies poderiam ser agrupadas segundo o tipo de formação vegetal e verificamos em qual escala espacial de diversidade haveria um maior fluxo de espécies. Observamos que, de forma geral houveram correlações significativas entre as variáveis relacionadas à vegetação e à composição de espécies. Dentre essas correlações, vimos que a caracterização da paisagem em fitofisionomias representou melhor os padrões de composição de espécies do que o índice de cobertura vegetal EVI2. Na análise discriminante, vimos que 27% de todas as amostras analisadas se mostraram estar restritas a uma determinada fitofisionomia. Além disso, a partição da diversidade mostrou que a substituição de espécies (diversidade beta) entre gradientes latitudinais e longitudinais foram maiores do que observado em nível de parcelas, tipos de vegetação e municípios, sugerindo que as variações ambientais em menores escalas explicam pouco das alterações na composição das comunidades de Isoptera no bioma Cerrado. The Cerrado is the second largest biome of Brazil and it is considered one of the biggest world biodiversity hotspot. In this Brazilian savannah, there is a great diversity and abundance of termites (Isoptera), which are considered key-species for maintenance of many ecosystem services. Despite the importance of termites exerted on the ecosystem, little is known about how the composition of species of termites varies depending on the different types of vegetation present in the Cerrado. Termites (Isoptera) are eusocial insects widely dispersed throughout the tropics. Even today, the termites are in the midst of a taxonomic review and, coupled with the low number of taxonomists, there is some difficulty in identifying some species. With this, in this study we elaborated two manuscripts adressing the problems exposed above. The first study aimed to verify the possibility of replacing termite identification to species level by other higher levels, through a sufficient analysis taxonomic. Correlated to species richness, the richness of genres (r = 0.98903) subfamilies (r = 0.7422) and trophic group (r = 0.77808), where we saw that there was a high correlation between the wealth of different levels. It evaluated the correlation between species composition and the other analyzed levels, and we saw that both the Mantel test: species x gender (r = 0.5323), x subfamily (r = 0.2718) x trophic group (r = 0.2847), and by Procrustes: x species genus (m²: 0.6344) x subfamily (m²: 0.8989) x trophic group (m²: 0.8043), the values indicated low correlations between the levels. In this article, we conclude that when working with the species composition, the replacement of identification by other levels would be frustrated by the low found overlapping values. And we find that that relative wealth, the high correlation between species and genera suggests the possibility of replacing the identification of the species level by gender. In the second article, we used termite samples collected in 15 municipalities in the Midwest region of the Cerrado and correlated with environmental variables of altitude, geographic distribution, vegetation index, perimeter and fragment area collected and type of vegetation. We also a discriminant analysis and a partition diversity. In these analyzes, we seek to see whether the species could be grouped according to the type of plant formation and in which spatial scale of diversity would be a greater flow of species. In this study, we concluded that in general there were significant correlations between variables related to vegetation and species composition. Among these correlations, we saw that the characterization of landscape by phytophysiognomies best represents the species composition patterns, then the vegetation index EVI2. We saw in the discriminant analysis that 27% of all samples are restricted to a particular physiognomy. Furthermore, the partition diversity showed that substitution of the species (beta diversity) between latitudinal and longitudinal gradients was higher than that observed in level of parts, types of vegetation and municipalities, suggesting that environmental variations at smaller scales bit representing the changes in the composition the Isoptera communities in the Cerrado biome.

FREIRE, K. de M. F.; ARAÚJO, A. R. da R. Analysis of marine catches off the State of Sergipe (1950-2010). Arquivos de Ciências do Mar, v. 49, n.1, p. 13-29, jan. 2016. The state of Sergipe has no official electronic version of the database of catch statistics available in printed national bulletins. Thus, the objective of this study was to update its statistics on fish production of a previously reconstructed national database to obtain a time series for 1950-2010, analyzing catch composition with higher taxonomic resolution, and estimating some missing components of fisheries. Reconstructed total catches were higher than original catches and indicated an increase in catches from 1950 to 1979. In the 1980s and 1990s a stabilization was observed, and decreasing catches from 2005 to 2010. Catches were almost exclusively artisanal. The better taxonomic resolution of the reconstructed database allowed for the identification of the following species with the highest catches in 2010: Xiphopenaeus kroyeri, Mugil curema, Ucides cordatus, Goniopsis cruentata and Macrodon ancylodon. Catches for these species amounted for about 50% of the total extracted off Sergipe in 2010. Recreational catches were estimated at 16 t in 2010, and annual discards at 818 t in the 1980s/1990s. Ornamental and subsistence catches were not estimated. Our analysis indicated that taxonomic losses are observed in two stages: when local data are compiled into a national database, and then from a national to an international one. O estado de Sergipe não dispõe de uma versão eletrônica oficial do banco de dados de estatística de captura disponível em boletins nacionais impressos. Assim, o objetivo desse trabalho foi atualizar a parte referente ao estado de Sergipe de um banco de dados nacional eletrônico reconstruído, a fim de obter uma série histórica para 1950-2010, analisando a composição da captura com maior resolução taxonômica e estimando componentes ausentes da pesca. As capturas totais reconstruídas foram sempre mais elevadas do que as originais e indicaram um aumento nas capturas de 1950 a 1979. Nas décadas de 1980 and 1990, foi observada uma estabilização nas capturas, e uma queda de 2005 a 2010. As capturas foram extraídas quase exclusivamente pela frota artesanal. A melhor resolução taxonômica permitiu a identificação das seguintes espécies com as de maiores capturas em 2010: Xiphopenaeus kroyeri, Mugil curema, Ucides cordatus, Goniopsis cruentata e Macrodon ancylodon. As capturas para essas espécies representaram cerca de 50% do total extraído em Sergipe em 2010. Capturas recreativas foram estimadas em 16 t em 2010, e descartes anuais em 818 t nas décadas de 1980 e 1990. Capturas ornamentais e de subsistência não foram estimadas. Nossa análise indicou que perdas taxonômicas foram observadas em duas etapas: quando dados locais são incorporados em um banco nacional e posteriormente, de um banco nacional para um internacional.

Matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) has been shown to be a rapid, effective, and sensitive tool for characterizing diverse bacteria. Historically, the primary application of this technology has been to identify bacteria at the genus and species levels in a few minutes. The most commonly used identification method involves matching mass spectra of unknown bacteria to reference spectra in commercially available databases with the assistance of manufacturer-created algorithms. Recently, there has been keen interest in enhancing the taxonomic resolution of MALDI to characterize bacteria at the strain and subspecies levels. Often, categorization of strains sharing similar traits, differentiation of closely related strains, and/or identification of a single strain are desired. Strain-level characterization is important in the development of counter-bioterrorism strategies, prevention of food contamination, and rapid diagnosis of bacterial infections. This chapter focuses on factors, including culture medium, sample preparation, data acquisition, and data analysis that affect strain-level characterization. In addition, the chapter highlights techniques and treatments that offer promise to improve the taxonomic resolution of MALDI-TOF MS-enabled approaches to bacterial characterization.

Since the advent of the use of matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry (TOF MS) as a tool for microbial characterization, efforts to increase the taxonomic resolution of the approach have been made. The rapidity and efficacy of the approach have suggested applications in counter-bioterrorism, prevention of food contamination, and monitoring the spread of antibiotic-resistant bacteria. Strain-level resolution has been reported with diverse bacteria, using library-based and bioinformatics-enabled approaches. Three types of characterization at the strain level have been reported: strain categorization, strain differentiation, and strain identification. Efforts to enhance the library-based approach have involved sample pre-treatment and data reduction strategies. Bioinformatics approaches have leveraged the ever-increasing amount of publicly available genomic and proteomic data to attain strain-level characterization. Bioinformatics-enabled strategies have facilitated strain characterization via intact biomarker identification, bottom-up, and top-down approaches. Rigorous quantitative and advanced statistical analyses have fostered success at the strain level with both approaches. Library-based approaches can be limited by effects of sample preparation and culture conditions on reproducibility, whereas bioinformatics-enabled approaches are typically limited to bacteria, for which genetic and/or proteomic data are available. Biological molecules other than proteins produced in strain-specific manners, including lipids and lipopeptides, might represent other avenues by which strain-level resolution might be attained. Immunological and lectin-based chemistries have shown promise to enhance sensitivity and specificity. Whereas the limits of the taxonomic resolution of MALDI TOF MS profiling of bacteria appears bacterium-specific, recent data suggest that these limits might not yet have been reached. © 2012 Wiley Periodicals, Inc., Mass Spec Rev 32:188–217, 2013

The ecology of the freshwater phytoplankton — communities of freely-dispersed, plant-functioning microbes — has attracted attention in Britain for over 100 years. Here an outline history is given, with reference to persons and places, types of water-body involved, and the approaches adopted. The last include taxonomic resolution and composition with range of morphotypes; physiology of growth, photosynthesis and nutrition in relation to environmental variables; population sampling, dynamics and controlling factors; experimental mesocosms; and synecological aspects of communities. Reductionist and autecological approaches have been accompanied by more abstract generalisation, including phytoplankton viewed as a model community.

Understanding seabird marine habitat affinities, at-sea behavior, variability in repro- ductive success, migratory patterns, phenology, and other life history traits depends primarily on knowledge of the prey that they consume. Traditionally, estimating diets has been done through classification and enumeration of prey remains found in stomach contents of seabirds collected at sea, as well as chick meals, pellets, and feces collected at breeding colonies. These techniques have the advantage of high taxonomic resolution of prey, but suffer from biases due to the under - estimation of soft-bodied or small prey that are digested completely and overestimation of prey with durable parts that are retained for long periods of time. Recent innovations in 2 biochemical assays of seabird tissues—stable isotope and fatty acid analyses—have greatly expanded knowledge of seabird diets and have advanced our understanding of the ways in which seabirds can indicate in- ter-seasonal, annual, decadal, and longer shifts in oceanographic conditions over varying spatial scales. Advances in statistical approaches to these data have provided new ways in which prey can be identified and quantified. When applied in combination, these 3 techniques (traditional diet sampling, and stable isotope and fatty acid analyses) have the potential to reveal pathways of energy flux across marine ecosystems and to provide new insight into marine ecosystem dynamics. We review the basic principles of these approaches to determining seabird diet and emphasize the need for more formal conceptual and statistical integration of methods to advance this field.

Summary 1. Taxonomic sufficiency concerns the use of higher-taxon diversity as a surrogate for species diversity. It represents a fast and cost-effective method to assess community responses to natural and anthropogenic environmental drivers. In spite of the potential applications of using higher taxa as surrogates for species, little research has been carried out to determine the underlying reasons that might make taxonomic surrogacy effective for detecting diversity changes. 2. Here, we determine whether the effectiveness of higher taxa as species surrogates relies mostly on taxonomic relatedness of species (i.e. the relative closeness of species in the Linnaean taxonomic hierarchy) or depends simply on the numerical ratio between species and higher taxa (i.e. the degree of species aggregation). We reviewed the current literature on taxonomic sufficiency to check for any correlation between the effectiveness of higher taxa and the degree of species aggregation across different types of organisms. Tests based on random simulations from diverse marine mollusc assemblages were also carried out to ascertain whether the ability of higher taxa to detect variation in the multivariate structure of assemblages depended on the degree of species aggregation. 3. Mollusc data showed that information loss and the ensuing decrease in statistical power to detect natural or human-driven changes in assemblages at higher taxonomic levels depend on the degree of species aggregation, rather than on the taxonomic resolution employed. Analyses of the literature suggested that such outcomes could be generalizable to a wide range of organisms and environmental settings. 4. Our findings do not support the idea of a direct relationship between taxonomic relatedness and ecological similarity among species. This indicates that taxonomic ranks higher than species may not provide ecologically meaningful information, because higher taxa can behave as random groups of species unlikely to convey consistent responses to natural or human-driven environmental changes. 5. Synthesis and applications. Surrogates of species-level information can be based on the ‘highest practicable aggregation’ of species, irrespective of their taxonomic relatedness. Our findings cast doubt on static taxonomical groupings, legitimizing the use of alternative ways to aggregate species to maximize the use of species surrogacy.

A recent collection of a red alga from Bermuda showed great similarities to Leptofauchea brasiliensis from Brazil, providing the impetus for a morphological and anatomical evaluation of the two. Based on these studies, the two appear to be congeneric. Molecular phylogenetic analyses of the Bermudian plants showed them to be to be a new genus and species of the Phyllophoraceae (Gigartinales), Archestenogramma profundum C.W. Schneider, Chengsupanimit & G.W. Saunders. In light of our anatomical observations, our phylogenetic results also proved instructive as to the disposition of L. brasiliensis, a species that was suggested to be incorrectly assigned to the Rhodymeniales for over a quarter of a century and even recently excluded from Leptofauchea. The morphological and anatomical similarity of L. brasiliensis to A. profundum suggested its movement from the Faucheaceae to a new taxonomic placement in the Phyllophoraceae, as A. brasiliense (A.B. Joly) C.W. Schneider, Chengsupanimit & G.W. Saunders, comb. nov.

The analysis of sedimentary chironomid assemblages is an approach that has been widely adopted for inferring past environmental conditions. However, there is an ongoing discussion in the literature about whether this approach could become more sensitive at detecting past environmental changes if paleolimnologists conducted finer taxonomic analyses of their specimens. To advance this discussion, we conducted comparative analyses of larval chironomid assemblages resolved to two levels of taxonomic resolution. For this exercise, we chose to use live assemblages (as opposed to sub-fossil assemblages) because fine taxonomic resolution of live assemblages is more easily obtained. Our specific aims were to (i) determine if finely resolved taxa comprising a coarsely resolved group have similar ecological niches, (ii) determine if different environmental predictors of community composition are identified when two different levels of taxonomic resolution are applied and (iii) evaluate whether the variance explained by environmental variables differs substantially between levels of taxonomic resolution. We found that there was substantial dispersion among finely resolved taxa belonging to a single coarse group, which suggests that the merging of these taxa results in the loss of ecological information, and therefore warrants higher taxonomic precision. However, the identification of significant environmental predictors and the proportion of variance explained by these did not differ greatly between our two levels of taxonomic resolution. Overall our results show that coarse-resolution analyses may be adequate for some applications, but if the aim is to infer subtle environmental changes (as is the case in most paleolimnological studies) we recommend the highest possible level of taxonomic resolution.

Daphnia subfossils from lake sediments are useful for exploring the impacts of environmental stressors on aquatic ecosystems. Unfortunately, taxonomic resolution of Daphnia remains is coarse, as only a small portion of the animal is preserved, and so the identification of daphniid subfossils typically relies upon postabdominal claws. Daphniid claws can be assigned to one of two species complexes: D. longispina or D. pulex. Both complexes contain species with differing environmental optima, and therefore improved taxonomic resolution of subfossil daphniid claws would aid paleolimnological analyses. To identify morphological features that may be used to help differentiate between species within complexes, we used species presence/absence data from net tows to select lakes in central Ontario (Canada) containing only a single species from a particular complex, then used remains preserved in surface sediments of these lakes to isolate four Daphnia species: D. ambigua and D. mendotae from the D. longispina complex, and D. pulicaria and D. catawba from the D. pulex complex. Our analyses demonstrate that, within the D. longispina complex, postabdominal claw length (PCL) and spinule length can be used to distinguish D. mendotae from D. ambigua. In addition, within the D. pulex complex, there are differences between D. pulicaria and D. catawba in the relative lengths of the proximal and middle combs on the postabdominal claw. However, the number of stout spines on the middle comb is an unreliable character for differentiating species. Overall, our data demonstrate that greater resolution within Daphnia species complexes is possible using postabdominal claws; however, the process is arduous, and applicability will likely decrease with the number of taxa present.

New fossil turtle material from the Early Cretaceous of (Valanginian) of Colombia is described here. The material consists of carapace bones discovered in shallow marine sequences of the Rosablanca Formation, Eastern Cordillera, Zapatoca, Department of Santander. These fossils represent the oldest record of eucryptodiran turtles for the northernmost part of South America. Although detailed taxonomic resolution cannot be defined within Eucryptodira, the material resembles marine turtles in morphology and histology particularly to Protostegidae clade. Eucryptodires are the new element in the reptilian fauna of the Rosablanca Formation, which also has panpleurodires turtles, undescribed fish, plesiosaurs, and ichthyosaurs.

The linkage of trait responses to stressor gradients has potential to expand biomonitoring approaches beyond traditional taxonomically based assessments that identify ecological effect to provide a causal diagnosis. Traits-based information may have several advantages over taxonomically based methods. These include providing mechanistic linkages of biotic responses to environmental conditions, consistent descriptors or metrics across broad spatial scales, more seasonal stability compared with taxonomic measures, and seamless integration of traits-based analysis into assessment programs. A traits-based biomonitoring approach does not require a new biomonitoring framework, because contemporary biomonitoring programs gather the basic site-by-species composition matrices required to link community data to the traits database. Impediments to the adoption of traits-based biomonitoring relate to the availability, consistency, and applicability of existing trait data. For example, traits generalizations among taxa across biogeographical regions are rare, and no consensus exists relative to the required taxonomic resolution and methodology for traits assessment. Similarly, we must determine if traits form suites that are related to particular stressor effects, and whether significant variation of traits occurs among allopatric populations. Finally, to realize the potential of traits-based approaches in biomonitoring, a concerted effort to standardize terminology is required, along with the establishment of protocols to ease the sharing and merging of broad, geographical trait information.

Vessel traffic is the primary pathway for non-indigenous marine species introductions to New Zealand, with hull fouling recognised as being an important mechanism. This article describes hull fouling on seven slow-moving commercial vessels sampled over a 1 year period. Sampling involved the collection of images and fouling specimens from different hull locations using a standardised protocol developed to assess vessel biofouling in New Zealand. A total of 29 taxa was identified by expert taxonomists, of which 24% were indigenous to New Zealand and 17% non-indigenous. No first records to New Zealand were reported, however 59% of species were classified as 'unknown' due to insufficient taxonomic resolution. The extent of fouling was low compared to that described for other slow-movers. Fouling cover, biomass and richness were on average 17.1% (SE = 1.8%), 5.2 g (SE = 1.1 g) and 0.8 (SE = 0.07) per photoquadrat (200 x 200 mm), respectively. The fouling extent was lowest on the main hull areas where the antifouling paint was in good condition. In contrast, highest levels of fouling were associated with dry-docking support strips and other niche areas of the hull where the paint condition was poor. Future studies should target vessels from a broader range of bioregions, including vessels that remain idle for extended periods (ie months) between voyages, to increase understanding of the biosecurity risks posed by international commercial slow-movers.

Although appendicularians are relevant primary consumers and are part of every zooplankton community, there is a lack of information on the species present in different ocean regions. Thus, regional identification guides are useful to develop datasets with high taxonomic resolution. Appendicularian species were identified in 33 epipelagic samples of zooplankton collected in several locations of Costarican waters. Eighteen appendicularian species were identified, of which 15 were found in the Pacific and only three in the Caribbean. Seven species are new records for Costa Rican Pacific waters (Appendicularia sicula, Fritillaria charybdae, F. cf. pacifica, F. tenella, F. pellucida f. omani, Oikoipleura fusiformis f. cornutogastra and Pelagopleura verticalis). Data for each species distribution in Costa Rica is presented together with a key for the identification of appendicularian species recorded in the Inter-American seas and the Eastern Tropical Pacific.

The resolution achievable for chironomid identifications has increased in recent years because of significant improvements in taxonomic literature. However, high taxonomic resolution requires more training for analysts. Furthermore, with greater taxonomic resolution, misidentifications and the number of rare, poorly represented taxa in chironomid calibration datasets may increase. We assessed the effects of various levels of taxonomic resolution on the performance of chironomid-based temperature inference models (transfer functions) and temperature reconstruction. A calibration dataset consisting of chironomid assemblage and temperature data from 100 lakes was examined at four levels of taxonomic detail. The coarsest taxonomic resolution primarily represented identifications to genus or suprageneric level. At the highest level of taxonomic resolution, identification to genus level was possible for 37% of taxa, and identification below genus was possible for 60% of taxa. Transfer functions were obtained using Weighted Averaging (WA) and Weighted Averaging-Partial Least Squares (WA-PLS) regression. Cross-validated performance statistics, such as the root mean square error of prediction (RMSEP) and the coefficient of determination (r2) between inferred and observed values improved considerably from the lowest taxonomic resolution level (WA: RMSEP 1.91°C, r2 0.78; WA-PLS: RMSEP 1.59°C, r2 0.86) to the highest taxonomic resolution level (WA: RMSEP 1.66°C, r2 0.84; WA-PLS: RMSEP 1.41°C, r2 0.89). Reconstructed July air temperatures during the Lateglacial period based on fossil chironomid assemblages from Hijkermeer (The Netherlands) were similar for all levels of taxonomic resolution, except the coarsest level. At the coarsest taxonomic level, reconstruction failed to infer one of the known Lateglacial cold episodes in the record. Also, the difference in reconstructed values based on lowest and highest taxonomic resolutions exceeded sample-specific estimated standard errors of prediction in several instances. Our results suggest that chironomid-based transfer functions at the highest taxonomic resolution outperform models based on lower-resolution calibration data. However, transfer functions of intermediate taxonomic resolution produced results very similar to models based on high-resolution taxonomic data. In studies that include analysts with different levels of expertise, inference models based on intermediate taxonomic resolution, therefore, might provide an alternative to transfer functions of maximum taxonomic detail in order to ensure taxonomic consistency between calibration datasets and down-core records produced by different analysts.

The goal of the present study was to evaluate whether the Eastern Canadian Diatom Index (IDEC: Indice Diatomees de l’Est du Canada), which was built on fine-scale taxonomic resolution and included all observed diatom taxa, would perform similarly if a number of taxa were excluded from the analyses or if a reduced level of taxonomic resolution was used. The effects of excluding taxa and reducing the taxonomic resolution were evaluated by studying community structure variations in ordination analyses, and more specifically by comparing IDEC values calculated from the original diatom matrix with IDEC values obtained from simplified diatom matrices. The results showed that the exclusion of taxa based on the relative abundance criterion is the most appropriate, while the exclusion of taxa based on the frequency of occurrence criterion greatly affected the structure of the ordination. More specifically, taxa with a maximum relative abundance

Lithified marine sediments are not equitably distributed through time, raising the possibility that lithification masks biological signals when data from unlithified and lithified sediments are compared or combined. Using mollusk-dominated assemblages from the early Cenozoic of the Gulf Coastal Plain, we find that lithification conceals small taxa, decreases taxonomic resolution, and exacerbates the undersampling of rare taxa. Lithified assemblages appear less diverse and have less even abundance distributions than coeval unlithified samples. These limitations cannot be overcome by standardization procedures, nor are they likely to be circumvented by collecting larger samples. The effects of this bias, however, can be mitigated by restricting analyses to a single lithification state or to specific size classes. Since lithification selectively obscures small taxa, the magnitude of this bias will be most severe when organisms are particularly small, such as in the aftermath of mass extinctions. In the study area, lithification artificially protracts the recovery period following the Cretaceous-Paleogene mass extinction by ~7 m.y.

This paper examines how the use of various taxonomic levels and morphological functional groups influences the interpretation of multivariate analyses when comparing macroalgal assemblages in different regions in the Northeast Pacific. We found that for intertidal assemblages, within-site variation was high at the species level and regions only became discernable from the genus level to the order level. Above order level, regions were less well distinguished. Differentiating assemblages at the genus level were similar to results from functional group analyses. This implies that various levels and morphological functional groups can be used to distinguish intertidal assemblages among regions. Intertidal strata differences could be discerned at all taxonomic levels and using functional groups. In contrast to the intertidal, only a few regions were significantly different for subtidal assemblages, independent of taxonomic resolution used. Functional grouping in subtidal assemblages yielded the same resolution as taxonomic levels. Conversely to the intertidal assemblages, strata differences in the subtidal were found at the species and genus levels and with functional groups but not at the family and higher levels. Overall, these results demonstrate differences in regional and strata comparisons in intertidal and subtidal assemblage analyses and that typically species-level analyses are not required.

Changing the taxonomic scale of a biotic-assemblage dataset influences our ability to detect ecological patterns. In bioassessments, a test-site’s biological community is compared against a benchmark to indicate ecosystem condition, but the taxonomic resolution needed to judge impairment reliably is the subject of much scientific debate. This paper reviews taxonomic sufficiency for freshwater benthic-macroinvertebrate bioassessments. Three main issues are discussed: (1) the ecological significance of different taxonomic aggregations; (2) trade-offs involving taxonomic detail and information content versus money, time, expertise, and data quality; and (3) sampling- and analytical-method-specific factors affecting taxonomic sufficiency. Although Species should be the default taxonomic level for bioassessments, taxonomic sufficiency is chiefly determined by a study’s purpose, and pragmatism often dictates reduced detail. When a taxonomic-minimalism approach is necessary, a quantitative criterion for taxonomic sufficiency should be specified; this criterion should be based on an optimization of cost-benefit trade-offs associated with different taxonomic scales. Mixed-level aggregations, as well as morpho-species and ecological-trait classifications should be considered in this optimization process. Looking to the future, closer ties between taxonomists and bioassessment researchers would benefit both of their disciplines. Such coordination would provide the autoecological information and better diagnostic tools (such as keys and molecular methods) needed for biomonitoring, and better (and more widespread) biomonitoring would fuel taxonomy’s resurgence.

Phylogenetic trees underlie our understanding of yeast evolution and are also proving instrumental in the development of a more robust yeast classification system based upon natural (i.e. evolutionary) relationships. In an effort to refine/improve taxonomic resolution, recent studies have focused on the use of multigene rather than single gene sequencing. Nevertheless, searches to determine 'the tree' remain problematic, as they can often overlook conflicts in the dataset. In such instances, phylogenetic networks such as neighbor-nets and consensus networks can provide a more useful and indeed more informative alternative means of analysis. In this study, we have used the latter two phylogenetic network techniques to reanalyze the multigene sequence dataset of Kurtzman & Robnett, which was used to redefine the taxonomy of the family Saccharomycetaceae. Results from our analyses show that, in general, established clades are robust. However, they also reveal conflict between mitochondrial- and nuclear-encoded genes and indicate the existence of complex patterns of hybridization and introgression not detected in the original study. These patterns are discussed in relation to how they may impact upon the current classification of this group of yeasts.

Automated identification and quantification of algae in microscopic images is a tool that allows high taxonomic resolution with reasonable technical efforts. However, in samples containing various non-algal objects, this is still not a satisfactorily solved problem. We show that autofluorescence information improves discrimination of algae from non-algal objects as well as phycoerythrin (PE) containing algae from others. We analyse the stability of the autofluorescence to estimate its constraints. Cold and dark storage of glutaraldehyde fixed samples maintains autofluorescence sufficiently for 3 weeks. Under repeated excitations, chlorophyll a (Chl a) or PE autofluorescence show an exponential decrease followed by an intermediate maximum. A peak also occurs in emission wavelength ranges without chlorophyll and PE fluorescence. The unspecific autofluorescence causing the peaks is at least partly identical with the blue-green fluorescence (BGF) in plant cells. BGF interferes with identification of algae, thus correction of pigment autofluorescence with such unspecific fluorescence allows a more reliable algal discrimination procedure. A classification scheme for discrimination of Chl a and PE-containing algae shows a high performance in a test with natural samples. Integration of fluorescence and bright-field image information provides a powerful tool for phytoplankton analysis in complex samples.

In addition to evidence for bipedality in some fossil taxa, molar enamel thickness is among the few characters distinguishing (thick-enameled) hominins from the (thin-enameled) African apes. Despite the importance of enamel thickness in taxonomic discussions and a long history of scholarship, measurements of enamel thickness are performed almost exclusively on molars, with relatively few studies examining premolars and anterior teeth. This focus on molars has limited the scope of enamel thickness studies (i.e., there exist many fossil hominin incisors, canines, and premolars). Increasing the available sample of teeth from which to compare enamel thickness measurements from the fossil record could substantially increase our understanding of this aspect of dental biology, and perhaps facilitate greater taxonomic resolution of early hominin fossils. In this study, we report absolute and relative (size-scaled) enamel thickness measurements for the complete dentition of modern humans and chimpanzees. In accord with previous studies of molars, chimpanzees show lower relative enamel thickness at each tooth position, with little overlap between the two taxa. A significant trend of increasing enamel thickness from anterior to posterior teeth is apparent in both humans and chimpanzees, indicating that inter-taxon comparisons should be limited to the same tooth position in order to compare homologous structures. As nondestructive imaging techniques become commonplace (facilitating the examination of increasing numbers of fossil specimens), studies may maximize available samples by expanding beyond molars.

One of the commonly quoted weaknesses of pollen analysis is its poor taxonomic resolution, which can be achieved with the Light Microscope (LM). This prevents detailed palaeoecological interpretations from being made. Although the Scanning Electron Microscope (SEM) has been widely available for almost 40 years, it is rarely used in routine palaeopalynological research. The usual reason given is that single-grain techniques are too time-consuming. However, this need not be the case. By combining LM and SEM, fossil pollen grains can be identified more accurately. Moreover, it is possible to distinguish between similar, but botanically distinct, taxa. In this way, palaeopalynology can supply phylogeneticists and palaeoclimatologists with a plethora of useful data.

Complex multi-dimensional datasets are now pervasive in science and elsewhere in society. Better interactive tools are needed for visual data exploration so that patterns in such data may be easily discovered, data can be proofread, and subsets of data can be chosen for algorithmic analysis. In particular, synthetic research such as ecological interaction research demands effective ways to examine multiple datasets. This paper describes our integration of hundreds of food-web datasets into a common platform, and the visualization software, EcoLens, we developed for exploring this information. This publicly-available application and integrated dataset have been useful for our research predicting large complex food webs, and EcoLens is favorably reviewed by other researchers. Many habitats are not well represented in our large database. We confirm earlier results about the small size and lack of taxonomic resolution in early food webs but find that they and a non-food-web source provide trophic information about a large number of taxa absent from more modern studies. Corroboration of Tuesday Lake trophic links across studies is usually possible, but lack of links among congeners may have several explanations. While EcoLens does not provide all kinds of analytical support, its label- and item-based approach is effective at addressing concerns about the comparability and taxonomic resolution of food-web data.

espanolDurante los meses de verano de tres anos consecutivos se estudiaron las caracteristicas fisicoquimicas de cuatro pozas efimeras, de poca profundidad y su fauna de invertebrados. El muestreo de los invertebrados se llevo a cabo por succion del agua con una maquina de bombeo. Desde el punto de vista fisicoquimico, las pozas estudiadas resultaron ser microlimnotopos heliotopicos, mesotroficos y mesopoikilohalinos. Su estratificacion termica resulto ser de caracter monomictico, con pocos grados de diferencia termica entre la superficie y el fondo. Se encontro que sus caracteristicas quimicas las situan entre habitats dulceacuicolas y verdaderamente salinos. Las pozas mostraron alto contenido de fosfato, Ca y sulfato, seguido por los niveles de fluoruro, Fe, K, Mg, Cl y nitrato. El contenido de los solidos totales suspendidos fue igualmente alto. Por el contrario, el contenido de bicarbonato y CN fue bajo. Al parecer, las propiedades geoquimicas de las montanas que rodean a la vega juegan un papel importante en la hidroquimica de estos cuerpos de agua. En general, las abundancias totales por taxon fueron bajas. Se registraron cinco taxones superiores. Cladoceros (e.g., Alona spp.), seguido por los dipteros quironomidos y los copepodos ciclopoideos y harpacticoideos fueron los grupos dominantes. Grupos menos abundantes fueron los anfipodos (e.g., Hyperia spp.) y los ostracodos Cyprididae. Algunos de los taxones reportados en este trabajo se registran por primera vez en este tipo de habitat. Sin embargo, debido a sus caracteristicas, se necesitan estudios con una resolucion taxonomica mas fina con el fin de dilucidar la presencia de generos o especies propias de estos sistemas. En comparacion con los cuerpos loticos encontrados en la zona, las pozas arrojaron una menor riqueza taxonomica. Este resultado puede deberse a diferencias en la dinamica de las condiciones abioticas observadas entre los dos habitats. La variabilidad entre pozas, asociada a la abundancia, fue alta para la mayoria de los taxones registrados. Esta variabilidad puede ser un reflejo de la condicion general de la vega estudiada, lo que sugiere que estas pozas son fuente importante de la alta biodiversidad observada en estas unidades de paisaje. Como las vegas de la zona estan conectadas en red, tambien contribuyen a la biodiversidad de todo el sistema de montana. A partir de este argumento, resulta claro que las estrategias de conservacion de las vegas andinas necesitan incluir a estas pequenas unidades de paisaje. EnglishThe physical-chemical features of four temporary shallow ponds and their invertebrate fauna were studied during the summer months of three consecutive years. Invertebrate sampling was conducted by suction of pond water with a pump. From the physical-chemical point of view, the study ponds were heliotopic, mesotrophic and mesopoikilohaline microlimnotopes. Their thermal stratification is monomic-tic, with few degrees of difference in water temperature between surface and bottom. The chemical characteristics of pond water were in between those of freshwater and truly saline ponds. The study ponds exhibited high content of phosphate, Ca, and sulfate content, followed by fluoride, Fe, K, Mg, Cl, nitrate, and total suspended solids. They were low in bicarbonate and CN content. Apparently, the geochemical properties of the surrounding mountains play a role in the hydrochemistry of these water bodies. Total abundance per taxon was mostly low. We recorded five higher taxa. Cladocerans (e.g., Alona spp.), followed by dipterans (e.g., chironomid flies), and copepods (e.g., cyclopoids and harpactoids) were the dominant groups. Less abundant groups were amphipods (e.g., Hyperia spp.), and ostracods (e.g., Cyprididae). Some of the taxa reported in this work are recorded for first time in this type of habitat. Nevertheless, given the habitat characteristics, studies at finer taxonomic resolution are needed to search for site-specific genera or species. We obtained lower taxono-mic richness compared to lotic systems found in the area. This result may be due to differences in the dynamics of abiotic conditions observed between the two habitats. The variability in abundance among ponds was high for most of the recorded taxa. This variability may be a reflection of the general condition of the wet pasture we studied, suggesting that the ponds are important sources of the high biodiversity found in these landscape units. As the wet pastures of the area are networked, also contribute to biodiversity of the entire mountain system. From this, it is clear that conservation strategies of Andean wet pastures need to include these small landscape units.

ISI Document Delivery No.: CF3II Times Cited: 0 Cited Reference Count: 52 Cited References: Szoecs Eduard, 2012, SCIENCE OF THE TOTAL ENVIRONMENT, V437, P121 Szoecs, Eduard Van den Brink, Paul J. Lagadic, Laurent Caquet, Thierry Roucaute, Marc Auber, Arnaud Bayona, Yannick Liess, Matthias Ebke, Peter Ippolito, Alessio ter Braak, Cajo J. F. Brock, Theo C. M. Schafer, Ralf B. Interface Recherche-Expertise pour l'Evaluation du Risque en Ecotoxicologie; Ministry of Ecology, Sustainable Development and Energy; TOTAL S.A. [10, 11]; Region Bretagne; INRA; Dutch Ministry of Economic Affairs; TOTAL S.A.; [BO-20-002-001] The authors gratefully acknowledge the contributions from scientists and technicians from the INRA Experimental Unit of Aquatic Ecology and Ecotoxicology and Ecotoxicology and Quality and Aquatic Research Group during mesocosm experiments. These experiments were conducted in programmes funded by the Interface Recherche-Expertise pour l'Evaluation du Risque en Ecotoxicologie coordinated by the Structure Scientifique Mixte INRA-Direction Generale de l'Alimentation (Study no. 8), by the Ministry of Ecology, Sustainable Development and Energy through its "Pesticides" research programme (Study Nos. 3, 4), and by TOTAL S.A. (Study Nos. 10, 11). A. Auber and Y. Bayona PhDs were funded through a grant from The Region Bretagne and INRA and by TOTAL S.A., respectively. The studies conducted at Wageningen UR (Study nos. 1, 7 and 9) were financially supported by the Dutch Ministry of Economic Affairs, as well as the contribution of Paul Van den Brink and Theo Brock to this paper (Project BO-20-002-001). The data sets of these studies are available upon request. Springer Dordrecht Environmental Sciences & Ecology; Toxicology; International audience; Mesocosm experiments that study the ecological impact of chemicals are often analysed using the multivariate method 'Principal Response Curves' (PRCs). Recently, the extension of generalised linear models (GLMs) to multivariate data was introduced as a tool to analyse community data in ecology. Moreover, data aggregation techniques that can be analysed with univariate statistics have been proposed. The aim of this study was to compare their performance. We compiled macroinvertebrate abundance datasets of mesocosm experiments designed for studying the effect of various organic chemicals, mainly pesticides, and re-analysed them. GLMs for multivariate data and selected aggregated endpoints were compared to PRCs regarding their performance and potential to identify affected taxa. In addition, we analysed the inter-replicate variability encountered in the studies. Mesocosm experiments characterised by a higher taxa richness of the community and/or lower taxonomic resolution showed a greater inter-replicate variability, whereas variability decreased the more zero counts were encountered in the samples. GLMs for multivariate data performed equally well as PRCs regarding the community response. However, compared to first axis PRCs, GLMs provided a better indication of individual taxa responding to treatments, as separate models are fitted to each taxon. Data aggregation methods performed considerably poorer compared to PRCs. Multivariate community data, which are generated during mesocosm experiments, should be analysed using multivariate methods to reveal treatment-related community-level responses. GLMs for multivariate data are an alternative to the widely used PRCs.

We report the application of a molecular barcode method (ZooMS) to identify fragmentary bone remains (>2.5 cm) from a Middle to Upper Palaeolithic sequence at Les Cottes, France. ZooMS uses peptide mass fingerprinting of collagen (the most abundant protein in bone) to discriminate fauna (typically to genus level). Using previously reported peptide markers we initially conducted a blind test using 34 morphologically identified bones, followed by the application of ZooMS on 145 morphologically unidentified bone specimens. For the blind test, ZooMS was in agreement with morphological identifications in all cases, but in some instances taxonomic resolution is lower than morphological identifications. Further, 93.8% (136/145) of spectra obtained for morphologically unidentified bone specimens result in identifications that cannot be taxonomically improved by ZooMS. These include ten bone specimens showing signs of carnivore digestion. Focussing on the unidentified bone specimens of the Châtelperronian unit at Les Cottes (US06), ZooMS identified an additional ≈30% of the total number of bones discovered, increasing the total number of identified bone specimens to 61.8%. Further, ZooMS revealed higher taxonomic richness compared to morphological identifications for US06, thereby providing a more informed interpretation of the faunal community present at Les Cottes during the Châtelperronian.

Chironomids (non-biting midges) have been used in palaeoenvironmental studies in Eurasia since the 1920s. Initially changes in chironomid assemblages were largely interpreted as a response to changes in trophic status or water depth. It was only with the advent of chironomid-temperature inference models in the early 1990s that their potential as palaeoclimatic indicators was fully exploited. This paper provides a brief review of the pioneering studies but focuses on the most recent advances. Better taxonomic resolution of fossil midges, expansion of modern training sets, use of air temperature data derived from meteorological stations rather than surface-water temperature data, and Bayesian statistical approaches have lead to improvements in the performance of chironomid-temperature transfer functions. Applications of these transfer functions to derive chironomid-inferred temperature estimates from Lateglacial (ca 15,000–11,200 cal. yr BP) and Holocene (11,200 cal. yr BP to Present) sequences from throughout Eurasia are reviewed in this paper. Chironomid-inferred Lateglacial reconstructions closely reflect oxygen isotope records from Greenland ice cores. Holocene reconstructions are less consistent. Some closely follow instrumental records or corroborate other proxy data, while other reconstructions are less successful. As a result of soil development during the Holocene, changes in pH, nutrients, DO and DOC had a greater influence than temperature on the composition of some midge assemblages. One way to mitigate this is through consensus temperature reconstructions from several sites in the same region. The challenge for future workers is for further improvement in taxonomic resolution of sub-fossil chironomid larvae, to improve further the performance of chironomid-temperature inference models, to develop training sets for southern Europe and Russia and to improve our understanding of the ecological responses of chironomids.

Studies conducted along the southern Iberian coastline validate macrobenthic community analyses at taxonomic levels higher than that of species. Twelve studies on littoral benthic communities, carried out by the same research team, were selected spanning both a variety of sampling strategies (spatial, temporal, spatiotemporal) and substrate/habitat types (sediment, rock, algae). In order to establish differences between the results obtained at the taxonomic levels of species, family and order, similarities among stations were calculated using Spearman’s coefficient for ranges. A subset of three studies was selected to investigate possible differences in ‘best-explaining’ environmental variables with taxonomic level. The environmental variables selected at species level were the same as those found at levels of family and order. It is concluded that studies at the different levels of taxonomic resolution (species, family, order) lead to similar results both with regard to relative community distributions and the environmental variables associated with these. The importance of this result for monitoring similar benthic communities is discussed.

Several studies in semi-natural coastal lagoons in the Ria Formosa lagoonal system have been carried out. These man-made water reservoirs behave as small lagoons with one opening to the tidal channels, which may be intermittent. Because of their size, these reservoirs are ideal sites for ecological studies. Water quality and macrobenthic fauna were analysed in five water reservoirs. All reservoirs received the same incoming water through a tidal channel, but they differed in water renewal regime. Multidimensional Scaling (MDS) and Discriminant Analysis were used to evaluate the similarity among sites, stations and sampling occasions. Different levels of taxonomic resolution (family, large taxonomic groups and phylum level) were also evaluated. The separation of sites and stations became unclear using high taxonomic levels. Results from the multivariate analyses suggest a slight differentiation of the stations according to sampling occasion but a clear differentiation of the several water reservoirs. Some of the lagoons studied with low water renewal rates showed strong environmental variations. They were characterised by low diversity indexes and abundance of small-sized organisms. Other lagoons, with high water renewal rates, showed low environmental variation and well diversified and structured benthic communities. The main environmental factor that seems to affect the benthic communities was the variation in salinity between neap and spring tides, which is related with the water renewal regime. Coastal lagoons offer a protected shallow habitat, which can be highly productive. Well structured communities, controlled by k-strategists, can develop and settle in leaky lagoons, that is, lagoons with wide entrance channels and tidal currents which guarantee a good water renewal. In these lagoons, biomass can accumulate in large organisms. In contrast, lagoons with a single narrow entrance, that may be closed for long periods, are characterised by persistent physical stress and are dominated by communities of small-sized r-strategists.

1. Sampling and processing of benthic macroinvertebrate samples is time consuming and expensive. Although a number of cost-cutting options exist, a frequently asked question is how representative a subset of data is of the whole community, in particular in areas where habitat diversity is high (like Dutch surface water habitats). 2. Weighted averaging was used to reassign 650 samples to a typology of 40 community types, testing the representativeness of different subsets of data: (i) four different types of data (presence/absence, raw, (2)log- and ln-transformed abundance), (ii) three subsets of 'indicator' taxa (taxa with indicator weights 4-12, 7-12, and 10-12) and (iii) single taxonomic groups (n = 14) by determining the classification error. 3. (2)log- and ln-transformed abundances resulted in the lowest classification error, whilst the use of qualitative data resulted in a reduction of 10% of the samples assigned to their original community type compared to the use of ln-transformed abundance data. 4. Samples from community types with a high number of unique indicator taxa had the lowest classification error, and classification error increased as similarity among community types increased. Using a subset of indicator taxa resulted in a maximum increase of the classification error of 15% when only taxa with an indicator weight 10-12 were included (error = 49.1%). 5. Use of single taxonomic groups resulted in high classification error, the lowest classification error was found using Trichoptera (68%), and was related to the frequency of the taxonomic group among samples and the indicator weights of the taxa. 6. Our findings that the use of qualitative data, subsets of indicator taxa or single taxonomic groups resulted in high classification error implies low taxonomic redundancy, and supports the use of all taxa in characterising a macroinvertebrate community, in particular in areas where habitat diversity is high.

Using lake trout ( Salvelinus namaycush ) and walleye ( Sander vitreus ) we examined the extent of error that is created when non-population-specific or non-sex-specific data are used to develop fishery sustainability models. To put biases in perspective we first compared relative differences in sustainable harvest rate estimates of fast and slow growing populations to the mean difference between species. Few estimates of early mortality exist for either species, and a sensitivity analysis indicated that sustainable harvest rate estimates varied by more than 90% with those available. To evaluate biases created by predicting life history traits we estimated maturation age from asymptotic length in populations whose life history parameters had been measured directly. Incorporating species-specific information produced maturation ages that were closer to those measured (mean difference 22%) than did the estimates from inter-specific relationships (mean difference 42%). This resulted in sustainability estimates from species-specific predictions being closer to those estimated using actual maturation data. In evaluating problems associated with using non-sex-specific data we found that estimates of maximum sustainable harvest rates increased when female-specific life history data were used (could only be done for walleye) instead of combined-sex data (mean change in the two populations was 7%). Analyses indicate that it is desirable to collect life history data on specific populations of lake trout and walleye. If this is not possible, estimates of maximum sustainable harvest rates are most influenced by variation in estimates of early mortality, followed by the taxonomic resolution used to estimate co-variation among life history traits, and finally the use of combined-sex versus female-specific data.

The idea of using nucleotide sequences as barcodes for species identification has stirred up debates in the community of taxonomists and systematists. We argue that barcodes are potentially extremely useful tools for taxonomy for several reasons. Barcodes may, for example, help to identify cryptic and polymorphic species and give means to associate life history stages of unknown identity. Barcode systems would thus be particularly helpful in cases when morphology is ambiguous or uninformative and would provide tools for higher taxonomic resolution of disparate life forms. Comparative analysis of short DNA sequences may also represent heuristic access cards to a deeper understanding of evolutionary relationships between organisms. However, barcodes are the “essence” of species identities no more than taxonomic holotypes are “the species”. It makes no sense to think that morphology and other biological information about organisms can be made obsolete by barcode systems. The biological significance of matchi...