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2.
Trends Ecol Evol ; 33(12): 945-957, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-30314916

RESUMO

Ecological communities change in time and space, but long-term dynamics at the century-to-millennia scale are poorly documented due to lack of relevant data sets. Nevertheless, understanding long-term dynamics is important for explaining present-day biodiversity patterns and placing conservation goals in a historical context. Here, we use recent examples and new perspectives to highlight how environmental DNA (eDNA) is starting to provide a powerful new source of temporal data for research questions that have so far been overlooked, by helping to resolve the ecological dynamics of populations, communities, and ecosystems over hundreds to thousands of years. We give examples of hypotheses that may be addressed by temporal eDNA biodiversity data, discuss possible research directions, and outline related challenges.


Assuntos
Biodiversidade , DNA/análise , Meio Ambiente , Ecologia , Ecossistema
3.
Mol Ecol Resour ; 18(6): 1415-1426, 2018 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-30155977

RESUMO

Rapid environmental change in highly biodiverse tropical regions demands efficient biomonitoring programmes. While existing metrics of species diversity and community composition rely on encounter-based survey data, eDNA recently emerged as alternative approach. Costs and ecological value of eDNA-based methods have rarely been evaluated in tropical regions, where high species richness is accompanied by high functional diversity (e.g., the use of different microhabitats by different species and life stages). We first tested whether estimation of tropical frogs' community structure derived from eDNA data is compatible with expert field assessments. Next, we evaluated whether eDNA is a financially viable solution for biodiversity monitoring in tropical regions. We applied eDNA metabarcoding to investigate frog species occurrence in five ponds in the Chiquitano dry forest region in Bolivia and compared our data with a simultaneous visual and audio encounter survey (VAES). We found that taxon lists and community structure generated with eDNA and VAES correspond closely, and most deviations are attributable to different species' life histories. Cost efficiency of eDNA surveys was mostly influenced by the richness of local fauna and the number of surveyed sites: VAES may be less costly in low-diversity regions, but eDNA quickly becomes more cost-efficient in high-diversity regions with many sites sampled. The results highlight that eDNA is suitable for large-scale biodiversity surveys in high-diversity areas if life history is considered, and certain precautions in sampling, genetic analyses and data interpretation are taken. We anticipate that spatially extensive, standardized eDNA biodiversity surveys will quickly emerge in the future.


Assuntos
Anfíbios/classificação , Anfíbios/genética , Biota , Código de Barras de DNA Taxonômico/métodos , Metagenômica/métodos , Animais , Bolívia , Custos e Análise de Custo , Código de Barras de DNA Taxonômico/economia , Metagenômica/economia , Clima Tropical
4.
Parasit Vectors ; 11(1): 81, 2018 02 05.
Artigo em Inglês | MEDLINE | ID: mdl-29402295

RESUMO

BACKGROUND: As ectothermic animals, temperature influences insects in almost every aspect. The potential disease spreading Asian bush mosquito (Aedes japonicus japonicus) is native to temperate East Asia but invasive in several parts of the world. We report on the previously poorly understood temperature-dependence of its life history under laboratory conditions to understand invasion processes and to model temperature niches. RESULTS: To evaluate winter survival, eggs were exposed between 1 day and 14 days to low temperatures (5 °C, 0 °C, -5 °C and -9 °C). Hatching success was drastically decreased after exposure to 0 °C and -5 °C, and the minimal hatching success of 0% was reached at -9 °C after two days. We then exposed larvae to 14 temperatures and assessed their life trait parameters. Larval survival to adulthood was only possible between 10 °C and 31 °C. Based on this, we modelled the optimal (25 °C), minimal (7 °C) and maximal (31 °C) temperature for cumulative female survival. The time to adult emergence ranges from 12 days to 58 days depending on temperature. We used an age-at-emergence-temperature model to calculate the number of potential generations per year for the Asian bush mosquito in Germany with an average of 4.72 potential generations. At lower temperatures, individuals grew larger than at higher temperatures with female R1 length ranging from 3.04 ± 0.1 mm at 31 °C to 4.26 ± 0.2 mm at 15 °C. CONCLUSIONS: Reduced egg hatch after exposure to sub-zero temperatures prohibits the establishment of the Asian bush mosquito in large parts of Germany. Larval overwintering is not possible at temperature ≤ 5 °C. The many potential generations displayed per year may contribute to the species' invasion success. This study on the thermal ecology of the Asian bush mosquito adds to our knowledge on the temperature dependence of the species and data could be incorporated in epidemiological and population dynamic modelling.


Assuntos
Aedes/fisiologia , Espécies Introduzidas , Larva/fisiologia , Temperatura , Aedes/crescimento & desenvolvimento , Animais , Temperatura Baixa , Feminino , Alemanha , Mosquitos Vetores/crescimento & desenvolvimento , Mosquitos Vetores/fisiologia , Oócitos/fisiologia , Estações do Ano
5.
Ecol Evol ; 8(3): 1786-1793, 2018 02.
Artigo em Inglês | MEDLINE | ID: mdl-29435253

RESUMO

Properly designed (randomized and/or balanced) experiments are standard in ecological research. Molecular methods are increasingly used in ecology, but studies generally do not report the detailed design of sample processing in the laboratory. This may strongly influence the interpretability of results if the laboratory procedures do not account for the confounding effects of unexpected laboratory events. We demonstrate this with a simple experiment where unexpected differences in laboratory processing of samples would have biased results if randomization in DNA extraction and PCR steps do not provide safeguards. We emphasize the need for proper experimental design and reporting of the laboratory phase of molecular ecology research to ensure the reliability and interpretability of results.

6.
Forensic Sci Med Pathol ; 14(1): 76-84, 2018 03.
Artigo em Inglês | MEDLINE | ID: mdl-29349723

RESUMO

In forensic entomology, many studies analyze fly activity and succession on dead bodies by using pig cadavers and a variety of small baited traps. Data on real human bodies are very rare. To address this shortcoming, we analyzed the fly fauna of 51 human bodies in Germany. Sex, age, place of discovery, and presumed time of death were noted. Larvae were sampled during autopsy according to body region or tissue. For every infested region, the total number of fly larvae were estimated and classified into categories of 1-10, 11-50, and 50+. All samples were identified to the species level. Besides a descriptive analysis of their occurrence patterns, a categorical PCA was performed, and multispecies generalized linear models and a latent variable model were run. Our results highlight the most forensically important blow flies on human bodies in Central Europe (Lucilia sericata, L. ampullacea, Phormia regina, Calliphora vicina); prove, for the first time, the general transferability of species lists based on succession studies on pig cadavers; recommend a certain set of species, such as the so-far neglected L. ampullacea, for future developmental studies; and reveal competitive occurrence of up to six species on the same body as a potential factor of influence. Assignment to a certain body region was often possible and our data clearly indicate certain tissues, e.g. brain, as of high interest for future developmental studies. Focusing on real scenario settings helps direct research to forensically relevant questions and appraises the plausibility of vital laboratory studies.


Assuntos
Biodiversidade , Dípteros , Comportamento Alimentar , Mudanças Depois da Morte , Adulto , Idoso , Animais , Restos Mortais , Entomologia , Feminino , Ciências Forenses , Alemanha , Humanos , Larva , Masculino , Pessoa de Meia-Idade
7.
Microb Ecol ; 75(2): 468-478, 2018 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-28785816

RESUMO

Using terrestrial model ecosystems (TMEs), we investigated how reduced moisture conditions impact soil fungal communities from a temperate grassland over the course of an entire season. Starting at about 65% of the soil's maximum water holding capacity (WHCmax), TME soils were adjusted to three moisture levels for 15 weeks: 70% WHCmax, approximating starting conditions, 50% WHCmax, and 30% WHCmax, representing reduced moisture conditions. Diversity and abundances of soil fungi at the start and at the end of the experiment were characterized using Illumina meta-barcoding. Community diversity at the end of the experiment did not differ between experimental moisture levels and was comparable to diversity measures from the field. However, fungal communities did change compositionally in both abundances and presence/absence of species. Analyzing class-level and individual contributions of fungi to these changes revealed that only a minor portion reacted significantly, indicating that most compositional change was likely driven by many consistent small-scale shifts in presence/absences or abundances. Together, our results show that prolonged reduction in soil moisture conditions will trigger compositional changes in soil fungal communities but not necessarily change overall diversity. We highlight the cumulative contribution of minor but consistent changes among community members, as opposed to significant responses of individual species. We also detected a strong general experimental effect on soil fungi that are moved from the field to experimental TMEs, suggesting the importance of acclimatization effects in these communities under laboratory conditions.


Assuntos
Fungos/isolamento & purificação , Microbiologia do Solo , Biodiversidade , Secas , Ecossistema , Fungos/classificação , Fungos/genética , Pradaria , Micobioma , Filogenia , Estações do Ano , Solo/química , Água/análise
8.
BMC Evol Biol ; 17(1): 129, 2017 06 06.
Artigo em Inglês | MEDLINE | ID: mdl-28587671

RESUMO

BACKGROUND: Taxonomy offers precise species identification and delimitation and thus provides basic information for biological research, e.g. through assessment of species richness. The importance of molecular taxonomy, i.e., the identification and delimitation of taxa based on molecular markers, has increased in the past decade. Recently developed exploratory tools now allow estimating species-level diversity in multi-locus molecular datasets. RESULTS: Here we use molecular species delimitation tools that either quantify differences in intra- and interspecific variability of loci, or divergence times within and between species, or perform coalescent species tree inference to estimate species-level entities in molecular genetic datasets. We benchmark results from these methods against 14 morphologically readily differentiable species of a well-defined subgroup of the diverse Drusinae subfamily (Trichoptera, Limnephilidae). Using a 3798 bp (6 loci) molecular data set we aim to corroborate a geographically isolated new species by integrating comparative morphological studies and molecular taxonomy. CONCLUSIONS: Our results indicate that only multi-locus species delimitation provides taxonomically relevant information. The data further corroborate the new species Drusus zivici sp. nov. We provide differential diagnostic characters and describe the male, female and larva of this new species and discuss diversity patterns of Drusinae in the Balkans. We further discuss potential and significance of molecular species delimitation. Finally we argue that enhancing collaborative integrative taxonomy will accelerate assessment of global diversity and completion of reference libraries for applied fields, e.g., conservation and biomonitoring.


Assuntos
Insetos/classificação , Insetos/genética , Animais , Península Balcânica , Feminino , Insetos/anatomia & histologia , Insetos/crescimento & desenvolvimento , Larva/genética , Masculino , Filogenia
9.
FEMS Microbiol Rev ; 40(5): 686-700, 2016 09.
Artigo em Inglês | MEDLINE | ID: mdl-27358393

RESUMO

With high-throughput sequencing (HTS), we are able to explore the hidden world of microscopic organisms to an unpre-cedented level. The fast development of molecular technology and statistical methods means that microbial ecologists must keep their toolkits updated. Here, we review and evaluate some of the more widely adopted and emerging techniques for analysis of diversity and community composition, and the inference of species interactions from co-occurrence data generated by HTS of marker genes. We emphasize the importance of observational biases and statistical properties of the data and methods. The aim of the review is to critically discuss the advantages and disadvantages of established and emerging statistical methods, and to contribute to the integration of HTS-based marker gene data into community ecology.


Assuntos
Archaea/genética , Bactérias/genética , Fungos/genética , Marcadores Genéticos/genética , Microbiota/genética , Archaea/classificação , Bactérias/classificação , Biodiversidade , Interpretação Estatística de Dados , Fungos/classificação , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Análise de Sequência de DNA/métodos
10.
Zookeys ; (559): 107-24, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27006607

RESUMO

In this paper we describe Drusus sharrensis sp. n., from the Sharr Mountains in Kosovo. Males of the new species are morphologically most similar to Drusus krusniki Malicky, 1981, Drusus kerek Oláh, 2011 and Drusus juliae Oláh, 2011 but differ mainly in exhibiting (1) a differently shaped spinose area on tergite VIII; (2) intermediate appendages anteriorly curved in lateral view with broad tips in dorsal view; (3) inferior appendages with a distinct dorsal protrusion in the proximal half. Females of the new species are morphologically most similar to Drusus krusniki, Drusus kerek, Drusus juliae, and Drusus plicatus Radovanovic, 1942 but mainly differ in (1) segment X that is longer than the supragenital plate with distinctly pointed tips; (2) supragenital plate quadrangular with a distinct round dorsal protrusion; (3) a vulvar scale with a small median lobe. Results of phylogenetic species delimitation support monophyly of Drusus sharrensis sp. n. and recover it as sister to a clade comprising (Drusus pelasgus Oláh, 2010 + Drusus juliae + Drusus arbanios Oláh, 2010 + Drusus plicatus + (Drusus dacothracus Oláh, 2010 + Drusus illyricus Oláh, 2010)). The new species is a micro-endemic of the Sharr Mountains, a main biodiversity hotspot in the Balkan Peninsula. Main threats to the aquatic ecosystems of this part of the Balkan Peninsula are discussed.

11.
Zootaxa ; 4083(4): 483-500, 2016 Feb 23.
Artigo em Inglês | MEDLINE | ID: mdl-26985141

RESUMO

Drusinae (Trichoptera, Limnephilidae) are highland caddisflies inhabiting high-gradient, turbulent running water and spring habitats. They are disjunctly distributed over the Eurasian mountain ranges, and the majority of species is endemic to particular mountain areas. The most diverse of three main groups of the Drusinae, the grazer clade, consists of species in which larvae feed on epiltihic biofilm and algae. In this paper we describe three previously unknown grazer-clade Drusinae larvae: Drusus krusniki Malicky 1981 (endemic to the Dinaric western Balkans), D. vernonensis Malicky 1989 (endemic to the Hellenic western Balkans), and D. vespertinus Marinkovic 1976 (endemic to the Dinaric western Balkans). The larvae of these species have toothless mandibles typical of the Drusinae grazer clade. Larvae and adults were unambiguously associated using molecular genetic data, i.e., the mitochondrial cytochrome oxidase I gene fragment (mtCOI3-P). Morphological characteristics of the larvae are described and the diagnostic features enabling species-level identification are illustrated. We further discuss the ecology and distribution of three Western Balkan endemic species.


Assuntos
Insetos/anatomia & histologia , Animais , Península Balcânica , Ecologia , Ecossistema , Larva
12.
Proc Biol Sci ; 283(1825): 20152413, 2016 Feb 24.
Artigo em Inglês | MEDLINE | ID: mdl-26888029

RESUMO

The evolutionary speed hypothesis (ESH) proposes a causal mechanism for the latitudinal diversity gradient. The central idea of the ESH is that warmer temperatures lead to shorter generation times and increased mutation rates. On an absolute time scale, both should lead to an acceleration of selection and drift. Based on the ESH, we developed predictions regarding the distribution of intraspecific genetic diversity: populations of ectothermic species with more generations per year owing to warmer ambient temperatures should be more differentiated from each other, accumulate more mutations and show evidence for increased mutation rates compared with populations in colder regions. We used the multivoltine insect species Chironomus riparius to test these predictions with cytochrome oxidase I (COI) sequence data and found that populations from warmer regions are indeed significantly more differentiated and have significantly more derived haplotypes than populations from colder regions. We also found a significant correlation of the annual mean temperature with the population mutation parameter θ that serves as a proxy for the per generation mutation rate under certain assumptions. This pattern could be corroborated with two nuclear loci. Overall, our results support the ESH and indicate that the thermal regime experienced may be crucially driving the evolution of ectotherms and may thus ultimately govern their speciation rate.


Assuntos
Evolução Biológica , Chironomidae/fisiologia , Clima , Distribuição Animal , Animais , Chironomidae/genética , Europa (Continente) , Haplótipos , Temperatura
13.
Zootaxa ; 4032(5): 551-68, 2015 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-26624385

RESUMO

The Balkan Peninsula is one of the most important European hotspots of freshwater biodiversity. The region is, however, to a large extent insufficiently investigated. Here we present data on distribution of caddisflies in one particularly understudied area, the Republic of Kosovo. Our data include the first records of Adicella altandroconia Botosaneanu & Novak and Halesus tessellatus (Rambur) for the Kosovo caddisfly fauna, and a new locality for the recently described Ecclisopteryx keroveci Previsic, Graf, & Vitecek. Further, we describe the new caddisfly species Drusus dardanicus sp. nov. from the Kopaonik Mountains. The new species belongs to the D. discophorus Species Group and differs morphologically from its most similar congeners (D. discophorus Radovanovic, D. balcanicus Kumanski, and D. bureschi Kumanski) mainly in exhibiting (1) subtrianglar superior appendages; (2) a narrow, dorsal spinate area of tergite VIII; and (3) evenly rounded tips of intermediate appendages in caudal view. In phylogenetic analysis, D. dardanicus sp. nov. is well delineated and recovered as a sister taxon to D. osogovicus Kumanski, a species recorded from Bulgaria. The recent discovery of a new species and other rare or microendemic species presents important contributions to the knowledge on the rich freshwater biodiversity in Kosovo. These species face increasing anthropogenic pressure and threats to their conservation.


Assuntos
Insetos/classificação , Distribuição Animal , Estruturas Animais/anatomia & histologia , Estruturas Animais/crescimento & desenvolvimento , Animais , Biodiversidade , Tamanho Corporal , Ecossistema , Feminino , Insetos/anatomia & histologia , Insetos/genética , Insetos/crescimento & desenvolvimento , Masculino , Tamanho do Órgão , Filogenia
14.
Mol Phylogenet Evol ; 93: 249-260, 2015 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-26265260

RESUMO

The caddisfly subfamily Drusinae BANKS comprises roughly 100 species inhabiting mountain ranges in Europe, Asia Minor and the Caucasus. A 3-gene phylogeny of the subfamily previously identified three major clades that were corroborated by larval morphology and feeding ecologies: scraping grazers, omnivorous shredders and filtering carnivores. Larvae of filtering carnivores exhibit unique head capsule complexities, unknown from other caddisfly larvae. Here we assess the species-level relationships within filtering carnivores, hypothesizing that head capsule complexity is derived from simple shapes observed in the other feeding groups. We summarize the current systematics and taxonomy of the group, clarify the systematic position of Cryptothrix nebulicola, and present a larval key to filtering carnivorous Drusinae. We infer relationships of all known filtering carnivorous Drusinae and 34 additional Drusinae species using Bayesian species tree analysis and concatenated Bayesian phylogenetic analysis of 3805bp of sequence data from six gene regions (mtCOI5-P, mtCOI3-P, 16S mrDNA, CADH, WG, 28S nrDNA), morphological cladistics from 308 characters, and a total evidence analysis. All analyses support monophyly of the three feeding ecology groups but fail to fully resolve internal relationships. Within filtering carnivores, variation in head setation and frontoclypeus structure may be associated with progressive niche adaptation, with less complex species recovered at a basal position. We propose that diversification of complex setation and frontoclypeus shape represents a recent evolutionary development, hypothetically enforcing speciation and niche specificity within filtering carnivorous Drusinae.


Assuntos
Insetos/genética , Distribuição Animal , Animais , Teorema de Bayes , Carnivoridade , Europa (Continente) , Evolução Molecular , Feminino , Genes de Insetos , Especiação Genética , Cabelo/anatomia & histologia , Insetos/anatomia & histologia , Larva/anatomia & histologia , Larva/genética , Masculino , Filogenia , Análise de Sequência de DNA
15.
Zookeys ; (513): 79-104, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26257570

RESUMO

Two new species of the genus Drusus (Trichoptera, Limnephilidae, Drusinae) from the Western Balkans are described. Additionally, observations on the biodiversity and threats to the region's endemic aquatic fauna are discussed. Drususkrpachi sp. n. is a micro-endemic of the Korab Mountains, Macedonia, and Drususmalickyi sp. n. is a micro-endemic of the Prokletije Mountains, Albania. Both new species are most similar to Drususmacedonicus but differ from the latter in the shape of segment IX, the shape of the tips of the intermediate appendages in lateral view, the shape of the inferior appendages, and the form and shape of the parameres. In addition, males of the European species of filtering carnivore Drusinae are diagnosed and illustrated, including Cryptothrixnebulicola McLachlan, Drususchrysotus Rambur, Drususdiscolor Rambur, Drususmacedonicus Schmid, Drususmeridionalis Kumanski, Drususmuelleri McLachlan, Drususromanicus Murgoci and Botosaneanu, and Drusussiveci Malicky. These additions to the Western Balkan fauna demonstrate the significance of this region for European biodiversity and further highlight the importance of faunistic studies in Europe.

16.
Zookeys ; (496): 85-103, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-25931956

RESUMO

New species are described in the genera Wormaldia (Trichoptera, Philopotamidae) and Drusus (Trichoptera, Limnephilidae, Drusinae). Additionally, the larva of the new species Drususcrenophylax sp. n. is described, and a key provided to larval Drusus species of the bosnicus-group, in which the new species belongs. Observations on the threats to regional freshwater biodiversity and caddisfly endemism are discussed. The new species Wormaldiasarda sp. n. is an endemic of the Tyrrhenian island of Sardinia and differs most conspicuously from its congeners in the shape of segment X, which is trilobate in lateral view. The new species Drususcrenophylax sp. n. is a micro-endemic of the Western Balkans, and increases the endemism rate of Balkan Drusinae to 79% of 39 species. Compared to other Western Balkan Drusus, males of the new species are morphologically most similar to Drususdiscophorus Radovanovic and Drususvernonensis Malicky, but differ in the shape of superior and intermediate appendages. The females of Drususcrenophylax sp. n. are most similar to those of Drususvernonensis, but differ distinctly in the outline of segment X. Larvae of Drususcrenophylax sp. n. exhibit toothless mandibles, indicating a scraping grazing-feeding ecology.

17.
Eur J Entomol ; 112(2): 344-361, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26997882

RESUMO

In a recent 3-gene phylogeny of the Trichoptera subfamily Drusinae Banks, 1916 molecular data clearly correlated with the morphology and feeding ecology of larvae. The largest of three main groups, the Drusinae grazer clade, exhibits an unusual larval feeding ecology for Limnephilidae, and is the most diverse group. In this paper we describe four previously unknown Drusinae larvae from this clade: Drusus balcanicus Kumanski, 1973 (micro-endemic to Eastern Balkans); Drusus botosaneanui Kumanski, 1968 (Dinaric Western Balkans, Hellenic and Eastern Balkan, Asia Minor), Drusus serbicus Marinkovic-Gospodnetic, 1971a (micro-endemic to Dinaric Western Balkans); and Drusus tenellus (Klapálek, 1898) (Carpathians, Dinaric Eastern Balkans). Characteristically, the larvae of these species develop toothless mandibles typical for the Drusinae grazer clade. Larvae and adults were unambiguously associated by a phylogenetic approach based on two mitochondrial (mtCOI, mtLSU= 16S rDNA) and two nuclear genes (nuWG, nuCAD). In addition, information on the morphology of the larvae is given and the diagnostic features necessary for identification are illustrated.

18.
Mol Ecol ; 24(1): 235-48, 2015 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-25443313

RESUMO

Micro-organisms associated with plants and animals affect host fitness, shape community structure and influence ecosystem properties. Climate change is expected to influence microbial communities, but their reactions are not well understood. Host-associated micro-organisms are influenced by the climate reactions of their hosts, which may undergo range shifts due to climatic niche tracking, or may be actively relocated to mitigate the effects of climate change. We used a common-garden experiment and rDNA metabarcoding to examine the effect of host relocation and high-latitude warming on the complex fungal endophytic microbiome associated with leaves of an ecologically dominant boreal forest tree (Populus balsamifera L.). We also considered the potential effects of poplar genetic identity in defining the reactions of the microbiome to the treatments. The relocation of hosts to the north increased the diversity of the microbiome and influenced its structure, with results indicating enemy release from plausible pathogens. High-latitude warming decreased microbiome diversity in comparison with natural northern conditions. The warming also caused structural changes, which made the fungal communities distinct in comparison with both low-latitude and high-latitude natural communities, and increased the abundance of plausible pathogens. The reactions of the microbiome to relocation and warming were strongly dependent on host genetic identity. This suggests that climate change effects on host-microbiome systems may be mediated by the interaction of environmental factors and the population genetic processes of the hosts.


Assuntos
Fungos/classificação , Aquecimento Global , Microbiota , Populus/microbiologia , Biodiversidade , Canadá , Endófitos/classificação , Modelos Lineares , Folhas de Planta/microbiologia , Árvores/microbiologia
19.
Ecol Evol ; 4(13): 2642-53, 2014 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-25077016

RESUMO

High-throughput metabarcoding studies on fungi and other eukaryotic microorganisms are rapidly becoming more frequent and more complex, requiring researchers to handle ever increasing amounts of raw sequence data. Here, we provide a flexible pipeline for pruning and analyzing fungal barcode (ITS rDNA) data generated as paired-end reads on Illumina MiSeq sequencers. The pipeline presented includes specific steps fine-tuned for ITS, that are mostly missing from pipelines developed for prokaryotes. It (1) employs state of the art programs and follows best practices in fungal high-throughput metabarcoding; (2) consists of modules and scripts easily modifiable by the user to ensure maximum flexibility with regard to specific needs of a project or future methodological developments; and (3) is straightforward to use, also in classroom settings. We provide detailed descriptions and revision techniques for each step, thus giving the user maximum control over data treatment and avoiding a black-box approach. Employing this pipeline will improve and speed up the tedious and error-prone process of cleaning fungal Illumina metabarcoding data.

20.
Evol Appl ; 7(6): 702-13, 2014 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-25067951

RESUMO

The Lusitanian slug, presumed to be native to south-west Europe, was ranked among the 100 worst invading species in Central Europe. However, from the very beginning of its recognition in the presumed invasion area, there was little evidence that the species was actually anthropogenically introduced. We investigated the invasive status of the species by comparing specific predictions on the population genetic structure in the invasion area with the pattern actually found. In a DNA-taxonomy approach, the species could not be found in its presumed native range. Using statistical phylogeographic techniques on a mitochondrial (COI) and nuclear (ZF) marker and species distribution modelling, we could show that the species is with very high probability not an invasor, but native to Central Europe. The study underlines the value of statistical phylogeography in rigorously testing hypotheses on the dynamics of biological invasions.

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