scholarly journals Comparing metatranscriptomics, PCR-based methods, and morphology in estimating diversity and composition of zooplankton mock communities

2021 ◽  
Vol 4 ◽  
Author(s):  
Mark Louie Lopez ◽  
Ya-Ying Lin ◽  
Ryuji Machida
Keyword(s):  
Species Richness ◽  
Species Diversity ◽  
Massively Parallel Sequencing ◽  
Pcr Amplification ◽  
Abundant Species ◽  
Morphological Data ◽  
Sequence Variant ◽  
Field Samples ◽  
Diversity Estimates ◽  
Mock Communities

Studying complex metazoan communities requires taxonomic expertise and laborious work if done using the traditional morphological approach. Nowadays, the popular use of molecular25 based methods accompanied by massively parallel sequencing (MPS) provides rapid and higher resolution diversity analyses. However, diversity estimates derived from the molecular-based approach can be biased by the co-detection of environmental DNA (eDNA), pseudogene contamination, and PCR amplification biases. Here, we constructed microcrustacean zooplankton mock communities to compare species diversity and composition estimates from PCR-based methods using genomic (gDNA) and complementary DNA (cDNA), metatranscriptomic transcripts, and morphology data. Mock community analyses show that gDNA mitochondrial cytochrome c oxidase I (mtCOI) amplicons inflate species richness due to environmental and nontarget species sequence contamination. Significantly higher amplicon sequence variant (ASV) and nucleotide diversity in gDNA amplicons than cDNA indicated the presence of putative pseudogenes. Last, PCR-based methods failed to detect the most abundant species in mock communities due to priming site mismatch. Overall, metatranscriptomic transcripts provided estimates of species richness and composition that closely resembled morphological data. The use of metatranscriptomic transcripts was further tested in field samples. The results showed that it could provide consistent species diversity estimates among biological and technical replicates while allowing monitoring of the zooplankton temporal species composition changes using different mitochondrial markers. These findings show that community characterization based on metatranscriptomic transcripts reflects the actual community more than PCR-based approaches.

scholarly journals Metatranscriptomics provides closer diversity and composition estimates with morphology than PCR-based methods: a zooplankton mock community case study

2020 ◽  
Author(s):  
Mark Louie Lopez ◽  
Ya-Ying Lin ◽  
Mitsuhide Sato ◽  
Fuh-Kwo Shiah ◽  
Chih-hao Hsieh ◽  
...  
Keyword(s):  
Species Richness ◽  
Species Diversity ◽  
Massively Parallel Sequencing ◽  
Pcr Amplification ◽  
Morphological Data ◽  
Sequence Variant ◽  
Mock Community ◽  
Field Samples ◽  
Diversity Estimates ◽  
Mock Communities

Studying complex metazoan communities requires taxonomic expertise and laborious work if done using the traditional morphological approach. Nowadays, the popular use of molecular-based methods accompanied by massively parallel sequencing (MPS) provides rapid and higher resolution diversity analyses. However, diversity estimates derived from the molecular-based approach can be biased by the co-detection of environmental DNA (eDNA), pseudogene contamination, and PCR amplification biases. Here, we constructed microcrustacean zooplankton mock communities to compare species diversity and composition estimates from PCR-based methods using genomic (gDNA) and complementary DNA (cDNA), metatranscriptomic transcripts, and morphology data. Mock community analyses show that gDNA mitochondrial cytochrome c oxidase I (mtCOI) amplicons inflate species richness due to environmental and nontarget species sequence contamination. Significantly higher amplicon sequence variant (ASV) and nucleotide diversity in gDNA amplicons than cDNA indicated the presence of putative pseudogenes. Last, PCR-based methods failed to detect the most abundant species in mock communities due to priming site mismatch. Overall, metatranscriptomic transcripts provided estimates of species richness and composition that closely resembled morphological data. The use of metatranscriptomic transcripts was further tested in field samples. The results showed that it could provide consistent species diversity estimates among biological and technical replicates while allowing monitoring of the zooplankton temporal species composition changes using different mitochondrial markers. These findings show that community characterization based on metatranscriptomic transcripts reflects the actual community more than PCR-based approaches.

Macrofungal diversity of a temperate oak forest: a test of species richness estimators

1999 ◽  
Vol 77 (7) ◽  
pp. 1014-1027 ◽  
Author(s):  
John Paul Schmit ◽  
John F Murphy ◽  
Gregory M Mueller
Keyword(s):  
Species Richness ◽  
Species Diversity ◽  
Deciduous Forest ◽  
Hardwood Forests ◽  
Oak Forest ◽  
Species Richness Estimation ◽  
Indiana Dunes ◽  
Richness Estimators ◽  
Diversity Estimates ◽  
Better Than

Two 0.1-ha plots, each divided into 10 contiguous subplots, were established in a Quercus-dominated deciduous forest in the Indiana Dunes National Lakeshore. Macrofungi were surveyed on these plots at weekly intervals during the fruiting season over 3 years. During this survey 177 species were recorded, including 30 species inhabiting leaf litter, 36 ectomycorrhizal species, 29 non-mycorrhizal soil-inhabiting species, and 79 wood-inhabiting species. This species richness is comparable to, but slightly higher than, that reported by other plot-based studies undertaken in hardwood forests. We compared the ability of seven species-richness estimation techniques to determine the true species richness on these plots. While some estimators performed better than others, in general the estimations were too low based on the following year's data and were not consistent from year to year. We found some evidence of spatial autocorrelation of communities of fungi found in adjacent subplots. This indicates that the benefit of using contiguous subplots to increase the homogeneity of the area sampled needs to be balanced against the possibility of underestimating the species richness of an area because of spatial autocorrelation.Key words: macrofungi, species diversity, diversity estimates, Indiana Dunes.

scholarly journals Short Communication: The species diversity and composition of roadside trees in five cities in Sumatra, Indonesia

2018 ◽  
Vol 19 (5) ◽  
pp. 1615-1621 ◽  
Author(s):  
WIRYONO . ◽  
YANSEN . ◽  
ADITYA . ◽  
DAVID JUARA LAMHOT ◽  
JURIAH HUTAHAEAN
Keyword(s):  
Species Richness ◽  
Species Diversity ◽  
Introduced Species ◽  
Native Species ◽  
Short Communication ◽  
Diversity Index ◽  
Wiener Index ◽  
Abundant Species ◽  
Number Of Individuals ◽  
Aesthetic Values

Wiryono, Yansen, Aditya, Lamhot DJ, Hutahaean J. 2018. Short Communication: The species diversity and composition ofroadside trees in five cities in Sumatra, Indonesia. Biodiversitas 19: 1615-1621. Roadside trees make living in a city more enjoyable dueto their aesthetic values and ecosystem services. The ecological benefits of roadside trees may be enhanced by increasing the speciesdiversity and the proportion of native species. The objective of this study was to know the species diversity and composition of roadsidetrees in the cities of Palembang, Bengkulu, Curup, Pematang Siantar and Argamakmur, in Sumatra Island, Indonesia, varying in size andaltitude. Data of trees were collected from selected streets and analyzed to determine the species richness (S), Shannon-Wiener index ofdiversity (Hʹ) and Ellenberg index of community similarity (ISE). The results showed that the species richness in a city ranged from 7 to26, with the diversity index between 1.05 and 2.08. The large and medium cities had higher S and Hʹ. More introduced species werefound, both in number of species and number of individuals, than the native ones. The similarity among cities in species compositionranged from 47 to 82%. Overall, Swietenia macrophylla, an introduced species, was the most abundant species. The S and Hʹ values ofall cities were considered low and the composition of tree species did not support the conservation of native species. It is, therefore,essential to increase the species diversity of street trees, especially by planting native species.

scholarly journals Diversity of Predators Associated with the Mealybug Complex in Cassava Growing Districts of Tamil Nadu, India

2021 ◽  
pp. 62-79
Author(s):  
A. Thennarasi ◽  
S. Jeyarani ◽  
N. Sathiah
Keyword(s):  
Species Richness ◽  
Species Diversity ◽  
Tamil Nadu ◽  
Abundant Species ◽  
Phenacoccus Manihoti ◽  
Species Evenness ◽  
Cryptolaemus Montrouzieri ◽  
Species Association ◽  
Extensive Survey ◽  
Index Of Diversity

An extensive survey was carried to study the diversity of predators associated with the mealybug complex in the cassava growing districts viz., Salem, Namakkal, Erode, Tiruppur and Coimbatore of Tamil Nadu, India from January to September, 2021. The survey revealed the dominance of Phenacoccus manihoti Matile-Ferrero 1977 (Hemiptera: Pseudococcidae) than other mealybug species in all the surveyed districts. The incidence of P. manihoti ranged from 12 to 90 per cent while Paracoccus marginatus Williams and Granara de Willink 1992 (Hemiptera: Pseudococcidae) incidence was found to be between 8 and 54 per cent. The incidence of Ferrisia virgata Cockerell 1893 (Hemiptera: Pseudococcidae) was found to be very low (8-16%) compared to other mealybug species. Association of total predators with P. manihoti were found to be maximum (30.87%) followed by the total predators with P. marginatus (6.49%) whereas 0.53 per cent of total predators associated with F. virgata. The  fourteen different predators viz., Cryptolaemus montrouzieri  Mulsant 1853 (Coleoptera: Coccinellidae), Menocheilus sexmaculatus Fabricius 1781 (Coleoptera: Coccinellidae), Anegleis cardoni Weise 1892 (Coleoptera: Coccinellidae), Hyperaspis maindroni Sicard 1929 (Coleoptera: Coccinellidae), Brumoides suturalis Fabricius 1798 (Coleoptera: Coccinellidae), Scymnus spp. (Coleoptera: Coccinellidae), Chrysoperla spp. (Neuroptera: Chrysopidae), Mallada spp. (Neuroptera: Chrysopidae), Spalgis epeus Westwood 1851 (Lepidoptera: Lycaenidae), Geocoris spp. (Hemiptera: Geocoridae), Cardiastethus spp. (Hemiptera: Anthocoridae), Diadiplosis spp. (Diptera: Cecidomyiidae), Oxyopes spp. (Araneae: Oxyopidae) and Argiope spp. (Araneae: Araneidae) were found to associated with the mealybug species viz.,P. manihoti, P. marginatus and  F. virgata. Among the predators of the mealybug complex, the most relative abundant species were H. maindroni (11.74%) associated with P. manihoti and C. montrouzieri (6.49%) associated with P. marginatus followed by S. epeus (0.67%) associated with F. virgata. The diversity of predators assessed through Simpson’s Index of Diversity, Shannon-Wiener, Pielou’s Evenness and Margalef indices revealed highest species diversity, species richness and species evenness in Namakkal district.

scholarly journals Sheep nemabiome diversity and its response to anthelmintic treatment in Swedish sheep herds

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Peter Halvarsson ◽  
Johan Höglund
Keyword(s):  
Species Richness ◽  
Diversity Index ◽  
Nematode Species ◽  
Abundant Species ◽  
Anthelmintic Treatment ◽  
Host Age ◽  
Larval Culture ◽  
Nematode Parasites ◽  
South Central ◽  
Nematode Diversity

Abstract Background A novel way to study the species composition and diversity of nematode parasites in livestock is to perform deep sequencing on composite samples containing a mixture of different species. Herein we describe for the first time the nematode community structures (nemabiomes) inhabiting Swedish sheep and how these are/were affected by host age and recent anthelmintic treatments. Methods A total of 158 fecal samples were collected (n = 35 in 2007 and n = 123 in 2013–2016) and cultured from groups of sheep on 61 commercial farms in the south-central part of the country where most animals are grazed. Among the samples, 2 × 44 (56%) were paired collections from the same groups pre- and post-treatment with anthelmintics such as macrocyclic lactones, benzimidazoles or levamisole. Samples were analyzed for their nemabiome using the PacBio platform followed by bioinformatic sequence analysis with SCATA. Species richness and diversity were calculated and analyzed in R. Results Nematode ITS2 sequences were found in all larval culture samples except two, even though the fecal egg counts were below the McMaster threshold in 20 samples. Sequencing yielded, on average, 1008 sequences per sample. In total, 16 operational taxonomical units (OTU), all with ≥ 98 % identity to sequences in the NCBI database, were recognized. The OTUs found represented nematode species of which ten are commonly associated with sheep. Multiple species were identified in all pre-anthelmintic treatment larval culture samples. No effects on nematode diversity were found in relation to host age. On the other hand, recent anthelmintic treatment lowered species richness, especially after use of ivermectin and albendazole. Interestingly, despite zero egg counts after use of levamisole, these samples still contained nematode DNA and especially H. contortus. Conclusions Our findings provide evidence that nemabiome analysis combined with diversity index analysis provides an objective methodology in the study of the efficacy of anthelmintic treatment as both high and low abundant species were detected.

Carabidae (Coleoptera) in Nova Scotia, Canada wild blueberry fields: prospects for biological control

2012 ◽  
Vol 144 (6) ◽  
pp. 779-791 ◽  
Author(s):  
G.C. Cutler ◽  
J.M. Renkema ◽  
C.G. Majka ◽  
J.M. Sproule
Keyword(s):  
Biological Control ◽  
Nova Scotia ◽  
Species Diversity ◽  
Insect Pests ◽  
Abundant Species ◽  
Conservation Biological Control ◽  
Carabid Beetles ◽  
Eastern Canada ◽  
Wild Blueberries ◽  
Wild Blueberry

AbstractThe Carabidae (Coleoptera) are a diverse family of beetles with almost 300 species identified in Nova Scotia, Canada. Carabid beetle communities have been studied in several agricultural systems, but not wild blueberries, an important crop in eastern Canada. In the interest of potentially developing conservation biological control programs in wild blueberry, we collected Carabidae in crop (fruit-bearing) and sprout (vegetative) blueberry fields in Nova Scotia in order to assess species diversity and abundance over space and time. Over 3200 specimens were collected, representing 51 species. A large portion of collected specimens (39%) were nonnative, and the most abundant species were generally predacious and synanthropic. Species diversity tended to be higher near forest edges than further into fields, but not for all abundant species. Several of the most prominent predators showed significant differences in preference of crop versus sprout fields, distribution throughout fields, and seasonable abundance. These findings have implications for conservation biological control efforts with carabid beetles against several insect pests in wild blueberry.

scholarly journals What Does Productivity Really Mean? Towards an Integrative Paradigm in the Search for Biodiversity-Productivity Relationships

2013 ◽  
Vol 41 (1) ◽  
pp. 36 ◽  
Author(s):  
Liangjun HU ◽  
Qinfeng GUO
Keyword(s):  
Species Richness ◽  
Species Diversity ◽  
Biomass Production ◽  
Real Root ◽  
Spatial Scaling ◽  
Ecological Processes ◽  
The Real ◽  
Community Or ◽  
Per Se ◽  
Underlying Mechanisms

How species diversity relates to productivity remains a major debate. To date, however, the underlying mechanisms that regulate the ecological processes involved are still poorly understood. Three major issues persist in early efforts at resolution. First, in the context that productivity drives species diversity, how the pathways operate is poorly-explained. Second, productivity  per se varies with community or ecosystem maturity. If diversity indeed drives productivity, the criterion of choosing appropriate measures for productivity is not available. Third, spatial scaling suggests that sampling based on small-plots may not be suitable for formulating species richness-productivity relationships (SRPRs). Thus, the long-standing assumption simply linking diversity with productivity and pursuing a generalizing pattern may not be robust. We argue that productivity, though defined as ‘the rate of biomass production’, has been measured in two ways environmental surrogates and biomass production leading to misinterpretations and difficulty in the pursuit of generalizable SRPRs. To tackle these issues, we developed an integrative theoretical paradigm encompassing richer biological and physical contexts and clearly reconciling the major processes of the systems, using proper productivity measures and sampling units. We conclude that loose interpretation and confounding measures of productivity may be the real root of current SRPR inconsistencies and debate.

scholarly journals Composition and diversity of anurans in the Restinga of the Conde municipality, northern coast of the state of Bahia, northeastern Brazil

2016 ◽  
Vol 16 (3) ◽  
Author(s):  
Felipe Augusto Trindade Gondim-Silva ◽  
Alessandra Rodrigues Santos Andrade ◽  
Rafael Oliveira Abreu ◽  
Jamile Santos Nascimento ◽  
Geovane Paixão Corrêa ◽  
...  
Keyword(s):  
Species Richness ◽  
Species Diversity ◽  
Species Composition ◽  
Rainy Season ◽  
Dominant Species ◽  
The State ◽  
Northeastern Brazil ◽  
Freshwater Wetland ◽  
Northern Coast ◽  
Anuran Species

Abstract The Conde municipality is located in the northern coast of the state of Bahia (NC), northeastern Brazil, and is part of the Atlantic Tropical domain. The anuran fauna of the northern portion of the NC is still poorly known if compared to the southern portion. The Restinga is one of the predominant environments of the coastal plains of the NC and it is characterized essentially by presenting sandy soil covered by herbaceous and shrubby vegetation. The objective of this study was to determine the anuran species composition and diversity for the Restinga of the Conde municipality. Sampling was carried out at night by active search over four periods of five consecutive days each, two over the 'main rainy season' and two in a 'lesser rainy season', using 14 sample units (SUs) and five extra sample plots (EPs). We calculated dominance and species diversity using the Berger-Parker and Shannon-Wiener H' indices, respectively. We used accumulation curves and the Jackknife 1 estimator to estimate anuran species richness, considering only the data obtained from the SUs. We recorded 713 anuran specimens distributed within 33 species, 13 genera and five families (Bufonidae, Craugastoridae, Hylidae, Leptodactylidae and Microhylidae). The Hylidae and Leptodactylidae families had the highest species richness. Considering only the SUs (Jackknife 1 estimator in brackets), we recorded 28 species in the study area (33.9 ± 2.3), 13 in Shrubby Vegetation Zones - SVZ (20.8 ± 2.9) and 25 in Freshwater Wetland Zones - FWZ (28.9 ± 1.9). The abundance and species diversity of the FWZ (n = 638 specimens; H'= 2.4) were higher than those recorded for the SVZ (n = 52 specimens; H' = 1.9). The SVZ and FWZ showed distinct dominant species, wherein Pristimantis paulodutrai was the dominant species in SVZ and Scinax fuscomarginatus in FWZ. The Restinga of the Conde municipality stands out as the one with the highest anuran species richness already recorded considering only SVZ and FWZ. Moreover, its anuran species composition represented 55% of the anuran species known for the NC and included taxa common to three different morphoclimatic domains (Tropical Atlantic, Cerrado and Caatinga).

scholarly journals Fish species diversity in headwaters streams of Paraguay and Paraná Basins

2007 ◽  
Vol 50 (6) ◽  
pp. 1033-1042 ◽  
Author(s):  
Yzel Rondon Súarez ◽  
Sabrina Bigatão Valério ◽  
Karina Keyla Tondado ◽  
Alexandro Cezar Florentino ◽  
Thiago Rota Alves Felipe ◽  
...  
Keyword(s):  
Species Richness ◽  
Species Diversity ◽  
Environmental Factors ◽  
Fish Species ◽  
Total Species Richness ◽  
Paraná Basin ◽  
Parana Basin ◽  
Number Of Individuals ◽  
Total Species ◽  
Fish Species Diversity

The influence of spatial, temporal and environmental factors on fish species diversity in headwater streams in Paraguay and Paraná basins, Brazil was examined. A total of 4,605 individuals were sampled, distributed in 60 species. The sampled streams in Paraná basin presented a larger total species richness (42) than Paraguay streams (40). However the estimated richness was larger in Paraguay basin (53) than Paraná streams (50). The streams of Paraná basin had a greater mean species richness and evenness, while more individuals per sample were found in the Paraguay basin. Difference between the sub-basins were found in the Paraguay basin, while for the basin of Paraná, richness and evenness vary significantly between the sub-basins, but the number of individuals varied seasonally. The most important environmental factors to species diversity and abundance were altitude, water temperature, stream width and stream depth for both the basins.

Diverse perennial crop mixtures sustain higher productivity over time based on ecological complementarity

2011 ◽  
Vol 26 (4) ◽  
pp. 317-327 ◽  
Author(s):  
Valentín D. Picasso ◽  
E. Charles Brummer ◽  
Matt Liebman ◽  
Philip M. Dixon ◽  
Brian J. Wilsey
Keyword(s):  
Species Richness ◽  
Species Diversity ◽  
Biomass Production ◽  
Cropping Systems ◽  
Individual Species ◽  
Selection Effects ◽  
Complementarity Effect ◽  
Change Over Time ◽  
Diversity Effects ◽  
Over Time

AbstractCropping systems that rely on renewable energy and resources and are based on ecological principles could be more stable and productive into the future than current monoculture systems with serious unintended environmental consequences such as soil erosion and water pollution. In nonagricultural systems, communities with higher species diversity have higher productivity and provide other ecosystem services. However, communities of well-adapted crop species selected for biomass production may respond differently to increasing diversity. Diversity effects may be due to complementarity among species (complementary resource use and facilitative interactions) or positive selection effects (e.g., species with higher productivity dominate the mixture), and these effects may change over time or across environments. Our goal was to identify the ecological mechanisms causing diversity effects in a biodiversity experiment using agriculturally relevant species, and evaluate the implications for the design of sustainable cropping systems. We seeded seven perennial forage species in a replicated field experiment at two locations in Iowa, USA, and evaluated biomass productivity of monocultures and two- to six-species mixtures over 3 years after the establishment year under management systems of contrasting intensity: one or three harvests per year. Productivity increased with seeded species richness in all environments, and the positive relationship did not change over time. Polyculture overyielding was due to complementarity among species in the community rather than to selection effects of individual species. Complementarity increased as a log-linear function of species richness in all environments, and this trend was consistent across years. Legume–grass facilitation may explain much of this complementarity effect. Although individual species with high biomass production had a major effect on productivity of mixtures, the species producing the highest biomass in monoculture changed over the years in most environments. Furthermore, transgressive overyielding was observed and was more prevalent in later years, in some environments. We conclude that choosing a single well-adapted species for maximizing productivity may not be the best alternative over the long term and that high levels of species diversity should be included in the design of productive and ecologically sound agricultural systems.

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