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.

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 ◽  
Oak Forest ◽  
Richness Estimators

scholarly journals Plant community diversity and composition provide little resistance to Juniperus encroachment

Botany ◽  
2008 ◽  
Vol 86 (12) ◽  
pp. 1416-1426 ◽  
Author(s):  
Amy C. Ganguli ◽  
David M. Engle ◽  
Paul M. Mayer ◽  
Eric C. Hellgren
Keyword(s):  
Species Richness ◽  
Species Diversity ◽  
Species Composition ◽  
Plant Species ◽  
Plant Community ◽  
Tallgrass Prairie ◽  
Abiotic Factors ◽  
Community Diversity ◽  
Oak Forest ◽  
Old Field

Widespread encroachment of the fire-intolerant species Juniperus virginiana  L. into North American grasslands and savannahs where fire has largely been removed has prompted the need to identify mechanisms driving J. virginiana encroachment. We tested whether encroachment success of J. virginiana is related to plant species diversity and composition across three plant communities. We predicted J. virginiana encroachment success would (i) decrease with increasing diversity, and (ii) J. virginiana encroachment success would be unrelated to species composition. We simulated encroachment by planting J. virginiana seedlings in tallgrass prairie, old-field grassland, and upland oak forest. We used J. virginiana survival and growth as an index of encroachment success and evaluated success as a function of plant community traits (i.e., species richness, species diversity, and species composition). Our results indicated that J. virginiana encroachment success increased with increasing plant richness and diversity. Moreover, growth and survival of J. virginiana seedlings was associated with plant species composition only in the old-field grassland and upland oak forest. These results suggest that greater plant species richness and diversity provide little resistance to J. virginiana encroachment, and the results suggest resource availability and other biotic or abiotic factors are determinants of J. virginiana encroachment success.

scholarly journals Mammals from the Tarascan Plateau, Michoacán, México.

1999 ◽  
Vol 4 (1) ◽  
pp. 53 ◽  
Author(s):  
Constantino Orduña Trejo ◽  
Alondra Castro Campillo ◽  
José Ramírez Pulido
Keyword(s):  
Species Diversity ◽  
Species Composition ◽  
Key Words ◽  
Deciduous Forest ◽  
First Record ◽  
The State ◽  
Rodent Species ◽  
Tropical Deciduous Forest ◽  
Oak Forest ◽  
Mountain Range

 Resumen: Se examinaron 568 ejemplares de mamíferos nativos de 49 especies, procedentes de 49 localidades de la Meseta Tarasca o Sierra Purépecha del Estado de Michoacán, México. Las especies encontradas en esta región del Eje Volcánico Transversal incluyen 1 marsupial, 2 insectívoros, 17 quirópteros, 2 carnívoros, 24 roedores y 1 lagomorfo. Para calcular la diversidad de especies en los cuatro hábitats muestreados, se utilizaron las 2 especies de insectívoros y 21 de roedores. De mayor a menor diversidad, en el bosque de pino-encino se recolectaron 201 individuos de 15 especies (H’ = 2.49), en el bosque tropical caducifolio 142 de 15 especies (H’ = 2.43), en el bosque de oyamel 92 individuos de 10 especies (H’ = 2.01) y en las áreas de ecotono 52 individuos de cuatro especies (H’ = 1.15). El registro de Hylonycteris underwoodi es el primero para las partes altas del Estado de Michoacán. Abstract: We examined 568 specimens of native mammals belonging to 47 species from 49 localities of the Tarascan Plateau or Sierra Purépecha mountain range in the State of Michoacán, México. Species composition of this enclave in the Transvolcanic Belt is 1 marsupial, 2 insectivores, 17 bats, 2 carnivores, 24 rodents, and 1 lagomorph. To calculate the species diversity according to the four sampled habitats, only the 2 insectivore and 21 rodent species were included. From higher to lower diversity values, we found 201 specimens from 15 species in pine-oak forest (H’ = 2.49), 142 from 15 species in tropical deciduous forest (H’ = 2.43), 92 specimens belonging to 10 species fir forest (H’ = 2.01), and 52 from four species in an ecotonal area (H’ =1.15). Hylonycteris underwoodi is the first record for the highlands from the State of Michoacan. Key words: Mammals, distribution, diversity, Tarascan Plateau, Michoacán.

scholarly journals Estimating Diversity Through Time Using Molecular Phylogenies: Old and Species-Poor Frog Families are the Remnants of a Diverse Past

2019 ◽  
Author(s):  
O Billaud ◽  
D S Moen ◽  
T L Parsons ◽  
H Morlon
Keyword(s):  
Species Richness ◽  
Probabilistic Approach ◽  
R Package ◽  
Extinction Rate ◽  
Competitive Effects ◽  
Phenotypic Divergence ◽  
Poor Group ◽  
Diversity Dynamics ◽  
Diversity Estimates ◽  
Better Than

Abstract Estimating how the number of species in a given group varied in the deep past is of key interest to evolutionary biologists. However, current phylogenetic approaches for obtaining such estimates have limitations, such as providing unrealistic diversity estimates at the origin of the group. Here, we develop a robust probabilistic approach for estimating diversity through time curves and uncertainty around these estimates from phylogenetic data. We show with simulations that under various realistic scenarios of diversification, this approach performs better than previously proposed approaches. We also characterize the effect of tree size and undersampling on the performance of the approach. We apply our method to understand patterns of species diversity in anurans (frogs and toads). We find that Archaeobatrachia—a species-poor group of old frog clades often found in temperate regions—formerly had much higher diversity and net diversification rate, but the group declined in diversity as younger, nested clades diversified. This diversity decline seems to be linked to a decline in speciation rate rather than an increase in extinction rate. Our approach, implemented in the R package RPANDA, should be useful for evolutionary biologists interested in understanding how past diversity dynamics have shaped present-day diversity. It could also be useful in other contexts, such as for analyzing clade–clade competitive effects or the effect of species richness on phenotypic divergence.

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.

Edge influence on herbaceous plant species, diversity and soil properties in sparse oak forest fragments in Iran

2021 ◽  
Author(s):  
Gelareh Valadi ◽  
Javad Eshaghi Rad ◽  
Yahia Khodakarami ◽  
Mostafa Nemati Peykani ◽  
Karen A. Harper
Keyword(s):  
Species Richness ◽  
Species Diversity ◽  
Organic Carbon ◽  
Species Composition ◽  
Soil Properties ◽  
Plant Species ◽  
Herbaceous Plants ◽  
Oak Forest ◽  
Forest Fragments ◽  
Edge Influence

Abstract Aims Forest edges have been well studied in temperate and tropical forests, but less so in open canopy forests. We investigated edge influence on plant species diversity and soil properties in sparse oak forest fragments. Methods Data were collected along three transects from the edge to the interior of three small (under 10 ha) and three large (over 10 ha) oak forest fragments in Kermanshah province, Iran. We measured herbaceous plants (< 0.5 m in height) and soil attributes at 0 (forest edge), 25, 50, 100 and 150 m. We quantified species diversity using the Shannon index, used rarefaction to compare species richness between two different sizes of fragments and applied non-metric multidimensional scaling ordination to investigate the variation in species composition. We estimated the distance of edge influence using randomization tests. Generalized linear mixed models with post-hoc Tukey's HSD tests were used to assess the effects of distance from edge and fragment size on diversity and soil properties. Important findings We found greater species richness, diversity and evenness at the edge of both small and large fragments, and lower nitrogen and organic carbon at the edge compared to the interior of large fragments, with most changes within 50 m of the edge. Species composition, organic carbon and total nitrogen were significantly different between small and large fragments. Our findings of significant edge influence on herbaceous plants and soil properties in these sparse forests provide a significant contribution to the literature on edges, especially in relation to herbaceous plants.

scholarly journals Species composition and community structure of dung beetles (Coleoptera: Scarabaeidae: Scarabaeinae) compared among savanna and forest formations in the southwestern Brazilian Cerrado

2020 ◽  
Vol 37 ◽  
pp. 1-12
Author(s):  
Jorge Luiz da Silva ◽  
Ricardo José da Silva ◽  
Izaias Médice Fernandes ◽  
Wesley Oliveira de Sousa ◽  
Fernando Zagury Vaz-de-Mello
Keyword(s):  
Species Richness ◽  
Species Diversity ◽  
Deciduous Forest ◽  
Dung Beetle ◽  
Dung Beetles ◽  
Gallery Forest ◽  
Brazilian Cerrado ◽  
Habitat Types ◽  
Mato Grosso ◽  
Species Richness And Abundance

Although dung beetles are important members of ecological communities and indicators of ecosystem quality, species diversity, and how it varies over space and habitat types, remains poorly understood in the Brazilian Cerrado. We compared dung beetle communities among plant formations in the Serra Azul State Park (SASP) in the state of Mato Grosso, Brazil. Sampling (by baited pitfall and flight-interception traps) was carried out in 2012 in the Park in four habitat types: two different savanna formations (typical and open) and two forest formations (seasonally deciduous and gallery). A total of 5,400 individuals collected comprised 57 species in 22 genera. Typical savanna had the greatest species richness and abundance, followed by open savanna and deciduous forest, while the gallery forest had the fewest species but high abundance. Tunnelers (one of three main nesting behavior guilds) showed the greatest richness and abundance (except in the gallery forest, where one dweller species was extremely abundant) in all plant formations. We found that species richness and abundance of the dung beetle community are influenced by differences among plant formations. Habitat heterogeneity in the different plant formations along with anthropic influences (fire, habitat fragmentation) are cited as important factors that explain guild and species richness and distribution patterns. These results emphasize the importance of protected areas, such as SASP, for the maintenance and conservation of species diversity in the Brazilian Cerrado.

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 Preferences for Northern Hardwood Silviculture among Family Forest Owners in Michigan’s Upper Peninsula

2020 ◽  
Author(s):  
Alexander C Helman ◽  
Matthew C Kelly ◽  
Mark D Rouleau ◽  
Yvette L Dickinson
Keyword(s):  
Species Diversity ◽  
Hardwood Forests ◽  
Family Forest Owners ◽  
Forest Owners ◽  
Upper Peninsula ◽  
Northern Hardwood Forests ◽  
Family Forest ◽  
Northern Hardwood ◽  
Single Tree ◽  
Single Tree Selection

Abstract Managing northern hardwood forests using high-frequency, low-intensity regimes, such as single-tree selection, favors shade-tolerant species and can reduce tree species diversity. Management decisions among family forest owners (FFO) can collectively affect species and structural diversity within northern hardwood forests at regional scales. We surveyed FFOs in the Western Upper Peninsula of Michigan to understand likely future use of three silvicultural treatments—single-tree selection, shelterwood, and clearcut. Our results indicate that FFOs were most likely to implement single-tree selection and least likely to implement clearcut within the next 10 years. According to logistic regression, prior use of a treatment and perceived financial benefits significantly increased the odds for likely use for all three treatments. Having received professional forestry assistance increased likely use of single-tree selection but decreased likely use of shelterwood. We discuss these results within the context of species diversity among northern hardwood forests throughout the region.

Catalogue of aquatic Oligochaeta (Annelida: Clitellata) of Montenegro, exclusive of Naidinae and Pristininae

Zootaxa ◽  
2011 ◽  
Vol 2985 (1) ◽  
pp. 1
Author(s):  
DANIJELA ŠUNDIĆ ◽  
BRANKO M. RADUJKOVIĆ ◽  
JASMINA KRPO–ĆETKOVIĆ
Keyword(s):  
Species Richness ◽  
Black Sea ◽  
Adriatic Sea ◽  
First Record ◽  
Aquatic Oligochaeta ◽  
The Black Sea ◽  
Drainage Basins ◽  
Aquatic Oligochaete ◽  
Balkan Region ◽  
Richness Estimators

The aquatic oligochaete fauna of Montenegro was recently studied in order to improve the knowledge of this group in the Balkan region. This study was carried out on sediments collected from 70 sampling sites (the Black Sea and the Adriatic Sea drainage basins) during three years (2005–2008). Forty-one species were identified, from seven following families: Naididae, Enchytraeidae, Haplotaxidae, Lumbriculidae, Lumbricidae, Criodrilidae and Branchiobdellidae (exclusive of Naidinae and Pristininae). Sixteen of them represent first record for the Montenegrin oligochaete fauna: Embolocephalus velutinus, Ilyodrilus templetoni, Psammoryctides deserticola, Spirosperma ferox, Tubifex ignotus, Bathydrilus adriaticus, Bothrioneurum vejdovskyanum, Rhyacodrilus coccineus, Cernosvitoviella atrata, Enchytraeus buchholzi, Mesenchytraeus armatus, Haplotaxis gordioides, Rhynchelmis limosella, Stylodrilus heringianus, Tatriella slovenica and Trichodrilus strandi. The list of species from the subfamilies Naidinae and Pristininae was published previously (Šundić et al. 2011), and it comprises 36 species. Altogether, the present study and literature data show that Montenegrin aquatic oligochaete fauna consists of 77 species. Concerning similarity, values of Jaccard’s index are the highest between Montenegrin and Serbian oligochaete fauna (57 %), and the lowest between Montenegrin and Albanian oligochaete fauna (27.77 %). Species richness estimators (Mao Tau, Uniques Mean, Chao 1, Chao 2, Jack 1, Jack 2, Bootstrap, ACE and ICE) indicate that findings of new oligochaete species in Montenegro are expected.

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