Estimates Of Diversity Research Articles

Morphology, nuclear SNPs and mate selection reveal that COI barcoding overestimates species diversity in a Mediterranean freshwater amphipod by an order of magnitude.

DNA sequence information has revealed many morphologically cryptic species worldwide. For animals, DNA-based assessments of species diversity usually rely on the mitochondrial cytochrome c oxidase subunit I (COI) gene. However, a growing amount of evidence indicate that mitochondrial markers alone can lead to misleading species diversity estimates due to mito-nuclear discordance. Therefore, reports of putative species based solely on mitochondrial DNA should be verified by other methods, especially in cases where COI sequences are identical for different morphospecies or where divergence within the same morphospecies is high. Freshwater amphipods are particularly interesting in this context because numerous putative cryptic species have been reported. Here, we investigated the species status of the numerous mitochondrial molecular operational taxonomic units (MOTUs) found within Echinogammarus sicilianus. We used an integrative approach combining DNA barcoding with mate selection observations, detailed morphometrics and genome-wide double digest restriction site-associated DNA sequencing (ddRAD-seq). Within a relatively small sampling area, we detected twelve COI MOTUs (divergence=1.8-20.3%), co-occurring in syntopy at two-thirds of the investigated sites. We found that pair formation was random and there was extensive nuclear gene flow among the ten MOTUs co-occurring within the same river stretch. The four most common MOTUs were also indistinguishable with respect to functional morphology. Therefore, the evidence best fits the hypothesis of a single, yet genetically diverse, species within the main river system. The only two MOTUs sampled outside the focal area were genetically distinct at the nuclear level and may represent distinct species. Our study reveals that COI-based species delimitation can significantly overestimate species diversity, highlighting the importance of integrative taxonomy for species validation, especially in hyperdiverse complexes with syntopically occurring mitochondrial MOTUs.

Unravelling the fungal darkness in a tropical cave: richness and the description of one new genus and six new species.

Caves are special environments that harbour an incredible diversity of life, including fungal species. Brazilian caves have been demonstrated to be biodiversity hotspots for known and unknown fungal species. We investigated the richness of culturable fungi in a tropical cave in Brazil by isolating these microorganisms from the sediment and air. The fungal abundance of colony-forming units (CFUs) was 3178 in sediment and 526 in air. We used morphological features and phylogenetic analyses of actin (actA), calmodulin (cmdA), internal transcribed spacer regions and intervening 5.8S rRNA (ITS), large subunit (LSU) rDNA, RNA polymerase II second largest subunit (rpb2), translation elongation factor 1-alpha (tef1), and β-tubulin (tub2) genes to identify these isolates. Forty-one species belonging to 17 genera of Ascomycota and two of Basidiomycota were identified, and the genus Aspergillus was most commonly observed in the cave (13 taxa). Twenty-four species were found in sediment (16 exclusives) and 25 species were found in air (17 exclusives). In this study, we introduced a new genus (Pseudolecanicillium gen. nov.) in the family Cordycipitaceae and six new species (14 % of the total taxa identified) of fungal isolates obtained from sediment and air: Aspergillus lebretii sp. nov., Malbranchea cavernosa sp. nov., Pseudohumicola cecavii sp. nov., Pseudolecanicillium caatingaense sp. nov., Talaromyces cavernicola sp. nov., and Tritirachium brasiliense sp. nov. In addition, we built a checklist of the fungal taxa reported from Brazilian caves. Our results highlight the contribution of Brazilian caves to the estimation of national and global fungal diversity. Citation: Alves VCS, Lira RA, Lima JMS, Barbosa RN, Bento DM, Barbier E, Bernard E, Souza-Motta CM, Bezerra JDP (2022). Unravelling the fungal darkness in a tropical cave: richness and the description of one new genus and six new species. Fungal Systematics and Evolution 10: 139-167. doi: 10.3114/fuse.2022.10.06.

Spatial and Temporal Patterns of Genetic Diversity and Structure in Danish Populations of the Alcon Blue Butterfly Phengaris alcon (Denis & Schiffermüller)

Phengaris alcon is an endangered, ant-associated butterfly found, amongst other places, in Denmark, where it has undergone a severe decline during the last century. However, the population genetic consequences of this decline remain unknown. To explore past and current patterns in population structure in relation to the decline, we analyzed DNA microsatellite data from 184 recent and 272 historical P. alcon specimens from 44 spatiotemporal locations in Denmark. We thus generated the most temporally and spatially comprehensive population genetic dataset for P. alcon in Denmark so far. Our results for the Bayesian population assignment of recent samples revealed three major current genetic clusters: western Jutland, northern Jutland, and the island of Læsø. Estimates of genetic diversity showed signs of inbreeding in several extant populations. When including data from museum specimens, only a single locatSion showed a decline in heterozygosity between 1967 and 2021. We suggest that the two distinct clusters in western and northern Jutland indicate two temporally separated Holocene colonizations of Denmark, the latter of which may have been aided by changes in agricultural practice in the late Neolithic period. The unique genetic signature of the Læsø populations may be a result of the admixture of northern Jutland and western Swedish populations.

Генетическое разнообразие домашнего северного оленя по маркерам двух типов

Abstract. The purpose of the study was to evaluate and compare the genetic diversity of populations of domestic reindeer by hereditary polymorphism of proteins and ISSR DNA fragments. Methodology and methods. The polymorphism of proteins and enzymes was studied by electrophoresis in starch and polyacrylamide gels. Polymorphism of ISSR DNA fragments was studied by the standard method of flanking by inverted repetition of microsatellite loci of DNA sites. Data processing and plotting were performed using standard computer programs Gclstats, Genepop, Exsel. Results. According to the transferrin locus (Tf), nine alleles were identified in the deer of the Little-Earth and Big-Earth tundra. Island Kolguev and mainland Chukchi deer have five and seven alleles, respectively. According to the allelic diversity of hepatic esterase (Est-P3) and ISSR DNA fragments, the examined populations did not differ. Judging by the values of the Shannon indices and effective elements, the level of genetic diversity of the Chukchi mainland tundra and Kolguev Island populations was lower than that of the Eastern European tundra mainland populations. Relative to the reindeer of the mainland tundra of Eastern Europe, the Chukchi mainland and Kolguev island populations diverged in opposite directions according to the frequencies of 10 out of 11 ISSR DNA fragments, Est-P3 alleles, as well as rare Tf alleles. Comparison of estimates of genetic diversity by different types of markers in the examined populations using Shannon indices and effective elements gave ambiguous results. Scientific novelty. According to the level of genetic diversity in the time interval of 40–50 years, similar trends in the divergence of the mainland Chukchi and island Kolguev populations relative to the mainland populations of the Little and Big-Earth tundra of Eastern Europe were revealed.

Landscape or local? Distinct responses of flower visitor diversity and interaction networks to different land use scales in agricultural tropical highlands

Land use change has been identified as a cause for biodiversity loss and has significant effects on pollinators and their interactions with plants. Interaction network analyses complement diversity estimators by providing information on the stability and functionality of the plant-pollinator community in an ecosystem. However, how land use changes affect insect diversity, and the structure of their plant-insect interaction networks, could depend on the intensity of the disturbance but also may be a matter of scale. Our study was carried out in a tropical highland landscape dominated by intense, yet diverse, small-scale agriculture. We studied the effects of land use, at a landscape scale, and local cover and plant ecological descriptors, at a local scale; on diversity descriptors of insect pollinator communities, the abundance of the most frequent flower visitors, and their interaction networks. Seminatural vegetation favored insect flower visitors at both scales. At the landscape scale, human settlements positively influenced bee diversity, and seminatural areas favored the abundance of frequent hoverfly and bumblebee species. At the local scale, bare soil cover negatively influenced honeybee abundance while flower-rich covers positively related to bumblebee abundance. Only local scale variables had influence on network metrics. Bare soil cover was related to higher network specialization, probably due to a low rate of honeybee interactions. Flower-rich covers negatively influenced network connectance but favored modularity. These results suggest that flower resources, provided by weed areas and flowering crops, promote a high rate of interactions between trophic levels and a non-random structure in the interaction networks that may be helping to sustain network stability. Our results highlight the role of seminatural vegetation, at both scales, in maintaining stable insect pollinator communities and interactions in heterogeneous agricultural landscapes of the tropics.

Agro-morphological traits and SSR markers reveal genetic variations in germplasm accessions of Indian mustard – An industrially important oilseed crop

Indian mustard is an economic and highly important industrial oilseed crop. In this study, genetic diversity among 135 Indian mustard germplasm accessions was evaluated using 11 agro-morphological descriptors and 227 SSRs. Morphological characterization of Indian mustard germplasm accessions exhibited a broad range of variation for characters including biological yield (CV = 25.63%), seed yield (CV = 23.23% and 1000-seed weight (CV = 23.14%); whereas traits such as days to maturity (CV = 2.91%) showed lowest degree of variation. Out of 227 SSR markers evaluated, a total of 159 (70.04%) SSRs produced polymorphic products and 68 (29.96%) SSRs resulted into monomorphic amplicons. The polymorphic markers amplified 575 alleles and the number of alleles ranged from 2-7 with 3.61 average number of alleles per locus. SSR markers BRMS-030, Ra2-E11, Ra2-G05, Ni4-G10 and Ol10B11 generated the highest number of alleles (7). SSR marker Ra2-G05 was having the highest allele frequency (0.84), while BRMS-002 was having the lowest major allele frequency (0.33). Polymorphism information content (PIC) values ranged from 0.24-0.61 with an average value of 0.39 per primer pair. Unweighted pair group method with arithmetic mean (UPGMA) cluster analysis based on morphological traits grouped Indian mustard genotypes into three clusters, while two clusters were obtained based on SSR based clustering. Population structure analysis provided a better estimate of genetic diversity and divided all the genotypes into five subpopulations. Genetically diverse accessions identified may be used for hybridization in Indian mustard crop improvement programs in future.

Evaluation of Genetic Diversity in Dog Breeds Using Pedigree and Molecular Analysis: A Review

Domestic dogs are important for many economic and social reasons, and they have become a well-known model species for human disease. According to research, dog breeds exhibit significant levels of inbreeding and genetic diversity loss, decreasing the population’s ability to adapt in certain conditions, and indicating the need of conservation strategies. Before the development of molecular markers, pedigree information was used for genetic diversity management. In recent years, genomic tools are frequently applied for accurate estimation of genetic diversity and improved genetic conservation due to incomplete pedigrees and pedigree errors. The most frequently used molecular markers include PCR-based microsatellite markers (STRs) and DNA sequencing-based single-nucleotide polymorphism markers (SNP). The aim of this review was to highlight genetic diversity studies on dog breeds conducted using pedigree and molecular markers, as well as the importance of genetic diversity conservation in increasing the adaptability and survival of dog breed populations.

A 16S rRNA amplicon approach to the structural and functional diversity of bacterial communities associated with horse gram crop for drought mitigation and sustainable productivity.

In this study, 16S rRNA amplicon sequencing analyses were performed to determine the diversity of the bacterial community present in the soil, rhizosphere region, root nodules and seeds of the horse gram plant. We observed the dominance of Proteobacteria, Actinobacteria, Firmicutes, Acidobacteria, Bacteroidetes, Planctomycetes and Gemmatimonadetes across all four domains of the horse gram plant. For community analyses, the significance of the alpha diversity was estimated using the Shannon index, Simpson index and Chao1 index, which revealed no significant difference among the samples. However, the estimation of the beta diversity indicated a significant difference among the samples, with p < 0.001 and R2 =1. A strong positive correlation was found between the rhizosphere and root nodule samples. Comparative genomics of the 16S rRNA gene showed that ammonium-oxidizing metabolism (amoA), nitrite-reducing metabolism (nirK) and nitrogen-fixing metabolism (nifH) were prominent mechanisms in all samples. The genes involved in the biosynthesis of amino acids, purine metabolism and nitrogen metabolism were identified as the key genes associated with the functional traits of microbial domains in horse gram. The culturable microbes associated with horse gram can be used as a substitute for synthetic fertilizers to maintain soil fertility and ecological health in agricultural practices. Determining the survival strategies of bacterial communities that positively respond to multiple gate selection helps in understanding the structural diversity and functional traits primarily focused on the development of beneficial microbial consortium for promoting plant growth.

Short-range multispectral imaging is an inexpensive, fast, and accurate approach to estimate biodiversity in a temperate calcareous grassland.

Image sensing technologies are rapidly increasing the cost-effectiveness of biodiversity monitoring efforts. Species differences in the reflectance of electromagnetic radiation can be used as a surrogate estimate plant biodiversity using multispectral image data. However, these efforts are often hampered by logistical difficulties in broad-scale implementation. Here, we investigate the utility of multispectral imaging technology from commercially available unmanned aerial vehicles (UAVs, or drones) in estimating biodiversity metrics at a fine spatial resolution (0.1-0.5cm pixel resolution) in a temperate calcareous grassland in Oxfordshire, UK. We calculate a suite of moments (coefficient of variation, standard deviation, skewness, and kurtosis) for the distribution of radiance from multispectral images at five wavelength bands (Blue 450 ± 16 nm; Green 560 ± 16 nm; Red 650 ± 16 nm; Red Edge 730 ± 16 nm; Near Infrared 840 ± 16 nm) and test their effectiveness at estimating ground-truthed biodiversity metrics from in situ botanical surveys for 37-1 × 1m quadrats. We find positive associations between the average coefficient of variation in spectral radiance and both the Shannon-Weiner and Simpson's biodiversity indices. Furthermore, the average coefficient of variation in spectral radiance is consistent and highly repeatable across sampling days and recording heights. Positive associations with biodiversity indices hold irrespective of the image recording height (2-8m), but we report reductions in estimates of spectral diversity with increases to UAV recording height. UAV imaging reduced sampling time by a factor of 16 relative to in situ botanical surveys. We demonstrate the utility of multispectral radiance moments as an indicator of biodiversity in this temperate calcareous grassland at a fine spatial resolution using a widely available UAV monitoring system with a coarse spectral resolution. The use of UAV technology with multispectral sensors has far-reaching potential to provide cost-effective and high-resolution monitoring of biodiversity.

A brief history of population genetic research in California and an evaluation of its utility for conservation decision-making.

A recently published macrogenetic dataset of California's flora and fauna, CaliPopGen, comprehensively summarizes population genetic research published between 1985 and 2020. Integrating these genetic data into the requisite "best available science" upon which conservation professionals rely should facilitate the prioritization of populations based on genetic health. We evaluate the extent to which the CaliPopGen Dataset provides genetic diversity estimates that are 1) unbiased, 2) sufficient in quantity, 3) cover entire species' ranges, and 4) include potentially adaptive loci. We identified genetic diversity estimates for 4,462 spatially referenced populations of 432 species, confirming California's rich published history of population genetics research. Most recent studies used microsatellites markers, which have uniquely high levels of variation, and estimates of all genetic metrics varied significantly across marker types. Most studies used less than 10 loci for inferences, rendering parameter estimates potentially unreliable, and covered small spatial extents that include only a fraction of the studied species' California distribution (median 16.3%). In contrast, the ongoing California Conservation Genomics Project (CCGP) aims to cover the full geographical and environmental breadth of each species' occupied habitats, and uses a consistent approach based on whole-genome data. However, the CCGP will sequence only 12% of the number of individuals, and covers only about half the evolutionary diversity, of the CaliPopGen Database. There is clearly a place in the evaluation of the genetic health of California for both approaches going forward, especially if differences among studies can be minimized, and overlap emphasized. A complementary use of both datasets is warranted to inform optimal conservation decision-making. Finally, a synopsis of the available population genetic data for California, all other US states and 241 other countries, allows us to identify states and countries for which meaningful data summaries, such as CaliPopGen, could be collated and others, which have limited published data available and are prime targets for future, empirical work.

Updated estimates of biotic diversity and endemism for Madagascar—revisited after 20 years

AbstractThe terrestrial and marine biotypes of Madagascar are critical priorities for conservation, with almost unparalleled levels of endemism, species diversity and human threat for a land area of its size. Field inventories and molecular-based research conducted from the mid 1980s to present have greatly expanded knowledge of the country's biota, for some groups with nearly exponential growth in measures of species diversity. I provide updated measures of estimated species diversity between a book with 289 contributors, published in 2003 (The Natural History of Madagascar), and a full-scale update with 539 contributors, published in 2022 (The New Natural History of Madagascar). I compare biodiversity information presented in the new book with data from the earlier book, providing insight into scientific advancements, and revised estimates of species richness and endemism of a range of taxonomic groups.

Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non-model organisms.

Despite the increasing accessibility of high-throughput sequencing, obtaining high-quality genomic data on non-model organisms without proximate well-assembled and annotated genomes remains challenging. Here, we describe a workflow that takes advantage of distant genomic resources and ingroup transcriptomes to select and jointly enrich long open reading frames (ORFs) and ultraconserved elements (UCEs) from genomic samples for integrative studies of microevolutionary and macroevolutionary dynamics. This workflow is applied to samples of the African unionid bivalve tribe Coelaturini (Parreysiinae) at basin and continent-wide scales. Our results indicate that ORFs are efficiently captured without prior identification of intron-exon boundaries. The enrichment of UCEs was less successful, but nevertheless produced substantial data sets. Exploratory continent-wide phylogenetic analyses with ORF supercontigs (>515,000 parsimony informative sites) resulted in a fully resolved phylogeny, the backbone of which was also retrieved with UCEs (>11,000 informative sites). Variant calling on ORFs and UCEs of Coelaturini from the Malawi Basin produced ~2000 SNPs per population pair. Estimates of nucleotide diversity and population differentiation were similar for ORFs and UCEs. They were low compared to previous estimates in molluscs, but comparable to those in recently diversifying Malawi cichlids and other taxa at an early stage of speciation. Skimming off-target sequence data from the same enriched libraries of Coelaturini from the Malawi Basin, we reconstructed the maternally-inherited mitogenome, which displays the gene order inferred for the most recent common ancestor of Unionidae. Overall, our workflow and results provide exciting perspectives for integrative genomic studies of microevolutionary and macroevolutionary dynamics in non-model organisms.

Eusociality as a neglected aspect of wild bee α‐diversity and its potential impact on diversity estimation

Abstract Bees provide important ecosystem services and are subjects of extensive studies on their α‐diversity, which is generally calculated with indices that integrate the number of species with their abundances. Variation in social behaviour, though expected to impact genetic diversity, is still largely neglected in such studies. We propose a simple method to show how sociality may affect diversity indices, when a surrogate of genetic diversity is taken into account. This method weighs the number of sampled females (N) to obtain new abundance values (NW), by taking into account relevant biological traits affecting genetic structure of populations, that is, the number of (natal) nests from which the sampled females originated (which depends on brood productivity and sex ratio) and the genetic relatedness among such females. Solitary species tend to have greater NW than eusocial ones especially at larger sample sizes. Across studies on 121 bee communities, we found that Taxonomic distinctness, Shannon–Wiener diversity and Gini–Simpson dominance tended to be greater when based on NW rather than on N. Such differences increased in communities with decreasing number of eusocial species and with increasing proportion of individuals from eusocial species. The results suggest that taking into account the social organisation of wild bees may have important consequences in estimating α‐diversity, thus claiming for future efforts in collecting biological data on as many wild bee species as possible to improve the precision of NW estimations. For example, stressors affecting more solitary bees could impoverish communities dominated by few but abundant eusocial species, more than expected by using unweighted abundances.

Microsatellite Characterization and Panel Selection for Brown Bear (Ursus arctos) Population Assessment.

An assessment of the genetic diversity and structure of a population is essential for designing recovery plans for threatened species. Italy hosts two brown bear populations, Ursus arctos marsicanus (Uam), endemic to the Apennines of central Italy, and Ursus arctos arctos (Uaa), in the Italian Alps. Both populations are endangered and occasionally involved in human-wildlife conflict; thus, detailed management plans have been in place for several decades, including genetic monitoring. Here, we propose a simple cost-effective microsatellite-based protocol for the management of populations with low genetic variation. We sampled 22 Uam and 22 Uaa individuals and analyzed a total of 32 microsatellite loci in order to evaluate their applicability in individual identification. Based on genetic variability estimates, we compared data from four different STR marker sets, to evaluate the optimal settings in long-term monitoring projects. Allelic richness and gene diversity were the highest for the Uaa population, whereas depleted genetic variability was noted for the Uam population, which should be regarded as a conservation priority. Our results identified the most effective STR sets for the estimation of genetic diversity and individual discrimination in Uam (9 loci, PIC 0.45; PID 2.0 × 10-5), and Uaa (12 loci, PIC 0.64; PID 6.9 × 10-11) populations, which can easily be utilized by smaller laboratories to support local governments in regular population monitoring. The method we proposed to select the most variable markers could be adopted for the genetic characterization of other small and isolated populations.

Analysis of genetic diversity and population structure in worldwide coconut germplasm (Cocos nucifera L.) using microsatellite markers

A collection of 96 palms, representing 16 diverse coconut accessions from the International Coconut Genebank for South Asia and the Middle East (ICG-SAME), Kidu, India, was analyzed for genetic diversity and population structure based on 35 simple sequence repeat (SSR) loci. The accessions exhibited high genetic diversity. The number of alleles ranged from 2 to 22, with an average of 6.2 per locus. The effective number of alleles per locus ranged from 1.04 to 3.58, with a mean of 1.86. Gene diversity estimates ranged from 0.224 to 0.457, with a mean of 0.355. Polymorphism information content (PIC) value varied from 0.04 to 0.66 with an average of 0.36. Hierarchical clustering analysis grouped the genotypes into two major clusters with two sub-groups, which corresponded with the geographic origins. The first cluster comprised the dwarf accessions, and the second cluster comprised all the tall accessions. STRUCTURE analysis was consistent with the result of the cluster analysis with the presence of two major populations (K = 2). The results indicated the potential of SSR markers for assessing genetic diversity and marker-assisted selection in coconut.

The Estimation of Diversity and Potential Utilization of Agroforestry Plants in Batara Village, Timor-Leste

In the context of conservation, the government of Timor-Leste and its partners work together to implement an agroforestry program to address the problem of forest loss which continues to be graded every year. This study aimed to estimate the level of plant species diversity and the potential benefits of agroforestry for the Batara Village community. Data collection was carried out on agroforestry land owned by farmers in Batara Village from December 2021 to January 2022 and data collection using the single plot method and census method, namely 10m x 10m seedlings, 40m x 40m sapling, 60m x 60m pole and 113,14m x 113,14m tree. Data for plant diversity can be analyzed using the margalef index, shannon wiener, and evenness, and the potential benefits of agroforestry using descriptive analysis. Based on the results of research on the diversity of plant species in agroforestry land in Batara village, 33 species of seedling and understorey, sapling level 19 species, pole level 17 species, and tree level 15 species and overall found 42 species of plants with 25 families and the results of descriptive analysis of respondents' interviews show that agroforestry can contribute from an economic point of view by 54.28%, from an ecological perspective to 32.95%, from a social perspective to 24.18% and from a cultural perspective to 6.1%.

DArTSeq SNP-based genetic diversity and population structure studies among taro [(Colocasia esculenta (L.) Schott] accessions sourced from Nigeria and Vanuatu.

Taro is a valuable staple food crop among resource-poor rural people in countries such as Nigeria and Ghana, among others. Characterization of genetic diversity is a prerequisite for proper management of breeding programs and conservation of genetic resources. Two hundred seventy one taro accessions obtained from Nigeria and Vanuatu were genotyped using DArTseq-based SNP markers with the objectives of investigating the genetic diversity and population structure. In the analysis, 10,391 SNP markers were filtered from the sequence and used. The analysis revealed higher transition than transversion types of SNPs in the ratio of 1.43:1. The polymorphism ranged from 0.26 to 0.29 for the markers, indicating moderate genetic diversity. A model-based Bayesian clustering analysis of taro accessions yielded five subgroups and revealed the admixture situation in 19.19% of all accessions in the study. Vanuatu taro accessions exhibited more genetic diversity than Nigerian taro accessions. The population diversity estimate (PhiPt) was relatively higher (0.52) for accessions originating from Vanuatu than for Nigerian accessions. Analysis of molecular variance (AMOVA) revealed that most variation existed among individuals within a population at 52%. Nei's genetic distance showed that relatedness is based on geographical proximity. Collection of taro genetic resources should give more emphasis to within regions to utilize diversity in taro breeding program. This study also demonstrated the efficiency of DArTseq-based SNP genotyping for large-scale genome analysis in taro. The genotypic markers provided in this study are useful for association mapping studies.

Mutualistic dinoflagellates with big disparities in ribosomal DNA variation may confound estimates of symbiont diversity and ecology in the jellyfish Cotylorhiza tuberculata

Mutualistic dinoflagellates with big disparities in ribosomal DNA variation may confound estimates of symbiont diversity and ecology in the jellyfish Cotylorhiza tuberculata

Repeated subsamples during DNA extraction reveal increased diversity estimates in DNA metabarcoding of Malaise traps.

With increased application of DNA metabarcoding in biodiversity assessment, various laboratory protocols have been optimized, and their further evaluation is subject of current research. Homogenization of bulk samples and subsequent DNA extraction from a subsample of destructed tissue is a common first stage of the metabarcoding process. This can either be conducted using sample material soaked in a storage fixative, e.g., ethanol (here referred to as "wet" treatment) or from dried individuals ("dry"). However, it remains uncertain if perfect mixing and equal distribution of DNA within the tube is ensured during homogenization and to what extent incomplete mixing and resulting variations in tissue composition affect diversity assessments if only a fraction of the destructed sample is processed in the downstream metabarcoding workflow. Here we investigated the efficiency of homogenization under wet and dry conditions and tested how variations in destructed tissue composition might affect diversity assessments of complex arthropod samples. We considered five time intervals of Malaise trap bulk samples and process nine different subsamples of homogenized tissue (20 mg each) in both treatments. Results indicate a more consistent diversity assessment from dried material, but at the cost of a higher processing time. Both approaches detected comparable OTU diversity and revealed similar taxa compositions in a single tissue extraction. With an increased number of tissue subsamples during DNA extraction, OTU diversity increased for both approaches, especially for highly diverse samples obtained during the summer. Here, particularly the detection of small and low-biomass taxa increased. The processing of multiple subsamples in the metabarcoding protocol can therefore be a helpful procedure to enhance diversity estimates and counteract taxonomic bias in biodiversity assessments. However, the process induces higher costs and time effort and the application in large-scale biodiversity assessment, e.g., in monitoring schemes needs to be considered on project-specific prospects.

Comparative analysis of the myriapod fauna (Diplopoda, Chilopoda) of the Shumen Plateau and the Madara Plateau (Northeastern Bulgaria)

Abstract At present, the inventory lists of the Myriapoda of many geographical areas in Bulgaria and the comparative analyzes of the similarity between such local faunas are scarce or completely missing. The present paper presents the results of the comparative analysis of α- and β-diversity of the myriapoda communities in natural habitats in two regions in Northeastern Bulgaria – the Shumen Plateau and the Madara Plateau. The compared habitats in these plateaus have similar geographical, soil and climatic conditions, and similar species composition of plant formations. The analysis of the structure of the myriapoda communities included estimation of species diversity by determining the Shannon-Wiever index (H’) and the Berger-Parker index (d). The degree of similarity between the species composition of the communities was analyzed by the Czekanowski-Dice-Sörensen, Jaccard, Bray-Curtis, Horn, Morisita-Horn indices and the corrected Chao-Sörensen and Chao-Jaccard indices. The species diversity of the millipede community in the Shumen Plateau is much greater than that of the Madara Plateau, while the diversity of the centipede communities in the two plateaus does not differ significantly. In both classes the greatest species diversity is registered in deciduous and mixed deciduous-coniferous forests. Chao-Sörensen and Chao-Jaccard indices of similarity for the myriapod communities in these habitats are the highest, approaching 1, in contrast to the other sites where the registered species composition of the centipedes is smaller and the degree of similarity is about 0.6.