Richness Estimates Research Articles

Enhancing semi-aquatic species representativeness beyond protected areas: dragonflies in networks of conservation corridors

Complementarity is crucial when prioritizing sites for biodiversity conservation. Networks of conservation corridors (CCs) can contribute to regional representativeness by complementing biodiversity features included in existing protected areas (PAs). We ask whether criteria important for CC management and design are effective at prioritizing complementary sites, and how the consideration of species represented in PAs influence criteria performance. We focused on species turnover of generalist and specialist dragonflies across 88 riverine sites. Criteria assessed included site-level estimates of dragonfly species richness, estimates of local habitat quality and corridor width. Measures of local habitat quality were based on either dragonfly indicator species or proportion of alien vegetation. Results showed that CCs complement dragonfly diversity in PAs by contributing unrepresented generalist species. Of the criteria, corridor width was the most efficient at prioritizing complementary sites, while prioritization based on dragonfly indicator species or species richness underperformed. When aiming to prioritize CC sites that also complement sites situated in established PAs, wide corridors with low levels of alien vegetation should be favoured.

Uneven species occurrence and richness of lowland snakes (Serpentes, Squamata) in Terengganu, Peninsular Malaysia, with new locality records.

This study documents information on the composition, diversity, richness, and temporal occurrence of snakes at Sekayu's lowland forest (SLF), Terengganu, Peninsular Malaysia for the first time. The snakes recorded within the SLF were sampled opportunistically from 2013 to 2019, employing the Visual Encounter Survey method (VES) and L-shape pitfall traps with drift fences. Forty-six snake species from 37 genera belonging to the nine families were recorded, of which 11 were new records to Terengganu. Individual-based rarefaction and extrapolation curves were not reaching asymptote, indicating that additional species can be recorded at the study area. Non-parametric species richness estimators estimated and produced a range between 51 and 57 species. ACE was the best estimator based on the quantitative evaluation. All species showed some variations of occurrence patterns across months. Fourteen species were only encountered once across the sampling years, and interestingly 11 of them were only detected during the rainy season (late October to January). In general, the number of species richness, abundance, and rare species were high during this season. Species richness of snakes is high at SLF but sampling effort should be intensified, especially during these rainy months, to obtain a robust estimated snake species richness in SLF. Terengganu harbor considerably high species richness of snakes with a total of 71 species to date (excluding marine snakes), but snake diversity is still underestimated as only a few localities were surveyed in the past years, primarily at the northern part. Future surveys should be commenced at the central and southern parts of Terengganu to complement the current investigation.

Not all who wander are lost: Trail bias in community science.

The exponential growth and interest in community science programs is producing staggering amounts of biodiversity data across broad temporal and spatial scales. Large community science datasets such as iNaturalist and eBird are allowing ecologists and conservation biologists to answer novel questions that were not possible before. However, the opportunistic nature of many of these enormous datasets leads to biases. Spatial bias is a common problem, where observations are biased towards points of access like roads and trails. iNaturalist-a popular biodiversity community science platform-exhibits strong spatial biases, but it is unclear how these biases affect the quality of biodiversity data collected. Thus, we tested whether fine-scale spatial bias due to sampling from trails affects taxonomic richness estimates. We compared timed transects with experienced iNaturalist observers on and off trails in British Columbia, Canada. Using generalized linear mixed models, we found higher overall taxonomic richness on trails than off trails. In addition, we found more exotic as well as native taxa on trails than off trails. There was no difference between on and off trail observations for species that are rarely observed. Thus, fine-scale spatial bias from trails does not reduce the quality of biodiversity measurements, a promising result for those interested in using iNaturalist data for research and conservation management.

Difficult times for amphibians: Effects of land-use change at the local and landscape scales in the Iberá Wetlands

Land-use change and management practices have led to habitat loss, one of the greatest factors in biodiversity decline. Particularly, amphibians comprise the highest number of threatened vertebrate species at the global scale. In this work, amphibian communities were analysed in three differing landscapes: a protected wetland, a livestock-impaired rangeland and a pine afforestation. In each landscape, amphibian species were sampled. Land-cover type and composition, as well as primary vegetation types were characterised at the landscape and local scale, respectively. The relationship between these environmental variables and the amphibian communities was analysed. Twenty-one amphibian species were identified; the protected and afforested landscapes were the richest, whereas the rangeland showed the lowest species richness and diversity estimates. At the local scale, vegetation, water coverage and land-use category explained the higher presence of amphibian species and their abundance. These results show how different land-uses, especially livestock farming, modify the composition of amphibian communities. This work constitutes a foundation for the development of sustainable management practices for conserving amphibians in landscape-level altered habitats.

Fish species richness is a key predictor of community biomass and productivity in littoral regions of Severn Sound, an embayment of southern Georgian Bay, Lake Huron

Catches from standardized littoral electrofishing (EF) surveys (1990–2016) at various locales in Severn Sound, Georgian Bay, were analyzed. Catches were adjusted for size-selectivity using published results of laboratory immobilization experiments. Adjusted abundance-mean size relationships were consistent with the metabolic theory of ecology where body size has a central role in structuring community features. Relationships among species richness and areal estimates of biomass and annual production of the adjusted catches were assessed. Richness was the key variable driving other community metrics and was, in turn, largely driven by habitat fetch metrics and sampling time of day. Richness, biomass, and production decreased with increasing maximum effective fetch. Richness increased with time after sunset. Year and locale had smaller roles in variation of community metrics with more vegetated/ less urbanized areas having higher values. Higher fish production is expected in sheltered areas where the contributions of allochthonous and benthic primary production are expected to be greater. Further analyses using additional EF datasets from Great Lakes’ littoral zones should increase understanding of the differences between littoral and offshore fish productivity and help guide management of littoral habitats to ensure healthy fish communities.

A comparison of biomonitoring methodologies for surf zone fish communities.

Surf zones are highly dynamic marine ecosystems that are subject to increasing anthropogenic and climatic pressures, posing multiple challenges for biomonitoring. Traditional methods such as seines and hook and line surveys are often labor intensive, taxonomically biased, and can be physically hazardous. Emerging techniques, such as baited remote underwater video (BRUV) and environmental DNA (eDNA) are promising nondestructive tools for assessing marine biodiversity in surf zones of sandy beaches. Here we compare the relative performance of beach seines, BRUV, and eDNA in characterizing community composition of bony (teleost) and cartilaginous (elasmobranch) fishes of surf zones at 18 open coast sandy beaches in southern California. Seine and BRUV surveys captured overlapping, but distinct fish communities with 50% (18/36) of detected species shared. BRUV surveys more frequently detected larger species (e.g. sharks and rays) while seines more frequently detected one of the most abundant species, barred surfperch (Amphistichus argenteus). In contrast, eDNA metabarcoding captured 88.9% (32/36) of all fishes observed in seine and BRUV surveys plus 57 additional species, including 15 that frequent surf zone habitats. On average, eDNA detected over 5 times more species than BRUVs and 8 times more species than seine surveys at a given site. eDNA approaches also showed significantly higher sensitivity than seine and BRUV methods and more consistently detected 31 of the 32 (96.9%) jointly observed species across beaches. The four species detected by BRUV/seines, but not eDNA were only resolved at higher taxonomic ranks (e.g. Embiotocidae surfperches and Sygnathidae pipefishes). In frequent co-detection of species between methods limited comparisons of richness and abundance estimates, highlighting the challenge of comparing biomonitoring approaches. Despite potential for improvement, results overall demonstrate that eDNA can provide a cost-effective tool for long-term surf zone monitoring that complements data from seine and BRUV surveys, allowing more comprehensive surveys of vertebrate diversity in surf zone habitats.

Valuation of the Diversity of Native Plants and the Cultural-Archaeological Richness as an Integrative Approach for a Potential Use in Ecotourism in the Inter-Andean Valley of Cusco, Southern Peru

In recent years, ecological tourism has become very important as it contributes significantly to sustainable development. In order to assess the potential for ecotourism and cultural-archaeological attributes, we studied the plant diversity of 10 traditionally visited natural routes of the valley of Cusco, Peru. Plant gamma diversity was represented by 384 species of vascular plants, with 220 genera, and 69 families; the most diverse were: Asteraceae with 93 species, Poaceae (36), and Fabaceae (15). The species with the highest frequency in the 10 routes are: Amaranthus caudatus, Escallonia resinosa, Stenomesson pearcei, and Baccharis buxifolia. Route 2 (Picol-Huaqoto) was the one with the greatest alpha diversity with 120 species. The CHAO-1 richness estimator estimates a gamma diversity of 570 species for all of the Cusco Valley. The Bray–Curtis beta diversity shows a high similarity (55%) and three floristic groups as determined by a non-metric multidimensional analysis (NMDS) and cluster analysis. The highest concentration of flowering plant species is grouped mainly during the rainy season (R2 = 0.19), and this relationship is significantly different from the dry season (p < 0.005). The integrative biological–cultural analysis identified routes R8, R10, R6, R7, and R2 as those with the greatest potential for ecotourism use in the Cusco Valley. The plant diversity and cultural–archaeological offerings along the tourist routes documented in this study present significant opportunities for the city of Cusco to attract both national and foreign tourists. Additionally, this study highlights the importance of prioritizing conservation and preservation efforts for these areas.

Interrogating 1000 insect genomes for NUMTs: A risk assessment for estimates of species richness.

The nuclear genomes of most animal species include NUMTs, segments of the mitogenome incorporated into their chromosomes. Although NUMT counts are known to vary greatly among species, there has been no comprehensive study of their frequency/attributes in the most diverse group of terrestrial organisms, insects. This study examines NUMTs derived from a 658 bp 5' segment of the cytochrome c oxidase I (COI) gene, the barcode region for the animal kingdom. This assessment is important because unrecognized NUMTs can elevate estimates of species richness obtained through DNA barcoding and derived approaches (eDNA, metabarcoding). This investigation detected nearly 10,000 COI NUMTs ≥ 100 bp in the genomes of 1,002 insect species (range = 0-443). Variation in nuclear genome size explained 56% of the mitogenome-wide variation in NUMT counts. Although insect orders with the largest genome sizes possessed the highest NUMT counts, there was considerable variation among their component lineages. Two thirds of COI NUMTs possessed an IPSC (indel and/or premature stop codon) allowing their recognition and exclusion from downstream analyses. The remainder can elevate species richness as they showed 10.1% mean divergence from their mitochondrial homologue. The extent of exposure to "ghost species" is strongly impacted by the target amplicon's length. NUMTs can raise apparent species richness by up to 22% when a 658 bp COI amplicon is examined versus a doubling of apparent richness when 150 bp amplicons are targeted. Given these impacts, metabarcoding and eDNA studies should target the longest possible amplicons while also avoiding use of 12S/16S rDNA as they triple NUMT exposure because IPSC screens cannot be employed.

Comparison of Oxford Nanopore Technologies and Illumina MiSeq sequencing with mock communities and agricultural soil

Illumina MiSeq is the current standard for characterizing microbial communities in soil. The newer alternative, Oxford Nanopore Technologies MinION sequencer, is quickly gaining popularity because of the low initial cost and longer sequence reads. However, the accuracy of MinION, per base, is much lower than MiSeq (95% versus 99.9%). The effects of this difference in base-calling accuracy on taxonomic and diversity estimates remains unclear. We compared the effects of platform, primers, and bioinformatics on mock community and agricultural soil samples using short MiSeq, and short and full-length MinION 16S rRNA amplicon sequencing. For all three methods, we found that taxonomic assignments of the mock community at both the genus and species level matched expectations with minimal deviation (genus: 80.9–90.5%; species: 70.9–85.2% Bray–Curtis similarity); however, the short MiSeq with error correction (DADA2) resulted in the correct estimate of mock community species richness and much lower alpha diversity for soils. Several filtering strategies were tested to improve these estimates with varying results. The sequencing platform also had a significant influence on the relative abundances of taxa with MiSeq resulting in significantly higher abundances Actinobacteria, Chloroflexi, and Gemmatimonadetes and lower abundances of Acidobacteria, Bacteroides, Firmicutes, Proteobacteria, and Verrucomicrobia compared to the MinION platform. When comparing agricultural soils from two different sites (Fort Collins, CO and Pendleton, OR), methods varied in the taxa identified as significantly different between sites. At all taxonomic levels, the full-length MinION method had the highest similarity to the short MiSeq method with DADA2 correction with 73.2%, 69.3%, 74.1%, 79.3%, 79.4%, and 82.28% of the taxa at the phyla, class, order, family, genus, and species levels, respectively, showing similar patterns in differences between the sites. In summary, although both platforms appear suitable for 16S rRNA microbial community composition, biases for different taxa may make the comparison between studies problematic; and even with a single study (i.e., comparing sites or treatments), the sequencing platform can influence the differentially abundant taxa identified.

A species richness estimator for sample‐based incidence data sampled without replacement

Abstract The accurate estimation of species richness in a target region is still a statistical challenge, especially in a highly heterogeneous community. Most richness estimators have been developed based on the assumption that data are randomly sampled with replacement or that data are sampled from an infinite population. However, in reality, most sampling schemes in the field are implemented as sampling without replacement (SWOR). As such, estimators derived based on sampling with replacement may cause overestimation as the sampling fraction increases and not converge to the true richness as the sampling fraction approaches one. Sample‐based incidence data, in which the sampling unit is a plot, and only the presence or absence of a species in each chosen plot is recorded, is one of the most commonly used data types for assessing species diversity in ecological studies. In this manuscript, according to sample‐based incidence data collected through SWOR, a new richness estimator is proposed using a truncated beta‐binomial mixture model. The new estimator was obtained through the moment approach, which avoids using iterative numerical algorithms for parameter estimation and presents a closed‐form estimator as an alternative to the maximum likelihood method. Although the newly proposed method is a parametric‐based richness estimator, similar to nonparametric estimators, only the rare species in the sample (i.e. the frequencies of uniques and duplicates) are required to estimate undetected richness. Based on the hypothetical models, the statistical performances of the proposed estimator are evaluated under varying degrees of heterogeneity and different mean species detection rates. Compared to other widely used nonparametric and parametric estimators, the simulation results indicate that the proposed estimator has a smaller bias and lower root mean square error when the sampling fraction is greater than 10%, particularly in highly heterogeneous communities. In addition, one ForestGEO permanent forest plot dataset is used to evaluate and compare the proposed approach with other estimators discussed in the study. The results demonstrate that the proposed estimator, in comparison to other widely used estimators, produces less biased estimate of true richness, along with more accurate 95% confidence interval.

Local variability, human factor or vague procedure? Searching for the reasons of excessive mortality in free living aquatic insects, resulting from biological monitoring

During the analysis of the biomonitoring data of Polish watercourses, it was found that the vast majority of aquatic insects (83–95% of more than 8.8 million individuals collected between 2012 and 2019) die unnecessarily during sampling, as a result of the sub-sampling procedure. Great, in some cases 30-fold differences in the mortality of insects, including those belonging to protected taxa, were observed between the samples analyzed by various regional laboratories. The most important reason for these differences appears to be factors that can be collectively referred to as the ‘human factor’, related to removing insects from the sphere of ethical protection, makes their killing an activity ethically neutral. This kind of attitude, which does not attach any importance to the life and suffering of insects interacts with the lack of precise requirements for the sampling equipment used. Those factors seem to be the most important in explaining the causes of excessive mortality of aquatic insects during sampling and the huge differences between laboratories. Principal component analysis and the analysis of variability measures showed that ecological differences between sampling sites can only be considered as a secondary determinant.Implications for insect conservationImproperly planned and conducted monitoring procedures, through excessive mortality of free-living aquatic insects, have or may have a negative impact on the environment and biodiversity. Therefore, it seems very important to promote alternative solutions that reduce such mortality in biological monitoring, such as: non-lethal methods of animal sampling, the use of pre-sampling areas to estimate the density of animals before sampling and estimation of the maximum abundance of a sample necessary for a reliable estimate of taxonomic richness using rarefaction.

Engineered Bacillus subtilis alleviates intestinal oxidative injury through Nrf2-Keap1 pathway in enterotoxigenic Escherichia coli (ETEC) K88-infected piglet.

Engineered probiotics can serve as therapeutics based on their ability of produce recombinant immune-stimulating properties. In this study, we built the recombinant Bacillus subtilis WB800 expressing antimicrobial peptide KR32 (WB800-KR32) using genetic engineering methods and investigated its protective effects of nuclear factor-E2-related factor 2 (Nrf2)‍-Kelch-like ECH-associated protein 1 (Keap1) pathway activation in intestinal oxidative disturbance induced by enterotoxigenic Escherichia coli (ETEC) K88 in weaned piglets. Twenty-eight weaned piglets were randomly distributed into four treatment groups with seven replicates fed with a basal diet. The feed of the control group (CON) was infused with normal sterilized saline; meanwhile, the ETEC, ETEC+WB800, and ETEC+WB800-KR32 groups were orally administered normal sterilized saline, 5×1010 CFU (CFU: colony forming units) WB800, and 5×1010 CFU WB800-KR32, respectively, on Days 1‍‒‍14 and all infused with ETEC K88 1×1010 CFU on Days 15‍‒‍17. The results showed that pretreatment with WB800-KR32 attenuated ETEC-induced intestinal disturbance, improved the mucosal activity of antioxidant enzyme (catalase (CAT), superoxide dismutase (SOD), and glutathione peroxidase (GPx)) and decreased the content of malondialdehyde (MDA). More importantly, WB800-KR32 downregulated genes involved in antioxidant defense (GPx and SOD1). Interestingly, WB800-KR32 upregulated the protein expression of Nrf2 and downregulated the protein expression of Keap1 in the ileum. WB800-KR32 markedly changed the richness estimators (Ace and Chao) of gut microbiota and increased the abundance of Eubacterium_rectale_ATCC_33656 in the feces. The results suggested that WB800-KR32 may alleviate ETEC-induced intestinal oxidative injury through the Nrf2-Keap1 pathway, providing a new perspective for WB800-KR32 as potential therapeutics to regulate intestinal oxidative disturbance in ETEC K88 infection.

Effects of dietary α-ketoglutarate on the growth performance, digestive enzymes, tor signaling pathway and intestinal microbiota of juvenile mirror carp (Cyprinus carpio) fed low phosphorus diets

The present study evaluated the effects of dietary α-ketoglutarate (AKG) on the growth performance, digestive enzymes, target of rapamycin (tor) signaling pathway and intestinal microbiota of juvenile mirror carp (Cyprinus carpio) fed low phosphorus diets. An eight week 2 × 3 two-factorial experiment was conducted to investigate the interaction between AKG levels at 0 or 0.6%, and dietary phosphorus levels at 0.27%, 0.55% or 0.76%. The results showed that the final body weight (FBW) and weight growth rate (WGR) were significantly improved and the feed conversion ratio (FCR) was significantly decreased by the dietary AKG or phosphorus (P < 0.05). The crude ash and phosphorous content were significantly increased with increasing available phosphorus supplement from 0.27% to 0.76%, whereas crude lipid was decreased as dietary phosphorus levels increased (P < 0.05). Fish fed a diet supplemented with 0.6% AKG showed a significant increase in crude protein, crude ash and phosphorous content compared to the diet without AKG group (P < 0.05). The mRNA expression of IIb sodium-dependent phosphate cotransporter (NaPi-IIb) was decreased by dietary AKG or phosphorus (P < 0.05).The activities of trypsin was significantly improved by dietary AKG or phosphorus (P < 0.05). The mRNA expression of tor, insulin growth factor I (igfI) and growth hormone (gh) were significantly increased by dietary AKG or phosphorus (P < 0.05). The richness estimate of Ace and Chao, and the diversity estimators of Simpson were significantly decreased with increasing phosphorus levels from 0.27% to 0.55% (P < 0.05). Compared with the 0.27% phosphorus group, the abundance of Fusobacteriota and Bacteroidota were relatively increased and the abundance of Proteobacteria, Actinobacteriota and Cyanobacteria were relatively decreased in 0.27% phosphorus added 0.6% AKG group. The abundance of Fusobacteriota and Actinobacteriota in 0.27% phosphorus group was relatively lower than that in 0.55% phosphorus group. On the contrary, the abundance of Firmicutes, Bacteroidota and Cyanobacteria in 0.27% phosphorus group was relatively higher than that in 0.55% phosphorus groups. These results indicated that dietary supplementation with 0.6% AKG could improve growth performance by increasing the activities of trypsin and promoting the formation of beneficial intestinal microbiota, and the tor, gh/igf-I gene expression in liver of mirror carp fed low phosphorus diets.

Theory and application of an improved species richness estimator.

Species richness is an essential biodiversity variable indicative of ecosystem states and rates of invasion, speciation and extinction both contemporarily and in fossil records. However, limited sampling effort and spatial aggregation of organisms mean that biodiversity surveys rarely observe every species in the survey area. Here we present a non-parametric, asymptotic and bias-minimized richness estimator, Ω by modelling how spatial abundance characteristics affect observation of species richness. Improved asymptotic estimators are critical when both absolute richness and difference detection are important. We conduct simulation tests and applied Ω to a tree census and a seaweed survey. Ω consistently outperforms other estimators in balancing bias, precision and difference detection accuracy. However, small difference detection is poor with any asymptotic estimator. An R-package, Richness, performs the proposed richness estimations along with other asymptotic estimators and bootstrapped precisions. Our results explain how natural and observer-induced variations affect species observation, how these factors can be used to correct observed richness using the estimator Ω on a variety of data, and why further improvements are critical for biodiversity assessments. This article is part of the theme issue 'Detecting and attributing the causes of biodiversity change: needs, gaps and solutions'.

Code and Data for Theory and application of an improved species richness estimator

Code and Data for Theory and application of an improved species richness estimator

An updated catalogue of the Collembola (Hexapoda) from Colombia and a perspective for unexplored richness.

An updated catalog of Collembola nominal species recorded in Colombia is herein provided, including two new records for the country: Entomobrya linda Soto-Adames, 2002 and Folsomides centralis (Denis, 1931), both found in Reserva Natural Mesenia - Paramillo (Antioquia Department). The data were obtained from the original descriptions, as well as secondary records surveyed until December 2022. I considered localities whose studies contained identification at generic level, but disregarded those who only contained records at family level. For each species, its type locality and general distribution were provided, in addition to the site of record in Colombia, which were plotted on a map. I also present the cumulative number of nominal species recorded and described from Colombia from 1929 to 2022. Colombia has now 38 nominal species (20 endemic) in 21 genera (one endemic, plus 19 without nominal species) and 16 families of Collembola distributed in 22 sites of the 11 departments and five regions. Of this total of families, Bourletiellidae, Collophoridae, Hypogastruridae and Sminthuridae only has generic records, no nominal species. Based on these data, an estimate of the species richness was made suggesting that at the current rate of species records, to recognize 231 to 250 more species (6-7 species every 10 years), it will take about 300 years, and even so this time will not be sufficient to unveil the real fauna of Collembola of the country. For that reason, these results suggest that the Collembola fauna from Colombia is still underestimated in relation to other countries from South America.

Using baited remote underwater videos to survey freshwater turtles

AbstractNew and innovative techniques utilizing underwater cameras have the potential to track changes in turtle populations whilst being less invasive and time intensive than traditional trapping surveys. In this study, we trialled the use of Baited Remote Underwater Videos (BRUVs) in five upland streams to test if BRUVs could be used for abundance, size and sex estimates of freshwater turtles. We also compared BRUVs to cathedral traps and identified key considerations for future use of this method, such as whether the time of day influenced results. Our study successfully detected 83 turtles from 52 h of footage and identified all species known to occur in the study area. The deployment time did not significantly influence relative abundance. BRUVs also produced statistically similar catch per unit effort estimates to cathedral trapping techniques. No small turtles (i.e. juveniles) were detected, and difficulties with visibility, sex accuracy and carapace measurements are discussed for future BRUV use. Our study shows that BRUVs are a useful, time effective, non‐invasive technique to collect relative abundance and species richness estimates for freshwater turtles.

Finding the sweet spot in camera trapping: A global synthesis and meta‐analysis of minimum sampling effort

SummaryCamera traps are one of the most common tools in wildlife and conservation biology. Sampling can document and measure animal presence and activity. Captures can be used to estimate population parameters such as presence, abundance, habitat suitability, and resident species richness of specific populations. Effective camera trapping is relevant to conservation for many reasons. For instance, they can be used to inform pre‐ and post‐restoration efforts, monitor the use of artificial structures by species and assess behaviours like predator–prey interactions. This sampling approach can aid in assessing diversity change, habitat change, pre‐ and post‐restoration efforts, artificial structure effects, species presence, and animal behaviour. We reviewed the literature to collect data and estimate incidence effect size measures for both vertebrate abundance and vertebrate richness to examine the relative efficacy of deploying more camera traps for a given period in different ecosystems. Increasing sampling effort through an increased number of cameras significantly increased net positive abundance detection rates in grasslands and mixed ecosystems. Net richness detection rates in mixed, tropical, deciduous, and grassland ecosystems similarly increased with the number of cameras deployed. The total number of days, however, was not a significant predictor of abundance or richness rates detected in any ecosystem. These findings suggest that deploying relatively more cameras for relatively fewer days provides the most effective estimates of vertebrate abundance and richness for a region.

Ichthyoplankton metabarcoding: An efficient tool for early detection of invasive species establishment.

Detection of invasive species is critical for management but is often limited by challenges associated with capture, processing and identification of early life stages. DNA metabarcoding facilitates large-scale monitoring projects to detect establishment early. Here, we test the use of DNA metabarcoding to monitor invasive species by sequencing over 5000 fishes in bulk ichthyoplankton samples (larvae and eggs) from four rivers of ecological and cultural importance in southern Canada. We were successful in detecting species known from each river and three invasive species in two of the four rivers. This includes the first detection of early life-stage rudd in the Credit River. We evaluated whether sampling gear affected the detection of invasive species and estimates of species richness, and found that light traps outperform bongo nets in both cases. We also found that the primers used for the amplification of target sequences and the number of sequencing reads generated per sample affect the consistency of species detections. However, these factors have less impact on detections and species richness estimates than the number of samples collected and analysed. Our analyses also show that incomplete reference databases can result in incorrectly attributing DNA sequences to invasive species. Overall, we conclude that DNA metabarcoding is an efficient tool for monitoring the early establishment of invasive species by detecting evidence of reproduction but requires careful consideration of sampling design and the primers used to amplify, sequence and classify the diversity of native and potentially invasive species.

Distribution and Species Richness of Benthic Polychaeta and Sipuncula in the Northwestern Pacific

Polychaeta and Sipuncula are abundant inhabitants of benthic marine habitats and have been increasingly sampled in the Northwest Pacific (NWP). However, polychaete and sipunculan species richness, composition, and distribution patterns still require further investigation, despite previous studies due to increasing deep-sea data flow. Using occurrence records for Polychaeta and Sipuncula from the Ocean Biodiversity Information System (OBIS) and the Global Biodiversity Information Facility (GBIF), we analyzed sampling effort (the number of distribution records), alpha (the number of species per 700,000 km2 hexagon cells) and gamma (the number of species per 5° latitudinal band) species diversity, and estimated species richness along latitudinal and bathymetric gradients. The species richness estimations were also correlated with multiple environmental and topographic variables, including depth, temperature, dissolved oxygen, chlorophyll, primary production, phytoplankton, current velocity, light, iron, nitrate, phosphate, silicate, and salinity. The dataset included over 30,000 distribution records belonging to polychaete (31,114 records, 98%) and sipunculan (690 records, 2%) species. Half of the distribution records were reported at a species level. The area around the island of Hainan and South Korea showed the highest alpha species richness (the number of species per 700,000 km2 hexagon cell), yet the estimated species richness (ES50) indicated that there might be many unknown, unsampled, or non-digitized species throughout the whole NWP. Correspondingly, most distribution records (sampling effort) and gamma species richness were found between latitudes 20 and 40° and decreased towards higher latitudes. Sipuncula were reported relatively more frequently from the deep sea than Polychaeta (62.8% vs. 12%). Overall, the number of species and records decreased with increasing depth, with a peak at about 5000 m. The alpha species richness had the strongest positive correlations with temperature, chlorophyll, primary production, and phytoplankton concentration. Here, we provide an overview of the species richness and distribution of Polychaeta in comparison with Sipuncula in the NWP, in both shallow and deep environments. This study demonstrates where further sampling efforts are needed to fill our knowledge gaps on annelids’ distribution and diversity along the NWP. This could improve the analyses of the distribution and diversity of annelids to better understand the current environmental drivers of biodiversity, as well as predicting potential future drivers. The outcome of the environmental correlation provides thus valuable knowledge for predicting the future impacts of global warming on potential distribution shifts of annelids into new environments such as the Arctic Sea, possibly resulting in biological invasions.