Abstract
Sampling is one of the most important and fundamental processes in field biology. Among many sampling methods in entomology, window traps have long been considered one of the most effective ...and standardized methods. Unfortunately, the DNA quality of samples collected by window traps is typically low due to incursion by water, mainly via rainfall. Water cannot be avoided in long‐term surveys, even with a roof, due to wind and condensation. As we move into the genomics era, this shortfall in DNA quality has become problematic for molecular biomonitoring, and solutions are urgently needed.
In this study, we developed the Water‐Exclusion Trap (WET), a 3D printable long‐term storable bottom collector for window or pitfall traps. The collection medium in WETs does not dilute because water is excluded and evaporation is limited, maximizing DNA preservation.
Our field tests show that the WET outperforms conventional traps in preserving DNA quality. Insect samples preserved in WETs in the field had significantly higher PCR success rates and DNA Integrity Numbers compared to conventional traps.
The WET addresses a critical challenge in the use of window traps, DNA degradation caused by water intrusion, and represents a significant advancement in fieldwork for genomic research in entomology. We provide the 3D printing template of the WET, enabling immediate, free use for all. Furthermore, it can be easily customized for different environments and purposes, and can be adapted to a variety of other traps, including pitfall traps, funnel traps and more.
Abstract
Metazoan metabarcoding is emerging as an essential strategy for inventorying biodiversity, with diverse projects currently generating massive quantities of community-level data. The ...potential for integrating across such data sets offers new opportunities to better understand biodiversity and how it might respond to global change. However, large-scale syntheses may be compromised if metabarcoding workflows differ from each other. There are ongoing efforts to improve standardization for the reporting of inventory data. However, harmonization at the stage of generating metabarcode data has yet to be addressed. A modular framework for harmonized data generation offers a pathway to navigate the complex structure of terrestrial metazoan biodiversity. Here, through our collective expertise as practitioners, method developers, and researchers leading metabarcoding initiatives to inventory terrestrial biodiversity, we seek to initiate a harmonized framework for metabarcode data generation, with a terrestrial arthropod module. We develop an initial set of submodules covering the 5 main steps of metabarcode data generation: (i) sample acquisition; (ii) sample processing; (iii) DNA extraction; (iv) polymerase chain reaction amplification, library preparation, and sequencing; and (v) DNA sequence and metadata deposition, providing a backbone for a terrestrial arthropod module. To achieve this, we (i) identified key points for harmonization, (ii) reviewed the current state of the art, and (iii) distilled existing knowledge within submodules, thus promoting best practice by providing guidelines and recommendations to reduce the universe of methodological options. We advocate the adoption and further development of the terrestrial arthropod module. We further encourage the development of modules for other biodiversity fractions as an essential step toward large-scale biodiversity synthesis through harmonization.
A correlation of species and genetic diversity has been proposed but not uniformly supported. Large-scale DNA barcoding provides qualitatively novel data to test for correlations across hierarchical ...levels (genes, genealogies and species), and may help to unveil the underlying processes. Here we analyse sequence variation in communities of aquatic beetles across Europe (>5,000 individuals) to test for self-similarity of beta diversity patterns at multiple hierarchical levels. We show that community similarity at all levels decreases exponentially with geographic distance, and initial similarity is correlated with the lineage age, consistent with a molecular clock. Log-log correlations between lineage age, number of lineages, and range sizes, reveal a fractal geometry in time and space, indicating a spatio-temporal continuum of biodiversity across scales. Simulations show that these findings mirror dispersal-constrained models of haplotype distributions. These novel macroecological patterns may be explained by neutral evolutionary processes, acting continuously over time to produce multi-scale regularities of biodiversity.
DNA sequences provide a universal character system in taxonomy for associating all developmental stages of organisms, but ambiguity arises due to genetic variation within species. The problem is ...compounded where target groups are less well studied or incompletely represented in DNA databases. Here we investigate the utility of DNA for larval–adult species associations within chafer (Coleoptera: Scarabaeidae) communities from four sites in the tropical lowlands of Nepal. We sequenced
ca. 1600
bp of mitochondrial
cox1 and
rrnL and 700
bp of nuclear 28S rRNA from 250 larval and adult specimens. Individuals were grouped into putative species using statistical parsimony analysis and population aggregation analysis (PAA), whereby specimens from each locality were grouped according to the presence of diagnostic nucleotides. In addition, species membership was determined based on shifts in branching rates on clock-constrained trees to detect the putative transition from speciation to population coalescence patterns. Using these two methods we delineated between 48 and 56 groups, of which 16–20 were composed of larval and adult individuals. Nuclear and mtDNA-based groups were highly congruent; variation of 28S rRNA within groups was very low, while one widespread 28S rRNA genotype was universally found in a paraphyletic group of five mtDNA clusters. Linnean names could be assigned to 19 groups, and hence between 86.1% and 92.7% of larval specimens could be associated to species by their membership in clearly delineated groups that contained fully identified adults. The remaining larvae were delineated as five species, four of which could be assigned to
Anomala or
Adoretus based on their phylogenetic position. We conclude that the sequence variation was highly structured in this complex assemblage of chafers and that any given individual (larva or adult) can be readily associated with a particular DNA group using the criterion of diagnosability. The association of different developmental stages therefore becomes a matter of determining the extent of the DNA-based groups, rather than matching of sequences from adult and larval individuals. This indicates the need for a purely sequence-based taxonomic system when associating different life stages via DNA.
Background
Various devices have been developed to facilitate liver transection and reduce blood loss in liver resections. None of these has proven superiority compared with the classical ...clamp‐crushing technique. This randomized clinical trial compared the effectiveness and safety of stapler transection with that of clamp‐crushing during open liver resection.
Methods
Patients admitted for elective open liver resection between January 2010 and October 2011 were assigned randomly to stapler transection or the clamp‐crushing technique. The primary endpoint was the total amount of intraoperative blood loss. Secondary endpoints included transection time, duration of operation, complication rates and resection margins.
Results
A total of 130 patients were enrolled, 65 to clamp‐crushing and 65 to stapler transection. There was no difference between groups in total intraoperative blood loss: median (i.q.r.) 1050 (525–1650) versus 925 (450–1425) ml respectively (P = 0·279). The difference in total intraoperative blood loss normalized to the transection surface area was not statistically significant (P = 0·092). Blood loss during parenchymal transection was significantly lower in the stapler transection group (P = 0·002), as were the parenchymal transection time (mean(s.d.) 30(21) versus 9(7) min for clamp‐crushing and stapler transection groups respectively; P < 0·001) and total duration of operation (mean(s.d.) 221(86) versus 190(85) min; P = 0·047). There were no significant differences in postoperative morbidity (P = 0·863) or mortality (P = 0·684) between groups.
Conclusion
Stapler transection is a safe technique but does not reduce intraoperative blood loss in elective liver resection compared with the clamp‐crushing technique. Registration number: NCT01049607 (http://www.clinicaltrials.gov).
Stapler technique does not reduce blood loss
Large-scale sequencing of short mtDNA fragments for biodiversity inventories ('DNA barcoding') indicates that sequence variation in animal mtDNA is highly structured and partitioned into discrete ...genetic clusters that correspond broadly to species-level entities. Here we explore how the migration rate, an important demographic parameter that is directly related to population isolation, might affect variation in the strength of mtDNA clustering among taxa. Patterns of mtDNA variation were investigated in two groups of beetles that both contain lineages occupying habitats predicted to select for different dispersal abilities: predacious diving beetles (Dytiscidae) in the genus Bidessus from lotic and lentic habitats across Europe and darkling beetles (Tenebrionidae) in the genus Eutagenia from sand and other soil types in the Aegean Islands. The degree of genetic clustering was determined using the recently developed 'mixed Yule coalescent' (MYC) model that detects the transition from between-species to within-population branching patterns. Lineages from presumed stable habitats, and therefore displaying lower dispersal ability and migration rates, showed greater levels of mtDNA clustering and geographical subdivision than their close relatives inhabiting ephemeral habitats. Simulations of expected patterns of mtDNA variation under island models showed that MYC clusters are only detected when the migration rates are much lower than the value of Nm=1 typically used to define the threshold for neutral genetic divergence. Therefore, discrete mtDNA clusters provide strong evidence for independently evolving populations or species, but their formation is suppressed even under very low levels of dispersal.
AIM: Neotropical highland streams have shown diminished ecosystem functioning after amphibian extirpation infected by the chytrid fungus Batrachochytrium dendrobatidis. The loss of amphibians could ...affect communities of aquatic insects co‐occurring in these streams in various ways. We examined patterns of species and genetic diversity of these communities and their evolutionary history along the chytrid expansion gradient to elucidate potential community responses. LOCATION: Six streams over a 320‐km transect in Panama affected by chytrid expansion from west to east for up to 14 years, and two apparently chytrid‐free streams in the east. METHODS: Patterns of α‐ and β‐diversity were investigated at three hierarchical levels: genus, species and haplotypes. Genus identification was based on morphology, and putative species were inferred by grouping the DNA barcodes (749 cox1 sequences) with the GMYC method on all collected individuals of Ephemeroptera, Trichoptera, Coleoptera and Plecoptera. RESULTS: A total of 96 genera in 43 families (9 orders) of insects were encountered. Genus‐level α‐diversity was higher in the easternmost streams, possibly due to a separate biogeographical history, whereas β‐diversity was constant along the chytrid expansion gradient. Community DNA barcoding resulted in 426 cox1 haplotypes and 154 putative species, most of them limited to single sites. High β‐diversity along the gradient at both species and haplotype levels argues against community homogenization by migration in the wake of amphibian declines. In contrast, phylo‐β‐diversity was low, indicating community similarity at deep levels. MAIN CONCLUSIONS: Aquatic insect communities in this region are influenced by long‐term limited dispersion that generated high endemicity. The pattern persists mostly unperturbed after disease‐driven amphibian declines; hence, if indeed insects fill the niches vacated by tadpoles, they would originate from local communities rather than immigration. Given the unique evolutionary history and physical isolation of local assemblages, the ecosystem deterioration carries the risk of losing unique diversity.
We introduce a general approach for investigating the role of geography in speciation, based on analyzing the geography of sister clades across all nodes in a species‐level phylogeny. We examine the ...predictions of allopatric, sympatric, and peripatric models of speciation in several animal groups, using patterns of range overlap and range size symmetry between sister clades. A simple model of cladogenesis incorporating random movements of species' ranges is used to illustrate the effects of range changes on expected patterns. We find evidence for a predominantly allopatric mode of speciation in our study groups, with sympatry arising through postspeciational range changes. In addition, we find that relatively recent speciation events are characterized by greater asymmetry in range size between sister clades than expected under our null models, providing potential support for the peripatric model of speciation. We discuss the possible confounding effects of postspeciational range changes on our conclusions.
Rhinorhipidae Lawrence, 1988 is an enigmatic beetle family represented by a single species,
Lawrence, 1988, from Australia, with poorly established affinities near the superfamily Elateroidea (click ...beetles, soldier beetles and fireflies) or the more inclusive series (infraorder) Elateriformia. Its evolutionary position may inform the basal relationships of the suborder Polyphaga, the largest clade of Coleoptera.
We analyzed four densely sampled DNA datasets of major coleopteran lineages for mitogenomes, rRNA genes and single copy nuclear genes. Additionally, genome sequencing was used for incorporation of
into a set of 4220 orthologs for 24 terminals representing 12 polyphagan superfamilies. Topologies differed to various degrees, but all consistently refute the proposed placement of Rhinorhipidae in Elateroidea and instead indicate either sister relationships with other Elateriformia, frequently together with Nosodendridae, another divergent small family hitherto placed in Derodontoidea, or in an isolated position among the deepest lineages of Polyphaga. The phylogenomic analyses recovered
in a sister position to all other Elateriformia composed of five superfamilies. Therefore, we erect the new superfamily Rhinorhipoidea Lawrence, 1988,
, with the type-family Rhinorhipidae. The origins of the Rhinorhipidae were dated to the Upper Triassic/Lower Jurassic at the very early phase of polyphagan diversification.
Thus, Rhinorhipidae adds another example to several recently recognized ancient relict lineages which are interspersed within contemporaneous hugely species-rich lineages of Coleoptera.
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