How will the 'molecular revolution' contribute to biological recording?

© 2015 The Linnean Society of London. Soaring throughput, plummeting costs, and increased sensitivity for assaying degraded or low-concentration DNA are driving a revolution in the way that we monitor biodiversity. Arguably the biggest 'game-changer' is environmental DNA (e DNA), which refers to free-floating DNA released by organisms into their environment. Rare or elusive species can be detected with greater sensitivity and accuracy using eDNA than by most conventional methods, and we have the capability to screen and describe whole communities, as well as perform targeted monitoring of single species. This paper discusses the basic approaches for molecular monitoring of biodiversity, provides case studies to demonstrate the effectiveness of the techniques, and considers any challenges and limitations that could impact molecular biological recording. It is argued that eDNA surveys offer exciting new opportunities to engage the public in biological recording and that molecular approaches will complement conventional surveys, enabling unprecedented insights into species distributions. Finally, with the number of eDNA studies increasing at a rapid pace, it is argued that there is a need to rapidly establish ways of managing molecular records. Integrating molecular records into existing biological records databases would enhance our understanding of species distributions and may be something that the Biological Records Centre should be considering to mark its landmark anniversary

Climate shaped the worldwide distribution of human mitochondrial DNA sequence variation

There is an ongoing discussion in the literature on whether human mitochondrial DNA (mtDNA) evolves neutrally. There have been previous claims for natural selection on human mtDNA based on an excess of non-synonymous mutations and higher evolutionary persistence of specific mitochondrial mutations in Arctic populations. However, these findings were not supported by the reanalysis of larger datasets. Using a geographical framework, we perform the first direct test of the relative extent to which climate and past demography have shaped the current spatial distribution of mtDNA sequences worldwide. We show that populations living in colder environments have lower mitochondrial diversity and that the genetic differentiation between pairs of populations correlates with difference in temperature. These associations were unique to mtDNA; we could not find a similar pattern in any other genetic marker. We were able to identify two correlated non-synonymous point mutations in the ND3 and ATP6 genes characterized by a clear association with temperature, which appear to be plausible targets of natural selection producing the association with climate. The same mutations have been previously shown to be associated with variation in mitochondrial pH and calcium dynamics. Our results indicate that natural selection mediated by climate has contributed to shape the current distribution of mtDNA sequences in humans

Motivations of citizen scientists to engage in projects on invasive alien species

The ongoing transport and spread of alien species worldwide are among the distinguishing characteristics of the Anthropocene. Likewise, despite its long history, citizen science (CS) is increasingly being recognized as a 21st century phenomenon. The critical mass of citizen scientists is evident by the steady increase in the number of projects depending on volunteer participation. The same is true of projects dealing with the problem of invasive alien species (IAS), which rely heavily on volunteers’ help for the initial detection of new invaders and their subsequent control and eradication. However, despite their importance for the success of many CS IAS projects, little is known about the motivations guiding volunteers to participate in IAS projects. Consequently, the goal of this research was to uncover the main motivations leading volunteers to take part in IAS projects and thus ensure a better and more successful design of future IAS CS project initiatives. A meta-synthesis approach was used to search for, analyze and synthesize the results obtained from the selected publications. Relevant studies were searched for using multiple databases (Web of Science, Scopus, Google Scholar and Google), using a search string encompassing (through a set of relevant synonyms) the three relevant topics: motivations, citizen science and invasive alien species. Filtering of the resulting documents was performed on several levels, aiming to finally include only those studies with empirical evidence pertaining to the participants’ motivations, leading to the final set of 27 relevant publications. A list of 202 statements pertaining to volunteer motivations was retrieved from the selected documents, and the listed motivations were further assigned to broader motivation categories using an iterative coding approach. The process of iterative categorization of the motivation statements yielded 16 different motivations affecting the participation of volunteers in IAS CS actions. These motivations have been further divided into those which are primarily environmental (supporting IAS management, helping the environment and protecting native species and habitats), those with a social connotation (social interaction, community responsibility and contribution to science) and those which are more personal (learning something new, personal and career development, feeling of accomplishment, health and wellbeing, enjoyment and fun). Some of the listed motivations are influenced by more than one aspect. For example, outdoor recreation, contact with nature and attachment to a particular place are motivations which refer to both a personal and an environmental aspect, while wanting to share existing knowledge and livelihood/food/income protection or opportunities are equally part of the social and personal aspect of motivations. An important outcome of this research is its recognition of previously unreported motivations, unique to IAS CS initiatives: 1) supporting invasive alien species (IAS) management, 2) protecting native species and habitats, and 3) livelihood/food/income protection or opportunities, as these aspects could be the cornerstones of future IAS CS project campaign

A review of volunteers’ motivations to monitor and control invasive alien species

People make an important contribution to the study and management of biological invasions, as many monitoring and control projects rely heavily on volunteer assistance. Understanding the reasons why people participate in such projects is critical for successful recruitment and retention of volunteers. We used a meta-synthesis approach to extract, analyze and synthesize the available information from 28 selected studies investigating motivations of volunteers to engage in monitoring and control of invasive alien species (IAS). Our findings show how motivations fit three broad themes, reflecting environmental concerns, social motivations, and personal reasons. An important outcome of this study is the description of motivations that are unique to the IAS context: supporting IAS management, protecting native species and habitats, and livelihood/food/income protection or opportunities. In addition, our study reflects on important methodological choices for investigating volunteer motivations as well as ethical issues that may arise in practice. We conclude with a set of recommendations for project design and future research on volunteer motivations in IAS contexts, emphasizing the importance of collaboration with social scientists

Comparing RADseq and microsatellites to infer complex phylogeographic patterns, an empirical perspective in the Crucian carp, Carassius carassius, L.

The conservation of threatened species must be underpinned by phylogeographic knowledge. This need is epitomized by the freshwater fish Carassius carassius, which is in decline across much of its European range. Restriction site-associated DNA sequencing (RADseq) is increasingly used for such applications; however, RADseq is expensive, and limitations on sample number must be weighed against the benefit of large numbers of markers. This trade-off has previously been examined using simulation studies; however, empirical comparisons between these markers, especially in a phylogeographic context, are lacking. Here, we compare the results from microsatellites and RADseq for the phylogeography of C. carassius to test whether it is more advantageous to genotype fewer markers (microsatellites) in many samples, or many markers (SNPs) in fewer samples. These data sets, along with data from the mitochondrial cytochrome b gene, agree on broad phylogeographic patterns, showing the existence of two previously unidentified C. carassius lineages in Europe: one found throughout northern and central-eastern European drainages and a second almost exclusively confined to the Danubian catchment. These lineages have been isolated for approximately 2.15 M years and should be considered separate conservation units. RADseq recovered finer population structure and stronger patterns of IBD than microsatellites, despite including only 17.6% of samples (38% of populations and 52% of samples per population). RADseq was also used along with approximate Bayesian computation to show that the postglacial colonization routes of C. carassius differ from the general patterns of freshwater fish in Europe, likely as a result of their distinctive ecology

Detection of a new non-native freshwater species by DNA metabarcoding of environmental samples — first record of Gammarus fossarum in the UK

© 2017 The Author(s). and 2017 REABIC. We report the discovery of a non-native gammarid, Gammarus fossarum (Koch, 1836) (Crustacea, Amphipoda), in UK rivers. Gammarus fossarum is a common freshwater gammarid in many parts of mainland Europe, but was previously considered absent from the UK. Gammarus fossarum was detected in a number of UK rivers following DNA metabarcoding of a mini-barcode region of the COI gene in macroinvertebrate kick samples, and environmental DNA (eDNA) from water and sediment samples. Subsequent morphological analysis and standard DNA barcoding showed that the species could be reliably identified and separated from Gammarus pulex (Linnaeus, 1758), the most dominant and widespread native freshwater gammarid in the UK. Our data demonstrate extensive geographical coverage of G. fossarum in the UK, spanning distant river catchments. At present there is no data to confirm the likely origin of G. fossarum’s introduction. Subsequent re-examination of historic archive material shows the species to have been present in the UK since at least 1964. This study is among the first to demonstrate the potential of eDNA metabarcoding for detection of new non-native species

Characteristics and drivers of high-altitude ladybird flight: insights from vertical-looking entomological radar

Understanding the characteristics and drivers of dispersal is crucial for predicting population dynamics, particularly in range-shifting species. Studying long-distance dispersal in insects is challenging, but recent advances in entomological radar offer unique insights. We analysed 10 years of radar data collected at Rothamsted Research, U.K., to investigate characteristics (altitude, speed, seasonal and annual trends) and drivers (aphid abundance, air temperature, wind speed and rainfall) of high-altitude flight of the two most abundant U.K. ladybird species (native Coccinella septempunctata and invasive Harmonia axyridis). These species cannot be distinguished in the radar data since their reflectivity signals overlap, and they were therefore analysed together. However, their signals do not overlap with other, abundant insects so we are confident they constitute the overwhelming majority of the analysed data. The target species were detected up to ~1100 m above ground level, where displacement speeds of up to ~60 km/h were recorded, however most ladybirds were found between ~150 and 500 m, and had a mean displacement of 30 km/h. Average flight time was estimated, using tethered flight experiments, to be 36.5 minutes, but flights of up to two hours were observed. Ladybirds are therefore potentially able to travel 18 km in a "typical" high-altitude flight, but up to 120 km if flying at higher altitudes, indicating a high capacity for long-distance dispersal. There were strong seasonal trends in ladybird abundance, with peaks corresponding to the highest temperatures of mid-summer, and warm air temperature was the key driver of ladybird flight. Climatic warming may therefore increase the potential for long-distance dispersal in these species. Low aphid abundance was a second significant factor, highlighting the important role of aphid population dynamics in ladybird dispersal. This research illustrates the utility of radar for studying high-altitude insect flight and has important implications for predicting long-distance dispersal. © 2013 Jeffries et al

Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods

Organisms continuously release DNA into their environments via shed cells, excreta, gametes and decaying material. Analysis of this ‘environmental DNA’ (eDNA) is revolutionizing biodiversity monitoring. eDNA outperforms many established survey methods for targeted detection of single species, but few studies have investigated how well eDNA reflects whole communities of organisms in natural environments. We investigated whether eDNA can recover accurate qualitative and quantitative information about fish communities in large lakes, by comparison to the most comprehensive long-term gill-net data set available in the UK. Seventy-eight 2L water samples were collected along depth profile transects, gill-net sites and from the shoreline in three large, deep lakes (Windermere, Bassenthwaite Lake and Derwent Water) in the English Lake District. Water samples were assayed by eDNA metabarcoding of the mitochondrial 12S and cytochrome b regions. Fourteen of the 16 species historically recorded in Windermere were detected using eDNA, compared to four species in the most recent gill-net survey, demonstrating eDNA is extremely sensitive for detecting species. A key question for biodiversity monitoring is whether eDNA can accurately estimate abundance. To test this, we used the number of sequence reads per species and the proportion of sampling sites in which a species was detected with eDNA (i.e. site occupancy) as proxies for abundance. eDNA abundance data consistently correlated with rank abundance estimates from established surveys. These results demonstrate that eDNA metabarcoding can describe fish communities in large lakes, both qualitatively and quantitatively, and has great potential as a complementary tool to established monitoring methods

Generating and testing ecological hypotheses at the pondscape with environmental DNA metabarcoding: A case study on a threatened amphibian

Background: Environmental DNA (eDNA) metabarcoding is revolutionizing biodiversity monitoring, but has unrealized potential for ecological hypothesis generation and testing. Aims: Here, we validate this potential in a large-scale analysis of vertebrate community data generated by eDNA metabarcoding of 532 UK ponds. Materials & Methods: We test biotic associations between the threatened great crested newt (Triturus cristatus) and other vertebrates as well as abiotic factors influencing T.cristatus detection at the pondscape. Furthermore, we test the status of T.cristatus as an umbrella species for pond conservation by assessing whether vertebrate species richness is greater in ponds with T.cristatus and higher T.cristatus Habitat Suitability Index (HSI) scores. Results: Triturus cristatus detection was positively correlated with amphibian and waterfowl species richness. Specifically, T.cristatus was positively associated with smooth newt (Lissotriton vulgaris), common coot (Fulica atra), and common moorhen (Gallinula chloropus), but negatively associated with common toad (Bufo bufo). Triturus cristatus detection did not significantly decrease as fish species richness increased, but negative associations with common carp (Cyprinus carpio), three-spined stickleback (Gasterosteus aculeatus), and ninespine stickleback (Pungitius pungitius) were identified. Triturus cristatus detection was negatively correlated with mammal species richness, and T.cristatus was negatively associated with gray squirrel (Sciurus carolinensis). Triturus cristatus detection was negatively correlated with larger pond area, presence of inflow, and higher percentage of shading, but positively correlated with HSI score, supporting its application to T.cristatus survey. Vertebrate species richness was significantly higher in T.cristatus ponds and broadly increased as T.cristatus HSI scores increased. Discussion: We reaffirm reported associations (e.g., T.cristatus preference for smaller ponds) but also provide novel insights, including a negative effect of pond inflow on T.cristatus. Conclusion: Our findings demonstrate the prospects of eDNA metabarcoding for ecological hypothesis generation and testing at landscape scale, and dramatic enhancement of freshwater conservation, management, monitoring, and research

Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds.

The sampling of environmental DNA (eDNA) coupled with cost-efficient and ever-advancing sequencing technology is propelling changes in biodiversity monitoring within aquatic ecosystems. Despite the increasing number of eDNA metabarcoding approaches, the ability to quantify species biomass and abundance in natural systems is still not fully understood. Previous studies have shown positive but sometimes weak correlations between abundance estimates from eDNA metabarcoding data and from conventional capture methods. As both methods have independent biases a lack of concordance is difficult to interpret. Here we tested whether read counts from eDNA metabarcoding provide accurate quantitative estimates of the absolute abundance of fish in holding ponds with known fish biomass and number of individuals. Environmental DNA samples were collected from two fishery ponds with high fish density and broad species diversity. In one pond, two different DNA capture strategies (on-site filtration with enclosed filters and three different preservation buffers versus lab filtration using open filters) were used to evaluate their performance in relation to fish community composition and biomass/abundance estimates. Fish species read counts were significantly correlated with both biomass and abundance, and this result, together with information on fish diversity, was repeatable when open or enclosed filters with different preservation buffers were used. This research demonstrates that eDNA metabarcoding provides accurate qualitative and quantitative information on fish communities in small ponds, and results are consistent between different methods of DNA capture. This method flexibility will be beneficial for future eDNA-based fish monitoring and their integration into fisheries management