Nathan K. Truelove

Testing the accuracy of non-experts in biodiversity monitoring exercises using fern species richness in the Ecuadorian Amazon

Assessing environmental change is often constrained by time, money and expertise. Community-based monitoring schemes attempt to address these limitations by providing local communities with the skills to measure changes in natural resources and contribute locally relevant information for local and regional management decisions. Despite the increasing popularity of community-based monitoring schemes, there is little information about the accuracy of the data they produce. In this study we use visual guides and hands-on training to teach groups of leaders from local communities in the Ecuadorian Amazon to measure the species richness of ferns. We compare their results to data obtained by experienced field biologists and show strong positive correlations in species richness estimates between the results obtained by groups receiving visual guides, groups receiving hands-on training and biologists. Our results show that, even with relatively little training, communities can use simple and cost-effective methodologies to yield data that accurately reflect levels of species richness.

Co-Occurrence Patterns of Common and Rare Leaf-Litter Frogs, Epiphytic Ferns and Dung Beetles across a Gradient of Human Disturbance

Indicator taxa are commonly used to identify priority areas for conservation or to measure biological responses to environmental change. Despite their widespread use, there is no general consensus about the ability of indicator taxa to predict wider trends in biodiversity. Many studies have focused on large-scale patterns of species co-occurrence to identify areas of high biodiversity, threat or endemism, but there is much less information about patterns of species co-occurrence at local scales. In this study, we assess fine-scale co-occurrence patterns of three indicator taxa (epiphytic ferns, leaf litter frogs and dung beetles) across a remotely sensed gradient of human disturbance in the Ecuadorian Amazon. We measure the relative contribution of rare and common species to patterns of total richness in each taxon and determine the ability of common and rare species to act as surrogate measures of human disturbance and each other. We find that the species richness of indicator taxa changed across the human disturbance gradient but that the response differed among taxa, and between rare and common species. Although we find several patterns of co-occurrence, these patterns differed between common and rare species. Despite showing complex patterns of species co-occurrence, our results suggest that species or taxa can act as reliable indicators of each other but that this relationship must be established and not assumed.

A Galaxy-based bioinformatics pipeline for optimised, streamlined microsatellite development from Illumina next-generation sequencing data

Microsatellites are useful tools for ecologists and conservationist biologists, but are taxa-specific and traditionally expensive and time-consuming to develop. New methods using next-generation sequencing (NGS) have reduced these problems, but the plethora of software available for processing NGS data may cause confusion and difficulty for researchers new to the field of bioinformatics. We developed a bioinformatics pipeline for microsatellite development from Illumina paired-end sequences, which is packaged in the open-source bioinformatics tool Galaxy. This optimises and streamlines the design of a microsatellite panel and provides a user-friendly graphical user interface. The pipeline utilises existing programs along with our own novel program and wrappers to: quality-filter and trim reads (Trimmomatic); generate sequence quality reports (FastQC); identify potentially-amplifiable microsatellite loci (Pal_finder); design primers (Primer3); assemble pairs of reads to enhance marker amplification success rates (PANDAseq); and filter optimal loci (Pal_filter). The complete pipeline is freely available for use via a pre-configured Galaxy instance, accessible at https://palfinder.ls.manchester.ac.uk.

Information Flows in Community-Based Monitoring Exercises in the Ecuadorian Amazon

Community-based monitoring schemes provide alternatives to costly scientific monitoring projects. While evidence shows that local community inhabitants can consistently measure environmental changes, few studies have examined how learned monitoring skills get passed on within communities. Here, we trained members of indigenous Kichwa communities in the Ecuadorian Amazon to measure fern and dung beetle species richness and examined how well they could pass on the information they had learned to other members of their community. We subsequently compared locally gathered species richness data to estimates gathered by trained biologists. Our results provide further evidence that devolved monitoring protocols can provide similar data to that gathered by scientists. In addition, our results show that local inhabitants can effectively pass on learned information to other community members, which is particularly important for the longevity of community-based monitoring initiatives.

Isolation and Characterization of Eight Polymorphic Microsatellites for the Spotted Spiny Lobster, Panulirus guttatus

Microsatellite sequences were isolated from enriched genomic libraries of the spotted spiny lobster, Panulirus guttatus using 454 pyrosequencing. Twenty-nine previously developed polymerase chain reaction primer pairs of Panulirus argus microsatellite loci were also tested for cross-species amplification in Panulirus guttatus. In total, eight consistently amplifying, and polymorphic loci were characterized for 57 individuals collected in the Florida Keys and Bermuda. The number of alleles per locus ranged from 8 to 20 and observed heterozygosities ranged from 0.409 to 0.958. Significant deviations from Hardy–Weinberg equilibrium were found in one locus from Florida and three loci from Bermuda. Quality control testing indicated that all loci were easy to score, highly polymorphic and showed no evidence of linkage disequilibrium. Null alleles were detected in three loci with moderate frequencies ranging from (20% to 22%). These eight microsatellites provide novel molecular markers for future conservation genetics research of P. guttatus.

Isolation and characterization of 10 polymorphic microsatellite loci for the endangered Galapagos-endemic whitespotted sandbass (Paralabrax albomaculatus)

The white-spotted sandbass (Paralabrax albomaculatus) is a commercially important species in the Galapagos Marine Reserve, but is classified as endangered in the IUCN Red List. For this study, 10 microsatellite loci were isolated and characterized using Illumina paired-end sequencing. These loci can be used for genetic studies of population structure and connectivity to aid in the management of the white-spotted sandbass and other closely-related species. The 10 characterized loci were polymorphic, with 11–49 alleles per locus, and observed heterozygosity ranged from 0.575 to 0.964. This set of markers is the first to be developed for this species.

Empowering conservation practice with efficient and economical genotyping from poor quality samples

Moderate to high density genotyping (100+ SNPs) is widely used to determine and measure individual identity, relatedness, fitness, population structure and migration in wild populations. However, these important tools are difficult to apply when high-quality genetic material is unavailable. Most genomic tools are developed for high quality DNA sources from labor medical settings. As a result, most genetic data from market or field settings is limited to easily amplified mitochondrial DNA or a few microsatellites. To enable genotyping in conservation contexts, we used next-generation sequencing of multiplex PCR products from very low-quality DNA extracted from feces, hair, and cooked samples. We demonstrated utility and wide-ranging potential application in endangered wild tigers and tracking commercial trade in Caribbean queen conch. We genotyped 100 SNPs from degraded tiger samples to identify individuals, discern close relatives, and detect population differentiation. Co-occurring carnivores do not amplify (e.g. Indian wild dog/Dhole) or are monomorphic (e.g. leopard). 62 SNPs from conch fritters and field-collected samples were used to test relatedness and detect population structure. We provide proof-of-concept for a rapid, simple, cost-effective, and scalable method (for both samples and number of loci), a framework that can be applied to other conservation scenarios previously limited by low quality DNA samples. These approaches provide a critical advance for wildlife monitoring and forensics, open the door to field-ready testing, and will strengthen the use of science in policy decisions and wildlife trade.

Evaluating tools for the spatial management of fisheries

1. The ability to define the spatial dynamics of fish stocks is critical to fisheries man- agement. Combating illegal, unreported and unregulated fishing and the regula- tion of area-based management through physical patrols and port side controls are growing areas of management attention. Augmenting the existing approaches to fisheries management with forensic techniques has the potential to increase compliance and enforcement success rates. 2. We tested the accuracy of three techniques (genotyping, otolith microchemistry and morphometrics) that can be used to identify geographic origin. We used fish caught from three fishing grounds, separated by a minimum of 5 km and a maxi- mum of 60 km, to test the accuracy of these approaches at relatively small spatial scales. 3. Using nearest-neighbour analyses, morphometric analysis was the most accurate (79.5%) in assigning individual fish to their fishing ground of origin. Neither otolith microchemistry (54.0%) or genetic analyses (52.4%) had sufficient accuracy at the spatial scales we examined. 4. Synthesis and applications. The combination of accuracy and minimal resource re- quirements make morphometric analysis a promising tool for assessing compli- ance with area-based fishing restrictions at the scale of kilometres. Furthermore, this approach has promising application, in small-scale fisheries through to com- munity-based management approaches where technical and financial resources are limited.