Choosing and Using Introns in Molecular Phylogenetics

Introns are now commonly used in molecular phylogenetics in an attempt to recover gene trees that are concordant with species trees, but there are a range of genomic, logistical and analytical considerations that are infrequently discussed in empirical studies that utilize intron data. This review outlines expedient approaches for locus selection, overcoming paralogy problems, recombination detection methods and the identification and incorporation of LVHs in molecular systematics. A range of parsimony and Bayesian analytical approaches are also described in order to highlight the methods that can currently be employed to align sequences and treat indels in subsequent analyses. By covering the main points associated with the generation and analysis of intron data, this review aims to provide a comprehensive introduction to using introns (or any non-coding nuclear data partition) in contemporary phylogenetics

A common garden design reveals population-specific variability in potential impacts of hybridisation between populations of farmed and wild Atlantic salmon, Salmo salar L

Released individuals can have negative impacts on native populations through various mechanisms; including competition, disease transfer and introduction of maladapted gene-complexes. Previous studies indicate that the level of farmed Atlantic salmon introgression in native populations is population-specific. However few studies have explored the potential role of population diversity or river characteristics, such as temperature, on the consequences of hybridisation. We compared freshwater growth of multiple families derived from two farmed, five wild, and two F1 hybrid salmon populations at three contrasting temperatures (7°C, 12°C, and 16°C) in a common garden experiment. As expected, farmed salmon outgrew wild salmon at all temperatures, with hybrids displaying intermediate growth. However, differences in growth were population-specific and some wild populations performed better than others relative to the hybrid and farmed populations at certain temperatures. Therefore, the competitive balance between farmed and wild salmon may depend both on the thermal profile of the river and the genetic characteristics of the respective farmed and wild strains. While limited to F1 hybridisation, the present study shows the merits in adopting a more complex spatially resolved approach to risk management of local populations

Plastic and heritable variation in shell thickness of the intertidal gastropod Nucella lapillus associated with risks of crab predation and wave action, and sexual maturation

The intertidal snail Nucella lapillus generally has thicker shells at sites sheltered from wave action, where crabs are abundant and pose a high risk of predation, than at exposed sites where crabs are rare. We studied two populations showing the opposite trend. We reciprocally transplanted snails between field sites and measured shell length, width and lip thickness of those recaptured 12 months later. Snails transplanted to the sheltered site grew larger than sheltered-site residents, which in turn grew larger than transplants to the exposed site. Relative shell-lip thickness was greater in residents at the exposed site than at the sheltered site. Transplants from shelter to exposure developed relatively thicker shells than their controls and relatively thinner shells from exposure to shelter. Progeny of the two populations were reared for 12 months in a common garden experiment presenting effluent from crabs feeding on broken conspecifics as the treatment and fresh sea-water as the control. The crab-effluent treatment decreased foraging activity, concomitantly reducing cumulative somatic growth and reproductive output. Juveniles receiving crab-effluent grew slower in shell length while developing relatively thicker shell lips than controls, the level of response being similar between lineages. F(2) progeny of the exposed-site lineage showed similar trends to the F(1)s; sheltered-site F(2)s were too few for statistical analysis. At sexual maturity, shell-lip thickness was greater in snails receiving crab-effluent than in controls, indicating plasticity, but was also greater in the exposed-site than in the sheltered-site lineage, indicating heritable variation, probably in degree of sexual thickening of the shell lip. Results corroborate hypotheses that 'defensive' shell thickening is a passive consequence of starvation and that heritable and plastic control of defensive shell morphology act synergistically. Shell thickening of juveniles was similar between lineages, contrary to hypotheses predicting differential strengths of plasticity in populations from low- or high-risk habitats.publishe

Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes

AimMeiofaunal communities that inhabit the marine benthos offer unique opportunities to simultaneously study the macroecology of numerous phyla that exhibit different life-history strategies. Here, we ask: (1) if the macroecology of meiobenthic communities is explained mainly by dispersal constraints or by environmental conditions; and (2) if levels of meiofaunal diversity surpass existing estimates based on morphological taxonomy. LocationUK and mainland European coast. MethodsNext-generation sequencing techniques (NGS; Roche 454 FLX platform) using 18S nuclear small subunit ribosomal DNA (rDNA) gene. Pyrosequences were analysed using AmpliconNoise followed by chimera removal using Perseus. ResultsRarefaction curves revealed that sampling saturation was only reached at 15% of sites, highlighting that the bulk of meiofaunal diversity is yet to be discovered. Overall, 1353 OTUs were recovered and assigned to 23 different phyla. The majority of sampled sites had c. 60-70 unique operational taxonomic units (OTUs) per site, indicating high levels of beta diversity. The environmental parameters that best explained community structure were seawater temperature, geographical distance and sediment size, but most of the variability (R-2=70%-80%) remains unexplained. Main conclusionsHigh percentages of endemic OTUs suggest that meiobenthic community composition is partly niche-driven, as observed in larger organisms, but also shares macroecological features of microorganisms by showing high levels of cosmopolitanism (albeit on a much smaller scale). Meiobenthic communities exhibited patterns of isolation by distance as well as associations between niche, latitude and temperature, indicating that meiobenthic communities result from a combination of niche assembly and dispersal processes. Conversely, isolation-by-distance patterns were not identified in the featured protists, suggesting that animals and protists adhere to radically different macroecological processes, linked to life-history strategies.Natural Environment Research Council (NERC) [NE/E001505/1, NE/F001266/1, MGF-167]; Portuguese Foundation for Science and Technology (FCT) [SFRH/BD/27413/2006, SFRH/BPD/80447/2014]; EPSRC [EP/H003851/1]; BBSRC CASE studentship; Unilever; Biotechnology and Biological Sciences Research Council [987347]; Engineering and Physical Sciences Research Council [EP/H003851/1]; Natural Environment Research Council [NE/F001290/1, NE/F001266/1, NE/E001505/1, NBAF010002]info:eu-repo/semantics/publishedVersio

Seasonal progression and differences in major floral resource use by bees and hoverflies in a diverse horticultural and agricultural landscape revealed by DNA metabarcoding

12 pages, 6 figures, 2 tables, supporting information .-- Data Availability Statement: Raw sequence data are available on the Sequence Read Archive at PRJNA763761. Data available via the Dryad Digital Repository https://doi.org/10.5061/dryad.rjdfn2z9s (Lowe et al., 2022). All code is available at https://github.com/colford/nbgw-plant-illumina-pipelineGardens are important habitats for pollinators, providing floral resources and nesting sites. There are high levels of public support for growing ‘pollinator-friendly’ plants but while plant recommendation lists are available, they are usually inconsistent, poorly supported by scientific research and target a narrow group of pollinators. In order to supply the most appropriate resources, there is a clear need to understand foraging preferences, for a range of pollinators, across the season within horticultural landscapes. Using an innovative DNA metabarcoding approach, we investigated foraging preferences of four groups of pollinators in a large and diverse, horticultural and agricultural landscape, across the flowering season and over 2 years, significantly improving on the spatial and temporal scale that can be achieved using observational studies. Bumblebees, honeybees, non-corbiculate bees and hoverflies visited 191 plant taxa. Overall floral resources were shared between the different types of pollinators, but significant differences were seen between the plants used most abundantly by bees (Hymenoptera) and hoverflies (Diptera). Floral resource use by pollinators is strongly associated with seasonal changes in flowering plants, with pollinators relying on dominant plants found within each season, with preferences consistent across both years. The plants identified were categorised according to their native status to investigate the value of native and non-native plants. The majority of floral resources used were of native and near-native origin, but the proportion of horticultural and naturalised plants increased during late summer and autumn. Synthesis and applications. Plant recommendation lists for pollinators should distinguish between bees and hoverflies and provide evidence-based floral recommendations throughout the year that include native as well as non-native plants for use in the United Kingdom and Northern Europe. Specific management recommendations include reducing mowing to encourage plants such as dandelion Taraxacum officinale and buttercups Ranunculus spp., and reducing scrub management to encourage bramble Rubus fruticosusN.d.V., L.J. and A.L. have received funding through the Welsh Government Rural Communities – Rural Development Programme 2014–2020, which is funded by the European Agricultural Fund for Rural Development and the Welsh Government. A.L. was supported by a Knowledge Economy Skills Scholarship (KESS2), part-funded by the Welsh Government's European Social Fund (ESF). Pollinator icons contained in the plant recommendation list were created by Thomas McBride. We acknowledge the support of the Supercomputing Wales project, which is part-funded by the European Regional Development Fund (ERDF) via Welsh GovernmentWith the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)Peer reviewe

Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing

Understanding how biodiversity changes in time and space is vital to assess the effects of environmental change on benthic ecosystems. Due to the limitations of morphological methods, there has been a rapid expansion in the application of high-throughput sequencing methods to study benthic eukaryotic communities. However, the effect of sample size and small-scale spatial variation on the assessment of benthic eukaryotic diversity is still not well understood. Here, we investigate the effect of different sample volumes in the genetic assessment of benthic metazoan and non-metazoan eukaryotic community composition. Accordingly, DNA was extracted from five different cumulative sediment volumes comprising 100% of the top 2 cm of five benthic sampling cores, and used as template for Ilumina MiSeq sequencing of 18 S rRNA amplicons. Sample volumes strongly impacted diversity metrics for both metazoans and non-metazoan eukaryotes. Beta-diversity of treatments using smaller sample volumes was significantly different from the beta-diversity of the 100% sampled area. Overall our findings indicate that sample volumes of 0.2 g (1% of the sampled area) are insufficient to account for spatial heterogeneity at small spatial scales, and that relatively large percentages of sediment core samples are needed for obtaining robust diversity measurement of both metazoan and non-metazoan eukaryotes