Multi-locus phylogenetic analysis of Amphipoda indicates a single origin of the pelagic suborder Hyperiidea

Hyperiidea is an exclusively pelagic suborder of amphipod crustaceans, exhibiting a wide array of unique adaptations to life in the dark, open expanse of the oceanic midwater. No common morphological synapomorphy unites approximately 350 described species. Instead, hyperiid amphipods are defined only by their pelagic existence. Hyperiidea exhibits many of the characteristics of an adaptive radiation and could represent a midwater example of this phenomenon. Previous morphological and molecular analyses have led to uncertainty in the shared ancestry of Hyperiidea. The evolutionary history of their diverse adaptations, as well as their relationship to other amphipods, remains unknown. Here we present results of a multi-locus phylogenetic analysis of publicly available amphipod sequences for three nuclear loci (18S, 28S, and H3) and two mitochondrial loci (COI and 16S) from over 300 amphipod genera, 40 of which are hyperiids. We recover strong support for a monophyletic Hyperiidea as well as reciprocally monophyletic hyperiid infraorders Physocephalata and Physosomata (with enigmatic genera Cystisoma and Paraphronima more closely related to Physosomata). We also identify several benthic, commensal amphipods representing potential sister groups for Hyperiidea. These taxa have not previously been considered close hyperiid relatives and include the genera Amphilochus, Colomastix, Anamixis, Paranamixis, and Leucothoe. Our results support the current definition of Hyperiidea and inform the phylogenetic placement of the suborder within Amphipoda

Moving conferences online: lessons learned from an international virtual meeting

We consider the opportunities and challenges associated with organizing a conference online, using a case study of a medium-sized (approx. 400 participants) international conference held virtually in August 2020. In addition, we present quantifiable evidence of the participants’ experience using the results from an online post-conference questionnaire. Although the virtual meeting was not able to replicate the in-person experience in some aspects (e.g. less engagement between participants) the overwhelming majority of respondents found the meeting an enjoyable experience and would join similar events again. Notably, there was a strong desire for future inperson meetings to have at least some online component. Online attendance by lower-income researchers was higher compared with a past, similarthemed in-person meeting held in a high-income nation, but comparable to one held in an upper-middle-income nation. This indicates that online conferences are not a panacea for diversity and inclusivity, and that holding in-person meetings in developing economies can be at least as effective. Given that it is now relatively easy to stream contents of meetings online using low-cost methods, there are clear benefits in making all presented content accessible online, as well as organizing online networking events for those unable to attend in person

The role of taxonomic expertise in interpretation of metabarcoding studies

Abstract The performance of DNA metabarcoding approaches for characterizing biodiversity can be influenced by multiple factors. Here, we used morphological assessment of taxa in zooplankton samples to develop a large barcode database and to assess the congruence of taxonomic identification with metabarcoding under different conditions. We analysed taxonomic assignment of metabarcoded samples using two genetic markers (COI, 18S V1–2), two types of clustering into molecular operational taxonomic units (OTUs, ZOTUs), and three methods for taxonomic assignment (RDP Classifier, BLASTn to GenBank, BLASTn to a local barcode database). The local database includes 1042 COI and 1108 18S (SSU) barcode sequences, and we added new high-quality sequences to GenBank for both markers, including 109 contributions at the species level. The number of phyla detected and the number of taxa identified to phylum varied between a genetic marker and among the three methods used for taxonomic assignments. Blasting the metabarcodes to the local database generated multiple unique contributions to identify OTUs and ZOTUs. We argue that a multi-marker approach combined with taxonomic expertise to develop a curated, vouchered, local barcode database increases taxon detection with metabarcoding, and its potential as a tool for zooplankton biodiversity surveys

Supplementary material from "Stable genetic structure and connectivity in pollution-adapted and nearby pollution-sensitive populations of Fundulus heteroclitus"

Populations of the non-migratory estuarine fish Fundulus heteroclitus inhabiting the heavily polluted New Bedford Harbour (NBH) estuary have shown inherited tolerance to local pollutants introduced to their habitats in the past 100 years. Here we examine two questions: (i) Is there pollution-driven selection on the mitochondrial genome across a fine geographical scale? and (ii) What is the pattern of migration among sites spanning a strong pollution gradient? Whole mitochondrial genomes were analysed for 133 F. heteroclitus from seven nearby collection sites: four sites along the NBH pollution cline (approx. 5 km distance), which had pollution-adapted fish, as well as one site adjacent to the pollution cline and two relatively unpolluted sites about 30 km away, which had pollution-sensitive fish. Additionally, we used microsatellite analyses to quantify genetic variation over three F. heteroclitus generations in both pollution-adapted and sensitive individuals collected from two sites at two different time points (1999/2000 and 2007/2008). Our results show no evidence for a selective sweep of mtDNA in the polluted sites. Moreover, mtDNA analyses revealed that both pollution-adapted and sensitive populations harbour similar levels of genetic diversity. We observed a high level of non-synonymous mutations in the most polluted site. This is probably associated with a reduction in Ne and concomitant weakening of purifying selection, a demographic expansion following a pollution-related bottleneck or increased mutation rates. Our demographic analyses suggest that isolation by distance influences the distribution of mtDNA genetic variation between the pollution cline and the clean populations at broad spatial scales. At finer scales, population structure is patchy, and neither spatial distance, pollution concentration or pollution tolerance is a good predictor of mtDNA variation. Lastly, microsatellite analyses revealed stable population structure over the last decade

Suplemental figures and Tables from Stable genetic structure and connectivity in pollution-adapted and nearby pollution-sensitive populations of <i>Fundulus heteroclitus</i>

This file includes supplemental figures and tables included in our manuscrip

Microsatellites File S3 from Stable genetic structure and connectivity in pollution-adapted and nearby pollution-sensitive populations of <i>Fundulus heteroclitus</i>

Microsatellite file

Microsatellites File S1 from Stable genetic structure and connectivity in pollution-adapted and nearby pollution-sensitive populations of <i>Fundulus heteroclitus</i>

Microsatellite file

Microsatellites File S2 from Stable genetic structure and connectivity in pollution-adapted and nearby pollution-sensitive populations of <i>Fundulus heteroclitus</i>

Microsatellite file

Suplemental figures and Tables from Stable genetic structure and connectivity in pollution-adapted and nearby pollution-sensitive populations of <i>Fundulus heteroclitus</i>

This file includes supplemental figures and tables included in our manuscrip

Moving conferences online: lessons learned from an international virtual meeting

We consider the opportunities and challenges associated with organizing a conference online, using a case study of a medium-sized (approx. 400 participants) international conference held virtually in August 2020. In addition, we present quantifiable evidence of the participants' experience using the results from an online post-conference questionnaire. Although the virtual meeting was not able to replicate the in-person experience in some aspects (e.g. less engagement between participants) the overwhelming majority of respondents found the meeting an enjoyable experience and would join similar events again. Notably, there was a strong desire for future in-person meetings to have at least some online component. Online attendance by lower-income researchers was higher compared with a past, similar-themed in-person meeting held in a high-income nation, but comparable to one held in an upper-middle-income nation. This indicates that online conferences are not a panacea for diversity and inclusivity, and that holding in-person meetings in developing economies can be at least as effective. Given that it is now relatively easy to stream contents of meetings online using low-cost methods, there are clear benefits in making all presented content accessible online, as well as organizing online networking events for those unable to attend in person