First record of Seira dowlingi (Wray, 1953) (Collembola, Entomobryidae, Seirinae) from China and mitogenome comparison with the New World specimens

Here, the first record of Seira dowlingi from Asia is reported and its newly generated mitogenome is compared with Neotropical specimens. Molecular analyses were performed based on low-coverage whole-genome sequencing and the complete mitogenome was assembled using NovoPlasty. Our results show that the Chinese specimens have the same color pattern, chaetotaxy, and almost identical mitogenomes, differing only on three nucleotides located in protein-coding genes. A maximum-likelihood phylogeny based on 13 mitochondrial genes was made and the specimens’ similarity was confirmed, as well as its phylogenetic position. Considering the large geographic distance between the American and the Asiatic populations, we believe that the presence of S. dowlingi in China is a result of anthropogenic introduction. The data generated here can be useful for further phylogeographic studies related to Seirinae subfamily or Collembola fauna in general.

First report of downy mildew, caused by Peronospora chenopodii-ambrosioidis on epazote (Dysphania ambrosioides) in North Carolina

In this brief, we report the observation of downy mildew caused by Peronospora chenopodii-ambrosioidis on epazote (Dysphania ambrosioides) in North Carolina, USA. We performed morphological characterization of the sporangia and sporangiophores for identification. We also confirmed the identity of the pathogen by performing an alignment and generating a Maximum Likelihood phylogeny of the concatenated internal transcribed spacer (ITS) region and cytochrome c oxidase subunit I (cox1) sequences.

Genetic Analysis of Formosan Subterranean Termite (Blattodea: Rhinotermitidae) Populations in California

A new infestation of the Formosan subterranean termite, Coptotermes formosanus Shiraki (Blattodea: Rhinotermitidae), was discovered in Canyon Lake, Riverside County, California. We used three mitochondrial DNA (COI, COII, and 16S) and seven polymorphic microsatellite markers to characterize the genetic relationship of the colony with two other colonies that were collected in 1992 and 2018 in La Mesa, San Diego County. Maximum likelihood phylogeny of C. formosanus based on concatenated COI and COII sequences revealed that the two La Mesa populations (CA01 and CA02) and the Canyon Lake population (CA03) were from different maternal lineages. Based on the 14 COII haplotypes of C. formosanus found world-wide, CA01 and CA02 belonged to a haplotype widely distributed across the United States, while CA03 was grouped under a haplotype predominantly found in Asia. Microsatellite allele frequencies across all loci for both La Mesa populations were relatively similar, but significant genetic differences were found between CA02 and CA03 colonies (FST = 0.24; Dest = 0.30; G″ ST = 0.55; P < 0.01).

Fossil-calibrated molecular phylogeny of atlantid heteropods (Gastropoda, Pterotracheoidea)

Background The aragonite shelled, planktonic gastropod family Atlantidae (shelled heteropods) is likely to be one of the first groups to be impacted by imminent ocean changes, including ocean warming and ocean acidification. With a fossil record spanning at least 100 Ma, atlantids have experienced and survived global-scale ocean changes and extinction events in the past. However, the diversification patterns and tempo of evolution in this family are largely unknown. Results Based on a concatenated maximum likelihood phylogeny of three genes (cytochrome c oxidase subunit 1 mitochondrial DNA, 28S and 18S ribosomal rRNA) we show that the three extant genera of the family Atlantidae, Atlanta, Protatlanta and Oxygyrus, form monophyletic groups. The genus Atlanta is split into two groups, one exhibiting smaller, well ornamented shells, and the other having larger, less ornamented shells. The fossil record, in combination with a fossil-calibrated phylogeny, suggests that large scale atlantid extinction was accompanied by considerable and rapid diversification over the last 25 Ma, potentially driven by vicariance events. Conclusions Now confronted with a rapidly changing modern ocean, the ability of atlantids to survive past global change crises gives some optimism that they may be able to persist through the Anthropocene.

Fossil-calibrated molecular phylogeny of atlantid heteropods (Gastropoda, Pterotracheoidea)

Background: The aragonite shelled, planktonic gastropod family Atlantidae (shelled heteropods) is likely to be one of the first groups to be impacted by imminent ocean changes, including ocean warming and ocean acidification. With a fossil record spanning at least 100 Million years (Ma), atlantids have experienced and survived global-scale ocean changes and extinction events in the past. However, the diversification patterns and tempo of evolution in this family are largely unknown. Results: Based on a concatenated maximum likelihood phylogeny of three genes (cytochrome c oxidase subunit 1 mitochondrial DNA, 28S and 18S ribosomal rRNA) we show that the three extant genera of the family Atlantidae, Atlanta, Protatlanta and Oxygyrus, form monophyletic groups. The genus Atlanta is split into two groups, one exhibiting smaller, well ornamented shells, and the other having larger, less ornamented shells. The fossil record, in combination with a fossil-calibrated phylogeny, suggests that large scale atlantid extinction was accompanied by considerable and rapid diversification over the last 25 Ma, potentially driven by vicariance events. Conclusions: Now confronted with a rapidly changing modern ocean, the ability of atlantids to survive past global change crises gives some optimism that they may be able to persist through the Anthropocene.

Fossil-calibrated molecular phylogeny of atlantid heteropods (Gastropoda, Pterotracheoidea)

The aragonite shelled, planktonic gastropod family Atlantidae (shelled heteropods) is likely to be one of the first groups to be impacted by imminent ocean changes, including ocean warming and ocean acidification. With a fossil record spanning at least 100 Million years (Ma), atlantids have experienced and survived global-scale ocean changes and extinction events in the past. However, the diversification patterns and tempo of evolution in this family are largely unknown. Based on a concatenated maximum likelihood phylogeny of three genes (cytochrome c oxidase subunit 1 mitochondrial DNA, 28S and 18S ribosomal rRNA) we show that the three extant genera of the family Atlantidae, Atlanta, Protatlanta and Oxygyrus, form monophyletic clades. The genus Atlanta is split into two groups, one exhibiting smaller, well ornamented shells, and the other having larger, less ornamented shells. The fossil record, in combination with a fossil-calibrated phylogeny suggest that large scale atlantid extinction was accompanied by considerable and rapid diversification over the last 25 Ma, potentially driven by vicariance events. Now confronted with a rapidly changing modern ocean, the ability of atlantids to survive past global change crises gives some optimism that they may be able to persist through the Anthropocene.

Beyond Wallace: a new lineage of Chrysorthenches (Lepidoptera: Yponomeutoidea: Glyphipterigidae) reveals a journey tracking its host-plants, Podocarpus (Pinopsida: Podocarpaceae)

A northward trans-Wallacean radiation is demonstrated for Chrysorthenches, a member of the Orthenches group. Here we review Chrysorthenches and allied genera resulting in a generic transfer of Diathryptica callibrya to Chrysorthenches and two new congeners: C. muraseaeSohn & Kobayashisp. nov. from Japan and C. smaragdinaSohnsp. nov. from Thailand. We review morphological characters of Chrysorthenches and allied genera, and find polyphyly of Diathryptica and the association of the Orthenches-group with Glyphipterigidae. These findings were supported in a maximum likelihood phylogeny of DNA barcodes from ten yponomeutoids. We analysed 30 morphological characters for 12 species of Chrysorthenches, plus one outgroup, via a cladistic approach. The resulting cladogram redefined two pre-existing Chrysorthenches species-groups and identified one novel lineage: the C. callibrya species-group. We review the host associations between Chrysorthenches and Podocarpaceae, based on mapping the working phylogenies. Our review suggests that ancestral Chrysorthenches colonized Podocarpus and later shifted to other podocarp genera. Biogeographical patterns of Chrysorthenches show that they evolved long after the Podocarpaceae radiation. Disjunctive trans-Wallacean distribution of the C. callibrya species-group is possibly related to the tracking of their host-plants and the complicated geological history of the island-arc system connecting Australia and East Asia.

The Genomics of Streptococcus Pneumoniae Carriage Isolates from UK Children and Their Household Contacts, Pre-PCV7 to Post-PCV13

We used whole genome sequencing (WGS) analysis to investigate the population structure of 877 Streptococcus pneumoniae isolates from five carriage studies from 2002 (N = 346), 2010 (N = 127), 2013 (N = 153), 2016 (N = 187) and 2018 (N = 64) in UK households which covers the period pre-PCV7 to post-PCV13 implementation. The genomic lineages seen in the population were determined using multi-locus sequence typing (MLST) and PopPUNK (Population Partitioning Using Nucleotide K-mers) which was used for local and global comparisons. A Roary core genome alignment of all the carriage genomes was used to investigate phylogenetic relationships between the lineages. The results showed an influx of previously undetected sequence types after vaccination associated with non-vaccine serotypes. A small number of lineages persisted throughout, associated with both non-vaccine and vaccine types (such as ST199), or that could be an example of serotype switching from vaccine to non-vaccine types (ST177). Serotype 3 persisted throughout the study years, represented by ST180 and Global Pneumococcal Sequencing Cluster (GPSC) 12; the local PopPUNK analysis and core genome maximum likelihood phylogeny separated them into two clades, one of which is only seen in later study years. The genomic data showed that serotype replacement in the carriage studies was mostly due to a change in genotype as well as serotype, but that some important genetic lineages, previously associated with vaccine types, persisted.

Salt- and alkaline-tolerance are linked in Acacia

Saline or alkaline soils present a strong stress on plants that together may be even more deleterious than alone. Australia's soils are old and contain large, sometimes overlapping, areas of high salt and alkalinity. Acacia and other Australian plant lineages have evolved in this stressful soil environment and present an opportunity to understand the evolution of salt and alkalinity tolerance. We investigate this evolution by predicting the average soil salinity and pH for 503 Acacia species and mapping the response onto a maximum-likelihood phylogeny. We find that salinity and alkalinity tolerance have evolved repeatedly and often together over 25 Ma of the Acacia radiation in Australia. Geographically restricted species are often tolerant of extreme conditions. Distantly related species are sympatric in the most extreme soil environments, suggesting lack of niche saturation. There is strong evidence that many Acacia have distributions affected by salinity and alkalinity and that preference is lineage specific.