Australian Lineages Research Articles

Vicars in the desert: Substrate specialisation and paleo-erosion underpin cryptic speciation in an Australian arid-zone lizard lineage (Diplodactylidae: Diplodactylus)

Vicars in the desert: Substrate specialisation and paleo-erosion underpin cryptic speciation in an Australian arid-zone lizard lineage (Diplodactylidae: Diplodactylus)

Avian influenza viruses in New Zealand wild birds, with an emphasis on subtypes H5 and H7: Their distinctive epidemiology and genomic properties.

The rapid spread of highly pathogenic avian influenza (HPAI) A (H5N1) viruses in Southeast Asia in 2004 prompted the New Zealand Ministry for Primary Industries to expand its avian influenza surveillance in wild birds. A total of 18,693 birds were sampled between 2004 and 2020, including migratory shorebirds (in 2004-2009), other coastal species (in 2009-2010), and resident waterfowl (in 2004-2020). No avian influenza viruses (AIVs) were isolated from cloacal or oropharyngeal samples from migratory shorebirds or resident coastal species. Two samples from red knots (Calidris canutus) tested positive by influenza A RT-qPCR, but virus could not be isolated and no further characterization could be undertaken. In contrast, 6179 samples from 15,740 mallards (Anas platyrhynchos) tested positive by influenza A RT-qPCR. Of these, 344 were positive for H5 and 51 for H7. All H5 and H7 viruses detected were of low pathogenicity confirmed by a lack of multiple basic amino acids at the hemagglutinin (HA) cleavage site. Twenty H5 viruses (six different neuraminidase [NA] subtypes) and 10 H7 viruses (two different NA subtypes) were propagated and characterized genetically. From H5- or H7-negative samples that tested positive by influenza A RT-qPCR, 326 AIVs were isolated, representing 41 HA/NA combinations. The most frequently isolated subtypes were H4N6, H3N8, H3N2, and H10N3. Multivariable logistic regression analysis of the relations between the location and year of sampling, and presence of AIV in individual waterfowl showed that the AIV risk at a given location varied from year to year. The H5 and H7 isolates both formed monophyletic HA groups. The H5 viruses were most closely related to North American lineages, whereas the H7 viruses formed a sister cluster relationship with wild bird viruses of the Eurasian and Australian lineages. Bayesian analysis indicates that the H5 and H7 viruses have circulated in resident mallards in New Zealand for some time. Correspondingly, we found limited evidence of influenza viruses in the major migratory bird populations visiting New Zealand. Findings suggest a low probability of introduction of HPAI viruses via long-distance bird migration and a unique epidemiology of AIV in New Zealand.

Genomic characterization of a unique Panton-Valentine leucocidin-positive community-associated methicillin-resistant Staphylococcus aureus lineage increasingly impacting on Australian indigenous communities.

In 2010 a single isolate of a trimethoprim-resistant multilocus sequence type 5, Panton-Valentine leucocidin-positive, community-associated methicillin-resistant Staphylococcus aureus (PVL-positive ST5 CA-MRSA), colloquially named WA121, was identified in northern Western Australia (WA). WA121 now accounts for ~14 % of all WA MRSA infections. To gain an understanding of the genetic composition and phylogenomic structure of WA121 isolates we sequenced the genomes of 155 WA121 isolates collected 2010-2021 and present a detailed genomic description. WA121 was revealed to be a single clonally expanding lineage clearly distinct from sequenced ST5 strains reported outside Australia. WA121 strains were typified by the presence of the distinct PVL phage φSa2wa-st5, the recently described methicillin resistance element SCCmecIVo carrying the trimethoprim resistance (dfrG) transposon Tn4791, the novel β-lactamase transposon Tn7702 and the epidermal cell differentiation inhibitor (EDIN-A) plasmid p2010-15611-2. We present evidence that SCCmecIVo together with Tn4791 has horizontally transferred to Staphylococcus argenteus and evidence of intragenomic movement of both Tn4791 and Tn7702. We experimentally demonstrate that p2010-15611-2 is capable of horizontal transfer by conjugative mobilization from one of several WA121 isolates also harbouring a pWBG749-like conjugative plasmid. In summary, WA121 is a distinct and clonally expanding Australian PVL-positive CA-MRSA lineage that is increasingly responsible for infections in indigenous communities in northern and western Australia. WA121 harbours a unique complement of mobile genetic elements and is capable of transferring antimicrobial resistance and virulence determinants to other staphylococci.

Two sympatric lineages of Australian Cnestus solidus share Ambrosiella symbionts but not Wolbachia

Sympatric lineages of inbreeding species provide an excellent opportunity to investigate species divergence patterns and processes. Many ambrosia beetle lineages (Curculionidae: Scolytinae) reproduce by predominant inbreeding through sib mating in nests excavated in woody plant parts wherein they cultivate symbiotic ambrosia fungi as their sole source of nutrition. The Xyleborini ambrosia beetle species Cnestus solidus and Cnestus pseudosolidus are sympatrically distributed across eastern Australia and have overlapping morphological variation. Using multilocus sequencing analysis of individuals collected from 19 sites spanning their sympatric distribution, we assessed their phylogenetic relationships, taxonomic status and microbial symbionts. We found no genetic differentiation between individuals morphologically identified as C. solidus and C. pseudosolidus confirming previous suggestions that C. pseudosolidus is synonymous to C. solidus. However, within C. solidus we unexpectedly discovered the sympatric coexistence of two morphologically indistinguishable but genetically distinct lineages with small nuclear yet large mitochondrial divergence. At all sites except one, individuals of both lineages carried the same primary fungal symbiont, a new Ambrosiella species, indicating that fungal symbiont differentiation may not be involved in lineage divergence. One strain of the maternally inherited bacterial endosymbiont Wolbachia was found at high prevalence in individuals of the more common lineage but not in the other, suggesting that it may influence host fitness. Our data suggest that the two Australian Cnestus lineages diverged allopatrically, and one lineage then acquired Wolbachia. Predominant inbreeding and Wolbachia infection may have reinforced reproductive barriers between these two lineages after their secondary contact contributing to their current sympatric distribution.

Nuclear exchange generates population diversity in the wheat leaf rust pathogen Puccinia triticina

In clonally reproducing dikaryotic rust fungi, non-sexual processes such as somatic nuclear exchange are postulated to play a role in diversity but have been difficult to detect due to the lack of genome resolution between the two haploid nuclei. We examined three nuclear-phased genome assemblies of Puccinia triticina, which causes wheat leaf rust disease. We found that the most recently emerged Australian lineage was derived by nuclear exchange between two pre-existing lineages, which originated in Europe and North America. Haplotype-specific phylogenetic analysis reveals that repeated somatic exchange events have shuffled haploid nuclei between long-term clonal lineages, leading to a global P. triticina population representing different combinations of a limited number of haploid genomes. Thus, nuclear exchange seems to be the predominant mechanism generating diversity and the emergence of new strains in this otherwise clonal pathogen. Such genomics-accelerated surveillance of pathogen evolution paves the way for more accurate global disease monitoring.

Divergent east-west lineages in an Australian fruit fly, (Bactrocera jarvisi), associated with the Carpentaria Basin divide.

Bactrocera jarvisi is an endemic Australian fruit fly species (Diptera: Tephritidae). It occurs commonly across tropical and subtropical coastal Australia, from far-northern Western Australia, across the 'Top End' of the Northern Territory, and then down the Queensland east coast. Across this range, its distribution crosses several well documented biogeographic barriers. In order to better understand factors leading to the divergence of Australian fruit fly lineages, we carried out a population genetic study of B. jarvisi from across its range using genome-wide SNP analysis, utilising adult specimens gained from trapping and fruit rearing. Populations from the Northern Territory (NT) and Western Australia were genetically similar to each other, but divergent from the genetically uniform east-coast (= Queensland, QLD) population. Phylogenetic analysis demonstrated that the NT population derived from the QLD population. We infer a role for the Carpentaria Basin as a biogeographic barrier restricting east-west gene flow. The QLD populations were largely panmictic and recognised east-coast biogeographic barriers play no part in north-south population structuring. While the NT and QLD populations were genetically distinct, there was evidence for the historically recent translocation of flies from each region to the other. Flies reared from different host fruits collected in the same location showed no genetic divergence. While a role for the Carpentaria Basin as a barrier to gene flow for Australian fruit flies agrees with existing work on the related B. tryoni, the reason(s) for population panmixia for B. jarvisi (and B. tryoni) over the entire Queensland east coast, a linear north-south distance of >2000km, remains unknown.

Revised taxonomy of the tribe Leptospermeae (Myrtaceae) based on morphological and DNA data

AbstractNew insights into relationships in the tribe Leptospermeae (Myrtaceae) are presented based on phylogenetic analyses of a 6‐locus, 109‐taxon dataset comprising 98 taxa sampled from all nine genera currently recognised in tribe Leptospermeae, including 76 accessions of Leptospermum s.l., and 11 outgroups representing five related tribes. Maximum parsimony and Bayesian inference analyses of separate plastid and nuclear datasets resolved five major lineages within Leptospermum, which was found to be polyphyletic with respect to other genera in the tribe, including Homalospermum, Kunzea and Neofabricia. These results concur with relationships identified in the companion phylogenomic study of the tribe by Binks & al. We also tested congruence of ovule/seed characters with the clades and the possible synapomorphy of hemitropous ovules for Asteromyrtus + Agonis s.l. To better reflect the wide variation seen in Leptospermum s.l., the genus is here restricted to members of the clade of woody‐fruited taxa found in eastern Australia, New Zealand, the Cook Islands and Malesia. To accommodate the four distinct clades of non‐woody‐fruited taxa, Leptospermopsis is reinstated for one western Australian lineage, and three new genera Apectospermum, Aggreflorum, and Gaudium are created for the other western and two largely eastern lineages, respectively, and 45 new combinations made. A key to Leptospermum and the newly segregated genera is presented. Additionally, eight names are lectotypified.

Invasion history of Lycium ferocissimum in Australia: The impact of admixture on genetic diversity and differentiation

AbstractAimWe investigated the invasion history of Lycium ferocissimum, a spine‐covered shrub native to South Africa that was introduced to Australia in the mid‐1800s, and has since developed into a damaging invasive plant of undisturbed landscapes and pastures. In addition to identifying the provenance of the Australian plants, we tested for evidence of admixture, and contrasted genetic diversity and structuring across the native and introduced ranges.LocationSamples were collected across South Africa (24 localities) and Australia (26 localities).MethodsWe used genotyping‐by‐sequencing (3117 SNPs across 381 individuals) to assess population genetic structuring in L. ferocissimum across Australia and South Africa. Coalescent analyses were used to explicitly test contrasting invasion scenarios.ResultsClear geographic genetic structuring was detected across South Africa, with distinct clusters in the Eastern and Western Cape provinces. The L. ferocissimum plants in Australia form their own genetic cluster, with a similar level of genetic diversity as plants in South Africa. Coalescent analyses demonstrated that the lineage in Australia was formed by admixture between Eastern Cape and Western Cape plants, with most of the genetic material from the Australian lineage originating from the Western Cape. Our analyses suggest that L. ferocissimum plants were originally introduced to South Australia, though it is unclear whether admixture occurred before or after its introduction to Australia. We detected little evidence of geographic genetic structure across Australia, although many of the populations were genetically distinct from one another.Main ConclusionsOur results illustrate how admixture can result in genetically diverse and distinct invasive populations. The complex invasion history of L. ferocissimum in Australia poses particular challenges for biological control. We suggest potential biological control agents should be screened against admixed plants (in addition to plants from the Eastern and Western Cape) to test whether they provide effective control of the genetically distinct invasive lineage.

Revisión Taxonómica y Estado de Conservación de las Especies de Eryngium (Apiaceae, Saniculoideae) Presentes en Chile

Eryngium L. comprises ca. 250 species and is distributed in every continent, except Antarctica. The species of the genus that inhabit Chile are mostly endemic to that country and are phylogenetically closely related to species from the west coast of the United States of America and Australia. Taxonomic studies of the North American and Australian lineages of Eryngium are in press or in preparation. However, the Eryngium species from Chile have not been revised taxonomically for more than a century. Moreover, many of the species of the genus endemic to Chile show restricted distributions and, therefore, deserve particular attention to evaluate if they are in any category of threat in order to develop conservation policies. The objective of this study is to perform a taxonomic revision of the species of Eryngium from Chile, including an analysis of their conservation status. For this purpose, the vegetative and reproductive morphology and the geographic distribution and habitat of ca. 750 herbarium specimens were analyzed. In addition, the conservation status of the species was evaluated following the Red List categories and criteria of the International Union for Conservation of Nature. In total, 17 species of Eryngium were recognized in Chile, of which 15 are endemic to that country and two also grow in Argentina. A key for the recognition of species is provided. For each species, a list of accepted synonyms, a morphological description, illustration, distribution map, habitats, phenology, and vernacular names are presented. Six new synonyms are proposed (Eryngium polyrhizum Clos and all varieties of E. depressum Hook. & Arn. are synonymized with E. depressum, E. amethystinodes Kuntze is synonymized with E. rostratum Cav., and E. delarocheanum H. Wolff is synonymized with E. paniculatum Cav. & Dombey ex F. Delaroche), and nomenclature problems were analyzed and resolved, including the typification of 23 names. The distribution ranges of six species (Eryngium anomalum Hook. & Arn., E. coquimbanum Phil. ex Urb., E. depressum, E. humifusum Clos, E. pulchellum Phil., and E. rostratum) are rectified. Aproximately 60% of the Eryngium species from Chile belong to a category of threat, and most of them are critically endangered, so they should be special targets for conservation.

Whole genome characterization and evolutionary analysis of bovine ephemeral fever virus isolated in Iran.

Bovine ephemeral fever virus (BEFV) is an economically important arthropod-borne virus of cattle and water buffaloes which is enzootic in Africa, Australia, and Asia. We characterized the entire length of BEFV BA/RZ/IR strain genome isolated in Iran and compared to the all BEFV full genomes available in the GenBank. The BEFV genomes were phylogenetically classified as 4 lineages including the Middle Eastern, East Asian, Australian, and South African lineages. The Iranian BA/RZ/IR strain, which displayed maximum sequence identity (96.72%) to the Chinese JT02L strain was clustered as a separate branch in the East Asian lineage of the virus. Using Shannon entropy analysis, amino acid variations were detected in the all proteins encoded by BEFV genomes. Particularly, the polymerase L and the accessory proteins Gns, α2 and β exhibited the highest amino acid variations suggesting their significance in the viral replication efficiency. Our bioinformatics analyses also predict the occurrence of recombination event within the East Asian lineage of BEFV genomes. Our data show that the Chinese Henan 1 may be a hybrid strain constructed of the Chinese JT02L and Iranian BA/RZ/IR BEFV strains as the major and minor parents, respectively. These computational analyses suggest that the homologous recombination may be an evolutionary mechanism for BEFV as a member of the Rhabdoviridae family.

An annotated checklist of Australian Mesozoic tetrapods

In 2020, the Australasian palaeontological association Australasian Palaeontologists (AAP) joined the Australian government-supported Australian National Species List (auNSL) initiative to compile the first Australian Fossil National Species List (auFNSL) for the region. The goal is to assemble comprehensive systematic data on all vertebrate, invertebrate and plant fossil taxa described to date, and to present the information both within a continuously updated open-access online framework, and as a series of primary reference articles in AAP’s flagship journal Alcheringa. This paper spearheads these auFNSL Alcheringa publications with an annotated checklist of Australian Mesozoic tetrapods. Complete synonymy, type material, source locality, geological age and bibliographical information are provided for 111 species formally named as of 2022. In addition, chronostratigraphically arranged inventories of all documented Australian Mesozoic tetrapod fossil occurrences are presented with illustrations of significant, exceptionally preserved and/or diagnostic specimens. The most diverse order-level clades include temnospondyl amphibians (34 species), saurischian (13 species) and ornithischian (12 species) dinosaurs (excluding ichnotaxa), and plesiosaurian marine reptiles (11 species). However, numerous other groups collectively span the earliest Triassic (earliest Induan) to Late Cretaceous (late Maastrichtian) and incorporate antecedents of modern Australian lineages, such as chelonioid and chelid turtles and monotreme mammals. Although scarce in comparison to records from other continents, Australia’s Mesozoic tetrapod assemblages are globally important because they constitute higher-palaeolatitude faunas that evince terrestrial and marine ecosystem evolution near the ancient South Pole. The pace of research on these assemblages has also accelerated substantially over the last 20 years, and serves to promote fossil geoheritage as an asset for scientific, cultural and economic development. The auFNSL augments the accessibility and utility of these palaeontological resources and provides a foundation for ongoing exploration into Australia’s unique natural history. Stephen F. Poropat [stephenfporopat@gmail.com], Western Australian Organic and Isotope Geochemistry Centre, School of Earth and Planetary Science, Curtin University, Bentley, Western Australia 6102, Australia, and Australian Age of Dinosaurs Museum of Natural History, Lot 1 Dinosaur Drive, Winton, Queensland 4735, Australia; Phil R. Bell [pbell23@une.edu.au], Palaeoscience Research Centre, School of Environmental and Rural Science, University of New England, Armidale, New South Wales 2351, Australia; Lachlan J. Hart [l.hart@unsw.edu.au], Earth and Sustainability Science Research Centre, School of Biological, Earth and Environmental Sciences (BEES), University of New South Wales, Kensington, New South Wales 2052, Australia, and Australian Museum Research Institute, 1 William Street, Sydney, New South Wales 2010, Australia; Steven W. Salisbury [s.salisbury@uq.edu.au] School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia; Benjamin P. Kear [benjamin.kear@em.uu.se] The Museum of Evolution, Uppsala University, Norbyvägen 16, Uppsala SE-752 36, Sweden.

Characterization of centromeric DNA of Gossypium anomalum reveals sequence-independent enrichment dynamics of centromeric repeats.

Centromeres in eukaryotes are composed of highly repetitive DNAs, which evolve rapidly and are thought to achieve a favorable structure in mature centromeres. However, how the centromeric repeat evolves into an adaptive structure is largely unknown. We characterized the centromeric sequences of Gossypium anomalum through chromatin immunoprecipitation against CENH3 antibodies. We revealed that the G. anomalum centromeres contained only retrotransposon-like repeats but were depleted in long arrays of satellites. These retrotransposon-like centromeric repeats were present in the African-Asian and Australian lineage species, suggesting that they might have arisen in the common ancestor of these diploid species. Intriguingly, we observed a substantial increase and decrease in copy numbers among African-Asian and Australian lineages, respectively, for the retrotransposon-derived centromeric repeats without apparent structure or sequence variation in cotton. This result indicates that the sequence content is not a decisive aspect of the adaptive evolution of centromeric repeats or at least retrotransposon-like centromeric repeats. In addition, two active genes with potential roles in gametogenesis or flowering were identified in CENH3 nucleosome-binding regions. Our results provide new insights into the constitution of centromeric repetitive DNA and the adaptive evolution of centromeric repeats in plants.

Phylogenetic relationships in the Eugongylini (Squamata: Scincidae): generic limits and biogeography

Skinks (Family Scincidae) are the most diverse family of lizards (~1745 described species worldwide), and the Australasian region (Australia, New Caledonia, New Zealand) is a recognised global hotspot (>600 species) for skinks. Here we focus on determining the phylogenetic relationships and biogeography within the tribe Eugongylini, one of three lineages in the region. We used mtDNA (ND2) and nuclear (RAG-1, c-mos) DNA sequences and phylogenetic analyses to reveal the presence of three well-supported lineages of Australian Eugongylini. We found a sister relationship between the monotypic genera Eroticoscincus and Harrisoniascincus, and that the monotypic Anepischetosia has close affinities with Carinascincus coventryi and Pseudemoia. C. coventryi represents a separate lineage from the main Carinascincus radiation. Emoia was not found to be monophyletic, with Emoia s.s. part of an Australian lineage, and the remainder of the genus representing an older divergence within the tribe. The widespread and speciose Cryptoblepharus represented a well-supported lineage within an Australian lineage. Our analyses confirm previous suggestions that four Sphenomorphus species (louisiadensis, minutus, bignelli, and aignanus) are misplaced, and are part of the Eugongylini. Our phylogenetic analyses support the hypothesis that the origin of the tribe lies in Asia, with dispersal events to Africa, Australasia, and Oceania.

Evidence for flock transmission of individual subtypes and strains of avian influenza viruses: A monitoring study of wild birds in Kazakhstan

An active surveillance study of avian influenza viruses (AIVs) in wild birds was carried out in Kazakhstan in 2018–2019. In total, 866 samples were collected from wild birds and analyzed for influenza viruses using molecular and virological tests. Genome segments of Asian, European, and Australian lineages were detected in 25 (4.6%) out of 541 waterfowl samples positive for subtype H3N8, and in two (0.6%) out of 325 H3N8 positive samples from terrestrial birds. No highly pathogenic avian influenza virus (AIV) was detected.The results indicated transmission of closely related strains or identical subtypes of AIVs by a flock-unit of migratory birds or annual cyclical pattern of subtype dominance. The simultaneous circulation of genome segments of the Asian, European and Australian genetic lineages of H3N8 AIVs in wild birds in Kazakhstan indicated the important role of Central Asia as a transmission hub of AI viruses linking the East Asian migratory flyways with European flyways and vice versa.

Systematic revision, molecular phylogeny and biogeography of the antlion tribe Acanthoplectrini (Neuroptera: Myrmeleontidae: Dendroleontinae), with emphasis on the Oriental lineage

AbstractThe tribe Acanthoplectrini (Myrmeleontidae: Dendroleontinae) includes a group of antlion genera widely distributed across the Australasian and Oriental regions. The intergeneric and interspecific relationships between or within the Australian and Oriental lineages of this tribe as well as their historical biogeography remain largely unexplored. Here, we present a molecular phylogenetic and biogeographic analyses of Acanthoplectrini to infer the diversification history of this tribe, with emphasis on the Oriental lineage. Both the Oriental and Australian lineages are monophyletic and recovered as sister groups. Ancestral area reconstruction suggests that the ancestor of Acanthoplectrini might have been once widely distributed from Indochina to Australia and then split into the Oriental and Australian lineages during the early‐Miocene. Our analyses recovered northeastern Indochina and south China as the ancestral range of the Oriental Acanthoplectrini. During the mid‐Miocene to the mid‐Pliocene, orographic events such as the rising of mountain ranges (including the Himalayas) and the formation of major islands in southeastern Asia triggered several dispersal and vicariance events in the Oriental Acanthoplectrini, driving their speciation. We revise the classification of the Oriental Acanthoplectrini, establishing the new genus Paralayahima gen. n., which is recovered sister to Layahima Navás. Moreover, we describe four new species of Layahima, Layahima aspoeckorum sp. n., Layahima monba sp. n., Layahima lhoba sp. n. and Layahima xinliae sp. n., and we reinstate two previously synonymized species, Layahima melanocoris (Yang) stat. rev. and comb. n. and Layahima nebulosa Navás stat. rev.

Biogeographic history predicts bee community structure across floral resource gradients in south‐east Australia

AbstractAimPlant populations are declining in their native ranges around the globe through the expansion of agriculture, urbanization, and plant invasions. We test the hypothesis that animal species that have spent more of their evolutionary history in a region are more dependent on native plants, particularly those plants that have spent more of their evolutionary history in the region, and are therefore more negatively impacted by native plant decline.LocationYarra Valley landscapes, Australia.MethodsWe test the presence and pattern of phylogenetic signal in native bee community responses to local flower density of ancient Australian plant lineages and the amount of native vegetation in the surrounding landscape across farm and native vegetation sites. We also test phylogenetic signal in the frequency of bee visitation to flowers from ancient Australian plant lineages. We compare the patterns of phylogenetic signal to the current understanding of bee biogeographic histories to evaluate our hypothesis.ResultsThere was significant phylogenetic signal in responses to flower density of plants from ancient Australian lineages, and the frequency of visitation to these flowers, with most species from the ancient Australian bee clade being positively associated with these flowers. This is consistent with our hypothesis. Significant phylogenetic signal in response to native vegetation in the surrounding landscape was driven primarily by the more recently arrived bee linages, with ancient lineages able to persist on some farms where ancient Australian flowers were present (e.g. on roadsides).Main conclusionsBee species that have spent more of their evolutionary history in Australia are more dependent on ancient Australian plant lineages and so most negatively impacted by the decline of these plants. This may be a broader phenomenon because phylogenetic conservatism in host plant use, the main assumption underlying our hypothesis, is common among herbivorous arthropods (~500,000 species).

Recombinant parechovirus A3 possibly causes various clinical manifestations, including myalgia; findings in Yamagata, Japan in 2019

Background Parechovirus A3 was first reported in 2004 and has been recognized as a causative agent of mild and severe infections in children. Since we first reported an outbreak of adult parechovirus A3-associated myalgia in Yamagata, Japan in 2008, this disease has since been recognized across Japan, but has not yet been reported from other countries. Aim We analysed 19 cases of parechovirus A3 infections identified in Yamagata in 2019 to further clarify the epidemiology of this disease. Methods We performed phylogenetic analyses of parechovirus A3 isolates and analysed the clinical manifestations and the genomic clusters. Results There were two clusters, with cluster 2019B replacing 2019 A around October/November. Phylogenetic analysis revealed that 2019B cluster strains and Australian recombinant strains, which appeared between 2012 and 2013, were grouped in one cluster at non-structural protein regions, suggesting that the ancestor to these regions of 2019B cluster strains were Australian recombinant lineage strains. The strains from both clusters caused various infections in children including myalgia. These findings strongly support that parechovirus A3 strains cause myalgia and other paediatric infections irrespective of the virus strains involved, including recombinant strains. Conclusions We have reported repeatedly sporadic cases of myalgia and here showed that recombinant strains also cause myalgia. We hope our experiences will help better understand these infections and possibly result in detection of more cases in the world.

Phylogenomics resolves timing and patterns in the evolution of Australasian Cerambycinae (Coleoptera: Cerambycidae), and reveals new insights into the subfamily-level classification and historical biogeography of longhorn beetles

Cerambycinae is the second-largest subfamily of longhorn beetles in the Southern Hemisphere. The phylogeny of Cerambycinae is poorly known, resulting in a highly artificial tribal-level classification and a largely speculative evolutionary history. We reconstructed the phylogenetic relationships of Cerambycinae at the generic level using anchored hybrid enrichment data from hundreds of nuclear genes, with a primary focus on the extraordinarily diverse faunas of Australia and New Zealand. We also estimated divergence times by incorporating fossil calibrations in our analyses. We identified two main clades within Cerambycinae, which can also be separated morphologically by a distinct type of antennal foramen. We recovered a Late Jurassic origin of crown Cerambycinae. Dorcasominae, which was newly found to have representatives in Australia, was notably derived from within Cerambycinae. We recovered two independent origins of Australian Cerambycinae: one clade originated in the Early Cretaceous and is likely endemic to the Southern Hemisphere, while the other clade appears to have immigrated to Australia, perhaps from the Northern Hemisphere. Within the Australian lineages were multiple independent origins of New Zealand taxa, all of which are relative host-plant generalists. Tribal relationships and assignments are discussed, and based on our results, the following major nomenclatural acts were made: Dorcasominae Lacordaire, 1868 is downgraded to a tribe Dorcasomini of Cerambycinae Latreille, 1804; Neostenini Lacordaire, 1868 syn. nov. is treated as a junior synonym of Uracanthini Blanchard, 1851.

Cryptic species of pondweeds (Potamogetonaceae) at an intercontinental scale revealed by molecular phylogenetic analyses

AbstractCryptic species are morphologically indistinguishable but genetically divergent entities that constitute an important part of Earth's biodiversity. They occur in all kingdoms of life, especially when morphological characters are scarce. Compared to the high number of plant species, relatively few cryptic species have been detected so far. Here, we report cryptic species in pondweeds (Potamogeton), freshwater aquatic angiosperms that are characterized by reduced morphology. Using four molecular markers (ITS, 5S‐NTS, rpl20‐5′rps12, trnT‐trnL), three of them unlinked, we found that the widespread P. octandrus consists of three divergent lineages that correspond to the geographic origins of samples from Africa, Asia, and Australia, respectively. Relatively high genetic divergence between these lineages, reciprocal monophyly and many fixed diagnostic characters indicate that P. octandrus consists of three cryptic species. We formally distinguish the African lineage as P. parvifolius and the Australian lineage as P. tenuicaulis from Asian P. octandrus s.str. Potamogeton tenuicaulis is paraphyletic with the Asian species P. cristatus, which differs by unique fruit characters. We assume that the ancestor of P. cristatus originated from Australia and reached Asia by long‐distance dispersal. Quality criteria for assigning species status to cryptic species and their formal taxonomic recognition are discussed.

First Evidence of Cryptic Species Diversity and Population Structuring of Selaroides leptolepis in the Tropical Western Pacific

The yellowstripe scad,Selaroides leptolepis(Carangidae), is an important fish commodity in the Tropical Western Pacific (TWP). It has a latitudinal Pacific range from south of Japan down to northern Australia, with the highest concentration in Southeast Asia. However, its TWP fishing grounds have long been a hotspot of unsustainable exploitations, thus threatening the remaining wild populations. Despite the species’ commercial significance, there is limited understanding of its genetic structure and diversity. Herein, the genetic structure ofS. leptolepiswas examined using mitochondrialCOIandCytBsequences. Both markers denoted significant genetic structuring based on high overall FSTvalues. Hierarchical analysis of molecular variance (AMOVA), maximum likelihood (ML) phylogenetic trees, and median-joining (MJ) haplotype networks strongly supported the occurrence of two allopatrically distributed lineages. These comprised of a widespread Asian lineage and an isolated Australian lineage. Within-lineage distances were low (K2P < 1%) whereas across-lineage distances were remarkably high (K2P > 6%), already comparable to that of interspecific carangid divergences. Haplotype sequence memberships, high genetic variations, and the geographic correlation suggested that the Australian lineage was a putative cryptic species. Historical demographic inferences also revealed that the species experienced rapid expansion commencing on the late Pleistocene, most likely during the end of the Last Glacial Maximum (∼20,000 years ago). The present study encouraged the application of lineage-specific management efforts, as the lineages are experiencing different evolutionary pressures. Overall, accurate knowledge of the species’ genetic distribution is fundamental in protecting its diversity and assuring stock sustainability.