Minor Lineages Research Articles

A new lineage nomenclature to aid genomic surveillance of dengue virus.

Dengue virus (DENV) is currently causing epidemics of unprecedented scope in endemic settings and expanding to new geographical areas. It is therefore critical to track this virus using genomic surveillance. However, the complex patterns of viral genomic diversity make it challenging to use the existing genotype classification system. Here, we propose adding 2 sub-genotypic levels of virus classification, named major and minor lineages. These lineages have high thresholds for phylogenetic distance and clade size, rendering them stable between phylogenetic studies. We present assignment tools to show that the proposed lineages are useful for regional, national, and subnational discussions of relevant DENV diversity. Moreover, the proposed lineages are robust to classification using partial genome sequences. We provide a standardized neutral descriptor of DENV diversity with which we can identify and track lineages of potential epidemiological and/or clinical importance. Information about our lineage system, including methods to assign lineages to sequence data and propose new lineages, can be found at: dengue-lineages.org.

Bronze Art, Cultural Norms, and Group Identity: A Group of Late Western Zhou and Early Spring and Autumn He Vessels Analyzed in Their Temporal and Spatial Contexts

abstract: A new generation of scholars has called into question the homogeneous nature of Western Zhou culture and the sweeping imposition of this culture over a large region that covers much of present-day China. Our study contributes to this debate by focusing on a coherent group of bronze vessels dated to the end of the Western Zhou and beginning of the Spring and Autumn periods. He (盉) vessels with drum-shaped bodies, bird-like lids, and human-like legs are among the most unique and artistically innovative artifacts of this period. While these unique artifacts have been found in and near the center of the Western Zhou polity, they are not associated with the rituals of the royal house, but rather with those of other aristocratic lineages. We argue that the artistic style of the vessels was part of the culture developed around the royal Zhou house and in areas close to it, although it is not strictly representative of the royal culture of the Western Zhou, being instead associated with minor lineages. A multi-dimensional analysis of this group of vessels, addressing their geographical distribution, location within their archaeological context, and social associations, combined with an analysis of their decorative scheme and the inscriptions cast inside them, enables us to better understand the sociocultural landscape of this period. Our study suggests that diversity existed not only in remote border areas or among the lower strata of society, but also within the cultural core of the Western Zhou polity and among the highest echelons of the aristocracy. Such processes of diversification are associated with the development of local and regional identities and with the growth of the political independence of aristocratic lineages during the final years of the transition from the Western Zhou to the Spring and Autumn periods.

Bronze Art, Cultural Norms, and Group Identity: A Group of Late Western Zhou and Early Spring and Autumn He Vessels Analyzed in Their Temporal and Spatial Contexts

A new generation of scholars has called into question the homogeneous nature of Western Zhou culture and the sweeping imposition of this culture over a large region that covers much of present-day China. Our study contributes to this debate by focusing on a coherent group of bronze vessels dated to the end of the Western Zhou and beginning of the Spring and Autumn periods. He (盉) vessels with drum-shaped bodies, bird-like lids, and human-like legs are among the most unique and artistically innovative artifacts of this period. While these unique artifacts have been found in and near the center of the Western Zhou polity, they are not associated with the rituals of the royal house, but rather with those of other aristocratic lineages. We argue that the artistic style of the vessels was part of the culture developed around the royal Zhou house and in areas close to it, although it is not strictly representative of the royal culture of the Western Zhou, being instead associated with minor lineages. A multi-dimensional analysis of this group of vessels, addressing their geographical distribution, location within their archaeological context, and social associations, combined with an analysis of their decorative scheme and the inscriptions cast inside them, enables us to better understand the socio-cultural landscape of this period. Our study suggests that diversity existed not only in remote border areas or among the lower strata of society, but also within the cultural core of the Western Zhou polity and among the highest echelons of the aristocracy. Such processes of diversification are associated with the development of local and regional identities and with the growth of the political independence of aristocratic lineages during the final years of the transition from the Western Zhou to the Spring and Autumn periods. KEYWORDS: homogeneous culture, ritual and identity, bronze art, he vessels, winged animal and human figurines, Western Zhou and Spring and Autumn periods

Skeleton phylogeny reconstructed with transcriptomes for the tribe Drosophilini (Diptera: Drosophilidae)

The family Drosophilidae is one of the most important model systems in evolutionary biology. Thanks to advances in high-throughput sequencing technology, a number of molecular phylogenetic analyses have been undertaken by using large data sets of many genes and many species sampled across this family. Especially, recent analyses using genome sequences have depicted the family-wide skeleton phylogeny with high confidence. However, the taxon sampling is still insufficient for minor lineages and non-Drosophila genera. In this study, we carried out phylogenetic analyses using a large number of transcriptome-based nucleotide sequences, focusing on the largest, core tribe Drosophilini in the Drosophilidae. In our analyses, some noise factors against phylogenetic reconstruction were taken into account by removing putative paralogy from the datasets and examining the effects of missing data, i.e. gene occupancy and site coverage, and incomplete lineage sorting. The inferred phylogeny has newly resolved the following phylogenetic positions/relationships at the genomic scale: (i) the monophyly of the subgenus Siphlodora including Zaprionus flavofasciatus to be transferred therein; (ii) the paraphyly of the robusta and melanica species groups within a clade comprised of the robusta, melanica and quadrisetata groups and Z. flavofasciatus; (iii) Drosophila curviceps (representing the curviceps group), D. annulipes (the quadrilineata subgroup of the immigrans group) and D. maculinotata clustered into a clade sister to the Idiomyia + Scaptomyza clade, forming together the expanded Hawaiian drosophilid lineage; (iv) Dichaetophora tenuicauda (representing the lineage comprised of the Zygothrica genus group and Dichaetophora) placed as the sister to the clade of the expanded Hawaiian drosophilid lineage and Siphlodora; and (v) relationships of the subgenus Drosophila and the genus Zaprionus as follows: (Zaprionus, (the quadrilineata subgroup, ((D. sternopleuralis, the immigrans group proper), (the quinaria radiation, the tripunctata radiation)))). These results are to be incorporated into the so-far published phylogenomic tree as a backbone (constraint) tree for grafting much more species based on sequences of a limited number of genes. Such a comprehensive, highly confident phylogenetic tree with extensive and dense taxon sampling will provide an essential framework for comparative studies of the Drosophilidae.

Ancient Components and Recent Expansion in the Eurasian Heartland: Insights into the Revised Phylogeny of Y-Chromosomes from Central Asia.

In the past two decades, studies of Y chromosomal single nucleotide polymorphisms (Y-SNPs) and short tandem repeats (Y-STRs) have shed light on the demographic history of Central Asia, the heartland of Eurasia. However, complex patterns of migration and admixture have complicated population genetic studies in Central Asia. Here, we sequenced and analyzed the Y-chromosomes of 187 male individuals from Kazakh, Kyrgyz, Uzbek, Karakalpak, Hazara, Karluk, Tajik, Uyghur, Dungan, and Turkmen populations. High diversity and admixture from peripheral areas of Eurasia were observed among the paternal gene pool of these populations. This general pattern can be largely attributed to the activities of ancient people in four periods, including the Neolithic farmers, Indo-Europeans, Turks, and Mongols. Most importantly, we detected the consistent expansion of many minor lineages over the past thousand years, which may correspond directly to the formation of modern populations in these regions. The newly discovered sub-lineages and variants provide a basis for further studies of the contributions of minor lineages to the formation of modern populations in Central Asia.

Immunophenotypic assessment of PNH clones in major and minor cell lineages in the peripheral blood of patients with paroxysmal nocturnal hemoglobinuria.

Flow cytometric immunophenotyping is essential for the diagnosis of paroxysmal nocturnal hemoglobinuria (PNH). Most cases have easy to interpret flow cytometry profiles with red cells, neutrophils and monocytes showing complete deficiency of glycophosphatidylinositol (GPI) linked antigen expression. Some cases are more challenging to interpret due to the presence of multiple populations of PNH cells and variable levels of GPI antigen expression. We studied 46 known PNH patients, many with complex immunophenotypic profiles using a novel, single tube, multi-parameter 7-color immunophenotyping assay that allowed simultaneous detection and assessment of PNH clones within multiple lineages of peripheral blood leucocytes. Red cell PNH clones were also assessed in total and immature (CD71+) components by CD59 expression. For individual patients, total PNH clones in each cell lineage were highly correlated. Monocytes, eosinophils and basophils showed the highest proportions of PNH cells. Red cell PNH clones were typically smaller than monocyte and neutrophil PNH clones. In most cases, PNH clones were detectable in minor leucocyte populations where multiple populations of PNH cells were present, variability in the proportions of type II and type III cells was seen across different cell lineages, even though total PNH clones remained similar. This study shows that PNH patients with multiple PNH clones do not always display the same abnormality across all cell lineages routinely tested. There is no simple explanation for this but is likely due to a combination of complex molecular, genetic and biochemical dysfunction in different blood cell types.

Integrative Study of Genotypic and Phenotypic Diversity in the Eurasian Orchid Genus Neotinea.

Knowledge of population variation across species’ ranges is a prerequisite for correctly assessing the overall variability of any group of organisms and provides an invaluable basis for unraveling evolutionary history, optimizing taxonomy and devising effective conservation strategies. Here, we examine the genus Neotinea, which represents a relatively recently delimited monophyletic genus of orchids, for which a detailed study of its overall variability was lacking. We applied a suite of biosystematic methods, consisting of flow cytometry, multivariate and geometric morphometrics, and analysis of genomic SNP data, to identify phylogenetic lineages within the genus, to delineate phenotypic variation relevant to these lineages, and to identify potential cryptic taxa within lineages. We found clear differentiation into four major lineages corresponding to the groups usually recognized within the genus: Neotinea maculata as a distinct and separate taxon, the Neotinea lactea group comprising two Mediterranean taxa N. lactea and Neotinea conica, the Neotinea ustulata group comprising two phenologically distinct varieties, and the rather complex Neotinea tridentata group comprising two major lineages and various minor lineages of unclear taxonomic value. N. conica constitutes both a monophyletic group within N. lactea and a distinct phenotype within the genus and merits its proposed subspecies-level recognition. By contrast, the spring and summer flowering forms of N. ustulata (var. ustulata and var. aestivalis) were confirmed to be distinct only morphologically, not phylogenetically. The most complex pattern emerged in the N. tridentata group, which splits into two main clades, one containing lineages from the Balkans and eastern Mediterranean and the other consisting of plants from Central Europe and the central Mediterranean. These individual lineages differ in genome size and show moderate degrees of morphological divergence. The tetraploid Neotinea commutata is closely related to the N. tridentata group, but our evidence points to an auto- rather than an allopolyploid origin. Our broad methodological approach proved effective in recognizing cryptic lineages among the orchids, and we propose the joint analysis of flow cytometric data on genome size and endopolyploidy as a useful and beneficial marker for delineating orchid species with partial endoreplication.

Reassessment of the Columnea latent viroid (CLVd) Taxonomic Classification.

Columnea latent viroid (CLVd) is a member of the Pospiviroid family and its naked circular RNA genome typically forms native “rod-like” secondary structures. In this work, the CLVd taxonomy was reevaluated based on sequence similarity and phylogenetic analysis, as well as the evaluation of the symptom development and disease severity of four selected CLVd isolates in a range of host species. The phylogenetic analysis showed that all CLVd isolates were clustered into five distinct clades: (I) severe isolates originally found in tomato crops in Thailand, (II) ornamental isolates, (III) mild isolates originally found in tomato crops in Thailand, and two clades (IV and V) containing mild isolates originating mainly from tomato crops in European countries, with different virulence levels on several hosts. Our analysis demonstrated that some CLVd isolates have a sequence similarity of less than 90% within the species taxon, as well as distinct biological characteristics (symptom development and virulence), both of which are important ICTV criteria for viroid classification. For these reasons, we propose that CLVd should be re-classified into at least three main taxonomic lineages: a “CLVd-tomato Asian lineage” (I), a “CLVd-tomato European lineage” (IV) and a “CLVd-ornamental European lineage” (II), plus two minor lineages (III and V), fitting the ICTV criteria.

Aegilops tauschii Coss. molecular phylogeny: nuclear gene Got2 versus chloroplast DNA data

Aegilops tauschii Coss. phylogenetic tree based on DNA sequences of nuclear gene Got2, about 3000 b.p., studied in 114 accessions of the species was constructed and compared with the tree previously built using non-coding chloroplast DNA (cpDNA), about 3000 b.p. in total, in 111 Ae. tauschii accessions. (110 accessions are the same on both trees.) The two trees differ greatly, implying that despite of Ae. tauschii being mostly self-pollinating species, cross pollination played an important role in the species evolutionary history. Got2 tree rather well corresponds to Ae. tauschii intraspecies systematics based on spike morphology, while cpDNA tree is in contradiction with this systematics. Ae. tauschii phylogeographic patterns essentially differ in Ae. tauschii subsp. tauschii and Ae. tauschii subsp. strangulata. As revealed by Got2 DNA data, subsp. strangulata presents five major common phylogenetic lineages sharing the subspecies range between each other, and minor relict lineages in addition. Subspecies tauschii presents single major lineage occupying all the subspecies range, and additional relict lineages.

Among-Population Genetic Diversity of Rice Blast Fungus Based on Fingerprinting of Virulence-related genes

In this study, 189 strains of rice blast fungus isolated from rice-growing fields in five counties within the Jiangxi Province, China, were amplified with 16 pairs of virulence gene-specific primers. Fifteen pairs were able to amplify their target bands. The percentage of polymorphic sites was as high as 93.75%, and the frequency of amplification varied greatly. Cluster analysis classified the 189 strains, represented by 108 different haplotypes, into 21 genetic lineages at a genetic similarity level of 0.80. JXH16 was the dominant haplotype. The 21 genetic lineages included 1 dominant, 2 subdominant, 12 secondary, and 6 minor lineages. At the population level, rich genetic diversity was observed among the 189 strains from different geographic regions (H = 0.2890; I = 0.4398). At a genetic distance of 0.02, the five populations were clustered into three groups that were unrelated to geographical distribution. A certain level of genetic differentiation was found to exist within each blast fungus population (HT = 0.2842). Within-population genetic diversity was higher than that among populations (Hs = 0.2210; Dst = 0.0632), with 77.75% of the total genetic variation originates within populations (Gst = 0.2225). Some within-population gene flow were detected (Nm = 1.7473). The results of our study, which revealed the genetic structure and diversity of rice blast fungal strains in five major rice cultivation areas of Jiangxi Province and their relationship to geographical distribution, can serve as a basis for rice blast resistance breeding and the selection of suitable varieties for these regions, including Duchang County, Jinggangshan City, Fengcheng City, Wan ‘an County and Wuyuan County.

Paternal heritage of the Han Chinese in Henan province (Central China): high diversity and evidence of in situ Neolithic expansions

Background: Due to their long history, complex admixture processes and large population sizes, more research is required to explore the fine genetic structure of Han populations from different geographic locations of China.Aim: To characterise the paternal genetic structure of the Han Chinese in Henan province, which was once the central living region of the ancient Huaxia population, the precursors of the Han Chinese.Subjects and methods: We sequenced Y chromosomes of 60 males from Zhengzhou, Henan Province, and reconstructed a phylogenetic tree for these samples with age estimation.Results: We observed high diversity of paternal lineages in our collection. We found that the in situ Neolithic expansion of the “Major lineages” contributed to a large portion of the paternal gene pool of the Han population in Henan Province. We also detected a large number of “Minor lineages” that diverged in the Palaeolithic Age.Conclusion: We suggest that the high genetic diversity in the paternal gene pool of modern Han populations is mainly attributed to the reservation of a larger number of lineages that diverged in the Palaeolithic Age, while the recent expansion of limited lineages contributed to the majority of the gene pool of modern Han populations. We propose that such a structure is a basal characteristic for the genetic structure of modern Han populations.

Multiple origins of reverse transcriptases linked to CRISPR-Cas systems

ABSTRACT Prokaryotic genomes harbour a plethora of uncharacterized reverse transcriptases (RTs). RTs phylogenetically related to those encoded by group-II introns have been found associated with type III CRISPR-Cas systems, adjacent or fused at the C-terminus to Cas1. It is thought that these RTs may have a relevant function in the CRISPR immune response mediating spacer acquisition from RNA molecules. The origin and relationships of these RTs and the ways in which the various protein domains evolved remain matters of debate. We carried out a large survey of annotated RTs in databases (198,760 sequences) and constructed a large dataset of unique representative sequences (9,141). The combined phylogenetic reconstruction and identification of the RTs and their various protein domains in the vicinity of CRISPR adaptation and effector modules revealed three different origins for these RTs, consistent with their emergence on multiple occasions: a larger group that have evolved from group-II intron RTs, and two minor lineages that may have arisen more recently from Retron/retron-like sequences and Abi-P2 RTs, the latter associated with type I-C systems. We also identified a particular group of RTs associated with CRISPR-cas loci in clade 12, fused C-terminally to an archaeo-eukaryotic primase (AEP), a protein domain (AE-Prim_S_like) forming a particular family within the AEP proper clade. Together, these data provide new insight into the evolution of CRISPR-Cas/RT systems.

Familias, linajes y poder señorial: aspectos de movilidad y articulación de los entornos rurales a los urbanos en el espacio cantábrico

El siguiente trabajo analiza, en forma comparada, las dinámicas de movilidad socio-territoriales que presentan los linajes menores del área cantábrica asociados a la casa señorial de los Velasco (duques de Frías) en función de la centralidad que presentan las ciudades en el espacio septentrional analizando la dinámica de ascenso y movilización de sus descendientes. Para ello se utiliza el análisis de redes y la comparación de trayectorias y recorridos -colectivos y personales- para componer un cuadro dinámico de interrelaciones y movilidad.

Bacterial community in ancient permafrost alluvium at the Mammoth Mountain (Eastern Siberia)

Permanently frozen (approx. 3.5Ma) alluvial Neogene sediments exposed in the Aldan river valley at the Mammoth Mountain (Eastern Siberia) are unique, ancient, and poorly studied permafrost environments. So far, the structure of the indigenous bacterial community has remained unknown. Use of 16S metagenomic analysis with total DNA isolation using DNA Spin Kit for Soil (MO-Bio) and QIAamp DNA Stool Mini Kit (Qiagen) has revealed the major and minor bacterial lineages in the permafrost alluvium sediments. In sum, 61 Operational Taxonomic Units (OTUs) with 31,239 reads (Qiagen kit) and 15,404 reads (Mo-Bio kit) could be assigned to the known taxa. Only three phyla, Bacteroidetes, Proteobacteria and Firmicutes, comprised >5% of the OTUs abundance and accounted for 99% of the total reads. OTUs pertaining to the top families (Chitinophagaceae, Caulobacteraceae, Sphingomonadaceae, Bradyrhizobiaceae, Halomonadaceae) held >90% of reads. The abundance of Actinobacteria was less (0.7%), whereas members of other phyla (Deinococcus-Thermus, Cyanobacteria/Chloroplast, Fusobacteria, and Acidobacteria) constituted a minor fraction of reads. The bacterial community in the studied ancient alluvium differs from other permafrost sediments, mainly by predominance of Bacteroidetes (>52%). The diversity of this preserved bacterial community has the potential to cause effects unknown if prompted to thaw and spread with changing climate. Therefore, this study elicits further reason to study how reintroduction of these ancient bacteria could affect the surrounding ecosystem, including current bacterial species.

Population genomic insights into variation and evolution of Xanthomonas oryzae pv. oryzae

Xanthomonas oryzae pv. oryzae ( Xoo) is a serious pathogen of rice causing bacterial leaf blight disease. Resistant varieties and breeding programs are being hampered by the emergence of highly virulent strains. Herein we report population based whole genome sequencing and analysis of 100 Xoo strains from India. Phylogenomic analysis revealed the clustering of Xoo strains from India along with other Asian strains, distinct from African and US Xo strains. The Indian Xoo population consists of a major clonal lineage and four minor but highly diverse lineages. Interestingly, the variant alleles, gene clusters and highly pathogenic strains are primarily restricted to minor lineages L-II to L-V and in particularly to lineage L-III. We could also find the association of an expanded CRISPR cassette and a highly variant LPS gene cluster with the dominant lineage. Molecular dating revealed that the major lineage, L-I is youngest and of recent origin compared to remaining minor lineages that seems to have originated much earlier in the past. Further, we were also able to identify core effector genes that may be helpful in efforts towards building durable resistance against this pathogen.

High occurrence of Pacearchaeota and Woesearchaeota (Archaea superphylum DPANN) in the surface waters of oligotrophic high-altitude lakes.

We carried out a regional survey on the archaea composition from surface waters of > 300 high-altitude Pyrenean lakes (average altitude 2300 m, pH range 4.4-10.1) by 16S rRNA gene tag sequencing. Relative Archaea abundances ranged between 0% and 6.3% of total prokaryotes amplicons in the polymerase chain reaction (PCR) mixture, and we detected 769 operational taxonomic units (OTUs; grouped at 97% identity) that split into 13 different lineages, with altitude and pH having a significant effect on the community composition. Woesearchaeota and Pacearchaeota (formerly Euryarchaeota DHVEG-6 cluster) dominated the data set (83% of total OTUS), showed a high occurrence (presence in c. 75% of the lakes) and had relative abundances significantly and positively correlated with the phylogenetic diversity of bacterial communities. Micrarchaeota-Diapherotrites (formerly Euryarchaeota MEG cluster), Methanomicrobia, Thermoplasmata and ammonia-oxidizing thaumarchaeota (AOA) showed relative abundances between 1% and 3% and occurrences between 14% and 26%. Minor lineages were SM1K20, Aenigmarchaeota (formerly Euryarchaeota DSEG cluster), Methanobacteria, Bathyarchaeota and SCG. Environmental preferences substantially differed among lineages, with Aenigmarchaeota and Methanomicrobia having the largest habitat breadth, and Thermoplasmata, AOA and Micrarchaeota having the smallest. Pacearchaeota and Woesearchaeota had been mostly reported from saline habitats and sediments, but surface waters of oligotrophic alpine lakes are suitable environments for such ecologically spread and genetically diverse archaeal lineages.

Contrasted Genetic Diversity, Relevance of Climate and Host Plants, and Comments on the Taxonomic Problems of the Genus Picoa (Pyronemataceae, Pezizales).

The species concept within the genus Picoa Vittad. is here revisited in light of new molecular and ecological data obtained from samples collected throughout the Mediterranean basin. Two highly diverse widespread clades and four additional minor lineages were significantly supported by three genes dataset (ITS, 28s LSU and RPB2) inferences for 70 specimens. The two widespread clades occur in very different geographical and ecological areas associated with exclusive host plants in the genus Helianthemum. SEM study of spore surface morphology in these lineages revealed the existence of smooth ascospores in the majority of these clades. However the most frequent lineage in Europe and coastal North Africa displayed either smooth or verrucose spores. Hence this morphological criterion cannot be reliably used to discriminate between the different clades. In addition, SEM observations made on ascospores from several original collections of P. juniperi and P. lefebvrei supported the hypothesis that ornamentation depends on the degree of maturity in some of these lineages. Geographical and ecological, rather than morphological data are here suggested as the most useful characters to separate the different lineages in Picoa. Further studies focusing on these features are needed before the names P. juniperi and P. lefebvrei can be unambiguously linked with the genetic lineages observed.

Phylogeny and systematics of mitriform gastropods (Mollusca: Gastropoda: Neogastropoda)

With about 800 Recent species, ‘miters’ are a widely distributed group of tropical and subtropical gastropods that are most diverse in the Indo-West Pacific. They include the two families Mitridae and Costellariidae, similar in shell morphology and traditionally treated as close relatives. Some genera of deep-water Ptychatractidae and Volutomitridae are close to miters in shell morphology, and the term ‘mitriform gastropods’ has been introduced to refer to Mitridae, Costellariidae, and this assortment of convergent forms. The present study aimed at the reconstruction of phylogenetic relationships of mitriform gastropods based on representative taxon sampling. Four genetic markers [cytochrome c oxidase subunit I (COI), 16S and 12S rRNA mitochondrial genes, and H3 (Histone 3) nuclear gene] were sequenced for over 90 species in 20 genera, and the molecular data set was supplemented by studies of radula morphology. Our analysis recovered Mitridae as a monophyletic group, whereas the genus Mitra was found to be polyphyletic. Of 42 mitrid species included in the analysis, 37 formed a well-supported ‘core Mitridae’ consisting of four major clades, three of them consistent with the subfamilies Cylindromitrinae, Imbricariinae, and Mitrinae, and Strigatella paupercula standing out by itself. Basal to the ‘core Mitridae’ are four minor lineages, with the genus Charitodoron recognized as sister group to all other Mitridae. The deep-water family Pyramimitridae shows a sister relationship to the Mitridae, with high support for a Pyramimitridae + Mitridae clade. Our results recover the monophyly of the Costellariidae, which form a well-supported clade that also includes Ptychatractidae, Columbariinae, and Volutomitridae, but not Mitridae. Most derived and diverse amongst Costellariidae are species of Vexillum, characterized by a bow-shaped, multicuspidate rachidian tooth. Several previously unrecognized deep-water costellariid lineages are revealed. Their members retain some plesiomorphies – in particular a tricuspidate rachidian tooth – that makes them morphologically intermediate between ptychatractids and Vexillum. The taxa of Ptychatractidae included in the analysis are not monophyletic, but form three well-supported, unrelated groupings, corresponding respectively to Ceratoxancus + Latiromitra, Exilia, and Exiliodea. None of them shows an affinity to Pseudolividae. © 2015 The Linnean Society of London

Evolutionary Drivers of Diversification and Distribution of a Southern Temperate Stream Fish Assemblage: Testing the Role of Historical Isolation and Spatial Range Expansion

This study used phylogenetic analyses of mitochondrial cytochrome b sequences to investigate genetic diversity within three broadly co-distributed freshwater fish genera (Galaxias, Pseudobarbus and Sandelia) to shed some light on the processes that promoted lineage diversification and shaped geographical distribution patterns. A total of 205 sequences of Galaxias, 177 sequences of Pseudobarbus and 98 sequences of Sandelia from 146 localities across nine river systems in the south-western Cape Floristic Region (South Africa) were used. The data were analysed using phylogenetic and haplotype network methods and divergence times for the clades retrieved were estimated using *BEAST. Nine extremely divergent (3.5–25.3%) lineages were found within Galaxias. Similarly, deep phylogeographic divergence was evident within Pseudobarbus, with four markedly distinct (3.8–10.0%) phylogroups identified. Sandelia had two deeply divergent (5.5–5.9%) lineages, but seven minor lineages with strong geographical congruence were also identified. The Miocene-Pliocene major sea-level transgression and the resultant isolation of populations in upland refugia appear to have driven widespread allopatric divergence within the three genera. Subsequent coalescence of rivers during the Pleistocene major sea-level regression as well as intermittent drainage connections during wet periods are proposed to have facilitated range expansion of lineages that currently occur across isolated river systems. The high degree of genetic differentiation recovered from the present and previous studies suggest that freshwater fish diversity within the south-western CFR may be vastly underestimated, and taxonomic revisions are required.

Fusarium Damage in Cereal Grains from Western Canada. 1. Phylogenetic Analysis of Moniliformin-Producing Fusarium Species and Their Natural Occurrence in Mycotoxin-Contaminated Wheat, Oats, and Rye

Harvest samples of common wheat (Triticum aestivum), oats (Avena sativa), and rye (Secale cereale) from producers in western Canada were analyzed for fungal infection by toxigenic Fusarium species and contamination by trichothecenes and moniliformin (MON). Fusarium graminearum and F. avenaceum were the two most frequently isolated species from samples of rye and wheat collected in 2010. F. poae and F. sporotrichioides were more commonly detected in randomly selected oat seeds. Other toxigenic Fusarium species including F. acuminatum, F. culmorum, and F. pseudograminearum as well as Phaeosphaeria nodorum (a.k.a. Septoria nodorum) were recovered primarily from fusarium-damaged kernels of wheat. Pure cultures of F. avenaceum, F. acuminatum, and other related species known to produce moniliformin were isolated from incubated seeds based on micro- and macromorphological criteria. The phylogenetic analysis inferred from partial DNA sequences of the acl1 and tef-1α genes revealed two major clades representing F. avenaceum and F. acuminatum, respectively. These clades comprised all Canadian isolates of the two species and a number of reference cultures studied earlier for their propensity to form moniliformin in vitro and in planta. However, some reference cultures previously reported to produce significant amounts of moniliformin formed minor phylogenetic lineages that represent rather distinct but closely related species. Concomitantly, cereal samples were analyzed for the presence of deoxynivalenol and moniliformin. These two Fusarium toxins were observed most frequently in common wheat, at concentrations up to 1.1 and 4.0 mg/kg, respectively. There was no apparent relationship between moniliformin concentrations and detection of F. avenaceum and F. acuminatum in rye and oat samples. Geographical analysis of the distribution of moniliformin and F. avenaceum and F. acuminatum across the Canadian Prairies also did not indicate a strong relationship.