Monitoring the mutation dynamics of human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical in understanding its infectivity, virulence and pathogenicity for development of a vaccine. In an "age of mobility," the pandemic highlights the importance and vulnerability of regionalization and labor market interdependence in Southeast Asia. We intend to characterize the genetic variability of viral populations within the region to provide preliminary information for regional surveillance in the future. By analyzing 142 complete genomes from South East Asian (SEA) countries, we identified three central variants distinguished by nucleotide and amino acid changes.
The spatial dissemination of three prevalent taxa of sooty blotch and flyspeck (SBFS) fungi under several levels of precipitation was compared during 2015 and 2016 in an Iowa apple orchard. Overhead irrigation was used to supplement ambient precipitation in order to insure SBFS spore dissemination and colony development. There were five irrigation levels, involving 1-min-long periods of irrigation that were imposed either once or twice per hour at intervals of 3, 6, or 12 h, as well as a nonirrigated control. Preselected apple fruit were inoculated with one of the three SBFS taxa to serve as sources of inoculum. Dissemination from these inoculated apple fruit was assessed at harvest by counting SBFS colonies on water-sprayed and nontreated fruit. As a further control, additional fruit were enclosed in fruit bags throughout the fruit development period. In both 2015 and 2016, the number of colonies of the SBFS fungus Peltaster gemmifer per apple increased sharply as the duration of irrigation increased, whereas the number of colonies of Microcyclosporella mali increased to a lesser extent and Stomiopeltis sp. RS1 showed no increase. In 2015, the linear relationship between the duration of irrigation-imposed precipitation levels and the number of colonies on the water-sprayed apple fruit was similar for P. gemmifer (slope = 0.09), Stomiopeltis sp. RS1 (slope = 0.07), and Microcyclosporella mali (slope = 0.13); whereas, in 2016, the slope was higher for P. gemmifer (0.28) than for Stomiopeltis sp. RS1 (-0.09) or M. mali (0.06). The results indicated that dissemination of P. gemmifer increased sharply in response to increased irrigation-imposed precipitation, and that dissemination patterns differed considerably among the three SBFS taxa. The apparent advantage of P. gemmifer in precipitation-triggered dissemination may stem from its ability to produce spores rapidly by budding. To our knowledge, this is the first article to assess splash dispersal by SBFS fungi in the field and the first to document taxon-specific patterns of dissemination in this pathogen complex.
The complete mitochondrial genomes of four fish species of the commercially important family Latidae were sequenced using the Illumina MiSeq, thereby significantly increasing the mitogenomic resources for the family. Whole mitogenome-based phylogenetic analysis supports the monophyly of the genus Lates and more generally the family Latidae. The mitogenome sequences from this study will be useful for future assessments of the diversity within and between Lates species and studies of phylogenetic relationships within the diverse and taxonomically challenging perciform fishes.
Acute hepatopancreatic necrosis disease (AHPND) is a severe disease affecting recently stocked cultured shrimps. The disease is mainly caused by V. parahaemolyticus that harbors the pVA1 plasmid; this plasmid contains the pirA and pirB genes, which encode a delta-endotoxin. AHPND originated in China in 2009 and has since spread to several other Asian countries and recently to Latin America (2013). Many Asian strains have been sequenced, and their sequences are publicly accessible in scientific databases, but only four strains from Latin America have been reported. In this study, we analyzed nine pVA1-harboring V. parahaemolyticus sequences from strains isolated in Mexico along with the 38 previously available pVA1-harboring V. parahaemolyticus sequences and the reference strain RIMD 2210633. The studied sequences were clustered into three phylogenetic clades (Latin American, Malaysian, and Cosmopolitan) through pangenomic and phylogenomic analysis. The nucleotide sequence alignment of the pVA1 plasmids harbored by the Asian and Latin American strains confirmed that the main structural difference in the plasmid between the Asian and Latin American strains is the absence of the Tn3 transposon in the Asian strains; in addition, some deletions in the pirAB region were found in two of the Latin American strains. Our study represents the most robust and inclusive phylogenomic analysis of pVA1-harboring V. parahaemolyticus conducted to date and provides insight into the epidemiology of AHPND. In addition, this study highlights that disease diagnosis through the detection of the pirA and pirB genes is an inadequate approach due to the instability of these genes.
BACKGROUND: Resistance to colistin, the last line therapy for infections caused by multidrug-resistant Gram-negative bacteria, represents a major public health threat. Citrobacter freundii B9-C2 which was isolated from the stool of preterm neonate on the first week of life, displayed resistance to almost all major antibiotics, including colistin. Through whole genome sequencing (WGS), we characterised the genome features that underline the antibiotic-resistance phenotype of this isolate.
METHODS: Genome of C. freundii B9-C2 was sequenced on an Illumina MiSeq platform. The assembled genome was annotated and deposited into GenBank under the accession number CP027849.
RESULTS: Multiple antimicrobial resistance genes including blaCMY-66 were identified. Further, the presence of 15 antibiotic efflux pump-encoding resistance genes, including crp, baeR, hns, patA, emrB, msbA, acrA, acrB, emrR, mdtC, mdtB, mdtG, kdpE, mdfA and msrB, were detected and likely to account for the observed cephalosporins, carbapenems, aminoglycosides and monobactams resistance in C. freundii B9-C2. The isolate also presented unique virulence genes related to biofilm formation, motility and iron uptake. The genome was compared to publicly available genomes and it was closely related to strains with environmental origins.
CONCLUSION: To the best of our knowledge, this is the first report of intestinal carriage of colistin-resistant C. freundii from the stool of a neonate in Malaysia. Using genomic analysis, we have contributed to the understanding of the potential mechanism of resistance and the phylogenetic relationship of the isolates with draft genomes available in the public domain.
Rhaphidophora megasperma Engl., a species hitherto regarded as endemic to Sarawak, East Malaysia, is published as a new record for Peninsular Malaysia. It is the first species in the Rhaphidophora Spathacea group recorded for western Sunda. The species is illustrated and a key to the perforate-laminated Rhaphidophora in Peninsular Malaysia is presented.
Chikungunya virus (CHIKV) is a mosquito-borne alphavirus which causes fever, rash, and arthralgia. In the past, life-threatening complications were very rarely reported. However, during the recent worldwide outbreaks, there have been several reports of unusually severe complications and deaths. Malaysia is experiencing a nationwide outbreak of CHIKV, with over 10 000 patients affected since April 2008. We report the first case of culture-confirmed CHIKV-associated death in Malaysia, in a patient with fever, rash, acute exacerbation of pre-existing heart failure, rhabdomyolysis, and multiple organ failure. CHIKV infections may cause atypical, severe or fatal presentations.
BACKGROUND: Marine bacteriophages play key roles in the community structure of microorganisms, biogeochemical cycles, and the mediation of genetic diversity through horizontal gene transfer. Recently, traditional isolation methods, complemented by high-throughput sequencing metagenomics technology, have greatly increased our understanding of the diversity of bacteriophages. Oceanospirillum, within the order Oceanospirillales, are important symbiotic marine bacteria associated with hydrocarbon degradation and algal blooms, especially in polar regions. However, until now there has been no isolate of an Oceanospirillum bacteriophage, and so details of their metagenome has remained unknown.
RESULTS: Here, we reported the first Oceanospirillum phage, vB_OliS_GJ44, which was assembled into a 33,786 bp linear dsDNA genome, which includes abundant tail-related and recombinant proteins. The recombinant module was highly adapted to the host, according to the tetranucleotides correlations. Genomic and morphological analyses identified vB_OliS_GJ44 as a siphovirus, however, due to the distant evolutionary relationship with any other known siphovirus, it is proposed that this virus could be classified as the type phage of a new Oceanospirivirus genus within the Siphoviridae family. vB_OliS_GJ44 showed synteny with six uncultured phages, which supports its representation in uncultured environmental viral contigs from metagenomics. Homologs of several vB_OliS_GJ44 genes have mostly been found in marine metagenomes, suggesting the prevalence of this phage genus in the oceans.
CONCLUSIONS: These results describe the first Oceanospirillum phage, vB_OliS_GJ44, that represents a novel viral cluster and exhibits interesting genetic features related to phage-host interactions and evolution. Thus, we propose a new viral genus Oceanospirivirus within the Siphoviridae family to reconcile this cluster, with vB_OliS_GJ44 as a representative member.
We collected two specimens of an undescribed species of Lygosoma from pitfall traps in an urban rainforest in Kuching and from the base of a forested hill in western Sarawak, East Malaysia. The new species is diagnosable from all south-east Asian congeners by morphological characters, and most closely resembles Lygosoma herberti from the Thai-Malay Peninsula. The new species shows substantial molecular divergence from its closest relatives in two protein-coding genes, one mitochondrial (ND1) and one nuclear (R35) that we sequenced for several south-east Asian congeners. We describe the new species on the basis of this distinct morphology and genetic divergence. It is the third species of Lygosoma known from Borneo, and highlights the continuing rise in lizard species diversity on the island. In addition, the discovery of this species from a small urban rainforest underscores the importance of preserving intact rainforest areas of any size in maintaining species diversity.
A new species of Asian rock gecko, genus Cnemaspis, is described from Padawan, western Sarawak, Malaysian Borneo. The new species forms a clade with C. paripari and C. nigridia of the C. nigridia group in a mitochondrial DNA phylogeny and is similar to them morphologically in some characters such as caudal scalation. It differs from the other Asian Cnemaspis species in its unique combination of snout-vent length (up to 62.7 mm), 4-9 precloacal pores in males, keeled subcaudals with an enlarged, smooth, median row, presence of ventrolateral caudal tubercles, and coloration (head and upper flanks dark-yellow; anterior portion of tail black; posterior portion of tail white with black, paravertebral blob). Phylogenetic relationships within the C. nigridia group and the distributional ranges of species within the group suggest allopatric speciation by geographic isolation.
Lednice virus (LEDV) has been detected in Culex modestus mosquitoes in several European countries within the last six decades. In this study, phylogenetic analyses of the complete genome segments confirm that LEDV belongs to the Turlock orthobunyavirus (Orthobunyavirus, Peribunyaviridae) species and is closely related to Umbre, Turlock, and Kedah viruses.
A new species of limestone karst-adapted gecko of the Cyrtodactylus pulchellus complex, C. dayangbuntingensis sp. nov., is described from Dayang Bunting Island of the Langkawi Archipelago off the northwest coast of Peninsular Malaysia. It is the third species of the group to be described from the archipelago after C. langkawiensis and C. macrotuberculatus. The new species can be distinguished from all other species of Cyrtodactylus based on molecular evidence from the mitochondrial gene ND2 and its flanking tRNAs as well as having unique combinations of morphological and color pattern characteristics. This discovery underscores the need for continued surveys of the many islands in the archipelago to properly ascertain its true herpetological diversity.
Molecular phylogenetic analyses of the sister species Sphenomorphus stellatus and S. praesignis based on the mitochondrial genes 12S and 16S rRNA recover the former as paraphyletic with respect to the latter in that a specimen of S. stellatus from the type locality in Peninsular Malaysia is more closely related to S. praesignis than to Indochinese populations of S. stellatus. Furthermore, the phylogeny indicates that the Indochinese populations represent two species, thus resulting in four major lineages within this clade. These relationships are consistent with multivariate and univariate analyses of morphological and discrete color pattern data which statistically define and diagnose the four lineages and together with the molecular data, provide the foundation for robust, testable, species-level hypotheses. As such, S. stellatus is herein restricted to Peninsular Malaysia; S. annamiticus is resurrected for the circum-continental populations ranging through southeastern Thailand, southern Cambodia, and southern Vietnam; a new species-S. preylangensis sp. nov.-is described from an isolated mountain, Phnom Chi, from the Prey Lang Wildlife Sanctuary in central Cambodia; and the taxonomy of S. praesignis remains unchanged. The description of S. preylangensis sp. nov. underscores the necessity to conserve this remnant of lowland evergreen rainforest in the Prey Lang Wildlife Sanctuary.
An integrative taxonomic analysis of Subdoluseps herberti from southern Thailand and Peninsular Malaysia and S. samajaya from Sarawak, East Malaysia (Borneo) recovers the former as paraphyletic with respect to the latter. The analyses recover the three southernmost populations of S. herberti in Peninsular Malaysia as conspecific and the sister lineage of S. samajaya, whereas S. herberti from Thailand and northern Peninsular Malaysia constitute the sister species to S. samajaya plus the southern three Peninsular Malaysian populations. As such, the southern populations are described herein as S. malayana sp. nov. and all three species are referred to as the S. herberti group. Clade boundaries and breaks within this group on the Thai-Malay Peninsula occurring at the Isthmus of Kra, across the Kangar-Pattani line, and between the Thai-Malay Peninsula and Borneo are consistent with phylogeographic patterns of other Sundaic taxa. The discovery of S. malayana sp. nov. continues to underscore the fact that, despite the well-studied nature of the lizard fauna of Peninsular Malaysia, much of it still remains unrealized and for conservation efforts to move forward, field research followed by expeditiously revised taxonomies must continue.
This overview of the Luciolinae addresses the fauna of S. E. Asia including India, Sri Lanka, China, Japan, Malaysia, Thailand, Laos, Cambodia, Vietnam, Indonesia, the Philippines, the Republic of Palau, Federated States of Micronesia, and the Australopacific area of Australia, Papua New Guinea, Solomon Islands, New Caledonia, Vanuatu and Fiji.Of the 28 genera now recognised in the Luciolinae we address 27 genera from the study area as defined above, including three new genera which are described herein, and 222 species including 13 species newly described herein. Photuroluciola Pic from Madagascar is the only Luciolinae genus not addressed here. A key to genera is presented. Keys to species are either included here or referenced in existing literature. Twelve genera have had no new taxonomic decisions made nor are any new species records listed, and are addressed in an abbreviated fashion, with short diagnoses and plates of features of life stages: Aquatica Fu et al. 2010, Australoluciola Ballantyne 2013, Convexa Ballantyne 2009, Emeia Fu et al. 2012a, Inflata Boontop 2015, Lloydiella Ballantyne 2009, Missimia Ballantyne 2009, Pteroptyx Olivier 1902, Pyrophanes Olivier 1885, Sclerotia Ballantyne 2016, Triangulara Pimpasalee 2016, and Trisinuata Ballantyne 2013. Abscondita Ballantyne 2013 contains 8 species, and includes new records for Abs. anceyi (Olivier 1883), Abs. chinensis (L.) (which is newly synonymised with Luciola succincta Bourgeois), Abs. terminalis (Olivier 1883) including a first record from both Laos and Thailand, and Abs. perplexa (Walker 1858). Luciola pallescens Gorham 1880 is transferred to Abscondita and the pronotal colour range is addressed from a wide range of localities. Abs. berembun Nada sp. nov. and Abs. jerangau Nada sp. nov. are described from Malaysia. Hooked bursa plates are described for pallescens and berembun. Aquilonia Ballantyne 2009 is expanded to include 3 species. Gilvainsula Ballantyne 2009, represented by two species from the south eastern coast of New Guinea is synonymised under Aquilonia Ballantyne 2009, which is briefly redescribed and keyed from: Aquil. costata (Lea) from northern Australia, including many new records, Aquil. messoria (Ballantyne) comb. nov. and Aquil. similismessoria (Ballantyne) comb. nov. Asymmetricata Ballantyne 2009 now includes 4 species. As. bicoloripes (Pic 1927) comb. nov. and As. humeralis (Walker 1858) comb. nov. are transferred from Luciola, with L. doriae Olivier 1885, L. impressa Olivier 1910b and L. notatipennis Olivier 1909a newly synonymised with As. humeralis. Luciola aemula Olivier 1891 is synonymised with As. ovalis (Hope 1831). The variation in the extent of the anterior median emargination of the light organ in ventrite 7, and the possibility of a bipartite light organ in males of As. circumdata (Motsch. 1854) is explored. Females of both As. circumdata and As. ovalis (Hope 1831) are without bursa plates and the distinctively shaped median oviduct plate in each is described. Records from Thailand are recorded for both As. circumdata and As. ovalis. Atyphella Olliff 1890 now contains 28 species with 4 transferred from other genera, and one new species: Aty. abdominalis (Olivier 1886) comb. nov. and Aty. striata (Fabricius 1801) comb. nov. are transferred from Luciola, with Aty. carolinae Olivier 1911b and Aty. rennellia (Ballantyne 2009) comb. nov. transferred from Magnalata Ballantyne 2009. Atyphella telokdalam Ballantyne sp. nov. from Indonesia is described herein. Atyphella is now known from records in the Philippines and Indonesia as well as Australia and New Guinea. Colophotia Motschulsky 1853 is considered here from seven species for which intact types can be located for three. An abbreviated revision based on the United States National Museum collection only is presented, with specimens of C. bakeri Pic 1924, C. brevis Olivier 1903a, C. plagiata (Erichson 1834) and C. praeusta (Eschscholtz 1822) redescribed, using where possible features of males, females and larvae. Colophotia particulariventris Pic 1938 is newly synonymised with C. praeusta. Colophotia miranda Olivier 1886 and L. truncata Olivier 1886 are treated as species incertae sedis. Curtos Motschulsky 1845 includes 19 species with suggestions made, but not yet formalised, for the possible transfer of the following seven species from Luciola: Luciola complanata Gorham 1895, L. costata Pic 1929, L. delauneyi Bourgeois 1890, L. deplanata Pic 1929, L. extricans Walker 1858, L. multicostulata Pic 1927 and L. nigripes Gorham 1903. Curtos is not revised here. Emarginata Ballantyne gen nov. is described for E. trilucida (Jeng et al. 2003b) comb. nov., transferred from Luciola and characterised by the emarginated elytral apex. An extended range of specimens from Thailand is listed. Kuantana Ballantyne gen. nov. from Selangor, Malaysia is described from K. menayah gen. et sp. nov. having bipartite light organs in ventrite 7 and an asymmetrical tergite 8 which is not emarginated on its left side. Female has no bursa plates. Luciola Laporte 1833 s. stricto as defined by a population of the type species Luciola italica (L. 1767) from Pisa, Italy, is further expanded and considered to comprise the following19 species: L. antipodum (Bourgeois 1884), L. aquilaclara Ballantyne 2013, L. chapaensis Pic 1923 which is synonymised with L. atripes Pic 1929, L. curtithorax Pic 1928, L. filiformis Olivier 1913c, L. horni Bourgeois 1905, L. hypocrita Olivier 1888, L. italica (L. 1767), L. kagiana Matsumura 1928, L. oculofissa Ballantyne 2013, L. pallidipes Pic 1928 which is synonymised with L. fletcheri Pic 1935, L. parvula Kiesenwetter 1874, L. satoi Jeng Yang 2003, L. tuberculata Yiu 2017, and two species treated as near L. laticollis Gorham 1883, and near L. nicollieri Bugnion 1922. The following are described as new: L. niah Jusoh sp. nov., L. jengai Nada sp. nov. and L. tiomana Ballantyne sp. nov. Luciola niah sp. nov. female has two wide bursa plates on each side of the bursa. Luciola s. lato (as defined here) consists of 36 species. Twenty-seven species formerly standing under Luciola have been assigned to other genera or synonymised. Seven species are recommended for transfer to Curtos, and 32 species now stand under species incertae sedis. Magnalata Ballantyne is reduced to the type species M. limbata and redescribed. Medeopteryx Ballantyne 2013 is expanded to 20 species with the addition of two new combinations, Med. semimarginata (Olivier 1883) comb. nov. and Med. timida (Olivier 1883) comb. nov., both transferred from Luciola, and one new species, Med. fraseri Nada sp. nov. from Malaysia. The range of this genus now extends from Australia and the island of New Guinea to SE Asia. Medeopteryx semimarginata females have wide paired bursa plates. Pygoluciola Wittmer 1939 now includes 19 species with 5 new species: P. bangladeshi Ballantyne sp. nov., P. dunguna Nada 2018, P. matalangao Ballantyne sp. nov. (scored by the code name 'Jeng Matalanga' in Ballantyne Lambkin 2013), P. phupan Ballantyne sp. nov. and P. tamarat Jusoh sp. nov. Six species are transferred from Luciola: P. abscondita (Olivier 1891) comb. nov., P. ambita (Olivier 1896) comb. nov., P. calceata (Olivier 1905) comb. nov., P. insularis (Olivier 1883) comb. nov., P. nitescens (Olivier 1903b) comb. nov. and P. vitalisi (Pic 1934) comb. nov., and redescribed from males, and includes female reproductive anatomy for P. nitescens comb. nov. and P. dunguna, both of which have hooked bursa plates. Serratia Ballantyne gen. nov. is erected for S. subuyania gen. et sp. nov. and characterised by the serrate nature of certain antennal flagellar segments in the male. The following 37 species listed under species incertae sedis are further explored: Colophotia miranda Olivier 1886, Lampyris serraticornis Boisduval 1835, Luciola angusticollis Olivier 1886, L. antennalis Bourgeois 1905, L. antica (Boisduval 1835), L. apicalis (Eschscholtz 1822), L. aurantiaca Pic 1927, L. bicoloriceps Pic 1924, L. binhana Pic 1927, L. bourgeoisi Olivier 1895, L. dilatata Pic 1929, L. exigua (Gyllenhall 1817), L. exstincta Olivier 1886, L. fissicollis Fairmaire 1891, L. flava Pic 1929, L. flavescens (Boisduval 1835), L. fukiensis Pic 1955, L. immarginata Bourgeois 1890, L. incerta (Boisduval 1835), L. infuscata (Erichson 1834), L. intricata (Walker 1858), L. japonica (Thunberg 1784), L. klapperichi Pic 1955, L. lata Olivier 1883, L. limbalis Fairmaire 1889, L. marginipennis (Boisduval 1835), L. melancholica Olivier 1913a, L. robusticeps Pic 1928, L. ruficollis (Boisduval 1835), L. spectralis Gorham 1880, L. stigmaticollis Fairmaire 1887, L. tincticollis Gorham 1895, L. trivandrensis Raj 1947, L. truncata Olivier 1886, L. vittata (Laporte 1833) Pteroptyx atripennis Pic 1923 and P. curticollis Pic 1923. While phylogenetic analyses indicate their distinctiveness, no further taxonomic action is taken with Luciola cruciata Motschulsky 1854 and L. owadai Sâtô et Kimura 1994 from Japan given the importance of the former as a national icon. Analyses also indicate that Lampyroidea syriaca Costa 1875 belongs in Luciola s. str. A much wider taxonomic analysis of this genus including all the species is necessary before any further action can be taken.
An anatomical study was carried out on 14 taxa belonging to Selaginellaceae in an attempt to study their stipe anatomical characteristics and to provide anatomical data for the selected taxa in Selaginellaceae. Out of 29 taxa of Selaginellaceae recorded in Peninsular Malaysia, 14 taxa have been selected namely Selaginella alutacia, S. argentea, S. frondosa, S. intermedia var. intermedia, S. intermedia var. dolichocentrus, S. mayeri, S. morganii, S. ornata, S. plana, S. polita, S. roxburghii var. roxburghii, S. stipulata, S. wallichii and S. willdenowii. Method used in this study was sectioning using sliding microtome. Findings in this study have shown that Selaginellaceae species studied can be clustered into two groups based on the stipe stellar systems, which are monostelic and tristelic groups. There are some variations exist in the cross sections of the stipes of the same species due to the presence and absence of the leaf trace. Each species is proved to have distinct stipe anatomical characteristics that can be used to differentiate species in Selaginellaceae.
Microcystins (MCs) are secondary metabolites produced by cyanobacteria and have been well-documented in temperate and tropical regions. However, knowledge of the production of MCs in extremely cold environments is still in its infancy. Recently, examination of 100-year-old Antarctic cyanobacterial mats collected from Ross Island and the McMurdo Ice Shelf during Captain R.F. Scott's Discovery Expedition revealed that the presence of MCs in Antarctica is not a new phenomenon. Here, morphological and molecular phylogenetic analyses are used to identify a new microcystin-producing freshwater cyanobacterium, Anagnostidinema pseudacutissimum. The strain was isolated from a deep-frozen (-15 °C) sample collected from a red-brown cyanobacterial mat in a frozen pond at Cape Crozier (Ross Island, continental Antarctica) in 1984-1985. Amplification of the mcyE gene fragment involved in microcystin biosynthesis from A. pseudacutissimum confirmed that it is identical to the sequence from other known microcystin-producing cyanobacteria. Analysis of extracts from this A. pseudacutissimum strain by HPLC-MS/MS confirmed the presence of MC-LR and -YR at concentrations of 0.60 μg/L and MC-RR at concentrations of 0.20 μg/L. This is the first report of microcystin production from a species of Anagnostidinema from Antarctica.
PREMISE: Unique among vascular plants, some species of Selaginella have single giant chloroplasts in their epidermal or upper mesophyll cells (monoplastidy, M), varying in structure between species. Structural variants include several forms of bizonoplast with unique dimorphic ultrastructure. Better understanding of these structural variants, their prevalence, environmental correlates and phylogenetic association, has the potential to shed new light on chloroplast biology unavailable from any other plant group.
METHODS: The chloroplast ultrastructure of 76 Selaginella species was studied with various microscopic techniques. Environmental data for selected species and subgeneric relationships were compared against chloroplast traits.
RESULTS: We delineated five chloroplast categories: ME (monoplastidy in a dorsal epidermal cell), MM (monoplastidy in a mesophyll cell), OL (oligoplastidy), Mu (multiplastidy, present in the most basal species), and RC (reduced or vestigial chloroplasts). Of 44 ME species, 11 have bizonoplasts, cup-shaped (concave upper zone) or bilobed (basal hinge, a new discovery), with upper zones of parallel thylakoid membranes varying subtly between species. Monoplastidy, found in 49 species, is strongly shade associated. Bizonoplasts are only known in deep-shade species (<2.1% full sunlight) of subgenus Stachygynandrum but in both the Old and New Worlds.
CONCLUSIONS: Multiplastidic chloroplasts are most likely basal, implying that monoplastidy and bizonoplasts are derived traits, with monoplastidy evolving at least twice, potentially as an adaptation to low light. Although there is insufficient information to understand the adaptive significance of the numerous structural variants, they are unmatched in the vascular plants, suggesting unusual evolutionary flexibility in this ancient plant genus.
Rapidly accumulating genetic data from environmental sequencing approaches have revealed an extraordinary level of unsuspected diversity within marine phytoplankton,1-11 which is responsible for around 50% of global net primary production.12,13 However, the phenotypic identity of many of the organisms distinguished by environmental DNA sequences remains unclear. The rappemonads represent a plastid-bearing protistan lineage that to date has only been identified by environmental plastid 16S rRNA sequences.14-17 The phenotypic identity of this group, which does not confidently cluster in any known algal clades in 16S rRNA phylogenetic reconstructions,15 has remained unknown since the first report of environmental sequences over two decades ago. We show that rappemonads are closely related to a haptophyte microalga, Pavlomulina ranunculiformis gen. nov. et sp. nov., and belong to a new haptophyte class, the Rappephyceae. Organellar phylogenomic analyses provide strong evidence for the inclusion of this lineage within the Haptophyta as a sister group to the Prymnesiophyceae. Members of this new class have a cosmopolitan distribution in coastal and oceanic regions. The relative read abundance of Rappephyceae in a large environmental barcoding dataset was comparable to, or greater than, those of major haptophyte species, such as the bloom-forming Gephyrocapsa huxleyi and Prymnesium parvum, and this result indicates that they likely have a significant impact as primary producers. Detailed characterization of Pavlomulina allowed for reconstruction of the ancient evolutionary history of the Haptophyta, a group that is one of the most important components of extant marine phytoplankton communities.
Human populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10%-40%.1 It is assumed that this high mortality affected the gene pools of these populations. First, local population crashes reduced genetic diversity. Second, a change in frequency is expected for sequence variants that may have affected survival or susceptibility to the etiologic agent (Yersinia pestis).2 Third, mass mortality might alter the local gene pools through its impact on subsequent migration patterns. We explored these factors using the Norwegian city of Trondheim as a model, by sequencing 54 genomes spanning three time periods: (1) prior to the plague striking Trondheim in 1,349 CE, (2) the 17th-19th century, and (3) the present. We find that the pandemic period shaped the gene pool by reducing long distance immigration, in particular from the British Isles, and inducing a bottleneck that reduced genetic diversity. Although we also observe an excess of large FST values at multiple loci in the genome, these are shaped by reference biases introduced by mapping our relatively low genome coverage degraded DNA to the reference genome. This implies that attempts to detect selection using ancient DNA (aDNA) datasets that vary by read length and depth of sequencing coverage may be particularly challenging until methods have been developed to account for the impact of differential reference bias on test statistics.