Extant Canis lupus genetic diversity can be grouped into three phylogenetically distinct clades: Eurasian and American wolves and domestic dogs.1 Genetic studies have suggested these groups trace their origins to a wolf population that expanded during the last glacial maximum (LGM)1-3 and replaced local wolf populations.4 Moreover, ancient genomes from the Yana basin and the Taimyr peninsula provided evidence of at least one extinct wolf lineage that dwelled in Siberia during the Pleistocene.35 Previous studies have suggested that Pleistocene Siberian canids can be classified into two groups based on cranial morphology. Wolves in the first group are most similar to present-day populations, although those in the second group possess intermediate features between dogs and wolves.67 However, whether this morphological classification represents distinct genetic groups remains unknown. To investigate this question and the relationships between Pleistocene canids, present-day wolves, and dogs, we resequenced the genomes of four Pleistocene canids from Northeast Siberia dated between >50 and 14 ka old, including samples from the two morphological categories. We found these specimens cluster with the two previously sequenced Pleistocene wolves, which are genetically more similar to Eurasian wolves. Our results show that, though the four specimens represent extinct wolf lineages, they do not form a monophyletic group. Instead, each Pleistocene Siberian canid branched off the lineage that gave rise to present-day wolves and dogs. Finally, our results suggest the two previously described morphological groups could represent independent lineages similarly related to present-day wolves and dogs.
Zeugodacus caudatus is a pest of pumpkin flowers. It has a Palearctic and Oriental distribution. We report here the complete mitochondrial genome of the Malaysian and Indonesian samples of Z. caudatus determined by next-generation sequencing of genomic DNA and determine their taxonomic status as sibling species and phylogeny with other taxa of the genus Zeugodacus. The whole mitogenome of both samples possessed 37 genes (13 protein-coding genes-PCGs, 2 rRNA and 22 tRNA genes) and a control region. The mitogenome of the Indonesian sample (15,885 bp) was longer than that of the Malaysian sample (15,866 bp). In both samples, TΨC-loop was absent in trnF and DHU-loop was absent in trnS1. Molecular phylogeny based on 13 PCGs was concordant with 15 mitochondrial genes (13 PCGs and 2 rRNA genes), with the two samples of Z. caudatus forming a sister group and the genus Zeugodacus was monophyletic. The Malaysian and Indonesian samples of Z. caudatus have a genetic distance of p = 7.8 % based on 13 PCGs and p = 7.0 % based on 15 mitochondrial genes, indicating status of sibling species. They are proposed to be accorded specific status as members of a species complex.
Forty-eight isolates of Pseudo-nitzschia species were established from the Miri coast of Sarawak (Malaysian Borneo) and underwent TEM observation and molecular characterization. Ten species were found: P. abrensis, P. batesiana, P. fukuyoi, P. kodamae, P. lundholmiae, P. multistriata, P. pungens, P. subfraudulenta, as well as two additional new morphotypes, herein designated as P. bipertita sp. nov. and P. limii sp. nov. This is the first report of P. abrensis, P. batesiana, P. kodamae, P. fukuyoi, and P. lundholmiae in coastal waters of Malaysian Borneo. Pseudo-nitzschia bipertita differs from its congeners by the number of sectors that divide the poroids, densities of band striae, and its cingular band structure. Pseudo-nitzschia limii, a pseudo-cryptic species in the P. pseudodelicatissima complex sensu lato, is distinct by having wider proximal and distal mantles, a higher number of striae, and greater poroid height in the striae of the valvocopula. The species were further supported by the phylogenetic reconstructions of the nuclear-encoded large subunit ribosomal gene and the second internal transcribed spacer. Phylogenetically, P. bipertita clustered with its sister taxa (P. subpacifica + P. heimii); P. limii appears as a sister taxon to P. kodamae and P. hasleana in the ITS2 tree. Pairwise comparison of ITS2 transcripts with its closest relatives revealed the presence of both hemi- and compensatory base changes. Toxicity analysis showed detectable levels of domoic acid in P. abrensis, P. batesiana, P. lundholmiae, and P. subfraudulenta, but both new species tested below the detection limit.
Toxoplasmosis is a widespread parasitic infection by Toxoplasma gondii, a parasite with at least three distinct clonal lineages. This article reports the whole genome sequencing and de novo assembly of T. gondii RH (type I representative strain), as well as genome-wide comparison across major T. gondii lineages. Genomic DNA was extracted from tachyzoites of T. gondii RH strain and its identity was verified by PCR and LAMP. Subsequently, whole genome sequencing was performed, followed by sequence filtering, genome assembly, gene annotation assignments, clustering of gene orthologs and phylogenetic tree construction. Genome comparison was done with the already archived genomes of T. gondii. From this study, the genome size of T. gondii RH strain was found to be 69.35Mb, with a mean GC content of 52%. The genome shares high similarity to the archived genomes of T. gondii GT1, ME49 and VEG strains. Nevertheless, 111 genes were found to be unique to T. gondii RH strain. Importantly, unique genes annotated to functions that are potentially critical for T. gondii virulence were found, which may explain the unique phenotypes of this particular strain. This report complements the genomic archive of T. gondii. Data obtained from this study contribute to better understanding of T. gondii and serve as a reference for future studies on this parasite.
Mitochondrial DNA (mtDNA) serves as a powerful tool for exploring matrilineal phylogeographic ancestry, as well as for analyzing highly degraded samples, because of its polymorphic nature and high copy numbers per cell. The recent advent of complete mitochondrial genome sequencing has led to improved techniques for phylogenetic analyses based on mtDNA, and many multiplex genotyping methods have been developed for the hierarchical analysis of phylogenetically important mutations. However, few high-resolution multiplex genotyping systems for analyzing East-Asian mtDNA can be applied to extremely degraded samples. Here, we present a multiplex system for analyzing mitochondrial single nucleotide polymorphisms (mtSNPs), which relies on a novel amplified product-length polymorphisms (APLP) method that uses inosine-flapped primers and is specifically designed for the detailed haplogrouping of extremely degraded East-Asian mtDNAs. We used fourteen 6-plex polymerase chain reactions (PCRs) and subsequent electrophoresis to examine 81 haplogroup-defining SNPs and 3 insertion/deletion sites, and we were able to securely assign the studied mtDNAs to relevant haplogroups. Our system requires only 1×10-13 g (100 fg) of crude DNA to obtain a full profile. Owing to its small amplicon size (<110 bp), this new APLP system was successfully applied to extremely degraded samples for which direct sequencing of hypervariable segments using mini-primer sets was unsuccessful, and proved to be more robust than conventional APLP analysis. Thus, our new APLP system is effective for retrieving reliable data from extremely degraded East-Asian mtDNAs.
Plasmodium knowlesi and P. cynomolgi are simian malaria parasites capable of causing symptomatic human infections. The interaction between the Duffy binding protein alpha on P. knowlesi merozoite and the Duffy-antigen receptor for chemokine (DARC) on human and macaque erythrocyte membrane is prerequisite for establishment of blood stage infection whereas DARC is not required for erythrocyte invasion by P. cynomolgi. To gain insights into the evolution of the PkDBP gene family comprising PkDBPα, PkDBPβ and PkDBPγ, and a member of the DBP gene family of P. cynomolgi (PcyDBP1), the complete coding sequences of these genes were analyzed from Thai field isolates and compared with the publicly available DBP sequences of P. vivax (PvDBP). The complete coding sequences of PkDBPα (n=11), PkDBPβ (n=11), PkDBPγ (n=10) and PcyDBP1 (n=11) were obtained from direct sequencing of the PCR products. Nucleotide diversity of DBP is highly variable across malaria species. PcyDBP1 displayed the greatest level of nucleotide diversity while all PkDBP gene members exhibited comparable levels of diversity. Positive selection occurred in domains I, II and IV of PvDBP and in domain V of PcyDBP1. Although deviation from neutrality was not detected in domain II of PkDBPα, a signature of positive selection was identified in the putative DARC binding site in this domain. The DBP gene families seem to have arisen following the model of concerted evolution because paralogs rather than orthologs are clustered in the phylogenetic tree. The presence of identical or closely related repeats exclusive for the PkDBP gene family suggests that duplication of gene members postdated their divergence from the ancestral PcyDBP and PvDBP lineages. Intragenic recombination was detected in all DBP genes of these malaria species. Despite the limited number of isolates, P. knowlesi from Thailand shared phylogenetically related domain II sequences of both PkDBPα and PkDBPγ with those from Peninsular Malaysia, consistent with their geographic proximity.
Anaplasma spp. infects a wide variety of wildlife and domestic animals. This study describes the identification of a novel species of Anaplasma (Candidatus Anaplasma pangolinii) from pangolins (Manis javanica) and Anaplasma bovis from wild boars (Sus scrofa) in Malaysia. Based on 16S rRNA gene sequences, Candidatus Anaplasma pangolinii is identified in a distinct branch within the family Anaplasmataceae, exhibiting the closest sequence similarity with the type strains of Anaplasma bovis (97.7%) and Anaplasma phagocytophilum (97.6%). The sequence also aligned closely (99.9%) with that of an Anaplasma spp. (strain AnAj360) detected from Amblyomma javanense ticks. The nearly full length sequence of the 16S rRNA gene derived from two wild boars in this study demonstrated the highest sequence similarity (99.7%) to the A. bovis type strain. Partial 16S rRNA gene fragments of A. bovis were also detected from a small population of Haemaphysalis bispinosa cattle ticks in this study. Our finding suggests a possible spread of two Anaplasma species in the Malaysian wildlife and ticks. The zoonotic potential of the Anaplasma species identified in this study is yet to be determined.
The areolate Oriental family Heteropterygidae Kirby, 1893 is critically reviewed and the results of the present study contradict the arrangement suggested by Zompro (2004), but in most aspects agree with a molecular study presented by Whiting et al (2003) and a phylogenetic study presented by Bradler (2009). The family is critically discussed and new hypotheses are presented for the phylogeny and intra-familiar relationships, placing the subfamily Dataminae Rehn & Rehn, 1939 as the basalmost clade of Heteropterygidae. The subfamilies Obriminae Brunner v. Wattenwyl, 1893 and Heteropteryginae Kirby, 1893 together represent the sister-group of Dataminae. Arguments and a tree are presented to support this hypothesis. New diagnoses and lists of genera are provided for all three subfamilies contained in Heteropterygidae, along with keys to distinguish between them. The subfamily Obriminae is critically reviewed and the distinction between the three tribes Obrimini Brunner v. Wattenwyl, 1893, Eubulidini Zompro, 2004 and Miroceramiini Zompro, 2004 introduced by Zompro (2004) is shown to be poorly supported. While Obrimini sensu Zompro, 2004 is generally accepted (but now also contains genera that were placed in Eubulidini or Miroceramiini by Zompro (2004)), the tribes Eubulidini and Miroceramiini are not supported. A new arrangement is introduced, which is based on morphological characters neglected or overlooked by Zompro (2004) but were partly discussed by Bradler (2009). The genus Mearnsiana Rehn & Rehn, 1939 is removed from Miroceramiini and transferred to Obrimini. The genera Eubulides Stål, 1877, Heterocopus Redtenbacher, 1906, Theramenes Stål, 1875 and Stenobrimus Redtenbacher, 1906 are removed from Eubulidini and also transferred to Obrimini. Consequently, Eubulidini is synonymised with Obrimini (n. syn.). Miroceramiini is a monotypical tribe and only includes the Wallacean genus Miroceramia Günther, 1934. The new tribe Tisamenini n. trib. is established for the three basal genera Tisamenus Stål, 1875, Ilocano Rehn & Rehn, 1939 and Hoploclonia Stål, 1875 all of which were placed in Eubulidini by Zompro (2004). The latter genus differs from the other two genera by the morphology of the female genitalia, which is unique amongst the entire family. Three generic groups are recognized within Obrimini, the Obrimus-group, Stenobrimus-group and Theramenes-group. Keys are presented to distinguish between the three tribes now contained in the Obriminae, i.e. Obrimini, Tisamenini n. trib. and Miroceramiini. The genus Hennobrimus Conle, 2006 is synonymised with Mearnsiana Rehn & Rehn, 1939, based on the fact that the type-species of both genera are conspecific (n. syn.). Hennobrimus hennemanni Conle, 2006, the type-species of Hennobrimus, and Trachyaretaon manobo Lit & Eusebio, 2005 are synonymised with Mearnsiana bullosa Rehn & Rehn, 1939, the type-species of Mearnsiana (n. syn.). Theramenes dromedarius Stål, 1877 from the Philippines is removed from synonymy with the Wallacean Theramenes olivaceus (Westwood, 1859) and re-established as a valid species (rev. stat.). The subfamily Heteropteryginae Kirby, 1896 is revised at the species-level and a new diagnosis is presented. Keys to the two genera and all 16 known species are provided along with new descriptions, differential diagnoses, lists of examined material, detailed information on the known distributions, measurements and illustrations of the insects and eggs. The intra-subfamiliar and intra-generic relationships are discussed and a cladogram is presented. Heteropteryginae contains two genera: Heteropteryx Gray, 1835 (Type-species: Phasma dilatatum Parkinson, 1798) and Haaniella Kirby, 1896 (Type-species: Phasma (Heteropteryx) muelleri de Haan, 1842). The distribution of this subfamily is restricted to Sundaland with the exception of a single species that is found in Vietnam. All other species are distributed in Borneo, Sumatra, the Mentawai Islands, Singapore, Peninsular Malaysia and Thailand. Heteropteryginae contains the largest and most striking members of the entire family Heteropteryginae, some of which are amongst the heaviest insects known. The subfamily is characterized by apomorphies such as the presence of wings, having a tympanal area (= stridulatory organ) in the basal portion of the alae, straight profemora, strongly shortened tarsi, lack of rough sensory-areas on the prosternum and typically X-shaped micropylar plate of the eggs. The sister-group of Heteropteryginae is represented by the Obriminae, with which it shares a beak-like secondary ovipositor in the females and presence of a medio-apical spine on the area apicalis. Both features are synapomorphies of Heteropteryginae + Obriminae. The genus Haaniella Kirby, 1904 contains 16 known species, five of which are newly described herein. The genus Miniopteryx Zompro, 2004 (Type-species: Haaniella parva Günther, 1944) is synonymised with Haaniella on the basis that the distinguishing feature mentioned in the original description is a character that is frequently found throughout the genus (n. syn.). The type-species H. parva Günther, 1944 is automatically retransferred to Haaniella (rev. stat.). Haaniella aculeata n. sp. from western Sumatra is described from the male. Haaniella macroptera n. sp. from Singapore and the Johor state in southern Peninsular Malaysia is described from both sexes and the eggs. Haaniella gintingi n. sp. from Central Sumatra is described from both sexes and the eggs and Haaniella kerincia n. sp. from Western Sumatra is described from the insects only, the eggs being still unknown. One new species, Haaniella gorochovi n. sp., is the only representative of the genus and subfamily Heteropteryginae known from Vietnam and both sexes as well as the eggs are described. Haaniella erringtoniae (Redtenbacher, 1906) is endemic in Peninsular Malaysia, here removed from synonymy with H. muelleri (de Haan, 1842) and re-established as a valid species (rev. stat.). The Sumatran Haaniella glaber (Redtenbacher, 1906) is removed from synonymy with H. muelleri (Haan, 1842) and re-established as a valid species (rev. stat.). Leocrates glaber Redtenbacher, 1906 and Haaniella muelleri simplex Günther, 1944 are removed from synonymy with H. muelleri (Haan, 1842) (rev. stat.) and synonymised with H. glaber. Haaniella mecheli (Redtenbacher, 1906) and H. rosenbergii (Kaup, 1871) are removed from synonymy with H. muelleri (Haan, 1842) and re-established as valid species (rev. stat.). Haaniella erringtoniae novaeguineae Günther, 1934 and Haaniella muelleri var. b. (Haan, 1842) are synonymized with H. rosenbergii (Kaup, 1871) (n. syn.). The type-species Haaniella muelleri (Haan, 1842) is shown to be a fairly rare species that is restricted to Sumatra. All subsequent records of H. muelleri from outside Sumatra and references to captive breeding of stock originating from Peninsular Malaysia in Europe relate to H. erringtoniae (Redtenbacher, 1906). The previously unknown males and eggs of H. rosenbergii (Kaup, 1871) as well as the previously unknown females and eggs of H. parva Günther, 1944 are described and illustrated for the first time. Based on morphological characters of the insects and eggs three distinct species-groups are recognized within Haaniella. The muelleri species-group contains nine species that are distributed throughout Sumatra, the Mentawei Islands, Singapore and Peninsular Malaysia. These are characterized by the smooth ventral surface of the meso- and metafemora and lemon-shaped eggs which entirely lack the setae seen in the two other species-groups. The grayii species-group comprises four species, two of which are endemic in Borneo, one endemic in Sumatra and the fourth species being the only known representative of the subfamily in Vietnam. These species are characteristic for the prominent pair of spines on the abdominal tergites II-IV of males and long apically multidentate epiproct of females. The echinata species-group contains three exceptionally Bornean species, which are characterized by the long and apically pointed subgenital plate of females, which clearly projects beyond the epiproct, as well as the sub-basal lateral tooth of the anal segment of males. The muelleri species-group is sister to the remainder two species-groups. Heteropteryx Gray, 1853 is a monotypical genus and only contains the type-species H. dilatata (Parkinson, 1798), which is found throughout Peninsular Malaysia, Thailand, Sumatra and Northeastern Borneo. This genus differs from Haaniella by the strongly conically elevated head, which posteriorly projects over the anterior margin of the pronotum, females being bright green or yellow in colour with plain and translucent pink alae and having distinct spines on the abdominal tergites, and males having a strongly shortened mesothorax and dull pink alae. Lectotypes are designated for Haaniella parva Günther, 1944, Heteropteryx echinata Redtenbacher, 1906, Heteropteryx saussurei Redtenbacher, 1906 and Heteropteryx scabra Redtenbacher, 1906 to guarantee stability of these names. Information on the habitats, host-plants, biology, life cycle, parasitism and captive breeding of the species of Heteropteryginae is presented and a list summarising all taxonomic changes presented herein.
This study was done to understand the dynamics of rotavirus genotype distribution in Turkish children. Samples were collected from January 2006 through August 2011 from children at a hospital in Ankara. Rotavirus was detected in 28 % (241/889) of the samples. Genotype G9P[8] was predominant (28 %), followed by G1P[8] (16.3 %) and G2P[8] (15.9 %). G9 was absent in the samples from 2006 and 2007 and then re-emerged in 2008 and increased gradually. Phylogenetic analysis showed that Turkish G9 rotaviruses of the present study formed a sublineage with strains from Italy and Ethiopia, possibly indicating spread of a clone in these countries.
The vertical structure of a tropical rain forest is complex and multilayered, with strong variation of micro-environment with height up to the canopy. We investigated the relation between morphological traits of leaf surfaces and tree ecological characteristics in a Malaysian tropical rain forest. The shapes and densities of stomata and trichomes on the abaxial leaf surfaces and their relation with leaf characteristics such as leaf area and leaf mass per area (LMA) were studied in 136 tree species in 35 families with different growth forms in the tropical moist forest. Leaf physiological properties were also measured in 50 canopy and emergent species. Most tree species had flat type (40.4 %) or mound type (39.7 %) stomata. In addition, 84 species (61.76 %) in 22 families had trichomes, including those with glandular (17.65 %) and non-glandular trichomes (44.11 %). Most leaf characteristics significantly varied among the growth form types: species in canopy and emergent layers and canopy gap conditions had higher stomatal density, stomatal pore index (SPI), trichome density and LMA than species in understory and subcanopy layers, though the relation of phylogenetically independent contrasts to each characteristic was not statistically significant, except for leaf stomatal density, SPI and LMA. Intrinsic water use efficiency in canopy and emergent tree species with higher trichome densities was greater than in species with lower trichome densities. These results suggest that tree species in tropical rain forests adapt to a spatial difference in their growth forms, which are considerably affected by phylogenetic context, by having different stomatal and trichome shapes and/or densities.
Genetic variation in mitochondrial genes could underlie metabolic adaptations because mitochondrially encoded proteins are directly involved in a pathway supplying energy to metabolism. Macquarie perch from river basins exposed to different climates differ in size and growth rate, suggesting potential presence of adaptive metabolic differences. We used complete mitochondrial genome sequences to build a phylogeny, estimate lineage divergence times and identify signatures of purifying and positive selection acting on mitochondrial genes for 25 Macquarie perch from three basins: Murray-Darling Basin (MDB), Hawkesbury-Nepean Basin (HNB) and Shoalhaven Basin (SB). Phylogenetic analysis resolved basin-level clades, supporting incipient speciation previously inferred from differentiation in allozymes, microsatellites and mitochondrial control region. The estimated time of lineage divergence suggested an early- to mid-Pleistocene split between SB and the common ancestor of HNB+MDB, followed by mid-to-late Pleistocene splitting between HNB and MDB. These divergence estimates are more recent than previous ones. Our analyses suggested that evolutionary drivers differed between inland MDB and coastal HNB. In the cooler and more climatically variable MDB, mitogenomes evolved under strong purifying selection, whereas in the warmer and more climatically stable HNB, purifying selection was relaxed. Evidence for relaxed selection in the HNB includes elevated transfer RNA and 16S ribosomal RNA polymorphism, presence of potentially mildly deleterious mutations and a codon (ATP6113) displaying signatures of positive selection (ratio of nonsynonymous to synonymous substitution rates (dN/dS) >1, radical change of an amino-acid property and phylogenetic conservation across the Percichthyidae). In addition, the difference could be because of stronger genetic drift in the smaller and historically more subdivided HNB with low per-population effective population sizes.
The gram-positive, mesophilic and non-motile coccus Streptococcus gordonii is an important causative agent of infective endocarditis (IE). This pioneer species of dental plaque also causes bacteraemia in immune-supressed patients. In this study, we analysed the genome of a representative strain, Streptococcus gordonii SK12 that was originally isolated from the oral cavity. To gain a better understanding of the biology, virulence and phylogeny, of this potentially pathogenic organism, high-throughput Illumina HiSeq technology and different bioinformatics approaches were performed. Genome assembly of SK12 was performed using CLC Genomic Workbench 5.1.5 while RAST annotation revealed the key genomic features. The assembled draft genome of Streptococcus gordonii SK12 consists of 27 contigs, with a genome size of 2,145,851 bp and a G+C content of 40.63%. Phylogenetic inferences have confirmed that SK12 is closely related to the widely studied strain Streptococcus gordonii Challis. Interestingly, we predicted 118 potential virulence genes in SK12 genome which may contribute to bacterial pathogenicity in infective endocarditis. We also discovered an intact prophage which might be recently integrated into the SK12 genome. Examination of genes present in genomic islands revealed that this oral strain
might has potential to acquire new phenotypes/traits including strong defence system, bacitracin
resistance and collateral detergent sensitivity. This detailed analysis of S. gordonii SK12 further improves our understanding of the genetic make-up of S. gordonii as a whole and may help to elucidate how this species is able to transition between living as an oral commensal and potentially causing the lifethreatening condition infective endocarditis.
Rodent models have been used extensively to study West Nile virus (WNV) infection because they develop severe neurological symptoms similar to those observed in human WNV neuroinvasive disease. Most of this research has focused on old lineage (L) 1 strains, while information about pathogenicity is lacking for the most recent L1 and L2 strains, as well as for newly defined lineages. In this study, 4-week-old Swiss mice were inoculated with a collection of 12 WNV isolates, comprising 10 old and recent L1 and L2 strains, the putative L6 strain from Malaysia and the proposed L7 strain Koutango (KOU). The intraperitoneal inoculation of 10-fold dilutions of each strain allowed the characterization of the isolates in terms of LD50, median survival times, ID50, replication in neural and extraneural tissues and antibody production. Based on these results, we classified the isolates in three groups: high virulence (all L1a strains, recent L2 strains and KOU), moderate virulence (B956 strain) and low virulence (Kunjin and Malaysian isolates). We determined that the inoculation of a single dose of 1000 p.f.u. would be sufficient to classify WNV strains by pathotype. We confirmed the enhanced virulence of the KOU strain with a high capacity to cause rapid systemic infection. We also corroborated that differences in pathogenicity among strains do not correlate with phylogenetic lineage or geographic origin, and confirmed that recent European and African WNV strains belonging to L1 and L2 are highly virulent and do not differ in their pathotype profile compared to the prototype NY99 strain.
Frullania subgenus Microfrullania is a clade of ca. 15 liverwort species occurring in Australasia, Malesia, and southern South America. We used combined nuclear and chloroplast sequence data from 265 ingroup accessions to test species circumscriptions and estimate the biogeographic history of the subgenus. With dense infra-specific sampling, we document an important role of long-distance dispersal in establishing phylogeographic patterns of extant species. At deeper time scales, a combination of phylogenetic analyses, divergence time estimation and ancestral range estimation were used to reject vicariance and to document the role of long-distance dispersal in explaining the evolution and biogeography of the clade across the southern Hemisphere. A backbone phylogeny for the subgenus is proposed, providing insight into evolution of morphological patterns and establishing the basis for an improved sectional classification of species within Microfrullania. Several species complexes are identified, the presence of two undescribed but genetically and morphologically distinct species is noted, and previously neglected names are discussed.
Weedy rice is a conspecific form of cultivated rice (Oryza sativa L.) that infests rice fields and results in severe crop losses. Weed strains in different world regions appear to have originated multiple times from different domesticated and/or wild rice progenitors. In the case of Malaysian weedy rice, a multiple-origin model has been proposed based on neutral markers and analyses of domestication genes for hull color and seed shattering. Here, we examined variation in pericarp (bran) color and its molecular basis to address how this trait evolved in Malaysian weeds and its possible role in weed adaptation. Functional alleles of the Rc gene confer proanthocyanidin pigmentation of the pericarp, a trait found in most wild and weedy Oryzas and associated with seed dormancy; nonfunctional rc alleles were strongly favored during rice domestication, and most cultivated varieties have nonpigmented pericarps. Phenotypic characterizations of 52 Malaysian weeds revealed that most strains are characterized by the pigmented pericarp; however, some weeds have white pericarps, suggesting close relationships to cultivated rice. Phylogenetic analyses indicate that the Rc haplotypes present in Malaysian weeds likely have at least three distinct origins: wild O. rufipogon, white-pericarp cultivated rice, and red-pericarp cultivated rice. These diverse origins contribute to high Rc nucleotide diversity in the Malaysian weeds. Comparison of Rc allelic distributions with other rice domestication genes suggests that functional Rc alleles may confer particular fitness benefits in weedy rice populations, for example, by conferring seed dormancy. This may promote functional Rc introgression from local wild Oryza populations.
Reliable species identification provides a sounder basis for use of species in the order Odonata as biological indicators and for their conservation, an urgent concern as many species are threatened with imminent extinction. We generated 134 COI barcodes from 36 morphologically identified species of Odonata collected from Mindanao Island, representing 10 families and 19 genera. Intraspecific sequence divergences ranged from 0 to 6.7% with four species showing more than 2%, while interspecific sequence divergences ranged from 0.5 to 23.3% with seven species showing less than 2%. Consequently, no distinct gap was observed between intraspecific and interspecific DNA barcode divergences. The numerous islands of the Philippine archipelago may have facilitated rapid speciation in the Odonata and resulted in low interspecific sequence divergences among closely related groups of species. This study contributes DNA barcodes for 36 morphologically identified species of Odonata reported from Mindanao including 31 species with no previous DNA barcode records.
In an attempt to determine whether or not genetic variants of the Tasmanian strain of Atlantic salmon aquareovirus (TSRV) exist, 14 isolates of TSRV, originating from various locations in Tasmania, covering a 20-year period (1990-2010), obtained from various host species and tissues, and isolated on different cell lines, were selected for this study. Two categories, termed "typical" and "atypical", of variants of TSRV were identified based on preliminary genotypic and phenotypic characterization carried out on these 14 different isolates. In addition, electron microscopic examination indicated the existence of at least three variants based on viral particle size. Finally, this study demonstrated the existence of at least one new variant of TSRV isolates, other than the more commonly isolated typical TSRV isolates, in farmed Tasmanian Atlantic salmon.
The Southeast Asian species of Hypsugo are rare bats, except for H. cadornae and H. pulveratus, which are distributed throughout the Indomalayan region. Hypsugo macrotis is restricted to Peninsular Malaysia, Sumatra, Java and adjacent islands, and is known only from a handful of specimens. Here we report a new locality record of the species from Seremban, Peninsular Malaysia, which also represents the first known building-dweller colony of any Hypsugo from the region. We discuss the taxonomic status of two morphologically similar species, H. macrotis and H. vordermanni, and provide the first COI and cyt b gene sequences for H. macrotis and reconstruct the species' phylogenetic relationships.
The karyotypes have been determined of 16 of the 32 species of the genus Varanus, including animals from Africa, Israel, Malaya and Australia. A constant chromosome number of 2n = 40 was observed. The karyotype is divided into eight pairs of large chromosomes and 12 paris of microchromosomes. A series of chromosomal rearrangements have become established in both size groups of the karyotype and are restricted to centromers shifts, probably caused by pericentric inversion. Species could be placed in one of six distinct karyotype groups which are differentiated by these rearrangements and whose grouping does not always correspond with the current taxonomy. An unusual sex chromosome system of the ZZ/ZW type was present in a number of the species examined. The evolutionary significance of these chromosomal rearrangements, their origin and their mode of establishment are discussed and related to the current taxonomic groupings. The most likely phylogenetic model based on chromosome morphology, fossil evidence and the current distribution of the genus Varanus is presented.
Polygonum minus (syn. Persicaria minor) is a herbal plant that is well known for producing sesquiterpenes, which contribute to its flavour and fragrance. This study describes the cloning and functional characterisation of PmSTPS1 and PmSTPS2, two sesquiterpene synthase genes that were identified from P. minus transcriptome data mining. The full-length sequences of the PmSTPS1 and PmSTPS2 genes were expressed in the E. coli pQE-2 expression vector. The sizes of PmSTPS1 and PmSTPS2 were 1098 bp and 1967 bp, respectively, with open reading frames (ORF) of 1047 and 1695 bp and encoding polypeptides of 348 and 564 amino acids, respectively. The proteins consist of three conserved motifs, namely, Asp-rich substrate binding (DDxxD), metal binding residues (NSE/DTE), and cytoplasmic ER retention (RxR), as well as the terpene synthase family N-terminal domain and C-terminal metal-binding domain. From the in vitro enzyme assays, using the farnesyl pyrophosphate (FPP) substrate, the PmSTPS1 enzyme produced multiple acyclic sesquiterpenes of β-farnesene, α-farnesene, and farnesol, while the PmSTPS2 enzyme produced an additional nerolidol as a final product. The results confirmed the roles of PmSTPS1 and PmSTPS2 in the biosynthesis pathway of P. minus, to produce aromatic sesquiterpenes.