Displaying publications 141 - 160 of 171 in total

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  1. Meiotic drive does not cause condition-dependent reduction of the sexual ornament in stalk-eyed flies
    Finnegan SR, Mondani M, Fowler K, Pomiankowski A
    J Evol Biol, 2021 05;34(5):736-745.
    PMID: 33559198 DOI: 10.1111/jeb.13770
    Meiotic drive systems are associated with low-frequency chromosomal inversions. These are expected to accumulate deleterious mutations due to reduced recombination and low effective population size. We test this prediction using the 'sex-ratio' (SR) meiotic drive system of the Malaysian stalk-eyed fly Teleopsis dalmanni. SR is associated with a large inversion (or inversions) on the X chromosome. In particular, we study eyespan in males carrying the SR chromosome, as this trait is a highly exaggerated, sexually dimorphic trait, known to have heightened condition-dependent expression. Larvae were raised in low and high larval food stress environments. SR males showed reduced eyespan under the low and high stress treatments, but there was no evidence of a condition-dependent decrease in eyespan under high stress. Similar but more complex patterns were observed for female eyespan, with evidence of additivity under low stress and heterosis under high stress. These results do not support the hypothesis that reduced sexual ornament size in meiotic drive males is due to a condition-dependent response to the putative increase in mutation load. Instead, reduced eyespan likely reflects compensatory resource allocation to different traits in response to drive-mediated destruction of sperm.
    Matched MeSH terms: Biological Evolution
  2. Eggplant Domestication: Pervasive Gene Flow, Feralization, and Transcriptomic Divergence
    Page A, Gibson J, Meyer RS, Chapman MA
    Mol Biol Evol, 2019 07 01;36(7):1359-1372.
    PMID: 31039581 DOI: 10.1093/molbev/msz062
    In the context of food security, examining the genomics of domestication will help identify genes underlying adaptive and economically important phenotypes, for example, larger fruit, improved taste, and loss of agronomically inferior phenotypes.  Examination of genome-scale single nucleotide polymorphisms demonstrates the relationships between wild ancestors of eggplant (Solanum melongena L.), confirming that Solanum insanum L. is the wild progenitor. This species is split roughly into an Eastern (Malaysian, Thai, and Vietnamese) and Western (Indian, Madagascan, and Sri Lankan) group, with domesticates derived from the former. Additional "wild" accessions from India appear to be feral escapes, derived multiple times from domesticated varieties through admixture. Accessions with small egg-shaped fruit are generally found intermixed with East Asian Solanum insanum confirming they are primitive relative to the large-fruited domesticates.  Comparative transcriptomics was used to track the loci under selection. Sequence analysis revealed a genetic bottleneck reducing variation by almost 50% in the primitive accessions relative to the wild species and a further 10% in the landraces. We also show evidence for selection on genes with a role in response to wounding and apoptosis.  Genes showing a significant difference in expression between wild and primitive or between primitive and landrace genepools were mostly (>75%) downregulated in the derived populations and enriched for gene ontologies related to defense, flowering, signaling, and response to biotic and abiotic stimuli.  This work reveals genomic changes involved in crop domestication and improvement, and the population genetics work explains why defining the eggplant domestication trajectory has been so challenging.
    Matched MeSH terms: Biological Evolution
  3. Fulltext Mapping black panthers: Macroecological modeling of melanism in leopards (Panthera pardus)
    da Silva LG, Kawanishi K, Henschel P, Kittle A, Sanei A, Reebin A, et al.
    PLoS One, 2017;12(4):e0170378.
    PMID: 28379961 DOI: 10.1371/journal.pone.0170378
    The geographic distribution and habitat association of most mammalian polymorphic phenotypes are still poorly known, hampering assessments of their adaptive significance. Even in the case of the black panther, an iconic melanistic variant of the leopard (Panthera pardus), no map exists describing its distribution. We constructed a large database of verified records sampled across the species' range, and used it to map the geographic occurrence of melanism. We then estimated the potential distribution of melanistic and non-melanistic leopards using niche-modeling algorithms. The overall frequency of melanism was ca. 11%, with a significantly non-random spatial distribution. Distinct habitat types presented significantly different frequencies of melanism, which increased in Asian moist forests and approached zero across most open/dry biomes. Niche modeling indicated that the potential distributions of the two phenotypes were distinct, with significant differences in habitat suitability and rejection of niche equivalency between them. We conclude that melanism in leopards is strongly affected by natural selection, likely driven by efficacy of camouflage and/or thermoregulation in different habitats, along with an effect of moisture that goes beyond its influence on vegetation type. Our results support classical hypotheses of adaptive coloration in animals (e.g. Gloger's rule), and open up new avenues for in-depth evolutionary analyses of melanism in mammals.
    Matched MeSH terms: Biological Evolution
  4. Species delimitation and biogeography of a southern hemisphere liverwort clade, Frullania subgenus Microfrullania (Frullaniaceae, Marchantiophyta)
    Carter BE, Larraín J, Manukjanová A, Shaw B, Shaw AJ, Heinrichs J, et al.
    Mol Phylogenet Evol, 2017 02;107:16-26.
    PMID: 27744015 DOI: 10.1016/j.ympev.2016.10.002
    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.
    Matched MeSH terms: Biological Evolution
  5. Natural infection in primates: helminths and problems in primate phylogeny, ecology, and behavior
    Dunn FL
    Lab Anim Care, 1970 Apr;20(2):383-8.
    PMID: 4245583
    Matched MeSH terms: Biological Evolution
  6. Malaria of the orang-utan (Pongo pygmaeus) in Borneo
    Peters W
    Philos Trans R Soc Lond B Biol Sci, 1976 Sep 28;275(941):439-82.
    PMID: 10589
    The primary objective of this project was to study the life cycle and ecology of Plasmodium pitheci, a malaria parasite of the orang-utan. The field work was based on the orang-utan rehabilitation centre in the Sepilok Forest Reserve of eastern Sabah. Two visits were made to Sepilok, the first in February and March, 1972, and the second (by W.P.) in January 1974. On the first visit two species of "surrogate host" were taken to Sabah, i.e. chimpanzees and Aotus monkeys for experimental work. The arboreal habitat of the orang-utan in the dipterocarp forests of eastern Sabah is described. In the Sepilok Forest Reserve dwell gibbons and leaf-monkeys, in addition to a small population of semi-domesticated and wild, free-ranging orang-utans of various ages. Although numerous species of anopheline mosquitoes have been collected in eastern Sabah, longitudinal studies are not available. Anopheles balabacensis was caught both attracted to orang-utans and to man at Sepilok. This species which is the main vector of human malaria in the north of Borneo, is suspected also of transmitting orang-utan malaria in this part of Sabah. Repeated blood examinations have been made on a number of orang-utans in the centre since 1966 and a high prevalence of infection was recorded with Plasmodium pitheci. In 1966 10 out of 19 animals had demonstrable parasitaemia. Detailed case histories are presented to show the course of parasitaemia in several orang-utans. Infections of P. pitheci were found to run a very chronic course. During the 1972 expedition a second, previously undescribed malaria parasite of the orang-utan was discovered, and was named P. silvaticum. The new parasite was successfully transmitted both by blood inoculation and, later, by sporozoite inoculation, into splenectomized chimpanzees. Although both species of malaria parasite may cause transitory signs of illness, orang-utans in general appear to be little discomforted by the infection. The animals do however suffer from other infectious diseases such as amoebic and balantidial dysentery, and melioidosis is a serious natural hazard which may have accounted for several deaths of wild orang-utans. An unidentified, intraerythrocytic structure that appeared in the blood of one chimpanzee, which had been inoculated with blood from an orang-utan, may have contributed to its death. Detailed descriptions and illustrations of P. pitheci and P. silvaticum are given. All stages of the life cycle of P. silvaticum are known (the tissue stages having been described in the liver of a "surrogate host", the chimpanzee) but only the blood and sporogonic stages of P. pitheci have been seen. This species was not infective to a chimpanzee, although there is an earlier report of a transient infection in this host by other workers. In the blood both parasites showed a tertian periodicity. From the appearance of the tissue schizonts on the seventh day it was estimated that the complete pre-erythrocytic cycle of P. silvaticum in the chimpanzee would occupy 8 days. P...
    Matched MeSH terms: Biological Evolution
  7. Venom proteome of the yellow-lipped sea krait, Laticauda colubrina from Bali: Insights into subvenomic diversity, venom antigenicity and cross-neutralization by antivenom
    Tan CH, Wong KY, Tan KY, Tan NH
    J Proteomics, 2017 08 23;166:48-58.
    PMID: 28688916 DOI: 10.1016/j.jprot.2017.07.002
    The venom proteome of Laticauda colubrina (Bali, Indonesia) was elucidated by nano-ESI-LCMS/MS of the venom reverse-phase HPLC fractions. Altogether 31 distinct forms of proteins were identified and clustered into three toxin families: three-finger toxin (3FTX, 66.12% of total venom proteins), phospholipase A2 (PLA2, 33.26%) and cysteine-rich secretory protein (CRiSP, 0.05%). The 3FTX were α-neurotoxins (five long neurotoxins, LNTX, 48.87%; two short neurotoxins, SNTX, 16.94%) and a trace amount of two cytotoxins (CTX, 0.31%). PLA2 were present with a large diversity of homologues (≥20 forms), however none was annotated to the lethal proteoform reported previously. The venom is highly lethal in mice (LD50=0.10μg/g) and this is driven primarily by the SNTX and LNTX (LD50=0.05-0.13μg/g), since the PLA2 proteins were non-lethal up to 2μg/g (20-time the venom LD50). The SNTX and LNTX were effectively cross-neutralized by the heterologous Sea Snake Antivenom (SSAV, Australian product) (potency=0.27mg toxin per ml antivenom, and 0.40mg/ml, respectively), corroborating the cross-neutralization of the whole venom (potency=1.09mg/ml) and its antigenic immunoreactivity toward SSAV. Furthermore, compared with earlier studies, the present work reveals geographical variation of venom composition for L. colubrina which may have implication for the evolution and conservation of the species.

    BIOLOGICAL SIGNIFICANCE: Laticauda colubrina (yellow-lipped sea krait) is a widely distributed, semi-aquatic venomous snake species. The venom proteome at the level of protein family is unsophisticated and consistent with its restricted prey selection. Nonetheless, the subproteomic findings revealed geographical variability of the venom for this widely distributed species. In contrast to two previous reports, the results for the Balinese L. colubrina venom showed that LNTX Neurotoxin a and Neurotoxin b were co-existent while the PLA2 lethal subtype (PLA-II) was undetected by means of LCMS/MS and by in vivo assay. This is an observable trait of L. colubrina considered divergent from specimens previously studied for the Philippines and the Solomon Islands. The stark geographical variation might be reflective of trophic adaptation following evolutionary arms race between the snake and the prey (eels) in different localities. The preferred trait would likely propagate and remain significant within the geographical population, since the strong behaviour of site fidelity in the species would have minimized gene flow between distant populations. Meanwhile, the in vivo neutralization study verified that the efficacy of the heterologous Sea Snake Antivenom (Australian product) is attributable to the cross-neutralization of SNTX and LNTX, two principal lethal toxins that made up the bulk of L. colubrina venom proteins. The findings also implied that L. colubrina, though could be evolutionarily more related to the terrestrial elapids, has evolved a much streamlined, neurotoxin- and PLA2-predominated venom arsenal, with major antigenicity shared among the true sea snakes and the Australo-Papuan elapids. The findings enrich our current understanding of the complexity of L. colubrina venom and the neutralizing spectrum of antivenom against the principal toxins from this unique elapid lineage.

    Matched MeSH terms: Biological Evolution
  8. Why have the peninsular "negritos" remained distinct?
    Benjamin G
    Hum Biol, 2013 Feb-Jun;85(1-3):445-84.
    PMID: 24297237
    The primary focus of this article is on the so-called negritos of Peninsular Malaysia and southern Thailand, but attention is also paid to other parts of Southeast Asia. I present a survey of current views on the "negrito" phenotype--is it single or many? If the phenotype is many (as now seems likely), it must have resulted from parallel evolution in the several different regions where it has been claimed to exist. This would suggest (contrary to certain views that have been expressed on the basis of very partial genetic data) that the phenotype originated recently and by biologically well-authenticated processes from within the neighboring populations. Whole-genome and physical-anthropological research currently support this view. Regardless of whether the negrito phenotype is ancient or recent-and to the extent that it retains any valid biological reality (which is worth questioning)-explanations are still needed for its continued distinctiveness. In the Malay Peninsula, a distinctive "Semang" societal pattern followed by most, but not all, so-called negritos may have been responsible for this by shaping familial, breeding, and demographic patterns to suit the two main modes of environmental appropriation that they have followed, probably for some millennia: nomadic foraging in the forest, and facultative dependence on exchange or labor relations with neighboring populations. The known distribution of "negritos" in the Malay Peninsula is limited to areas within relatively easy reach of archaeologically authenticated premodern transpeninsular trading and portage routes, as well as of other non-negrito, Aslian-speaking populations engaged in swidden farming. This suggests that their continued distinctiveness has resulted from a wish to maintain a complementary advantage vis-à-vis other, less specialized populations. Nevertheless, a significant degree of discordance exists between the associated linguistic, societal-tradition, and biological patterns which suggests that other factors have also been at play.
    Matched MeSH terms: Biological Evolution
  9. Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity
    Harrisson KA, Amish SJ, Pavlova A, Narum SR, Telonis-Scott M, Rourke ML, et al.
    Mol Ecol, 2017 Nov;26(22):6253-6269.
    PMID: 28977721 DOI: 10.1111/mec.14368
    Adaptive differences across species' ranges can have important implications for population persistence and conservation management decisions. Despite advances in genomic technologies, detecting adaptive variation in natural populations remains challenging. Key challenges in gene-environment association studies involve distinguishing the effects of drift from those of selection and identifying subtle signatures of polygenic adaptation. We used paired-end restriction site-associated DNA sequencing data (6,605 biallelic single nucleotide polymorphisms; SNPs) to examine population structure and test for signatures of adaptation across the geographic range of an iconic Australian endemic freshwater fish species, the Murray cod Maccullochella peelii. Two univariate gene-association methods identified 61 genomic regions associated with climate variation. We also tested for subtle signatures of polygenic adaptation using a multivariate method (redundancy analysis; RDA). The RDA analysis suggested that climate (temperature- and precipitation-related variables) and geography had similar magnitudes of effect in shaping the distribution of SNP genotypes across the sampled range of Murray cod. Although there was poor agreement among the candidate SNPs identified by the univariate methods, the top 5% of SNPs contributing to significant RDA axes included 67% of the SNPs identified by univariate methods. We discuss the potential implications of our findings for the management of Murray cod and other species generally, particularly in relation to informing conservation actions such as translocations to improve evolutionary resilience of natural populations. Our results highlight the value of using a combination of different approaches, including polygenic methods, when testing for signatures of adaptation in landscape genomic studies.
    Matched MeSH terms: Biological Evolution
  10. Variation of C-bands in the chromosomes of several subspecies of Rattus rattus
    Yosida TH, Sagai T
    Chromosoma, 1975;50(3):283-300.
    PMID: 1149576
    All subspecies of black rats (Rattus rattus) used in the present study are characterized by having large and clear C-bands at the centromeric region. The appearance of the bands, however, is different in the subspecies. Chromosome pair No. 1 in Asian type black rats (2n=42), which are characterized by an acrocentric and subtelocentric polymorphism, showed C-band polymorphism. In Phillipine rats (R. rattus mindanensis) the pair was subtelocentric with C-bands, but in Malayan black rats (R. rattus diardii) it was usually acrocentric with C-bands. In Hong-Kong (R. rattus flavipectus) and Japanese black rats (R. rattus tanezumi) it was polymorphic with respect to the presence of acrocentrics with C-bands or subtelocentrics without C-bands. The other chromosomes pairs showed clear C-bands, but in Hong-Kong black rats the pairs No. 2 and 5 were polymorphic with and without C-bands. In Japanese black rats, 6 chromosome pairs (No. 3, 4, 7, 9, 11 and 13) were polymorphic in regard to presence and absence of C-bands, but the other 5 chromosome pairs (No. 2, 5, 6, 8 and 10) showed always absence of C-bands. Only pair No. 12 usually showed C-bands. C-bands in small metacentric pairs (No. 14 to 20) in Asian type black rats generally large in size, but those in the Oceanian (2n=38) and Ceylon type black rats (2n=40) were small. In the hybrids between Asian and Oceanian type rats, heteromorphic C-bands, one large and the other small, were observed. Based on the consideration of karyotype evolution in the black rats, the C-band is suggested to have a tendency toward the diminution as far as the related species are concerned.
    Matched MeSH terms: Biological Evolution
  11. A multi-locus approach resolves the phylogenetic relationships of the Simulium asakoae and Simulium ceylonicum species groups in Malaysia: evidence for distinct evolutionary lineages
    Low VL, Takaoka H, Adler PH, Ya'cob Z, Norma-Rashid Y, Chen CD, et al.
    Med Vet Entomol, 2015 Sep;29(3):330-7.
    PMID: 25968459 DOI: 10.1111/mve.12120
    A multi-locus approach was used to examine the DNA sequences of 10 nominal species of blackfly in the Simulium subgenus Gomphostilbia (Diptera: Simuliidae) in Malaysia. Molecular data were acquired from partial DNA sequences of the mitochondria-encoded cytochrome c oxidase subunit I (COI), 12S rRNA and 16S rRNA genes, and the nuclear-encoded 18S rRNA and 28S rRNA genes. No single gene, nor the concatenated gene set, resolved all species or all relationships. However, all morphologically established species were supported by at least one gene. The multi-locus sequence analysis revealed two distinct evolutionary lineages, conforming to the morphotaxonomically recognized Simulium asakoae and Simulium ceylonicum species groups.
    Matched MeSH terms: Biological Evolution
  12. Fulltext A draft genome sequence of the elusive giant squid, Architeuthis dux
    da Fonseca RR, Couto A, Machado AM, Brejova B, Albertin CB, Silva F, et al.
    Gigascience, 2020 Jan 01;9(1).
    PMID: 31942620 DOI: 10.1093/gigascience/giz152
    BACKGROUND: The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea-dwelling species will allow several pending evolutionary questions to be unlocked.

    FINDINGS: We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome.

    CONCLUSIONS: This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.

    Matched MeSH terms: Biological Evolution
  13. Fulltext A Method for Quantifying, Visualising, and Analysing Gastropod Shell Form
    Liew TS, Schilthuizen M
    PLoS One, 2016;11(6):e0157069.
    PMID: 27280463 DOI: 10.1371/journal.pone.0157069
    Quantitative analysis of organismal form is an important component for almost every branch of biology. Although generally considered an easily-measurable structure, the quantification of gastropod shell form is still a challenge because many shells lack homologous structures and have a spiral form that is difficult to capture with linear measurements. In view of this, we adopt the idea of theoretical modelling of shell form, in which the shell form is the product of aperture ontogeny profiles in terms of aperture growth trajectory that is quantified as curvature and torsion, and of aperture form that is represented by size and shape. We develop a workflow for the analysis of shell forms based on the aperture ontogeny profile, starting from the procedure of data preparation (retopologising the shell model), via data acquisition (calculation of aperture growth trajectory, aperture form and ontogeny axis), and data presentation (qualitative comparison between shell forms) and ending with data analysis (quantitative comparison between shell forms). We evaluate our methods on representative shells of the genera Opisthostoma and Plectostoma, which exhibit great variability in shell form. The outcome suggests that our method is a robust, reproducible, and versatile approach for the analysis of shell form. Finally, we propose several potential applications of our methods in functional morphology, theoretical modelling, taxonomy, and evolutionary biology.
    Matched MeSH terms: Biological Evolution
  14. Fulltext Anti-inflammatory and antiplatelet activities of plasma are conserved across twelve mammalian species
    Ahmed S, Gul S, Idris F, Hussain A, Zia-Ul-Haq M, Jaafar HZ, et al.
    Molecules, 2014;19(8):11385-94.
    PMID: 25090125 DOI: 10.3390/molecules190811385
    Human plasma inhibits arachidonic acid metabolism and platelet aggregation. This helps human form a haemostatic control system that prevents the progress of certain aggregatory or inflammatory reactions. Whether this property of plasma is unique to human or extends to other species is not well known. It is speculated that this protective ability of plasma remains evolutionarily conserved in different mammals. In order to confirm this, the effect of plasma from 12 different mammalian species was investigated for its inhibitory potential against arachidonic acid metabolism and platelet aggregation. Metabolism of arachidonic acid by cyclooxygenase and lipoxygenase pathways was studies using radio-immuno assay and thin layer chromatography while platelet aggregation in the plasma of various mammals was monitored following turbedmetric method in a dual channel aggregometer. Results indicate that inhibition of AA metabolism and platelet aggregation is a common feature of plasma obtained from different mammalian species, although there exists large interspecies variation. This shows that besides human, other mammals also possess general protective mechanisms against various aggregatory and inflammatory conditions and this anti-inflammatory property of the plasma is evolutionarily conserved in mammalian species. The most likely candidates responsible for these properties of plasma include haptoglobin, albumin and lipoproteins.
    Matched MeSH terms: Biological Evolution
  15. Origin and evolution of Nipah virus
    Lo Presti A, Cella E, Giovanetti M, Lai A, Angeletti S, Zehender G, et al.
    J Med Virol, 2016 Mar;88(3):380-8.
    PMID: 26252523 DOI: 10.1002/jmv.24345
    Nipah virus, member of the Paramyxoviridae family, is classified as a Biosafety Level-4 agent and category C priority pathogen. Nipah virus disease is endemic in south Asia and outbreaks have been reported in Malaysia, Singapore, India, and Bangladesh. Bats of the genus Pteropus appear to be the natural reservoir of this virus. The aim of this study was to investigate the genetic diversity of Nipah virus, to estimate the date of origin and the spread of the infection. The mean value of Nipah virus N gene evolutionary rate, was 6.5 × 10(-4) substitution/site/year (95% HPD: 2.3 × 10(-4)-1.18 × 10(-3)). The time-scaled phylogenetic analysis showed that the root of the tree originated in 1947 (95% HPD: 1888-1988) as the virus entered in south eastern Asiatic regions. The segregation of sequences in two main clades (I and II) indicating that Nipah virus had two different introductions: one in 1995 (95% HPD: 1985-2002) which correspond to clade I, and the other in 1985 (95% HPD: 1971-1996) which correspond to clade II. The phylogeographic reconstruction indicated that the epidemic followed two different routes spreading to the other locations. The trade of infected pigs may have played a role in the spread of the virus. Bats of the Pteropus genus, that are able to travel to long distances, may have contributed to the spread of the infection. Negatively selected sites, statistically supported, could reflect the stability of the viral N protein.
    Matched MeSH terms: Biological Evolution
  16. Sequence changes in six variants of rice tungro bacilliform virus and their phylogenetic relationships
    Cabauatan PQ, Melcher U, Ishikawa K, Omura T, Hibino H, Koganezawa H, et al.
    J Gen Virol, 1999 Aug;80 ( Pt 8):2229-37.
    PMID: 10466823
    The DNA of three biological variants, G1, Ic and G2, which originated from the same greenhouse isolate of rice tungro bacilliform virus (RTBV) at the International Rice Research Institute (IRRI), was cloned and sequenced. Comparison of the sequences revealed small differences in genome sizes. The variants were between 95 and 99% identical at the nucleotide and amino acid levels. Alignment of the three genome sequences with those of three published RTBV sequences (Phi-1, Phi-2 and Phi-3) revealed numerous nucleotide substitutions and some insertions and deletions. The published RTBV sequences originated from the same greenhouse isolate at IRRI 20, 11 and 9 years ago. All open reading frames (ORFs) and known functional domains were conserved across the six variants. The cysteine-rich region of ORF3 showed the greatest variation. When the six DNA sequences from IRRI were compared with that of an isolate from Malaysia (Serdang), similar changes were observed in the cysteine-rich region in addition to other nucleotide substitutions and deletions across the genome. The aligned nucleotide sequences of the IRRI variants and Serdang were used to analyse phylogenetic relationships by the bootstrapped parsimony, distance and maximum-likelihood methods. The isolates clustered in three groups: Serdang alone; Ic and G1; and Phi-1, Phi-2, Phi-3 and G2. The distribution of phylogenetically informative residues in the IRRI sequences shared with the Serdang sequence and the differing tree topologies for segments of the genome suggested that recombination, as well as substitutions and insertions or deletions, has played a role in the evolution of RTBV variants. The significance and implications of these evolutionary forces are discussed in comparison with badnaviruses and caulimoviruses.
    Matched MeSH terms: Biological Evolution
  17. Fulltext A standardized dataset for conservation prioritization of songbirds to support CITES
    Juergens J, Bruslund S, Staerk J, Oegelund Nielsen R, Shepherd CR, Leupen B, et al.
    Data Brief, 2021 Jun;36:107093.
    PMID: 34041313 DOI: 10.1016/j.dib.2021.107093
    In this article we present a standardized dataset on 6659 songbirds (Passeriformes) highlighting information relevant to species conservation prioritization with a main focus to support the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Data were collected from both scientific and grey literature as well as several online databases. The data are structured into six knowledge categories: Conventions and Treaties, Human Use, Extinction Risk, Management Opportunities, Biological Information, and Intrinsic Values. The Conventions and Treaties category includes the listings for two international conventions, CITES and the Convention on the Conservation of Migratory Species of Wild Animals (CMS), as well as EU listings for the EU Wildlife Trade Regulations and the EU Birds Directive. The Human Use category contains information on both regulated trade collected from the CITES Trade Database and the United States' Law Enforcement Management Information System (LEMIS), and highly aggregated data on seizures which we obtained from TRAFFIC, the United Nations Office on Drugs and Crime (UNODC) and two data sources on traditional medicine. We also present, for the first time, the complete Songbirds in Trade Database (SiTDB), a trade database curated by taxon expert S. Bruslund based on expert knowledge, literature review, market surveys and sale announcements. Data on the types of human use, including traditional medicine are also provided. The knowledge area on Extinction Risk contains data on the species' IUCN Red List status, the Alliance for Zero Extinction Trigger Species status, site and population at the site, the species' IUCN Climate Change Vulnerability Assessment, and the listing of priority species at the Asian Songbird Crisis Summit. In the Management Opportunities category, we gathered data on ex-situ management from Species360 zoo holdings as well as species management plans from the European and North American Zoo Associations (EAZA and AZA, respectively). Biological Information includes data on body mass, clutch size, diet, availability of data from the IUCN Red List on habitat systems, extent of occurrence, generation length, migration pattern, distribution, and biological data from the Demographic Species Knowledge Index, number of occurrences recorded by the Global Biodiversity Information Facility (GBIF) as well as genomic data from the Bird 10 000K Genomes (B10K) project, Vertebrate Genome Project (VGP) and GenBank. Information on invasive species is also part of this knowledge area. The Intrinsic Value category refers to two measures of the species' intrinsic value, namely Ecological and Evolutionary Distinctiveness. In order to make these knowledge areas comparable, we standardized data following the taxonomy of the Handbook of the Birds of the World and Birdlife (Version 4, 2019). The data enable a broad spectrum of analyses and will be useful to scientists for further research and to policymakers, zoos and other conservation stakeholders for future prioritization decisions.
    Matched MeSH terms: Biological Evolution
  18. Fulltext Possible Roles of New Mutations Shared by Asian and American Zika Viruses
    Yokoyama S, Starmer WT
    Mol Biol Evol, 2017 03 01;34(3):525-534.
    PMID: 28087772 DOI: 10.1093/molbev/msw270
    Originating in Africa, the Zika virus (ZIKV) has spread to Asia, Pacific Islands and now to the Americas and beyond. Since the first isolation in 1947, ZIKV strains have been sampled at various times in the last 69 years, but this history has not been reflected in studying the patterns of mutation accumulation in their genomes. Implementing the viral history, we show that the ZIKV ancestor appeared sometime in 1930-1945 and, at that point, its mutation rate was probably less than 0.2 × 10-3/nucleotide site/year and subsequently increased significantly in most of its descendants. Sustaining a high mutation rate of 4 × 10-3/site/year throughout its evolution, the Ancestral Asian strain, which was sampled from a mosquito in Malaysia, accumulated 13 mutations in the 3'-untranslated region of RNA stem-loops prior to 1963, seven of which generate more stable stem-loop structures and are likely to inhibit cellular antiviral activities, including immune and RNA interference (RNAi) pathways. The seven mutations have been maintained in all Asian and American strains and may be responsible for serious medical problems we are facing today and offer testable hypotheses to examine their roles in molecular interactions during brain development.
    Matched MeSH terms: Biological Evolution
  19. Fulltext Malagasy Genetic Ancestry Comes from an Historical Malay Trading Post in Southeast Borneo
    Brucato N, Kusuma P, Cox MP, Pierron D, Purnomo GA, Adelaar A, et al.
    Mol Biol Evol, 2016 09;33(9):2396-400.
    PMID: 27381999 DOI: 10.1093/molbev/msw117
    Malagasy genetic diversity results from an exceptional protoglobalization process that took place over a thousand years ago across the Indian Ocean. Previous efforts to locate the Asian origin of Malagasy highlighted Borneo broadly as a potential source, but so far no firm source populations were identified. Here, we have generated genome-wide data from two Southeast Borneo populations, the Banjar and the Ngaju, together with published data from populations across the Indian Ocean region. We find strong support for an origin of the Asian ancestry of Malagasy among the Banjar. This group emerged from the long-standing presence of a Malay Empire trading post in Southeast Borneo, which favored admixture between the Malay and an autochthonous Borneo group, the Ma'anyan. Reconciling genetic, historical, and linguistic data, we show that the Banjar, in Malay-led voyages, were the most probable Asian source among the analyzed groups in the founding of the Malagasy gene pool.
    Matched MeSH terms: Biological Evolution
  20. Pollen structure and development in Nymphaeales: insights into character evolution in an ancient angiosperm lineage
    Taylor ML, Cooper RL, Schneider EL, Osborn JM
    Am J Bot, 2015 Oct;102(10):1685-702.
    PMID: 26419810 DOI: 10.3732/ajb.1500249
    A knowledge of pollen characters in early-diverging angiosperm lineages is essential for understanding pollen evolution and the role of pollen in angiosperm diversification. In this paper, we report and synthesize data on mature pollen and pollen ontogeny from all genera of Nymphaeales within a comparative, phylogenetic context and consider pollen evolution in this early-diverging angiosperm lineage. We describe mature pollen characters for Euryale, Barclaya, and Nymphaea ondinea, taxa for which little to no structural data exist.
    Matched MeSH terms: Biological Evolution
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