Displaying publications 21 - 40 of 171 in total

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  1. Fulltext Acoustic communication at the water's edge: evolutionary insights from a mudskipper
    Polgar G, Malavasi S, Cipolato G, Georgalas V, Clack JA, Torricelli P
    PLoS One, 2011;6(6):e21434.
    PMID: 21738663 DOI: 10.1371/journal.pone.0021434
    Coupled behavioural observations and acoustical recordings of aggressive dyadic contests showed that the mudskipper Periophthalmodon septemradiatus communicates acoustically while out of water. An analysis of intraspecific variability showed that specific acoustic components may act as tags for individual recognition, further supporting the sounds' communicative value. A correlative analysis amongst acoustical properties and video-acoustical recordings in slow-motion supported first hypotheses on the emission mechanism. Acoustic transmission through the wet exposed substrate was also discussed. These observations were used to support an "exaptation hypothesis", i.e. the maintenance of key adaptations during the first stages of water-to-land vertebrate eco-evolutionary transitions (based on eco-evolutionary and palaeontological considerations), through a comparative bioacoustic analysis of aquatic and semiterrestrial gobiid taxa. In fact, a remarkable similarity was found between mudskipper vocalisations and those emitted by gobioids and other soniferous benthonic fishes.
    Matched MeSH terms: Biological Evolution*
  2. Fulltext Rethinking megafauna
    Moleón M, Sánchez-Zapata JA, Donázar JA, Revilla E, Martín-López B, Gutiérrez-Cánovas C, et al.
    Proc Biol Sci, 2020 03 11;287(1922):20192643.
    PMID: 32126954 DOI: 10.1098/rspb.2019.2643
    Concern for megafauna is increasing among scientists and non-scientists. Many studies have emphasized that megafauna play prominent ecological roles and provide important ecosystem services to humanity. But, what precisely are 'megafauna'? Here, we critically assess the concept of megafauna and propose a goal-oriented framework for megafaunal research. First, we review definitions of megafauna and analyse associated terminology in the scientific literature. Second, we conduct a survey among ecologists and palaeontologists to assess the species traits used to identify and define megafauna. Our review indicates that definitions are highly dependent on the study ecosystem and research question, and primarily rely on ad hoc size-related criteria. Our survey suggests that body size is crucial, but not necessarily sufficient, for addressing the different applications of the term megafauna. Thus, after discussing the pros and cons of existing definitions, we propose an additional approach by defining two function-oriented megafaunal concepts: 'keystone megafauna' and 'functional megafauna', with its variant 'apex megafauna'. Assessing megafauna from a functional perspective could challenge the perception that there may not be a unifying definition of megafauna that can be applied to all eco-evolutionary narratives. In addition, using functional definitions of megafauna could be especially conducive to cross-disciplinary understanding and cooperation, improvement of conservation policy and practice, and strengthening of public perception. As megafaunal research advances, we encourage scientists to unambiguously define how they use the term 'megafauna' and to present the logic underpinning their definition.
    Matched MeSH terms: Biological Evolution
  3. Fulltext Salmonella Typhi genomics: envisaging the future of typhoid eradication
    Yap KP, Thong KL
    Trop Med Int Health, 2017 08;22(8):918-925.
    PMID: 28544285 DOI: 10.1111/tmi.12899
    Next-generation whole-genome sequencing has revolutionised the study of infectious diseases in recent years. The availability of genome sequences and its understanding have transformed the field of molecular microbiology, epidemiology, infection treatments and vaccine developments. We review the key findings of the publicly accessible genomes of Salmonella enterica serovar Typhi since the first complete genome to the most recent release of thousands of Salmonella Typhi genomes, which remarkably shape the genomic research of S. Typhi and other pathogens. Important new insights acquired from the genome sequencing of S. Typhi, pertaining to genomic variations, evolution, population structure, antibiotic resistance, virulence, pathogenesis, disease surveillance/investigation and disease control are discussed. As the numbers of sequenced genomes are increasing at an unprecedented rate, fine variations in the gene pool of S. Typhi are captured in high resolution, allowing deeper understanding of the pathogen's evolutionary trends and its pathogenesis, paving the way to bringing us closer to eradication of typhoid through effective vaccine/treatment development.
    Matched MeSH terms: Biological Evolution
  4. Fulltext Phylogenetic and Transcripts Profiling of Glucose Sensing Related Genes in Candida glabrata
    Ng TS, Mohd Desa MN, Sandai D, Chong PP, Than LT
    Jundishapur J Microbiol, 2015 Nov;8(11):e25177.
    PMID: 26855740 DOI: 10.5812/jjm.25177
    BACKGROUND: The sensing mechanism of glucose in Saccharomyces cerevisiae is well studied. However, such information is scarcely found in other yeast species such as Candida glabrata.

    OBJECTIVES: This study aimed to identify the glucose sensing pathway related genes of C. glabrata and to analyze the regulation pattern of these genes in response to different surrounding glucose concentrations through the quantitative real time polymerase chain reaction (qRT-PCR).

    MATERIALS AND METHODS: Phylogenetic analysis was carried out on predicted amino acid sequences of C. glabrata and S. cerevisiae to compare their degree of similarity. In addition, the growth of C. glabrata in response to different amounts of glucose (0%, 0.01%, 0.1%, 1% and 2%) was evaluated via the spot dilution assay on prepared agar medium. Besides, the SNF3 and RGT2, which act as putative glucose sensors, and the RGT1 and MIG1, which act as putative transcriptional regulators and selected downstream hexose transporters (HXTs), were analysed through qRT-PCR analysis for the gene expression level under different glucose concentrations.

    RESULTS: Comparative analysis of predicted amino acids in the phylogenetic tree showed high similarity between C. glabrata and S cerevisiae. Besides, C. glabrata demonstrated the capability to grow in glucose levels as low as 0.01% in the spot dilution assay. In qRT-PCR analysis, differential expressions were observed in selected genes when C. glabrata was subjected to different glucose concentrations.

    CONCLUSIONS: The constructed phylogenetic tree suggests the close evolutionary relationship between C. glabrata and S. cerevisiae. The capability of C. glabrata to grow in extremely low glucose environments and the differential expression of selected glucose-sensing related genes suggested the possible role of these genes in modulating the growth of C. glabrata in response to different glucose concentrations. This study helps deepen our understanding of the glucose sensing mechanism in C. glabrata and serves to provide fundamental data that may assist in unveiling this mechanism as a potential drug target.

    Matched MeSH terms: Biological Evolution
  5. "Complement fractionation" in natural diploid orchid species
    Teoh SB
    Theor Appl Genet, 1982 Mar;61(1):91-5.
    PMID: 24271380 DOI: 10.1007/BF00261517
    Four out of 10 diploid orchid species showed "complement fractionation" a complex cytological phenomenon, hitherto reported only in polyploid plants. The manifestation of this phenomenon during meiosis is the formation of chromosome subgroups resulting eventually in cells with more than the usual four sporads; five or six being the optimum number in the investigated orchid species. No implications whatsoever can be deduced as to the genetic or genomic constitution of the end products. The presence of the phenomenon in these orchid species could perhaps indicate a polyploid ancestry or concealed hybridity. The operation of "complement fractionation", however, could be interpreted as an alternative evolutionary pathway opposed to polyploidy.
    Matched MeSH terms: Biological Evolution
  6. 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
  7. 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
  8. Genetic divergence and evolutionary relationship in Fejervarya cancrivora from Indonesia and other Asian countries inferred from allozyme and MtDNA sequence analyses
    Kurniawan N, Islam MM, Djong TH, Igawa T, Daicus MB, Yong HS, et al.
    Zoolog Sci, 2010 Mar;27(3):222-33.
    PMID: 20192690 DOI: 10.2108/zsj.27.222
    To elucidate genetic divergence and evolutionary relationship in Fejervarya cancrivora from Indonesia and other Asian countries, allozyme and molecular analyses were carried out using 131 frogs collected from 24 populations in Indonesia, Thailand, Bangladesh, Malaysia, and the Philippines. In the allozymic survey, seventeen enzymatic loci were examined for 92 frogs from eight representative localities. The results showed that F. cancrivora is subdivided into two main groups, the mangrove type and the large- plus Pelabuhan ratu types. The average Nel's genetic distance between the two groups was 0.535. Molecular phylogenetic trees based on nucleotide sequences of the 16S rRNA and Cyt b genes and constructed with the ML, MP, NJ, and BI methods also showed that the individuals of F. cancrivora analyzed comprised two clades, the mangrove type and the large plus Pelabuhan ratu / Sulawesi types, the latter further split into two subclades, the large type and the Pelabuhan ratu / Sulawesi type. The geographical distribution of individuals of the three F. cancrivora types was examined. Ten Individuals from Bangladesh, Thailand, and the Philippines represented the mangrove type; 34 Individuals from Malaysia and Indonesia represented the large type; and 11 individuals from Indonesia represented the Pelabuhan ratu / Sulawesi type. Average sequence divergences among the three types were 5.78-10.22% for the 16S and 12.88-16.38% for Cyt b. Our results suggest that each of the three types can be regarded as a distinct species.
    Matched MeSH terms: Biological Evolution
  9. Evolutionary and biogeographic history of the black fly Simulium wayani (Diptera: Simuliidae) on the island of Timor
    Adler PH, Takaoka H, Sofian-Azirun M, Chen CD, Suana IW
    Acta Trop, 2019 May;193:1-6.
    PMID: 30772330 DOI: 10.1016/j.actatropica.2019.02.017
    A recently described species of black fly, Simulium wayani Takaoka and Chen, from the island of Timor was chromosomally mapped to provide insights into its evolutionary and biogeographic history. The morphologically based species status of S. wayani is supported by a suite of fixed chromosomal rearrangements and unique sex chromosomes derived primarily from a large pool of polymorphisms in the S. ornatipes complex in Australia. The banding patterns of its polytene chromosomes indicate that S. wayani is closely related to a pair of homosequential cryptic species (S. norfolkense Dumbleton and S. ornatipes cytoform A2) in the S. ornatipes Skuse complex on mainland Australia; all three species uniquely share the same amplified band in their chromosomal complement. The low level of polymorphism and heterozygosity in S. wayani, relative to Australian populations of the S. ornatipes complex, suggests few colonization events from the larger land mass.
    Matched MeSH terms: Biological Evolution*
  10. Fulltext Emergence and adaptive evolution of Nipah virus
    Li K, Yan S, Wang N, He W, Guan H, He C, et al.
    Transbound Emerg Dis, 2020 Jan;67(1):121-132.
    PMID: 31408582 DOI: 10.1111/tbed.13330
    Since its first emergence in 1998 in Malaysia, Nipah virus (NiV) has become a great threat to domestic animals and humans. Sporadic outbreaks associated with human-to-human transmission caused hundreds of human fatalities. Here, we collected all available NiV sequences and combined phylogenetics, molecular selection, structural biology and receptor analysis to study the emergence and adaptive evolution of NiV. NiV can be divided into two main lineages including the Bangladesh and Malaysia lineages. We formly confirmed a significant association with geography which is probably the result of long-term evolution of NiV in local bat population. The two NiV lineages differ in many amino acids; one change in the fusion protein might be involved in its activation via binding to the G protein. We also identified adaptive and positively selected sites in many viral proteins. In the receptor-binding G protein, we found that sites 384, 386 and especially 498 of G protein might modulate receptor-binding affinity and thus contribute to the host jump from bats to humans via the adaption to bind the human ephrin-B2 receptor. We also found that site 1645 in the connector domain of L was positive selected and involved in adaptive evolution; this site might add methyl groups to the cap structure present at the 5'-end of the RNA and thus modulate its activity. This study provides insight to assist the design of early detection methods for NiV to assess its epidemic potential in humans.
    Matched MeSH terms: Biological Evolution
  11. Ornament size and colour as alternative strategies for effective communication in gliding lizards
    Klomp DA, Ord TJ, Das I, Diesmos A, Ahmad N, Stuart-Fox D
    J Evol Biol, 2016 Sep;29(9):1689-700.
    PMID: 27234454 DOI: 10.1111/jeb.12908
    Sexual ornamentation needs to be conspicuous to be effective in attracting potential mates and defending territories and indeed, a multitude of ways exists to achieve this. Two principal mechanisms for increasing conspicuousness are to increase the ornament's colour or brightness contrast against the background and to increase the size of the ornament. We assessed the relationship between the colour and size of the dewlap, a large extendible throat-fan, across a range of species of gliding lizards (Agamidae; genus Draco) from Malaysia and the Philippines. We found a negative relationship across species between colour contrast against the background and dewlap size in males, but not in females, suggesting that males of different species use increasing colour contrast and dewlap size as alternative strategies for effective communication. Male dewlap size also increases with increasing sexual size dimorphism, and dewlap colour and brightness contrast increase with increasing sexual dichromatism in colour and brightness, respectively, suggesting that sexual selection may act on both dewlap size and colour. We further found evidence that relative predation intensity, as measured from predator attacks on models placed in the field, may play a role in the choice of strategy (high chromatic contrast or large dewlap area) a species employs. More broadly, these results highlight that each component in a signal (such as colour or size) may be influenced by different selection pressures and that by assessing components individually, we can gain a greater understanding of the evolution of signal diversity.
    Matched MeSH terms: Biological Evolution*
  12. Fulltext Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania
    Reich D, Patterson N, Kircher M, Delfin F, Nandineni MR, Pugach I, et al.
    Am J Hum Genet, 2011 Oct 07;89(4):516-28.
    PMID: 21944045 DOI: 10.1016/j.ajhg.2011.09.005
    It has recently been shown that ancestors of New Guineans and Bougainville Islanders have inherited a proportion of their ancestry from Denisovans, an archaic hominin group from Siberia. However, only a sparse sampling of populations from Southeast Asia and Oceania were analyzed. Here, we quantify Denisova admixture in 33 additional populations from Asia and Oceania. Aboriginal Australians, Near Oceanians, Polynesians, Fijians, east Indonesians, and Mamanwa (a "Negrito" group from the Philippines) have all inherited genetic material from Denisovans, but mainland East Asians, western Indonesians, Jehai (a Negrito group from Malaysia), and Onge (a Negrito group from the Andaman Islands) have not. These results indicate that Denisova gene flow occurred into the common ancestors of New Guineans, Australians, and Mamanwa but not into the ancestors of the Jehai and Onge and suggest that relatives of present-day East Asians were not in Southeast Asia when the Denisova gene flow occurred. Our finding that descendants of the earliest inhabitants of Southeast Asia do not all harbor Denisova admixture is inconsistent with a history in which the Denisova interbreeding occurred in mainland Asia and then spread over Southeast Asia, leading to all its earliest modern human inhabitants. Instead, the data can be most parsimoniously explained if the Denisova gene flow occurred in Southeast Asia itself. Thus, archaic Denisovans must have lived over an extraordinarily broad geographic and ecological range, from Siberia to tropical Asia.
    Matched MeSH terms: Biological Evolution
  13. 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
  14. Fulltext When West Meets East: The Origins and Spread of Weedy Rice Between Continental and Island Southeast Asia
    Neik TX, Chai JY, Tan SY, Sudo MPS, Cui Y, Jayaraj J, et al.
    G3 (Bethesda), 2019 09 04;9(9):2941-2950.
    PMID: 31292156 DOI: 10.1534/g3.119.400021
    Weedy crop relatives are among the world's most problematic agricultural weeds, and their ability to rapidly evolve can be enhanced by gene flow from both domesticated crop varieties and wild crop progenitor species. In this study, we examined the role of modern commercial crop cultivars, traditional landraces, and wild relatives in the recent emergence and proliferation of weedy rice in East Malaysia on the island of Borneo. This region of Malaysia is separated from the Asian continent by the South China Sea, and weedy rice has become a major problem there more recently than on the Malaysian peninsular mainland. Using 24 polymorphic SSR loci and genotype data from the awn-length domestication gene An-1, we assessed the genetic diversity, population structure and potential origins of East Malaysian weeds; 564 weedy, cultivated and wild rice accessions were analyzed from samples collected in East Malaysia, Peninsular Malaysia and neighboring countries. While there is considerable evidence for contributions of Peninsular Malaysian weed ecotypes to East Malaysian populations, we find that local crop cultivars and/or landraces from neighboring countries are also likely contributors to the weedy rice infestations. These findings highlight the implications of genetic admixture from different cultivar source populations in the spread of weedy crop relatives and the urgent need for preventive measurements to maintain sustainable crop yields.
    Matched MeSH terms: Biological Evolution
  15. Fulltext Contrasting evolutionary patterns between two haplogroups of Haematobia exigua (Diptera: Muscidae) from the mainland and islands of Southeast Asia
    Low VL, Tan TK, Prakash BK, Vinnie-Siow WY, Tay ST, Masmeatathip R, et al.
    Sci Rep, 2017 07 19;7(1):5871.
    PMID: 28724923 DOI: 10.1038/s41598-017-05921-w
    Uncovering the hidden diversity and evolutionary history of arthropods of medico-veterinary importance could have significant implications for vector-borne disease control and epidemiological intervention. The buffalo fly Haematobia exigua is an obligate bloodsucking ectoparasite of livestock. As an initial step towards understanding its population structures and biogeographic patterns, we characterized partial cytochrome c oxidase subunit I (COI) and cytochrome b (Cytb) sequences of H. exigua from three distinct geographic regions in Southeast Asia. We detected two distinct mitochondrial haplogroups of H. exigua in our surveyed geographic regions. Haplogroup I is widespread in the Southeast Asian mainland whereas haplogroup II is generally restricted to the type population Java Island. Both haplogroups were detected co-occurring on Borneo Island. Additionally, both haplogroups have undergone contrasting evolutionary histories, with haplogroup I exhibited a high level of mitochondrial diversity indicating a population expansion during the Pleistocene era dating back to 98,000 years ago. However, haplogroup II presented a low level of mitochondrial diversity which argues against the hypothesis of recent demographic expansion.
    Matched MeSH terms: Biological Evolution*
  16. 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
  17. Fulltext Phylogeography and phylogeny of Rhinoviruses collected from Severe Acute Respiratory Infection (SARI) cases over successive epidemic periods in Tunisia
    Haddad-Boubaker S, Ben Hamda C, Ghedira K, Mefteh K, Bouafsoun A, Boutiba-Ben Boubaker I, et al.
    PLoS One, 2021;16(11):e0259859.
    PMID: 34807924 DOI: 10.1371/journal.pone.0259859
    Rhinoviruses (RV) are a major cause of Severe Acute Respiratory Infection (SARI) in children, with high genotypic diversity in different regions. However, RV type diversity remains unknown in several regions of the world. In this study, the genetic variability of the frequently circulating RV types in Northern Tunisia was investigated, using phylogenetic and phylogeographic analyses with a specific focus on the most frequent RV types: RV-A101 and RV-C45. This study concerned 13 RV types frequently circulating in Northern Tunisia. They were obtained from respiratory samples collected in 271 pediatric SARI cases, between September 2015 and November 2017. A total of 37 RV VP4-VP2 sequences, selected among a total of 49 generated sequences, was compared to 359 sequences from different regions of the world. Evolutionary analysis of RV-A101 and RV-C45 showed high genetic relationship between different Tunisian strains and Malaysian strains. RV-A101 and C45 progenitor viruses' dates were estimated in 1981 and 1995, respectively. Since the early 2000s, the two types had a wide spread throughout the world. Phylogenetic analyses of other frequently circulating strains showed significant homology of Tunisian strains from the same epidemic period, in contrast with earlier strains. The genetic relatedness of RV-A101 and RV-C45 might result from an introduction of viruses from different clades followed by local dissemination rather than a local persistence of an endemic clades along seasons. International traffic may play a key role in the spread of RV-A101, RV-C45, and other RVs.
    Matched MeSH terms: Biological Evolution
  18. Two new Bent-toed Geckos of the Cyrtodactylus pulchellus complex from Peninsular Malaysia and multiple instances of convergent adaptation to limestone forest ecosystems
    Grismer LL, Wood PL, Anuar S, Grismer MS, Quah ES, Murdoch ML, et al.
    Zootaxa, 2016 Apr 25;4105(5):401-29.
    PMID: 27394789 DOI: 10.11646/zootaxa.4105.5.1
    A new species of limestone cave-adapted gecko of the Cyrtodactylus pulchellus complex, C. hidupselamanya sp. nov., is described from an isolated karst formation at Felda Chiku 7, Kelantan, Peninsular Malaysia. This formation is scheduled to be completely quarried for its mineral content. From what we know about the life history of C. hidupselamanya sp. nov., this will result in its extinction. A new limestone forest-adapted species, C. lenggongensis sp. nov., from the Lenggong Valley, Perak was previously considered to be conspecific with C. bintangrendah but a re-evaluation of morphological, color pattern, molecular, and habitat preference indicates that it too is a unique lineage worthy of specific recognition. Fortunately C. lenggongensis sp. nov. is not facing extinction because its habitat is protected by the UNESCO Archaeological Heritage of the Lenggong Valley due to the archaeological significance of that region. Both 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. Using a time-calibrated BEAST analysis we inferred that the evolution of a limestone habitat preference and its apparently attendant morphological and color pattern adaptations evolved independently at least four times in the C. pulchellus complex between 26.1 and 0.78 mya.
    Matched MeSH terms: Biological Evolution
  19. Fulltext Malaria parasites of long-tailed macaques in Sarawak, Malaysian Borneo: a novel species and demographic and evolutionary histories
    Nada Raja T, Hu TH, Zainudin R, Lee KS, Perkins SL, Singh B
    BMC Evol. Biol., 2018 04 10;18(1):49.
    PMID: 29636003 DOI: 10.1186/s12862-018-1170-9
    BACKGROUND: Non-human primates have long been identified to harbour different species of Plasmodium. Long-tailed macaques (Macaca fascicularis), in particular, are reservoirs for P. knowlesi, P. inui, P. cynomolgi, P. coatneyi and P. fieldi. A previous study conducted in Sarawak, Malaysian Borneo, however revealed that long-tailed macaques could potentially harbour novel species of Plasmodium based on sequences of small subunit ribosomal RNA and circumsporozoite genes. To further validate this finding, the mitochondrial genome and the apicoplast caseinolytic protease M genes of Plasmodium spp. were sequenced from 43 long-tailed macaque blood samples.

    RESULTS: Apart from several named species of malaria parasites, long-tailed macaques were found to be potentially infected with novel species of Plasmodium, namely one we refer to as "P. inui-like." This group of parasites bifurcated into two monophyletic clades indicating the presence of two distinct sub-populations. Further analyses, which relied on the assumption of strict co-phylogeny between hosts and parasites, estimated a population expansion event of between 150,000 to 250,000 years before present of one of these sub-populations that preceded that of the expansion of P. knowlesi. Furthermore, both sub-populations were found to have diverged from a common ancestor of P. inui approximately 1.5 million years ago. In addition, the phylogenetic analyses also demonstrated that long-tailed macaques are new hosts for P. simiovale.

    CONCLUSIONS: Malaria infections of long-tailed macaques of Sarawak, Malaysian Borneo are complex and include a novel species of Plasmodium that is phylogenetically distinct from P. inui. These macaques are new natural hosts of P. simiovale, a species previously described only in toque monkeys (Macaca sinica) in Sri Lanka. The results suggest that ecological factors could affect the evolution of malaria parasites.

    Matched MeSH terms: Biological Evolution*
  20. Fulltext Extended survival of Pleistocene Siberian wolves into the early 20th century on the island of Honshū
    Niemann J, Gopalakrishnan S, Yamaguchi N, Ramos-Madrigal J, Wales N, Gilbert MTP, et al.
    iScience, 2021 Jan 22;24(1):101904.
    PMID: 33364590 DOI: 10.1016/j.isci.2020.101904
    The Japanese or Honshū wolf was one the most distinct gray wolf subspecies due to its small stature and endemicity to the islands of Honshū, Shikoku, and Kyūshū. Long revered as a guardian of farmers and travellers, it was persecuted from the 17th century following a rabies epidemic, which led to its extinction in the early 20th century. To better understand its evolutionary history, we sequenced the nuclear genome of a 19th century Honshū wolf specimen to an average depth of coverage of 3.7✕. We find Honshū wolves were closely related to a lineage of Siberian wolves that were previously believed to have gone extinct in the Late Pleistocene, thereby extending the survival of this ancient lineage until the early 20th century. We also detected significant gene flow between Japanese dogs and the Honshū wolf, corroborating previous reports on Honshū wolf dog interbreeding.
    Matched MeSH terms: Biological Evolution
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