Displaying publications 1 - 20 of 171 in total

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  1. Automatic generation of controllers for embodied legged organisms: a Pareto evolutionary multi-objective approach
    Teo J, Abbass HA
    Evol Comput, 2004;12(3):355-94.
    PMID: 15355605
    In this paper, we investigate the use of a self-adaptive Pareto evolutionary multi-objective optimization (EMO) approach for evolving the controllers of virtual embodied organisms. The objective of this paper is to demonstrate the trade-off between quality of solutions and computational cost. We show empirically that evolving controllers using the proposed algorithm incurs significantly less computational cost when compared to a self-adaptive weighted sum EMO algorithm, a self-adaptive single-objective evolutionary algorithm (EA) and a hand-tuned Pareto EMO algorithm. The main contribution of the self-adaptive Pareto EMO approach is its ability to produce sufficiently good controllers with different locomotion capabilities in a single run, thereby reducing the evolutionary computational cost and allowing the designer to explore the space of good solutions simultaneously. Our results also show that self-adaptation was found to be highly beneficial in reducing redundancy when compared against the other algorithms. Moreover, it was also shown that genetic diversity was being maintained naturally by virtue of the system's inherent multi-objectivity.
    Matched MeSH terms: Biological Evolution*
  2. Fulltext Dragonfly Algorithm and Its Hybrids: A Survey on Performance, Objectives and Applications
    Emambocus BAS, Jasser MB, Mustapha A, Amphawan A
    Sensors (Basel), 2021 Nov 13;21(22).
    PMID: 34833621 DOI: 10.3390/s21227542
    Swarm intelligence is a discipline which makes use of a number of agents for solving optimization problems by producing low cost, fast and robust solutions. The dragonfly algorithm (DA), a recently proposed swarm intelligence algorithm, is inspired by the dynamic and static swarming behaviors of dragonflies, and it has been found to have a higher performance in comparison to other swarm intelligence and evolutionary algorithms in numerous applications. There are only a few surveys about the dragonfly algorithm, and we have found that they are limited in certain aspects. Hence, in this paper, we present a more comprehensive survey about DA, its applications in various domains, and its performance as compared to other swarm intelligence algorithms. We also analyze the hybrids of DA, the methods they employ to enhance the original DA, their performance as compared to the original DA, and their limitations. Moreover, we categorize the hybrids of DA according to the type of problem that they have been applied to, their objectives, and the methods that they utilize.
    Matched MeSH terms: Biological Evolution
  3. Fulltext Advances on bank erosion studies: a review
    Abdul-Kadir, M.A., Ariffin, J.
    ASM Science Journal, 2012;6(2):128-137.
    MyJurnal
    This paper reviews the advances made on studies related to bank erosion. Bank erosion has been an area of interest by researchers in geological, geotechnical, hydraulic, hydrology and river engineering disciplines. With anticipated global challenges from climate change impacts, bank erosion studies could support challenges faced in ensuring sustainable environmental management. The evolution in the theoretical and laboratory findings have led to the advances in bank erosion and contributed to new knowledge in the said field. This review summarises the findings of previous investigators including measurements approach and prediction of rates of bank erosion through the use of physical models and numerical approach.
    Matched MeSH terms: Biological Evolution
  4. Fulltext An evolutionary firefly algorithm for the estimation of nonlinear biological model parameters
    Abdullah A, Deris S, Anwar S, Arjunan SN
    PLoS One, 2013;8(3):e56310.
    PMID: 23469172 DOI: 10.1371/journal.pone.0056310
    The development of accurate computational models of biological processes is fundamental to computational systems biology. These models are usually represented by mathematical expressions that rely heavily on the system parameters. The measurement of these parameters is often difficult. Therefore, they are commonly estimated by fitting the predicted model to the experimental data using optimization methods. The complexity and nonlinearity of the biological processes pose a significant challenge, however, to the development of accurate and fast optimization methods. We introduce a new hybrid optimization method incorporating the Firefly Algorithm and the evolutionary operation of the Differential Evolution method. The proposed method improves solutions by neighbourhood search using evolutionary procedures. Testing our method on models for the arginine catabolism and the negative feedback loop of the p53 signalling pathway, we found that it estimated the parameters with high accuracy and within a reasonable computation time compared to well-known approaches, including Particle Swarm Optimization, Nelder-Mead, and Firefly Algorithm. We have also verified the reliability of the parameters estimated by the method using an a posteriori practical identifiability test.
    Matched MeSH terms: Biological Evolution*
  5. Fulltext Disappearance of Imported Cases of Omicron Lineage BA.2.40 in West Kalimantan, Indonesia
    Liana DF, Novianry V, Andriani A, Mahyarudin M, Astuti P
    Iran J Med Sci, 2024 Mar;49(3):176-185.
    PMID: 38584647 DOI: 10.30476/ijms.2023.97513.2935
    BACKGROUND: The World Health Organization has declared Omicron as the fifth variant of concern with more than 50 mutations, particularly in the spike protein. Given increased viral infectivity due to mutations, worldwide genomic surveillance and detection of severe acute respiratory syndrome 2 (SARS-CoV-2) is essential. The present study aimed to track Omicron lineage BA.2.40 in West Kalimantan, Indonesia.

    METHODS: In May-August 2022, nasopharyngeal swab samples (n=3,642) were collected from international travelers to West Kalimantan (active surveillance), and patients hospitalized due to SARS-CoV-2 infection (baseline surveillance). The samples were tested for Omicron lineages based on ORF1ab, N, and HV69-70del genes, followed by whole-genome sequencing. The sequences were then identified using two genomic databases, aligned against the reference genome (Wuhan/Hu-1/2019), and then compared with BA.2.40 lineage detected across the world. Phylogenetic analysis between the samples and other SARS-CoV-2 isolates was performed using molecular evolutionary genetics analysis software.

    RESULTS: Based on the genomic databases, 10 isolates were identified as BA.2.40. All samples tested positive for the ORF1ab and N genes, but negative for the HV69-70del gene, which is a marker to detect the Omicron variant. Phylogenetic analysis showed the isolates were closely related to an isolate from Malaysia, an area dominated by BA.2.40.

    CONCLUSION: Omicron lineage BA.2.40 has no HV69-70 deletion in the spike protein, a marker used to screen for the Omicron variant. BA.2.40 showed a high similarity to an isolate from Malaysia and was detected only during certain periods, indicating the effect of internationally imported cases.

    Matched MeSH terms: Biological Evolution
  6. Evolutionary origin of Ceratonova shasta and phylogeny of the marine myxosporean lineage
    Fiala I, Hlavničková M, Kodádková A, Freeman MA, Bartošová-Sojková P, Atkinson SD
    Mol Phylogenet Evol, 2015 May;86:75-89.
    PMID: 25797924 DOI: 10.1016/j.ympev.2015.03.004
    In order to clarify the phylogenetic relationships among the main marine myxosporean clades including newly established Ceratonova clade and scrutinizing their evolutionary origins, we performed large-scale phylogenetic analysis of all myxosporean species from the marine myxosporean lineage based on three gene analyses and statistical topology tests. Furthermore, we obtained new molecular data for Ceratonova shasta, C. gasterostea, eight Ceratomyxa species and one Myxodavisia species. We described five new species: Ceratomyxa ayami n. sp., C. leatherjacketi n. sp., C. synaphobranchi n. sp., C. verudaensis n. sp. and Myxodavisia bulani n. sp.; two of these formed a new, basal Ceratomyxa subclade. We identified that the Ceratomyxa clade is basal to all other marine myxosporean lineages, and Kudoa with Enteromyxum are the most recently branching clades. Topologies were least stable at the nodes connecting the marine urinary clade, the marine gall bladder clade and the Ceratonova clade. Bayesian inference analysis of SSU rDNA and the statistical tree topology tests suggested that Ceratonova is closely related to the Enteromyxum and Kudoa clades, which represent a large group of histozoic species. A close relationship between Ceratomyxa and Ceratonova was not supported, despite their similar myxospore morphologies. Overall, the site of sporulation in the vertebrate host is a more accurate predictor of phylogenetic relationships than the morphology of the myxospore.
    Matched MeSH terms: Biological Evolution*
  7. Crocodylian conservation and evolution insights from an anatomical and histological examination of phalli from male false gharial (Tomistoma schlegelii)
    Moore BC, Fitri WN, Augustine L
    Anat Histol Embryol, 2020 May;49(3):390-401.
    PMID: 32154618 DOI: 10.1111/ahe.12542
    As wild population threats for the endangered false gharial (Tomistoma schlegelii) persist, conservation breeding programs, including developing semen collection techniques for subsequent artificial insemination, are becoming important species conservation measures. Developing reproductive biology understanding of a species is important to developing best practices and hopefully maximizing reproductive successes. However, information on crocodylians functional copulatory anatomy in general is lacking. To that end, zoological facilities and conservation centres have the exceptional opportunity to contribute new understandings that may not otherwise be attainable regarding crocodylian reproductive anatomy, particularly during routine physical examinations or post-mortem necropsies. Therefore, to better understand T. schlegelii reproductive biology, to contribute knowledge in support of zoo breeding conservation efforts and to contribute to what is known overall about crocodylian reproduction, we investigated phallic anatomy of adult male Tomistoma from two zoological populations, the St. Louis Zoo, USA and Sungai Dusun Wildlife Reserve, Peninsular Malaysia. Here, we present the gross anatomical features and histological analysis of underlying tissue-level details in pursuit of a better understanding of copulatory function and associated gamete transfer mechanisms. While much of the overall Tomistoma phallic morphology and inferred function corresponds to that of other crocodylian species and speaks to conserved aspects of functional anatomy across taxa, species-specific aspects of glans and glans tip morphology are also identified. These novelties are discussed in a general function and overall broader evolutionary contexts.
    Matched MeSH terms: Biological Evolution
  8. MitoPhAST, a new automated mitogenomic phylogeny tool in the post-genomic era with a case study of 89 decapod mitogenomes including eight new freshwater crayfish mitogenomes
    Tan MH, Gan HM, Schultz MB, Austin CM
    Mol Phylogenet Evol, 2015 Apr;85:180-8.
    PMID: 25721538 DOI: 10.1016/j.ympev.2015.02.009
    The increased rate at which complete mitogenomes are being sequenced and their increasing use for phylogenetic studies have resulted in a bioinformatic bottleneck in preparing and utilising such data for phylogenetic analysis. Hence, we present MitoPhAST, an automated tool that (1) identifies annotated protein-coding gene features and generates a standardised, concatenated and partitioned amino acid alignment directly from complete/partial GenBank/EMBL-format mitogenome flat files, (2) generates a maximum likelihood phylogenetic tree using optimised protein models and (3) reports various mitochondrial genes and sequence information in a table format. To demonstrate the capacity of MitoPhAST in handling a large dataset, we used 81 publicly available decapod mitogenomes, together with eight new complete mitogenomes of Australian freshwater crayfishes, including the first for the genus Gramastacus, to undertake an updated test of the monophyly of the major groups of the order Decapoda and their phylogenetic relationships. The recovered phylogenetic trees using both Bayesian and ML methods support the results of studies using fragments of mtDNA and nuclear markers and other smaller-scale studies using whole mitogenomes. In comparison to the fragment-based phylogenies, nodal support values are generally higher despite reduced taxon sampling suggesting there is value in utilising more fully mitogenomic data. Additionally, the simple table output from MitoPhAST provides an efficient summary and statistical overview of the mitogenomes under study at the gene level, allowing the identification of missing or duplicated genes and gene rearrangements. The finding of new mtDNA gene rearrangements in several genera of Australian freshwater crayfishes indicates that this group has undergone an unusually high rate of evolutionary change for this organelle compared to other major families of decapod crustaceans. As a result, freshwater crayfishes are likely to be a useful model for studies designed to understand the evolution of mtDNA rearrangements. We anticipate that our bioinformatics pipeline will substantially help mitogenome-based studies increase the speed, accuracy and efficiency of phylogenetic studies utilising mitogenome information. MitoPhAST is available for download at https://github.com/mht85/MitoPhAST.
    Matched MeSH terms: Biological Evolution
  9. Fulltext Absence of evidence is not evidence of absence: Nanopore sequencing and complete assembly of the European lobster (Homarus gammarus) mitogenome uncovers the missing nad2 and a new major gene cluster duplication
    Gan HM, Grandjean F, Jenkins TL, Austin CM
    BMC Genomics, 2019 May 03;20(1):335.
    PMID: 31053062 DOI: 10.1186/s12864-019-5704-3
    BACKGROUND: The recently published complete mitogenome of the European lobster (Homarus gammarus) that was generated using long-range PCR exhibits unusual gene composition (missing nad2) and gene rearrangements among decapod crustaceans with strong implications in crustacean phylogenetics. Such atypical mitochondrial features will benefit greatly from validation with emerging long read sequencing technologies such as Oxford Nanopore that can more accurately identify structural variation.

    RESULTS: We re-sequenced the H. gammarus mitogenome on an Oxford Nanopore Minion flowcell and performed a long-read only assembly, generating a complete mitogenome assembly for H. gammarus. In contrast to previous reporting, we found an intact mitochondrial nad2 gene in the H. gammarus mitogenome and showed that its gene organization is broadly similar to that of the American lobster (H. americanus) except for the presence of a large tandemly duplicated region with evidence of pseudogenization in one of each duplicated protein-coding genes.

    CONCLUSIONS: Using the European lobster as an example, we demonstrate the value of Oxford Nanopore long read technology in resolving problematic mitogenome assemblies. The increasing accessibility of Oxford Nanopore technology will make it an attractive and useful tool for evolutionary biologists to verify new and existing unusual mitochondrial gene rearrangements recovered using first and second generation sequencing technologies, particularly those used to make phylogenetic inferences of evolutionary scenarios.

    Matched MeSH terms: Biological Evolution*
  10. Fulltext Applying an evolutionary mismatch framework to understand disease susceptibility
    Lea AJ, Clark AG, Dahl AW, Devinsky O, Garcia AR, Golden CD, et al.
    PLoS Biol, 2023 Sep;21(9):e3002311.
    PMID: 37695771 DOI: 10.1371/journal.pbio.3002311
    Noncommunicable diseases (NCDs) are on the rise worldwide. Obesity, cardiovascular disease, and type 2 diabetes are among a long list of "lifestyle" diseases that were rare throughout human history but are now common. The evolutionary mismatch hypothesis posits that humans evolved in environments that radically differ from those we currently experience; consequently, traits that were once advantageous may now be "mismatched" and disease causing. At the genetic level, this hypothesis predicts that loci with a history of selection will exhibit "genotype by environment" (GxE) interactions, with different health effects in "ancestral" versus "modern" environments. To identify such loci, we advocate for combining genomic tools in partnership with subsistence-level groups experiencing rapid lifestyle change. In these populations, comparisons of individuals falling on opposite extremes of the "matched" to "mismatched" spectrum are uniquely possible. More broadly, the work we propose will inform our understanding of environmental and genetic risk factors for NCDs across diverse ancestries and cultures.
    Matched MeSH terms: Biological Evolution
  11. Fulltext Recommendations on otorhinolaryngology procedural-based services during covid-19 pandemic
    Sobani Din, Fadzilah Ismail, Teh, Carren Sui Lin, Raudha Ezaty Ruslan, Shiraz Qamil Muhammad Abdul Kadar, Azuin Izzati Arshad
    Borneo Journal of Medical Sciences, 2021;15(1):67-71.
    MyJurnal
    The current COVID-19 pandemic has forced many clinical disciplines to evolve to function safely and still provide the necessary care. Otorhinolaryngology (ORL) is a field that has been greatly affected by this highly transmissible viral pathogen. Aerosolizing procedures, proximity examination and other common procedures must be revamped to suit current time. The usual norm ORL procedures need also be altered to incorporate safeguards to protect both patient and healthcare workers. This recommendation for current practices aims to give a practical approach to modify current practices to maintain safety during the pandemic. These recommendations are the consensus amongst ORL practitioners in Hospital Sungai Buloh which is the designated COVID-19 centre for Malaysia’s central region and is currently being practised.
    Matched MeSH terms: Biological Evolution
  12. 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
  13. 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
  14. Comparative morphology of spermatozoa and reproductive systems of zorapteran species from different world regions (Insecta, Zoraptera)
    Dallai R, Gottardo M, Mercati D, Machida R, Mashimo Y, Matsumura Y, et al.
    Arthropod Struct Dev, 2014 Jul;43(4):371-83.
    PMID: 24657729 DOI: 10.1016/j.asd.2014.03.001
    The male and female reproductive apparatus of Zorotypus magnicaudelli (Malaysia), Zorotypus huxleyi (Ecuador) and Zorotypus weidneri (Brazil) were examined and documented in detail. The genital apparatus and sperm of the three species show only minor differences. The testes are larger in Z. magnicaudelli. Z. huxleyi lacks the helical appendage in the accessory glands. A long cuticular flagellum is present in Z. magnicaudelli and in the previously studied Zorotypus caudelli like in several other species, whereas it is absent in Z. weidneri, Z. huxleyi, Zorotypus hubbardi, Zorotypus impolitus and Zorotypus guineensis. Characteristic features of the very similar sperm are the presence of: a) two dense arches above the axoneme; b) a 9 + 9+2 axoneme with detached subtubules A and B of doublets 1 and 6; c) the axonemal end degenerating with enlarging accessory tubules; d) accessory tubules with 17 protofilaments; e) three accessory bodies beneath the axoneme; and f) two mitochondrial derivatives of equal shape. The first characteristic (a) is unknown outside of Zoraptera and possibly autapomorphic. The sperm structure differs distinctly in Z. impolitus and Z. hubbardi, which produce giant sperm and possess a huge spermatheca. The presence of the same sperm type in species either provided with a sclerotized coiled flagellum in males or lacking this structure indicates that a different organization of the genital apparatus does not necessarily affect the sperm structure. The flagellum and its pouch has probably evolved within Zoraptera, but it cannot be excluded that it is a groundplan feature and was reduced several times. The fossil evidence and our findings suggest that distinct modifications in the genital apparatus occurred before the fragmentation of the Gondwanan landmass in the middle Cretaceous.
    Matched MeSH terms: Biological Evolution*
  15. Fulltext Signature selection forces and evolutionary divergence of immune-survival genes compared between two important shrimp species
    Soo TCC, Bhassu S
    PLoS One, 2023;18(1):e0280250.
    PMID: 36634148 DOI: 10.1371/journal.pone.0280250
    In recent years, shrimp aquaculture industry had grown significantly to become the major source of global shrimp production. Despite that, shrimp aquaculture production was impeded by various shrimp diseases over the past decades. Interestingly, different shrimp species demonstrated variable levels of immune strength and survival (immune-survival) ability towards different diseases, especially the much stronger immune-survival ability shown by the ancient shrimp species, Macrobrachium rosenbergii compared to other shrimp species. In this study, two important shrimp species, M. rosenbergii and Penaeus monodon (disease tolerant strain) (uninfected control and VpAHPND-infected) were compared to uncover the potential underlying genetic factors. The shrimp species were sampled, followed by RNA extraction and cDNA conversion. Five important immune-survival genes (C-type Lectin, HMGB, STAT, ALF3, and ATPase 8/6) were selected for PCR, sequencing, and subsequent genetics analysis. The overall genetic analyses conducted, including Analysis of Molecular Variance (AMOVA) and population differentiation, showed significant genetic differentiation (p<0.05) between different genes of M. rosenbergii and P. monodon. There was greater genetic divergence identified between HMGB subgroups of P. monodon (uninfected control and VpAHPND-infected) compared to other genes. Besides that, based on neutrality tests conducted, purifying selection was determined to be the main evolutionary driving force of M. rosenbergii and P. monodon with stronger purifying selection exhibited in M. rosenbergii genes. Potential balancing selection was identified for VpAHPND-infected HMGB subgroup whereas directional selection was detected for HMGB (both species) and ATPase 8/6 (only P. monodon) genes. The divergence times between M. rosenbergii and P. monodon genes were estimated through Bayesian molecular clock analysis, which were 438.6 mya (C-type Lectin), 1885.4 mya (HMGB), 432.6 mya (STAT), 448.1 mya (ALF3), and 426.4 mya (ATPase 8/6) respectively. In conclusion, important selection forces and evolutionary divergence information of immune-survival genes between M. rosenbergii and P. monodon were successfully identified.
    Matched MeSH terms: Biological Evolution*
  16. Phylogeny of the most species-rich freshwater bivalve family (Bivalvia: Unionida: Unionidae): Defining modern subfamilies and tribes
    Lopes-Lima M, Froufe E, Do VT, Ghamizi M, Mock KE, Kebapçı Ü, et al.
    Mol Phylogenet Evol, 2017 01;106:174-191.
    PMID: 27621130 DOI: 10.1016/j.ympev.2016.08.021
    Freshwater mussels of the order Unionida are key elements of freshwater habitats and are responsible for important ecological functions and services. Unfortunately, these bivalves are among the most threatened freshwater taxa in the world. However, conservation planning and management are hindered by taxonomic problems and a lack of detailed ecological data. This highlights the urgent need for advances in the areas of systematics and evolutionary relationships within the Unionida. This study presents the most comprehensive phylogeny to date of the larger Unionida family, i.e., the Unionidae. The phylogeny is based on a combined dataset of 1032bp (COI+28S) of 70 species in 46 genera, with 7 of this genera being sequenced for the first time. The resulting phylogeny divided the Unionidae into 6 supported subfamilies and 18 tribes, three of which are here named for the first time (i.e., Chamberlainiini nomen novum, Cristariini nomen novum and Lanceolariini nomen novum). Molecular analyses were complemented by investigations of selected morphological, anatomical and behavioral characters used in traditional phylogenetic studies. No single morphological, anatomical or behavioral character was diagnostic at the subfamily level and few were useful at the tribe level. However, within subfamilies, many tribes can be recognized based on a subset of these characters. The geographical distribution of each of the subfamilies and tribes is also presented. The present study provides important advances in the systematics of these extraordinary taxa with implications for future ecological and conservation studies.
    Matched MeSH terms: Biological Evolution
  17. Fulltext Divergence of iron metabolism in wild Malaysian yeast
    Lee HN, Mostovoy Y, Hsu TY, Chang AH, Brem RB
    G3 (Bethesda), 2013 Dec 09;3(12):2187-94.
    PMID: 24142925 DOI: 10.1534/g3.113.008011
    Comparative genomic studies have reported widespread variation in levels of gene expression within and between species. Using these data to infer organism-level trait divergence has proven to be a key challenge in the field. We have used a wild Malaysian population of S. cerevisiae as a test bed in the search to predict and validate trait differences based on observations of regulatory variation. Malaysian yeast, when cultured in standard medium, activated regulatory programs that protect cells from the toxic effects of high iron. Malaysian yeast also showed a hyperactive regulatory response during culture in the presence of excess iron and had a unique growth defect in conditions of high iron. Molecular validation experiments pinpointed the iron metabolism factors AFT1, CCC1, and YAP5 as contributors to these molecular and cellular phenotypes; in genome-scale sequence analyses, a suite of iron toxicity response genes showed evidence for rapid protein evolution in Malaysian yeast. Our findings support a model in which iron metabolism has diverged in Malaysian yeast as a consequence of a change in selective pressure, with Malaysian alleles shifting the dynamic range of iron response to low-iron concentrations and weakening resistance to extreme iron toxicity. By dissecting the iron scarcity specialist behavior of Malaysian yeast, our work highlights the power of expression divergence as a signpost for biologically and evolutionarily relevant variation at the organismal level. Interpreting the phenotypic relevance of gene expression variation is one of the primary challenges of modern genomics.
    Matched MeSH terms: Biological Evolution
  18. Deep biogeographic barriers explain divergent global vertebrate communities
    Williams PJ, Zipkin EF, Brodie JF
    Nat Commun, 2024 Mar 28;15(1):2457.
    PMID: 38548741 DOI: 10.1038/s41467-024-46757-z
    Biogeographic history can lead to variation in biodiversity across regions, but it remains unclear how the degree of biogeographic isolation among communities may lead to differences in biodiversity. Biogeographic analyses generally treat regions as discrete units, but species assemblages differ in how much biogeographic history they share, just as species differ in how much evolutionary history they share. Here, we use a continuous measure of biogeographic distance, phylobetadiversity, to analyze the influence of biogeographic isolation on the taxonomic and functional diversity of global mammal and bird assemblages. On average, biodiversity is better predicted by environment than by isolation, especially for birds. However, mammals in deeply isolated regions are strongly influenced by isolation; mammal assemblages in Australia and Madagascar, for example, are much less diverse than predicted by environment alone and contain unique combinations of functional traits compared to other regions. Neotropical bat assemblages are far more functionally diverse than Paleotropical assemblages, reflecting the different trajectories of bat communities that have developed in isolation over tens of millions of years. Our results elucidate how long-lasting biogeographic barriers can lead to divergent diversity patterns, against the backdrop of environmental determinism that predominantly structures diversity across most of the world.
    Matched MeSH terms: Biological Evolution
  19. Craniodental affinities of Southeast Asia's "negritos" and the concordance with their genetic affinities
    Bulbeck D
    Hum Biol, 2013 Feb-Jun;85(1-3):95-133.
    PMID: 24297222
    Genetic research into Southeast Asia's "negritos" has revealed their deep-rooted ancestry, with time depth comparable to that of Southwest Pacific populations. This finding is often interpreted as evidence that negritos, in contrast to other Southeast Asians, can trace much of their ancestry directly back to the early dispersal of Homo sapiens in the order of 70 kya from Africa to Pleistocene New Guinea and Australia. One view on negritos is to lump them and Southwest Pacific peoples into an "Australoid" race whose geographic distribution had included Southeast Asia prior to the Neolithic incursion of "Mongoloid" farmers. Studies into Semang osteology have revealed some hints of Southwest Pacific affinities in cranial shape, dental morphology, and dental metrical "shape." On the other hand, the Andamanese have been shown to resemble Africans in their craniometrics and South Asians in their dental morphology, while Philippine negritos resemble Mongoloid Southeast Asians in these respects and also in their dental metrics. This study expands the scope of negrito cranial comparisons by including Melayu Malays and additional coverage of South Asians. It highlights the distinction between the Mongoloid-like Philippine negritos and the Andamanese and Semang (and Senoi of Malaya) with their non-Mongoloid associations. It proposes that the early/mid-Holocene dispersal of the B4a1a mitochondrial DNA clade across Borneo, the Philippines, and Taiwan may be important for understanding the distinction between Philippine and other negritos.
    Matched MeSH terms: Biological Evolution*
  20. Fulltext Data set of phylogenetic analysis inferred based on the complete genomes of the family Nodaviridae
    Low CF, Bunawan H
    Data Brief, 2016 Sep;8:1454-61.
    PMID: 27617282 DOI: 10.1016/j.dib.2016.08.025
    In this article, nine complete genomes of viruses from the genus Alphanodavirus and Betanodavirus (Family Nodaviridae) were comparatively analyzed and the data of their evolutionary origins and relatedness are reported. The nucleotide sequence alignment of the complete genomes from all species and their deduced evolutionary relationships are presented. High sequence similarity within the genus Betanodavirus compared to the genus Alphanodavirus was revealed in multiple sequence alignment of the Nodaviridae genomes. The amino acid sequence similarity for both RNA1 and RNA2 ORF is more conserved in Betanodavirus, compared to Alphanodavirus. The conserved and variable regions within the virus genome that were defined based on the multiple sequence alignments are presented in this dataset.
    Matched MeSH terms: Biological Evolution
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