Displaying publications 1 - 20 of 171 in total

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  1. Characterisation of the mitochondrial genome and phylogenetic analysis of Toxocara apodemi (Nematoda: Ascarididae)
    Gao Y, Hu Y, Xu S, Liang H, Lin H, Yin TH, et al.
    J Helminthol, 2024 Apr 15;98:e33.
    PMID: 38618902 DOI: 10.1017/S0022149X24000221
    We first sequenced and characterised the complete mitochondrial genome of Toxocara apodeme, then studied the evolutionary relationship of the species within Toxocaridae. The complete mitochondrial genome was amplified using PCR with 14 specific primers. The mitogenome length was 14303 bp in size, including 12 PCGs (encoding 3,423 amino acids), 22 tRNAs, 2 rRNAs, and 2 NCRs, with 68.38% A+T contents. The mt genomes of T. apodemi had relatively compact structures with 11 intergenic spacers and 5 overlaps. Comparative analyses of the nucleotide sequences of complete mt genomes showed that T. apodemi had higher identities with T. canis than other congeners. A sliding window analysis of 12 PCGs among 5 Toxocara species indicated that nad4 had the highest sequence divergence, and cox1 was the least variable gene. Relative synonymous codon usage showed that UUG, ACU, CCU, CGU, and UCU most frequently occurred in the complete genomes of T. apodemi. The Ka/Ks ratio showed that all Toxocara mt genes were subject to purification selection. The largest genetic distance between T. apodemi and the other 4 congeneric species was found in nad2, and the smallest was found in cox2. Phylogenetic analyses based on the concatenated amino acid sequences of 12 PCGs demonstrated that T. apodemi formed a distinct branch and was always a sister taxon to other congeneric species. The present study determined the complete mt genome sequences of T. apodemi, which provide novel genetic markers for further studies of the taxonomy, population genetics, and systematics of the Toxocaridae nematodes.
    Matched MeSH terms: Biological Evolution
  2. 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
  3. 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
  4. Menno Schilthuizen
    Schilthuizen M
    Curr Biol, 2024 Jan 22;34(2):R40-R41.
    PMID: 38262351 DOI: 10.1016/j.cub.2023.11.040
    Interview with Menno Schilthuizen, who studies the evolutionary ecology of morphological diversification in related species at the Naturalis Biodiversity Center and Leiden University.
    Matched MeSH terms: Biological Evolution*
  5. Fulltext The vulnerability assessment and obstacle factor analysis of urban agglomeration along the Yellow River in China from the perspective of production-living-ecological space
    Yang L, Meng H, Wang J, Wu Y, Zhao Z
    PLoS One, 2024;19(4):e0299729.
    PMID: 38578727 DOI: 10.1371/journal.pone.0299729
    Urban agglomerations are sophisticated territorial systems at the mature stage of city development that are concentrated areas of production and economic activity. Therefore, the study of vulnerability from the perspective of production-living-ecological space is crucial for the sustainable development of the Yellow River Basin and global urban agglomerations. The relationship between productivity, living conditions, and ecological spatial quality is fully considered in this research. By constructing a vulnerability evaluation index system based on the perspectives of production, ecology, and living space, and adopting the entropy value method, comprehensive vulnerability index model, and obstacle factor diagnostic model, the study comprehensively assesses the vulnerability of the urban agglomerations along the Yellow River from 2001 to 2020. The results reveal that the spatial differentiation characteristics of urban agglomeration vulnerability are significant. A clear three-level gradient distribution of high, medium, and low degrees is seen in the overall vulnerability; these correspond to the lower, middle, and upper reaches of the Yellow River Basin, respectively. The percentage of cities with higher and moderate levels of vulnerability did not vary from 2001 to 2020, while the percentage of cities with high levels of vulnerability did. The four dimensions of economic development, leisure and tourism, resource availability, and ecological pressure are the primary determinants of the urban agglomeration's vulnerability along the Yellow River. And the vulnerability factors of various urban agglomerations showed a significant evolutionary trend; the obstacle degree values have declined, and the importance of tourism and leisure functions has gradually increased. Based on the above conclusions, we propose several suggestions to enhance the quality of urban development along the Yellow River urban agglomeration. Including formulating a three-level development strategy, paying attention to ecological and environmental protection, developing domestic and foreign trade, and properly planning and managing the tourism industry.
    Matched MeSH terms: Biological Evolution
  6. Evolutionarily labile dispersal behavior and discontinuous habitats enhance population differentiation in island versus continentally distributed swallows
    Broyles GG, Myers BM, Friedman NR, Gawin DF, Mohd-Taib FS, Sahlan PGM, et al.
    Evolution, 2023 Dec 02;77(12):2656-2671.
    PMID: 37801637 DOI: 10.1093/evolut/qpad179
    The causes of population divergence in vagile groups remain a paradox in evolutionary biology: dispersive species should be able to colonize new areas, a prerequisite for allopatric speciation, but dispersal also facilitates gene flow, which erodes population differentiation. Strong dispersal ability has been suggested to enhance divergence in patchy habitats and inhibit divergence in continuous landscapes, but empirical support for this hypothesis is lacking. Here we compared patterns of population divergence in a dispersive clade of swallows distributed across both patchy and continuous habitats. The Pacific Swallow (Hirundo tahitica) has an insular distribution throughout Southeast Asia and the Pacific, while its sister species, the Welcome Swallow (H. neoxena), has a continental distribution in Australia. We used whole-genome data to demonstrate strong genetic structure and limited introgression among insular populations, but not among continental populations. Demographic models show that historic changes in habitat connectivity have contributed to population structure within the clade. Swallows appear to exhibit evolutionarily labile dispersal behavior in which they reduce dispersal propensity after island colonization despite retaining strong flight ability. Our data support the hypothesis that fragmented habitats enhance population differentiation in vagile groups, and suggest that labile dispersal behavior is a key mechanism underlying this pattern.
    Matched MeSH terms: Biological Evolution
  7. 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
  8. Fulltext Historic Sampling of a Vanishing Beast: Population Structure and Diversity in the Black Rhinoceros
    Sánchez-Barreiro F, De Cahsan B, Westbury MV, Sun X, Margaryan A, Fontsere C, et al.
    Mol Biol Evol, 2023 Sep 01;40(9).
    PMID: 37561011 DOI: 10.1093/molbev/msad180
    The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north-south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity.
    Matched MeSH terms: Biological Evolution*
  9. Fulltext Marine-montane transitions coupled with gill and genetic convergence in extant crustacean
    Liu H, Zheng Y, Zhu B, Tong Y, Xin W, Yang H, et al.
    Sci Adv, 2023 Jun 23;9(25):eadg4011.
    PMID: 37352347 DOI: 10.1126/sciadv.adg4011
    Marine-terrestrial transition represents an important aspect of organismal evolution that requires numerous morphological and genetic innovations and has been hypothesized to be caused by geological changes. We used talitrid crustaceans with marine-coastal-montane extant species at a global scale to investigate the marine origination and terrestrial adaptation. Using genomic data, we demonstrated that marine ancestors repeatedly colonized montane terrestrial habitats during the Oligocene to Miocene. Biological transitions were well correlated with plate collisions or volcanic island formation, and top-down cladogenesis was observed on the basis of a positive relationship between ancestral habitat elevation and divergence time for montane lineages. We detected convergent variations of convoluted gills and convergent evolution of SMC3 associated with montane transitions. Moreover, using CRISPR-Cas9 mutagenesis, we proposed that SMC3 potentially regulates the development of exites, such as talitrid gills. Our results provide a living model for understanding biological innovations and related genetic regulatory mechanisms associated with marine-terrestrial transitions.
    Matched MeSH terms: Biological Evolution*
  10. Dissecting the Biology of Rafflesia Species: Current Progress and Future Directions Made Possible with High-Throughput Sequencing Data
    Mursyidah AK, Hafizzudin-Fedeli M, Nor Muhammad NA, Latiff A, Firdaus-Raih M, Wan KL
    Plant Cell Physiol, 2023 Apr 17;64(4):368-377.
    PMID: 36611267 DOI: 10.1093/pcp/pcad004
    The angiosperm Rafflesia exhibits a unique biology, including a growth strategy that involves endophytic parasitism of a specific host, with only the gigantic flower externally visible. The Rafflesia possesses many unique evolutionary, developmental and morphological features that are rooted in yet-to-be-explained physiological processes. Although studies on the molecular biology of Rafflesia are limited by sampling difficulties due to its rarity in the wild and the short life span of its flower, current advances in high-throughput sequencing technology have allowed for the genome- and transcriptome-level dissection of the molecular mechanisms behind the unique characteristics of this parasitic plant. In this review, we summarize major findings on the cryptic biology of Rafflesia and provide insights into future research directions. The wealth of data obtained can improve our understanding of Rafflesia species and contribute toward the conservation strategy of this endangered plant.
    Matched MeSH terms: Biological Evolution*
  11. Large haploblocks underlie rapid adaptation in the invasive weed Ambrosia artemisiifolia
    Battlay P, Wilson J, Bieker VC, Lee C, Prapas D, Petersen B, et al.
    Nat Commun, 2023 Mar 27;14(1):1717.
    PMID: 36973251 DOI: 10.1038/s41467-023-37303-4
    Adaptation is the central feature and leading explanation for the evolutionary diversification of life. Adaptation is also notoriously difficult to study in nature, owing to its complexity and logistically prohibitive timescale. Here, we leverage extensive contemporary and historical collections of Ambrosia artemisiifolia-an aggressively invasive weed and primary cause of pollen-induced hayfever-to track the phenotypic and genetic causes of recent local adaptation across its native and invasive ranges in North America and Europe, respectively. Large haploblocks-indicative of chromosomal inversions-contain a disproportionate share (26%) of genomic regions conferring parallel adaptation to local climates between ranges, are associated with rapidly adapting traits, and exhibit dramatic frequency shifts over space and time. These results highlight the importance of large-effect standing variants in rapid adaptation, which have been critical to A. artemisiifolia's global spread across vast climatic gradients.
    Matched MeSH terms: Biological Evolution
  12. Fulltext Female cooperative labour networks in hunter-gatherers and horticulturalists
    Kraft TS, Cummings DK, Venkataraman VV, Alami S, Beheim B, Hooper P, et al.
    Philos Trans R Soc Lond B Biol Sci, 2023 Jan 16;378(1868):20210431.
    PMID: 36440571 DOI: 10.1098/rstb.2021.0431
    Cooperation in food acquisition is a hallmark of the human species. Given that costs and benefits of cooperation vary among production regimes and work activities, the transition from hunting-and-gathering to agriculture is likely to have reshaped the structure of cooperative subsistence networks. Hunter-gatherers often forage in groups and are generally more interdependent and experience higher short-term food acquisition risk than horticulturalists, suggesting that cooperative labour should be more widespread and frequent for hunter-gatherers. Here we compare female cooperative labour networks of Batek hunter-gatherers of Peninsular Malaysia and Tsimane forager-horticulturalists of Bolivia. We find that Batek foraging results in high daily variation in labour partnerships, facilitating frequent cooperation in diffuse networks comprised of kin and non-kin. By contrast, Tsimane horticulture involves more restricted giving and receiving of labour, confined mostly to spouses and primary or distant kin. Tsimane women also interact with few individuals in the context of hunting/fishing activities and forage mainly with spouses and primary kin. These differences give rise to camp- or village-level networks that are more modular (have more substructure when partitioned) among Tsimane horticulturalists. Our findings suggest that subsistence activities shape the formation and extent of female social networks, particularly with respect to connections with other women and non-kin. We discuss the implications of restricted female labour networks in the context of gender relations, power dynamics and the adoption of farming in humans. This article is part of the theme issue 'Cooperation among women: evolutionary and cross-cultural perspectives'.
    Matched MeSH terms: Biological Evolution
  13. 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*
  14. Fulltext Ancient proteins resolve controversy over the identity of Genyornis eggshell
    Demarchi B, Stiller J, Grealy A, Mackie M, Deng Y, Gilbert T, et al.
    Proc Natl Acad Sci U S A, 2022 Oct 25;119(43):e2109326119.
    PMID: 35609205 DOI: 10.1073/pnas.2109326119
    The realization that ancient biomolecules are preserved in "fossil" samples has revolutionized archaeological science. Protein sequences survive longer than DNA, but their phylogenetic resolution is inferior; therefore, careful assessment of the research questions is required. Here, we show the potential of ancient proteins preserved in Pleistocene eggshell in addressing a longstanding controversy in human and animal evolution: the identity of the extinct bird that laid large eggs which were exploited by Australia's indigenous people. The eggs had been originally attributed to the iconic extinct flightless bird Genyornis newtoni (†Dromornithidae, Galloanseres) and were subsequently dated to before 50 ± 5 ka by Miller et al. [Nat. Commun. 7, 10496 (2016)]. This was taken to represent the likely extinction date for this endemic megafaunal species and thus implied a role of humans in its demise. A contrasting hypothesis, according to which the eggs were laid by a large mound-builder megapode (Megapodiidae, Galliformes), would therefore acquit humans of their responsibility in the extinction of Genyornis. Ancient protein sequences were reconstructed and used to assess the evolutionary proximity of the undetermined eggshell to extant birds, rejecting the megapode hypothesis. Authentic ancient DNA could not be confirmed from these highly degraded samples, but morphometric data also support the attribution of the eggshell to Genyornis. When used in triangulation to address well-defined hypotheses, paleoproteomics is a powerful tool for reconstructing the evolutionary history in ancient samples. In addition to the clarification of phylogenetic placement, these data provide a more nuanced understanding of the modes of interactions between humans and their environment.
    Matched MeSH terms: Biological Evolution
  15. 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
  16. Deep-time convergent evolution in animal communication presented by shared adaptations for coping with noise in lizards and other animals
    Ord TJ, Klomp DA, Summers TC, Diesmos A, Ahmad N, Das I
    Ecol Lett, 2021 Sep;24(9):1750-1761.
    PMID: 34196091 DOI: 10.1111/ele.13773
    Convergence in communication appears rare compared with other forms of adaptation. This is puzzling, given communication is acutely dependent on the environment and expected to converge in form when animals communicate in similar habitats. We uncover deep-time convergence in territorial communication between two groups of tropical lizards separated by over 140 million years of evolution: the Southeast Asian Draco and Caribbean Anolis. These groups have repeatedly converged in multiple aspects of display along common environmental gradients. Robot playbacks to free-ranging lizards confirmed that the most prominent convergence in display is adaptive, as it improves signal detection. We then provide evidence from a sample of the literature to further show that convergent adaptation among highly divergent animal groups is almost certainly widespread in nature. Signal evolution is therefore curbed towards the same set of adaptive solutions, especially when animals are challenged with the problem of communicating effectively in noisy environments.
    Matched MeSH terms: Biological Evolution
  17. Fulltext Phylogeography, colouration, and cryptic speciation across the Indo-Pacific in the sea urchin genus Echinothrix
    Coppard SE, Jessop H, Lessios HA
    Sci Rep, 2021 Aug 16;11(1):16568.
    PMID: 34400682 DOI: 10.1038/s41598-021-95872-0
    The sea urchins Echinothrix calamaris and Echinothrix diadema have sympatric distributions throughout the Indo-Pacific. Diverse colour variation is reported in both species. To reconstruct the phylogeny of the genus and assess gene flow across the Indo-Pacific we sequenced mitochondrial 16S rDNA, ATPase-6, and ATPase-8, and nuclear 28S rDNA and the Calpain-7 intron. Our analyses revealed that E. diadema formed a single trans-Indo-Pacific clade, but E. calamaris contained three discrete clades. One clade was endemic to the Red Sea and the Gulf of Oman. A second clade occurred from Malaysia in the West to Moorea in the East. A third clade of E. calamaris was distributed across the entire Indo-Pacific biogeographic region. A fossil calibrated phylogeny revealed that the ancestor of E. diadema diverged from the ancestor of E. calamaris ~ 16.8 million years ago (Ma), and that the ancestor of the trans-Indo-Pacific clade and Red Sea and Gulf of Oman clade split from the western and central Pacific clade ~ 9.8 Ma. Time since divergence and genetic distances suggested species level differentiation among clades of E. calamaris. Colour variation was extensive in E. calamaris, but not clade or locality specific. There was little colour polymorphism in E. diadema.
    Matched MeSH terms: Biological Evolution
  18. 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
  19. Enhancing mitogenomic phylogeny and resolving the relationships of extinct megafaunal placental mammals
    Phillips MJ, Shazwani Zakaria S
    Mol Phylogenet Evol, 2021 05;158:107082.
    PMID: 33482383 DOI: 10.1016/j.ympev.2021.107082
    Mitochondrial genomes provided the first widely used sequences that were sufficiently informative to resolve relationships among animals across a wide taxonomic domain, from within species to between phyla. However, mitogenome studies supported several anomalous relationships and fell partly out of favour as sequencing multiple, independent nuclear loci proved to be highly effective. A tendency to blame mitochondrial DNA (mtDNA) has overshadowed efforts to understand and ameliorate underlying model misspecification. Here we find that influential assessments of the infidelity of mitogenome phylogenies have often been overstated, but nevertheless, substitution saturation and compositional non-stationarity substantially mislead reconstruction. We show that RY coding the mtDNA, excluding protein-coding 3rd codon sites, partitioning models based on amino acid hydrophobicity and enhanced taxon sampling improve the accuracy of mitogenomic phylogeny reconstruction for placental mammals, almost to the level of multi-gene nuclear datasets. Indeed, combined analysis of mtDNA with 3-fold longer nuclear sequence data either maintained or improved upon the nuclear support for all generally accepted clades, even those that mtDNA alone did not favour, thus indicating "hidden support". Confident mtDNA phylogeny reconstruction is especially important for understanding the evolutionary dynamics of mitochondria themselves, and for merging extinct taxa into the tree of life, with ancient DNA often only accessible as mtDNA. Our ancient mtDNA analyses lend confidence to the relationships of three extinct megafaunal taxa: glyptodonts are nested within armadillos, the South American ungulate, Macrauchenia is sister to horses and rhinoceroses, and sabre-toothed and scimitar cats are the monophyletic sister-group of modern cats.
    Matched MeSH terms: Biological Evolution
  20. 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
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