Genomic comparisons confirm Giardia duodenalis sub-assemblage AII as a unique species

Frontiers in Cellular and Infection Microbiology, Journal Year: 2022, Volume and Issue: 12

Published: Oct. 17, 2022

Giardia duodenalis is a parasitic flagellated protozoan which infects wide range of mammalian hosts, including humans, and subdivided into at least eight genetic assemblages commonly thought to represent cryptic species. Molecular studies have shown that G. assemblage A, parasitizes humans animals, contains several phylogenetically distinct groupings known as sub-assemblages. employing poor phylogenetic-resolution markers routinely recover these sub-assemblages, implying they evolutionarily clades possibly species, hypothesis supported by epidemiologic trends. Here, we further tested this using available data from 41 whole genomes characterize sub-assemblages coalescent techniques for statistical estimation species boundaries coupled functional gene content analysis, thereby assessing the stability distinctiveness clades. Our analysis revealed two new sub-assemblage well novel signatures geared toward differential host adaptation population structuring via vertical inheritance rather than recombination or panmixia. We formally propose AII hominis , while preserving name AI. Additionally, our bioinformatic methods broadly address challenges identifying microbial advance understanding emerging disease epidemiology, should be applicable other lower eukaryotic taxa interest. n. sp. Zoobank LSID: urn:lsid: zoobank.org:pub:4298F3E1-E3EF-4977-B9DD-5CC59378C80E.

Language: Английский

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Systematics of the Little Red Tree Frog, Litoria rubella (Anura: Pelodryadidae), with the description of two new species from eastern Australia and arid Western Australia

Zootaxa, Journal Year: 2025, Volume and Issue: 5594(2), P. 269 - 315

Published: Feb. 27, 2025

The Litoria rubella species complex (L. capitula and L. rubella) is distributed across much of continental Australia, southern New Guinea, the Tanimbar Islands Indonesia, in habitats ranging from deserts to tropical forests. We carried out an appraisal molecular genetics, advertisement calls, morphological variation complex. Analyses thousands nuclear gene SNPs nucleotide sequences mitochondrial ND4 identified four reciprocally monophyletic lineages both marker types, two exclusively one Australia/New Guinea Islands. calls three on Australia have overlapping but significant differences number pulses notes, dominant frequency, call duration, particularly where come into contact. lineage genetically morphologically distinct represents capitula. Molecular data together support recognition Australia: a widespread central arid northern tropics lineage, western zone eastern mesic lineage. sensu stricto Kimberley Top End regions, zone, Murray Darling Basin, making it extreme climate-generalist. SNP indicates that has flow north Lake Eyre Basin not south, possible ring species. does differ appearance or geographically disjunct phylogenetically distinct. primarily east Great Dividing Range Cape York Queensland. redescribe stricto, describe as new species, pyrina sp. nov. larisonans respectively. Although are similar, they do overlap distribution, identification non-problematic. can be distinguished at contact zones by having with higher frequency. investigated history morphology type for mystacina designate nomen dubium. Australian likely conservation status Least Concern abundant, no threats. Little known about outside few existing museum specimens.

Language: Английский

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Cold, creeping things: deep phylogeographic structure in a naturally fragmented cool-adapted skink (Scincidae; Anepischetosia) from south-eastern Australia

Conservation Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: April 24, 2025

Abstract The temperate forests of eastern Australia have been extensively fragmented over the last 200 years and are now increasingly threatened by fire climate change. To understand manage impacts these threats, there is a need to patterns endemism diversity across an array ecologically divergent taxa. Anepischetosia monotypic genus scincid lizards that adapted cool, wet forest habitats in far south-eastern mainland Australia. Here we use reduced representation genomic data sequencing mitochondrial ND4 locus from museum tissue samples characterise phylogeographic structure population-level genetic this taxon. These reveal novel deep geographically localised structuring, including at least six ESUs spanning several candidate species. Many lineages associated with patches mesic habitat, especially north range, suggesting long histories persistence through major environmental change Plio-Pleistocene, similar observed some taxa non-glaciated landscapes northern hemisphere. Two putative ESUs, whose ranges overlap areas impacted recent high-intensity bushfires, low may be conservation concern. Additional seemingly isolated populations western Victoria remain poorly sampled comprise yet further or results highlight how analyses can overlooked concern leveraging collections – as well-sampled accessible even considered comparatively “well known”.

Language: Английский

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Are Pheromones Key to Unlocking Cryptic Lizard Diversity?

The American Naturalist, Journal Year: 2019, Volume and Issue: 194(2), P. 168 - 182

Published: April 17, 2019

Animals use mating traits to compete for, attract, and choose mates. Because influence mate choice, the divergence of between populations can result in reproductive isolation. This occur without associated morphological divergence, producing reproductively isolated cryptic species that are visually indistinguishable. Thus, identifying morphologically conservative groups is key resolving diversity speciation processes. Lizards contain many such groups, with phylogeographic studies often revealing highly divergent but lineages within species. Considering lizard be sympatric indistinguishable, we hypothesize candidate will exhibit pheromones have typically diverged more than morphology. To test this, used gas chromatography characterize (epidermal pore secretions) from 10 genetically Bynoe's gecko (Heteronotia binoei) complex northern Australia. Multivariate analyses pheromone blends morphology indicate lineage specific relatively Such specificity suggests behavioral isolation this radiation. These results suggest data may unlock tremendous currently being uncovered groups.

Language: Английский

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SODA: multi-locus species delimitation using quartet frequencies

Bioinformatics, Journal Year: 2020, Volume and Issue: 36(24), P. 5623 - 5631

Published: Nov. 21, 2020

Species delimitation, the process of deciding how to group a set organisms into units called species, is one most challenging problems in computational evolutionary biology. While many methods exist for species based on coalescent theory, few are scalable very large datasets, and that scale tend be not accurate. delimitation closely related tree inference from discordant gene trees, problem has enjoyed rapid advances recent years.In this article, we build accuracy scalability quartet-based estimation propose new method SODA delimitation. relies heavily recently developed testing zero branch length trees. In extensive simulations, show can easily datasets while maintaining high accuracy.The code data presented here available https://github.com/maryamrabiee/SODA.Supplementary at Bioinformatics online.

Language: Английский

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Phylogenomics, biogeography, and evolution of morphology and ecological niche of the eastern Asian–eastern North AmericanNyssa(Nyssaceae)

Journal of Systematics and Evolution, Journal Year: 2020, Volume and Issue: 58(5), P. 571 - 603

Published: May 9, 2020

Abstract Nyssa (Nyssaceae, Cornales) represents a classical example of the well‐known eastern Asian–eastern North American floristic disjunction. The genus consists three species in Asia, four America, and one Central America. Species are ecologically important trees Asian forests. distribution living rich fossil record make it an excellent model for understanding origin evolution However, despite small number species, relationships within have remained unclear not been elucidated using molecular approach. Here, we integrate data from 48 nuclear genes, fossils, morphology, ecological niche to resolve relationships, elucidate its biogeographical history, investigate morphology niches, aiming at better EA–ENA Results showed that (CAM) talamancana was sister remaining which were divided among three, rapidly diversified subclades. Estimated divergence times history suggested had ancestral range Eurasia western America late Paleocene. rapid diversification occurred early Eocene, followed by multiple dispersals between Erasian continents. experienced two major episodes extinction Oligocene end Neogene, respectively. N. relic lineage boreotropical flora Paleocene/Eocene boundary once results supported importance both Atlantic land bridge Bering (BLB) Paleogene Neogene dispersals, respectively, as well role refugia flora. total‐evidence‐based dated phylogeny pattern macroevolution coincided with paleoclimatic changes. We found evolutionary changes (including wood anatomy leaf traits) niches (precipitation temperature) disjunct, supporting selection driving trait evolutions after geographic isolation. also demonstrated challenges phylogenomic studies lineages histories. concatenation gene can lead inference strongly incongruent tree. conflicts genealogies did seem impose strong effect on time dating our case. Furthermore, events may be recovered analysis BEAST if critical constraints relevant nodes available. Our study provides complex bidirectional exchanges plants Paleogene, but “out Asia” migrations explain present disjunct EA ENA.

Language: Английский

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Speciation Hypotheses from Phylogeographic Delimitation Yield an Integrative Taxonomy for Seal Salamanders (Desmognathus monticola)

Systematic Biology, Journal Year: 2022, Volume and Issue: 72(1), P. 179 - 197

Published: Sept. 28, 2022

Abstract Significant advances have been made in species delimitation and numerous methods can test precisely defined models of speciation, though the synthesis phylogeography taxonomy is still sometimes incomplete. Emerging consensus treats distinct genealogical clusters genome-scale data as strong initial evidence speciation most cases, a hypothesis that must therefore be falsified under an explicit evolutionary model. We now hypotheses linking trait differentiation to specific mechanisms divergence with increasingly large sets. Integrative can, therefore, reflect understanding how each axis variation relates underlying processes, nomenclature for lineages. illustrate this approach here Seal Salamanders (Desmognathus monticola) introduce new unsupervised machine-learning delimitation. Plethodontid salamanders are renowned their morphological conservatism despite extensive phylogeographic divergence. discover 2 geographic genetic clusters, which demographic spatial ecology gene flow provide robust support ecogeographic limited phenotypic These integrated (e.g., spatially localized reduced migration) reflected emergent properties expected reinforcement ethological isolation selection against hybrids). Their prima facie species-level distinctiveness, supported by along axes such behavior, geography, climate suggest ecological basis subsequent through prezygotic isolation. As sets grow more comprehensive, species-delimitation tested, rejected, or corroborated hypotheses, providing reciprocal illumination processes integrative taxonomies. [Desmognathus; taxonomy; machine learning; delimitation.]

Language: Английский

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Phylogenomic analysis provides diagnostic tools for the identification of Anastrepha fraterculus (Diptera: Tephritidae) species complex

Evolutionary Applications, Journal Year: 2023, Volume and Issue: 16(9), P. 1598 - 1618

Published: Aug. 30, 2023

Insect pests cause tremendous impact to agriculture worldwide. Species identification is crucial for implementing appropriate measures of pest control but can be challenging in closely related species. True fruit flies the genus

Language: Английский

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Plotting for change: an analytical framework to aid decisions on which lineages are candidate species in phylogenomic species discovery

Biological Journal of the Linnean Society, Journal Year: 2021, Volume and Issue: 135(1), P. 117 - 137

Published: June 29, 2021

Abstract A recent study argued that coalescent-based models of species delimitation mostly delineate population structure, not species, and called for the validation candidate using biological information additional to genetic information, such as phenotypic or ecological data. Here, we introduce a framework interrogate genomic datasets trees presence in situations where data are unavailable, unobtainable uninformative. For de novo studies boundaries, propose six steps: (1) visualize affinities among individuals identify both discrete admixed groups from first principles hold aside involved contemporary admixture independent consideration; (2) apply phylogenetic techniques lineages; (3) assess diagnosability those lineages potential species; (4) interpret diagnosable geographical context (sympatry, parapatry, allopatry); (5) significance difference trends sampling intensity; (6) adopt holistic approach available evidence inform decisions on status difficult cases allopatry. We this distinguish within-species widespread complex Australian freshwater fishes (Retropinna spp.). Our addresses two cornerstone issues systematics often discussed explicitly discovery: how determine it, what criteria should be used decide whether conspecific represent different species.

Language: Английский

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Gene flow throughout the evolutionary history of a colour polymorphic and generalist clownfish

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(14)

Published: June 14, 2024

Abstract Even seemingly homogeneous on the surface, oceans display high environmental heterogeneity across space and time. Indeed, different soft barriers structure marine environment, which offers an appealing opportunity to study various evolutionary processes such as population differentiation speciation. Here, we focus Amphiprion clarkii (Actinopterygii; Perciformes), most widespread of clownfishes that exhibits highest colour polymorphism. Clownfishes can only disperse during a short pelagic larval phase before their sedentary adult lifestyle, might limit connectivity among populations, thus facilitating speciation events. Consequently, taxonomic status A . has been under debate. We used whole‐genome resequencing data 67 specimens spread Indian Pacific Oceans characterize species' structure, demographic history found from Indo‐Pacific Ocean following stepping‐stone dispersal gene flow was pervasive throughout its history. Interestingly, patterns differed noticeably Indonesian populations two at extreme sampling distribution (i.e. Maldives New Caledonia), exhibited more comparable despite geographic genetic distances. Our emphasizes how studies uncover intricate past wide‐ranging species with diverse phenotypes, shedding light complex nature concept paradigm.

Language: Английский

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