Unraveling the extensive phylogenetic discordance and evolutionary history of spurless taxa within the Aquilegia ecalcarata complex

New Phytologist, Journal Year: 2025, Volume and Issue: unknown

Published: March 7, 2025

Parallel evolution of the same, or at least very similar, phenotype(s) in different lineages is often interpreted as evidence for action natural selection. However, caution required when inferring parallel based on uncertain potentially incorrect phylogenetic frameworks. Here, by conducting extensive phylogenomic and population genetic analyses, we aim to clarify evolutionary history spurless taxa within Aquilegia ecalcarata complex. We observed substantial discordance patterns across entire genome, primarily attributed ancient introgression incomplete lineage sorting. Additionally, identified several whose positions were distorted admixture events. Using a backbone tree demographic modeling, determined that these independently originated twice this group. Intriguingly, our investigation revealed experienced expansion during global cooling, while their spurred sister groups underwent contraction. The losses petal spurs, therefore, may be linked adaptations low-temperature conditions. These findings emphasize importance comprehensive population-level analyses inference provide valuable insights into dynamics trait loss its implications adaptive strategies.

Language: Английский

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Candidate‐species delimitation in Desmognathus salamanders reveals gene flow across lineage boundaries, confounding phylogenetic estimation and clarifying hybrid zones

Ecology and Evolution, Journal Year: 2022, Volume and Issue: 12(2)

Published: Feb. 1, 2022

Dusky Salamanders (genus

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Novel phylogenomic inference and ‘Out of Asia’ biogeography of cobras, coral snakes and their allies

Royal Society Open Science, Journal Year: 2024, Volume and Issue: 11(8)

Published: Aug. 1, 2024

Estimation of evolutionary relationships among lineages that rapidly diversified can be challenging, and, in such instances, inaccurate or unresolved phylogenetic estimates lead to erroneous conclusions regarding historical geographical ranges lineages. One example underscoring this issue has been the challenge posed by untangling biogeographic origin elapoid snakes, which includes numerous dangerously venomous species as well not known dangerous humans. The worldwide distribution lineage makes it an ideal group for testing hypotheses related faunal exchanges many continents and other landmasses occupied contemporary species. We developed a novel suite genomic resources, included sampling, inferred robust estimate relationships, we leveraged quantitatively range evolution through deep-time history remarkable radiation. Our biogeographical definitively reject lingering former ‘Out Africa’ hypothesis support Asia’ scenario involving multiple between Asia, Africa, Australasia, Americas Europe.

Language: Английский

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Predicting the invasiveness of alpine newts in the UK

Biological Invasions, Journal Year: 2025, Volume and Issue: 27(3)

Published: March 1, 2025

Abstract Predicting invasion risk to novel environments is essential for management and conservation decision making but the evolutionary lineage at which make these predictions often unclear. Here we predict current suitability across United Kingdom (UK) alpine newt Ichthyosaura alpestris , a species with complex history, broad native range, growing number of introduced populations anecdotal reports ecological consequences amphibian communities. We use distribution niche modelling environmental in UK both species-level lineage-level quantify overlap. show good model transferability parts UK—especially central eastern England northern Scotland—to be highly environmentally suitable newt. Our findings provide evidence differences lineage-level, Greek being distinct from most other lineages, low confidence maxent Greek, Balkan Italian lineages due high levels extrapolation. In contrast, records appear share same as Central lineage. find 66% currently known fall within areas predicted species-level, providing series testable hypotheses better understand ecology this UK.

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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Unsupervised machine learning for species delimitation, integrative taxonomy, and biodiversity conservation

Molecular Phylogenetics and Evolution, Journal Year: 2023, Volume and Issue: 189, P. 107939 - 107939

Published: Oct. 5, 2023

Language: Английский

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Gene drive in species complexes: defining target organisms

Trends in biotechnology, Journal Year: 2022, Volume and Issue: 41(2), P. 154 - 164

Published: July 19, 2022

Engineered gene drives share many environmental risk assessment considerations with other transgenes in genetically modified organisms, but they can differ significantly their potential to spread, increase frequency, and persist target populations.Recently, introduction of mosquitoes an engineered drive completely suppressed caged wild type laboratory populations the malaria vector Anopheles gambiae, belonging a species complex containing both nonvector that produce fertile interspecific hybrids.As sequences are conserved amongst all this complex, vertical transfer vectors nonvectors is plausible. This challenges notion simple dichotomy between organism nontarget organism.Using as specific case study, options on defining organisms complexes developed here, including proposal new concept complex. drives, which bias own inheritance frequency populations, being control mosquito vectors. Such belong hybrids, making (VGDT) sibling biologically While VGDT could positively impact human health protection goals, might challenge biodiversity ones. Therefore, use invites more nuanced than for not intended populations. Incorporating offers flexibility when assessing impacts from VGDT. Gene (see Glossary) allow genes, transgenes, or genetic traits be transmitted offspring at greater Mendelian frequencies, property modification interest spread through interbreeding [1.Burt A. Site-specific selfish genes tools engineering natural populations.Proc. Biol. Sci. 2003; 270: 921-928Crossref PubMed Scopus (442) Google Scholar, 2.Burt et al.Gene reduce transmission sub-Saharan Africa.J. Responsible Innov. 2018; 5: S66-S80Crossref (44) 3.Wang G.H. al.Symbionts drive: two strategies combat vector-borne disease.Trends Genet. 2022; 38: 708-723Abstract Full Text PDF (16) Scholar]. In particular, there considerable harnessing diseases such (Box 1) [4.African Union Development Agency – New Partnership Africa's Drives Malaria Control Elimination Africa.2018Google Scholar,5.World Health Organization Evaluation Genetically Modified Mosquitoes Vector-Borne Diseases. WHO, 2020Google Scholar].Box 1Malaria drivesThe World (WHO) has reported 2020 were 241 million cases worldwide, associated estimated 627 000 deaths [68.World Report. 2021Google Countries WHO African Region continue carry disproportionately high global burden, 95% 96% deaths. Plasmodium falciparum major pathogen responsible causing humans via bites infected female blood-feed hosts provide essential nutrients development eggs. As result insecticide-treated bed nets indoor insecticide spraying, well prophylactic therapeutic pharmaceutical treatments, been steady decline prevalence over last decade. However, progress recently stalled remains under further threat resistance behavioural adaptations, increased zoophilic responses, mosquitoes, drugs, invoking need complementary approaches burden disease, novel [3.Wang 4.African 5.World Scholar,68.World Scholar].Current include encoding CRISPR-Cas9 endonuclease expressed germline promoter, along ubiquitously constitutively gRNAs, together cleave genome [2.Burt Scholar,69.Hammond A.M. Galizi R. fight malaria: current state future directions.Pathog. Glob. Health. 111: 412-423Crossref (62) Once transgene introduced into its genomic location one pair homologous chromosomes, gRNA Cas9 act concert germ cells cause double-stranded break DNA site wild-type chromosome. When lesion repaired by homology directed repair using transgenic chromosome template, entire transgene, flanking either side pasted homologous, formerly wild-type, process homing create mostly pairs parental chromosomes homozygous so proportion would otherwise case, leading super-Mendelian progeny. Thus, once mating population, capable will drive, within assuming any fitness costs do outweigh The Current Before release considered regulators, decision-makers stakeholders, (ERA), whether probabilistic, qualitative, combination thereof, must conducted evaluate risks health, animal environment [6.National Academies Sciences, Engineering, Medicine Horizon: Advancing Science, Navigating Uncertainty, Aligning Research Public Values. National Press, 2016Google 7.Landis W.G. al.A general risk-based adaptive management scheme incorporating Bayesian Network Relative Risk Model South River, Virginia, study.Integr. Environ. Assess. Manag. 2017; 13: 115-126Crossref (26) 8.James S. al.Pathway deployment biocontrol tool elimination Sub-Saharan Africa: recommendations Scientific Working Group.Am. J. Trop. Med. Hyg. 98: 1-49Crossref (122) 9.EFSA Panel Organisms al.Adequacy sufficiency evaluation existing EFSA guidelines molecular characterisation, post-market monitoring insects drives.EFSA 2020; 18e06297Google 10.James S.L. al.Toward definition efficacy safety criteria advancing drive-modified field testing.Vector Borne Zoonotic Dis. 20: 237-251Crossref (38) 11.World Guidance Framework Testing Mosquitoes.2nd edn. 12.Ickowicz al.Predicting persistence dominant sterile male mosquitoes.Parasit. Vectors. 2021; 14: 480Crossref (4) 13.Connolly J.B. al.Recommendations applications control.Malar. 21: 152Crossref (9) A prerequisite effective ERA (GMOs) define unintended effects intervention (TOs) (NTOs) [9.EFSA Scholar,10.James Scholar,14.Romeis al.The value regulatory frameworks agricultural pest drives.Environ. Policy. 108: 19-36Crossref (23) 15.Devos Y. organisms: developing practical guidance.Trends Biotechnol. 39: 853-856Abstract (12) 16.Devos al.Potential against disease vectors, pests invasive poses assessment.Crit. Rev. : 1-17Google 17.Devos al.Risk releases insects.Biotechnol. Adv. 107807Crossref paradigm typically applied qualitative GM plants, where, general, clear distinction targeted, TOs, those NTOs. same GMOs, non-gene (GMMs), designed addition, most significant contain [18.Davidson G. species.Bull. Organ. 1964; 31: 625-634PubMed 19.Besansky N.J. al.Semipermeable boundaries gambiae arabiensis: evidence multilocus sequence variation.Proc. Natl. Acad. U. 100: 10818-10823Crossref (170) 20.Small S.T. al.Radiation reticulation marks origin vector.Proc. 117: 31583-31590Crossref (13) 21.Antonio-Nkondjio C. Simard F. Highlights anopheles nili moucheti, Africa.in: - insights IntechOpen, 2013Crossref 22.Crawford J.E. al.Reticulate speciation barriers introgression complex.Genome Evol. 2015; 7: 3116-3131Crossref (27) Scholar], some combinations hybridisation hybrids. semipermeable porous facilitate [19.Besansky Scholar,20.Small Scholar,23.Thelwell al.Evidence mitochondrial bwambae gambiae.Insect Mol. 2000; 9: 203-210Crossref (24) Scholar] plausibly lead species, nonvectors. represents binary choice TO NTO complexes. Depending how goals defined, evaluated number different ways ERA. Here, study involving population suppression sensu lato (s.l.) [24.Kyrou K. targeting doublesex causes complete mosquitoes.Nat. 36: 1062-1066Crossref (425) Scholar,25.Hammond al.Gene-drive large cages bridge lab field.Nat. Commun. 12: 4589Crossref (39) used illustrate these differing possibilities consequences 2).Box 2Case study: gambiaeThere principal control. replacement disrupt endogenous cargo prevent pathogens [69.Hammond density introducing cost sex bias. example, gRNAs haplosufficient fertility genes. Transgenic heterozygous females disrupted copy remain fertile. Via homing, rates males population. They therefore increasingly likely mate another, generating increasing proportions transgenics, sterile. progeny decreases suppressed.Early attempts suppress led caused mutations simultaneously retained functionality protein targeted [70.Hammond system reproduction gambiae.Nat. 2016; 34: 78-83Crossref (733) Recently, determination locus s.l. investigated drive. locus, highly conserved, encodes transcripts, (AgdsxM), (AgdsxF) spans intron–exon boundary, mutation selectively disrupts AgdsxF isoform, intersex, unable blood feed. laboratory, small eliminations after 9–11 generations recent cage experiments closely mimic feeding reproductive environments field, overlapping, age-structured collapse year without [25.Hammond There suppressed. Early Africa coluzzii, stricto (s.s.), arabiensis, funestus (all Diptera: Culicidae) [26.Sinka M.E. Africa, Europe Middle East: occurrence data, distribution maps bionomic precis.Parasit. 2010; 3: 117Crossref (503) Scholar,27.Afrane al.Secondary continent?.in: Rodriguez-Morales A.J. Topics Malaria. 2016Crossref s.s., arabiensis currently active [28.Burt Crisanti evolved synthetic.ACS Chem. 343-346Crossref (49) All three members 3). also contains species. Most have examined producing hybrids Some found albeit low frequencies [23.Thelwell Scholar,29.White G.B. Chromosomal hybridization complex.Nature. 1971; 231: 184-185Crossref (41) 30.Costantini al.Living edge: biogeographic patterns habitat segregation conform niche expansion gambiae.BMC Ecol. 2009; 16Crossref (156) 31.Pombi M. al.Dissecting functional components isolation among related sympatric complex.Evol. Appl. 10: 1102-1120Crossref (29) 32.Epopa P.S. al.Seasonal dynamics western Burkina Faso.Malar. 2019; 18: 113Crossref thus representing route.Box 3Anopheles complexThe recognised least nine morphologically indistinguishable shared common ancestor less 2 years ago [71.Fontaine M.C. al.Mosquito genomics. Extensive revealed phylogenomics.Science. 3471258524Crossref (337) Scholar]: amharicus, bwambae, fontenillei; melas, merus, quadriannulatus.A. coluzzii regional sections Scholar,72.Sinka map vectors.Parasit. 2012; 69Crossref (395) geographically restricted, local [48.White sp.n., Semliki Valley, Uganda, relationships An. (Diptera: Culicidae).Syst. Entomol. 1985; 501-522Crossref

Language: Английский

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Systematic revision of the Spotted and Northern Dusky Salamanders (Plethodontidae: Desmognathus conanti and D. fuscus), with six new species from the eastern United States

Zootaxa, Journal Year: 2023, Volume and Issue: 5311(4), P. 451 - 504

Published: July 2, 2023

Spotted and Northern Dusky Salamanders (Desmognathus conanti D. fuscus) have a long complex taxonomic history. At least 10 other currently recognized species in the genus were either described from populations previously considered fuscus, as or later subspecies thereof, synonyms before ultimately being distinct. Recent molecular analyses also revealed extensive cryptic diversity within both species, which are polyphyletic assemblages of 13 distinct mitochondrial lineages with 5.7-10.3% uncorrected 'p' distances COI barcode locus. Based on phylogenomic data population-clustering considering admixture between lineages, 11 candidate circumscribed by recent authors. Those ecomorphologically variable, comprising large, robust, keel-tailed populations, small, gracile, round-tailed forms. Evaluating their distinctiveness based genetic, geographic, morphological evidence, we conclude that six candidates represent new species: Desmognathus anicetus sp. nov., bairdi campi catahoula lycos tilleyi nov. Consequently, recognize eight total formerly associated nominal re-delimited concepts contain additional phylogeographic lineage may further species. In addition to existing nuclear phylogenetic, network, clustering results, present preliminary linear morphometrics bolster diagnostic specificity phenotypic characteristics. These changes stabilize paraphyletic taxonomy species-level Desmognathus, though exist here, elsewhere genus.

Language: Английский

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The Artefactual Branch Effect and Phylogenetic Conflict: Species Delimitation with Gene Flow in Mangrove Pit Vipers (Trimeresurus purpureomaculatus-erythrurus Complex)

Systematic Biology, Journal Year: 2023, Volume and Issue: 72(6), P. 1209 - 1219

Published: July 13, 2023

Mangrove pit vipers of the Trimeresurus purpureomaculatus-erythrurus complex are only species viper known to naturally inhabit mangroves. Despite serving integral ecological functions in mangrove ecosystems, evolutionary history, distribution, and boundaries remain poorly understood, partly due overlapping distributions, confusing phenotypic variations, lack focused studies. Here, we present first genomic study on introduce a robust hypothesis-driven delimitation framework that considers gene flow phylogenetic uncertainty conjunction with novel application new class speciation-based model implemented through program Delineate. Our results showed produced conflict our focal substantiates artefactual branch effect where highly admixed populations appear as divergent nonmonophyletic lineages arranged stepwise manner at basal position clades. confounding effects flow, were able obtain unequivocal support for recognition based intersection congruence multiple lines evidence. This demonstrates an integrative approach predicated consideration plausible histories, population structure/differentiation, implementation can effectively delimit presence conflict.

Language: Английский

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Different patterns of introgression in a three species hybrid zone among European cave salamanders

Ecology and Evolution, Journal Year: 2023, Volume and Issue: 13(8)

Published: Aug. 1, 2023

Hybrid zones occur where genetically distinct populations meet, mate and produce offspring with mixed ancestry. In Plethodontid salamanders, introgressive hybridization is a common phenomenon, hybrids backcross parental leading to the spread of new alleles into genomes. Whereas many hybrid have been reported in American only single zone has documented European plethodontids so far, which located at Apuan Alps Italian Peninsula. Here, we describe previously unreported Northern Apennines involving all three salamander species inhabiting We found 21 Speleomantes sites occurrence, from hitherto unexplored area boundaries between ranges. Using mitochondrial (Cytb ND2 genes) nuclear markers (two diagnostic SNPs NCX1 gene), revealed three-way contact mainland hybridize: S. strinatii, ambrosii italicus. observed strong mitonuclear discordance, showing conspicuous geographic pattern, while coexisted both same individuals, providing evidence possible combinations. The introgression asymmetric, italicus mitogenome usually associated a. and, lesser extent, strinatii alleles. This finding confirms that are group choice investigate mechanisms suggests behavioural, genetic ecological components may concur determining direction extent introgression.

Language: Английский

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