What are fungal species and how to delineate them?

Fungal Diversity, Год журнала: 2021, Номер 109(1), С. 1 - 25

Опубликована: Июль 1, 2021

Язык: Английский

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Species boundaries in plant pathogenic fungi: a Colletotrichum case study

BMC Evolutionary Biology, Год журнала: 2016, Номер 16(1)

Опубликована: Апрель 14, 2016

Accurate delimitation of plant pathogenic fungi is critical for the establishment quarantine regulations, screening genetic resistance to pathogens, and study ecosystem function. Concatenation analysis multi-locus DNA sequence data represents a powerful commonly used approach recognizing evolutionary independent lineages in fungi. It however possible mask discordance between individual gene trees, thus speciation events might be erroneously estimated if one simply recognizes well supported clades as distinct species without implementing careful examination boundary. To investigate this phenomenon, we studied Colletotrichum siamense s. lat., which cosmopolitan pathogen causing serious diseases on many economically important hosts. Presently there are significant disagreements among mycologists what constitutes C. with number accepted ranging from seven. In study, multiple approaches were test null hypothesis “C. complex”, using global strain collection. Results molecular analyses based Genealogical Concordance Phylogenetic Species Recognition (GCPSR) coalescent methods (e.g. Generalized Mixed Yule-coalescent Poisson Tree Processes) do not support recognition any within lat. species, rejecting hypothesis. This conclusion reinforced by recombination, cross fertility, comparison ecological morphological characters. Our results indicate that reproductive isolation, geographic host barriers flow absent discovery emphasized importance polyphasic when describing novel morphologically conserved genera

Язык: Английский

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The Multispecies Coalescent Over-Splits Species in the Case of Geographically Widespread Taxa

Systematic Biology, Год журнала: 2019, Номер 69(1), С. 184 - 193

Опубликована: Июнь 5, 2019

Many recent species delimitation studies rely exclusively on limited analyses of genetic data analyzed under the multispecies coalescent (MSC) model, and results from these often are regarded as conclusive support for taxonomic changes. However, most MSC-based methods have well-known unmet assumptions. Uncritical application genetic-based approaches (without due consideration sampling design, effects a priori group designations, isolation by distance, cytoplasmic-nuclear mismatch, population structure) can lead to over-splitting species. Here, we argue that in many common biological scenarios, researchers must be particularly cautious regarding limitations, especially cases well-studied, geographically variable, parapatrically distributed complexes. We consider points with respect historically controversial group, American milksnakes (Lampropeltis triangulum complex), using analysis (Ruane et al. 2014). show over-reliance program Bayesian Phylogenetics Phylogeography, without adequate its assumptions resulted this study. Several hypothesized instead appear represent arbitrary slices continuous geographic clines. conclude best available evidence supports three, rather than seven, within complex. More generally, recommend coalescent-based incorporate thorough variation carefully examine putative contact zones among delimited before making

Язык: Английский

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Phylogenetic Systematics and Evolution of the Spider Infraorder Mygalomorphae Using Genomic Scale Data

Systematic Biology, Год журнала: 2019, Номер 69(4), С. 671 - 707

Опубликована: Сен. 13, 2019

Abstract The infraorder Mygalomorphae is one of the three main lineages spiders comprising over 3000 nominal species. This ancient group has a worldwide distribution that includes among its ranks large and charismatic taxa such as tarantulas, trapdoor spiders, highly venomous funnel-web spiders. Based on past molecular studies using Sanger-sequencing approaches, numerous mygalomorph families (e.g., Hexathelidae, Ctenizidae, Cyrtaucheniidae, Dipluridae, Nemesiidae) have been identified non-monophyletic. However, these data were unable to sufficiently resolve higher-level (intra- interfamilial) relationships necessary changes in classification could be made with confidence. Here, we present comprehensive phylogenomic treatment spider Mygalomorphae. We employ 472 loci obtained through anchored hybrid enrichment reconstruct all estimate timeframe their diversification. sampled nearly currently recognized families, which allowed us assess status, result, propose new scheme. Our generic-level sampling also provided an evolutionary framework for revisiting questions regarding silk use first analysis within strict phylogenetic shows sheet web likely plesiomorphic condition mygalomorphs, well providing insights ancestral foraging behavior divergence time estimates, concomitant detailed biogeographic analysis, suggest both continental-level vicariance more recent dispersal events played important role shaping modern day distributional patterns. our results, relimit generic composition Nemesiidae. elevate five subfamilies family rank: Anamidae (NEW RANK), Euagridae Ischnothelidae Pycnothelidae Bemmeridae RANK). Three Entypesidae FAMILY), Microhexuridae Stasimopidae subfamily Australothelinae SUBFAMILY) are newly proposed. Such major rearrangement classification, recognizing nine established family-level rank taxa, largest seen decades. [Biogeography; clocks; phylogenomics; foraging; taxonomy.]

Язык: Английский

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Impact of Model Violations on the Inference of Species Boundaries Under the Multispecies Coalescent

Systematic Biology, Год журнала: 2017, Номер 67(2), С. 269 - 284

Опубликована: Сен. 2, 2017

The use of genetic data for identifying species-level lineages across the tree life has received increasing attention in field systematics over past decade. multispecies coalescent model provides a framework understanding process lineage divergence and become widely adopted delimiting species. However, because these studies lack an explicit assessment fit, many cases, accuracy inferred species boundaries are unknown. This is concerning given large amount empirical theory that highlight complexity speciation process. Here, we seek to fill this gap by using simulation characterize sensitivity inference under (MSC) several violations assumptions thought be common data. We also assess fit MSC context delimitation. Our results show substantial variation sets. Posterior predictive tests find poorest performance sets were hypothesized impacted violations. while inferences assuming robust minor violations, such can biased some biologically plausible scenarios. Taken together, suggest researchers identify individual which delimitation likely problematic, thereby highlighting cases where additional lines evidence particularly important collect. study supports growing body work importance checking phylogenetics, usefulness tailoring reliability particular inferences. [Populations structure, gene flow, demographic changes, posterior prediction, simulation, genetics.].

Язык: Английский

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A demonstration of unsupervised machine learning in species delimitation

Molecular Phylogenetics and Evolution, Год журнала: 2019, Номер 139, С. 106562 - 106562

Опубликована: Июль 16, 2019

Язык: Английский

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Incorporating the speciation process into species delimitation

PLoS Computational Biology, Год журнала: 2021, Номер 17(5), С. e1008924 - e1008924

Опубликована: Май 13, 2021

The “multispecies” coalescent (MSC) model that underlies many genomic species-delimitation approaches is problematic because it does not distinguish between genetic structure associated with species versus of populations within species. Consequently, as both the and spatial resolution data increases, a proliferation artifactual results within-species population lineages, detected due to restrictions in gene flow, are identified distinct toll this extends beyond systematic studies, getting magnified across disciplines rely upon an accurate framework Here we present first new class addresses issue by incorporating extended speciation process for delimitation. We formation lineages their subsequent development into independent separate processes provide way incorporate current understanding boundaries system through specification identities subset lineages. As result, can be discriminated entire system, assigned remaining unknown affinities quantified probabilities. In addition identification units nature, primary goal delimitation, incorporation also allows us insights links species-level processes. By explicitly accounting flow only between, but within, species, address limits delimiting Specifically, while alone sufficient when considered conjunction other information able learn about boundaries, tempo itself.

Язык: Английский

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Integrating phylogenomic and morphological data to assess candidate species-delimitation models in brown and red-bellied snakes (Storeria)

Zoological Journal of the Linnean Society, Год журнала: 2016, Номер 177(4), С. 937 - 949

Опубликована: Фев. 23, 2016

Systematics at the species level is still marked by theoretical and empirical tensions amongst desires to identify geographical lineages, delimit species, estimate their relationships. These goals are often confounded because each relies, least some extent, on others being known. However, recently developed methods can simultaneously address all three. Furthermore, next-generation genomic sequencing allows us generate large-scale molecular data sets examine variation within a fine scale. Finally, renaissance in morphological validation integrate historical definitions with coalescent models for delimitation. Here, we investigate applicability of these an case, Nearctic snake genus Storeria. Integrating trait into delimitation reduces number delimited from alone. Whereas support eight distinct species-level including this four. The taxa Storeria dekayi, occipitomaculata, storerioides, victa considered distinct, monotypic no subspecies recognized. We highlight need careful assessment delimitation, combining both computational genetic as well traditional character-based descriptions. It now possible phylogeographical using data, relationships single coherent set analyses. Moving forward, will allow more rapid objective assessments cryptic diversity level.

Язык: Английский

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Multilocus sequence data reveal dozens of putative cryptic species in a radiation of endemic Californian mygalomorph spiders (Araneae, Mygalomorphae, Nemesiidae)

Molecular Phylogenetics and Evolution, Год журнала: 2015, Номер 91, С. 56 - 67

Опубликована: Май 27, 2015

Язык: Английский

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Phylogenomics and species delimitation for effective conservation of manta and devil rays

Molecular Ecology, Год журнала: 2020, Номер 29(24), С. 4783 - 4796

Опубликована: Ноя. 9, 2020

Abstract Practical biodiversity conservation relies on delineation of biologically meaningful units. Manta and devil rays (Mobulidae) are threatened worldwide, yet morphological similarities a succession recent taxonomic changes impede the development an effective strategy. Here, we generate genome‐wide single nucleotide polymorphism (SNP) data from geographically taxonomically representative set manta ray samples to reconstruct phylogenetic relationships evaluate species boundaries under general lineage concept. We show that nominal units supported by alternative sources constitute independently evolving lineages, find robust evidence for putative new in Gulf Mexico. Additionally, uncover substantial incomplete sorting indicating rapid speciation together with standing variation ancestral populations has driven uncertainty within Mobulidae. Finally, detect cryptic diversity distinct populations, demonstrating management below level may be warranted certain species. Overall, our study provides framework molecular genetic delimitation is relevant wide‐ranging taxa concern, highlights potential genomic support management, law enforcement strategies.

Язык: Английский

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