Finding Evolutionary Processes Hidden in Cryptic Species

Trends in Ecology & Evolution, Journal Year: 2017, Volume and Issue: 33(3), P. 153 - 163

Published: Dec. 11, 2017

Language: Английский

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Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

IMA Fungus, Journal Year: 2020, Volume and Issue: 11(1)

Published: July 10, 2020

True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of based on global richness estimates, with around 3 million predicted species. Compared to plants animals, have simple body plans often morphologically ecologically obscure structures. This poses challenges for accurate precise identifications. Here we provide a conceptual framework identification fungi, encouraging approach integrative (polyphasic) taxonomy species delimitation, i.e. combination genealogy (phylogeny), phenotype (including autecology), reproductive biology (when feasible). allows objective evaluation diagnostic characters, either phenotypic or molecular both. Verification identifications is crucial but neglected. Because clade-specific evolutionary histories, there currently no single tool although DNA barcoding using internal transcribed spacer (ITS) remains first diagnosis, particularly in metabarcoding studies. Secondary barcodes are increasingly implemented groups where ITS does not sufficient precision. Issues pairwise sequence similarity-based OTU clustering discussed, multiple alignment-based phylogenetic approaches subsequent verification recommended as more alternatives. In approaches, trade-off between speed accuracy precision must be carefully considered. Intragenomic variation other markers should properly documented, phylotype diversity necessarily proxy richness. Important strategies improve are: (1) broadly document intraspecific intragenomic markers; (2) substantially expand repositories, focusing undersampled clades missing taxa; (3) curation labels primary repositories increase number sequences verified material; (4) link data digital information voucher specimens including imagery. parallel, technological improvements genome sequencing offer promising alternatives future. Despite prevalence DNA-based fungal taxonomy, phenotype-based remain an important strategy catalog establish initial hypotheses.

Language: Английский

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Genetic Diversity and Conservation Units: Dealing With the Species-Population Continuum in the Age of Genomics

Frontiers in Ecology and Evolution, Journal Year: 2018, Volume and Issue: 6

Published: Oct. 23, 2018

Current approaches to biodiversity conservation are largely based on geographic areas, ecosystems, ecological communities and species, with less attention ongenetic diversity the evolutionary continuum from populations species. Conservation management generally rests discrete categories, such as identified and, for threated taxa, intraspecific units. Species, in particular, provide a common measure of yet both theory nature, speciation is typically protracted process progressing connected unambiguous species variable rates phenotypic, genetic divergence. Thus, most recognised not genetically uniform sometimes highly structured into historically isolated worthy consideration units that represent unique conservation. Genome screens offer unprecedented resolution structure across taxonomic boundaries complexes, have potential oversplit if interpreted conservatively. This highlights blurred line between can confound simple dichotomies 'species' versus 'not species'. At same time, like plants, there increasing evidence than even distantly related animal hybridize exchange genes. A review legislation reveals legal definitions quite flexible accommodate range infra-specific taxa divergent populations, well taxonomically For example, legislative definition around world include: subspecies, varieties, geographically and/or distinct populations. In principle, this flexibility allows protection maintenance processes at broad levels. However, biologists often fail adequately justify then translate their defined categories suited assessment under local legislation. We recommend (i). genomic data should be conservatively when formally naming (ii). concomitantly, stronger impetus more approach identifying clearly justified units, (iii). guidelines developed recognising labelling align best scientific practice, (iv). nuanced view emerging analyses communicated effectively by scientists decision makers.

Language: Английский

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Comparison of Methods for Molecular Species Delimitation Across a Range of Speciation Scenarios

Systematic Biology, Journal Year: 2018, Volume and Issue: 67(5), P. 830 - 846

Published: Feb. 15, 2018

Species are fundamental units in biological research and can be defined on the basis of various operational criteria. There has been growing use molecular approaches for species delimitation. Among most widely used methods, generalized mixed Yule-coalescent (GMYC) Poisson tree processes (PTP) were designed analysis single-locus data but often applied to concatenations multilocus data. In contrast, Bayesian multispecies coalescent approach software Phylogenetics Phylogeography (BPP) explicitly models evolution this study, we compare performance GMYC, PTP, BPP using synthetic generated by simulation under speciation scenarios. We show that absence gene flow, main factor influencing these methods is ratio population size divergence time, while number loci sample per have smaller effects. Given appropriate priors correct guide trees, shows lower rates overestimation underestimation, generally robust potential confounding factors except high levels flow. The single-threshold GMYC best strategy identified PTP perform well scenarios involving more than a single putative when flow absent, outperforms fewer involved. Both sensitive effects factors. Case studies bears bees further validate some findings from our reveal importance an informed starting point Our results highlight key affecting delimitation, with benefits within integrative taxonomic framework.

Language: Английский

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Inordinate Fondness Multiplied and Redistributed: the Number of Species on Earth and the New Pie of Life

The Quarterly Review of Biology, Journal Year: 2017, Volume and Issue: 92(3), P. 229 - 265

Published: Aug. 24, 2017

The number of species on Earth is one the most fundamental numbers in science, but that remains highly uncertain. Clearly, more exist than present formally described (approximately 1.5 million), projected differ dramatically among studies. Recent estimates range from about 2 million to approximately 1 trillion, project around 11 or fewer. Numerous studies have focused insects as a major component overall richness, and many excluded other groups, especially non-eukaryotes. Here, we re-estimate global biodiversity. We also estimate relative richness clades living organisms, summarized “Pie Life.” Unlike previous estimates, incorporate morphologically cryptic arthropod molecular-based delimitation. include numerous groups organisms not been simultaneously included those often associated with particular insect host (including mites, nematodes, apicomplexan protists, microsporidian fungi, bacteria). Our suggest there are likely be at least 6 billion Earth. Furthermore, contrast new Pie Life dominated by bacteria 70–90% species) only hyperdiverse groups.

Language: Английский

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The Spectre of Too Many Species

Systematic Biology, Journal Year: 2018, Volume and Issue: 68(1), P. 168 - 181

Published: July 4, 2018

Recent simulation studies examining the performance of Bayesian species delimitation as implemented in bpp program have suggested that may detect population splits but not divergences and it tends to over-split when data many loci are analyzed. Here, we confirm these results provide mathematical justifications. We point out distinction between made protracted speciation model (PSM) has no influence on generation gene trees sequence data, which explains why method can use such distinguish speciation. suggest PSM is unrealistic its mechanism for assigning status assumes instantaneous speciation, contradicting prevailing taxonomic practice. suggestion, based simulation, case with flow, selection amount (the number loci) increases. discuss a recently proposed empirical genealogical divergence index (gdi) illustrate parameter estimates produced by full likelihood analysis much more reliable inference under gdi than approximate phrapl. estimation approach useful identifying sympatric cryptic species, while be used implement criteria determining among allopatric populations.

Language: Английский

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Resolving Fusarium: Current Status of the Genus

Annual Review of Phytopathology, Journal Year: 2019, Volume and Issue: 57(1), P. 323 - 339

Published: June 21, 2019

The fungal genus Fusarium is one of the most important groups plant-pathogenic fungi and affects a huge diversity crops in all climatic zones across globe. In addition, it also human pathogen produces several extremely mycotoxins food products that have deleterious effects on livestock humans. These been plagued over past century by different perspectives what constitutes how many species occur within genus. Currently, there are conflicting views generic boundaries defines impact disease diagnosis, management, biosecurity legislation. An approach to defining identifying places needs community users (especially, this case, phytopathologists) forefront presented review.

Language: Английский

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Species boundaries in the human pathogen Paracoccidioides

Fungal Genetics and Biology, Journal Year: 2017, Volume and Issue: 106, P. 9 - 25

Published: June 9, 2017

The use of molecular taxonomy for identifying recently diverged species has transformed the study speciation in fungi. pathogenic fungus Paracoccidioides spp been hypothesized to be composed five phylogenetic species, four which compose brasiliensis complex. Nuclear gene genealogies support this divergence scenario, but mitochondrial loci do not; while all from complex are differentiated at nuclear coding loci, they not loci. We addressed source incongruity using 11 previously published fragments, 10 newly-sequenced non-coding and microsatellites. further demonstrated that mito-nuclear incongruence results interspecific hybridization introgression, a common phenomenon eukaryotes. Additional population genetic analyses revealed possible introgression much less than seen mitochondrion. Our consistent with scenario secondary contact subsequent despite continued persistence boundaries. also suggest yeast morphology slightly-but significantly-differs across propose elevate these formally described taxonomic species.

Language: Английский

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The hitchhiker's guide to single‐locus species delimitation

Molecular Ecology Resources, Journal Year: 2018, Volume and Issue: 18(6), P. 1234 - 1246

Published: May 30, 2018

Molecular approaches to species delimitation are increasingly used ascertain the number of in a sample prior taxonomic, ecological or physiological studies. Although multilocus gaining fast popularity, single-gene methods still predominate literature. However, available simulation benchmarks these focus exclusively on species-poor samples and/or tree-based approaches: as result, travellers land single-locus lack comprehensive "hitchhiker's guide" highlighting sweet spots and dangers their road. To fill this gap, we compared performances distance-based (ABGD, "automatic barcode gap discovery"), allele sharing-based (haplowebs) (GMYC, "generalized mixed Yule-coalescent" PTP, "Poisson tree processes") detect interspecific boundaries 6, 60 120 simulated with various speciation rates, effective population sizes, mutation rates sampling patterns. We found that all performed poorly when sizes were large, haplowebs yielding best results followed by ABGD then approaches. The latter's error type was mostly oversplitting, whereas chiefly overlumped leaned either way depending parameters: such widely divergent patterns suggest that, if three types agree, resulting is probably correct. Perfect congruence being quite rare, search one-size-fit-all approach should forget it; however, our hitchhiker's guide raises hope delimitation's Holy Grail may be relatively uncharted nearby delimitation.

Language: Английский

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What are fungal species and how to delineate them?

Fungal Diversity, Journal Year: 2021, Volume and Issue: 109(1), P. 1 - 25

Published: July 1, 2021

Language: Английский

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