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Figure 7 from: Réblová M, Nekvindová J, Fournier J, Miller AN (2020) Delimitation, new species and teleomorph-anamorph relationships in Codinaea, Dendrophoma, Paragaeumannomyces and Striatosphaeria (Chaetosphaeriaceae). MycoKeys 74: 17-74. https://doi.org/10.3897/mycokeys.74.57824

Figure 7 Paragaeumannomyces granulatus (PDD 118744). A, B ascomata C, D vertical section of ascomal wall E papilla and the upper part of ascomal wall in surface view F, G asci H ascal apex with apical annulus I paraphyses J ascospores K colonies on CMD, MLA, OA and PCA after 4 wk (from left to right). Scale bars: 250 μm (A, B); 100 μm (C); 25 μm (G); 20 μm (D–F, I); 10 μm (H, J); 1 cm (K).

Figure 4 from: Réblová M, Nekvindová J, Fournier J, Miller AN (2020) Delimitation, new species and teleomorph-anamorph relationships in Codinaea, Dendrophoma, Paragaeumannomyces and Striatosphaeria (Chaetosphaeriaceae). MycoKeys 74: 17-74. https://doi.org/10.3897/mycokeys.74.57824

Figure 4 Paragaeumannomyces abietinus. A, B ascomata C, D, F vertical section of ascomal wall E vertical section of the ascomal wall and papilla with apical setae G, H ascospores I, J asci K, L ascal apex with apical ring M paraphyses N colonies on CMD, MLA, OA and PCA after 4 wk (from left to right). Images: PRA-16327 (A); CBS 145351 (B, F–L, N); PRA-16324 (C); PRA-16325 (D, E, M). Scale bars: 250 μm (A, B); 200 μm (C); 50 μm (D–F); 20 μm (I, J, M); 10 μm (G, H, K, L); 1 cm (N).

Figure 6 from: Réblová M, Nekvindová J, Fournier J, Miller AN (2020) Delimitation, new species and teleomorph-anamorph relationships in Codinaea, Dendrophoma, Paragaeumannomyces and Striatosphaeria (Chaetosphaeriaceae). MycoKeys 74: 17-74. https://doi.org/10.3897/mycokeys.74.57824

Figure 6 Paragaeumannomyces elegans. A, B ascomata C vertical section of ascomal wall D ascal apex with apical annulus E–G asci H ascospores I paraphyses. Images: PDD 118740 (A, B, D, H, I); PDD 118741 (C, E–G). Scale bars: 250 μm (A, B); 20 μm (C); 10 μm (D–I).

Figure 2 from: Réblová M, Nekvindová J, Fournier J, Miller AN (2020) Delimitation, new species and teleomorph-anamorph relationships in Codinaea, Dendrophoma, Paragaeumannomyces and Striatosphaeria (Chaetosphaeriaceae). MycoKeys 74: 17-74. https://doi.org/10.3897/mycokeys.74.57824

Figure 2 Combined phylogeny using ITS and 28S of 35 members of Paragaeumannomyces. Species names given in bold are new species; T and PT indicate ex-type and ex-paratype strains. Thickened branches indicate branch support with MLBS = 100%, PP values = 1.0 and MP = 100 %. Branch support of nodes ≥ 75 % ML and MPBS, and ≥ 0.95 PP is indicated above branches.

Figure 12 from: Réblová M, Nekvindová J, Fournier J, Miller AN (2020) Delimitation, new species and teleomorph-anamorph relationships in Codinaea, Dendrophoma, Paragaeumannomyces and Striatosphaeria (Chaetosphaeriaceae). MycoKeys 74: 17-74. https://doi.org/10.3897/mycokeys.74.57824

Figure 12 Dendrophoma cytisporoides (CBS 144107). A–C ascomata D vertical section of the ascomal wall with remnants of the periderm E–G asci H paraphyses, asci and ascogenous hyphae I, J ascal apex K, L sterile primordia of sporodochia on MLA after 6 mo M sporodochium on OA after 10 wk N conidia O colonies on CMD, MLA, OA and PCA after 4 wk (from left to right). Scale bars: 300 μm (A–C, K); 20 μm (D); 10 μm (E–H); 5 μm (I, J, N); 100 μm (L, M); 1 cm (O).

Figure 11 from: Réblová M, Nekvindová J, Fournier J, Miller AN (2020) Delimitation, new species and teleomorph-anamorph relationships in Codinaea, Dendrophoma, Paragaeumannomyces and Striatosphaeria (Chaetosphaeriaceae). MycoKeys 74: 17-74. https://doi.org/10.3897/mycokeys.74.57824

Figure 11 Striatosphaeria castanea (CBS 145352). A, B ascomata C asci D ascospores E ascal apex with apical annulus F colonies on CMA with an Urtica dioica stem after 8 wk G–J conidia K–Q conidiophores R colonies on CMD, MLA, OA and PCA after 4 wk (from left to right). Scale bars: 500 μm (A, B); 20 μm (C, E); 10 μm (D, G–Q); 1 cm (F, R).

Figure 10 from: Réblová M, Nekvindová J, Fournier J, Miller AN (2020) Delimitation, new species and teleomorph-anamorph relationships in Codinaea, Dendrophoma, Paragaeumannomyces and Striatosphaeria (Chaetosphaeriaceae). MycoKeys 74: 17-74. https://doi.org/10.3897/mycokeys.74.57824

Figure 10 Paragaeumannomyces smokiensis (ILLS00121398). A, B ascomata C globose cells of the outer layer of the ascomal wall and an ostiolar seta D, E asci F, G ascal apex with apical annulus H–K ascospores. Scale bars: 250 μm (A, B); 50 μm (C); 20 μm (D, E); 10 μm (F–K).

Figure 1 from: Réblová M, Nekvindová J, Fournier J, Miller AN (2020) Delimitation, new species and teleomorph-anamorph relationships in Codinaea, Dendrophoma, Paragaeumannomyces and Striatosphaeria (Chaetosphaeriaceae). MycoKeys 74: 17-74. https://doi.org/10.3897/mycokeys.74.57824

Figure 1 Combined phylogeny using ITS and 28S of selected members of the Chaetosphaeriaceae. Species names given in bold are taxonomic novelties; T, ET, IST and PT indicate ex-type, ex-epitype, ex-isotype and ex-paratype strains. Thickened branches indicate branch support with MLBS = 100%, PP values = 1.0 and MP = 100 %. Branch support of nodes ≥ 75 % ML and MPBS, and ≥ 0.95 PP is indicated above branches.

opencc-zeroDec 2020View details →

Genetic delimitation of Oreocharis species from Hainan Island

Hainan Island harbours an extraordinary diversity of Gesneriaceae with 14 genera and 23 species, among which two species and one variety are recognized in the genus Oreocharis. These three Oreocharis taxa are all Hainan-endemics and show complex geographical distribution pattern with considerable morphological intermixtures. In this study, we combined DNA (nuclear ITS sequences and cpDNA trnL-trnF and ycf1b) to evaluate genetic delimitation for 12 Oreocharis populations from the island, together with morphological similarity analysis using 16 morphological traits. The results showed Hainan Oreocharis taxa was monophyly with relative low genetic diversity within populations, highly significant genetic differentiation among populations and a significant phylogeographical structure. The 12 populations formed three genetically distinct groups, roughly correspondent to the currently recognized two species and one unknown lineage. The PCA analyses of morphological traits indicate three distinctive groups, differing mainly in petal color and corolla shape and types. The roles of river isolation in the origin and distribution of these three lineages are discussed.

Data from: Cryptic species or inadequate taxonomy? implementation of 2D geometric morphometrics based on integumental organs as landmarks for delimitation and description of copepod taxa

Discovery of cryptic species using molecular tools has become common in many animal groups but it is rarely accompanied by morphological revision, creating ongoing problems in taxonomy and conservation. In copepods, cryptic species have been discovered in most groups where fast-evolving molecular markers were employed. In this study at Yeelirrie in Western Australia we investigate a subterranean species complex belonging to the harpacticoid genus Schizopera Sars, 1905, using both the barcoding mitochondrial COI gene and landmark-based two-dimensional geometric morphometrics. Integumental organs (sensilla and pores) are used as landmarks for the first time in any crustacean group. Complete congruence between DNA-based species delimitation and relative position of integumental organs in two independent morphological structures suggests the existence of three distinct evolutionary units. We describe two of them as new species, employing a condensed taxonomic format appropriate for cryptic species. We argue that many supposedly cryptic species might not be cryptic if researchers focus on analyzing morphological structures with multivariate tools that explicitly take into account geometry of the phenotype. A perceived supremacy of molecular methods in detecting cryptic species is in our view a consequence of disparity of investment and unexploited recent advancements in morphometrics among taxonomists. Our study shows that morphometric data alone could be used to find diagnostic morphological traits and gives hope to anyone studying small animals with a hard integument or shell, especially opening the door to assessing fossil diversity and rich museum collections. We expect that simultaneous use of molecular tools with geometry-oriented morphometrics may yield faster formal description of species. Decrypted species in this study are a good example for urgency of formal descriptions, as they display short-range endemism in small groundwater calcrete aquifers in a paleochannel, where their conservation may be threatened by proposed mining.

opencc-zeroDec 2013View details →

Data from: Species detection and individual assignment in species delimitation: can integrative data increase efficacy?

Statistical species delimitation usually relies on singular data, primarily genetic, for detecting putative species and individual assignment to putative species. Given the variety of speciation mechanisms, singular data may not adequately represent the genetic, morphological and ecological diversity relevant to species delimitation. We describe a methodological framework combining multivariate and clustering techniques that uses genetic, morphological and ecological data to detect and assign individuals to putative species. Our approach recovers a similar number of species recognized using traditional, qualitative taxonomic approaches that are not detected when using purely genetic methods. Furthermore, our approach detects groupings that traditional, qualitative taxonomic approaches do not. This empirical test suggests that our approach to detecting and assigning individuals to putative species could be useful in species delimitation despite varying levels of differentiation across genetic, phenotypic and ecological axes. This work highlights a critical, and often overlooked, aspect of the process of statistical species delimitation—species detection and individual assignment. Irrespective of the species delimitation approach used, all downstream processing relies on how individuals are initially assigned, and the practices and statistical issues surrounding individual assignment warrant careful consideration.

opencc-zeroDec 2013View details →

Data from: Bayesian species delimitation can be robust to guide tree inference errors

The Bayesian method of species delimitation (Yang and Rannala, 2010) uses a so-called guide tree to reduce the number of models to be evaluated in the reversible-jump Markov chain Monte Carlo (rjMCMC) algorithm (Green, 1995). It has been pointed out that the method tends to over-split if a random population tree is used as the guide tree (Fujita and Leaché, 2011). Here we conduct a simulation study to examine the performance of the method under more realistic scenarios, that is, when the guide tree is inferred from the sequence data. We found that Bayesian species delimitation is in general robust to errors in the inferred guide tree.

opencc-zeroDec 2012View details →

Data from: Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent approach: a revised method and evaluation on simulated data sets

DNA barcoding-type studies assemble single-locus data from large samples of individuals and species, and have provided new kinds of data for evolutionary surveys of diversity. An important goal of many such studies is to delimit evolutionarily significant species units, especially in biodiversity surveys from environmental DNA samples. The Generalized Mixed Yule Coalescent (GMYC) method is a likelihood method for delimiting species by fitting within- and between-species branching models to reconstructed gene trees. Although the method has been widely used, it has not previously been described in detail or evaluated fully against simulations of alternative scenarios of true patterns of population variation and divergence between species. Here, we present important reformulations to the GMYC method as originally specified, and demonstrate its robustness to a range of departures from its simplifying assumptions. The main factor affecting the accuracy of delimitation is the mean population size of species relative to divergence times between them. Other departures from the model assumptions, such as varying population sizes among species, alternative scenarios for speciation and extinction, and population growth or subdivision within species, have relatively smaller effects. Our simulations demonstrate that support measures derived from the likelihood function provide a robust indication of when the model performs well and when it leads to inaccurate delimitations. Finally, the so-called single-threshold version of the method outperforms the multiple-threshold version of the method on simulated data: we argue that this might represent a fundamental limit due to the nature of evidence used to delimit species in this approach. Together with other studies comparing its performance relative to other methods, our findings support the robustness of GMYC as a tool for delimiting species when only single-locus information is available.

opencc-zeroOct 2019View details →

Data from: Process-based species delimitation leads to identification of more biologically relevant species

Most approaches to species delimitation to-date have considered divergence-only models. While these models are appropriate for allopatric speciation, their failure to incorporate many of the population-level processes that drive speciation, such as gene flow (e.g. in sympatric speciation), places an unnecessary limit on our collective understanding of the processes that produce biodiversity. To consider these processes while inferring species boundaries, we introduce the R-package delimitR and apply it to identify species boundaries in the reticulate taildropper slug (Prophysaon andersoni). Results suggest that secondary contact is an important mechanism driving speciation in this system. By considering process, we both avoid erroneous inferences that can be made when population-level processes such as secondary contact drive speciation but only divergence is considered, and gain insight into the process of speciation in terrestrial slugs. Further, we apply delimitR to three published empirical datasets and find results corroborating previous findings. Finally, we evaluate the performance of delimitR using simulation studies, and find that error rates are near zero when comparing models that include lineage divergence and gene flow for three populations with a modest number of Single Nucleotide Polymorphisms (SNPs; 1,500) and moderate divergence times (< 100000 generations). When we apply delimitR to a complex model set (i.e. including divergence, gene flow, and population size changes), error rates are moderate (~0.15; 10000 SNPs), and, when present, misclassifications occur between highly similar models.

Data from: The species versus subspecies conundrum: quantitative delimitation from integrating multiple data types within a single Bayesian approach in Hercules beetles

With the recent attention and focus on quantitative methods for species delimitation, an overlooked but equally important issue regards what has actually been delimited. This study investigates the apparent arbitrariness of some taxonomic distinctions, and in particular how species and subspecies are assigned. Specifically, we use a recently developed Bayesian model-based approach to show that in the Hercules beetles (genus Dynastes) there is no statistical difference in the probability that putative taxa represent different species, irrespective of whether they were given species or subspecies designations. By considering multiple data types, as opposed to relying exclusively on genetic data alone, we also show that both previously recognized species and subspecies represent a variety of points along the speciation spectrum (i.e., previously recognized species are not systematically further along the continuum than subspecies). For example, based on evolutionary models of divergence, some taxa are statistically distinguishable on more than one axis of differentiation (e.g., along both phenotypic and genetic dimensions), whereas other taxa can only be delimited statistically from a single data type. Because both phenotypic and genetic data are analyzed in a common Bayesian framework, our study provides a framework for investigating whether disagreements in species boundaries among data types reflect (i) actual discordance with the actual history of lineage splitting, or instead (ii) differences among data types in the amount of time required for differentiation to become apparent among the delimited taxa. We discuss what the answers to these questions imply about what characters are used to delimit species, as well as the diverse processes involved in the origin and maintenance of species boundaries. With this in mind, we then reflect more generally on how quantitative methods for species delimitation are used to assign taxonomic status.

opencc-zeroDec 2015View details →

Data from: Species delimitation with gene flow

Species are commonly thought to be evolutionarily independent in a way that populations within a species are not. In recent years, studies that seek to identify evolutionarily independent lineages (i.e., to delimit species) using genetic data have typically adopted multispecies coalescent approaches that assume that evolutionary independence is formed by the differential sorting of ancestral alleles due to genetic drift. However, gene flow appears to be common among populations and nascent species, and while this process may inhibit lineage divergence (and thus independence), it is usually not explicitly considered when delimiting species. In this article, we apply Phylogeographic Inference using Approximate Likelihoods (PHRAPL), a recently described method for phylogeographic model selection, to species delimitation. We describe an approach to delimiting species using PHRAPL that attempts to account for both genetic drift and gene flow, and we compare the method's performance to that of a popular delimitation approach (BPP) using both simulated and empirical datasets. PHRAPL generally infers the correct demographic-delimitation model when the generating model includes gene flow between taxa, given a sufficient amount of data. When the generating model includes only isolation in the recent past, PHRAPL will in some cases fail to differentiate between gene flow and divergence, leading to model misspecification. Nevertheless, the explicit consideration of gene flow by PHRAPL is an important complement to existing delimitation approaches, particularly in systems where gene flow is likely important.

opencc-zeroDec 2016View details →

Data from: Cryptic diversity and discordance in single-locus species delimitation methods within horned lizards (Phrynosomatidae: Phrynosoma)

Biodiversity reduction and loss continues to progress at an alarming rate, and thus there is widespread interest in utilizing rapid and efficient methods for quantifying and delimiting taxonomic diversity. Single-locus species-delimitation methods have become popular, in part due to the adoption of the DNA barcoding paradigm. These techniques can be broadly classified into tree-based and distance-based methods depending on whether species are delimited based on a constructed genealogy. Although the relative performance of these methods has been tested repeatedly with simulations, additional studies are needed to assess congruence with empirical data. We compiled a large data set of mitochondrial ND4 sequences from horned lizards (Phrynosoma) to elucidate congruence using four tree-based (single-threshold GMYC, multiple-threshold GMYC, bPTP, mPTP) and one distance-based (ABGD) species delimitation models. We were particularly interested in cases with highly uneven sampling and/or large differences in intraspecific diversity. Results showed a high degree of discordance among methods, with multiple-threshold GMYC and bPTP suggesting an unrealistically high number of species (29 and 26 species within the P. douglasii complex alone). The single-threshold GMYC model was the most conservative, likely a result of difficulty in locating the inflection point in the genealogies. mPTP and ABGD appeared to be the most stable across sampling regimes and suggested the presence of additional cryptic species that warrant further investigation. These results suggest that the mPTP model may be preferable in empirical data sets with highly uneven sampling or large differences in effective population sizes of species.

Data from: Delimiting species-poor datasets using single molecular markers: a study of barcode gaps, haplowebs and GMYC

Most single-locus molecular approaches to species delimitation available to date have been designed and tested on data sets comprising at least tens of species, whereas the opposite case (species-poor data sets for which the hypothesis that all individuals are conspecific cannot by rejected beforehand) has rarely been the focus of such attempts. Here we compare the performance of barcode gap detection, haplowebs and generalized mixed Yule–coalescent (GMYC) models to delineate chimpanzees and bonobos using nuclear sequence markers, then apply these single-locus species delimitation methods to data sets of one, three, or six species simulated under a wide range of population sizes, speciation rates, mutation rates and sampling efforts. Our results show that barcode gap detection and GMYC models are unable to delineate species properly in data sets composed of one or two species, two situations in which haplowebs outperform them. For data sets composed of three or six species, bGMYC and haplowebs outperform the single-threshold and multiple-threshold versions of GMYC, whereas a clear barcode gap is only observed when population sizes and speciation rates are both small. The latter conditions represent a "sweet spot" for molecular taxonomy where all the single-locus approaches tested work well; however, the performance of these methods decreases strongly when population sizes and speciation rates are high, suggesting that multilocus approaches may be necessary to tackle such cases.

opencc-zeroDec 2008View details →

Data from: Sampling strategies for delimiting species: genes, individuals, and populations in the Liolaemus elongatus-kriegi complex (Squamata: Liolaemidae) in Andean-Patagonian South America

Recovery of evolutionary history and delimiting species boundaries in widely distributed, poorly-known groups requires extensive geographic sampling, but this is difficult to design a priori because evolutionary diversity is often "hidden" by an inadequate taxonomy. Large data sets are needed, and these provide unique challenges for analysis when they span intra and inter-specific levels of divergence. Protocols have been designed to combine methods of analysis for DNA sequences that exhibit both very shallow and relatively deeper divergences (Crandall and Fitzpatrick, 1996). In this study we combine several tree-based phylogeny reconstruction methods with nested clade analysis, to extract maximum historical signal at various levels, in the poorly-known Liolaemus elongatus-kriegi complex in temperate South America. We implement the basic protocol of Wiens and Penkrot (2002) to test for species boundaries, and propose modifications to accommodate large data sets and gene regions with heterogeneous substitution rates. Combining haplotype trees with nested-clade analyses allowed testing of species boundaries on the basis of a priori defined criteria, and this approach suggests that the number of putative species could be doubled. We discuss these findings in the context of the advantages and limitations of a combined approach for retrieval of maximum historical information in large data sets, in the context of the yet formidable unresolved issues of sampling strategies.

Data from: Coalescent-based species delimitation approach uncovers high cryptic diversity in the cosmopolitan lichen-forming fungal genus Protoparmelia (Lecanorales, Ascomycota)

Species recognition in lichen-forming fungi has been a challenge because of unsettled species concepts, few taxonomically relevant traits, and limitations of traditionally used morphological and chemical characters for identifying closely related species. Here we analyze species diversity in the cosmopolitan genus Protoparmelia s.l. The ~25 described species in this group occur across diverse habitats from the boreal -arctic/alpine to the tropics, but their relationship to each other remains unexplored. In this study, we inferred the phylogeny of 18 species currently assigned to this genus based on 160 specimens and six markers: mtSSU, nuLSU, ITS, RPB1, MCM7, and TSR1. We assessed the circumscription of species-level lineages in Protoparmelia s. str. using two coalescent-based species delimitation methods – BP&P and spedeSTEM. Our results suggest the presence of a tropical and an extra-tropical lineage, and eleven previously unrecognized distinct species-level lineages in Protoparmelia s. str. Several cryptic lineages were discovered as compared to phenotype-based species delimitation. Many of the putative species are supported by geographic evidence.