Criteria For Species Delimitation Research Articles

Next‐generation species delimitation and taxonomy: Implications for biogeography

AbstractAn accurate species‐level taxonomy is paramount for biogeographical research, and conversely, biogeographical data are of importance for species delimitation. We here review recent developments and future perspectives of taxonomy of direct relevance for biogeographers. The understanding that species are independently evolving segments of population‐level lineages, the rise of integrative approaches to delimit such lineages, and the advent of high‐throughput sequencing have considerably renewed the discipline of taxonomy. Using genome‐scale molecular datasets, the extent of admixture across hybrid zones can now be effectively assessed and the evolutionary independence of lineages inferred, leading to more reliable and comparable species delimitation criteria. Substantially divergent but admixing phylogeographical lineages can conveniently be named as subspecies, thus avoiding taxonomic oversplitting and taxonomic inflation. At the same time, comprehensive DNA barcoding and DNA metabarcoding efforts are uncovering an enormous proportion of undiscovered biotic diversity, and we encourage the development of bioinformatic pipelines that combine high‐throughput species discovery and delimitation with diagnosis and scientific naming, to approach a biotic inventory of the globe without abandoning the established Linnaean system.

Species catalogue of Drymaeus (Mesembrinus) Alberts, 1850 (Gastropoda: Bulimulidae) from Brazil and new data on morphology and distribution of Drymaeus (Mesembrinus) interpunctus (Martens, 1887).

Herein, we attempted to obtain detailed data on the distribution of the species of Drymaeus (Mesembrinus) in Brazil, using biodiversity databases, malacological collections and literature as sources of occurrence records. We provided a catalogue of species, along with distribution maps. We also estimated the suitable distribution of Drymaeus (Mesembrinus) interpunctus using the maximum entropy approach. A detailed description of the anatomy of the soft parts of this species was provided, with new data on the pallial system. For each species we provided information on the compiled data associated with museum collections and the literature. Distribution maps including geographic boundaries, Brazilian biomes and altitude were made with QGIS software 3.16.10 Hannover. For niche modelling, nineteen bioclimatic variables and a topographic variable were used as predictors. The models were performed with MaxEnt version 3.3.3k. Most of the species are represented by scarce material in malacological collections; for some species, these records correspond to type material, indicating that they have not been recollected. Most of the species were represented by shells making anatomical comparison and DNA analysis difficult, limiting our ability to provide new criteria for species delimitation. Our results allowed us to expand the known distribution area for three species, Drymaeus dutaillyi, D. gereti and D. oreades, with new occurrence records in Brazil. The MaxEnt model showed a thin area of high suitability to D. (M.) interpunctus in the Southeastern Brazil, corresponding to the Atlantic Forest. Minimum temperature of the coldest month and mean temperature of coldest quarter were the variables that most influenced the development of the model. Drymaeus interpunctus was described based on specimens collected in Brazil without mention to the exact localities. Herein the new records from databases allowed to expand the known geographic distribution for this species and to infer its potential distribution. Although the type locality of D. interpunctus is in Brazil, the anatomy of the soft parts of specimens from this country was not previously described. The anatomy of the reproductive system of the specimens analyzed herein mostly corresponds to a previous description for specimens from Paraguay, except for the absence of penial sheath and the relative length of the bursa copulatrix duct. The results of niche modeling showed a thin area of high suitability for D. interpunctus and a vast area of moderate suitability, indicating that this species present a niche breadth that favors its occurrence in a range of different biomes, including less suitable areas. The small number of records obtained for most of the species and their restricted ranges associated with habitat destruction may indicate that they are of conservation concern.

A plea for preregistration in taxonomy

There are notoriously many different definitions of species and methods of species delimitation, forcing taxonomists to make a long range of methodological decisions in species delimitation. Because of this, there are sometimes multiple viable competing methodological paths, which could lead to different ranking (or even grouping) decisions. As a result, it is often unclear what it means for a group to be recognized as a species, the groups recognized as species are not always comparable, and some have even called ranking decisions ‘subjective’. To mitigate the problems this causes for users of taxonomy and taxonomists, we propose that taxonomists across the tree of life should start preregistering their research design and criteria for species delimitation in advance of their research. We argue that even if it were to require additional effort, preregistering taxonomic research would strongly benefit taxonomy in the long term, by increasing the transparency and usability of taxonomic outcomes and by reducing the need for ad hoc methodological decisions.

Plumage assisted divergence in a vocally complex island endemic: The Dicrurus paradiseus species complex in Sri Lanka

Models of allopatric speciation within an island biogeographic framework suggest that the division of ancestral mainland populations leads to one or more allopatric island species predominantly through natural and sexual selection or genetic drift. Here we studied phenotypic divergence in a phylogenetic framework in the Dicrurus paradiseus allospecies complex in Sri Lanka, a continental island located in the Indian plate, to understand the complexity of phenotypic divergence on an island. Members of the genus Dicrurus are known as drongos and are conserved in morphology and plumage, but highly variable in vocalization due to vocal learning and mimicry. Two closely related drongos are found in Sri Lanka: the endemic D. lophorinus (or D. paradiseus lophorinus to many authors) found in the wet zone of the island and the widespread continental species D. paradiseus, which inhabits the dry zone. Sampling from all major populations, and voucher specimens from museums across their range in Sri Lanka, we examined phenotypic and genetic variation in this group. The phenotype showed two clusters: birds with a fish-like tail and erect crest (D. lophorinus), and birds with elongated tail streamers with backwardly curved crest (D. paradiseus). There was no significant difference in the vocal traits compared. The genetic variation was examined using two nuclear (Myo 2 and c-mos) and two mitochondrial (ND2 and Cytb) loci and the phylogenetic relationship was analyzed using the Bayesian inference coalescent-based species tree estimation method. The quantitative criteria for species delimitation provided a score sufficient to consider these two taxa as distinct species by considering measurements of body and plumage, acoustics, behaviour and distribution. The phylogeny supports distinct species status for the Sri Lanka Drongo (Dicrurus lophorinus) and that the D. lophorinus and D. paradiseus sister pair diverged since 1.35 mya. The variation in the crest and the tail plumage (components of phenotype) were the main contributors of the divergence, despite the similarity in general appearance and vocalization of the allopatric species.

Assessing Species Boundaries in the Freshwater Snail Family Physidae Using Coalescent-Based Delimitation Methods

A common issue for several freshwater snail families is the fact that, for some genera, the criteria for species delimitation are scarce, subjected to intraspecific and ontogenetic variation, or insufficiently discrete to allow a clear distinction between species. For these genera, the use of molecular approaches is decisive in recognizing valid species. Herein, we applied coalescent methods to delimit evolutionary significant units (ESUs) in Physidae. We used 496 sequences of the mitochondrial cytochrome oxidase subunit I (COI) gene available in GenBank, ascribed to six genera and 25 nominal species, and the algorithms GMYC (General Mixed Yule-Coalescent) with two criteria (single-threshold and multiple-threshold), PTP (Poisson Tree Process), and mPTP (multi-rate Tree Poisson Process). The method that presented the best performance was the mPTP. This method showed a higher frequency of taxonomic species recovery and has delimited a lower number of ESUs (25 ESUs from a dataset attributed to 25 nominal species). Physidae is a family of freshwater snails that presents several issues related to the recognition of species boundaries. Herein, the use of coalescent delimitation methods allowed us to address important taxonomic questions, opening new avenues for future taxonomic research. Our findings have shown that the morphological operational criteria used to delimit several valid species fall within the limits of intraspecific variability, demonstrating taxonomic inflation within this family. Our results also demonstrated the presence of cryptic diversity under the nominal species Physella acuta (Draparnaud, 1805), Beringophysa jennessi (Dall, 1919), Physella pomilia (Conrad, 1834), and Physella gyrina (Say, 1821).

Lineage and role in integrative taxonomy of a heterotrophic orchid complex.

Lineage-based species definitions applying coalescent approaches to species delimitation have become increasingly popular. Yet, the application of these methods and the recognition of lineage-only definitions have recently been questioned. Species delimitation criteria that explicitly consider both lineages and evidence for ecological role shifts provide an opportunity to incorporate ecologically meaningful data from multiple sources in studies of species boundaries. Here, such criteria were applied to a problematic group of mycoheterotrophic orchids, the Corallorhiza striata complex, analysing genomic, morphological, phenological, reproductive-mode, niche, and fungal host data. A recently developed method for generating genomic polymorphism data-ISSRseq-demonstrates evidence for four distinct lineages, including a previously unidentified lineage in the Coast Ranges and Cascades of California and Oregon, USA. There is divergence in morphology, phenology, reproductive mode, and fungal associates among the four lineages. Integrative analyses, conducted in population assignment and redundancy analysis frameworks, provide evidence of distinct genomic lineages and a similar pattern of divergence in the extended data, albeit with weaker signal. However, none of the extended data sets fully satisfy the condition of a significant role shift, which requires evidence of fixed differences. The four lineages identified in the current study are recognized at the level of variety, short of comprising different species. This study represents the most comprehensive application of lineage + role to date and illustrates the advantages of such an approach.

Integrative taxonomy reveals a new species of Cyphocharax (Characiformes: Curimatidae) from the Upper Paraíba do Sul River basin, Brazil

Abstract A new species of Cyphocharax is described from the Upper Paraíba do Sul River basin, São Paulo, Brazil based on integrated morphological and molecular delimitation criteria. It is morphologically distinguished from its congeners by the presence of a round, dark blotch at the midlength of the caudal peduncle not extending to the proximal portions of the median caudal-fin rays, 19–20 circumpeduncular scales, 34–41 perforated lateral-line scales, 6–7 longitudinal scale rows above and below the lateral line, greatest body depth corresponding to 34.7–39.9% of standard length (SL), and the caudal peduncle depth corresponding to 13.3–15.2% of SL. The lowest genetic distances between the new species and other congeners are: 2.5% from C. gilbert, followed by 3.0% from C. santacatarinae, and 3.2% from C. aff. gilbert. All species delimitation criteria employed herein corroborated the recognition of the new species. In addition, comments on its conservation status are provided.

How to Render Species Comparable Taxonomic Units Through Deep Time: A Case Study on Intraspecific Osteological Variability in Extant and Extinct Lacertid Lizards.

Generally, the species is considered to be the only naturally occurring taxon. However, species recognized and defined using different species delimitation criteria cannot readily be compared, impacting studies of biodiversity through Deep Time. This comparability issue is particularly marked when comparing extant with extinct species because the only available data for species delimitation in fossils are derived from their preserved morphology, which is generally restricted to osteology in vertebrates. Here, we quantify intraspecific, intrageneric, and intergeneric osteological variability in extant species of lacertid lizards using pairwise dissimilarity scores based on a data set of 253 discrete osteological characters for 99 specimens referred to 24 species. Variability is always significantly lower intraspecifically than between individuals belonging to distinct species of a single genus, which is in turn significantly lower than intergeneric variability. Average values of intraspecific variability and associated standard deviations are consistent (with few exceptions), with an overall average within a species of 0.208 changes per character scored. Application of the same methods to six extinct lacertid species (represented by 40 fossil specimens) revealed that intraspecific osteological variability is inconsistent, which can at least in part be attributed to different researchers having unequal expectations of the skeletal dissimilarity within species units. Such a divergent interpretation of intraspecific and interspecific variability among extant and extinct species reinforces the incomparability of the species unit. Lacertidae is an example where extant species recognized and defined based on a number of delimitation criteria show comparable and consistent intraspecific osteological variability. Here, as well as in equivalent cases, application of those skeletal dissimilarity values to paleontological species delimitation potentially provides a way to ameliorate inconsistencies created by the use of morphology to define species. [Intraspecific variation; Lacertidae; morphological disparity; osteology; species delimitation; taxonomic bias.].

Integrative taxonomy and geographic sampling underlie successful species delimitation

Abstract Species delimitation requires a broad assessment of population-level variation using multiple lines of evidence, a process known as integrative taxonomy. More specifically, studies of species limits must address underlying questions of what limits the distribution of populations, how traits vary in association with different environments, and whether the observed trait differences may lead to speciation through reproductive isolation. While genomic data have revolutionized the process of delimiting species, such data should be analyzed along with phenotypic, behavioral, and ecological traits that shape individuals across geographic and environmental space. The integration of multiple traits promotes taxonomic stability and should be a major guiding principle for species delimitation. Equally important, however, is thorough geographic sampling to adequately represent population-level variation—both in allopatry and across putative contact zones. We discuss the importance of both of these factors in the context of species concepts and traits and present different examples from birds that illustrate criteria for species delimitation. In addition, we review a decade of proposals for species-level taxonomic revisions considered by the American Ornithological Society’s North American Classification Committee, and summarize the basis for decisions on whether to split or lump species. Finally, we present recommendations and discuss challenges (specifically permits, time, and funding) for species delimitation studies. This is an exciting time to be studying species delimitation in birds: many species-level questions remain, and methodological advances along with increased access to data enable new approaches to studying age-old problems in avian taxonomy.

Homoplasy as an Auxiliary Criterion for Species Delimitation.

Homoplasy is a sort of noise in phylogenetic reconstructions, due to the accumulation of backmutations, convergent evolution and horizontal gene transfer (HGT), which is considered the major trigger of homoplasy in microorganism for its massive presence. It is also known that homoplasy increases with the complexity of the tree with both real and simulated data. In this paper, we analyzed the variation of homoplasy with the two widely used taxonomic markers ITS and LSU in four taxonomic models characterized by differences in the intra-specific distances. An algorithm (HomoDist) was developed to analyze the homoplasy index (HI) variation upon addition of a single element (strain or species) in increasing distance from a starting element. This algorithm allows to follow changes of the consistency index (CI), complementary to the HI, with the increase of the number of taxa and with the increase of the distance among elements. Results show that homoplasy increases—as expected—with the number of taxa, but also as a function of the overall distance among species, often with an almost linear relationship between distance and HI. No HI change was observed in trees with few taxa spanning through short distances, indicating that this noise is not prohibitive in this context, although the analysis of the ratio between HI and distance can be recommended as a criterion for tree acceptance. The absence of large changes of the HI within the species, and its increase when new species are added by HomoDist, suggest that homoplasy variation can be used as an auxiliary test in distance-based species delimitation with any type of marker.

DISTATIS: A Promising Framework to Integrate Distance Matrices in Molecular Phylogenetics.

Molecular phylogenetic algorithms frequently disagree with the approaches considering reproductive compatibility and morphological criteria for species delimitation. The question stems if the resulting species boundaries from molecular, reproductive and/or morphological data are definitively not reconcilable; or if the existing phylogenetic methods are not sensitive enough to agree morphological and genetic variation in species delimitation. We propose DISTATIS as an integrative framework to combine alignment-based (AB) and alignment-free (AF) distance matrices from ITS2 sequences/structures to shed light whether Gelasinospora and Neurospora are sister but independent genera. We aimed at addressing this standing issue by harmonizing genus-specific classification based on their ascospore morphology and ITS2 molecular data. To validate our proposal, three phylogenetic approaches: i) traditional alignment-based, ii) alignment-free and iii) novel distance integrative (DI)-based were comparatively evaluated on a set of Gelasinospora and Neurospora species. All considered species have been extensively characterized at both the morphological and reproductive levels and there are known incongruences between their ascospore morphology and molecular data that hampers genus-specific delimitation. Traditional AB phylogenetic analyses fail at resolving the Gelasinospora and Neurospora genera into independent monophyletic clades following ascospore morphology criteria. In contrast, AF and DI approaches produced phylogenetic trees that could properly delimit the expected monophyletic clades. The DI approach outperformed the AF one in the sense that it could also divide the Neurospora species according to their reproduction mode.

DNA barcoding elucidates the population genetic diversity of venomous cobra species (Reptilia: Elapidae) in Indo-Bangladesh region

The DNA barcode data of venomous cobra species (Naja naja and Naja kaouthia) are limited in the global database, especially from India and Bangladesh. Owing to the rapid success of DNA barcoding for discriminating a variety of species around the world, the present study aimed to generate the mitochondrial cytochrome c oxidase subunit I (COI) gene information of two morphologically identified deadly elapid species from the Mizoram state in northeast India and Rangpur in northern Bangladesh. The multiple species delimitation methods: Automatic Barcode Gap Discovery (ABGD), General Mixed Yule-Coalescent (GMYC), and Poisson-Tree-Processes (bPTP) revealed 14, 16, and 18 molecular operational taxonomic units (MOTUs) for 12 Naja species. The binocellate cobra, N. naja showed monophyletic clustering in both maximum-likelihood (ML) and Bayesian (BA) trees, single MOTU in ABGD and GMYC, and negligible intra-species genetic distance (0.2%) with two haplotypes. However, the monocellate cobra, N. kaouthia showed paraphyletic and polytomy in ML and BA phylogenies respectively; more than one MOTUs in ABGD, GMYC, and bPTP analyses; and sufficient intra-species genetic distances (0.6–2.3%) with five haplotypes related to the diverse geographical locations in Bangladesh, China, India, and Thailand. By superimposing the executed species delimitation criteria, the present molecular-based investigation concludes the presence of cryptic diversity of N. kaouthia in Indo-Bangladesh, China, and Thailand.

Vastly underestimated species richness of Amazonian salamanders (Plethodontidae: Bolitoglossa) and implications about plethodontid diversification

We present data showing that the number of salamander species in Amazonia is vastly underestimated. We used DNA sequences of up to five genes (3 mitochondrial and 2 nuclear) of 366 specimens, 189 corresponding to 89 non-Amazonian nominal species and 177 Amazonian specimens, including types or topotypes, of eight of the nine recognized species in the region. By including representatives of all known species of Amazonian Bolitoglossa, except for one, and 73% of the currently 132 recognized species of the genus, our dataset represents the broadest sample of Bolitoglossa species, specimens, and geographic localities studied to date. We performed phylogenetic analyses using parsimony with tree-alignment and maximum likelihood (ML) with similarity alignment, with indels as binary characters. Our optimal topologies were used to delimit lineages that we assigned to nominal species and candidate new species following criteria that maximize the consilience of the current species taxonomy, monophyly, gaps in branch lengths, genetic distances, and geographic distribution. We contrasted the results of our species-delimitation protocol with those of Automated Barcode Gap Discovery (ABGD) and multi-rate Poisson Tree Processes (mPTP). Finally, we inferred the historical biogeography of South American salamanders by dating the trees and using dispersal-vicariance analysis (DIVA). Our results revealed a clade including almost all Amazonian salamanders, with a topology incompatible with just the currently recognized nine species. Following our species-delimitation criteria, we identified 44 putative species in Amazonia. Both ABGD and mPTP inferred more species than currently recognized, but their numbers (23–49) and limits vary. Our biogeographic analysis suggested a stepping-stone colonization of the Amazonian lowlands from Central America through the Chocó and the Andes, with several late dispersals from Amazonia back into the Andes. These biogeographic events are temporally concordant with an early land bridge between Central and South America (~10–15 MYA) and major landscape changes in Amazonia during the late Miocene and Pliocene, such as the drainage of the Pebas system, the establishment of the Amazon River, and the major orogeny of the northern Andes.

Morphological and molecular species boundaries in the Hyalella species flock of Lake Titicaca (Crustacea: Amphipoda)

The Hyalella species diversity in the high-altitude water bodies of the Andean Altiplano is addressed using mitochondrial cox1 sequences and implementing different molecular species delimitation criteria. We have recorded the presence of five major genetic lineages in the Altiplano, of which one seems to be exclusive to Lake Titicaca and nearby areas, whereas the rest occur also in other regions of South America. Eleven out of 36 South American entities diagnosed by molecular delimitation criteria in our study are likely endemic to the Titicaca and neighbouring water bodies. We have detected a remarkable disagreement between morphology and genetic data in the Titicacan Hyalella, with occurrence of several cases of the same morpho-species corresponding to several Molecular Operational Taxonomic Units (MOTUs), some even distantly related, and other instances where a particular MOTU is shared by a morphologically heterogeneous array of species, including species with body smooth and others with body heavily armoured. Species diversification and incongruence between morphological and molecular boundaries within this species assemblage may be associated to the sharp changes in hydrological conditions experienced by the water bodies of the Altiplano in the past, which included dramatic fluctuations in water level and salinity of Lake Titicaca. Such environmental shifts could have triggered rapid morphological changes and ecological differentiation within the Hyalella assemblage, followed by phenotypic convergence among the diverse lineages. Factors such as phenotypic plasticity, incomplete lineage sorting or admixture between divergent lineages might lie also at the root of the morphological-genetic incongruence described herein.

Taxonomy needs pluralism, but a controlled and manageable one

What we accept as the units to be classified is not just an expression of our current aims and  practices but will also impact further classificatory research. The launch of Megataxa invites a dispassionate discussion about the units to be classified and the names associated to them. Specifically, we must address three challenges.—Challenge 1. Living with pluralism in biological classifications. Despite the enormous amount of ink spent on this issue, there is little hope of finding a species concept at the same time satisfactory from a theoretical point of view and reliable as a guide for taxonomic practice. This unavoidably causes a degree of pluralism in biological classification, as the taxonomic units generally described as species are not necessarily comparable. Also, different users of classification may have different expectations, better satisfied by alternative solutions rather than by a consensus classification. The obvious tension between these different expectations cannot be easily solved by authority or consensus, or simply hoping in the future availability of better criteria for species delimitation. - Challenge 2. Managing multiple classifications within one nomenclature system. Changing taxonomy is the source of ambiguity in the meaning of species names. As a consequence, Linnaean names may not be unique and universal labels for the taxa we recognize. The problem can be solved by specifying taxonomic concepts, i.e. by associating the names to the contexts in which these are used.—Challenge 3. Managing the nomenclature for provisionally circumscribed taxa. Molecular Operational Taxonomic Units (MOTUs) do not correspond necessarily to conventional taxonomic species and no simple or universal rule exists to ‘translate’ MOTUs into Linnaean species. Provisionally recognized MOTUs do not get a Linnaean name, but are labelled with a formula, in too many cases following no acknowledged standard and thus becoming useless for communication purposes. Non-Linnaean names, or formulas, for provisionally circumscribed taxa cannot be rejected, but some international consensus is needed. 

Defining the core group of the genus Gomphonema Ehrenberg with molecular and morphological methods

ABSTRACTIn order to understand the taxonomy and phylogeny of the genus Gomphonema, the type of the name of the genus, G. acuminatum, and related species complexes are studied with an integrative taxonomic approach. Sixty-seven unialgal Gomphonema strains were established from 34 different water bodies in Croatia, Faroe Islands, Finland, Iceland, Germany, Mexico, Spain, Switzerland and Korea, which provided molecular (18S and rbcL), morphometric and ultrastructural data. Our study was complemented by molecular data from INSDC, summing up the studied data to 82 freshwater Gomphonema strains from the G. acuminatum and related species complexes which are here defined as the Gomphonema core group. Except for outline variations which occur even within one clone, their micro-morphologies are indistinguishable. The molecular data of the two markers clustered the taxa of the core group into one clade, well differentiated from other Gomphonema taxa such as G. augur and G. parvulum. For differentiation within the clade, the plastid marker rbcL provided better species resolution comparable to traditionally recognized taxa. The combined analysis of the molecular as well as morphological data resulted in the defining of only 7 subclades in contrast to 20 currently assigned names for the taxa of the Gomphonema core group in this study. The Gomphonema core group has been overdescribed due to the use of outline as the main criterion for species delimitation. A polyphasic approach, combining molecular and micromorphological data for taxonomy, nomenclatural evaluation, and observations from clonal cultures can reveal the full intricacies of evolutionary relations.

Review and Interpretation of Trends in DNA Barcoding

Interpretations and analytical practices surrounding DNA barcoding are reviewed from a compilation of 3,756 papers (as of December 31, 2018) with “DNA Barcode” in the title since 2004. By examining the practice of DNA barcoding in natural history and biodiversity science over this period, we explore the extent to which its purposes, premises, rationale and application have evolved. The number of studies involving identification, taxonomic decisions and the discovery of cryptic species has driven the publication of DNA barcode studies overall. Forensic studies and papers on biological conservation involving DNA barcodes have tracked the ensemble number of studies but rose sharply in 2017. Although neighbor-joining and graphic (tree-based) criteria for species delimitation have been preeminent, analytical paradigms have diversified slightly following the growing availability of tools in the Barcode of Life Database (BoLD). We conclude that the paradigms of DNA barcoding data are likely to persist and, in groups such as Lepidoptera, DNA barcoding has become a widely used tool in taxonomic science. The degree to which systematists will avail themselves of tools for extracting diagnostic data from barcodes remains to be seen.

In defence of taxonomic governance

It is well known that taxonomists rely on many different methods and criteria for species delimitation, leading to different kinds of groups being recognised as species. While this state of relative disorder is widely acknowledged, there is no similar agreement about how it should be resolved. This paper considers the view that the disorder in species classification should be resolved by a system of taxonomic governance. I argue that such a system of governance is best seen as a combination of standardisation, unification and regulation, each of which can be implemented in different forms. I investigate the forms that these three components should take for taxonomic governance by looking into two successfully governed classification systems, namely, virus classification and enzyme classification. The last part of the paper then defends the governance view against five objections.

Novel primers improve species delimitation in Cercospora

The genus Cercospora includes many important plant pathogens that are commonly associated with leaf spot diseases on a wide range of cultivated and wild plant species. Due to the lack of useful morphological features and high levels of intraspecific variation, host plant association has long been a decisive criterion for species delimitation in Cercospora. Because several taxa have broader host ranges, reliance on host data in Cercospora taxonomy has proven problematic. Recent studies have revealed multi-gene DNA sequence data to be highly informative for species identification in Cercospora, especially when used in a concatenated alignment. In spite of this approach, however, several species complexes remained unresolved as no single gene proved informative enough to act as DNA barcoding locus for the genus. Therefore, the aims of the present study were firstly to improve species delimitation in the genus Cercospora by testing additional genes and primers on a broad set of species, and secondly to find the best DNA barcoding gene(s) for species delimitation. Novel primers were developed for tub2 and rpb2 to supplement previously published primers for these loci. To this end, 145 Cercospora isolates from the Iranian mycobiota together with 25 additional reference isolates preserved in the Westerdijk Fungal Biodiversity Institute were subjected to an eight-gene (ITS, tef1, actA, cmdA, his3, tub2, rpb2 and gapdh) analysis. Results from this study provided new insights into DNA barcoding in Cercospora, and revealed gapdh to be a promising gene for species delimitation when supplemented with cmdA, tef1 and tub2. The robust eight-gene phylogeny revealed several novel clades within the existing Cercospora species complexes, such as C. apii, C. armoraciae, C. beticola, C. cf. flagellaris and Cercospora sp. G. The C. apii s. lat. isolates are distributed over three clades, namely C. apii s. str, C. plantaginis and C. uwebrauniana sp. nov. The C. armoraciae s. lat. isolates are distributed over two clades, C. armoraciae s. str. and C. bizzozeriana. The C. beticola s. lat. isolates are distributed over two clades, namely C. beticola s. str. and C. gamsiana, which is newly described.

Description of two new species of allocreadiid trematodes (Digenea: Allocreadiidae) in middle American freshwater fishes using an integrative taxonomy approach.

Integrative taxonomy uses several sources of information to establish more robust species delimitation criteria. In this study, we followed that approach to describe two new species of allocreadiid trematodes from freshwater fish distributed in locations across Middle America. The new species were first recognized by using sequences of the domains D1-D3 of the ribosomal 28S rRNA gene and then, morphological data (light and scanning electron microscopy (SEM)), host association, and geographical distribution were considered as additional sources of information to complement the species delimitation and description. Auriculostoma tica n. sp. was found in the intestine of Gymnotus maculosus Albert and Miller in Costa Rica, while Wallinia anindoi n. sp. was found in the intestine of Astyanax aeneus (Günther) in Oaxaca and Chiapas, Mexico, as well as in a location of Guatemala. A phylogenetic analysis combining newly generated sequences of the two new species along with those available for other allocreadiids in GenBank, revealed that isolates of each species are reciprocally monophyletic, and also their interrelationships: Au. tica n. sp. is a sister taxon of Auriculostoma totonacapanensis Razo-Mendivil et al., 2014, and W. anindoi n. sp. is a sister taxon of Wallinia brasiliensis Dias, et al., 2018. Genetic distances for the 28S rRNA gene were estimated among the American species of allocreadiids and further supported the validity of the new species.