Macroecological correlates of taxonomic uncertainty in New World coralsnakes

Delimiting species boundaries is a major goal in evolutionary biology. An increasing volume of literature has focused on the challenges of investigating cryptic diversity within complex evolutionary scenarios of speciation, including gene flow and demographic fluctuations. New methods based on model selection, such as approximate Bayesian computation, approximate likelihoods, and machine learning are promising tools arising in this field. Here, we introduce a framework for species delimitation using the multispecies coalescent model coupled with a deep learning algorithm based on convolutional neural networks (CNNs). We compared this strategy with a similar ABC approach. We applied both methods to test species boundary hypotheses based on current and previous taxonomic delimitations as well as genetic data (sequences from 41loci) in Pilosocereus aurisetus, a cactus species complex with a sky-island distribution and taxonomic uncertainty. To validate our method, we also applied the same strategy on data from widely accepted species from the genus Drosophila. The results show that our CNN approach has a high capacity to distinguish among the simulated species delimitation scenarios, with higher accuracy than ABC. For the cactus data set, a splitter hypothesis without gene flow showed the highest probability in both CNN and ABC approaches, a result agreeing with previous taxonomic classifications and in line with the sky-island distribution and low dispersal of P.aurisetus. Our results highlight the cryptic diversity within the P.aurisetus complex and show that CNNs are a promising approach for distinguishing complex evolutionary histories, even outperforming the accuracy of other model-based approaches such as ABC.

ABSTRACTAimIn this study, we sought to understand how the Linnean shortfall (i.e., the lack of knowledge about species taxonomy) interacts with the Darwinian shortfall (i.e., the lack of knowledge about phylogenetic relationships among species), which potentially jeopardises geographical patterns in estimates of speciation rates.LocationNew World.TaxonCoralsnakes (Serpentes: Elapidae).MethodsWe created an index of taxonomic uncertainty (ITU) that measures the likelihood of current species being split after undergoing future taxonomic revisions. The ITU was used in simulations where species with higher taxonomic uncertainty had a higher likelihood of having their phylogenetic branches split, generating new hypothetical species along their geographic ranges. We estimated the speciation rates before and after the split of taxonomically uncertain species.ResultsWe found that a high number of coralsnake species display substantial taxonomic uncertainty, positively correlated with the latitude of the species' geographical range centroid. The estimated speciation rates based on currently available data have a weak relationship with latitude. However, after incorporating taxonomic uncertainty into the phylogeny, we detect a higher positive correlation between speciation rate and latitude.Main ConclusionsThe observed change in speciation rates following the incorporation of taxonomic uncertainty highlights how such uncertainty can undermine the empirical evaluation of geographical patterns in speciation rates, revealing an interaction between the latitudinal taxonomic gradient and the latitudinal diversity gradient. Given that taxonomic changes can alter the number of species recognised as valid over time, our study highlights the need to incorporate taxonomic uncertainty into macroecological and macroevolutionary studies, enhancing the robustness of patterns inferred from these data.

Simple SummaryOur study describes several species of Phaeosphaeriaceae found in terrestrial habitats in Sichuan Province, China. We used morphological and molecular data to accurately delimit these species and determine their taxonomic relationships within the family. Our findings contribute to understanding fungal diversity in China and provide a basis for future studies exploring the ecological roles and biotechnological potential of these fungi. Additionally, our multi-gene phylogenetic approach provides increased accuracy and resolution in the delimitation of species boundaries within Phaeosphaeriaceae.The family Phaeosphaeriaceae is a diverse group of ascomycetous fungi that are commonly found in terrestrial habitats worldwide. In recent years, there has been increasing interest in the biodiversity of Phaeosphaeriaceae in China, particularly in Sichuan Province, which has not been fully explored for its high fungal diversity. In our study, we conducted extensive surveys in Sichuan Province to identify and describe new species of Ascomycota with diverse habitats. Here, we present a taxonomic revision of Phaeosphaeriaceae with taxonomic novelties from terrestrial habitats in Sichuan Province based on a multi-gene phylogenetic approach. Our study focuses on the description of four new species of Phaeosphaeriaceae, representing novel additions to the diversity of this fungal family. Using a combination of morphological and molecular data, we provide detailed descriptions of the new taxa and their placement within the family. Additionally, we discuss the phylogenetic relationships of these new taxa with other members of Phaeosphaeriaceae, providing insights into the correct taxonomic classification of the family. Our taxonomic revision contributes to understanding fungal diversity in China and provides a foundation for future studies investigating the taxonomy and ecological roles of Phaeosphaeriaceae fungi. Furthermore, our multi-gene phylogenetic approach provides increased resolution and accuracy in the delimitation of species boundaries within the family. Our study highlights the importance of continued exploration and taxonomic revision in order to fully understand the diversity and distribution of fungal species in China and beyond. New species: Paraloratospora sichuanensis, Phaeosphaeria chengduensis, P. sichuanensis, and Septoriella shoemakeri. New combinations: Paraloratospora breonadiae, P. fructigena, Septoriella ammophilicola, S. asparagicola, S. festucae, S. luzulae, and S. verrucispora. New names: Septoriella paradactylidis, and S. neomuriformis.

Defining species boundaries, or delimiting species, is a complex and often difficult task. Indeed, when such studies incorporate approaches that consider evolutionary mechanisms, there is much to be learned about species diversity and how the processes that play critical roles in speciation can impact species delineation. In 2021, a virtual workshop on species delimitation was held at the Smithsonian Institution National Museum of Natural History to train natural history scientists and taxonomists on the appropriate analytical tools that can be used to help delimit species when using molecular data. This perspective highlights some of the main themes discussed during that workshop while detailing three processes that can challenge any species delimitation study. Specifically, we discuss incomplete lineage sorting, gene flow, and population structure when delimiting species boundaries using molecular data. We highlight empirical studies and methodological approaches that have successfully met these challenges under various scenarios. Finally, we provide recommendations and considerations for undertaking species delimitation studies in a variety of taxa. To this end, we recommend that taxonomists fully embrace process-based species delimitation, which can provide important insights into speciation in their study systems. For those developing analytical approaches, we hope they consider incorporating less well-known taxa, such as marine invertebrates, into method testing. Marine invertebrates encompass many dark taxa across the tree of life yet represent the majority of animal phyla, many of which are vulnerable to extinction due to global ocean change. Thus, advancing species delimitation to address taxonomic revisions in these organisms will support conservation decisions on keystone ecosystems. Furthermore, the diversity of their life history strategies, the lack of obvious barriers to gene flow in the ocean environment, and their occurrence in isolated habitat patches can better inform our knowledge of speciation and the evolutionary processes that play a role in generating diversity in nature.

Accurate species delimitation is crucial for our understanding of evolution, biodiversity and conservation. However, morphology-based species delimitation alone appears to be prone to taxonomic errors and ineffective for taxa with high interspecific morphological homogeneity or intraspecific morphological variations, as is the case for mesothele and mygalomorph spiders. Combined molecular–morphology species delimitation has shown great potential to delimit species boundaries in such ancient lineages. In the present study, molecular and morphological evidence were integrated to delimit species of the primitively segmented spider genus SongthelaOno, 2000. The cytochrome c oxidase subunit I gene (COI) was sequenced for 192 novel specimens belonging to 12 putative morphospecies. The evolutionary relationships within Songthela and the 12-morphospecies hypothesis were tested in two steps – species discovery and species validation – using four single-locus species delimitation approaches. All species delimitation analyses supported the 12-species hypothesis. Phylogenetic analyses yielded three major clades in Songthela, which are consistent with morphology. Accordingly, we assigned 19 known and 11 new species (S. aokoulong, sp. nov., S. bispina, sp. nov., S. dapo, sp. nov., S. huayanxi, sp. nov., S. lianhe, sp. nov., S. lingshang, sp. nov., S. multidentata, sp. nov., S. tianmen, sp. nov., S. unispina, sp. nov., S. xiujian, sp. nov., S. zizhu, sp. nov.) of Songthela to three species-groups: the bispina-group, the multidentata-group and the unispina-group. Another new species, S. zimugang, sp. nov., is not included in any species groups, but forms a sister lineage to the bispina- and unispina-groups. These results elucidate a high species diversity of Songthela in a small area and demonstrate that integrating morphology with COI-based species delimitation is fast and cost-effective in delimiting species boundaries. http://zoobank.org/urn:lsid:zoobank.org:pub:AF0F5B31-AFAF-4861-9844-445AE8678B67

Species delimitation is critical to our understanding of evolution, biodiversity, and conservation. However, delimiting species boundaries can be challenging, especially when intraspecific divergence is high (and interspecific divergence is low), and gene flow and incomplete lineage sorting are present. Mygalomorph spiders have become models for examining a variety of evolutionary and biogeographical questions. However, their extreme morphological homogeneity and high genetic structuring make delimiting mygalomorph species especially challenging. Integrative approaches to species delimitation, which combine multiple lines of evidence, have been used to infer the limits of many mygalomorph groups in an independent and reproducible way. Yet molecular species delimitation and phylogenetic relationships of the purseweb spider family Atypidae remain scarce. In this study, we explored the phylogeny and species delimitation of Calommata spiders from southern China using data sets including three mitochondrial (COI, 16S, and 12S) and two nuclear (28S, H3) markers. Our phylogenetic analyses yielded a well‐supported clade containing all southern Chinese Calommata and a sister relationship between C. signata and three new species within it. Based on the single‐locus and multilocus species delimitation analyses, we delimited four Calommata species from southern China: one known species (C. signata) and three new species (C. yuanjiangica sp. n., C. hangzhica sp. n. and C. jinggangica sp. n.). This study thus provides a framework for determining the limits of C. signata sensu lato species and calls for further study of systematics and evolutionary relationships within Calommata and other atypid lineages.

Accurately delimiting species boundaries is of critical importance in many areas of biology including population genetics, conservation biology, biogeography, and evolutionary biology because inaccurate species delimitation may significantly affect downstream inferences. The Cycas taiwaniana complex consists of six morphologically similar taxa (C. changjiangensis, C. fairylakea, C. hainanensis, C. lingshuigensis, C. szechuanensis, C. taiwaniana) that are distributed throughout a narrow region of South China. The members of this complex and the taxonomic status of their names have long been debated. In this study, combining morphological characteristics, we employed three distinct approaches to delimit species: haplotype phylogeny delimitation, Bayesian coalescent species delimitation (BPP), and population cluster analyses. To delimitate the species boundaries within the C. taiwaniana complex, we used 4 plastid intergenic spacers (cpDNA), 4 nuclear genes (nDNA) and 10 microsatellites. All three approaches revealed the presence of two distinct species in the C. taiwaniana complex under the unified species concept, C. taiwaniana and C. szechuanensis, largely corresponding to morphological differentiation. Cycas fairylakea was a synonym for C. szechuanensis, and the other three taxa were synonyms for C. taiwaniana. Species delimitation using molecular data was consistent with our preliminary morphological inference. This study thus optimally resolved the species boundaries and taxonomic treatment of the C. taiwaniana complex from an integrated perspective using multiple sources of molecular data and distinct analytical approaches.

Taxonomic inflation: its influence on macroecology and conservation

The delimitation of species boundaries, particularly those obscured by reticulation, is a critical step in contemporary biodiversity assessment. It is especially relevant for conservation and management of indigenous fishes in western North America, represented herein by two species with dissimilar life histories codistributed in the highly modified Colorado River (i.e., flannelmouth sucker, Catostomus latipinnis; bluehead sucker, C. (Pantosteus) discobolus). To quantify phylogenomic patterns and examine proposed taxonomic revisions, we first employed double‐digest restriction site‐associated DNA sequencing (ddRAD), yielding 39,755 unlinked SNPs across 139 samples. These were subsequently evaluated with multiple analytical approaches and by contrasting life history data. Three phylogenetic methods and a Bayesian assignment test highlighted similar phylogenomic patterns in each, but with considerable difference in presumed times of divergence. Three lineages were detected in bluehead sucker, supporting elevation of C. (P.) virescens to species status and recognizing C. (P.) discobolus yarrowi (Zuni bluehead sucker) as a discrete entity. Admixture in the latter necessitated a reevaluation of its contemporary and historic distributions, underscoring how biodiversity identification can be confounded by complex evolutionary histories. In addition, we defined three separate flannelmouth sucker lineages as ESUs (evolutionarily significant units), given limited phenotypic and genetic differentiation, contemporary isolation, and lack of concordance (per the genealogical concordance component of the phylogenetic species concept). Introgression was diagnosed in both species, with the Little Colorado and Virgin rivers in particular. Our diagnostic methods, and the agreement of our SNPs with previous morphological, enzymatic, and mitochondrial work, allowed us to partition complex evolutionary histories into requisite components, such as isolation versus secondary contact.

The taxonomy of the genus Paeonia in central Mediterranean islands has been controversial, with number of recognized taxa changing greatly from one species without infraspecific division to three species or five infraspecific taxa in one species, and with the number of synonyms as great as 30. In the present work, the taxonomic history is thoroughly reviewed and a taxonomic revision is made based on extensive field work, chromosome observation, population sampling, examination of a large amount of herbarium specimens, and subsequent statistic analysis. As a result of the studies P. corsica Sieber ex Tausch, an ignored specific name, is restored at specific rank, and the species is found distinct from all the three subspecies of P. mascula in this region in having mostly nine (vs ≥ 10) leaflets/segments, shorter hairs (1.5 mm vs 3 mm long) on carpels, rather densely holosericeous (vs glabrous or very sparsely hirsute) on the lower surface of leaves. It is a diploid, confined to Corsica France), Sardinia (Italy), Ionian Islands and Akarnania Province of Greece, whereas P. mascula is a tetraploid, widely distributed from Spain to Turkey and Iraq, but not in Corsica, Sardinia and W Greece. In addition, type specimens of four taxa are designated, and 29 botanic names are listed as synonyms of P. corsica in this paper. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

1. Methods that assess patterns of phylogenetic relatedness, as well as character distribution and evolution, allow one to infer the ecological processes involved in community assembly. Assuming niche conservatism, assemblages should shift from phylogenetic clustering to evenness with decreasing geographic scale because the relative importance of mechanisms that shape assemblages is hypothesized to be scale-dependent. Whereas habitat filtering is more likely to act at regional scales because of increased habitat heterogeneity that allows sorting of ecologically similar species in contrasting environments, competition is more likely to act at local scales because low habitat heterogeneity provides few opportunities for niche partitioning. 2. We used species lists to assess assemblage composition, data on ecologically-relevant traits, and a molecular phylogeny, to examine the phylogenetic structure of antbird (Thamnophilidae) assemblages at three different geographical scales: regional (ecoregions), intermediate (100-ha plots) and local (mixed-flocks). In addition, we used patterns of phylogenetic beta diversity and beta diversity to separate the factors that structure antbird assemblages at regional scales. 3. Contrary to previous findings, we found a shift from phylogenetic evenness to clustering with decreasing geographical scale. We argue that this does not reject the hypothesis that habitat filtering is the predominant force in regional community assembly, because analyses of trait evolution and structure indicated a lack of niche conservatism in antbirds. 4. In some cases, phylogenetic evenness at regional scales can be an effect of historical biogeographic processes instead of niche-based processes. However, regional patterns of beta diversity and phylogenetic beta diversity suggested that phylogenetic structure in our study cannot be explained by the history of speciation and dispersal of antbirds, further supporting the habitat-filtering hypothesis. 5. Our analyses suggested that competitive interactions might not play an important role locally, which would provide a plausible explanation for the high alpha diversity of antbirds in Amazonia. 6. Finally, we emphasize the importance of including trait information in studies of phylogenetic community structure to adequately assess the mechanisms that determine species co-existence.

This, the 9th edition of the Checklist of the Birds of Britain, referred to throughout as the British List, has been prepared as a statement of the status of those species and subspecies known to have occurred in Britain and its coastal waters (Fig. 1). It incorporates all the changes to the British List up to and including the 48th Report of the British Ornithologists’ Union Records Committee (BOURC) (BOU 2018), and detailed in BOURC reports published in Ibis since the publication of the 8th edition of the British List (BOU 2013a).

Delimiting species boundaries among closely related lineages often requires a range of independent data sets and analytical approaches. Similar to other organismal groups, robust species circumscriptions in fungi are increasingly investigated within an empirical framework. Here we attempt to delimit species boundaries in a closely related clade of lichen-forming fungi endemic to Asia, the Hypogymnia hypotrypa group (Parmeliaceae). In the current classification, the Hypogymnia hypotrypa group includes two species: H. hypotrypa and H. flavida, which are separated based on distinctive reproductive modes, the former producing soredia but absent in the latter. We reexamined the relationship between these two species using phenotypic characters and molecular sequence data (ITS, GPD, and MCM7 sequences) to address species boundaries in this group. In addition to morphological investigations, we used Bayesian clustering to identify potential genetic groups in the H. hypotrypa/H. flavida clade. We also used a variety of empirical, sequence-based species delimitation approaches, including: the “Automatic Barcode Gap Discovery” (ABGD), the Poisson tree process model (PTP), the General Mixed Yule Coalescent (GMYC), and the multispecies coalescent approach BPP. Different species delimitation scenarios were compared using Bayes factors delimitation analysis, in addition to comparisons of pairwise genetic distances, pairwise fixation indices (FST). The majority of the species delimitation analyses implemented in this study failed to support H. hypotrypa and H. flavida as distinct lineages, as did the Bayesian clustering analysis. However, strong support for the evolutionary independence of H. hypotrypa and H. flavida was inferred using BPP and further supported by Bayes factor delimitation. In spite of rigorous morphological comparisons and a wide range of sequence-based approaches to delimit species, species boundaries in the H. hypotrypa group remain uncertain. This study reveals the potential limitations of relying on distinct reproductive strategies as diagnostic taxonomic characters for Hypogymnia and also the challenges of using popular sequence-based species delimitation methods in groups with recent diversification histories.

Faced with a combination of increasing degradation of habitats and sparse knowledge of species and their distributions, biologists are struggling to find ways of predicting spatial patterns of diversity and then to devise effective strategies for conservation. Area-based conservation planning typically applies complementarity algorithms to identify one or more combinations of areas that effectively represent the known pattern of species diversity (Margules & Pressey 2000). Usually, high-quality distribution data are available for only a limited number of taxonomic groups (e.g. trees, birds, butterflies), so geographic patterns of diversity in these groups must act as a 'surrogate' for those of other taxa. Even this level of knowledge may be lacking for some areas, or at finer spatial scales, leading to the use of environmental (e.g. climate, soil, etc.) data in addition to, or in place of, species' occurrence information (Ferrier 2002; see also Faith et al. 2001). The efficiency of such surrogates appears to vary, especially at the finer spatial scales relevant to most conservation planning efforts (see, for example, van Jaarsveld et al. 1998; Moritz et al. 2001; Lund & Rahbeck 2002).

Species delimitation is at the core of biological sciences. During the last decade, molecular‐based approaches have advanced the field by providing additional sources of evidence to classical, morphology‐based taxonomy. However, taxonomy has not yet fully embraced molecular species delimitation beyond threshold‐based, single‐gene approaches, and taxonomic knowledge is not commonly integrated into multilocus species delimitation models. Here we aim to bridge empirical data (taxonomic and genetic) with recently developed coalescent‐based species delimitation approaches. We use the multispecies coalescent model as implemented in two Bayesian methods ( dissect/stacey and bp&p ) to infer species hypotheses. In both cases, we account for phylogenetic uncertainty (by not using any guide tree) and taxonomic uncertainty (by measuring the impact of using a priori taxonomic assignments to specimens). We focus on an entire Neotropical tribe of butterflies, the Haeterini (Nymphalidae: Satyrinae). We contrast divergent taxonomic opinion – splitting, lumping and misclassifying species – in the light of different phenotypic classifications proposed to date. Our results provide a solid background for the recognition of 22 species. The synergistic approach presented here overcomes limitations in both traditional taxonomy (e.g. by recognizing cryptic species) and molecular‐based methods (e.g. by recognizing structured populations, and not raising them to species). Our framework provides a step forward towards standardization and increasing reproducibility of species delimitations.