Taxonomic Recognition Research Articles

Probability-based preservational variations within the early Cambrian Chengjiang biota (China).

The Chengjiang biota (Yunnan Province, China) is a treasure trove of soft-bodied animal fossils from the earliest stages of the Cambrian explosion. The mechanisms contributing to its unique preservation, known as the Burgess Shale-type preservation, are well understood. However, little is known about the preservation differences between various animal groups within this biota. This study compares tissue-occurrence data of 11 major animal groups in the Chengjiang biota using a probabilistic methodology. The fossil-based data from this study is compared to previous decay experiments. This shows that all groups are not equally preserved with some higher taxa more likely to preserve soft tissues than others. These differences in fossil preservation between taxa can be explained by the interaction of biological and environmental characteristics. A bias also results from differential taxonomic recognition, as some taxa are easily recognized from even poorly preserved fragments while other specimens are difficult to assign to higher taxa even with exquisite preservation.

Relationships within Mcneillia Indicate a Complex Evolutionary History and Reveal a New Species of Minuartiella (Caryophyllaceae, Alsinoideae).

The genus Mcneillia has been recently segregated from Minuartia L. based on molecular results, also supported by morphology. However, to date, a comprehensive study on the phylogenetic relationships within this genus is lacking. In this paper, we provide a multigene phylogeny of all the species and subspecies of Mcneillia employing two nuclear and six chloroplast markers. We documented extensive gene flow between taxa, sometimes separated at specific rank. In addition, Mcneillia as currently circumscribed, is not monophyletic. In fact, Mcneillia graminifolia subsp. brachypetala, strictly endemic to Greece, truly belongs to Minuartiella, a genus otherwise limited to South-West Asia. Moreover, even after removal of this taxon, our results do not support the monophyly of the taxa included in M. graminifolia s.l., the most variable and widespread species of the genus. Further controversial subspecies of Mcneillia graminifolia, i.e., subsp. hungarica and subsp. rosanoi, are shown to deserve taxonomic recognition as separate species, whereas Mc. moraldoi is not distinct at specific rank. In addition, Mc. saxifraga subsp. tmolea is here regarded as a further distinct species. A consistent taxonomic treatment is therefore proposed with six new combinations and nomenclatural notes, providing the necessary typifications.

Cryptic Species of Freshwater Sculpin (Cottidae: Cottus) in California, USA.

The Riffle Sculpin (Cottus gulosus) is a small, bottom-dwelling fish regarded as widespread in the cool-water streams that flow into Californias Central Valley and into streams of the central California coast. Using population genomics, supported by other genetic, distributional, and meristic studies, we demonstrate that C. gulosus consists of three cryptic species with four subspecies (five lineages), all but one entirely endemic to California: Cottus pitensis, Pit Sculpin Bailey and Bond 1963 Cottus gulosus, Inland Riffle Sculpin (Girard 1854) g. gulosus: San Joaquin Riffle Sculpin (Girard 1854), nominate subspecies g. wintu: Sacramento Riffle Sculpin, Moyle and Campbell 2022, new subspecies Cottus ohlone, Coastal Riffle Sculpin Moyle and Campbell 2022, new species o. ohlone, Ohlone Riffle Sculpin Moyle and Campbell 2022, nominate subspecies o. pomo, Pomo Riffle Sculpin Moyle and Campbell 2022, new subspecies. The three species are endemic to California watersheds although the range of C. pitensis extends into southeastern Oregon. All are confined to cool headwater streams or to rivers with cold water releases below dams. Their populations are increasingly isolated from one another because of anthropogenic changes to Californias river systems and some are threatened with extinction. Providing taxonomic recognition of the distinct forms will improve conservation efforts on their behalf. This study also demonstrates how genomics can be used to resolve situations where signals from mitochondrial and nuclear DNA are in conflict.

Extensive Sampling Provides New Insights into Phylogenetic Relationships between Wild and Domesticated Zanthoxylum Species in China

Zanthoxylum, belonging to the Rutaceae family, is widely distributed in tropical and subtropical regions. The genus has high economic value as spices, oils, medicinal plants, and culinary applications. Zanthoxylum has a long history of domestication and cultivation in China. However, the phylogenetic relationships and origin of wild and cultivated Zanthoxylum species in China remain largely unknown. Moreover, there is still no clear molecular phylogenetic system for Zanthoxylum species. Herein, 373 Zanthoxylum samples were collected from all presently known provenances of Zanthoxylum in China. In this study, four chloroplast DNA (cpDNA) markers (matK, ndhH, psbB, rbcL) were used to comprehensively analyze the genetic diversity, relatedness, and geographical origin of Chinese Zanthoxylum species. The results were as follows: (1) The aligned length of the four pairs of cpDNA sequences was 3836 bp, and 68 haplotypes were identified according to 219 variable polymorphic sites, including 90 singleton variable sites, 129 parsimony informative sites, 3 Indels (insertions and deletions). (2) Phylogenetic tree and haplotype network strongly supported the division of Zanthoxylum species consistent with the taxonomic recognition of five species: Z. bungeanum, Z. piasezkii, Z. piperitum, Z. armatum, and Z. micranthum. (3) Divergence time estimation suggested that Zanthoxylum genus originated from the Late Eocene, and most Zanthoxylum species diverged after the Middle Miocene. (4) Haplotype 16 (H16) was at the bottom of the phylogenetic tree, had higher haplotype diversity (Hd) and nucleotide polymorphism (Pi) than other haplotypes, and was located in the center of the network figure. Therefore, we deduced that the cultivated Zanthoxylum species may originate in Zhouqu County, Gansu Province, China. Meanwhile, our research provided a scientific basis for the identification and breeding programs of Chinese Zanthoxylum species.

Updated taxonomy on Gerronema (Porotheleaceae, Agaricales) with three new taxa and one new record from China.

Only three Gerronema (Porotheleaceae) species have been previously recorded in China. Here, we report collections of a fourth species in China: G.nemorale Har. Takah., which is widely distributed in Chinese temperate to subtropical zones. We also formally describe three new species, collected from Anhui, Fujian, and Zhejiang provinces: G.baishanzuense sp. nov., G.microcarpum sp. nov., and G.zhujian sp. nov. Furthermore, we include the results of a phylogenetic analysis of Porotheleaceae based on a multi-locus (ITS + nLSU) dataset. The results, which indicate that Gerronema is polyphyletic, support the taxonomic recognition of the three new species. Morphological descriptions, photographs, line drawings, and comparisons with closely related taxa are presented for the new and newly recorded species. A key to the seven species of Gerronema in China is also provided.

Species delimitation, hybridization and possible apomixis in a rapid radiation of Western AustralianLeptospermum(Myrtaceae)

AbstractSpecies delimitation is challenging in rapid radiations because the typical markers of speciation are often obscured. Here, we use comprehensive sampling and genome-wide single nucleotide polymorphisms to assess species boundaries in a radiation of nine morphologically similar Leptospermum taxa that failed to be discriminated in previous phylogenomic analyses. Our data recovered clear separation of L. maxwellii, L. sericeum and L. inelegans as currently circumscribed. A phrase-named taxon, Leptospermum. sp. Peak Charles/Norseman, was not distinct from L. incanum, and we recommend their synonymization. Another pair, L. nitens and L. roei, were also indistinct and differ by a single morphological character that also varies in L. inelegans without taxonomic recognition. We recommend synonymization of L. nitens and L. roei and consistent treatment of this character as a non-diagnostic, variable trait. Difficulty arose in discriminating L. erubescens and L. oligandrum; we make three suggestions and recommend further morphological investigation to determine the most appropriate taxonomic outcome. As expected, hybridization was common across the complex, but, unexpectedly, many individual plants were genetically identical within, and sometimes between, populations of most species. We hypothesize that this is due to apomixis. Overall, this study demonstrates the value of population genomics in the integrative taxonomy toolbox for disentangling species in rapid radiations, while also offering insight to the evolution of this poorly known group of Australian Leptospermum.

Morphological-molecular incongruence in Sphagnum majus ssp. majus and ssp. norvegicum

Species delimitation is problematic in many plant groups and among the mosses, Sphagnum is one of the more contentious genera because of high levels of morphological variation. The allopolyploid species, Sphagnum majus, comprises one such problematic complex. Two morphologically differentiated but overlapping subspecies have been described. We conducted morphometric and molecular analyses with samples from around the Northern Hemisphere to test for phenotypic and phylogenetic differentiation between the subspecies. Although field collections of the two species can be statistically differentiated morphologically, there is substantial overlap. Genome-scale molecular data do not suggest any differentiation between S. majus ssp. majus and ssp. norvegicum, including samples assigned to the two taxa from sympatric sites. Sequence data from the plastid genome were employed to infer parentage of allopolyploid S. majus. Our results support the hypothesis that S. annulatum is the paternal parent and S. cuspidatum is the maternal parent. We conclude that the morphological differences between them are either plastic responses to habitat heterogeneity or segregating genetic variation within a single taxon. Formal taxonomic recognition of two taxa is not supported by our molecular data.

Cryptic species of pondweeds (Potamogetonaceae) at an intercontinental scale revealed by molecular phylogenetic analyses

AbstractCryptic species are morphologically indistinguishable but genetically divergent entities that constitute an important part of Earth's biodiversity. They occur in all kingdoms of life, especially when morphological characters are scarce. Compared to the high number of plant species, relatively few cryptic species have been detected so far. Here, we report cryptic species in pondweeds (Potamogeton), freshwater aquatic angiosperms that are characterized by reduced morphology. Using four molecular markers (ITS, 5S‐NTS, rpl20‐5′rps12, trnT‐trnL), three of them unlinked, we found that the widespread P. octandrus consists of three divergent lineages that correspond to the geographic origins of samples from Africa, Asia, and Australia, respectively. Relatively high genetic divergence between these lineages, reciprocal monophyly and many fixed diagnostic characters indicate that P. octandrus consists of three cryptic species. We formally distinguish the African lineage as P. parvifolius and the Australian lineage as P. tenuicaulis from Asian P. octandrus s.str. Potamogeton tenuicaulis is paraphyletic with the Asian species P. cristatus, which differs by unique fruit characters. We assume that the ancestor of P. cristatus originated from Australia and reached Asia by long‐distance dispersal. Quality criteria for assigning species status to cryptic species and their formal taxonomic recognition are discussed.

Populational Differentiation in Boana bischoffi (Anura, Hylidae): Revisiting the Issue Using Molecular, Morphological, and Acoustic Data

Boana bischoffi was originally described from the Brazilian state of Rio Grande do Sul and has Boana multilineata from São Paulo as a junior synonym. The history of its nomenclature reflects the varying interpretation of the dorsal color pattern of the two different populations. We reevaluate the problem of taxonomic recognition of Boana multilineata based on molecular, morphometric, and acoustic data. The molecular data revealed two major clades that are partially concordant with the morphological and acoustic differentiation. Morphometric analyses revealed elements of differentiation between populations in snout–vent length (SVL) and head shape, which were patterns not detected previously. Discrimination considering call features was substantial, even complete in a discriminant analysis. Despite these differences, we refrain from resurrecting the name B. multilineata due to the existence of putative introgression zones, the effect of SVL in call dominant frequency, and lack of taxonomically relevant differences. Boana bischoffi might represent a case of incipient speciation.

The Motor Action Analysis Based on Deep Learning

For the slow speed and low accuracy of slow motor action recognition methods, this study proposes a motor action analysis method based on the CNN network and the softmax classification model. First, in order to obtain motor action feature information, by using static spatial features of BN-inception based on CNN network extracted actions and high-dimensional features of 3D ConvNet, then based on softmax classifier structure and realizing taxonomic recognition of the motor actions. Finally, through the decision-layer fusion and time semantic continuity optimization strategy, the motion action recognition accuracy is further improved and the more efficient motion action classification recognition is realized. The results show that the proposed method can complete the motor action analysis and achieve the classification recognition accuracy to 83.11%, which has certain practical value.

Taxonomy, allometry, sexual dimorphism, and conservation of the trans-Andean watersnakeHelicops danieliAmaral, 1937 (Serpentes: Dipsadidae: Hydropsini)

The extensive lack of knowledge on the morphological aspects of South American watersnakes includes a poor understanding of phenotypic parameters, intraspecific variation, and conservation of the trans-Andean Helicops species, Daniel’s Keelback (Helicops danieli Amaral, 1937). For the first time, we provide a multidisciplinary view using key features (e.g., morphology and niche modeling) to improve the taxonomic recognition of this species, as well as describing ontogenetic color changes, allometry, sexual dimorphism, and the conservation status of this poorly studied snake. First, we emended the morphological diagnosis of H. danieli with 23 characters and detected that juvenile tail length is positively related to allometric growth, and that juveniles differ from adults through the presence of the white nuchal collar. Females are larger than males for snout–vent length, whereas males showed proportionally longer tails and smaller head length growth. Suitable areas for H. danieli are restricted to the trans-Andean regions from the Magdalena drainage to the Caribbean coast, which also showed high values of anthropic impacts. Our multidisciplinary approach provided new insights into this South American watersnake’s morphology, intraspecific variation, and distribution.

TaxoNERD: Deep neural models for the recognition of taxonomic entities in the ecological and evolutionary literature

Abstract Easy access to multi‐taxa information (e.g. distribution, traits, diet) in the scientific literature is essential to understand, map and predict all‐inclusive biodiversity. Tools are needed to automatically extract useful information from the ever‐growing corpus of ecological texts and feed this information to open data repositories. A prerequisite is the ability to recognise mentions of taxa in text, a special case of named entity recognition (NER). In recent years, deep learning‐based NER systems have become ubiquitous, yielding state‐of‐the‐art results in the general and biomedical domains. However, no such tool is available to ecologists wishing to extract information from the biodiversity literature. We propose a new tool called TaxoNERD that provides deep neural network (DNN) models to recognise taxon mentions in ecological documents. To achieve high performance, these models usually need to be trained on a large corpus of manually annotated text. Creating such a corpus is a laborious and costly process, with the result that manually annotated corpora in the ecological domain tend to be too small to learn an accurate DNN model from scratch. To address this issue, we leverage existing models pretrained on large biomedical corpora using transfer learning. The performance of our models is evaluated on four corpora and compared to the most popular taxonomic entity recognition tools. Our experiments suggest that existing taxonomic NER tools are not suited to the extraction of ecological information from text as they performed poorly on ecologically oriented corpora, either because they do not take account of the variability of taxon naming practices or because they do not generalise well to the ecological domain. Conversely, a domain‐specific DNN‐based tool like TaxoNERD outperformed the other approaches on an ecological information extraction task. Efforts are needed to raise ecological information extraction to the same level of performance as its biomedical counterpart. One promising direction is to leverage the huge corpus of unlabelled ecological texts to learn a language representation model that could benefit downstream tasks. These efforts could be highly beneficial to ecologists on the long term.

(2847) Proposal to conserve the name Anthurium microspadix against A. porrectum (Araceae)

(2847) Proposal to conserve the name <i>Anthurium microspadix</i> against <i>A. porrectum</i> (<i>Araceae</i>)

Machine learning approach for automatic recognition of tomato-pollinating bees based on their buzzing-sounds.

Bee-mediated pollination greatly increases the size and weight of tomato fruits. Therefore, distinguishing between the local set of bees-those that are efficient pollinators-is essential to improve the economic returns for farmers. To achieve this, it is important to know the identity of the visiting bees. Nevertheless, the traditional taxonomic identification of bees is not an easy task, requiring the participation of experts and the use of specialized equipment. Due to these limitations, the development and implementation of new technologies for the automatic recognition of bees become relevant. Hence, we aim to verify the capacity of Machine Learning (ML) algorithms in recognizing the taxonomic identity of visiting bees to tomato flowers based on the characteristics of their buzzing sounds. We compared the performance of the ML algorithms combined with the Mel Frequency Cepstral Coefficients (MFCC) and with classifications based solely on the fundamental frequency, leading to a direct comparison between the two approaches. In fact, some classifiers powered by the MFCC-especially the SVM-achieved better performance compared to the randomized and sound frequency-based trials. Moreover, the buzzing sounds produced during sonication were more relevant for the taxonomic recognition of bee species than analysis based on flight sounds alone. On the other hand, the ML classifiers performed better in recognizing bees genera based on flight sounds. Despite that, the maximum accuracy obtained here (73.39% by SVM) is still low compared to ML standards. Further studies analyzing larger recording samples, and applying unsupervised learning systems may yield better classification performance. Therefore, ML techniques could be used to automate the taxonomic recognition of flower-visiting bees of the cultivated tomato and other buzz-pollinated crops. This would be an interesting option for farmers and other professionals who have no experience in bee taxonomy but are interested in improving crop yields by increasing pollination.

Cultivating Resilience in the Biodiversity Heritage Library During the Global Pandemic: Improving access to existing content

The events of 2020, including the COVID-19 pandemic and social justice demonstrations around the world, helped the Biodiversity Heritage Library (BHL) refocus our priorities for implementing our 2020–2025 Strategic Plan, which was adopted in April 2020. BHL’s natural ecosystem relies on virtual coordination across our global community. For this reason, much of the work of the consortium could continue during lockdowns and telework mandates at many of our partner institutions. Though most digitization projects were placed on hold, staff were able to shift priority to metadata enhancements to improve access and discoverability of existing content. Long-planned improvements in the use of persistent identifiers were pushed to the forefront of technical development. Improvements to the data model and user interface to better support born-digital content and articles were also prioritized in the 2021 Technical Priorities. Back-end improvements to the BHL website, currently under development, will also facilitate easier metadata import and updates, making it faster and easier to add article-level metadata, which will improve search and discoverability for articles within the collection. These technical improvements will continue to define BHL as a tool to connect biodiversity data. Part of our collaborative resilience is our ability to adapt and adjust to changing priorities. Over the past year, BHL has been working to review and update our Collection Development Policy. Social justice movements and discussions concerning the harmful content in BHL’s collection are helping to inform the review of our collection development policy in ways we wouldn’t have anticipated prior to 2020. Our review now includes strategies to identify gaps in and improve representation of biodiversity information from underrepresented regions, languages, cultures, and perspectives. We are also working with colleagues to support larger efforts within the library profession to improve and broaden metadata such as subject headings. We will continue to address the problematic historical legacy of natural history collections through actions defined in our strategic plan. The isolation and work from home orders of 2020 and early 2021 provided opportunities for some to expand into deep research and contribute to collaborative projects as work assignments became digital and thus more versatile. For example, transcription projects were accelerated because staff had more time to contribute to these resource-intensive activities. One result of this work is that more handwritten materials such as field notes and correspondence are now available for full-text searching and taxonomic name recognition within BHL. Another strategic goal of BHL is to grow consortial partnerships and alliances to foster cross-institutional collaboration. BHL sought new partnerships that would integrate BHL data into existing and emerging biodiversity projects. This cross-institutional collaboration is another way to cultivate resilience and sow the seeds of sustainability. In this talk, we will describe how BHL shifted its focus to reflect on and respond to global events of 2020. We will share discussions around acknowledging and addressing the harmful legacy content in BHL collections, new technical developments, and examples of collaborative telework projects.

Ceratozamia aurantiaca (Zamiaceae): A New Cycad Species from the Northern Rainforests of Oaxaca, Mexico

Ceratozamia aurantiaca, a new cycad species from Oaxaca, Mexico, is described. The new species is endemic to lowland karst tropical rainforests of the northern mountains (Sierra Norte region). This species is related to C. subroseophylla and C. robusta, together considered part of the C. robusta species complex due to their shared characteristics: robust, upright trunk; large and long leaves with densely armed petioles and linear to subfalcate leaflets; and large megastrobili. Ceratozamia aurantiaca, as the epithet suggests, is easily distinguished from other species by the orange color of its emerging leaves, a trait unique in the genus. Additionally, C. aurantiaca is distinguished from C. subroseophylla and C. robusta by having significantly shorter petioles, wider spacing between leaflets, and wider median leaflets. The taxonomic recognition of this species represents a step toward clarifying species delimitation in the C. robusta complex.

A preliminary investigation of umbellate inflorescences in Vallisneria americana populations of Central Florida

Vallisneria americana typically produces solitary pistillate inflorescences; however, unusual umbellate flowers have been observed in sub-tropical populations and are reported as rare. There are multiple hypotheses regarding the origin or cause of umbellate inflorescences—they may be relics of ancestral stocks surviving through asexual reproduction, heritable traits worthy of taxonomic recognition, or teratological specimens resulting from injury during flower formation. Through surveys of Vallisneria populations in four lakes in Central Florida, USA, we show these umbellate flowers are broadly distributed and we document their physical and reproductive traits, contrasted with solitary capsules (capsule number, capsule length and width, seed number, germination). Umbellate inflorescences were found frequently across space and time—capsules were found in three of four lakes, 40–80 % of the times flowering was observed. Umbellate inflorescences produced fewer seeds than solitary capsules, despite having 2–33 capsules per inflorescence. Seeds from umbellate capsules were viable, but germination occurred more slowly and at a lower percentage than seeds from solitary capsules. Nematodes were not detected within sampled inflorescences. Chironomid larvae were detected at a high rate (75–80 %) in umbellate capsules from two of three lakes but were not found on solitary capsules, suggesting they may be a possible cause for teratological growth. We conclude umbellate inflorescences are broadly distributed in Central Florida lakes and, while not sterile, they may have reproductive costs. Further study is needed to fully evaluate the cause of umbellate formation, population-level effects, and their range within Vallisneria americana.

Revisiting the taxonomy of Strobilanthes homotropa (Acanthaceae) and a new species Strobilanthes pradeepiana from the Western Ghats, India

Strobilanthes homotropa is an intricate species reported from Nilgiris, India. This taxon was treated in various ways leading to ambiguity in its taxonomic recognition. The present study revisits the taxonomy of S. homotropa and provides an amended description for the species. While doing so, S. homotropa is segregated from the puzzling species S. sexennis and a new species S. pradeepiana is recognized.

Updated description of Atheniella (Mycenaceae, Agaricales), including three new species with brightly coloured pilei from Yunnan Province, southwest China.

An updated description of the genus Atheniella, combining macro- and micromorphological characters that elaborate on the original generic characterisation, is presented. Atheniella is characterised by a brightly coloured pileus, all tissues inamyloid and pileipellis covered with simple to branched excrescences. Previously, nine Atheniella species were known globally, of which three species were accepted in China. Three newly-recognised species classified in the genus are here formally described from Yunnan Province: Atheniella flavidasp. nov., A. rutilasp. nov. and A. taoyaosp. nov. The new species are characterised by a yellow, orange, pink or red pileus, fusiform cheilocystidia and pleurocystidia, non-smooth pileipellis, stipitipellis smooth or with cylindrical ornamentation, caulocystidia fusiform or subglobose, if present and all tissues inamyloid. Morphological descriptions, photographs, line drawings and comparisons with closely-related taxa are presented for the new species. A phylogenetic analysis of sequence data for the rDNA internal transcribed spacer region and nuclear large ribosomal subunit (ITS + nLSU) supported that Atheniella is resolved as monophyletic and also supported the taxonomic recognition of the new species. A key to the 12 species of Atheniella is also provided.

Sequence data from isolated lichen-associated melanized fungi enhance delimitation of two new lineages within Chaetothyriomycetidae

Lichen thalli provide a long-lived and stable habitat for colonization by a wide range of microorganisms. Increased interest in these lichen-associated microbial communities has revealed an impressive diversity of fungi, including several novel lineages which still await formal taxonomic recognition. Among these, members of the Eurotiomycetes and Dothideomycetes usually occur asymptomatically in the lichen thalli, even if they share ancestry with fungi that may be parasitic on their host. Mycelia of the isolates are characterized by melanized cell walls and the fungi display exclusively asexual propagation. Their taxonomic placement requires, therefore, the use of DNA sequence data. Here, we consider recently published sequence data from lichen-associated fungi and characterize and formally describe two new, individually monophyletic lineages at family, genus, and species levels. The Pleostigmataceae fam. nov. and Melanina gen. nov. both comprise rock-inhabiting fungi that associate with epilithic, crust-forming lichens in subalpine habitats. The phylogenetic placement and the monophyly of Pleostigmataceae lack statistical support, but the family was resolved as sister to the order Verrucariales. This family comprises the species Pleostigma alpinum sp. nov., P. frigidum sp. nov., P. jungermannicola, and P. lichenophilum sp. nov. The placement of the genus Melanina is supported as a lineage within the Chaetothyriales. To date, this genus comprises the single species M. gunde-cimermaniae sp. nov. and forms a sister group to a large lineage including Herpotrichiellaceae, Chaetothyriaceae, Cyphellophoraceae, and Trichomeriaceae. The new phylogenetic analysis of the subclass Chaetothyiomycetidae provides new insight into genus and family level delimitation and classification of this ecologically diverse group of fungi.