Linnaeus in the information age

Discovering marine biodiversity in the 21st century

Chapter

Nov 2022
ADV MAR BIOL

We review the current knowledge of the biodiversity of the ocean as well as the levels of decline and threat for species and habitats. The lack of understanding of the distribution of life in the ocean is identified as a significant barrier to restoring its biodiversity and health. We explore why the science of taxonomy has failed to deliver knowledge of what species are present in the ocean, how they are distributed and how they are responding to global and regional to local anthropogenic pressures. This failure prevents nations from meeting their international commitments to conserve marine biodiversity with the results that investment in taxonomy has declined in many countries. We explore a range of new technologies and approaches for discovery of marine species and their detection and monitoring. These include: imaging methods, molecular approaches, active and passive acoustics, the use of interconnected databases and citizen science. Whilst no one method is suitable for discovering or detecting all groups of organisms many are complementary and have been combined to give a more complete picture of biodiversity in marine ecosystems. We conclude that integrated approaches represent the best way forwards for accelerating species discovery, description and biodiversity assessment. Examples of integrated taxonomic approaches are identified from terrestrial ecosystems. Such integrated taxonomic approaches require the adoption of cybertaxonomy approaches and will be boosted by new autonomous sampling platforms and development of machine-speed exchange of digital information between databases.

Sizing the Knowledge Gap in Taxonomy: The Last Dozen Years of Aphidiinae Research

Article

Full-text available

Feb 2022

Andjeljko Petrović

Taxonomic impediment is one of the main roadblocks to managing the current biodiversity crisis. Insect taxonomy is the biggest contributor to the taxonomic impediment, both in terms of the knowledge gap and the lack of experts. With this study, we tried to size the knowledge gap by analyzing taxonomical studies on the subfamily Aphidiinae (Hymenoptera: Braconidae) conducted from 2010 to 2021. All available taxonomic knowledge gathered in this period is critically summarized: newly described species, detection of alien species, published identification keys, etc. All findings are discussed relative to the current state of general taxonomy. Future prospects for taxonomy are also discussed.

Accelerating Ocean Species Discovery and Laying the Foundations for the Future of Marine Biodiversity Research and Monitoring

Article

Full-text available

Sep 2023

Ocean Census is a new Large-Scale Strategic Science Mission aimed at accelerating the discovery and description of marine species. This mission addresses the knowledge gap of the diversity and distribution of marine life whereby of an estimated 1 million to 2 million species of marine life between 75% to 90% remain undescribed to date. Without improved knowledge of marine biodiversity, tackling the decline and eventual extinction of many marine species will not be possible. The marine biota has evolved over 4 billion years and includes many branches of the tree of life that do not exist on land or in freshwater. Understanding what is in the ocean and where it lives is fundamental science, which is required to understand how the ocean works, the direct and indirect benefits it provides to society and how human impacts can be reduced and managed to ensure marine ecosystems remain healthy. We describe a strategy to accelerate the rate of ocean species discovery by: 1) employing consistent standards for digitisation of species data to broaden access to biodiversity knowledge and enabling cybertaxonomy; 2) establishing new working practices and adopting advanced technologies to accelerate taxonomy; 3) building the capacity of stakeholders to undertake taxonomic and biodiversity research and capacity development, especially targeted at low- and middle-income countries (LMICs) so they can better assess and manage life in their waters and contribute to global biodiversity knowledge; and 4) increasing observational coverage on dedicated expeditions. Ocean Census, is conceived as a global open network of scientists anchored by Biodiversity Centres in developed countries and LMICs. Through a collaborative approach, including co-production of science with LMICs, and by working with funding partners, Ocean Census will focus and grow current efforts to discover ocean life globally, and permanently transform our ability to document, describe and safeguard marine species.

Holistic description of new deep sea megafauna (Cephalopoda: Cirrata) using a minimally invasive approach

Article

Full-text available

Apr 2021
BMC BIOL

Background In zoology, species descriptions conventionally rely on invasive morphological techniques, frequently leading to damage of the specimens and thus only a partial understanding of their structural complexity. More recently, non-destructive imaging techniques have successfully been used to describe smaller fauna, but this approach has so far not been applied to identify or describe larger animal species. Here, we present a combination of entirely non-invasive as well as minimally invasive methods that permit taxonomic descriptions of large zoological specimens in a more comprehensive manner. Results Using the single available representative of an allegedly novel species of deep-sea cephalopod (Mollusca: Cephalopoda), digital photography, standardized external measurements, high-field magnetic resonance imaging, micro-computed tomography, and DNA barcoding were combined to gather all morphological and molecular characters relevant for a full species description. The results show that this specimen belongs to the cirrate octopod (Octopoda: Cirrata) genus Grimpoteuthis Robson, 1932. Based on the number of suckers, position of web nodules, cirrus length, presence of a radula, and various shell characters, the specimen is designated as the holotype of a new species of dumbo octopus, G. imperator sp. nov. The digital nature of the acquired data permits a seamless online deposition of raw as well as derived morphological and molecular datasets in publicly accessible repositories. Conclusions Using high-resolution, non-invasive imaging systems intended for the analysis of larger biological objects, all external as well as internal morphological character states relevant for the identification of a new megafaunal species were obtained. Potentially harmful effects on this unique deep-sea cephalopod specimen were avoided by scanning the fixed animal without admixture of a contrast agent. Additional support for the taxonomic placement of the new dumbo octopus species was obtained through DNA barcoding, further underlining the importance of combining morphological and molecular datasets for a holistic description of zoological specimens.

DNA BARCODING: FOUNDATIONS AND APPLICATIONS FOR SOUTHEAST ASIAN FRESHWATER FISHES

Article

Jan 2016

Scanning holotypes from the Vertebrate Paleontology Collection at the Museu Paraense Emilio Goeldi (Brazil): Tools for research and science outreach

Article

Jun 2023

The scanning of paleontological collections is increasingly important for morphological studies and science outreach. In addition to ensuring data sharing, digitization contributes to preserving morphological information in case of damage to the original specimens. In this communication, we aim to report digital versions of the holotypes from the Vertebrate Paleontology Collection at the Museu Paraense Emilio Goeldi, Brazil. For this purpose, eighteen holotypes of Early/Middle Miocene Teleostei from Pirabas Formation, northern Brazil, were scanned using microtomography, and cybertypes were proposed. The CT‐Scan data were stored in a virtual repository, can be freely accessed, and are available for future studies on the morphology of these specimens. Furthermore, these specimens are tiny and fragile, and digital versions can be an alternative to safely handling them. Finally, the digitization of important specimens, at least of holotypes, needs to be a standard practice in museum collections over the next years.

Integration or minimalism: twenty-one new species of ghost spiders (Anyphaenidae: Anyphaena) from Mexico

Article

Full-text available

Apr 2023

The rhythm of biodiversity loss vastly surpasses the number of new species described per year, with several taxa going extinct without us even knowing about their existence. After more than 250 years of traditional taxonomy, it is clear that the rate of biodiversity description and discovery needs to be improved. Molecular data has greatly increased the speed of species discovery and accuracy of taxonomic delimitation. Phenotypic documentation, although relatively slower, is still crucial to identify species and communicate taxonomic discoveries to a broader audience. Here, we integrate these data sources to describe a relatively large number of new species of the spider genus Anyphaena and look into its internal phylogenetic relationships. Our findings support the existence of several species groups within Anyphaena (as currently defined), but failed to recover the monophyly of this genus, suggesting a more comprehensive revision of its species groups and closely related anyphaenid genera is necessary. The 21 new species described here are: Anyphaena adnani sp. nov., A. bifurcata sp. nov., A. dulceae sp. nov., A. epicardia sp. nov., A. fernandae sp. nov., A. franciscoi sp. nov., A. ibarrai sp. nov., A. jimenezi sp. nov., A. megamedia sp. nov., A. miniducta sp. nov., A. natachae sp. nov., A. noctua sp. nov., A. porta sp. nov., A. quadrata sp. nov., A. rebecae sp. nov., A. salgueiroi sp. nov., A. sofiae sp. nov., A. stigma sp. nov., A. tonoi sp. nov., A. triangularis sp. nov. and A. urieli sp. nov.

A non-fossilized science: new techniques applied in Palaeontology

Article

Full-text available

Mar 2021

Aunque la paleontología suele percibirse por un amplio sector de la sociedad como una ciencia clásica y poco innovadora, desde hace dos décadas esta imagen dista mucho de la realidad. Numerosas técnicas y metodologías creadas, a priori, en entornos de investigación o industria con propósitos diferentes, han sido incorporadas al día a día de la investigación paleontológica. Esto ha producido un gran cambio en la praxis de esta ciencia, tanto en trabajo de campo, como preparación, investigación o divulgación. Algunas de estas técnicas implican el uso de sistemas de georreferenciación o de escáneres y sistemas de digitalización para la creación de modelos informáticos tridimensionales. Con ellos se pueden realizar interesantes estudios acerca de las cavidades internas de los cráneos, reconstrucciones tridimensionales del sistema musculoesquelético o análisis biomecánicos complejos. Gracias a estas técnicas podemos "devolver a la vida" a animales extintos con mucho mayor rigor que antes en la historia de la paleontología. Igualmente, estas técnicas también ayudan en la puesta en valor, documentación y conservación de yacimientos y fósiles, a la vez que incorporan nueva información que optimizan los montajes esqueléticos en las exhibiciones de los museos, y ayudan a divulgar a la sociedad los resultados científicos de una manera más interactiva y visual. Es por ello que es importante dar a conocer esta nueva faceta de la paleontología, desechar la visión que se tiene de ella como una ciencia con un enfoque anticuado, y presentarla de nuevo como una ciencia multidisciplinar e innovadora, puesta al día en los avances tecnológicos. Palabras clave: Digitalización, divulgación científica, museología, paleontología virtual, preservación del patrimonio. Abstract (EN) Although a large sector of society sees paleontology as a classic, not very innovative science, changes over the last two decades are challenging this perception. Many techniques and methodologies conceived for different fields in research or industry have become well-established in paleontology. This has been game changing in paleontological praxis at all levels, from fieldwork to preparation, research or outreach. Some of these techniques make use of georeferencing systems or scanners and digitization systems to create three dimensional virtual models. These models allow performing non-invasive studies on the internal cavities of skulls, highly detailed three-dimensional musculoskeletal reconstructions and complex biomechanical analyses. This way, we can "bring back to life" extinct animals more rigorously than has ever been possible before. These techniques also are key in showcasing, documenting and preserving fossils and fossil sites, incorporating new information to refine skeletal mounts in museum exhibits and provide a more interactive and visual outreach of science. Therefore, it is important to showcase this new area of paleontology, change its perception as a science with dated methodology and present it as an innovative, up-to-date and multidisciplinary science.

Morphology, nuclear SNPs and mate selection reveal that COI barcoding overestimates species diversity in a Mediterranean freshwater amphipod by an order of magnitude

Article

Full-text available

Dec 2022

DNA sequence information has revealed many morphologically cryptic species worldwide. For animals, DNA‐based assessments of species diversity usually rely on the mitochondrial cytochrome c oxidase subunit I (COI) gene. However, a growing amount of evidence indicate that mitochondrial markers alone can lead to misleading species diversity estimates due to mito‐nuclear discordance. Therefore, reports of putative species based solely on mitochondrial DNA should be verified by other methods, especially in cases where COI sequences are identical for different morphospecies or where divergence within the same morphospecies is high. Freshwater amphipods are particularly interesting in this context because numerous putative cryptic species have been reported. Here, we investigated the species status of the numerous mitochondrial molecular operational taxonomic units (MOTUs) found within Echinogammarus sicilianus. We used an integrative approach combining DNA barcoding with mate selection observations, detailed morphometrics and genome‐wide double digest restriction site‐associated DNA sequencing (ddRAD‐seq). Within a relatively small sampling area, we detected twelve COI MOTUs (divergence = 1.8–20.3%), co‐occurring in syntopy at two‐thirds of the investigated sites. We found that pair formation was random and there was extensive nuclear gene flow among the ten MOTUs co‐occurring within the same river stretch. The four most common MOTUs were also indistinguishable with respect to functional morphology. Therefore, the evidence best fits the hypothesis of a single, yet genetically diverse, species within the main river system. The only two MOTUs sampled outside the focal area were genetically distinct at the nuclear level and may represent distinct species. Our study reveals that COI‐based species delimitation can significantly overestimate species diversity, highlighting the importance of integrative taxonomy for species validation, especially in hyperdiverse complexes with syntopically occurring mitochondrial MOTUs.

Standardized nuclear markers improve and homogenize species delimitation in Metazoa

Article

Full-text available

Dec 2022
Methods Ecol. Evol.

Species are the fundamental units of life and evolution. Their recognition is essential for science and society. Molecular methods have been increasingly used for the identification of animal species, despite several challenges. Here, we explore with genomic data from nine animal lineages a set of nuclear markers, namely metazoan-level universal single-copy orthologs (metazoan USCOs), for their use in species delimitation. Our data sets include arthropods and vertebrates. We use various data assembly strategies and use coalescent-based species inference as well as population admixture analyses and phenetic methods. We demonstrate that metazoan USCOs distinguish well closely related morphospecies and consistently outperform classical mitochondrial DNA barcoding in discriminating closely related species in different animal taxa, as judged by comparison with morphospecies delimitations. USCOs overcome the general shortcomings of mitochondrial DNA barcodes, and due to standardization across Metazoa, also those of other approaches. They accurately assign samples not only to lower but also to higher taxonomic levels. Metazoan USCOs provide a powerful and unifying framework for DNA-based species delimitation and taxonomy in animals and their employment could result in a more efficient use of research data and resources.

The contribution of the BIOTA/FAPESP Program to the advancement of the knowledge on terrestrial invertebrates Thematic Review

Article

Oct 2022

The contribution of the BIOTA/FAPESP Program to the advancement of the knowledge on terrestrial invertebrates. Biota Neotropica 22(spe): e20221398. https://doi. Abstract: The variability of the organisms living in a given area constitute what is referred to as biodiversity, one of nature's fundamental properties, responsible for the balance and stability of ecosystems. The loss of biodiversity has been of great concern to scientists, especially because of the role played by human activities in this regard, able to lead to irreversible circumstances. The São Paulo Research Foundation (Fundação de Amparo à Pesquisa do Estado de São Paulo, FAPESP) plays a major role in supporting research efforts in the most diverse branches of science. In the late 1990´s, FAPESP launched a major program to promote research on biodiversity, named BIOTA/ FAPESP. So far, this program has financed the conduction of 26 projects, involving research activities in most of Brazil, while focusing mainly the State of São Paulo. These projects have generated about 1140 publications in peer-reviewed journals of high standard, providing relevant information, including the original description of 1187 species and 76 genera, the complementary description of 350 species, as well as a number of inventory works, biological studies, etc. The program has also been instrumental in the establishment or adequacy of research facilities and training of new taxonomists. Most extensively studied groups of terrestrial invertebrates include Insecta of the orders Hymenoptera, Lepidoptera and Diptera, and Arachnida of the subclasses Araneae and Acari. Distinct projects have also contributed to the detection of organisms potentially useful as biological control agents and in the determination of maps of major interest for the establishment of public policies. In the future, priority groups for study should include the Annelida and the Nematoda, for the potential both have as beneficial organisms, or for the potential some Nematoda have as organisms harmful to plants and animals. A contribuição do Programa BIOTA/FAPESP para o avanço no conhecimento sobre os invertebrados terrestres Resumo: A variabilidade dos organismos em uma determinada área constitui o que se denomina biodiversidade, uma das propriedades fundamentais da natureza, responsável pelo equilíbrio e estabilidade dos ecossistemas. A perda da biodiversidade tem sido uma grande preocupação para os cientistas, principalmente pelo papel desempenhado pelas atividades humanas, com potencial para desencadear circunstâncias irreversíveis. A Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) desempenha um papel importante no apoio às pesquisas nos mais diversos ramos da ciência. No final da década de 1990, a FAPESP lançou um grande programa de fomento à pesquisa em biodiversidade, denominado BIOTA/FAPESP. Até o momento, este programa financiou a realização de 26 projetos, envolvendo atividades na maior parte do Brasil, embora tenham como foco principal o estado de São Paulo. Esses projetos geraram cerca de 1.140 publicações em periódicos de alto impacto, fornecendo informações relevantes que incluem a descrição original de 1.187 espécies e 76 gêneros e a descrição complementar de 350 espécies, além de diversos trabalhos de inventário, estudos biológicos etc. O programa também tem sido fundamental para o estabelecimento ou adequação de instalações de pesquisa científica e o treinamento de novos taxonomistas. Os grupos de invertebrados terrestres mais estudados incluem os Insecta das ordens Hymenoptera, Lepidoptera e Diptera, e os Arachnida das subclasses Araneae e Acari. Projetos distintos também têm contribuído para a detecção de organismos potencialmente úteis como agentes de controle biológico e na determinação de mapas de áreas preferenciais para o estabelecimento de políticas públicas. No futuro, os grupos prioritários de estudo devem incluir os Annelida e os Nematoda, pelo potencial que ambos têm como organismos benéficos, ou pelo potencial que alguns Nematoda têm como organismos prejudiciais a plantas e animais.

A revolutionary protocol to describe understudied hyperdiverse taxa and overcome the taxonomic impediment

Article

Full-text available

Jul 2019

Here we elucidate and justify a DNA barcode approach to insect species description that can be applied to name tens of thousands of species of Ichneumonoidea and many other species-rich taxa. Each description consists of a lateral habitus image of the specimen, a COI barcode diagnosis, and the holotype specimen information required by the International Code of Zoological Nomenclature. We believe this approach, or a slight modification of it, will be useful for many other underdescribed hyperdiverse taxa, especially in the tropics. Due to the extreme species-richness of the Ichneumonoidea, the very low percentage of described species, and the lack of detailed biological information for most described species, the standard taxonomic approach is inefficient and overwhelmingly time consuming. A DNA barcode-based approach to initial description will provide a solid foundation of species hypotheses from which more comprehensive descriptions can be developed as other data, time, and budgets permit. Here we elucidate this view and detailed methodology that can generally be applied to species-rich underdescribed taxa. A real example is given by describing species in two genera, Hemichoma and Zelomorpha , reared from the Área de Conservación Guanacaste in northwestern Costa Rica. The generic type species Zelomorphaarizonensis is given a DNA barcode diagnosis and the following new species are described: Zelomorphaangelsolisi , Zelomorphabobandersoni , Zelomorphadanjohnsoni , Zelomorphadonwindsori , Zelomorphaeffugia , Zelomorphajohnchemsaki , Zelomorphakellyanneae , Zelomorphalarrykirkendalli , Zelomorphamariyavladmirovnae , Zelomorphamikeiviei , Zelomorphamyricagaleae , Zelomorphanoahjaneae , Zelomorphapaulgoldsteini , Zelomorphaterryerwini , Zelomorphawillsflowersi , Hemichomadonwhiteheadi , Hemichomafrankhovorei , and Hemichomajohnkingsolveri .

Taxonomy—An irreplaceable tool for validation of herbal medicine revisited

Chapter

Jan 2022

Rainer W Bussmann

Over the last decades there has been an increasing recognition of the importance of herbal medicine around the globe. Apart from the obvious use of crude plant preparations or plant extracts, plant-based natural product research has become a common tool in drug development. Plant material for research is often sourced either directly from the wild, or form a wide variety of venders and providers, most commonly over the Internet. The quality of the source material is often highly variable, and it has been our experience that much of the available material lacks all, or at least careful, documentation, identification and vouchering. Many well-respected researchers in phytomedicine are deficient in plant taxonomy and might be convinced that the correct scientific name and vouchering of plant material sourced does not really matter, if only a consistent vernacular name is provided. In this chapter we explore the necessity of correct scientific identification of material in herbal medicine, point to common errors in the process, and suggest ways to avoid potentially disastrous mistakes. Most taxonomic errors are simply caused by orthographic mistakes, by citing synonyms instead of the correct scientific name, wrong or missing author citations, mistakes in family classification, and simple extrapolation from a common vernacular name to a possible scientific identification. Most of these problems can easily be avoided by using open access online databases. The identification of vouchering material should however always be done, or at least confirmed, by specialists. Taxonomy remains a crucial tool for the validation and safety of herbal medicine.

Article Tragedy of the Natural History Museum

Article

Full-text available

Jul 2022

Fred Naggs

Licensed under a Creative Commons Attribution-N.C. 4.0 International https://creativecommons.org/licenses/by-nc/4.0/ Megataxa 007 (1): 085-112 h t t p s : / / w w w. m a p r e s s. c o m / m t Abstract The remit of the Natural History Museum, London, encompasses the whole of the natural world and places it at the forefront of global concerns about human impact on the biosphere. The Museum's stature as a world leading institution for storing and recording living diversity brings responsibilities, obligations and new prospects. In addition to revealing the genetic evolution of life in considerable detail, advances in molecular biology and cryogenics offer exciting new opportunities to extend beyond the Museum's traditional role as a storehouse for recording living diversity and to take a lead in biodiversity conservation. In its strategy for the coming decade, the Museum has declared a planetary emergency for which we need an unprecedented response, asserting that we must act now, that we must act on scientific evidence and that we must act together. However, the Museum is no longer led by scientists; its relevant expertise and the prioritisation of its collection-based world-leading role is being rapidly dismantled. It has been taken over by an administrative structure and placed under a government Department that have no notion of the importance of this role. Much of the Museum's activity is no longer led by science intimately connected to its role as a collections-based institution and its public profile is dominated by journalistic presentations from sources that are widely available to a broad range of the media. Inappropriate leadership and recruitment have diverted its science base in directions that place much of its research within the activities of numerous other academic agencies, undermining the reason and justification for the Museum's existence. The move of about half of the collections and associated scientific staff to a location outside of London is a self-imposed act of institutional vandalism. It will mutilate a national treasure, not only inflicting a massive and permanent financial burden but also irrevocably damaging the Museum's, cultural identity and function as an integrated collections and research institution. Rather than responding to a planetary emergency, the Museum is tragically descending into irrelevance.

COI is not always right: integrative taxonomy reveals striking overestimation of species diversity in a Mediterranean freshwater amphipod

Preprint

Full-text available

Mar 2022

Background The emergence of DNA taxonomy sparked a paradigm shift in biodiversity assessments and revealed the existence of many morphologically cryptic species in all ecosystems worldwide. For animals, DNA-based assessments of species diversity usually rely on the mitochondrial cytochrome c oxidase subunit I (COI) gene. However, an increasing number of studies report patterns of mito-nuclear discordance originating for example from shared ancestral polymorphisms or introgression, leading to an over- or underestimation of true species diversity. Therefore, reports of mitochondrial lineages should be verified by other methods. Freshwater amphipods are ideal model organisms since putative cryptic species have been reported in many of the nominal taxa. In this study, we investigated the species status of the numerous mitochondrial molecular operational taxonomic units (MOTUs) found within the Mediterranean freshwater amphipod Echinogammarus sicilianus on Sicily. For validation, we used an integrative taxonomic approach combining DNA barcoding with behavioural data, detailed morphometrics and genome-wide double digest restriction site-associated DNA sequencing (ddRAD-seq). Results Within a relatively small sampling area (approx. 200 km²), we detected 12 divergent COI MOTUs, with genetic distances ranging from 1.8% to 20.3% and a mean distance of 11%. At 17 of the 25 sampling sites up to six MOTUs occurred in syntopy. The four most common MOTUs were analysed with high resolution morphometric data (49 measurements per specimen), but we found no clear evidence of morphological differentiation among them. We also observed a high level of MOTU intermixing (38%) in precopulatory pairs. Similarly, ten of the mitochondrial MOTUs were not supported by the genome-wide ddRAD-seq data. However, for the two remaining mitochondrial MOTUs found at sites outside of the main river stretch, ddRAD-seq and COI data were congruent, indicating that those MOTUs might indeed represent cryptic species. Conclusions Our study on the amphipod E. sicilianus reveals another prominent example of mito-nuclear discordance indicating that species delimitation based solely on mitochondrial markers can significantly overestimate species diversity. The study highlights that integrative taxonomy approaches are important for validating species status, especially in hyperdiverse species complexes, where many mitochondrial MOTUs occur in close proximity or even syntopy.

Estudio taxonómico de la familia Malvaceae en los municipios de Leonardo Bravo y Eduardo Neri, Guerrero, México

Thesis

Full-text available

Jun 2013

Daniel David Díaz Contreras Díaz

La familia Malvaceae posee cerca de 80 géneros y 1700 especies a nivel mundial, y es unos de los 15 grupos de angiospermas de mayor diversidad en México. Aproximadamente 50% de las especies de esta familia presentes en el país son endémicas. Este trabajo es una contribución al conocimiento de esta familia en el estado de Guerrero. Como resultado de la investigación bibliográfica de la familia Malvaceae en el estado de Guerrro y la revisión de material botánico depositado en el Herbario de la Facultad de Ciencias (FCME), el Herbario Nacional (MEXU) y el Herbario de la Escuela Nacional de Ciencias Biológicas (ENCB), se obtuvo una lista de 29 especies que pertenecen a 13 géneros. Se encontraron siete géneros y 12 especies, y nueve géneros y 24 especies en los municipios Leonardo Bravo y Eduardo Neri, respectivamente. Las especies Anoda pubescens Schltdl. y Kearnemalvastrum subtriflorum (Lag.) D. M. Bates se añaden como nuevos registros para el estado de Guerrero.

COI is not always right: integrative taxonomy reveals striking overestimation of species diversity in a Mediterranean freshwater amphipod

Preprint

Full-text available

Mar 2022

Background The emergence of DNA taxonomy sparked a paradigm shift in biodiversity assessments and revealed the existence of many morphologically cryptic species in all ecosystems worldwide. For animals, DNA-based assessments of species diversity usually rely on the mitochondrial cytochrome c oxidase subunit I (COI) gene. However, an increasing number of studies report patterns of mito-nuclear discordance originating for example from shared ancestral polymorphisms or introgression, leading to an over- or underestimation of true species diversity. Therefore, reports of mitochondrial lineages should be verified by other methods. Freshwater amphipods are ideal model organisms since putative cryptic species have been reported in many of the nominal taxa. In this study, we investigated the species status of the numerous mitochondrial molecular operational taxonomic units (MOTUs) found within the Mediterranean freshwater amphipod Echinogammarus sicilianus on Sicily. For validation, we used an integrative taxonomic approach combining DNA barcoding with behavioural data, detailed morphometrics and genome-wide double digest restriction site-associated DNA sequencing (ddRAD-seq). Results Within a relatively small sampling area (approx. 200 km²), we detected 12 divergent COI MOTUs, with genetic distances ranging from 1.8% to 20.3% and a mean distance of 11%. At 17 of the 25 sampling sites up to six MOTUs occurred in syntopy. The four most common MOTUs were analysed with high resolution morphometric data (49 measurements per specimen), but we found no clear evidence of morphological differentiation among them. We also observed a high level of MOTU intermixing (38%) in precopulatory pairs. Similarly, ten of the mitochondrial MOTUs were not supported by the genome-wide ddRAD-seq data. However, for the two remaining mitochondrial MOTUs found at sites outside of the main river stretch, ddRAD-seq and COI data were congruent, indicating that those MOTUs might indeed represent cryptic species. Conclusions Our study on the amphipod E. sicilianus reveals another prominent example of mito-nuclear discordance indicating that species delimitation based solely on mitochondrial markers can significantly overestimate species diversity. The study highlights that integrative taxonomy approaches are important for validating species status, especially in hyperdiverse species complexes, where many mitochondrial MOTUs occur in close proximity or even syntopy.

A taxonomy of hydrological processes and watershed function

Article

Full-text available

Mar 2022

Hilary Mcmillan

This paper presents a taxonomy (hierarchical organization) of hydrological processes; specifically, runoff generation processes in natural watersheds. Over 130 process names were extracted from a literature review of papers describing experimental watersheds, perceptual models, and runoff processes in a range of hydro‐climatic environments. Processes were arranged into a hierarchical structure, and presented as a spreadsheet and interactive diagram. For each process, additional information was provided: a list of alternative names for the same process, a classification into hydrological function (e.g. flux, storage, release) and a unique identifier similar to a hashtag. We hope that the proposed hierarchy will prompt collaboration and debate in the hydrologic community into naming and organizing processes, towards a comprehensive taxonomy. The taxonomy provides a method to label and search hydrological knowledge, thereby facilitating synthesis and comparison of processes across watersheds. This article is protected by copyright. All rights reserved.

Molecular species delimitation of the genera Anodus, Argonectes, Bivibranchia and Micromischodus (Ostariophysi: Characiformes)

Article

Full-text available

Dec 2021
NEOTROP ICHTHYOL

A good taxonomic assessment of specimens is an essential task to many biological studies and DNA data have provided additional sources of information to assist in the disentanglement of taxonomic problems among living organisms, as has been the case of some taxa of the megadiverse Neotropical ichthyofauna. Here we assessed all valid species in the Neotropical freshwater fish genera Anodus, Argonectes, Bivibranchia and Micromischodus of the family Hemiodontidae to establish molecular species boundaries among them. All species delimitation methods defined exactly only one MOTU for Anodus elongatus, Argonectes longiceps, A. robertsi, Bivibranchia bimaculata, B. notata, B. velox, and Micromischodus sugillatus, resulting in total congruence between nominal species and MOTUs for these seven taxa. The three species having discordant results across analyses: Anodus orinocensis, Bivibranchia fowleri, and Bivibranchia simulata, matched more than one MOTU per species in some methods, meaning that cryptic diversity may exist within these taxa. Overall, this great correspondence among morphological and molecular boundaries for thae species analysed seem to be indicative of a reasonably stable taxonomy within these Hemiodontidae genera. Keywords: Biodiversity; Cryptic species; DNA barcoding; Hemiodontidae; Taxonomy

Biodiversity, taxonomy and metagenomics

Article

Full-text available

Feb 2017

MicroCT 3D reconstruction of three described braconid species (Hymenoptera: Braconidae)

Article

Full-text available

Jul 2020

Traditionally, entomologists have used destructive methods especially dissection in order to investigate the important taxonomic characters of specimens. New technologies for imaging and analyzing in taxonomy, offer opportunities to deposit three-dimensional (3D) data to proposed for rare and valuable type materials in museums and collections. Micro-computed tomography, as a non-destructive imaging technique, has become an emerging and progressive technology in insect science. However, this technology is rarely used in entomology compared to in medical and industrial applications. In this study, MicroCT imaging protocols are explained in detail using three species of braconid wasps: Aleiodes arnoldii Tobias, 1976 (Braconidae: Rogadinae), Hormius moniliatus Nee, 1811 (Braconidae: Hormiinae) and Macrocentrus bicolor Curtis, 1833 (Braconidae: Macrocentrinae). MicroCT scan data of three braconid wasp species from Iran, depicted main identification of skeletal body parts. A brief step-by-step is provided on image acquisition, 3D reconstruction and mesh editing to create a virtual model of the species utilized for morphological and morphometric studies. As a result, the use of micro-computed tomography as a non-invasive virtual examination tool was explored. The complete datasets containing the raw TIFF MicroCT data, 3D models and 3D rotation videos available for download at

Repositories for Taxonomic Data: Where We Are and What is Missing

Article

Full-text available

Apr 2020
SYST BIOL

Natural history collections are leading successful large-scale projects of specimen digitization (images, metadata, DNA barcodes), transforming taxonomy into a big data science. Yet, little effort has been directed towards safeguarding and subsequently mobilizing the considerable amount of original data generated during the process of naming 15-20,000 species every year. From the perspective of alpha-taxonomists, we provide a review of the properties and diversity of taxonomic data, assess their volume and use, and establish criteria for optimizing data repositories. We surveyed 4113 alpha-taxonomic studies in representative journals for 2002, 2010, and 2018, and found an increasing yet comparatively limited use of molecular data in species diagnosis and description. In 2018, of the 2661 papers published in specialized taxonomic journals, molecular data were widely used in mycology (94%), regularly in vertebrates (53%), but rarely in botany (15%) and entomology (10%). Images play an important role in taxonomic research on all taxa, with photographs used in > 80% and drawings in 58% of the surveyed papers. The use of omics (high-throughput) approaches or 3D documentation is still rare. Improved archiving strategies for metabarcoding consensus reads, genome and transcriptome assemblies, and chemical and metabolomic data could help to mobilize the wealth of high-throughput data for alpha-taxonomy. Because long term - ideally perpetual - data storage is of particular importance for taxonomy, energy footprint reduction via less storage-demanding formats is a priority if their information content suffices for the purpose of taxonomic studies. Whereas taxonomic assignments are quasi-facts for most biological disciplines, they remain hypotheses pertaining to evolutionary relatedness of individuals for alpha-taxonomy. For this reason, an improved re-use of taxonomic data, including machine-learning-based species identification and delimitation pipelines, requires a cyberspecimen approach-linking data via unique specimen identifiers, and thereby making them findable, accessible, interoperable, and reusable for taxonomic research. This poses both qualitative challenges to adapt the existing infrastructure of data centers to a specimen-centered concept and quantitative challenges to host and connect an estimated ≤2 million images produced per year by alpha-taxonomic studies, plus many millions of images from digitization campaigns. Of the 30-40,000 taxonomists globally, many are thought to be non-professionals, and capturing the data for online storage and reuse therefore requires low-complexity submission workflows and cost-free repository use. Expert taxonomists are the main stakeholders able to identify and formalize the needs of the discipline; their expertise is needed to implement the envisioned virtual collections of cyberspecimens.

A New Species of Praying Mantis from Peru Reveals Impaling as a Novel Hunting Strategy in Mantodea (Thespidae: Thespini)

Article

Dec 2019

A new species of lichen-mimicking praying mantis, Carrikerella simpira n. sp., is described from Tingo María region in Peru. The new species differs from its congeners in having reduced tergal lobes, a relatively sinuous pronotum, and it is found in the highland tropical rainforest of the Central Andes. Behavioral observations conducted on captive individuals revealed that juveniles and adults hunt by impaling prey using modified foretibial structures. Anatomical examinations of the incumbent trophic structures revealed functional adaptations for prey impaling in the foretibiae, primarily consisting of prominent, forwardly oriented, barbed spines. We provide an overall description of this novel hunting behavior in Mantodea and hypothesize on its evolutionary origin and adaptive significance for the Thespidae.

The unbearable lightness of sequence-based identification

Article

Full-text available

May 2019

Using the basic GenBank local alignment search tool program (BLAST) to identify fungi collected in a recently protected beech forest at Montricher (Switzerland), the number of ITS sequences associated to the wrong taxon name appears to be around 30%, even higher than previously estimated. Such results rely on the in-depth re-examination of BLAST results for the most interesting species that were collected, viz. first records for Switzerland, rare or patrimonial species and problematic species (when BLAST top scores were equally high for different species), all belonging to Agaricomycotina. This paper dissects for the first time a number of sequence-based identifications, thereby showing in every detail-particularly to the user community of taxonomic information-why sequence-based identification in the context of a fungal inventory can easily go wrong. Our first conclusion is that in-depth examination of BLAST results is too time consuming to be considered as a routine approach for future inventories: we spent two months on verification of approx. 20 identifications. Apart from the fact that poor taxon coverage in public depositories remains the principal impediment for successful species identification, it can be deplored that even very recent fungal sequence deposits in GenBank involve an uncomfortably high number of misidentifications or errors with associated metadata. While checking the original publications associated with top score sequences for the few examples that were here reexamined , a positive consequence is that we uncovered over 80 type sequences that were not annotated as types in GenBank. Advantages and pitfalls of sequence-based identification are discussed, particularly in the light of undertaking fungal inventories. Recommendations are made to avoid or reduce some of the major problems with sequence-based identification. Nevertheless, the prospects for a more reliable sequence-based identification of fungi remain quite dim, unless authors are ready to check and update the metadata associated with previously deposited sequences in their publications.

Beyond the “Code”: A Guide to the Description and Documentation of Biodiversity in Ciliated Protists (Alveolata, Ciliophora)

Article

Full-text available

Jul 2017

Recent advances in molecular technology have revolutionized research on allaspects of the biology of organisms, including ciliates, and created unprecedented opportunities for pursuing a more integrative approach to investigationsof biodiversity. However, this goal is complicated by large gaps and inconsistencies that still exist in the foundation of basic information about biodiversityof ciliates. The present paper reviews issues relating to the taxonomy of ciliates and presents specific recommendations for best practice in the observation and documentation of their biodiversity. This effort stems from aworkshop that explored ways to implement six Grand Challenges proposed bythe International Research Coordination Network for Biodiversity of Ciliates(IRCN-BC). As part of its commitment to strengthening the knowledge base that supports research on biodiversity of ciliates, the IRCN-BC proposes topopulate The Ciliate Guide, an online database, with biodiversity-related dataand metadata to create a resource that will facilitate accurate taxonomic identifications and promote sharing of data.

Micro-computed tomography for natural history specimens: a handbook of best practice protocols

Article

Full-text available

Apr 2019

Micro-computed tomography (micro-CT or microtomography) is a non-destructive imaging technique using X-rays which allows the digitisation of an object in three dimensions. The ability of micro-CT imaging to visualise both internal and external features of an object, without destroying the specimen, makes the technique ideal for the digitisation of valuable natural history collections. This handbook serves as a comprehensive guide to laboratory micro-CT imaging of different types of natural history specimens, including zoological, botanical, palaeontological and geological samples. The basic European Journal of Taxonomy 522: 1-55

Unexpected systematic affinities and geographic expansion of a marine alien hydroid (Cnidaria: Hydrozoa)

Article

Full-text available

Apr 2019

Biological systematics provides taxonomic information and expertise for biogeography and biological invasion research and management. However, the systematic classification of most taxa, including some alien and invasive species, relies only on morphology. This applies for example to Sertularella tongensis Stechow, 1919, an alien hydrozoan recently reported in the Mediterranean. Its genus affiliation is still unclear and controversial. Historically, it has been assigned to several existing genera. However, molecular data (COI, 16S, 18S, 28S) provided here do not support these previous assignments. Instead, integrative analyses combining morphological and molecular data support reassigning this species to a new genus, Bicaularia gen. nov. A biogeographic review revealed that this species is widely distributed in the mid- and low-latitude waters of the Indo-Pacific region, and is spreading to some tropical and temperate regions including the Mediterranean and Caribbean Seas, as well as Korea and Japan. This expansion may be attributable to human activity such as shipping through the Suez and the Panama Canals. However, the new record attached to a floating Sargassum algal fragment in the surface water of the open Pacific, might suggest a neglected cryptic spread pathway with the assistance of floating biological organisms. Our findings shed light on the complexity of the phylogeny and spread pathway of the investigated hydrozoan species. We regard the fine systematics as the first step towards future global sampling for molecular studies aiming to elucidate the origins and pathways for alien and invasive species.

Scientific Contributions in Evolutionary Biology to Study the Roots of Variation in the Existing Life Forms

Article

Full-text available

Apr 2018

Nida Tabassum Khan

The CCB-ID approach to tree species mapping with airborne imaging spectroscopy

Article

Full-text available

Oct 2018

Christopher Benjamin Anderson

Background Biogeographers assess how species distributions and abundances affect the structure, function, and composition of ecosystems. Yet we face a major challenge: it is difficult to precisely map species across landscapes. Novel Earth observations could overcome this challenge for vegetation mapping. Airborne imaging spectrometers measure plant functional traits at high resolution, and these measurements can be used to identify tree species. In this paper, I describe a trait-based approach to species identification with imaging spectroscopy, the Center for Conservation Biology species identification (CCB-ID) method, which was developed as part of an ecological data science evaluation competition. Methods These methods were developed using airborne imaging spectroscopy data from the National Ecological Observatory Network (NEON). CCB-ID classified tree species using trait-based reflectance variation and decision tree-based machine learning models, approximating a morphological trait and dichotomous key method inspired by botanical classification. First, outliers were removed using a spectral variance threshold. The remaining samples were transformed using principal components analysis (PCA) and resampled to reduce common species biases. Gradient boosting and random forest classifiers were trained using the transformed and resampled feature data. Prediction probabilities were calibrated using sigmoid regression, and sample-scale predictions were averaged to the crown scale. Results CCB-ID received a rank-1 accuracy score of 0.919, and a cross-entropy cost score of 0.447 on the competition test data. Accuracy and specificity scores were high for all species, but precision and recall scores varied for rare species. PCA transformation improved accuracy scores compared to models trained using reflectance data, but outlier removal and data resampling exacerbated class imbalance problems. Discussion CCB-ID accurately classified tree species using NEON data, reporting the best scores among participants. However, it failed to overcome several species mapping challenges like precisely identifying rare species. Key takeaways include (1) selecting models using metrics beyond accuracy (e.g., recall) could improve rare species predictions, (2) within-genus trait variation may drive spectral separability, precluding efforts to distinguish between functionally convergent species, (3) outlier removal and data resampling can exacerbate class imbalance problems, and should be carefully implemented, (4) PCA transformation greatly improved model results, and (5) targeted feature selection could further improve species classification models. CCB-ID is open source, designed for use with NEON data, and available to support species mapping efforts.

21st Century Biological Nomenclature-the Enduring Power of Names

Article

Aug 2018
INTEGR COMP BIOL

Judith Ellen Winston

Synopsis: Nomenclature and taxonomy are complementary and distinct aspects of the study of biodiversity, but the two are often confused even by biologists. Taxonomy is the part of the science of systematics that deals with identifying, describing, and categorizing organisms from species to higher taxa. Nomenclature is a system of giving names to organisms based on rules established for the process. Adoption of a system of binomial nomenclature by end of the 18th century helped standardize the process of naming the wealth of new organisms collected during the Age of Exploration, but before the middle of the 19th century, the turmoil resulting from differences in procedures and philosophies among practicing taxonomists necessitated the development of codes of nomenclature to regulate naming. By the early 20th century, codified sets of rules for the names of both plants and animals, nowadays usually abbreviated as ICBN (Botanical Code) and ICZN (Zoological Code), were in place internationally. These codes worked reasonably well through most of the 20th century, under the aegis of various international bodies, in part because procedures exist to bypass them when their provisions threaten nomenclatural stability. They also inspired the development of other nomenclatural codes for specific groups of organisms like bacteria, and, alternatively, the proposal of unified codes for all organisms. The rapid development of electronic communications and various means of electronic publication at the end of the 20th century, combined with what may be the advent of a new age of biological extinction, resulted in pressure to revise the codes to allow at least some degree of electronic publication and speedier description of new taxa in the 21st century. Consistent and unambiguous names are the platforms on which biological research and conservation practices are built. As we pursue the goals of documenting and conserving biodiversity, for which a stable nomenclature is essential, we must do so without restricting the freedom of the science of systematics.

Balanophoraceae no Brasil

Thesis

May 2014

Leandro Jorge Telles Cardoso

EN: Balanophoraceae is the most representative botanic family of holoparasites in Brazil, and since the Flora Brasiliensis it lacks from a dedicated revision of its species in the country. The present study makes a compilation and generates new information about Balanophoraceae, treating its morphology, taxa delimitation, ecological information, and taxonomic remarks, as well as its species conservation status. There are six genera and 15 species circumscribed, where six are endemic. This total represents 1/3 of the world’s species of Balanophoraceae and almost 90% of its richness in the Neotropics. The species were recorded in all Brazilian biomes, except in the “campos sulinos”, and habiting preferentially the interior of forest and forested savannas, since sea level up to 2400 meters of altitude. In the present revision, Helosis brasiliensis is revalidated, the occurrence of Lophophytum weddellii is confirmed to Brazil, and new typifications plus a new combination are proposed to some traditionally accepted names in the literature. Five species were identified under some threat category, being three “Endangered” and two “Vulnerable”, which demonstrate the necessity of promoting actions toward its conservation. In general, outcomes of this study provide the morphology role in delimitating species, contributing to a future phylogenetic reconstruction of Balanophoraceae, and help to meet national and international goals to the biodiversity study and conservation. In global scope, this study fills an important gap in the knowledge of Balanophoraceae. PT: Balanophoraceae é a mais representativa família de holoparasitas do Brasil e desde a Flora Brasiliensis carece de uma revisão direcionada as suas espécies no país. O presente estudo compila e gera novas informações acerca da família, abordando morfologia, delimitação dos táxons e informações ecológicas, assim como o estado de conservação das espécies. Estão circunscritos seis gêneros e 15 espécies, seis destas endêmicas do Brasil. Esse total representa 1/3 das espécies de Balanophoraceae do mundo e quase 90% da riqueza neotropical da família. Excetuando-se os campos sulinos, suas espécies foram registradas em todos os biomas brasileiros, habitando preferencialmente o interior de florestas e savanas florestadas, desde o nível do mar até pouco mais de 2400 m de altitude. Neste estudo Helosis brasiliensis foi circunscrito de H. cayennensis, confirmou-se a ocorrência inédita de Lophophytum weddellii para a flora do Brasil e foram propostas novas tipificações e uma nova combinação. A avaliação de risco identificou cinco espécies ameaçadas de extinção, sendo três em perigo e duas vulneráveis, demonstrando a necessidade de promover ações de conservação direcionadas. De forma geral, os resultados subsidiam o papel da morfologia na delimitação das espécies, contribuindo para a futura reconstrução filogenética de Balanophoraceae, e atendem também as metas nacionais e internacionais para o estudo e conservação da biodiversidade. Em âmbito global, representam o preenchimento de uma importante lacuna no estudo da família Balanophoraceae.

Insect taxonomy, biodiversity research and the new taxonomic impediments

Article

Full-text available

Dec 2017

Paolo Audisio

No taxon left behind? - A critical taxonomic checklist of Carpinus and Ostrya (Coryloideae, Betulaceae)

Article

Full-text available

Dec 2017

Hornbeams (Carpinus) and hop-hornbeams (Ostrya) are trees or large shrubs from the northern hemisphere. Currently, 43 species of Carpinus (58 taxa including subdivisions) and 8 species of Ostrya (9 taxa including sudivisions) are recognized. These are based on 175 (plus 16 Latin basionyms of cultivars) and 21 legitimate basionyms, respectively. We present an updated checklist with publication details and type information for all accepted names and the vast majority of synonyms of Carpinus and Ostrya, including the designation of 54 lectotypes and two neotypes. Cultivars are listed if validly described under the rules of the ICN. Furthermore, we consider Carpinus hwai Hu & W.C.Cheng to be a synonym of Carpinus fargesiana var. ovalifolia (H.J.P.Winkl.) Holstein & Weigend comb. nov. During the course of our work, we found 30 legitimate basionyms of non-cultivars that have been consistently overlooked since their original descriptions, when compared with the latest checklists and floristic treatments. As regional floras are highly important for taxonomic practice, we investigated the number of overlooked names and found that 78 basionyms were omitted at least once in the eight regional treatments surveyed. More seriously, we found 4 basionyms of accepted species being overlooked in a major floristic treatment.

Another brick in the wall: population dynamics of a symbiotic species of Oxydromus (Annelida, Hesionidae), described as new based on morphometry

Article

Full-text available

Oct 2017
CONTRIB ZOOL

Oxydromus humesi is an annelid polychaete living as a strict bi-valve endosymbiont (likely parasitic) of Tellina nymphalis in Congolese mangrove swamps and of Scrobicularia plana and Macomopsis pellucida in Iberian saltmarshes. The Congolese and Iberian polychaete populations were previously considered as belonging to the same species, the latter showing regular distribution , intra-specific aggressive behaviour, and complex host-entering behaviour. The fresh Iberian samples enabled us to undertake consistent morphometric analyses, as well as to further analyse the characteristics of the association and the population dynamics of the Iberian population hosted by S. plana. Among the morphological differences between the Congolese and Iberian specimens, leading to the description of the latter as Oxydromus okupa sp. nov., the most important are: 1) longer cephalic appendages, 2) greater distance between the eyes, 3) larger dorsal cirrostyle in relation to the corresponding dorsal lobe and cirro-phore. Moreover, dorsal and ventral lobes are similar in length, with the tip of the former reaching the tip of the latter in O. okupa sp. nov., while the dorsal lobe is much shorter than the ventral one in O. humesi. Mature adults of O. okupa sp. nov. occurred during the whole study period, with a higher percentage of ripe females in spring and, particularly, in summer. Numerous host specimens showed the symbiont's most preferred shell length (>26-36 mm). However, the prevalence was very low (usually <5%) and showed a clear seasonal pattern, being lower during spring/summer. This suggests that males are able to leave their hosts during this period, most likely to improve fertilization by directly entering or approaching a host occupied by a ripe female , while females usually remain inside. Based on the new results , the current knowledge of symbiotic Hesionidae and their relationships with invertebrate hosts is updated and discussed.

What really hampers taxonomy and conservation? A riposte to Garnett and Christidis (2017)

Article

Full-text available

Sep 2017

Responding to purported taxonomic anarchy, in an article published in the widely read journal Nature, Garnett & Christidis (2017) [hereafter GC] opined on the need for “standardized global species lists”, at the behest of conservationists, and proposed the construction of a judicial committee to “restrict … freedom of taxonomic action” and promote taxonomic stability. Here we reflect on this perspective and contest that the view of GC conflicts with some basic and indisputable principles underpinning the philosophy of science, most notably: it must be free. They appear to believe that taxonomic revisions should be based on political, economic and conservation concerns, and they treat species as fixed real entities, instead of refutable scientific hypotheses. In addition to such theoretical misconceptions, GC did not consider important practical aspects of what they term taxonomic anarchy, most significantly the participation of conservationists as authors of taxonomic works, and the importance of alternative management units, a well-established discussion in conservation biology.

Next-generation morphological character discovery and evaluation: an X-ray micro-CT enhanced revision of the ant genus Zasphinctus Wheeler (Hymenoptera, Formicidae, Dorylinae) in the Afrotropics

Article

Full-text available

Aug 2017

New technologies for imaging and analysis of morphological characters offer opportunities to enhance revisionary taxonomy and better integrate it with the rest of biology. In this study, we revise the Afrotropical fauna of the ant genus Zasphinctus Wheeler, and use high-resolution X-ray microtomography (micro-CT) to analyse a number of morphological characters of taxonomic and biological interest. We recognise and describe three new species: Z. obamai sp. n., Z. sarowiwai sp. n., and Z. wilsoni sp. n. The species delimitations are based on the morphological examination of all physical specimens in combination with 3D scans and volume reconstructions. Based on this approach, we present a new taxonomic discrimination system for the regional fauna that consists of a combination of easily observable morphological characters visible at magnifications of around 80–100 ×, less observable characters that require higher magnifications, as well as characters made visible through virtual dissections that would otherwise require destructive treatment. Zasphinctus are rarely collected ants and the material available to us is comparatively scarce. Consequently, we explore the use of micro-CT as a non-invasive tool for the virtual examination, manipulation, and dissection of such rare material. Furthermore, we delineate the treated species by providing a diagnostic character matrix illustrated by numerous images and supplement that with additional evidence in the form of stacked montage images, 3D PDFs and 3D rotation videos of scans of major body parts and full body (in total we provide 16 stacked montage photographs, 116 images of 3D reconstructions, 15 3D rotation videos, and 13 3D PDFs). In addition to the comparative morphology analyses used for species delimitations, we also apply micro-CT data to examine certain traits, such as mouthparts, cuticle thickness, and thoracic and abdominal muscles in order to assess their taxonomic usefulness or gain insights into the natural history of the genus. The complete datasets comprising the raw micro-CT data, 3D PDFs, 3D rotation videos, still images of 3D models, and coloured montage photos have been made available online as cybertypes (Dryad, http://dx.doi.org/10.5061/dryad.4s3v1).

Integrative taxonomy by molecular species delimitation: multi-locus data corroborate a new species of Balkan Drusinae micro-endemics

Article

Full-text available

Jun 2017
BMC EVOL BIOL

Background Taxonomy offers precise species identification and delimitation and thus provides basic information for biological research, e.g. through assessment of species richness. The importance of molecular taxonomy, i.e., the identification and delimitation of taxa based on molecular markers, has increased in the past decade. Recently developed exploratory tools now allow estimating species-level diversity in multi-locus molecular datasets. Results Here we use molecular species delimitation tools that either quantify differences in intra- and interspecific variability of loci, or divergence times within and between species, or perform coalescent species tree inference to estimate species-level entities in molecular genetic datasets. We benchmark results from these methods against 14 morphologically readily differentiable species of a well-defined subgroup of the diverse Drusinae subfamily (Trichoptera, Limnephilidae). Using a 3798 bp (6 loci) molecular data set we aim to corroborate a geographically isolated new species by integrating comparative morphological studies and molecular taxonomy. Conclusions Our results indicate that only multi-locus species delimitation provides taxonomically relevant information. The data further corroborate the new species Drusus zivici sp. nov. We provide differential diagnostic characters and describe the male, female and larva of this new species and discuss diversity patterns of Drusinae in the Balkans. We further discuss potential and significance of molecular species delimitation. Finally we argue that enhancing collaborative integrative taxonomy will accelerate assessment of global diversity and completion of reference libraries for applied fields, e.g., conservation and biomonitoring. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0972-5) contains supplementary material, which is available to authorized users.

The Molecularisation of Security: Medical Countermeasures, Stockpiling and the Governance of Biological Threats

Book

Jul 2021

Christopher Long

Taxonomie intégrative des Turridae : phylogénie, délimitation d’espèces et barcoding

Thesis

Sep 2008

Nicolas Puillandre

Les Turridae constituent un groupe de gastéropodes marins très diversifié, et dont une grande partie des espèces sont encore non décrites. Les approches taxonomiques traditionnelles se heurtent à des problèmes liés à la variabilité de la coquille, difficile à interpréter, aussi bien au niveau spécifique (α-taxonomie) qu’aux niveaux supérieurs (phylogénie). Afin d’accélérer le rythme de description des espèces, l’objectif de la thèse est de renouveler les pratiques taxonomiques au sein des Turridae en adaptant de nouvelles méthodes et de nouveaux outils. La taxonomie devient intégrative, et associe caractères moléculaires, morphologiques et écologiques mais également les méthodes issues de la phylogénie et de la génétique des populations. Le projet barcoding participe à cette nouvelle dynamique, en offrant une méthode d’analyse standardisée de ladiversité génétique.Dans une première partie, plusieurs gènes mitochondriaux et nucléaires ont été séquencés pour reconstruire la phylogénie des Conoidea, groupe incluant les Turridae mais également le genre Conus et les Terebridae. Les résultats obtenus mettent en évidence des relations phylogénétiques inédites, et permettent de proposer une nouvelle classification pour le groupe.Dans une seconde partie, l’approche d’α-taxonomie intégrative est détaillée. Elle repose sur le cadre conceptuel suivant : les espèces sont des segments de lignées évolutives. De plus, les espèces acquièrent au cours de leur évolution différentes propriétés qui peuvent être utilisées pour proposer des hypothèses de délimitation d’espèces, notamment en utilisant des caractères moléculaires. Dans une première étape, le fragment barcode du gène COI a été séquencé. Il a été utilisé pour identifier des pontes de gastéropodes marins et pour tester les hypothèses de délimitation d’espèces déjà disponibles pour le genre Eumunida (Crustacea).Le barcode COI peut également permettre de proposer de nouvelles hypothèses de délimitation d’espèces. Principalement deux méthodes exploratoires, dont l’une a été développée au cours de cette thèse, ont été utilisées pour délimiter des groupes de spécimens. Ces groupes ont ensuite été testés dans une seconde étape en analysant systématiquement un gène nucléaire (28S ou ITS2), mais également la variabilité morphologique. Cette approche de taxonomie intégrative a été appliquée à quatre groupes de Turridae, pour lesquels un grand nombre d’échantillons collectés dans le Pacifique étaient disponibles : les genres Bathytoma, Benthomangelia et Xenuroturris, et la sous-famille des Turrinae. Au total, 111 espèces ont été délimitées au sein de ces groupes, dont environ 70 seraient nouvelles pour la science.Les caractères moléculaires ont donc été utiles pour éclaircir les relations phylogénétiques au sein de la famille des Turridae. Associés à l’analyse d’autres caractères, ils ont également permis d’analyser la diversité spécifique de ce groupe. La méthodologie mise au point au cours de la thèse est donc adaptée à un groupe hyperdiversifé comme les Turridae, et accélère le rythme de découverte et de description de nouvelles espèces.

How physics fakes design

Chapter

Mar 2014

Alex Rosenberg

Evolution - both the fact that it occurred and the theory describing the mechanisms by which it occurred - is an intrinsic and central component in modern biology. Theodosius Dobzhansky captures this well in the much-quoted title of his 1973 paper 'Nothing in biology makes sense except in the light of evolution'. The correctness of this assertion is even more obvious today: philosophers of biology and biologists agree that the fact of evolution is undeniable and that the theory of evolution explains that fact. Such a theory has far-reaching implications. In this volume, eleven distinguished scholars address the conceptual, metaphysical and epistemological richness of the theory and its ethical and religious impact, exploring topics including DNA barcoding, three grand challenges of human evolution, functionalism, historicity, design, evolution and development, and religion and secular humanism. The volume will be of great interest to those studying philosophy of biology and evolutionary biology.

Darwin’s theory and the value of mathematical formalization

Chapter

Mar 2014

R. Paul Thompson

Evolution - both the fact that it occurred and the theory describing the mechanisms by which it occurred - is an intrinsic and central component in modern biology. Theodosius Dobzhansky captures this well in the much-quoted title of his 1973 paper 'Nothing in biology makes sense except in the light of evolution'. The correctness of this assertion is even more obvious today: philosophers of biology and biologists agree that the fact of evolution is undeniable and that the theory of evolution explains that fact. Such a theory has far-reaching implications. In this volume, eleven distinguished scholars address the conceptual, metaphysical and epistemological richness of the theory and its ethical and religious impact, exploring topics including DNA barcoding, three grand challenges of human evolution, functionalism, historicity, design, evolution and development, and religion and secular humanism. The volume will be of great interest to those studying philosophy of biology and evolutionary biology.

DNA barcoding and taxonomic practice

Chapter

Mar 2014

David Castle

Evolution - both the fact that it occurred and the theory describing the mechanisms by which it occurred - is an intrinsic and central component in modern biology. Theodosius Dobzhansky captures this well in the much-quoted title of his 1973 paper 'Nothing in biology makes sense except in the light of evolution'. The correctness of this assertion is even more obvious today: philosophers of biology and biologists agree that the fact of evolution is undeniable and that the theory of evolution explains that fact. Such a theory has far-reaching implications. In this volume, eleven distinguished scholars address the conceptual, metaphysical and epistemological richness of the theory and its ethical and religious impact, exploring topics including DNA barcoding, three grand challenges of human evolution, functionalism, historicity, design, evolution and development, and religion and secular humanism. The volume will be of great interest to those studying philosophy of biology and evolutionary biology.

Religion, truth, and progress

Chapter

Mar 2014

Philip Kitcher

Evolution - both the fact that it occurred and the theory describing the mechanisms by which it occurred - is an intrinsic and central component in modern biology. Theodosius Dobzhansky captures this well in the much-quoted title of his 1973 paper 'Nothing in biology makes sense except in the light of evolution'. The correctness of this assertion is even more obvious today: philosophers of biology and biologists agree that the fact of evolution is undeniable and that the theory of evolution explains that fact. Such a theory has far-reaching implications. In this volume, eleven distinguished scholars address the conceptual, metaphysical and epistemological richness of the theory and its ethical and religious impact, exploring topics including DNA barcoding, three grand challenges of human evolution, functionalism, historicity, design, evolution and development, and religion and secular humanism. The volume will be of great interest to those studying philosophy of biology and evolutionary biology.

Human evolution: Whence and whither?

Chapter

Mar 2014

Francisco Ayala

Evolution - both the fact that it occurred and the theory describing the mechanisms by which it occurred - is an intrinsic and central component in modern biology. Theodosius Dobzhansky captures this well in the much-quoted title of his 1973 paper 'Nothing in biology makes sense except in the light of evolution'. The correctness of this assertion is even more obvious today: philosophers of biology and biologists agree that the fact of evolution is undeniable and that the theory of evolution explains that fact. Such a theory has far-reaching implications. In this volume, eleven distinguished scholars address the conceptual, metaphysical and epistemological richness of the theory and its ethical and religious impact, exploring topics including DNA barcoding, three grand challenges of human evolution, functionalism, historicity, design, evolution and development, and religion and secular humanism. The volume will be of great interest to those studying philosophy of biology and evolutionary biology.

Comparing surface digitization techniques in palaeontology using visual perceptual metrics and distance computations between 3D meshes

Article

Full-text available

Jan 2021

The use of surface digitization techniques and methods in palaeontology has increased in the last two decades, mainly due to recent improvements in devices and software. However, many digitization efforts are published only as 3D models, with only a few details on the exact protocols used and sometimes not even indicating how to access these digital data, thus reducing the long‐term reusability of the obtained files. It is important to include this information, as the applied techniques and workflows have significant effects on the final quality of 3D models. We compare 3D meshes created by seven different surface digitization techniques and protocols for a sauropod caudal vertebra and a testudine turtle in a flat slab of rock. These two specimens represent typical examples of objects in vertebrate palaeontology collections, making them a suitable sample for our tests. Besides these quantitative and topological comparisons we also have computed visual perceptual metrics, which aim to predict the visual quality of a 3D model as perceived by a human observer. Our results agree with previous works, confirming that photogrammetry is one of the most suitable options for obtaining high quality 3D models of fossils, producing higher quality meshes than current structured light 3D scanners.

Ozymandias: a biodiversity knowledge graph

Article

Full-text available

Apr 2019

Roderic Page

Enormous quantities of biodiversity data are being made available online, but much of this data remains isolated in silos. One approach to breaking these silos is to map local, often database-specific identifiers to shared global identifiers. This mapping can then be used to construct a knowledge graph, where entities such as taxa, publications, people, places, specimens, sequences, and institutions are all part of a single, shared knowledge space. Motivated by the 2018 GBIF Ebbe Nielsen Challenge I explore the feasibility of constructing a "biodiversity knowledge graph" for the Australian fauna. The data cleaning and reconciliation steps involved in constructing the knowledge graph are described in detail. Examples are given of its application to understanding changes in patterns of taxonomic publication over time. A web interface to the knowledge graph (called "Ozymandias") is available at https://ozymandias-demo.herokuapp.com.

Cytochrome Oxidase I Sequences from Northern and Southern California Suggest Cryptic Baetis (Ephemeroptera: Baetidae) Species

Article

Jul 2019

The geographically widespread mayfly genus Baetis occurs from the subarctic to tropical regions of the world. Many of the 20 described Baetis species in North America are known to show cryptic species diversity. However, studies of Baetis that have examined morphology and genetic diversity have found mixed results in terms of cryptic species, with some studies indicating a complex of related species and others suggesting a single widespread species. We used Bayesian analyses, intra- and interspecific genetic diversity values, and median-joining haplotype networks to compare cytochrome oxidase I (COI) sequences from Baetis specimens from parts of northern and southern California (n = 742). Our results suggest that genetic diversity at the COI gene region in populations from northern California supports the diversity indicated by morphology (Baetis tricaudatus and Baetis adonis); however, populations in southern California exhibit more genetic diversity than indicated by morphology alone (DNA divergence > 1%), which suggests cryptic species diversity. The putative species that was morphologically and genetically identified as Baetis tricaudatus was the only taxon that occurred in both regions. No haplotypes were shared between regions. Intraspecific diversity within putative species from northern California was >1%. In contrast, intraspecific diversity within species from southern California was always <1%. Such discrepancies highlight the need for locally derived reference libraries in using next-generation sequencing or environmental DNA as a method to examine genetic diversity.

Ozymandias: A biodiversity knowledge graph

Preprint

Full-text available

Dec 2018

Roderic Page

Enormous quantities of biodiversity data are being made available online, but much of this data remains isolated in their own silos. One approach to breaking these silos is to map local, often database-specific identifiers to shared global identifiers. This mapping can then be used to con-struct a knowledge graph, where entities such as taxa, publications, people, places, specimens, sequences, and institutions are all part of a single, shared knowledge space. Motivated by the 2018 GBIF Ebbe Nielsen Challenge I explore the feasibility of constructing a "biodiversity knowledge graph" for the Australian fauna. These steps involved in constructing the graph are described, and examples its application are discussed. A web interface to the knowledge graph (called "Ozymandias") is available at https://ozymandias-demo.herokuapp.com.

A Mobile Game-Based Virtual Reality for Learning Basic Plant Taxonomy: Contextual Analysis and Prototype Development

Chapter

Jan 2018

The Science of Insect Taxonomy: Prospects and Needs: Science and Society

Chapter

Jul 2017

This chapter begins by stating what taxonomists understand but few other scientists have yet recognized, that taxonomy is to the life sciences as cosmology is to the physical sciences. The goals of taxonomy sound deceptively simple: to discover, describe, and critically test species; to describe and interpret the origin and diversification of their characters; to place them in classifications that reflect phylogenetic hierarchy; to make them identifiable; to give them unambiguous names; and to make information about them reliable and accessible. The fragmented research resources, provincial collections, and individual scholar models of the past can give way to the elevation of taxonomy to an appropriate global scale. A combination of cyberinfrastructure and the kind of teamwork exhibited in the Planetary Biodiversity Inventory (PBI) projects, along with a possible alternative strategy for accelerating species inventories, point to a clear path to success.

Linnaeus in the information age

Abstract

No full-text available

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