Concepts of taxonomy and concepts of biodiversity: the problem of interaction

There is, or there should be, an interaction between concepts of taxonomy and biodiversity. On the one hand, taxonomy develops some general and particular classificatory paradigms, which own diversity is to be taken into account to understand the nature of variety of natural kinds. On the other hand, analysis of the properties of biodiversity may put forward nontrivial problems for taxonomy that cannot be deduced directly from its own statements. From the point view of taxonomy, it is argued that the current concept of biodiversity based entirely on the species concept is deeply rooted in reductionistic view of nature. It is outdated epistemologically and should be replaced by the modern taxonomic concept of the hierarchical phylogenetic pattern. Operationally, the latter presumes a possibility for each species to be assigned a certain "phylogenetic weight", according to its phylogenetic uniqueness. From the point view of biodiversity, it is argued that the global biodiversity is a three component entity, as it includes, in addition to phylogenetic and ecological hierarchies, a biomorphic hierarchy, as well. This calls for taxonomy to elaborate the general principles of classification of biomorphs.     

Biodiversity inventory and informatics in Southeast Asia

Rapidly changing land use in Southeast Asia threatens plant diversity, and reduces the time we have left to document it. Despite over 200 years of scientific plant exploration, many plant species have yet to be discovered. Moreover, we still have a very poor understanding of the distribution of known taxa in this biogeographically complex region. We review the current state of biodiversity exploration, using plants in Indonesia as an example. Traditional methods of collecting and describing species have provided a solid foundation for our understanding of plant biodiversity, but are insufficient for the pragmatic task of rapidly discovering and documenting today’s biodiversity before it is gone, because general collecting expeditions tend to be infrequent, and documentation of most new species must await taxonomic revisions many years in the future. Solutions to this exploration and documentation crisis (i) could use the abundant resource of enthusiastic, networked, national biology students, (ii) should employ biodiversity informatics tools to efficiently engage both specialists and parataxonomists, and (iii) might require adoption of new types of α-taxonomy, utilizing increasingly low-cost molecular methods and high resolution photographs. We describe emerging technologies that will facilitate this taxonomic development. We believe that a new golden age of biodiversity exploration may be dawning, just as biodiversity itself is most threatened, and are hopeful that increasing knowledge of biodiversity will be a positive force to slow its loss.     

Species limits in butterflies (Lepidoptera: Nymphalidae): reconciling classical taxonomy with the multispecies coalescent

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

Genes Suggest Ancestral Colour Polymorphisms Are Shared across Morphologically Cryptic Species in Arctic Bumblebees

Our grasp of biodiversity is fine-tuned through the process of revisionary taxonomy. If species do exist in nature and can be discovered with available techniques, then we expect these revisions to converge on broadly shared interpretations of species. But for the primarily arctic bumblebees of the subgenus Alpinobombus of the genus Bombus, revisions by some of the most experienced specialists are unusual for bumblebees in that they have all reached different conclusions on the number of species present. Recent revisions based on skeletal morphology have concluded that there are from four to six species, while variation in colour pattern of the hair raised questions as to whether at least seven species might be present. Even more species are supported if we accept the recent move away from viewing species as morphotypes to viewing them instead as evolutionarily independent lineages (EILs) using data from genes. EILs are recognised here in practice from the gene coalescents that provide direct evidence for their evolutionary independence. We show from fitting both general mixed Yule/coalescent (GMYC) models and Poisson-tree-process (PTP) models to data for the mitochondrial COI gene that there is support for nine species in the subgenus Alpinobombus. Examination of the more slowly evolving nuclear PEPCK gene shows further support for a previously unrecognised taxon as a new species in northwestern North America. The three pairs of the most morphologically similar sister species are separated allopatrically and prevented from interbreeding by oceans. We also find that most of the species show multiple shared colour patterns, giving the appearance of mimicry among parts of the different species. However, reconstructing ancestral colour-pattern states shows that speciation is likely to have cut across widespread ancestral polymorphisms, without or largely without convergence. In the particular case of Alpinobombus, morphological, colour-pattern, and genetic groups show little agreement, which may help to explain the lack of agreement among previous taxonomic revisions.     

Ten years inventorying the Iberian fauna: results and perspectives

The Iberian Peninsula is one of the richest European regions in animal species diversity. Since 1988, the objective of the nationally funded Fauna Ibérica project has been to carry out a well-documented inventory of the animal biodiversity in the Iberian-Balearic region. After 10 years of taxonomic work, this project has produced 20 monographs, which have reviewed and inventoried around 11% of the animal species that inhabit the Iberian territory. It has also described 418 new species and 519 species formerly unknown in the Iberian-Balearic region. Considering all the new Iberian species described, we estimate that the researchers involved in this project have so far completed one third of all Iberian taxonomic work. At this rate it would take at least 75 years to finish the taxonomic review of the Iberian fauna. We recommend: (i) uninterrupted public logistical and financial support for taxonomy; (ii) the promotion of a plan for the training of new specialists in the taxonomically little-known groups; (iii) the elaboration of checklists as a way to inventory the Iberian animal biodiversity more rapidly; and (iv) the use of computerized approaches to species inventories taxonomy.     

Biodiversity,biogeography, and connectivity of polychaetes in the world's largest marine minerals exploration frontier

Aim

The abyssal Clarion-Clipperton Zone (CCZ), Pacific Ocean, is an area of commercial importance owing to the growing interest in mining high-grade polymetallic nodules at the seafloor for battery metals. Research into the spatial patterns of faunal diversity, composition, and population connectivity is needed to better understand the ecological impacts of potential resource extraction. Here, a DNA taxonomy approach is used to investigate regional-scale patterns of taxonomic and phylogenetic alpha and beta diversity, and genetic connectivity, of the dominant macrofaunal group (annelids) across a 6 million km² region of the abyssal seafloor.

Location

The abyssal seafloor (3932–5055 m depth) of the Clarion-Clipperton Zone, equatorial Pacific Ocean.

Methods

We used a combination of new and published barcode data to study 1866 polychaete specimens using molecular species delimitation. Both phylogenetic and taxonomic alpha and beta diversity metrics were used to analyse spatial patterns of biodiversity. Connectivity analyses were based on haplotype distributions for a subset of the studied taxa.

Results

DNA taxonomy identified 291–314 polychaete species from the COI and 16S datasets respectively. Taxonomic and phylogenetic beta diversity between sites were relatively high and mostly explained by lineage turnover. Over half of pairwise comparisons were more phylogenetically distinct than expected based on their taxonomic diversity. Connectivity analyses in abundant, broadly distributed taxa suggest an absence of genetic structuring driven by geographical location.

Main Conclusions

Species diversity in abyssal Pacific polychaetes is high relative to other deep-sea regions. Results suggest that environmental filtering, where the environment selects against certain species, may play a significant role in regulating spatial patterns of biodiversity in the CCZ. A core group of widespread species have diverse haplotypes but are well connected over broad distances. Our data suggest that the high environmental and faunal heterogeneity of the CCZ should be considered in future policy decisions.     

Lack of adequate taxonomic knowledge may hinder endemic mammal conservation in the Brazilian Atlantic Forest

The Atlantic Forest is one of the most diverse and threatened ecosystems of the world, being thus classified as one of the most important biodiversity hotspots. However, habitat loss, overexploitation, alien species, disease and pollution are not the only threats faced by native fauna and flora. The lack of adequate taxonomic knowledge hinders conservation and management efforts of endemic species. This is true even for mammals, which is the most charismatic group of animals and traditionally receive a good deal of attention from scientists and the public in general. A few examples show how this gap in local fauna information can be demise for species conservation, even misguiding management strategies: molecular data reveal a hidden marsupial diversity; the lack of taxonomic studies at the species level seriously threatens rodent conservation; and the taxonomic rearrangement of the genusBrachyteles revealed a new species and had a great impact on management strategies. New species are discovered, described and taxonomically rearranged at an astounding rate. We can only be successful in biodiversity conservation if we have at least a minimum level of knowledge about what we are trying to preserve. That is true both for researchers and for the general public. Recent taxonomic revisions may represent the turning point in Neotropical fauna knowledge, which, coupled with a greater awareness of local people about the rich biodiversity that dot their backyards, can represent a better conservation prospect for the endemics of the Atlantic Forest.     

TAXONOMY OF QUATERNARY DEEP-SEA OSTRACODS FROM THE WESTERN NORTH ATLANTIC OCEAN

Abstract:  Late Quaternary sediments from Ocean Drilling Program (ODP) Hole 1055B, Carolina Slope, western North Atlantic (32°47.041' N, 76°17.179' W; 1798 m water depth) were examined for deep-sea ostracod taxonomy. A total of 13 933 specimens were picked from 207 samples and c . 120 species were identified. Among them, 87 species were included and illustrated in this paper. Twenty-eight new species are described. The new species are: Ambocythere sturgio , Argilloecia abba , Argilloecia caju , Argilloecia keigwini , Argilloecia robinwhatleyi , Aversovalva carolinensis , Bythoceratina willemvandenboldi , Bythocythere eugeneschornikovi , Chejudocythere tenuis , Cytheropteron aielloi , Cytheropteron demenocali , Cytheropteron didieae , Cytheropteron richarddinglei , Cytheropteron fugu , Cytheropteron guerneti , Cytheropteron richardbensoni , Eucytherura hazeli , Eucytherura mayressi , Eucytherura namericana , Eucytherura spinicorona , Posacythere hunti , Paracytherois bondi , Pedicythere atroposopetasi , Pedicythere kennettopetasi , Pedicythere klothopetasi , Pedicythere lachesisopetasi , Ruggieriella mcmanusi and Xestoleberis oppoae . Taxonomic revisions of several common species were made to reduce taxonomic uncertainty in the literature. This study provides a robust taxonomic baseline for application to palaeoceanographical reconstruction and biodiversity analyses in the deep and intermediate-depth environments of the North Atlantic Ocean.     

The taxonomist - an endangered race. A practical proposal for its survival

Background

Taxonomy or biological systematics is the basic scientific discipline of biology, postulating hypotheses of identity and relationships, on which all other natural sciences dealing with organisms relies. However, the scientific contributions of taxonomists have been largely neglected when using species names in scientific publications by not citing the authority on which they are based.

Discussion

Consequences of this neglect is reduced recognition of the importance of taxonomy, which in turn results in diminished funding, lower interest from journals in publishing taxonomic research, and a reduced number of young scientists entering the field. This has lead to the so-called taxonomic impediment at a time when biodiversity studies are of critical importance. Here we emphasize a practical and obvious solution to this dilemma. We propose that whenever a species name is used, the author(s) of the species hypothesis be included and the original literature source cited, including taxonomic revisions and identification literature - nothing more than what is done for every other hypothesis or assumption included in a scientific publication. In addition, we postulate that journals primarily publishing taxonomic studies should be indexed in ISI^SM.

Summary

The proposal outlined above would make visible the true contribution of taxonomists within the scientific community, and would provide a more accurate assessment for funding agencies impact and importance of taxonomy, and help in the recruitment of young scientists into the field, thus helping to alleviate the taxonomic impediment. In addition, it would also make much of the biological literature more robust by reducing or alleviating taxonomic uncertainty.     

Is coarse taxonomy sufficient for detecting macroinvertebrate patterns in floodplain lakes?

Taxonomic sufficiency (TS) — defined as the minimum taxonomic detail required to discern some ecological pattern of interest — has been used extensively in bioassessment and biodiversity studies as a way of avoiding a portion of the time and monetary costs associated with species diagnoses. The taxonomic sufficiency for detecting species-level patterns among floodplain-lake benthic-invertebrate assemblages remains unexplored. We examined cross-taxonomic-level congruence in assemblage-environment relationships among 23 Chinese floodplain lakes. Our objectives were: (1) to compare the correlation between species richness and density and those at coarser taxonomic resolution; (2) to identify whether assemblage-environment relationships depend on taxonomic scale; and (3) to test whether the proportion of between-lake variability accounted for by environmental variables was independent of taxonomic scale. When taxonomic structure was described using sequentially coarser taxonomic aggregations, species-level patterns of richness and abundance were sequentially obscured (i.e., genus-level taxonomy best preserved patterns in species composition, order- and class-level taxonomy poorly represented species composition). Similar environmental variables were important for distinguishing lake species assemblages and genus assemblages; however, different environmental variables were important for describing family-, order-, and class-level assemblage patters. Moreover, environmental variables accounted for a similar amount of biological variability, regardless of taxonomic scale. Our results suggest genus taxonomy as sufficient for rapid assessments of lake diversity. Numerical dominance of the species- and genus-rich Chironomidae, Tubificidae, and Naididae, may account for the marked loss of information that occurs when lake invertebrates are assigned only to their families. In summary, we describe taxonomic sufficiency to detecting patterns of richness and abundance among subtropical lake macroinvertebrate faunas. This study will interest Chinese benthologists concerned with conservation and bioassessment.     

Cryptic diversity in flathead fishes (Scorpaeniformes: Platycephalidae) across the Indo‐West Pacific uncovered by DNA barcoding

Identification of taxonomical units underpins most biological endeavours ranging from accurate biodiversity estimates to the effective management of sustainably harvested, protected or endangered species. Successful species identification is now frequently based on a combination of approaches including morphometrics and DNA markers. Sequencing of the mitochondrial COI gene is an established methodology with an international campaign directed at barcoding all fishes. We employed COI sequencing alongside traditional taxonomic identification methods and uncovered instances of deep intraspecific genetic divergences among flathead species. Sixty‐five operational taxonomic units (OTUs) were observed across the Indo‐West Pacific from just 48 currently recognized species. The most comprehensively sampled taxon, Platycephalus indicus, exhibited the highest levels of genetic diversity with eight lineages separated by up to 16.37% genetic distance. Our results clearly indicate a thorough reappraisal of the current taxonomy of P. indicus (and its three junior synonyms) is warranted in conjunction with detailed taxonomic work on the other additional Platycephalidae OTUs detected by DNA barcoding.     

Taxonomy in the Kunming Institute of Botany (KIB): Progress during the past decade (2008-2018) and perspectives on future development

The development of new taxonomical theories and approaches, particularly molecular phylogenetics, has led to the expansion of traditional morphology-based taxonomy into the concept of "integrative taxonomy." Taxonomic knowledge has assumed greater significance in recent years, particularly because of growing concerns over the looming biodiversity crisis. Since its establishment in 1938, the Kunming Institute of Botany (KIB), which is located in Yunnan province in Southwest China, has focused attention on the taxonomy and conservation of the flora of China. For the forthcoming 80th anniversary of KIB, we review the achievements of researchers at KIB and their associates with respect to the taxonomy of land plants, fungi, and lichen. Major taxonomic advances are summarized for families of Calymperaceae, Cryphaeaceae, Lembophyllaceae, Neckeraceae, Polytrichaceae and Pottiaceae of mosses, Pteridaceae and Polypodiaceae of ferns, Taxaceae and Cycadaceae of gymnosperms, Asteraceae, Begoniaceae, Ericaceae, Euphorbiaceae, Gesneriaceae, Lamiaceae, Orchidaceae, Orobanchaceae, Poaceae, Theaceae and Urticaceae of angiosperms, Agaricaceae, Amanitaceae, Boletaceae, Cantharellaceae, Physalacriaceae Russulaceae, Suillaceae and Tuberaceae of fungi, and Ophioparmaceae and Parmeliaceae of lichens. Regarding the future development of taxonomy at KIB, we recommend that taxonomists continue to explore the biodiversity of China, integrate new theories and technologies with traditional taxonomic approaches, and engage in creative monographic work, with support from institutions, funding agencies, and the public.     

Systematics,biological knowledge and environmental conservation

Systematics and taxonomy are essential: they respectively elucidate life's history, and organize and verify biological knowledge. This knowledge is built of interrelated concepts which are ultimately accounted for by biological specimens. Such knowledge is essential to decide how much and what biodiversity survives human onslaughts. The preservation of specimens in natural history collections is the essential part of the process which builds and maintains biological knowledge. These collections and the human expertise essential to interpret specimens are the taxonomic resources which maintain accurate and verifiable concepts of biological entities. Present and future knowledge of the complexities and diversity of the biosphere depends on the integrity of taxonomic resources, vet widespread ignorance and disregard for their fundamental value has created a global crisis. Preservation of specimens in natural history collections is chronically neglected and support to study and manage collections is very insufficient. The knowledge held by experienced taxonomists is not being passed on to younger recruits. Neglect of collections has destroyed countless specimens and threatens millions more. These threats to taxonomic resources not only impinge on systematics but all biology: this tragedy jeopardizes the integrity of biological knowledge. The consequences for environmental conservation and therefore humanity are also of dire severity and the biodiversity crisis adds unprecedented weight to the barely recognized crisis in taxonomy and systematics.Where correspondence should     

A multigene molecular assessment of cryptic biodiversity in the iconic freshwater blackfishes (Teleostei: Percichthyidae: Gadopsis) of south‐eastern Australia

Freshwater biodiversity is under ever increasing threat from human activities, and its conservation and management require a sound knowledge of species‐level taxonomy. Cryptic biodiversity is a common feature for aquatic systems, particularly in Australia, where recent genetic assessments suggest that the actual number of freshwater fish species may be considerably higher than currently listed. The freshwater blackfishes (genus Gadopsis) are an iconic group in south‐eastern Australia and, in combination with their broad, naturally divided distribution and biological attributes that might limit dispersal, as well as ongoing taxonomic uncertainty, they comprise an ideal study group for assessing cryptic biodiversity. We used a multigene molecular assessment including both nuclear (51 allozyme loci; two S7 introns) and matrilineal markers (cytb) to assess species boundaries and broad genetic substructure within freshwater blackfishes. Range‐wide examination demonstrates the presence of at least six candidate species across two nominal taxa, Gadopsis marmoratus and Gadopsis bispinosus. Phylogeographical patterns often aligned to purported biogeographical provinces but occasionally reflected more restricted and unexpected relationships. We highlight key issues with taxonomy, conservation, and management for a species group in a highly modified region. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 521–540.     

A warning for ecologists and conservation biologists using species checklists: How the European marine fauna ‘lost’ all of its 16 <Emphasis Type="Italic">Discodoris</Emphasis> species (Mollusca: Gastropoda)

The European marine fauna used to be considered to include 16 species of Discodoris sea slugs until a recent worldwide revision demonstrated that there is not a single Discodoris species in European waters. This exemplary case illustrates the fact that species checklists do not accurately represent biodiversity unless they are based on sound taxonomic work in which (1) the status of every available species name has been addressed, i.e. whether it is valid, synonymous, or of doubtful application, and (2) classification reflects phylogenetic relationships. It is argued that taxonomic revisions are critically needed, because the status of species names can only be addressed properly through revisions. It is discussed that fields which depend on taxonomic data, such as conservation biology and ecology, might be affected deeply if problematic species names (synonyms and nomina dubia) have not been recognized. Consequently, it is proposed that a taxon that has not been revised be red-flagged in checklists, so that non-taxonomists will know which species names should be applied with caution or not at all.     

Integrative taxonomy and conservation of cryptic beetles in the Mediterranean region (Hydrophilidae)

Arribas, P., Andújar, C., Sánchez‐Fernández, D., Abellán, P. & Millán, A. (2012). Integrative taxonomy and conservation of cryptic beetles in the Mediterranean region (Hydrophilidae). —Zoologica Scripta, 00, 000–000. Because biodiversity inventory forms the basis for the effective conservation of species and habitats, there is an imperative need to discover and describe new species. A significant part of presently unknown biodiversity is constituted by cryptic species complexes, where traditional taxonomy usually fails due to a lack of clear taxonomic characters in the external structures of specimens. Integrative taxonomy offers a powerful tool to shed light on this part of encrypted biodiversity, combining multiple operational criteria in an evolutionary context in order to delineate species boundaries. The present study used an integrative approach to explore the species boundaries in a water beetle complex (Enochrus falcarius species complex) inhabiting saline streams, a rare and threatened habitat across the Mediterranean region. First, hypotheses about the candidate species on the basis of phylogenetic analyses and biogeographical information were proposed. Second, lineage divergence was evaluated between candidate species using (i) molecular cluster delimitation, (ii) morphometry (both linear body morphometrics and pronotum outlines) and (iii) ecological niche similarity estimates. We found divergence between candidate species on the basis of molecular, biogeographical and niche information, and consequently, four species were delimited within the E. falcarius complex (i.e. Enochrus jesusarribasi sp. n., Enochrus blazquezae sp. n., Enochrus risii sp. n. and Enochrus falcarius), despite the fact that they showed high morphological similarity. Enochrus falcarius, as previously considered, had not been proposed to be of conservational concern, because until now, it had been regarded as a single broadly distributed species in the Mediterranean region. However, the four entities here delimited within this species complex displayed characteristics that categorised them as vulnerable taxa. Hence, these results show how applying integrative taxonomy approaches and rapid vulnerability assessments to lineages from threatened habitats with the potential to comprise cryptic diversity could become a fundamental tool for biodiversity conservation, driving the discovery of cryptic species and consequently the modification of previous, inadequately evaluated vulnerability categorisations.