Cryptic species across deep-sea habitats: a case study on two sympatric cryptic complexes of Gymnonereidinae (Annelida: Nereididae).

Integrative taxonomy was formally introduced in 2005 as a comprehensive framework to delimit and describe taxa by integrating information from different types of data and methodologies (Dayrat 2005; Will et al. 2005). Even if debate remains about the hierarchy of the types of characters and criteria to use for species delimitation (Schlick-Steiner et al., 2009; Padial et al., 2010; Yeates et al., 2011), most, if not all taxonomists agree that objectively evaluating several lines of evidence within a formalized framework is the most efficient and theoretically-grounded approach to defining robust species hypotheses (Samadi and Barberousse 2006; de Queiroz 2007).The last ten years have seen a renewal of taxonomy, illustrated by the increasing number of published articles related to species concepts, species delimitation methodology and its application. In the early 90s, many systematists began to suspect that the majority of species would remain undescribed (Costello et al. 2013a; Erwin 1982; Mora et al. 2011 – but see Costello et al. 2013b) and that some of them will probably go extinct before we have a chance to describe them (Barnosky et al., 2011; Leakey and Lewin, 1995; Pimm et al., 2006). The use of molecular data, and in particular molecular barcoding (Hebert et al., 2003), was presented as one answer to this “taxonomic impediment” (as defined in Rodman and Cody, 2003), and welcomed as such by taxonomists. It thus adds to the toolkit of taxonomy, which continues its development as a synergic discipline involving morphological taxonomists, field ecologists, naturalists, and statisticians (Knapp 2008). Integrative taxonomy, used for many decades by taxonomists but only recently formalized concomitantly with the molecular revolution, is organised following a three-step workflow (see also Evenhuis 2007): first, we need to accumulate data on numerous specimens (from various types of data: DNA, morphology, ecology…); second, we need to circumscribe groups of organisms using concepts that ensure that these groups correspond to species (this second step may be coupled with the first, as biological data are continuously accumulated and species hypotheses re-discussed); and third, we need to provide a species description, i.e. a diagnosis and a name for the species recognized as new. Naming new species is a fundamental step when describing biodiversity and is the only way to ensure that scientists are talking about the same entity, and that all the data linked to conspecific specimens but produced by different researchers (or amateurs) can be associated in a comparative analysis (Patterson et al., 2010; Satler et al., 2013; Schlick-Steiner et al., 2007). Not linking biological data (should they be molecular, morphological, or ecological) to a formal species name will result in these data losing tremendous value (Goldstein and DeSalle 2011). Indeed, when authors publish data on entities that are not defined within the framework of a referencing system (e.g. solely identified by an alphanumeric label), they make it very difficult for other authors to build on these data. The best example is the need for taxa to be named to have a chance to be listed in an endangered species list and to benefit from a conservation program: no name, no surviving (Mace 2004). Beyond the need for communication among scientists, names are also key to communicating with non-scientist audiences. While it is now widely recognized that integrating several lines of evidence is the most efficient and theoretically grounded way to delimit new species (e.g. de Queiroz, 2007; Schlick-Steiner et al., 2009; Yeates et al., 2011), the formal naming of new entities may have become decoupled from species delimitation. Indeed, we noted that in several cases new delimited species were not accompanied by formal species description (see also Goldstein and DeSalle 2011). The aim of this article is therefore to test the hypothesis that integrative taxonomy, as defined in 2005 (Dayrat 2005; Will et al. 2005), and in particular the use of molecular data, helped to alleviate the taxonomic impediment by delimiting and describing new species. We reviewed part of the “integrative taxonomy” literature of the last eight years (2006-2013) and tested if authors that delimit new species also name them. We also looked at how the number and type of characters used, across different taxa, varies across articles.

Recent advancements in deep-sea exploration are noteworthy, revealing a diversity of organisms inhabiting unique habitats. These advances are also notable in the Brazilian Continental margin, especially at the Santos Basin, the most prolific in oil and gas exploration. Deep-sea habitats found at the Santos Basin included carbonate mounds, pockmarks, exhumed salt diapirs and organic falls, the latter represented by whale bones and wood. Polychaete species dominate the fauna of these habitats in both diversity and abundance, with different species described in the last years. Still, few studies advanced in the connectivity and evolutionary history of annelids using molecular data, which is the main focus of the present dissertation. Different case studies from distinct species were analyzed, including an eyeless group of the genus Nereis (Nereididae) with three new species, which formed a monophyletic group. This clade includes a formerly known species from Brazilian deep waters, one species formerly described from China, and the tree new species, which distribution can be explained by water masses delimitation (Chapter 1). Two Siboglinum (Siboglinidae) species previously described from the Brazilian Continental margin, from which the type specimens were lost, have been redescribed based on newly collected material. Molecular data from Siboglinum besnardi was successfully extracted and results are reported in Chapter 2. Seven distinct Gymnonereidinae (Nereididae) species are reported from different habitats of the Santos Basin and organized as two cryptic complexes based on species delimitation and phylogenetic analyses. The Micronereides capensis cryptic complex includes three species and the Ceratocephale sp. 4 cryptic complex includes other four species. These reports, together with discussions on cryptic speciation are discussed in Chapter 3. The population genetics and connectivity of a widely distributed Aphelochaeta species (Cirratulidae), inhabiting various deep-sea habitats, were investigated using different molecular markers. The gene flow seems to be continuous without habitat delimitation (Chapter 4). A comprehensive dataset produced during this dissertation is made accessible through the ABYSSAL database, which structure and operation of the latter is explained in Chapter 5. Lastly, in the final remarks section, the findings are synthesized, including a general phylogeny and species, to serve as the basis for discussion.

Taxonomic data is essential to advance the discovery and description of biodiversity, as well as the study of evolutionary processes. Emerging large-scale datasets and new methods of analysis have provided different approaches to describe biodiversity. Here, we present a review of the taxonomic history in Cycadales including an analysis of historical taxonomic concepts and approaches used for species delimitation. We examine the trends in the publication of new species following taxonomic works in books, journals and horticultural catalogues, monographic projects and floras where species treatments were published. In addition, we review the studies concerning species delimitations using the literature available in scientific journals appearing in the database ISI Web of Knowledge. The approaches used were discussed throughout all research focused on empirical and theoretical considerations in each study. We review the current state of the studies on causal processes that have given rise to the currently recognized diversity. The trend shows that taxonomic work on discovery and description of species has been intensive in the last 40 years culminating in 38.8% of binomials published. As a result, we consider the relevance of the monographs and floras for identification of species for other biological disciplines and the content of these contributions is compared and discussed. A total of six criteria (diagnosability, phenetic, phylogenetic, genotypic cluster, niche specialization and coalescent) were detected from the following three approaches to species delimitation within Cycadales: traditional, integrative taxonomy, and monophyletic. In all cases, the results from these species delimitations not only provided a taxonomic treatment or proposed a new species, but also supposedly clarified the other species involved as a result of the new taxonomic concept of the new species described. Most investigations of species delimitation used the traditional approach or a phenetic criteria. Finally, we discuss evolutionary studies on causal processes involved in cycad diversity. This is considered in the context of species delimitation as hypothesis testing for a successful evaluation of variation in both genetic and morphological understanding.

The advent of molecular methods has revolutionised the field of species delimitation and description, one of the key tasks of systematic biology. In animal taxonomy, one marker, the mitochondrial DNA (mtDNA) molecule, has acquired and retained disproportionate influence. This is despite its uniparental, clonal mode of inheritance, as a result of which the entire molecule acts as a single locus, and that precludes its use as a test for admixture between putative lineages, a key consideration in species delimitation. To establish the extent to which the limitations of mtDNA affect present-day taxonomy in non-avian reptiles, I surveyed species descriptions and delimitations published during the years 2023–2024, determined the markers used, and whether analyses of different markers were set up to critically test or just to confirm mtDNA-inspired candidate species. Mitochondrial DNA remains the dominant molecular marker in reptile taxonomy, being used in 84% of species descriptions and delimitations, and as the sole molecular marker in 44%. Despite the immense progress in next generation sequencing (NGS) technologies and their increasing affordability, only 3.4% of descriptions used NGS approaches. In 61% of descriptions, taxa were identified primarily through mtDNA divergence, and additional data (morphology, single-copy nuclear gene sequences) were used as confirmatory evidence rather than as rigorous tests of mitochondrially inferred species limits. I reiterate the importance of truly integrative species delimitation that critically tests species limits first hypothesised from mtDNA, and suggest ways of improving the robustness of species delimitations by optimising the allocation of resources to more appropriate markers and through analytical approaches that critically test the evolutionary independence of putative species.

What is a species? This seemingly simple question has occupied the minds of numerous biologists and philosophers, resulting in the formulation of many species concepts. From a theoretical point of view, the species problem has been resolved by equating species with independently evolving lineages (i.e. the evolutionary species concept or the general lineage concept). However, the practical issues with describing and delineating species remain. The origin of species is a gradual process that typically requires thousands to millions of years, creating a grey zone of species delimitation in which taxonomy is often controversial. To account for this, an integrative taxonomy has been proposed in which different taxonomic concepts and methods are integrated in the delimitation of species. In this chapter, I argue that genomics provides another line of evidence in this pluralistic approach to species classification. Indeed, genomic data can be combined with classical species criteria, such as diagnosability, phylogeny and reproductive isolation. First, genomic data can provide an extra diagnostic feature in species delimitation. Compared to ‘old-school’ genetic markers, the use of genome-wide markers leads to a significant rise in statistical power. Second, phylogenomic analyses can resolve the evolutionary relationships within rapidly diverging or hybridizing groups of species while taking into account gene tree discordance. Third, genomic data can be used to pinpoint the genetic basis of reproductive isolation and provide a detailed description of the speciation process. All in all, the genomic era will supply avian taxonomists with a new tool box that can be applied to old concepts, leading to better informed decisions in cataloguing biodiversity.

Species delimitation—owing to the paramount role of the species rank in evolutionary, ecological, and nature conservation studies—is an essential contribution of taxonomy to biodiversity research. In an ‘integrative taxonomy’ approach to species delimitation on the diploid level, we searched for evolutionary significant units (the warps and wefts) that gave rise to the polyploid complex of European ox-eye daisies (Leucanthemum; Compositae-Anthemideae). Species discovery and validation methods based on genetic, ecological, geographical, and morphometric datasets were applied to test the currently accepted diploid morpho-species, i.e., morphologically delimited species, in Leucanthemum. Novel approaches were taken in the analyses of RADseq data (consensus clustering), morphometrics of reconstructed leaf silhouettes from digitized herbarium specimens, and quantification of species-distribution overlaps. We show that 17 of the 20 Leucanthemum morpho-species are supported by genetic evidence. The taxonomic rank of the remaining three morpho-species was resolved by combining genealogic, ecologic, geographic, and morphologic data in the framework of von Wettstein’s morpho-geographical species concept. We herewith provide a methodological pipeline for the species delimitation in an ‘integrative taxonomy’ fashion using sources of evidence from genealogical, morphological, ecological, and geographical data in the philosophy of De Queiroz’s “Unified Species Concept”.

The third Heidelberg Unseminars in Bioinformatics (HUB) was held on 18th October 2012, at Heidelberg University, Germany. HUB brought together around 40 bioinformaticians from academia and industry to discuss the 'Biggest Challenges in Bioinformatics' in a 'World Café' style event.

The Rhizocarpaceae, a family of lichenized fungi within the Ascomycota, comprises approximately 160 species within five genera: Catolechia, Epilichen, Haugania, Poeltinula, and Rhizocarpon. Rhizocarpon is the most species-rich, with about 150 species predominantly inhabiting siliceous rock in boreal and arctic-alpine environments. Molecular phylogenetic studies have revealed that current taxonomy, heavily reliant on morphology, chemistry, and life strategies, renders Rhizocarpon paraphyletic. This study aims to elucidate the phylogenetic relationships and clarify genus delimitation within the Rhizocarpaceae using an integrative taxonomic approach that combines three genetic markers and a diversity of taxa covering the morphological, chemical, and ecological spectrum of the family. Our comprehensive sampling includes 50 species across the Rhizocarpaceae collected from diverse geographical locations and ecological settings. Our phylogenetic hypothesis is based on a concatenated dataset of two nuclear (ITS and MCM7) and one mitochondrial (mtSSU) genetic marker. Ascospore characteristics and thallus pigmentation alongside secondary metabolite profiles were mapped onto this DNA-based evolutionary framework. Our results underscore significant refinements in the classification of the Rhizocarpaceae, highlighting the inadequacy of traditional taxonomic markers alone to infer robust phylogenetic affiliations. We advocate for new circumscriptions of Catolechia, Poeltinula, and Rhizocarpon based on the molecular phylogeny and propose synonymizing Epilichen with Catolechia, the transfer of the species in the R. hochstetteri complex to Poeltinula, and the resurrection of Rehmia. We hence propose 24 new combinations and three typifications. Collectively, this study sets the groundwork for future research and stability in the systematics of the Rhizocarpaceae, augmenting our understanding of their diversity and evolutionary dynamics. Citation: Möller EJ, Timdal E, Haugan R, Bendiksby M (2025). Integrative taxonomy and genus delimitation in the Rhizocarpaceae (lichenized Ascomycota). Fungal Systematics and Evolution 16: 215-231. doi: 10.3114/fuse.2025.16.12.

Significant advances have been made in species delimitation and numerous methods can test precisely defined models of speciation, though the synthesis of phylogeography and taxonomy is still sometimes incomplete. Emerging consensus treats distinct genealogical clusters in genome-scale data as strong initial evidence of speciation in most cases, a hypothesis that must therefore be falsified under an explicit evolutionary model. We can now test speciation hypotheses linking trait differentiation to specific mechanisms of divergence with increasingly large data sets. Integrative taxonomy can, therefore, reflect an understanding of how each axis of variation relates to underlying speciation processes, with nomenclature for distinct evolutionary lineages. We illustrate this approach here with Seal Salamanders (Desmognathus monticola) and introduce a new unsupervised machine-learning approach for species delimitation. Plethodontid salamanders are renowned for their morphological conservatism despite extensive phylogeographic divergence. We discover 2 geographic genetic clusters, for which demographic and spatial models of ecology and gene flow provide robust support for ecogeographic speciation despite limited phenotypic divergence. These data are integrated under evolutionary mechanisms (e.g., spatially localized gene flow with reduced migration) and reflected in emergent properties expected under models of reinforcement (e.g., ethological isolation and selection against hybrids). Their genetic divergence is prima facie evidence for species-level distinctiveness, supported by speciation models and divergence along axes such as behavior, geography, and climate that suggest an ecological basis with subsequent reinforcement through prezygotic isolation. As data sets grow more comprehensive, species-delimitation models can be tested, rejected, or corroborated as explicit speciation hypotheses, providing for reciprocal illumination of evolutionary processes and integrative taxonomies. [Desmognathus; integrative taxonomy; machine learning; species delimitation.].

Molecular Systematics and the Diatom Species

Integrative taxonomy in a rapid speciation group associated with mating system transition: A case study in the Primula cicutariifolia complex

Integrative species delimitation in practice: Revealing cryptic lineages within the short-nosed skink Plestiodon brevirostris (Squamata: Scincidae)

Although delimitations of plant species are traditionally based on the study of herbarium specimens, new species can also be identified using multiple lines of evidence (integrative taxonomy). An integrative approach was implemented to identify a new species of the orchid genus Satyrium from the Midlands area of KwaZulu-Natal, South Africa, described here as S. cernuum. This species shares an overall similar floral morphology with five other sympatric morphotypes within the S. longicauda complex reported from the type locality but can be diagnosed by a combination of vegetative and floral traits and flowering phenology. According to a published phylogeny based on DNA sequences, the new species forms a monophyletic clade that is nested within S. longicauda and is supported as sister to the other S. longicauda morphotype that is uniquely characterised by a single erect leaf. The new species differs from this morphotype by the orientation of its flowers which are obtuse (vs. right-angled) relative to the inflorescence stem, spreading (vs. spreading to recurved) sepals, relatively short (vs. long) spurs that lack nectar and by its production of elevated levels of diacetin, a fatty-acid derived compound. Other S. longicauda morphotypes differ in the number and position of their leaves and a later flowering period. In addition, the new species is exclusively pollinated diurnally by the oil-collecting bee species Rediviva neliana, rather than being pollinated nocturnally by settling moths and hawkmoths; it is thus reproductively isolated from sympatric morphotypes. The formal recognition of the new species, which is known from two adjacent populations in an area of occupancy ≤1 km2 makes it a matter of immediate conservation concern. An identification key to the morphotypes of the S. longicauda complex from KwaZulu-Natal, including the newly described species, is provided. This study shows the value of using integrative taxonomy in the South African flora for the recognition of recently diverged taxa.

Simple SummaryThe taxonomy of the sinica group of macaques has been unresolved due to inconsistencies between their physical traits and genetic relationships. To clarify this taxonomic issue, we analyzed DNA from previously unsampled populations of the macaques in the Himalayas. Our results revealed that the sinica group consists of seven distinct species, rather than the previously considered six species as the two subspecies of Assamese macaques (Macaca assamensis assamensis and M. a. pelops) are separate candidate species with strong genetic variations. The study also identified Arunachal macaques (M. munzala) in the Shannan area of Xizang Zizhiqu in China. Multiple analyses revealed complex historical patterns of species dispersal and separation, mostly linked to climatic changes during the Quaternary period. We propose a new hypothesis about the sinica group’s evolutionary history.Owing to the taxonomic incongruence between the morphological features and genetic relationships of the sinica group of macaques (genus Macaca), the taxonomy of this macaque group has remained inconclusive. We aimed to resolve the taxonomic quandary and improve our understanding of the historical biogeography of the group by including macaque DNA samples from previously unsampled areas in the Himalayas. We sequenced and analyzed three mitochondrial DNA loci [cytochrome b (CYTB), cytochrome oxidase subunit 1 (COI) and D-loop; 2898 bp] for sequence polymorphism, phylogenetics, species delimitation, and ancestral area reconstruction. We confirmed the occurrence of Arunachal macaque (Macaca munzala) on the southern slopes of the Eastern Himalayas in the Xizang Zizhiqu (Tibet Autonomous Region) of China. The results revealed that the sinica group of macaques is a parapatric species group composed of seven distinct species. Phylogenetic and species delimitation analyses revealed that the two previously considered subspecies of Assamese macaques (the eastern subspecies M. assamensis assamensis and the western subspecies M. a. pelops) are two distinct species. The eastern Assamese macaque is a sister species to the Tibetan macaque, whereas the western Assamese macaque and Arunachal macaque are the closest genetic sister species. The sinica group of macaques underwent five vicariance and seven dispersal radiations in the past, which mainly coincided with the Quaternary climatic oscillations between the late Pliocene and the late Pleistocene. By integrating our phylogenetic and ancestral area reconstruction results with findings from previous paleontological and molecular studies, we propose a robust hypothesis about the phylogeography of the sinica group of macaques.

Species in the genus Gracilaria that display conspicuously flattened vegetative morphologies are a taxonomically challenging group of marine benthic red algae. This is a result of their species richness, morphological similarity, and broad phenotypic plasticity. Within this group, the Gracilaria domingensis complex is one of the most common, conspicuous, and morphologically variable species along the tropical western Atlantic Ocean. Previous research has identified that members of this complex belong to two distantly related clades. However, despite this increased phylogentic resolution, species delimitations within each of these clades remain unclear. Our study assessed the species diversity within this difficult complex using morphological and molecular data from three genetic markers (cox1, UPA, and rbcL). We additionally applied six single-marker species delimitation methods (SDM: ABGD, GMYCs, GMYCm, SPN, bPTP, and PTP) to rbcL, which were largely in agreement regarding species delimitation. These results, combined with our analysis of morphology, indicate that the G.domingensis complex includes seven distinct species, each of which are not all most closely related: G.cervicornis; a ressurected G.ferox; G.apiculata subsp. apiculata; a new species, Gracilaria baiana sp. nov.; G.intermedia subsp. intermedia; G.venezuelensis; and G.domingensis sensu stricto, which includes the later heterotypic synonym, G.yoneshigueana. Our study demonstrates the value of multipronged strategies, including the use of both molecular and morphological approaches, to decipher cryptic species of red algae.