The mind of the species problem

The concepts and origins of cell mortality

Organismal death is foundational to the evolution of life, and many biological concepts such as natural selection and life history strategy are so fashioned only because individuals are mortal. Organisms, irrespective of their organization, are composed of basic functional units-cells-and it is our understanding of cell death that lies at the heart of most general explanatory frameworks for organismal mortality. Cell death can be exogenous, arising from transmissible diseases, predation, or other misfortunes, but there are also endogenous forms of death that are sometimes the result of adaptive evolution. These endogenous forms of death-often labeled programmed cell death, PCD-originated in the earliest cells and are maintained across the tree of life. Here, we consider two problematic issues related to PCD (and cell mortality generally). First, we trace the original discoveries of cell death from the nineteenth century and place current conceptions of PCD in their historical context. Revisions of our understanding of PCD demand a reassessment of its origin. Our second aim is thus to structure the proposed origin explanations of PCD into coherent arguments. In our analysis we argue for the evolutionary concept of PCD and the viral defense-immunity hypothesis for the origin of PCD. We suggest that this framework offers a plausible account of PCD early in the history of life, and also provides an epistemic basis for the future development of a general evolutionary account of mortality.

Phylogeography and cohesion species delimitation of California endemic trapdoor spiders within the Aptostichus icenoglei sibling species complex (Araneae: Mygalomorphae: Euctenizidae)

Species delimitation is an imperative first step toward understanding Earth's biodiversity, yet what constitutes a species and the relative importance of the various processes by which new species arise continue to be debatable. Species delimitation in spiders has traditionally used morphological characters; however, certain mygalomorph spiders exhibit morphological homogeneity despite long periods of population-level isolation, absence of gene flow, and consequent high degrees of molecular divergence. Studies have shown strong geographic structuring and significant genetic divergence among several species complexes within the trapdoor spider genus Aptostichus, most of which are restricted to the California Floristic Province (CAFP) biodiversity hotspot. Specifically, the Aptostichus icenoglei complex, which comprises the three sibling species, A. barackobamai, A. isabella, and A. icenoglei, exhibits evidence of cryptic mitochondrial DNA diversity throughout their ranges in Northern, Central, and Southern California. Our study aimed to explicitly test species hypotheses within this assemblage by implementing a cohesion species-based approach. We used genomic-scale data (ultraconserved elements, UCEs) to first evaluate genetic exchangeability and then assessed ecological interchangeability of genetic lineages. Biogeographical analysis was used to assess the likelihood of dispersal versus vicariance events that may have influenced speciation pattern and process across the CAFP's complex geologic and topographic landscape. Considering the lack of congruence across data types and analyses, we take a more conservative approach by retaining species boundaries within A. icenoglei.

Taxonomic practice, creativity and fashion: what’s in a spider name?

There is a secret pleasure in naming new species. Besides traditional etymologies recalling the sampling locality, habitat or morphology of the species, names may be tributes to some meaningful person, pop culture references and even exercises of enigmatography. Using a dataset of 48 464 spider etymologies, we tested the hypothesis that species names given by taxonomists are deeply influenced by their cultural background. Specifically, we asked whether naming practices change through space or have changed through time. In absolute terms, etymologies referring to morphology were the most frequently used. In relative terms, references to morphology peaked in 1850–1900 and then began to decline, with a parallel increase in etymologies dedicated to people and geography. We also observed a dramatic increase in etymologies referring to pop culture and other cultural aspects in 2000–2020, especially in Europe and the Americas. While such fashionable names often carry no biological information regarding the species itself, they help give visibility to taxonomy, a discipline currently facing a profound crisis in academia. Taxonomy is among the most unchanged disciplines across the last centuries in terms of tools, rules and writing style. Yet, our analysis suggests that taxonomists remain deeply influenced by their living time and space.

Lung Cell Atlases in Health and Disease

The human lung cellular portfolio, traditionally characterized by cellular morphology and individual markers, is highly diverse, with over 40 cell types and a complex branching structure highly adapted for agile airflow and gas exchange. While constant during adulthood, lung cellular content changes in response to exposure, injury, and infection. Some changes are temporary, but others are persistent, leading to structural changes and progressive lung disease. The recent advance of single-cell profiling technologies allows an unprecedented level of detail and scale to cellular measurements, leading to the rise of comprehensive cell atlas styles of reporting. In this review, we chronical the rise of cell atlases and explore their contributions to human lung biology in health and disease.

A refreshed approach to homology-Prioritizing epistemology over metaphysics

Unease with the inclusion of "sameness" in Owen's definition of homology characterizes a substantial part of the literature on this subject, where this term has acquired an increasingly strict metaphysical flavor. Taken for granted the existence of body features that are "the same," their existence has been explained by appealing to universal laws of form, as the product of common ancestry, or in terms of proximal causes responsible for the emergence of conserved developmental modules. However, a fundamentally different approach is possible, if we shift attention from metaphysics to epistemology. We may reword Owen's statement as follows: organs of different animals, in so far as they can be described as the same despite any difference in form and function, are called homologues. The proposed framework provides an umbrella for both the traditional, all-or-nothing concept of homology, and the less fashionable alternatives of factorial or partial homology, as well as for an extension of homology from form to function. No less attractive is the prospect to handle also ghost homologues, the body parts or organs of which there is non-objective evidence in a given clade, but can nevertheless be represented, in a description that encapsulates some of the traits observable in their extant homologue in the sister clade. Stripped of its different and constraining metaphysical explanations, homology survives as an anchor concept to which different nomadic disciplines and research agendas can be associated.

Cell types as species: Exploring a metaphor

The concept of "cell type," though fundamental to cell biology, is controversial. Cells have historically been classified into types based on morphology, physiology, or location. More recently, single cell transcriptomic studies have revealed fine-scale differences among cells with similar gross phenotypes. Transcriptomic snapshots of cells at various stages of differentiation, and of cells under different physiological conditions, have shown that in many cases variation is more continuous than discrete, raising questions about the relationship between cell type and cell state. Some researchers have rejected the notion of fixed types altogether. Throughout the history of discussions on cell type, cell biologists have compared the problem of defining cell type with the interminable and often contentious debate over the definition of arguably the most important concept in systematics and evolutionary biology, "species." In the last decades, systematics, like cell biology, has been transformed by the increasing availability of molecular data, and the fine-grained resolution of genetic relationships have generated new ideas about how that variation should be classified. There are numerous parallels between the two fields that make exploration of the "cell types as species" metaphor timely. These parallels begin with philosophy, with discussion of both cell types and species as being either individuals, groups, or something in between (e.g., homeostatic property clusters). In each field there are various different types of lineages that form trees or networks that can (and in some cases do) provide criteria for grouping. Developing and refining models for evolutionary divergence of species and for cell type differentiation are parallel goals of the two fields. The goal of this essay is to highlight such parallels with the hope of inspiring biologists in both fields to look for new solutions to similar problems outside of their own field.

Pan-Africanism vs. single-origin of Homo sapiens: Putting the debate in the light of evolutionary biology

The scenario of Homo sapiens origin/s within Africa has become increasingly complex, with a pan-African perspective currently challenging the long-established single-origin hypothesis. In this paper, we review the lines of evidence employed in support of each model, highlighting inferential limitations and possible terminological misunderstandings. We argue that the metapopulation scenario envisaged by pan-African proponents well describes a mosaic diversification among late Middle Pleistocene groups. However, this does not rule out a major contribution that emerged from a single population where crucial derived features-notably, a globular braincase-appeared as the result of a punctuated, cladogenetic event. Thus, we suggest that a synthesis is possible and propose a scenario that, in our view, better reconciles with consolidated expectations in evolutionary theory. These indicate cladogenesis in allopatry as an ordinary pattern for the origin of a new species, particularly during phases of marked climatic and environmental instability.

Species determination using AI machine-learning algorithms: Hebeloma as a case study

The genus Hebeloma is renowned as difficult when it comes to species determination. Historically, many dichotomous keys have been published and used with varying success rate. Over the last 20 years the authors have built a database of Hebeloma collections containing not only metadata but also parametrized morphological descriptions, where for about a third of the cases micromorphological characters have been analysed and are included, as well as DNA sequences for almost every collection. The database now has about 9000 collections including nearly every type collection worldwide and represents over 120 different taxa. Almost every collection has been analysed and identified to species using a combination of the available molecular and morphological data in addition to locality and habitat information. Based on these data an Artificial Intelligence (AI) machine-learning species identifier has been developed that takes as input locality data and a small number of the morphological parameters. Using a random test set of more than 600 collections from the database, not utilized within the set of collections used to train the identifier, the species identifier was able to identify 77% correctly with its highest probabilistic match, 96% within its three most likely determinations and over 99% of collections within its five most likely determinations.

Food biodiversity: Quantifying the unquantifiable in human diets

Dietary diversity is an established public health principle, and its measurement is essential for studies of diet quality and food security. However, conventional between food group scores fail to capture the nutritional variability and ecosystem services delivered by dietary richness and dissimilarity within food groups, or the relative distribution (i.e., evenness or moderation) of e.g., species or varieties across whole diets. Summarizing food biodiversity in an all-encompassing index is problematic. Therefore, various diversity indices have been proposed in ecology, yet these require methodological adaption for integration in dietary assessments. In this narrative review, we summarize the key conceptual issues underlying the measurement of food biodiversity at an edible species level, assess the ecological diversity indices previously applied to food consumption and food supply data, discuss their relative suitability, and potential amendments for use in (quantitative) dietary intake studies. Ecological diversity indices are often used without justification through the lens of nutrition. To illustrate: (i) dietary species richness fails to account for the distribution of foods across the diet or their functional traits; (ii) evenness indices, such as the Gini-Simpson index, require widely accepted relative abundance units (e.g., kcal, g, cups) and evidence-based moderation weighting factors; and (iii) functional dissimilarity indices are constructed based on an arbitrary selection of distance measures, cutoff criteria, and number of phylogenetic, nutritional, and morphological traits. Disregard for these limitations can lead to counterintuitive results and ambiguous or incorrect conclusions about the food biodiversity within diets or food systems. To ensure comparability and robustness of future research, we advocate food biodiversity indices that: (i) satisfy key axioms; (ii) can be extended to account for disparity between edible species; and (iii) are used in combination, rather than in isolation.Supplemental data for this article is available online at https://doi.org/10.1080/10408398.2022.2051163 .

The Enclosed Intestinal Microbiome: Semiochemical Signals from the Precambrian and Their Disruption by Heavy Metal Pollution

It is increasingly likely that many non-communicable diseases of humans and associated animals are due to the degradation of their intestinal microbiomes, a situation often referred to as dysbiosis. An analysis of the resultant diseases offers an opportunity to probe the function of these microbial partners of multicellular animals. In our view, it now seems likely that vertebrate animals and their microbiomes have coevolved throughout the Ediacaran–Cambrian transition and beyond, operating by semiochemical messaging between the multicellular host and its microbial community guest. A consideration of the overall role of the mutualistic intestinal microbiome as an enclosed bioreactor throws up a variety of challenging concepts. In particular: the significance of the microbiome with respect to the immune system suggests that microeukaryotes could act as microbial sentinel cells; the ubiquity of bacteriophage viruses implies the rapid turnover of microbial composition by a viral-shunt mechanism; and high microbial diversity is needed to ensure that horizontal gene transfer allows valuable genetic functions to be expressed. We have previously postulated that microbes of sufficient diversity must be transferred from mother to infant by seemingly accidental contamination during the process of natural birth. We termed this maternal microbial inheritance and suggested that it operates alongside parental genetic inheritance to modify gene expression. In this way, the adjustment of the neonate immune system by the microbiome may represent one of the ways in which the genome of a vertebrate animal interacts with its microbial environment. The absence of such critical functions in the neonate may help to explain the observation of persistent immune-system problems in affected adults. Equally, granted that the survival of the guest microbiome depends on the viability of its host, one function of microbiome-generated semiochemicals could be to facilitate the movement of food through the digestive tract, effectively partitioning nutrition between host and guest. In the event of famine, downregulation of microbial growth and therefore of semiochemical production would allow all available food to be consumed by the host. Although it is often thought that non-communicable diseases, such as type 2 diabetes, are caused by consumption of food containing insufficient dietary fibre, our hypothesis suggests that poor-quality food is not the prime cause but that the tendency for disease follows the degradation of the intestinal microbiome, when fat build-up occurs because the relevant semiochemicals can no longer be produced. It is the purpose of this paper to highlight the possibility that the origins of the microbiome lie in the Precambrian and that the disconnection of body and microbiome gives rise to non-communicable disease through the loss of semiochemical signalling. We further surmise that this disconnect has been largely brought about by heavy metal poisoning, potentially illuminating a facet of the exposome, the sum total of environmental insults that influence the expression of the genetic inheritance of an animal.

Species as a heuristic: reconciling theory and practice

Species are crucial to most branches of biological research, yet remain controversial in terms of definition, delimitation, and reality. The difficulty of resolving the “species problem” stems from the tension between their theoretical concept as groups of evolving and highly variable organisms and the practical need for a stable and comparable unit of biology. Here, we suggest that treating species as a heuristic can be consistent with a theoretical definition of what species are and with the practical means by which they are identified and delimited. Specifically, we suggest that theoretically species are heuristic since they comprise clusters of closely related individuals responding in a similar manner to comparable sets of evolutionary and ecological forces, whilst they are practically heuristic because they are identifiable by the congruence of contingent properties indicative of those forces. This reconciliation of the theoretical basis of species with their practical applications in biological research allows for a loose but relatively consistent definition of species based on the strategic analysis and integration of genotypic, phenotypic, and ecotypic data. [Cohesion; heuristic; homeostasis; lineage; species problem.]

Conceptual issues in hominin taxonomy: Homo heidelbergensis and an ethnobiological reframing of species

Efforts to name and classify Middle Pleistocene Homo, often referred to as "Homo heidelbergensis" are hampered by confusing patterns of morphology but also by conflicting paleoanthropological ideologies that are embedded in approaches to hominin taxonomy, nomenclature, and the species concept. We deconstruct these issues to show how the field's search for a "real" species relies on strict adherence to pre-Darwinian essentialist naming rules in a post-typological world. We then examine Middle Pleistocene Homo through the framework of ethnobiology, which examines on how Indigenous societies perceive, classify, and name biological organisms. This research reminds us that across human societies, taxonomies function to (1) identify and classify organisms based on consensus pattern recognition and (2) construct a stable nomenclature for effective storage, retrieval and communication of information. Naming Middle Pleistocene Homo as a "real" species cannot be verified with the current data; and separating regional groups into distinct evolutionary lineages creates taxa that are not defined by readily perceptible or universally salient differences. Based on ethnobiological studies of this kind of patterning, referring to these hominins above the level of the species according to their generic category with modifiers (e.g., "European Middle Pleistocene Homo") is consistent with observed human capabilities for cognitive differentiation, is both necessary and sufficient given the current data, and will allow for the most clear communication across ideologies going forward.

'Species' without species

Biological science uses multiple species concepts. Order can be brought to this diversity if we recognize two key features. First, any given species concept is likely to have a patchwork structure, generated by repeated application of the concept to new domains. We illustrate this by showing how two species concepts (biological and ecological) have been modified from their initial eukaryotic applications to apply to prokaryotes. Second, both within and between patches, distinct species concepts may interact and hybridize. We thus defend a semantic picture of the species concept as a collection of interacting patchwork structures. Thus, although not all uses of the term pick out the same kind of unit in nature, the diversity of uses reflects something more than mere polysemy. We suggest that the emphasis on the use of species to pick out natural units is itself problematic, because that is not the term's sole function. In particular, species concepts are used to manage inquiry into processes of speciation, even when these processes do not produce clearly delimited species.

Pliocene-Early Pleistocene Geological Events Structure Pacific Martens (Martes caurina)

The complex topography, climate, and geological history of Western North America have shaped contemporary patterns of biodiversity and species distributions in the region. Pacific martens (Martes caurina) are distributed along the northern Pacific Coast of North America with disjunct populations found throughout the Northwestern Forested Mountains and Marine West Coast Forest ecoregions of the West Coast. Martes in this region have been classified into subspecies; however, the subspecific designation has been extensively debated. In this study, we use genomic data to delineate conservation units of Pacific marten in the Sierra-Cascade-Coastal montane belt in the western United States. We analyzed the mitochondrial genome for 94 individuals to evaluate the spatial distribution and divergence times of major lineages. We further genotyped 401 individuals at 13 microsatellite loci to investigate major patterns of population structure. Both nuclear and mitochondrial DNA suggest substantial genetic substructure concordant with historical subspecies designations. Our results revealed that the region contains 2 distinct mitochondrial lineages: a Cascades/Sierra lineage that diverged from the Cascades/coastal lineage 2.23 (1.48-3.14 mya), consistent with orogeny of the Cascade Mountain chain. Interestingly, Pacific Martes share phylogeographic patterns similar with other sympatric taxa, suggesting that the complex geological history has shaped the biota of this region. The information is critical for conservation and management efforts, and further investigation of adaptive diversity is warranted following appropriate revision of conservation management designations.

Defining the speciation continuum

A primary roadblock to our understanding of speciation is that it usually occurs over a timeframe that is too long to study from start to finish. The idea of a speciation continuum provides something of a solution to this problem; rather than observing the entire process, we can simply reconstruct it from the multitude of speciation events that surround us. But what do we really mean when we talk about the speciation continuum, and can it really help us understand speciation? We explored these questions using a literature review and online survey of speciation researchers. Although most researchers were familiar with the concept and thought it was useful, our survey revealed extensive disagreement about what the speciation continuum actually tells us. This is due partly to the lack of a clear definition. Here, we provide an explicit definition that is compatible with the Biological Species Concept. That is, the speciation continuum is a continuum of reproductive isolation. After outlining the logic of the definition in light of alternatives, we explain why attempts to reconstruct the speciation process from present-day populations will ultimately fail. We then outline how we think the speciation continuum concept can continue to act as a foundation for understanding the continuum of reproductive isolation that surrounds us.

Quantifying the use of species concepts

Humans conceptualize the diversity of life by classifying individuals into types we call 'species'¹. The species we recognize influence political and financial decisions and guide our understanding of how units of diversity evolve and interact. Although the idea of species may seem intuitive, a debate about the best way to define them has raged even before Darwin². So much energy has been devoted to the so-called 'species problem' that no amount of discourse will ever likely solve it^2,3. Dozens of species concepts are currently recognized³, but we lack a concrete understanding of how much researchers actually disagree and the factors that cause them to think differently^1,2. To address this, we used a survey to quantify the species problem for the first time. The results indicate that the disagreement is extensive: two randomly chosen respondents will most likely disagree on the nature of species. The probability of disagreement is not predicted by researcher experience or broad study system, but tended to be lower among researchers with similar focus, training and who study the same organism. Should we see this diversity of perspectives as a problem? We argue that we should not.

The History of Botrytis Taxonomy, the Rise of Phylogenetics, and Implications for Species Recognition

Botrytis is one of the oldest, most well studied, and most economically important fungal taxa. Nonetheless, many species in this genus have remained obscured for nearly 300 years because of the difficulty in distinguishing these species by conventional mycological methods. Aided by the use of phylogenetic tools, the genus is currently undergoing a taxonomic revolution. The number of putative species in the genus has nearly doubled over the last 10 years and more species are likely to be discovered in the future. The implementation of phylogenetic species recognition concepts in Botrytis is providing for more resolution on the relatedness among species than ever before, and this has helped to overcome issues in historical species recognition using morphology, sexual crosses, and pathogenicity tests. Meanwhile, the use of genetic tools is helping to reveal surprising insight into this archetypal necrotroph's behavior, making these approaches increasingly important in species recognition and identification. As Botrytis taxonomy continues to evolve at a rapid pace, researchers should be encouraged to continue to employ the powerful tool of phylogenetics while considering how it fits into a larger framework of classical Botrytis species recognition. Starting points for discussion on how to move forward with Botrytis species recognition are included herein, with an emphasis on the implications and utility of new species descriptions.

The number of species of degus (genus Octodon) is currently underestimated: An appraisal of species limits and their phylogenetic relationships (Rodentia: Hystricomorpha: Octodontidae)

As currently understood, the genus Octodon contains five species degus, lunatus, bridgesii, pacificus, and ricardojeda. Previous phylogenetic studies suggest that genus specific diversity is underestimated. In order to evaluate the taxonomic diversity of Octodon, we implemented unilocus (cytochrome-b) and multilocus (cytochrome-b + 4 nuclear genes) species delimitation methods. Octodon degus was recovered as a sister of the other species of the genus. The unilocus bGMYC and mPTP methods, based on cytochrome-b sequences, delimits 11 and 7 candidate species respectively, and both methods fail to recognize O. pacificus from O. ricardojeda. Results of the multilocus analysis (BPP) vary as a function of the dataset used. When the five genes are used 11 species are delimited, while eight species are delimited when only the nuclear genes are used. Octodon bridgesii is shown as comprising at least two species (one on the Pacific coast and the typical form found on the Andean slopes), while O. ricardojeda may comprise two species (one on the Chilean side of the Andes and the other in Argentina). Likewise, both multilocus matrices recover O. pacificus as a distinct species. This shows that species diversity of Octodon is underestimated. Remarkably, many of the delimited species based on genetic data are morphologically differentiated in cranio-dental characteristics. However, a pair of species has not achieved morphological differentiation, being cryptic species. Finally, the incongruence between mitochondrial and nuclear phylogenies suggests that processes such as incomplete lineage sorting and/or introgression have been present during the radiation of the genus.

Barcoding a can of worms: testing cox1 performance as a DNA barcode of Nematoda

Accurate taxonomic identifications and species delimitations are a fundamental problem in biology. The complex taxonomy of Nematoda is primarily based on morphology, which is often dubious. DNA barcoding emerged as a handy tool to identify specimens and assess diversity, but its applications in Nematoda are incipient. We evaluated cytochrome c oxidase subunit I (cox1) efficiency as a DNA barcode for nematodes scrutinising 5241 sequences retrieved from BOLD and GenBank. The samples included genera with medical, agricultural, or ecological relevance: Anguillicola, Caenorhabditis, Heterodera, Meloidogyne, Onchocerca, Strongyloides, and Trichinella. We assessed cox1 performance through barcode gap and Probability of Correct Identification (PCI) analyses, and estimated species richness through Automatic Barcode Gap Discovery (ABGD). Each genus presented distinct gap ranges, mirroring the evolutionary diversity within Nematoda. Thus, to survey the diversity of the phylum, a careful definition of thresholds for lower taxonomic levels should be considered. PCIs were around 70% for both databases, highlighting operational biases and challenges in nematode taxonomy. ABGD inferred higher richness than the taxonomic labels informed by databases. The prevalence of specimen misidentifications and dubious species delimitations emphasise the value of integrative approaches to nematode taxonomy and systematics. Overall, cox1 is a relevant tool for integrative taxonomy of nematodes.

What Would a Tree Say About Its Size?

When developing theories, designing studies, and interpreting the results, researchers are influenced by their perception of tree size. For example, we may compare two trees of the same size belonging to different species, and attribute any differences to dissimilarities between the species. However, the meaning of “same size” depends on the measures of size used. Wood density influences certain measures, such as biomass, but does not influence e.g., trunk diameter. Therefore, the choice of the measure of size can reverse any conclusions. Hence, it is import to consider which measure of size should be used. I argue that the most common measure of size, i.e., trunk diameter, is often a bad choice when wood density varies, as diameter is then not directly related to processes important in evolution. When trees with equal diameters but differing wood densities are compared, the tree with denser wood is larger if the measure of size is related to construction cost or trunk strength, a proxy of leaf area. From this perspective, the comparison is then conducted between a biologically larger heavy-wooded tree and a smaller light-wooded tree, and the differences between the trees may be caused by size instead of wood density. Therefore, trunk biomass and strength may often be more suitable measures of size, as they reflect the construction cost and biomechanical potency linked to leaf area crown height, often too challenging to estimate more directly. To assess how commonly inadequate measures of tree size have been used, I reviewed 10 highly cited journal articles. None of these 10 articles discussed the impact of wood density on biological size, and instead based the analyses on diameters or basal areas. This led to conclusions that could change or even reverse in an analysis based on biomass or strength. Overall, I do not suggest avoiding the use of diameter, but I recommend considering result sensitivity to the measure of size, particularly in studies ones with variable wood densities.

Hydrography rather than lip morphology better explains the evolutionary relationship between Gymnogeophagus labiatus and G. lacustris in Southern Brazil (Cichlidae: Geophagini)

ABSTRACT Gymnogeophagus labiatus and G. lacustris have been long recognized as sister species exhibiting different ecological requirements. Gymnogeophagus labiatus occurs in rock bottom rivers in the hydrographic basins of Patos Lagoon (HBP) and Tramandaí River (HBT), while G. lacustris is exclusive from sand bottom coastal lagoons of the HBT. In this study, we used molecular markers, morphological measurements and data from nuptial male coloration to investigate the evolutionary relationship between these species in each hydrographic basin. We found, for all data sets, a closer relationship between G. labiatus and G. lacustris from the HBT than between G. labiatus populations from HBT and HBP. In particular, lip area had a large intraspecific plasticity, being uninformative to diagnose G. lacustris from G. labiatus. Molecular clock-based estimates suggest a recent divergence between species in the HBT (17,000 years ago), but not between G. labiatus from HBP and HBT (3.6 millions of years ago). Finally, we also found a divergent G. labiatus genetic lineage from the Camaquã River, in the HBP. These results show that the current taxonomy of G. labiatus and G. lacustris does not properly represent evolutionary lineages in these species.

The fungal sexual revolution continues: discovery of sexual development in members of the genus Aspergillus and its consequences

Asexuality was considered to be a common feature of a large part of fungi, including those of the genus Aspergillus. However, recent advances and the available genomic and genetic engineering technologies allowed to gather more and more indications of a hidden sexuality in fungi previously considered asexual. In parallel, the acquired knowledge of the most suitable conditions for crossings was shown to be crucial to effectively promote sexual reproduction in the laboratory. These discoveries not only have consequences on our knowledge of the biological processes ongoing in nature, questioning if truly asexual fungal species exist, but they also have important implications on other research areas. For instance, the presence of sexuality in certain fungi can have effects on their pathogenicity or on shaping the ecosystem that they normally colonize. For these reasons, further investigations of the sexual potential of Aspergillus species, such as the industrially important A. niger, will be carried on.

When all life counts in conservation

Conservation science involves the collection and analysis of data. These scientific practices emerge from values that shape who and what is counted. Currently, conservation data are filtered through a value system that considers native life the only appropriate subject of conservation concern. We examined how trends in species richness, distribution, and threats change when all wildlife count by adding so-called non-native and feral populations to the International Union for Conservation of Nature Red List and local species richness assessments. We focused on vertebrate populations with founding members taken into and out of Australia by humans (i.e., migrants). We identified 87 immigrant and 47 emigrant vertebrate species. Formal conservation accounts underestimated global ranges by an average of 30% for immigrants and 7% for emigrants; immigrations surpassed extinctions in Australia by 52 species; migrants were disproportionately threatened (33% of immigrants and 29% of emigrants were threatened or decreasing in their native ranges); and incorporating migrant populations into risk assessments reduced global threat statuses for 15 of 18 species. Australian policies defined most immigrants as pests (76%), and conservation was the most commonly stated motivation for targeting these species in killing programs (37% of immigrants). Inclusive biodiversity data open space for dialogue on the ethical and empirical assumptions underlying conservation science.

Towards reconciliation of the four world bird lists: hotspots of disagreement in taxonomy of raptors

There are currently four world bird lists referenced by different stakeholders including governments, academic journals, museums and citizen scientists. Consolidation of these lists is a conservation and research priority. In reconciling lists, care must be taken to ensure agreement in taxonomic concepts-the actual groups of individual organisms circumscribed by a given scientific epithet. Here, we compare species-level taxonomic concepts for raptors across the four lists, highlighting areas of disagreement. Of the 665 species-level raptor taxa observed at least once among the four lists, only 453 (68%) were consistent across all four lists. The Howard and Moore Checklist of the Birds of the World contains the fewest raptor species (528), whereas the International Ornithological Community World Bird List contains the most (580) and these two lists are in the most disagreement. Of the disagreements, 67% involved owls, and Indonesia was the country containing the most disagreed upon species (169). Finally, we calculated the amount of species-level agreement across lists for each avian order and found raptor orders spread throughout the rankings of agreement. Our results emphasize the need to reconcile the four world bird lists for all avian orders, highlight broad disagreements across lists and identify hotspots of disagreement for raptors, in particular.

Integrative species delimitation reveals cryptic diversity in the southern Appalachian Antrodiaetus unicolor (Araneae: Antrodiaetidae) species complex

Although species delimitation can be highly contentious, the development of reliable methods to accurately ascertain species boundaries is an imperative step in cataloguing and describing Earth's quickly disappearing biodiversity. Spider species delimitation remains largely based on morphological characters; however, many mygalomorph spider populations are morphologically indistinguishable from each other yet have considerable molecular divergence. The focus of our study, the Antrodiaetus unicolor species complex containing two sympatric species, exhibits this pattern of relative morphological stasis with considerable genetic divergence across its distribution. A past study using two molecular markers, COI and 28S, revealed that A. unicolor is paraphyletic with respect to A. microunicolor. To better investigate species boundaries in the complex, we implement the cohesion species concept and use multiple lines of evidence for testing genetic exchangeability and ecological interchangeability. Our integrative approach includes extensively sampling homologous loci across the genome using a RADseq approach (3RAD), assessing population structure across their geographic range using multiple genetic clustering analyses that include structure, principal components analysis and a recently developed unsupervised machine learning approach (Variational Autoencoder). We evaluate ecological similarity by using large-scale ecological data for niche-based distribution modelling. Based on our analyses, we conclude that this complex has at least one additional species as well as confirm species delimitations based on previous less comprehensive approaches. Our study demonstrates the efficacy of genomic-scale data for recognizing cryptic species, suggesting that species delimitation with one data type, whether one mitochondrial gene or morphology, may underestimate true species diversity in morphologically homogenous taxa with low vagility.

Species assignment in forensics and the challenge of hybrids

Forensic identification of species is in growing demand, particularly from law enforcement authorities in the areas of wildlife, fisheries and hunting as well as food authentication. Within the non-human forensic genetics expanding applications' field, the major current difficulties result from the lack of standards and genetic databases as well as the poor or absent taxonomic definition of several groups. Here we focus on a forensically important and overlooked problem in species identification: the exclusive use of uniparental markers, a common practice in current genetic barcoding methodologies, may lead to incorrect or impossible assignment whenever hybrids can occur (frequently, not only in domesticates, but also in the wild). For example, if one of these cases involves a mammal, and mitochondrial DNA alone is used (which in instances may be the only type of DNA sequence available in databases), the sample will be wrongfully assigned to the female parental species, completely missing the detection of a possible hybrid animal. The importance of this issue in the forensic contributions to food authentication, wildlife and conservation genetics is analyzed. We present a cautionary guidance on the forensic reporting of results avoiding this error.

Diversity within species: interpreting strains in microbiomes

Studying within-species variation has traditionally been limited to culturable bacterial isolates and low-resolution microbial community fingerprinting. Metagenomic sequencing and technical advances have enabled culture-free, high-resolution strain and subspecies analyses at high throughput and in complex environments. This holds great scientific promise but has also led to an overwhelming number of methods and terms to describe infraspecific variation. This Review aims to clarify these advances by focusing on the diversity within bacterial and archaeal species in the context of microbiomics. We cover foundational microevolutionary concepts relevant to population genetics and summarize how within-species variation can be studied and stratified directly within microbial communities with a focus on metagenomics. Finally, we describe how common applications of within-species variation can be achieved using metagenomic data. We aim to guide the selection of appropriate terms and analytical approaches to facilitate researchers in benefiting from the increasing availability of large, high-resolution microbiome genetic sequencing data.

Phylogenomics Reveals Clear Cases of Misclassification and Genus-Wide Phylogenetic Markers for Acinetobacter

The Gram-negative Acinetobacter genus has several species of clear medical relevance. Many fully sequenced genomes belonging to the genus have been published in recent years; however, there has not been a recent attempt to infer the evolutionary history of Acinetobacter with that vast amount of information. Here, through a phylogenomic approach, we established the most up-to-date view of the evolutionary relationships within this genus and highlighted several cases of poor classification, especially for the very closely related species within the Acinetobacter calcoaceticus-Acinetobacter baumannii complex (Acb complex). Furthermore, we determined appropriate phylogenetic markers for this genus and showed that concatenation of the top 13 gives a very decent reflection of the evolutionary relationships for the genus Acinetobacter. The intersection between our top markers and previously defined universal markers is very small. In general, our study shows that, although there seems to be hardly any universal markers, bespoke phylogenomic approaches can be used to infer the phylogeny of different bacterial genera. We expect that ad hoc phylogenomic approaches will be the standard in the years to come and will provide enough information to resolve intricate evolutionary relationships like those observed in the Acb complex.

Strengthening the Interaction of the Virology Community with the International Committee on Taxonomy of Viruses (ICTV) by Linking Virus Names and Their Abbreviations to Virus Species

The International Committee on Taxonomy of Viruses (ICTV) is tasked with classifying viruses into taxa (phyla to species) and devising taxon names. Virus names and virus name abbreviations are currently not within the ICTV's official remit and are not regulated by an official entity. Many scientists, medical/veterinary professionals, and regulatory agencies do not address evolutionary questions nor are they concerned with the hierarchical organization of the viral world, and therefore, have limited use for ICTV-devised taxa. Instead, these professionals look to the ICTV as an expert point source that provides the most current taxonomic affiliations of viruses of interests to facilitate document writing. These needs are currently unmet as an ICTV-supported, easily searchable database that includes all published virus names and abbreviations linked to their taxa is not available. In addition, in stark contrast to other biological taxonomic frameworks, virus taxonomy currently permits individual species to have several members. Consequently, confusion emerges among those who are not aware of the difference between taxa and viruses, and because certain well-known viruses cannot be located in ICTV publications or be linked to their species. In addition, the number of duplicate names and abbreviations has increased dramatically in the literature. To solve this conundrum, the ICTV could mandate listing all viruses of established species and all reported unclassified viruses in forthcoming online ICTV Reports and create a searchable webpage using this information. The International Union of Microbiology Societies could also consider changing the mandate of the ICTV to include the nomenclature of all viruses in addition to taxon considerations. With such a mandate expansion, official virus names and virus name abbreviations could be catalogued and virus nomenclature could be standardized. As a result, the ICTV would become an even more useful resource for all stakeholders in virology.

Redox traits characterize the organization of global microbial communities

Biological communities are conventionally described as assemblages of species, whose ecological roles are known or predictable from their observable morphology. In microbial ecology, such a taxonomic approach is hindered by limited capacity to discriminate among different microbes, which bear highly dynamic genomes and establish complex associations. Approaches based on culture-independent functional genes profiling might overcome these problems, but a set of usable established genes in a general situation is still lacking. We show that genes related to reduction-oxidation (redox) processes separate microbial communities into their corresponding biomes. This redox-based characterization is linked to the microbial energetics of ecosystems and to most biogeochemical cycles and might be useful for assessing the impact of environmental degradation on the ecosystem services, underpinned by microorganisms.

The structure of biological communities is conventionally described as profiles of taxonomic units, whose ecological functions are assumed to be known or, at least, predictable. In environmental microbiology, however, the functions of a majority of microorganisms are unknown and expected to be highly dynamic and collectively redundant, obscuring the link between taxonomic structure and ecosystem functioning. Although genetic trait-based approaches at the community level might overcome this problem, no obvious choice of gene categories can be identified as appropriate descriptive units in a general ecological context. We used 247 microbial metagenomes from 18 biomes to determine which set of genes better characterizes the differences among biomes on the global scale. We show that profiles of oxidoreductase genes support the highest biome differentiation compared with profiles of other categories of enzymes, general protein-coding genes, transporter genes, and taxonomic gene markers. Based on oxidoreductases’ description of microbial communities, the role of energetics in differentiation and particular ecosystem function of different biomes become readily apparent. We also show that taxonomic diversity is decoupled from functional diversity, e.g., grasslands and rhizospheres were the most diverse biomes in oxidoreductases but not in taxonomy. Considering that microbes underpin biogeochemical processes and nutrient recycling through oxidoreductases, this functional diversity should be relevant for a better understanding of the stability and conservation of biomes. Consequently, this approach might help to quantify the impact of environmental stressors on microbial ecosystems in the context of the global-scale biome crisis that our planet currently faces.

Game of clones: Is Wolbachia inducing speciation in a weevil with a mixed reproductive mode?

Parthenogenesis is widely distributed in Metazoa but it is especially frequent in weevils (Coleoptera, Curculionidae) with one fifth of all known cases. Previous studies have shown that in the tribe Naupactini parthenogenetic reproduction most likely originated with an infection of the endoparasitic bacterium Wolbachia pipientis. In particular, Pantomorus postfasciatus possess a mixed reproductive mode: some populations have males while in others they are absent, and females produce clones by thelytoky. To better understand this scenario, we studied the population structure and infection status in 64 individuals of P. postfasciatus from Argentina and Brazil. We sequenced two mitochondrial (COI and COII) and one nuclear (ITS-1) fragments and obtained two very divergent haplogroups, one corresponding to the sexual populations uninfected with Wolbachia, and another conforming a monophyletic parthenogenetic (or presumptively parthenogenetic) and infected clade. Each of these haplogroups was identified as an independently evolutionary unit by all species delimitation analyses accomplished: multilocus *BEAST and BP&P, and single locus GMYC and K/θ rule. Additionally, present evidence suggests that Wolbachia infection occurred at least twice in all-female populations of P. postfasciatus with two different bacterial strains. Speciation mediated by Wolbachia is a recently described phenomenon and the case of P. postfasciatus is the first known case in a diplo-diploid insect. A model that describes how thelytoky-inducing phenotypes of Wolbachia could generate new lineages is discussed.

Viral species, viral genomes and HIV vaccine design: is the rational design of biological complexity a utopia?

A common logical confusion is prevalent in the whole of biology, namely that biological species are viewed both as an abstract category in an hierarchical classification and as a concrete kind of organism. This is partly due to the fact that the vast majority of living organisms do not have common names that differ from the Latin name of the species to which the organism belongs. However, it is somewhat astonishing that the same confusion exists in virology since every virus has a common name, different from the species name to which the virus belongs, which could be used to refer to the infectious viral entity as a concrete material object. The original 1991 ICTV definition of virus species stated that a virus species is a polythetic class of viruses and thus that a species is a class, namely a conceptual construction of the mind and not a physical, real object located in space and time. In 2013, the ICTV redefined a virus species no longer as a class but as a material object consisting of a monophyletic group of viruses that were all physically part of the species. This new definition is reminiscent of an earlier school of thought known as bionominalism which considered species to be concrete individuals rather than classes. Both bionominalism and the new ICTV definition are based on the logical fallacy of reification which treats abstractions such as classes as if they were concrete physical entities. The implications of this new ontology of virus species for virus taxonomy and for the possibility of incorporating nucleotide metagenomic sequences in the current ICTV classification is discussed.

A clash of ideas - the varying uses of the 'species' term in virology and their utility for classifying viruses in metagenomic datasets

Species definitions of viruses are frequently descriptive, with assignments often being based on their disease manifestations, host range, geographical distribution and transmission routes. This method of categorizing viruses has recently been challenged by technology advances, such as high-throughput sequencing. These have dramatically increased knowledge of viral diversity in the wider environment that dwarfs the current catalogue of viruses classified by the International Committee for the Taxonomy of Viruses (ICTV). However, because such viruses are known only from their sequences without phenotypic information, it is unclear how they might be classified consistently with much of the existing taxonomy framework. This difficulty exposes deeper incompatibilities in how species are conceptualized. The original species assignments based on disease or other biological attributes were primarily descriptive, similar to principles used elsewhere in biology for species taxonomies. In contrast, purely sequence-based classifications rely on genetic metrics such as divergence thresholds that include or exclude viruses in individual species categories. These different approaches bring different preconceptions about the nature of a virus species, the former being more easily conceptualized as a category with a part/whole relationship of individuals and species, while species defined by divergence thresholds or other genetic metrics are essentially logically defined groups with specific inclusion and exclusion criteria. While descriptive species definitions match our intuitive division of viruses into natural kinds, rules-based genetic classifications are required for viruses known from sequence alone, whose incorporation into the ICTV taxonomy is essential if it is to represent the true diversity of viruses in nature.

The Bunocephalus coracoideus Species Complex (Siluriformes, Aspredinidae). Signs of a Speciation Process through Chromosomal, Genetic and Ecological Diversity

Bunocephalus is the most species-rich Aspredinidae genus, corresponding to a monophyletic clade with 13 valid species. However, many species have their classification put in question. Here, we analyzed individuals from four Amazonian populations of Bunocephalus coracoideus by cytogenetic and molecular procedures. The geographic distribution, genetic distances and karyotype data indicate that each population represents an Evolutionary Significant Unit (ESU). Cytogenetic markers showed distinct 2n and karyotype formulas, as well as different numbers and locations of the rDNA sites among ESUs. One of such populations (ESU-D) highlighted an extensive polymorphic condition, with several cytotypes probably due to chromosomal rearrangements and meiotic non-disjunctions. This resulted in several aneuploid karyotypes, which was also supported by the mapping of telomeric sequences. Phylograms based on Maximum Likelihood (ML) and Neighbor Joining (NJ) analyses grouped each ESU on particular highly supported clades, with the estimation of evolutionary divergence indicating values being higher than 3.8–12.3% among them. Our study reveals a huge degree of chromosomal and genetic diversity in B. coracoideus and highly points to the existence of four ESUs in allopatric and sympatric speciation processes. In fact, the high divergences found among the ESUs allowed us to delimitate lineages with taxonomic uncertainties in this nominal species.

What do Biologists Make of the Species Problem?

The concept of species is one of the core concepts in biology and one of the cornerstones of evolutionary biology, yet it is rife with conceptual problems. Philosophers of biology have been discussing the concept of species for decades, and in doing so they sometimes appeal to the views of biologists. However, their statements as to what biologists think are seldom supported by empirical data. In order to investigate what biologists actually think about the key issues related to the problem of species, we have conducted a survey on the sample of 193 biologists from the population of biologists from over 150 biology departments at universities in the US and the EU. This article presents and discusses the results of the survey. Some results confirm and others falsify the reiterated statements of philosophers of biology as to what biologists think, but all results we obtained should be informative and relevant for future discussions of the problem of species.

Intraspecific chemical communication in microalgae

Contents 516 I. 516 II. 518 III. 518 IV. 521 V. 523 VI. 523 VII. 526 526 References 526 SUMMARY: The relevance of infochemicals in the relationships between organisms is emerging as a fundamental aspect of aquatic ecology. Exchanges of chemical cues are likely to occur not only between organisms of different species, but also between conspecific individuals. Especially intriguing is the investigation of chemical communication in microalgae, because of the relevance of these organisms for global primary production and their key role in trophic webs. Intraspecific communication between algae has been investigated mostly in relation to sexuality and mating. The literature also contains information on other types of intraspecific chemical communication that have not always been explicitly tagged as ways to communicate to conspecifics. However, the proposed role of certain compounds as intraspecific infochemicals appears questionable. In this article, we make use of this plethora of information to describe the various instances of intraspecific chemical communication between conspecific microalgae and to identify the common traits and ecological significance of intraspecific communication. We also discuss the evolutionary implications of intraspecific chemical communication and the mechanisms by which it can be inherited. A special focus is the genetic diversity among conspecific algae, including the possibility that genetic diversity is an absolute requirement for intraspecific chemical communication.

One species or four? Yes!...and, no. Or, arbitrary assignment of lineages to species obscures the diversification processes of Neotropical fishes

Species are fundamental units in many biological disciplines, but there is continuing disagreement as to what species are, how to define them, and even whether the concept is useful. While some of this debate can be attributed to inadequate data and insufficient statistical frameworks in alpha taxonomy, an equal part results from the ambiguity over what species are expected to represent by the many who use them. Here, mtDNA data, microsatellite data, and sequence data from 17 nuclear loci are used in an integrated and quantitative manner to resolve the presence of evolutionary lineages, their contemporary and historical structure, and their correspondence to species, in a species complex of Amazonian peacock "bass" cichlids (Cichla pinima sensu lato). Results suggest that the historical narrative for these populations is more complex than can be portrayed by recognizing them as one, two, or four species: their history and contemporary dynamics cannot be unambiguously rendered as discrete units (taxa) at any level without both choosing the supremacy of one delimitation criterion and obscuring the very information that provides insight into the diversification process. This calls into question the utility of species as a rank, term, or concept, and suggests that while biologists may have a reasonable grasp of the structure of evolution, our methods of conveying these insights need updating. The lack of correspondence between evolutionary phenomena and discrete species should serve as a null hypothesis, and researchers should focus on quantifying the diversity in nature at whatever hierarchical level it occurs.

Managing marine mollusc diseases in the context of regional and international commerce: policy issues and emerging concerns

Marine mollusc production contributes to food and economic security worldwide and provides valuable ecological services, yet diseases threaten these industries and wild populations. Although the infrastructure for mollusc aquaculture health management is well characterized, its foundations are not without flaws. Use of notifiable pathogen lists can leave blind spots with regard to detection of unlisted and emerging pathogens. Increased reliance on molecular tools has come without similar attention to diagnostic validation, raising questions about assay performance, and has been accompanied by a reduced emphasis on microscopic diagnostic expertise that could weaken pathogen detection capabilities. Persistent questions concerning pathogen biology and ecology promote regulatory paralysis that impedes trade and which could weaken biosecurity by driving commerce to surreptitious channels. Solutions that might be pursued to improve shellfish aquaculture health management include the establishment of more broad-based surveillance programmes, wider training and use of general methods like histopathology to ensure alertness to emerging diseases, an increased focus on assay assessment and validation as fundamental to assay development, investment in basic research, and application of risk analyses to improve regulation. A continual sharpening of diagnostic tools and approaches and deepening of scientific knowledge is necessary to manage diseases and promote sustainable molluscan shellfish industries.

Conservation of genetic uniqueness of populations may increase extinction likelihood of endangered species: the case of Australian mammals

BACKGROUND

As increasingly fragmented and isolated populations of threatened species become subjected to climate change, invasive species and other stressors, there is an urgent need to consider adaptive potential when making conservation decisions rather than focussing on past processes. In many cases, populations identified as unique and currently managed separately suffer increased risk of extinction through demographic and genetic processes. Other populations currently not at risk are likely to be on a trajectory where declines in population size and fitness soon appear inevitable.

RESULTS

Using datasets from natural Australian mammal populations, we show that drift processes are likely to be driving uniqueness in populations of many threatened species as a result of small population size and fragmentation. Conserving and managing such remnant populations separately will therefore often decrease their adaptive potential and increase species extinction risk.

CONCLUSIONS

These results highlight the need for a paradigm shift in conservation biology practise; strategies need to focus on the preservation of genetic diversity at the species level, rather than population, subspecies or evolutionary significant unit. The introduction of new genetic variants into populations through in situ translocation needs to be considered more broadly in conservation programs as a way of decreasing extinction risk by increasing neutral genetic diversity which may increase the adaptive potential of populations if adaptive variation is also increased.

Horizontal gene transfer, dispersal and haloarchaeal speciation

The Halobacteria are a well-studied archaeal class and numerous investigations are showing how their diversity is distributed amongst genomes and geographic locations. Evidence indicates that recombination between species continuously facilitates the arrival of new genes, and within species, it is frequent enough to spread acquired genes amongst all individuals in the population. To create permanent independent diversity and generate new species, barriers to recombination are probably required. The data support an interpretation that rates of evolution (e.g., horizontal gene transfer and mutation) are faster at creating geographically localized variation than dispersal and invasion are at homogenizing genetic differences between locations. Therefore, we suggest that recurrent episodes of dispersal followed by variable periods of endemism break the homogenizing forces of intrapopulation recombination and that this process might be the principal stimulus leading to divergence and speciation in Halobacteria.