COMADRE: a global data base of animal demography

The open‐data scientific philosophy is being widely adopted and proving to promote considerable progress in ecology and evolution. Open‐data global data bases now exist on animal migration, species distribution, conservation status, etc. However, a gap exists for data on population dynamics spanning the rich diversity of the animal kingdom world‐wide. This information is fundamental to our understanding of the conditions that have shaped variation in animal life histories and their relationships with the environment, as well as the determinants of invasion and extinction.

Matrix population models (MPMs) are among the most widely used demographic tools by animal ecologists. MPMs project population dynamics based on the reproduction, survival and development of individuals in a population over their life cycle. The outputs from MPMs have direct biological interpretations, facilitating comparisons among animal species as different as Caenorhabditis elegans, Loxodonta africana and Homo sapiens.

Thousands of animal demographic records exist in the form of MPMs, but they are dispersed throughout the literature, rendering comparative analyses difficult. Here, we introduce the COMADRE Animal Matrix Database, an open‐data online repository, which in its version 1.0.0 contains data on 345 species world‐wide, from 402 studies with a total of 1625 population projection matrices. COMADRE also contains ancillary information (e.g. ecoregion, taxonomy, biogeography, etc.) that facilitates interpretation of the numerous demographic metrics that can be derived from its MPMs. We provide R code to some of these examples.

Synthesis: We introduce the COMADRE Animal Matrix Database, a resource for animal demography. Its open‐data nature, together with its ancillary information, will facilitate comparative analysis, as will the growing availability of databases focusing on other aspects of the rich animal diversity, and tools to query and combine them. Through future frequent updates of COMADRE, and its integration with other online resources, we encourage animal ecologists to tackle global ecological and evolutionary questions with unprecedented sample size.

The interplay of cognition and cooperation

Cooperation often involves behaviours that reduce immediate payoffs for actors. Delayed benefits have often been argued to pose problems for the evolution of cooperation because learning such contingencies may be difficult as partners may cheat in return. Therefore, the ability to achieve stable cooperation has often been linked to a species' cognitive abilities, which is in turn linked to the evolution of increasingly complex central nervous systems. However, in their famous 1981 paper, Axelrod and Hamilton stated that in principle even bacteria could play a tit-for-tat strategy in an iterated Prisoner's Dilemma. While to our knowledge this has not been documented, interspecific mutualisms are present in bacteria, plants and fungi. Moreover, many species which have evolved large brains in complex social environments lack convincing evidence in favour of reciprocity. What conditions must be fulfilled so that organisms with little to no brainpower, including plants and single-celled organisms, can, on average, gain benefits from interactions with partner species? On the other hand, what conditions favour the evolution of large brains and flexible behaviour, which includes the use of misinformation and so on? These questions are critical, as they begin to address why cognitive complexity would emerge when 'simple' cooperation is clearly sufficient in some cases. This paper spans the literature from bacteria to humans in our search for the key variables that link cooperation and deception to cognition.

The evolution of general intelligence

The presence of general intelligence poses a major evolutionary puzzle, which has led to increased interest in its presence in nonhuman animals. The aim of this review is to critically evaluate this question and to explore the implications for current theories about the evolution of cognition. We first review domain-general and domain-specific accounts of human cognition in order to situate attempts to identify general intelligence in nonhuman animals. Recent studies are consistent with the presence of general intelligence in mammals (rodents and primates). However, the interpretation of a psychometric g factor as general intelligence needs to be validated, in particular in primates, and we propose a range of such tests. We then evaluate the implications of general intelligence in nonhuman animals for current theories about its evolution and find support for the cultural intelligence approach, which stresses the critical importance of social inputs during the ontogenetic construction of survival-relevant skills. The presence of general intelligence in nonhumans implies that modular abilities can arise in two ways, primarily through automatic development with fixed content and secondarily through learning and automatization with more variable content. The currently best-supported model, for humans and nonhuman vertebrates alike, thus construes the mind as a mix of skills based on primary and secondary modules. The relative importance of these two components is expected to vary widely among species, and we formulate tests to quantify their strength.

A Hypothesis of the Co-evolution of Cooperation and Responses to Inequity

Recent evidence demonstrates that humans are not the only species to respond negatively to inequitable outcomes which are to their disadvantage. Several species respond negatively if they subsequently receive a less good reward than a social partner for completing the same task. While these studies suggest that the negative response to inequity is not a uniquely human behavior, they do not provide a functional explanation for the emergence of these responses due to similar characteristics among these species. However, emerging data support the hypothesis that an aversion to inequity is a mechanism to promote successful long-term cooperative relationships amongst non-kin. In this paper, I discuss several converging lines of evidence which illustrate the need to further evaluate this relationship. First, cooperation can survive modest inequity; in explicitly cooperative interactions, individuals are willing to continue to cooperate despite inequitable outcomes as long as the partner's overall behavior is equitable. Second, the context of inequity affects reactions to it in ways which support the idea that joint efforts lead to an expectation of joint payoffs. Finally, comparative studies indicate a link between the degree and extent of cooperation between unrelated individuals in a species and that species’ response to inequitable outcomes. This latter line of evidence indicates that this behavior evolved in conjunction with cooperation and may represent an adaptation to increase the payoffs associated with cooperative interactions. Together these data inform a testable working hypothesis for understanding decision-making in the context of inequity and provide a new, comparative framework for evaluating decision-making behavior.

Four principles of bio-musicology

As a species-typical trait of Homo sapiens, musicality represents a cognitively complex and biologically grounded capacity worthy of intensive empirical investigation. Four principles are suggested here as prerequisites for a successful future discipline of bio-musicology. These involve adopting: (i) a multicomponent approach which recognizes that musicality is built upon a suite of interconnected capacities, of which none is primary; (ii) a pluralistic Tinbergian perspective that addresses and places equal weight on questions of mechanism, ontogeny, phylogeny and function; (iii) a comparative approach, which seeks and investigates animal homologues or analogues of specific components of musicality, wherever they can be found; and (iv) an ecologically motivated perspective, which recognizes the need to study widespread musical behaviours across a range of human cultures (and not focus solely on Western art music or skilled musicians). Given their pervasiveness, dance and music created for dancing should be considered central subcomponents of music, as should folk tunes, work songs, lullabies and children's songs. Although the precise breakdown of capacities required by the multicomponent approach remains open to debate, and different breakdowns may be appropriate to different purposes, I highlight four core components of human musicality--song, drumming, social synchronization and dance--as widespread and pervasive human abilities spanning across cultures, ages and levels of expertise. Each of these has interesting parallels in the animal kingdom (often analogies but in some cases apparent homologies also). Finally, I suggest that the search for universal capacities underlying human musicality, neglected for many years, should be renewed. The broad framework presented here illustrates the potential for a future discipline of bio-musicology as a rich field for interdisciplinary and comparative research.

Language evolution: syntax before phonology?

Phonology and syntax represent two layers of sound combination central to language's expressive power. Comparative animal studies represent one approach to understand the origins of these combinatorial layers. Traditionally, phonology, where meaningless sounds form words, has been considered a simpler combination than syntax, and thus should be more common in animals. A linguistically informed review of animal call sequences demonstrates that phonology in animal vocal systems is rare, whereas syntax is more widespread. In the light of this and the absence of phonology in some languages, we hypothesize that syntax, present in all languages, evolved before phonology.

Multimodal communication and language origins: integrating gestures and vocalizations

The presence of divergent and independent research traditions in the gestural and vocal domains of primate communication has resulted in major discrepancies in the definition and operationalization of cognitive concepts. However, in recent years, accumulating evidence from behavioural and neurobiological research has shown that both human and non-human primate communication is inherently multimodal. It is therefore timely to integrate the study of gestural and vocal communication. Herein, we review evidence demonstrating that there is no clear difference between primate gestures and vocalizations in the extent to which they show evidence for the presence of key language properties: intentionality, reference, iconicity and turn-taking. We also find high overlap in the neurobiological mechanisms producing primate gestures and vocalizations, as well as in ontogenetic flexibility. These findings confirm that human language had multimodal origins. Nonetheless, we note that in great apes, gestures seem to fulfil a carrying (i.e. predominantly informative) role in close-range communication, whereas the opposite holds for face-to-face interactions of humans. This suggests an evolutionary shift in the carrying role from the gestural to the vocal stream, and we explore this transition in the carrying modality. Finally, we suggest that future studies should focus on the links between complex communication, sociality and cooperative tendency to strengthen the study of language origins.

ECOLOGICAL AND HISTORICAL ASSOCIATIONS OF GENE FLOW IN DARTERS (TELEOSTEI: PERCIDAE)

Life history should relate to gene flow (Nm) through its influence on dispersal and effective population size. Comparative studies designed to elucidate this relationship must contend with historical events that can yield misleading estimates of gene flow and statistical problems associated with inclusion of life-history traits correlated with phylogeny. We studied the relationships of life-history characters and gene flow in 15 species of darters, a monophyletic group of stream fishes. Populations of coexisting species were sampled in three geographic regions with different Pleistocene glaciation histories. Gene flow was estimated indirectly from allozymes using two methods, 8 and private alleles. Isolation-by-distance was also tested using regression of pairwise estimates of gene flow (M̂) on distance. Theta and private-alleles methods produced congruent estimates of Nm, except in a study region hypothesized to have been historically fragmented and then united following Pleistocene glaciation. A relatively weak association between life-history traits and Nm (based on θ) was observed when species from the historically fragmented region were included in stepwise regression analysis, because Nm was low despite life-history differences among taxa in this region. Excluding observations from this region produced stronger associations between clutch size and Nm (r² = 0.57), and between female size, egg size, and Nm (r² = 0.95). Additional analyses that corrected for female body size and phylogenetic nonindependence agreed that darters with high fecundity and small eggs exhibited high gene flow, whereas darters with small clutches and large eggs had low gene flow. The latter combination of life-history traits primarily is exhibited in species from headwater habitats where parental investment presumably confers survivorship on offspring. Reduced gene flow and genetic divergence among demes appear to be evolutionary consequences of this strategy.

Simultaneously estimating evolutionary history and repeated traits phylogenetic signal: applications to viral and host phenotypic evolution

Phylogenetic signal quantifies the degree to which resemblance in continuously-valued traits reflects phylogenetic relatedness. Measures of phylogenetic signal are widely used in ecological and evolutionary research, and are recently gaining traction in viral evolutionary studies. Standard estimators of phylogenetic signal frequently condition on data summary statistics of the repeated trait observations and fixed phylogenetics trees, resulting in information loss and potential bias. To incorporate the observation process and phylogenetic uncertainty in a model-based approach, we develop a novel Bayesian inference method to simultaneously estimate the evolutionary history and phylogenetic signal from molecular sequence data and repeated multivariate traits. Our approach builds upon a phylogenetic diffusion framework that model continuous trait evolution as a Brownian motion process and incorporates Pagel's λ transformation parameter to estimate dependence among traits. We provide a computationally efficient inference implementation in the BEAST software package. We evaluate the synthetic performance of the Bayesian estimator of phylogenetic signal against standard estimators, and demonstrate the use of our coherent framework to address several virus-host evolutionary questions, including virulence heritability for HIV, antigenic evolution in influenza and HIV, and Drosophila sensitivity to sigma virus infection. Finally, we discuss model extensions that will make useful contributions to our flexible framework for simultaneously studying sequence and trait evolution.

Functionally homologous representation of vocalizations in the auditory cortex of humans and macaques

How the evolution of speech has transformed the human auditory cortex compared to other primates remains largely unknown. While primary auditory cortex is organized largely similarly in humans and macaques,¹ the picture is much less clear at higher levels of the anterior auditory pathway,² particularly regarding the processing of conspecific vocalizations (CVs). A "voice region" similar to the human voice-selective areas^3,4 has been identified in the macaque right anterior temporal lobe with functional MRI;⁵ however, its anatomical localization, seemingly inconsistent with that of the human temporal voice areas (TVAs), has suggested a "repositioning of the voice area" in recent human evolution.⁶ Here we report a functional homology in the cerebral processing of vocalizations by macaques and humans, using comparative fMRI and a condition-rich auditory stimulation paradigm. We find that the anterior temporal lobe of both species possesses cortical voice areas that are bilateral and not only prefer conspecific vocalizations but also implement a representational geometry categorizing them apart from all other sounds in a species-specific but homologous manner. These results reveal a more similar functional organization of higher-level auditory cortex in macaques and humans than currently known.

Compared to what: What can we say about nonapeptide function and social behavior without a frame of reference?

Our understanding of behavior and mechanism is undermined by the absence of a frame of reference because relationships between individuals and species are without context. We highlight a need to be more comparative, using nonapeptide (vasopressin and oxytocin) modulation of social behavior as an example. We reconsider the use of model organisms and the term 'social' in this context, contrasting two popular models for nonapeptide regulation of social behavior. We then propose that a frame of reference should be established by studying mechanisms of behavior across taxa along the same continua. If we are to ever establish a unifying theory of behavior, we must transcend individual examples and determine the relative relationships of behavior and mechanism among and between species.

Genomic and Transcriptomic Analysis Identified Novel Putative Cassava lncRNAs Involved in Cold and Drought Stress

Long non-coding RNAs (lncRNAs) play important roles in the regulation of complex cellular processes, including transcriptional and post-transcriptional regulation of gene expression relevant for development and stress response, among others. Compared to other important crops, there is limited knowledge of cassava lncRNAs and their roles in abiotic stress adaptation. In this study, we performed a genome-wide study of ncRNAs in cassava, integrating genomics- and transcriptomics-based approaches. In total, 56,840 putative ncRNAs were identified, and approximately half the number were verified using expression data or previously known ncRNAs. Among these were 2229 potential novel lncRNA transcripts with unmatched sequences, 250 of which were differentially expressed in cold or drought conditions, relative to controls. We showed that lncRNAs might be involved in post-transcriptional regulation of stress-induced transcription factors (TFs) such as zinc-finger, WRKY, and nuclear factor Y gene families. These findings deepened our knowledge of cassava lncRNAs and shed light on their stress-responsive roles.

A vocalization-processing network in marmosets

Vocalizations play an important role in the daily life of primates and likely form the basis of human language. Functional imaging studies have demonstrated that listening to voices activates a fronto-temporal voice perception network in human participants. Here, we acquired whole-brain ultrahigh-field (9.4 T) fMRI in awake marmosets (Callithrix jacchus) and demonstrate that these small, highly vocal New World primates possess a similar fronto-temporal network, including subcortical regions, that is activated by the presentation of conspecific vocalizations. The findings suggest that the human voice perception network has evolved from an ancestral vocalization-processing network that predates the separation of New and Old World primates.

IGF1R levels in the brain negatively correlate with longevity in 16 rodent species

The insulin/insulin-like growth factor signaling (IIS) pathway is a major conserved regulator of aging. Nematode, fruit fly and mouse mutants with reduced IIS signaling exhibit extended lifespan. These mutants are often dwarfs leading to the idea that small body mass correlates with longevity within species. However, when different species are compared, larger animals are typically longer-lived. Hence, the role of IIS in the evolution of life history traits remains unresolved. Here we used comparative approach to test whether IGF1R signaling changes in response to selection on lifespan or body mass and whether specific tissues are involved. The IGF1R levels in the heart, lungs, kidneys, and brains of sixteen rodent species with highly diverse lifespans and body masses were measured via immunoblot after epitope conservation analysis. We report that IGF1R levels display strong negative correlation with maximum lifespan only in brain tissue and no significant correlations with body mass for any organ. The brain-IGF1R and lifespan correlation holds when phylogenetic non-independence of data-points is taken into account. These results suggest that modulation of IGF1R signaling in nervous tissue, but not in the peripheral tissues, is an important factor in the evolution of longevity in mammals.

Helping in humans and other animals: a fruitful interdisciplinary dialogue

Humans are arguably unique in the extent and scale of cooperation with unrelated individuals. While pairwise interactions among non-relatives occur in some non-human species, there is scant evidence of the large-scale, often unconditional prosociality that characterizes human social behaviour. Consequently, one may ask whether research on cooperation in humans can offer general insights to researchers working on similar questions in non-human species, and whether research on humans should be published in biology journals. We contend that the answer to both of these questions is yes. Most importantly, social behaviour in humans and other species operates under the same evolutionary framework. Moreover, we highlight how an open dialogue between different fields can inspire studies on humans and non-human species, leading to novel approaches and insights. Biology journals should encourage these discussions rather than drawing artificial boundaries between disciplines. Shared current and future challenges are to study helping in ecologically relevant contexts in order to correctly interpret how payoff matrices translate into inclusive fitness, and to integrate mechanisms into the hitherto largely functional theory. We can and should study human cooperation within a comparative framework in order to gain a full understanding of the evolution of helping.

"I don't need my patients' opinion to withdraw treatment": patient preferences at the end-of-life and physician attitudes towards advance directives in England and France

This paper presents the results of a qualitative interview study exploring English and French physicians' moral perspectives and attitudes towards end-of-life decisions when patients lack capacity to make decisions for themselves. The paper aims to examine the importance physicians from different contexts accord to patient preferences and to explore the (potential) role of advance directives (ADs) in each context. The interviews focus on (1) problems that emerge when deciding to withdraw/-hold life-sustaining treatment from both conscious and unconscious patients; (2) decision-making procedures and the participation of proxies/relatives; (3) previous experience with ADs and views on their usefulness; and (4) perspectives on ways in which the decision-making processes in question might be improved. The analysis reveals differences in the way patient preferences are taken into consideration and shows how these differences influence the reasons physicians in each country invoke to justify their reluctance to adhering to ADs. Identifying cultural differences that complicate efforts to develop the practical implementation of ADs can help to inform national policies governing ADs and to better adapt them to practice.

Climate predicts which sex acts as helpers among cooperatively breeding bird species

Among avian cooperative breeders, help in raising offspring is usually provided by males or by both sexes. Sex bias in helping should evolve in response to sex-specific ecological constraints on independent reproduction, with mate shortage for males and breeding vacancy shortage for each sex. Given that male-biased adult sex ratios are prevalent among birds, we predict that male-only helping mainly occurs in temperate species where fast population turnovers deriving from low adult annual survival allow all adult females to hold breeding vacancies, whereas some males overflow as helpers, and both-sex helping in tropical species where saturated habitats prevent not only males, but also females from breeding themselves. As expected, we found that across species, adult survival increased towards tropical zones and warmer climates, and higher adult survival tended to be associated with both-sex helping. Furthermore, sex bias in helping was predicted by latitude and ambient temperature. Our findings of demographic response of species to climate as a potential determinant of bias in helper sex uncover how ecological constraints operate to limit independent reproduction in sex-specific ways.

Climate change and ocean deoxygenation within intensified surface-driven upwelling circulations

Ocean deoxygenation often takes place in proximity to zones of intense upwelling. Associated concerns about amplified ocean deoxygenation arise from an arguable likelihood that coastal upwelling systems in the world's oceans may further intensify as anthropogenic climate change proceeds. Comparative examples discussed include the uniquely intense seasonal Somali Current upwelling, the massive upwelling that occurs quasi-continuously off Namibia and the recently appearing and now annually recurring 'dead zone' off the US State of Oregon. The evident 'transience' in causal dynamics off Oregon is somewhat mirrored in an interannual-scale intermittence in eruptions of anaerobically formed noxious gases off Namibia. A mechanistic scheme draws the three examples towards a common context in which, in addition to the obvious but politically problematic remedy of actually reducing 'greenhouse' gas emissions, the potentially manageable abundance of strongly swimming, finely gill raker-meshed small pelagic fish emerges as a plausible regulating factor.This article is part of the themed issue 'Ocean ventilation and deoxygenation in a warming world'.

Coordinating social action: a primer for the cross-species investigation of communicative repair

Human joint action is inherently cooperative, manifested in the collaborative efforts of participants to minimize communicative trouble through interactive repair. Although interactive repair requires sophisticated cognitive abilities, it can be dissected into basic building blocks shared with non-human animal species. A review of the primate literature shows that interactionally contingent signal sequences are at least common among species of non-human great apes, suggesting a gradual evolution of repair. To pioneer a cross-species assessment of repair this paper aims at (i) identifying necessary precursors of human interactive repair; (ii) proposing a coding framework for its comparative study in humans and non-human species; and (iii) using this framework to analyse examples of interactions of humans (adults/children) and non-human great apes. We hope this paper will serve as a primer for cross-species comparisons of communicative breakdowns and how they are repaired. This article is part of the theme issue 'Revisiting the human 'interaction engine': comparative approaches to social action coordination'.

Adaptive evolution to novel predators facilitates the evolution of damselfly species range shifts

Most species have evolved adaptations to reduce the chances of predation. In many cases, adaptations to coexist with one predator generate tradeoffs in the ability to live with other predators. Consequently, the ability to live with one predator may limit the geographic distributions of species, such that adaptive evolution to coexist with novel predators may facilitate range shifts. In a case study with Enallagma damselflies, we used a comparative phylogenetic approach to test the hypothesis that adaptive evolution to live with a novel predator facilitates range size shifts. Our results suggest that the evolution of Enallagma shifting from living in ancestral lakes with fish as top predators, to living in lakes with dragonflies as predators, may have facilitated an increase in their range sizes. This increased range size likely arose because lakes with dragonflies were widespread, but unavailable as a habitat throughout much of the evolutionary history of Enallagma because they were historically maladapted to coexist with dragonfly predators. Additionally, the traits that have evolved as defenses against dragonflies also likely enhanced damselfly dispersal abilities. While many factors underlie the evolutionary history of species ranges, these results suggest a role for the evolution of predator-prey interactions.

The Promise of an Evolutionary Perspective of Alcohol Consumption

The urgent need for medical treatments of alcohol use disorders has motivated the search for novel molecular targets of alcohol response. Most studies exploit the strengths of lab animals without considering how these and other species may have adapted to respond to alcohol in an ecological context. Here, we provide an evolutionary perspective on the molecular and genetic underpinnings of alcohol consumption by reviewing evidence that alcohol metabolic enzymes have undergone adaptive evolution at 2 evolutionary junctures: first, to enable alcohol consumption accompanying the advent of a frugivorous diet in a primate ancestor, and second, to decrease the likelihood of excessive alcohol consumption concurrent with the spread of agriculture and fermentation in East Asia. By similarly considering how diverse vertebrate and invertebrate species have undergone natural selection for alcohol responses, novel conserved molecular targets of alcohol are likely be discovered that may represent promising therapeutic targets.

No Evidence That Nitrogen Limitation Influences the Elemental Composition of Isopod Transcriptomes and Proteomes

The field of stoichiogenomics aims at understanding the influence of nutrient limitations on the elemental composition of the genome, transcriptome, and proteome. The 20 amino acids and the 4 nt differ in the number of nutrients they contain, such as nitrogen (N). Thus, N limitation shall theoretically select for changes in the composition of proteins or RNAs through preferential use of N-poor amino acids or nucleotides, which will decrease the N-budget of an organism. While these N-saving mechanisms have been evidenced in microorganisms, they remain controversial in multicellular eukaryotes. In this study, we used 13 surface and subterranean isopod species pairs that face strongly contrasted N limitations, either in terms of quantity or quality. We combined in situ nutrient quantification and transcriptome sequencing to test if N limitation selected for N-savings through changes in the expression and composition of the transcriptome and proteome. No evidence of N-savings was found in the total N-budget of transcriptomes or proteomes or in the average protein N-cost. Nevertheless, subterranean species evolving in N-depleted habitats displayed lower N-usage at their third codon positions. To test if this convergent compositional change was driven by natural selection, we developed a method to detect the strand-asymmetric signature that stoichiogenomic selection should leave in the substitution pattern. No such signature was evidenced, indicating that the observed stoichiogenomic-like patterns were attributable to nonadaptive processes. The absence of stoichiogenomic signal despite strong N limitation within a powerful phylogenetic framework casts doubt on the existence of stoichiogenomic mechanisms in metazoans.

Unlocking the Secrets of the Regenerating Fish Heart: Comparing Regenerative Models to Shed Light on Successful Regeneration

The adult human heart cannot repair itself after injury and, instead, forms a permanent fibrotic scar that impairs cardiac function and can lead to incurable heart failure. The zebrafish, amongst other organisms, has been extensively studied for its innate capacity to repair its heart after injury. Understanding the signals that govern successful regeneration in models such as the zebrafish will lead to the development of effective therapies that can stimulate endogenous repair in humans. To date, many studies have investigated cardiac regeneration using a reverse genetics candidate gene approach. However, this approach is limited in its ability to unbiasedly identify novel genes and signalling pathways that are essential to successful regeneration. In contrast, drawing comparisons between different models of regeneration enables unbiased screens to be performed, identifying signals that have not previously been linked to regeneration. Here, we will review in detail what has been learnt from the comparative approach, highlighting the techniques used and how these studies have influenced the field. We will also discuss what further comparisons would enhance our knowledge of successful regeneration and scarring. Finally, we focus on the Astyanax mexicanus, an intraspecies comparative fish model that holds great promise for revealing the secrets of the regenerating heart.

The Diatom Diversity and Ecological Status of a Tufa-Depositing River through eDNA Metabarcoding vs. a Morphological Approach-A Case Study of the Una River (Bosnia and Herzegovina)

Tufa deposits in karst rivers are unique habitats created by mutual interactions between specific environmental and biotope features and inhabited by diatoms as a highly abundant and diverse algal group. This pilot study aimed to investigate the diversity of diatom communities on tufa depositing habitats and assess the Una River's ecological status using a comparative molecular and morphological approach for diatom identification. The 312 base pairs of the rbcL gene were barcoded and analyzed using MiSeq reads and amplicon sequence variants (ASVs) obtained by the DADA2 pipeline. The reference database Diat.barcode v7 was used for taxonomic assignment. The morphological identification of the diatoms was carried out in parallel. In total, the combined dataset revealed 46 taxa identified at genus rank, 125 on the subgenus, and 145 on combined taxonomy rank. The metabarcoding approach mostly leads to a lower number of identified taxa at species rank (58 in molecular vs. 119 in optical inventory), resulting in higher values of beta diversity and heterogeneity in diatom assemblages in samples obtained by morphological approach. Despite the high percentage of taxonomically not assigned diatom ASVs to the species rank, high Shannon diversity index values and a similar number of taxa per locations compared to the morphological approach were obtained. Taxa Achnanthidium minutissimum (Kützing) Czarnecki, Achnanthidium pyrenaicum (Hustedt) H.Kobayasi, Amphora pediculus (Kützing) Grunow, Diatoma vulgaris Bory, Navicula cryptotenella Lange-Bertalot, and Navicula tripunctata (O.F.Müller) Bory were identified at all locations in both inventories. Although limited consistency in the diatom abundances between the two inventory datasets was found, a similar grouping of samples was observed connected to the river's longitudinal gradient. The data obtained using molecular approach in most sites indicated a mostly lower ecological status (good or moderate) compared to the data obtained from the morphological approach (high, good, and moderate). The potential of environmental DNA (eDNA) diatom metabarcoding for water monitoring and diversity studies is undeniable, but to fully realize the benefits of these methods in the future, it is essential to standardize protocols and expand the reference database for species found in specific habitats, such as tufa deposits.