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Protecting habitat of species-at-risk is critical to their recovery, but can be contentious. For example, protecting species that are locally imperilled but globally common (e.g. species that only occur in a jurisdiction at the edge of their geographic range) is often thought to distract from protecting globally-imperilled species. However, such perceived trade-offs are based on the assumption that threatened groups have little spatial overlap, which is rarely quantified. Here, we compile range maps of terrestrial species-at-risk in Canada to assess the geographic overlap of nationally and globally at-risk species with each other, among taxonomic groups, and with protected areas. While many nationally-at-risk taxa only occurred in Canada at their northern range edge (median=4% of range in Canada), nationally-at-risk species were not significantly more peripheral in Canada than globally-at-risk species. Further, 56% of hotspots of nationally-at-risk taxa were also hotspots of globally-at-risk taxa in Canada, undercutting the perceived trade-off in their protection. Hotspots of nationally-at-risk taxa also strongly overlapped with hotspots of individual taxonomic groups, though less so for mammals. While strong spatial overlap across threat levels and taxa should facilitate efficient habitat protection

1. We studied the natural history knowledge (NHK) of students (18-19 years), considering the salience of nature expressed through the knowledge of names of organisms, routes for knowledge transmission and acquisition, and the potential of specific taxa to represent a student's overall knowledge. 2. We report a two-year study of the NHK of 149 UK-resident first-year biology students surveyed by means of a free-listing exercise, facilitating the assessment of salience, prior to participation in a residential field-course run by the University of Oxford. 3. Each year, students anonymously completed a questionnaire asking them to name any five species in each of five taxonomic groups (birds, trees, mammals, butterflies and wildflowers) found wild in the British Isles, also stating if those named were native or introduced. Metadata were collected on the students' background and sources of knowledge (e.g., family, teachers, etc.). 4. Of the five taxonomic groups, birds were the best known by the students, while butterflies were the most poorly known group. However, although asked for names at species level, while 94% of students could name five British bird taxa, only 55.7% named them at species level, many giving folk-generics such as ‘duck’ or ‘seagull’ instead. For butterflies, only 12.8% of students correctly named five British species, and 47% named none. 5. Family influences, self-motivation and knowledge of birds, rather than formal education, best predicted students’ overall NHK. While urban/rural residency had a small effect on NHK, it strongly influenced the relative importance of other factors. 6. Factor Analysis showed NHK was best represented by knowledge of birds. Furthermore, the bird species named predicted students’ total NHK as well as the students’ knowledge of birds. Asked to name their favourite bird, students with family influence were significantly more likely to name native species. 7. We describe the complex interplay between context, family and formal education in developing nature salience; roles which we define as nature ‘advocacy’. In the urban context, the advocacy of family and teachers was essential to engage young people with nature, while this was not so in a rural context. We briefly consider the implications of our study for natural history education going forward.

Biological invasions are a major driver of biodiversity loss and socioeconomic burden globally. As invasion rates accelerate worldwide, understanding past invasion dynamics is essential to inform predictions of future invaders and impacts. Owing to a high diversity of pathways and current biosecurity gaps, aquatic systems near urban centres are especially susceptible to alien species establishments. Here, we compiled and compared alien species lists for three different aquatic recipient regions spanning the North Atlantic: Chesapeake Bay, Great Lakes-St. Lawrence River and North and Baltic Seas. Each system is a major trade centre, with a history of invasions, and characterised by a strong natural salinity gradient. Our goal was to compare the alien species across systems, to test for similarities in the taxonomic composition and geographic origin as well as species overlap among the three regions. We selected specific macroinvertebrate, algae and fish taxa for analysis, to control for uneven taxonomic and biogeographic resolution across regions. Cumulatively, we identified 326 individual alien species established in these aquatic systems, with the North and Baltic Seas most invaded overall (163), followed by Great Lakes-St. Lawrence River (84) and Chesapeake Bay (79). Most invasions were from Ponto-Caspian, Eurasian, Northwest Pacific, Northwest Atlantic and North American origins, and mostly comprised Arthropoda, Chordata, Mollusca and Annelida. However, origins and taxonomies differed significantly among destinations, with Ponto-Caspian species particularly successful invaders to the North and Baltic Seas then Great Lakes-St. Lawrence River, but less so to Chesapeake Bay. Nevertheless, approximately eight tenths of invaders established in only one region, indicating disparate invasion patterns and a high potential for future aliens to accrue from increasingly diverse source pools and pathways. These results support biosecurity strategies that consider a broad range of geographic origins and taxonomic groups to limit the translocation, arrival and spread of alien species worldwide.

Rodents are the largest order of mammals and contain several model organisms important to scientific research in a variety of fields, yet no large set of genomic markers have been designed for this group to date, hindering evolutionary studies into relationships of the group as a whole. Here we present a genomic probe set designed and optimized for rodents with a protocol that is easy to replicate with little laboratory investment. This design utilizes an anchored hybrid enrichment approach specifically targeting rodents to generate longer loci with a higher substitution rate than existing vertebrate probes to provide utility at various taxonomic levels. Using a test set of rodents from all five suborders, we successfully obtained alignments for 416 of the 418 target loci with an average of 1379 bp per locus and a total alignment of more than half a million base pairs. This genomic data set performed well in all phylogenetic analyses, especially in recent phylogenetic splits, with ample parsimony-informative sites within genera and even within species, showing more than four times as many single nucleotide polymorphisms per locus than a recent vertebrate ultraconserved elements study. Additional support is provided in resolving deeper clades in Rodentia. By providing this probe design, we hope that more laboratories can easily generate data for answering questions in rodents from species delimitation to understanding relationships among families in rapid radiations.

The integrity of the homestead pond supply depends on how various macrobenthic communities make their living more diversified and contribute to complex food webs. In addition, the macrobenthic community are significantly used as indicator organisms to detect the pollution impacts in aquatic ecosystems. In this study, we show the data about the diversity and community structure of macrobenthos and their relationship with environmental variables in homestead ponds of Noakhali coast from January 2019 to August 2019. The current study yielded 17 species belonging to seven taxonomic groups with a mean density of 3630 ind./m2. The Nematode community, comprising 48.86% of the total taxonomic groups with Prionchulus sp. as the dominant macrobenthic species represented more than 31% of the total macrobenthic taxa, and showed a significant negative correlation with the value of salinity, DO, pH. The environmental variables and diversity indices were detected significant variations (P

Pollen micromorphology is not only used to check the functional and structural evolution in plants but also to solve the taxonomic problem related to the classification of plants. Therefore, keeping in view the significance of pollen traits, selected taxa of the subfamily Caesalpiniaceae was collected from different geographical regions of Pakistan. The species were then analyzed under both light microscopy and scanning electron microscopy techniques to investigate the importance of micromorphological characters of pollen in the identification and classification of species. Great variation was recorded in equatorial shape, surface ornamentation, tectum, polar diameter, equatorial diameter, and exine thickness. However, little variation was observed in pollen type, polar shape, and fertility of pollen. The equatorial shape of five types was observed: prolate, prolate-spheroidal, spheroidal-subprolate, subspheroidal-prolate, and subspheroidal. Four types of surface ornamentation, psilate, granulate, clavate, and perforate, were recorded. Tectum of five types, intactate, reticulate regulate, medium reticulate, tactate, and striate, was observed. Sexine was thicker than nexine in all studied species. The largest polar diameter was observed in Caesalpinia pulcherrima 64.1 μm while the smallest in Parkinsonia aculeata 26.1 μm. The largest equatorial diameter was found in C. pulcherrima of 70.25 μm whereas the smallest in P. aculeata 27.57 μm. All the pollens analyzed were tricolporate. All studied species have a fertility ratio of more than 90%. A taxonomic key was developed to show the variation in pollen features and delimit species for the correct identification. In conclusion, the pollen traits were found useful to define species boundaries at various taxonomic ranks and will strengthen the taxonomy of this subfamily. Besides, this study also explored the palynological traits and their implication in the taxonomy of the subfamily Caesalpiniaceae.

O_LIVisualising data is a vital part of analysis, allowing researchers to find patterns, and assess and communicate the results of statistical modeling. In ecology, visualisation is often challenging when there are many variables (often for different species or other taxonomic groups) and they are not normally distributed (often counts or presence-absence data). Ordination is a common and powerful way to overcome this hurdle by reducing data from many response variables to just two or three, to be easily plotted. C_LIO_LIOrdination is traditionally done using dissimilarity-based methods, most commonly non-metric multidimensional scaling (nMDS). In the last decade however, model-based methods for unconstrained ordination have gained popularity. These are primarily based on latent variable models, with latent variables estimating the underlying, unobserved ecological gradients. C_LIO_LIDespite some major benefits, a major drawback of model-based ordination methods is their speed, as they typically taking much longer to return a result than dissimilarity-based methods, especially for large sample sizes. C_LIO_LIWe introduce copula ordination, a new, scalable model-based approach to unconstrained ordination. This method has all the desirable properties of model-based ordination methods, with the added advantage that it is computationally far more efficient. In particular, simulations show copula ordination is an order of magnitude faster than current model-based methods, and can even be faster than nMDS for large sample sizes, while being able to produce similar ordination plots and trends as these methods. C_LI

Genomicus is a database and web-server dedicated to comparative genomics in eukaryotes. Its main functionality is to graphically represent the conservation of genomic blocks between multiple genomes, locally around a specific gene of interest or genome-wide through karyotype comparisons. Since 2010 and its first release, Genomicus has synchronized with 60 Ensembl releases and seen the addition of functions that have expanded the type of analyses that users can perform. Today, five public instances of Genomicus are supporting a total number of 1029 extant genomes and 621 ancestral reconstructions from all eukaryotes kingdoms available in Ensembl and Ensembl Genomes databases complemented with four additional instances specific to taxonomic groups of interest. New visualization and query tools are described in this manuscript. Genomicus is freely available at http://www.genomicus.bio.ens.psl.eu/genomicus.

The unprecedented growth of human-dominated landscapes has led to population decline and the extinction of many animal species. A major paradigm shift that perceived wildlife as problem animals into threatened species that need protection triggered human-wildlife conflict studies. Although human-wildlife conflict incidences can be found globally, they have unique characteristics in each region of the world. However, little is known about the characteristics of human-wildlife conflicts in Southeast Asia, particularly Indonesia. There is a need for a comprehensive insight into human-wildlife conflict studies in Indonesia to understand past advancements and propose future priorities. This study examined the literature that provides the overall view of the human-wildlife conflict patterns in the country. The results showed that there was a comparatively small number of studies because this field was a relatively new subject in Indonesia. Furthermore, there were big gaps regarding animal species and the geographic distribution of study sites. A total of 35 species belonging to eight taxonomic groups experienced conflicts with humans. However, the studies heavily focused on three groups of animals and certain areas of the country. The predominant conflict sites were secondary forest, agroforestry, and farmlands. The conflicts in these areas unveiled the significance of local beliefs and social norms for formulating mitigation strategies.

Aim:Our current understanding of the causes of global extinction risk is mostly informed by the expert knowledge-based “threats classification scheme” of the IUCN Red List of Threatened Species. Studies based on this dataset came to different conclusions about the relative importance of threats to species, depending on which taxonomic groups and levels of extinction risk were considered, and which version of the database was used. A key reason may lie in data limitations as causes of threat are well known for charismatic and well-studied species, but not for the majority of species assessed. Here, we aim to fill current knowledge gaps about the importance of drivers of global extinction risks by focusing on endemic species.Location:Global.Methods:We examined country-level variation in the proportion of globally threatened and extinct endemic species (Index of Threat, IoT) with a range of spatially explicit information about anthropogenic pressures, mitigation measures and data limitations.Results:IoT coincided with several anthropogenic pressures, with substantial differences among kingdoms, life-forms, levels of extinction risk and geographic locations. IoT of plants, particularly tropical woody plants of moderate extinction risk, was higher in countries with higher GDP and more invasive species. Furthermore, IoT of animals, particularly tropical mammals and invertebrates of moderate extinction risk, was higher in countries with higher GDP and smaller roadless areas.Main conclusions:The extinction crisis for endemic species is associated with a complex network of potential drivers that need to be considered in concert in conservation policy and practice. Although our results require careful interpretation and remain sensitive to data limitations, we encourage similar studies at smaller scales to identify potential drivers of extinction risk at a higher resolution, particularly in regions where species assessments have been conducted consistently or on organisms with a uniform response time to pressures. published

We report an update of the Hymenoptera Genome Database (HGD; http://HymenopteraGenome.org), a genomic database of hymenopteran insect species. The number of species represented in HGD has nearly tripled, with fifty-eight hymenopteran species, including twenty bees, twenty-three ants, eleven wasps and four sawflies. With a reorganized website, HGD continues to provide the HymenopteraMine genomic data mining warehouse and JBrowse/Apollo genome browsers integrated with BLAST. We have computed Gene Ontology (GO) annotations for all species, greatly enhancing the GO annotation data gathered from UniProt with more than a ten-fold increase in the number of GO-annotated genes. We have also generated orthology datasets that encompass all HGD species and provide orthologue clusters for fourteen taxonomic groups. The new GO annotation and orthology data are available for searching in HymenopteraMine, and as bulk file downloads.

A successful restoration of riparian forests can recover the diversity of several groups of soil invertebrates. However, few studies have considered the recovery of the entire community of soil macrofauna and the relative effect in taxonomical and functional diversity. We evaluated how taxonomical diversity, in terms of abundance and richness, relates to trophic diversity in four patches of riparian forests that had been artificially recovered, and compared them to the reference site in Volta Grande Reservoir, Brazil. No relationship was found between taxonomic diversity and trophic diversity, suggesting functional redundancy among taxonomic groups. Nevertheless, we observed that the taxonomic group with more species presented higher trophic diversity than the rest, indicating low functional redundancy within this group. The abundance and the taxonomic and functional richness of the four restored sites was similar to the reference site. The forest recovery was efficient in recovering invertebrate soil community since the taxonomic and trophic composition recorded in our study were similar to the composition of natural areas. We emphasize the importance of studying edaphic fauna as a community in order to comprehend how it reacts to forest restoration.

A challenge for taxonomists all over the world and across all taxonomic groups is recognizing and delimiting species, and cryptic species are even more challenging. However, an accurate identification is fundamental for all biological studies from ecology to conversation biology. We used a multidisciplinary approach including genetics as well as morphological and ecological data to assess if an easily recognizable, widely distributed and euryoecious mite taxon represents one and the same species. According to phylogenetic (based on mitochondrial and nuclear genes) and species delimitation analyses, five distinct putative species were detected and supported by high genetic distances. These genetic lineages correlate well with ecological data, and each species could be associated to its own (micro)habitat. Subsequently, slight morphological differences were found and provide additional evidence that five different species occur in Central and Southern Europe. The minuteness and the characteristic habitus of Caleremaeus monilipes tempted to neglect potential higher species diversity. This problem might concern several other “well-known” euryoecious microarthropods. Five new species of the genus Caleremaeus are described, namely Caleremaeus mentobellus sp. nov., C. lignophilus sp. nov., C. alpinus sp. nov., C. elevatus sp. nov., and C. hispanicus sp. nov. Additionally, a morphological evaluation of C. monilipes is presented.

Diverse evolutionary forces have promoted the great diversity of vocal behaviour found in birds. The description of such behaviour is crucial for understanding both selective and non-selective pressures shaping acoustic signals in birds and their role in ecological and evolutionary processes. Here, we describe the vocal behaviour of the Sclater’s Wren (Campylorhynchus rufinucha humilis), a songbird species that lives in Neotropical dry forests. Using active and passive acoustic monitoring, we quantified sex-specific solo song repertoires, described the acoustic structural characteristics of the songs, assessed vocal activity during the dawn chorus including calls, solo songs, duets and sex contribution to duet formation, and tested whether the degree of song sharing varied with geographical distance between neighbouring territories. Our results based on 24 pairs suggest that Sclater’s Wrens have sexually dimorphic songs, and that both females and males combine their songs to produce duets. Most duets are initiated by males and answered by females. Females have only one song type in their repertoire, while males have multiple song types with a finite repertoire size of 49.7 ± 8.8 (calculated with simple enumeration; n = 8) or 55.4 ± 16.1 (calculated with the capture–recapture technique; n = 19) song types on average per bird. The vocal activity during the morning resembles the pattern of dawn chorus, although individuals usually start vocalising after sunrise, with both sexes contributing to the vocal activity during the morning. We also found that the number of songs that two males share decreases as geographic distance increases between territories, suggesting that males learn their songs from their parents or neighbouring tutors, a learned behaviour important in intra-sexual interactions. Our study adds to the accounts of Neotropical bird species that have detailed vocal descriptions and will facilitate comparisons with other taxonomic groups within the Rufous-naped Wren complex, shedding light on taxonomic disputes.

Despite the important role that species names play in multiple fields, there is no globally complete list of known and described species. This lack is a result simultaneously of the complexity of planetary biodiversity, the long history of naming species in publications from all over the world, the small number of taxonomists working on many important groups, the rapid and dynamic change in knowledge for a few well-studied groups, and the limited incentives for researchers to curate such lists. Recent papers have proposed that a more formal governance mechanism is needed to assist with the translation of taxonomic knowledge to user communities. The recommendation is for the taxonomic community to assist user groups by maintaining reviewed lists that reflect as far as possible consensus among practising taxonomists and incorporating new insights and understanding as these become widely accepted within the relevant taxonomic community. The Catalogue of Life (COL) is the most significant international partnership working to deliver a list of all species by engaging a broad network of taxonomists and databases to contribute expert-curated lists for different taxonomic groups. COL, which included 1,908,823 species as of May 2021, has great experience with developing such a list across all taxonomic groups and has been modernising its processes and tools since 2017 to reflect best practice in management of large digital information assets. This paper explores the alignment between the current state and directions of COL and the initiative to improve the governance of species lists.

The subfamily Barnadesioideae (Compositae) is endemic to South America, comprising 10 genera and 80 species of mostly spiny herbs, subshrubs, shrubs, trees, or woody vines distributed from Venezuela to Argentina. Three genera, Dasyphyllum (27 species), Chuquiraga (22 spp.) and Barnadesia (19 spp.) contain 85% of the species, while the other seven genera (Archidasyphyllum, Arnaldoa, Doniophyton, Duseniella, Fulcaldea, Huarpea, and Schlechtendalia) are represented by up to three species each. Most species are found in xeric areas in the Andean and Patagonian regions—as in the Páramos, Puna and Patagonian steppe vegetation—with a secondary center of diversity in eastern South America. Previous phylogenetic hypotheses have clarified the relationships within the subfamily, showing that there are many non-monophyletic groups in different taxonomic ranks. As a result, taxonomic changes have been proposed over recent decades in order to reflect classifications comprising only monophyletic groups. In the present study, we provide a generic synopsis of the subfamily Barnadesioideae based on the most recent generic circumscriptions, including a key, expanded morphological descriptions, information on geographical distribution and habitat, photographs and taxonomic notes for all genera.

This study is dedicated to genome size dynamics during evolution of plant and animal species belonging to the same genera. At the scale of the taxonomic categories of plant and animal kingdoms, genome size of species trends to decline, which means that species with small genomes significantly prevail. However, within genera of both plants and animals genome size can increase, decrease, or remain relatively stable during the entire time of genus evolution. These three patterns represent the basic components of intrageneric genome size dynamics. Aside of this simple dynamics with one component, there exists complex dynamics consisting of two or even three basic components. Genome size dynamics of diploids and polyploids within plant genera can significantly differ which reflects influence of different evolutionary factors. The reasons of the component change in the case of the complex dynamics is not completely clear, however one of those can be the global cooling which began three million years ago.

An important focus of community ecology, including invasion biology, is to investigate functional trait diversity patterns to disentangle the effects of environmental and biotic interactions. However, a notable limitation is that studies usually rely on a small and easy‐to‐measure set of functional traits, which might not immediately reflect ongoing ecological responses to changing abiotic or biotic conditions, including those that occur at a molecular or physiological level. We explored the potential of using the diversity of expressed genes—functional genomic diversity (FGD)—to understand ecological dynamics of a recent and ongoing alpine invasion. We quantified FGD based on transcriptomic data measured for 26 plant species occurring along adjacent invaded and pristine streambeds. We used an RNA‐seq approach to summarize the overall number of expressed transcripts and their annotations to functional categories, and contrasted this with functional trait diversity (FTD) measured from a suite of characters that have been traditionally considered in plant ecology. We found greater FGD and FTD in the invaded community, independent of differences in species richness. However, the magnitude of functional dispersion was greater from the perspective of FGD than from FTD. Comparing FGD between congeneric alien–native species pairs, we did not find many significant differences in the proportion of genes whose annotations matched functional categories. Still, native species with a greater relative abundance in the invaded community compared with the pristine tended to express a greater fraction of genes at significant levels in the invaded community, suggesting that changes in FGD may relate to shifts in community composition. Comparisons of diversity patterns from the community to the species level offer complementary insights into processes and mechanisms driving invasion dynamics. FGD has the potential to illuminate cryptic changes in ecological diversity, and we foresee promising avenues for future extensions across taxonomic levels and macro‐ecosystems., Functional trait diversity patterns have been central for understanding how communities respond to change. We explore the diversity of functional genomic traits in an invaded alpine ecosystem, exposing cryptic functional diversity that helps disentangle controversial hypotheses of invasion biology and community assembly.

Leeches play important roles in food webs due to their abundance, diversity and feeding habits. Studies using invertebrate-derived DNA (iDNA) extracted from leech gut contents to target vertebrate DNA have focused on the Indo-Pacific region and mainly leveraged the leech family Haemadipsidae, composed of bloodfeeding terrestrial leeches, while predatory, fluid/tissue-feeding and aquatic bloodfeeding species have been largely disregarded. While there is some general knowledge regarding the taxonomic groups that leeches prefer to feed on, detailed taxonomic resolution is missing and, therefore, their potential use for monitoring animals is unknown. In this study, 116 leeches from 12 species (six families) and spanning the three feeding habits were collected in Mexico and Canada. We used DNA metabarcoding to investigate their diet and assess their potential use for biodiversity monitoring. We detected vertebrates from five orders including fish, turtles and birds in the diet of aquatic bloodfeeding leeches; eight invertebrate orders of annelids, arthropods and molluscs in leeches that feed on body fluids and tissues; and ten orders of invertebrates belonging to Arthropoda and Annelida, as well as one vertebrate and one parasitic nematode, in predatory leeches. These results show the potential use of iDNA from aquatic bloodfeeding leeches for retrieving vertebrate taxa, and from predatory and fluid-feeding leeches for invertebrates. Our study provides information about the dietary range of freshwater leeches and one terrestrial leech and contributes proof-of-concept for the use of these leeches for animal monitoring, expanding our knowledge of the use of iDNA from leech gut contents to North America.

Type series of three nominal taxa of the hydrobiid gastropods inhabiting the Caspian Sea were traced recently in the uncatalogued part of the malacological collection of the Zoological Institute of Russian Academy of Sciences, Saint-Petersburg. Images of the holotypes and some paratypes of Pyrgula isseli Logvinenko & Starobogatov, 1969, P. sowinskyi Logvinenko & Starobogatov, 1969 and P. derzhavini Logvinenko & Starobogatov, 1969 are presented. The first two species belong to the genus Clathrocaspia (subfamily Caspiinae) and P. sowinskyi is considered a junior synonym of C. pallasii (Clessin & W. Dybowski in W. Dybowski, 1887). The attribution of the third species, P. derzhavini, to Laevicaspia (Pyrgulinae) is confirmed based on the newly discovered type material. Based on the additional information we update ecological data and distribution ranges of the species, provide comments on their nomenclature, systematic position and taxonomic rank.

The epithet “alpina” has been recurrently used in the genus Deschampsia to name plants located in northern regions of Europe, Asia and North America, as a species (Deschampsia alpina (L.) Roem. & Schult.), but also in infraspecific categories (Deschampsia cespitosa subsp. alpina Tzvel. and Deschampsia cespitosa var. alpina Schur.). The morphological and molecular available evidence suggests the existence of a single species, Deschampsia cespitosa (L.) P. Beauv., in which individuals belonging to the same morphological gradient have received different names in different taxonomic categories throughout its wide distribution range. An evaluation of the available names indicates that all uses of the epithet “alpina” are illegitimate. A new combination is proposed at the infraspecific level as Deschampsia cespitosa subsp. neoalpina Chiapella, Xue & Greimler.

Schall et al. (2020) assessed how a combination of different forest management systems in managed forest landscapes dominated by European beech may affect the biodiversity (alpha, beta and gamma) of 14 taxonomic groups. Current forest policy and nature conservation often demand for combining uneven-aged managed and unmanaged, set-aside for nature conservation, beech forests in order to promote biodiversity. In contrast to this, Schall et al. (2020) found even-aged shelterwood forests, represented by different developmental phases, to support highest regional (gamma) diversity. By pointing out that unmanaged forests included in our study are not old-growth forests, Bruun and Heilmann-Clausen (2021) challenge our conclusion as not providing sound scientific advice to societies. It is true that the studied unmanaged forests are not representing old-growth forests as defined in the literature. However, we demonstrate the representativeness of our unmanaged forests for current beech forest landscapes of Central Europe, where managed forests were more or less recently set-aside in order to develop old-growth structures. We also show that the managed and recently unmanaged forests in our study already differ distinctively in their forest structures. We use this response to stress the role of forest reserves for promoting certain species groups, and to emphasise their importance as valuable research sites today and in the future. Synthesis and applications. We see two main conclusions from our study. First, unmanaged forests still matter. We agree with Bruun and Heilmann-Clausen (2021) on the general importance of unmanaged, old-growth or long-untouched forests, and we do not question the importance of set-aside forests for biodiversity conservation. However, a complete complementarity to managed systems may only reveal after many decades of natural development. Second, safeguarding biodiversity in largely managed forest landscapes should focus on providing a landscape matrix of different developmental phases with varying environmental conditions rather than on maximising the vertical structure within stands. Such landscapes can partly compensate for structures that are still missing in vital, dense and closed forests recently set-aside or for unsuitable phases that may occur due to a cyclic synchronisation of forest structures in unmanaged forests. © 2021 The Authors. Journal of Applied Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society

The process of molecular identification of species known as DNA barcoding consists on discriminating taxa based on cumulative differences of their DNA sequences and is widely used within animals, including birds. Finding the best genomic tools, such as primers, to reach most of the species within the studied groups and evaluating the coverage breadth and physicochemical properties of primers before testing in the laboratory, can save time and financial resources. Therefore, this work aimed to retrieve the available primers for the COI gene currently used on the molecular identification of birds and evaluate them for its coverage range, physicochemical properties, and performance on in silico PCR. Afterwards, we provide the best primer subsets to cover the highest number of avian sequences and the best individual primers for each bird order in terms of coverage breadth. Thirty-one bird orders had at least one COI sequence to serve as template, 152 primers available for assessing the COI gene were evaluated, and 118 could bind to at least one template sequence. No primer subset alone could cover all template sequences; however, when combining two subsets, the complete coverage of avian COI sequences analyzed was achieved. We were able to find optimal primer subsets for more specific taxonomic groups or for analysis involving the complete avian group, in order to guide researchers in the process of choosing the best primer set for each individual barcoding goal.

Lichens are major components of high altitude/latitude ecosystems. However, accurately characterizing their biodiversity is challenging because these regions and habitats are often underexplored, there are numerous poorly known taxonomic groups, and morphological variation in extreme environments can yield conflicting interpretations. Using an iterative taxonomic approach based on over 800 specimens and incorporating both traditional morphology‐based identifications and information from the standard fungal DNA barcoding marker, we compiled a voucher‐based inventory of biodiversity of lichen‐forming fungi in a geographically limited and vulnerable alpine community in an isolated sky island in the Colorado Plateau, USA—the La Sal Mountains. We used the newly proposed Assemble Species by Automatic Partitioning (ASAP) approach to empirically delimit candidate species‐level lineages from family‐level multiple sequence alignments. Specimens comprising DNA‐based candidate species were evaluated using traditional taxonomically diagnostic phenotypic characters to identify specimens to integrative species hypotheses and link these, where possible, to currently described species. Despite the limited alpine habitat (ca. 3,250 ha), we document the most diverse alpine lichen community known to date from the southern Rocky Mountains, with up to 240 candidate species/species‐level lineages of lichen‐forming fungi. 139 species were inferred using integrative taxonomy, plus an additional 52 candidate species within 29 different putative species complexes. Over 68% of sequences could not be assigned to species‐level rank with statistical confidence, corroborating the limited utility of current sequence repositories for species‐level DNA barcoding of lichen‐forming fungi. By integrating vouchered specimens, DNA sequence data, and photographic documentation, we provide an important baseline of lichen‐forming fungal diversity for the limited alpine habitat in the Colorado Plateau. These data provide an important resource for subsequent research in the ecology and evolution of lichens alpine habitats, including DNA barcodes for most putative species/species‐level lineages occurring in the La Sal Mountains, and vouchered collections representing any potentially undescribed species that can be used for future taxonomic studies., Using an iterative taxonomic approach based on over 800 specimens and incorporating both traditional morphology‐based identifications and information from the standard fungal DNA barcoding marker, we compiled a voucher‐based inventory of biodiversity of lichen‐forming fungi in a geographically limited and vulnerable alpine community in an isolated sky island in the Colorado Plateau, USA—the La Sal Mountains. These data provide an important resource for subsequent lichen biodiversity research in alpine habitats, including DNA barcodes for the vast majority of putative species/species‐level lineages occurring in the La Sal Mountains, crucial information on species distributions, and vouchered collections representing any potentially undescribed species that can be used for future taxonomic studies.

Roots of different plant species are colonized by bacterial communities, that are distinct even when hosts share the same habitat. It remains unclear to what extent the host actively selects these communities and whether commensals are adapted to a specific plant species. To address this question, we assembled a sequence-indexed bacterial culture collection from roots and nodules of Lotus japonicus that contains representatives of most species previously identified using metagenomics. We analysed taxonomically paired synthetic communities from L. japonicus and Arabidopsis thaliana in a multi-species gnotobiotic system and detected signatures of host preference among commensal bacteria in a community context, but not in mono-associations. Sequential inoculation experiments revealed priority effects during root microbiota assembly, where established communities are resilient to invasion by latecomers, and that host preference of commensal bacteria confers a competitive advantage in their cognate host. Our findings show that host preference in commensal bacteria from diverse taxonomic groups is associated with their invasiveness into standing root-associated communities.

The formation of large-scale landscape-technical systems (LTchS), which territorially extended beyond river valleys, complicated the processes of exchange of matter, energy and information between valley-river and watershed types of areas, which led to the emergence of paradynamic landscape complexes of higher taxonomic rank. It is noted that on the territory of the Right Bank of Ukraine a significant number of anthropogenic paradynamic landscape complexes (APDLС) have been formed in the neighboring watersheds, which closely interact with each other. It was found that the formation and functioning of natural paradynamic landscape complexes of different taxonomic rank is due to many paradynamic and paragenetic connections. Longitudinal and anthropogenic paragenetic landscape complexes (APGLС) are characterized by longitudinal and transverse paragenetic connections, which are analyzed on the example of APGLС type "dam - pond - bridge - mill - island". There are three orders of basin APDLС: 1) basin APDLС of the 3rd order originate in the bottom of the river valley and gradually spread to watersheds; 2) basins of APDLС of the 2nd order unite among themselves APDLС which are located along the main stream; 3) basin APDLС of the 1st order arise due to a combination of landscape-technical systems in the valley of the main river with LTchS in the valleys of tributaries. The specifics of the functioning of the complex inter-basin APDLС "LTchS of the Right Bank of Ukraine", which is formed by the landscape and technical systems of the Dnieper, Dniester, Southern Bug, Danube, Vistula and Black Sea rivers, are considered. In each basin there are several centers (regional centers or centers of united territorial communities), which are subordinated to the central place (capital). The relationship between them is provided through a set of mechanical (movement of goods and passengers) and water (transportation of water through canals and water mains) paradynamic connections. Emphasis is placed on modern environmental problems in the catchment areas of the Right Bank of Ukraine. It is concluded that the study of paradynamic and paragenetic relationships within watersheds is aimed at the rational use of natural resources of river valleys. Control over the condition of APDLС should be entrusted to local basin administrations, where the leading role can be assigned to landscape engineers.Key words: anthropogenic landscape, landscape-technical system, paradynamic landscape complex, river valley, drainage basin. Формування значних за площею ландшафтно-технічних систем (ЛТчС), які територіально виходили за межі річкових долин, ускладнило процеси обміну речовиною, енергією та інформацією між долинно-річковими та вододільними типами місцевостей, що стало причиною виникнення парадинамічних ландшафтних комплексів вищого таксономічного рангу. Зазначено, що на території Правобережної України сформувалося значна кількість антропогенних парадинамічних ландшафтних комплексів (АПДЛК) у сусідніх водозбірних басейнах, які тісно взаємодіють між собою. Виявлено, що утворення та функціонування природних парадинамічних ландшафтних комплексів різного таксономічного рангу відбувається за рахунок множини парадинамічних і парагенетичних зв’язків. Для долинно-річкових антропогенних парагенетичних ландшафтних комплексів (АПГЛК) є характерними повздовжні та поперечні парагенетичні зв’язки, які проаналізовано на прикладі АПГЛК типу «гребля – ставок – міст – млин – острів». Виокремлено три порядки басейнових АПДЛК: 1) басейнові АПДЛК 3-го порядку зароджуються у днищі річ-кової долини і поступово поширюються на вододіли; 2) басейнові АПДЛК 2-го порядку об’єд-нують між собою АПДЛК, які розташовуються уздовж головного річища; 3) басейнові АПДЛК 1-го порядку виникають за рахунок поєднання ландшафтно-технічних систем у долині головного річища з ЛТчС в долинах приток. Розглянуто специфіку функціонування складного міжбасей-нового АПДЛК «ЛТчС Правобережної України», який сформований ландшафтно-технічними системами басейнів Дніпра, Дністра, Південного Бугу, Дунаю, Вісли та річок Причорномор’я. У кожному басейні виокремлюється кілька осередків (обласні центри або центри об’єднаних територіальних громад), які підпорядковуються центральному місцю (столиці). Взаємозв’язок між ними забезпечується через множину механічних (переміщенням вантажів і пасажирів) і водних (транспортування води каналами і водогонами) парадинамічних зв’язків. Акцентовано увагу на сучасних екологічних проблемах у водозбірних басейнах Правобережної України. Зроблено висновок про те, що дослідження парадинамічних і парагенетичних зв’язків у межах водозбірних басейнів спрямоване на раціональне використання природних ресурсів річкових долин. Контроль за станом АПДЛК має бути покладений на локальні басейнові управління, де провідна роль може відводиться інженерам-ландшафтознавцям.Ключові слова: антропогенний ландшафт, ландшафтно-технічна система, парадинамічний ландшафтний комплекс, річкова долина, водозбірний басейн.

Taxonomic spectra, i.e. relations between supraspecific taxa by the number of included species, remain poorly understood in aspect of the mathematical properties. We studied taxonomic spectra of plants (Magnoliophyta, Bryophyta), animals (Coleoptera, Aves), fungi (Agaricomycetes) and terrestrial protists (Myxomycetes), found in the Homilsha Forests National Nature Park (North-East of Ukraine), and concluded that they correspond to the hollow-curve distribution at the level of genera, families and orders. The spectra of most taxa, as shown by the Akaike information criterion, are closely approximated by the log-series distribution model at all taxonomic levels. This type of distribution is typical for the species abundance curves, based on collections made from small areas. At the same time, in the genera–families–orders row the similarity to the lognormal distribution increases. The central values and variability vary considerably between different taxonomic groups and ranks, however, without affecting the type of distribution. The number of orders in all taxa except Bryophyta has reached the saturation and coincides with the curve of the estimated number of orders according to the Chao1 coefficient. For families and especially genera the correspondence with estimated number of species is much lower. Our results do not confirm the assumption that hollow-curve distributions of taxonomic spectra result from the artificial fragmentation of taxa. These distributions neither depend on the insufficient knowledge about the species composition at the locality, nor reflect the size of the studied area. The presence of such distributions in both local and global biota of different groups may be explained by the common features of their evolution, especially by the existence of relict orphan groups. The fact that in Homilsha Forests the kurtosis and skewness of distributions decreases in the genera–families–orders row can therefore be explained by the relatively low percentage of the high-rank orphan taxa in the local biota. This may be a common feature of communities studied at small geographical scale, since orphan taxa often demonstrate a high level of endemism. Comparative studies of local communities from different climate zones may help to understand how universal are the patterns, described herein.

Analysis and comparison of the helminth assemblages in Antarctic rockcod Notothenia coriiceps collected near the UAS “Akademik Vernadsky” (Argentine Islands, West Antarctica) in 2002 and 2014–2015 were performed to characterise the parasite community and investigate the temporal changes in helminth assemblages and infection parameters. All specimens of N. coriiceps (n = 194) were caught at depths of 10–30 m. Parasites (22,856 helminth specimens and 15,057 cysts) were collected manually and identified based on their morphology. Statistical analysis of the quantitative data was performed using the Quantitative Parasitology 3.0 (QP 3.0), Paleontological Statistics (PAST v. 3.1), and PRIMER 6 software. Twenty-seven species of four taxonomic groups were recorded: trematodes (8 species), cestodes (4), nematodes (5), and acanthocephalans (10). Helminth samples collected in 2002 and 2014–2015 showed a rather high similarity in species composition. The species richness was higher in the sample collected in 2014–2015, while the evenness and diversity in the two samples were similar. The dissimilarity between helminth infracommunities in the two samples appeared to be statistically significant. Larval cestodes Diphyllobotrium sp., the acanthocephalan Metacanthocephalus rennicki, and the trematode Neoleoburia antarctica were found to make the most significant impact on the dissimilarity. The analysis of the composition and structure of helminth community in N. coriiceps revealed the changes that have happened during the last decade. At least some of the changes are attributed to the changes in marine ecosystems in Western Antarctica.

Some of the most impressive functional specializations in the human brain are found in the occipitotemporal cortex (OTC), where several areas exhibit selectivity for a small number of visual categories, such as faces and bodies, and spatially cluster based on stimulus animacy. Previous studies suggest this animacy organization reflects the representation of an intuitive taxonomic hierarchy, distinct from the presence of face- and body-selective areas in OTC. Using human functional magnetic resonance imaging, we investigated the independent contribution of these two factors-the face-body division and taxonomic hierarchy-in accounting for the animacy organization of OTC and whether they might also be reflected in the architecture of several deep neural networks that have not been explicitly trained to differentiate taxonomic relations. We found that graded visual selectivity, based on animal resemblance to human faces and bodies, masquerades as an apparent animacy continuum, which suggests that taxonomy is not a separate factor underlying the organization of the ventral visual pathway.SIGNIFICANCE STATEMENT Portions of the visual cortex are specialized to determine whether types of objects are animate in the sense of being capable of self-movement. Two factors have been proposed as accounting for this animacy organization: representations of faces and bodies and an intuitive taxonomic continuum of humans and animals. We performed an experiment to assess the independent contribution of both of these factors. We found that graded visual representations, based on animal resemblance to human faces and bodies, masquerade as an apparent animacy continuum, suggesting that taxonomy is not a separate factor underlying the organization of areas in the visual cortex. ispartof: JOURNAL OF NEUROSCIENCE vol:41 issue:33 pages:7103-7119 ispartof: location:United States status: published

Social networks research using non-human animals has grown over the past decade, utilizing a wide range of species to answer an array of pure and applied questions. Network approaches have relevance to conservation, evaluating social influences on fecundity, health, fitness and longevity. While the application of network approaches to in situ populations with conservation concern appears in published literature, the degree to which ex situ and zoo-housed populations are the focus of "social networks for conservation research" is limited. Captive environments provide scientists with an ability to understand the social behavior of species that may be hard to observe consistently in the wild. This paper evaluates the scope of network research involving ex situ populations, analyzing output from 2010 to 2019 to determine trends in questions and subjects using ex situ populations. We show that only 8.2% of ex situ social network analysis (SNA) implications are of conservation-focus, apparent in papers relating to birds, carnivores, bats, primates, reptiles, and ungulates. Husbandry and welfare questions predominate in ex situ network research, but over half of these papers have nonpractical application (basic science). The chance of a citation for a basic science paper was 95.4% more than for a conservation-based paper. For taxonomic groups, primate-focused papers had the most citations. The focus of ex situ conservation-based networks research may be driven by the needs of conservation programs (e.g., population recovery outcomes) or by a need to evaluate the efficacy of ex situ conservation goals. We evaluate our findings considering the IUCN's One Plan Approach to conservation to show how in situ and ex situ network research is applicable to global conservation efforts. We have identified that there is a lack of application and evaluation of SNA to wildlife conservation. We highlight future areas of research in zoos and hope to stimulate discussion and collaboration between relevant parties.

We present an open (publicly available) and updatable database of the karyotypes of Blattodea which is available at http://web.natur.cuni.cz/zoologie/arthropods/blattodeadatabase/index.html. This database currently contains data on chromosome numbers and sex chromosome systems for 355 (209 cockroaches and 146 termites) cytogenetically and/or geographically distinct populations of 229 species (138 cockroaches and 91 termites). When available, data on chromosome morphology and fundamental number are also included. As this summary of the data on Blattodea cytogenetics follows current taxonomy and phylogeny it enabled us to discuss hypotheses on karyotype evolution. We also point out some cytogenetically interesting phenomena such as extensive karyotype differentiation at low taxonomic levels in some lineages and the change from the X0 sex chromosome system, which is present in cockroaches, to systems with multiple neo-sex chromosomes, present in termites. We encourage the use of modern cytogenetic methods in research on Blattodea cytogenetics to uncover more detailed mechanisms of karyotype evolution in this insect order. We also provide a brief summary of the history of cytogenetic research in Blattodea.

Los estudios sobre las áreas de distribución geográfica (ADG) proporcionan información sobre cómo se establecen las especies en el espacio y tiempo, y los efectos del cambio de uso de suelo sobre los patrones geográficos de la biodiversidad. En la provincia biogeográfica de la Faja Volcánica Transmexicana (FVT) habita un alto número de especies endémicas; sin embargo, presenta altas tasas de deforestación. En el presente trabajo: (a) se describen cuantitativa y cualitativamente las ADG histórica de 167 especies de anfibios, aves, insectos, mamíferos y plantas endémicas de la FVT, y (b) se analiza el efecto del cambio de uso de suelo actual en esas distribuciones geográficas. En general, la clase Mammalia tuvo las mayores superficies ocupadas, el promedio más alto de las tres magnitudes y fue principalmente de distribución continental. Por otro lado, la mayoría de las especies fueron transicionales y discontinuas. Considerando el cambio en el uso del suelo, el 85% de las especies tuvo cambios en sus ADG históricas, de las que dos tercios tuvieron una pérdida mayor al 50%. Los grupos taxonómicos más afectados por pérdida total de su ADG histórica, fueron Insecta y Amphibia. La mayoría de las especies ocuparon altitudes elevadas y por lo tanto, los rangos altitudinales con mayor de superficie perdida fueron entre los 1,500 y 3,000 msnm. La variabilidad en el comportamiento distribucional de las especies sugiere patrones internos y diferenciados en la FVT, y mayor complejidad biológica, geológica y evolutiva de la esperada, con múltiples relaciones de la FVT con las provincias adyacentes. Los estudios areográficos pueden constituir un punto de partida para la preservación de áreas no transformadas, que cumpla el objetivo de prevenir la posible extirpación de las especies.

Major biogeographic and taxonomic biases are recurrent in biological surveys, including fragmentation studies. Detecting biases and subsequent gaps is crucial to steer future research and suitable conservation policies. We evaluated biogeographic and fragmentation-related biases on antbirds and non-flying small mammals in Brazil, two oversampled and vulnerable taxonomic groups, by surveying papers in the Scielo and the Web of Science. We found 566 articles published from 1945 to 2018, including 55 and 43 fragmentation studies for antbirds and small mammals, respectively. Considering the species richness for each group across the Brazilian biomes, the number of publications for small mammals tended to disproportionately increase while increasing richness. The Atlantic Forest, the most degraded and densely populated biome, contained the highest number of publications. However, the Amazon included a disproportionately high number of papers considering its low population density. Conversely, non-forest biomes such as the Caatinga, Pampa and Pantanal were mostly overlooked. Our results show that research effort for small mammals and antbirds in Brazil is biogeographically biased. We call future research to consider more studies across non-forest biomes and vast unexplored areas within forest biomes to overcome major knowledge gaps on diversity, distribution and ecology of antbirds and small mammals in Brazil.