Complete chloroplast genome of Tricyrtis xianjuensis Li, Chen & Ma 2014 (Liliaceae): a species endemic to Zhejiang province, China

Tricyrtis xianjuensis Li, Chen & Ma 2014 is a rare and endangered species endemic to Zhejiang province, with fewer than 200 individuals in the wild. In our present study, the complete chloroplast genome of T. xianjuensis was assembled by using high-throughput sequencing data, and its genomic features were described and comparative genomic analyses within Liliaceae family were performed. The complete chloroplast genome of T. xianjuensis was 155,748 bp in length, exhibiting a GC content of 37.3%. This genome structure contained two inverted repeats (IRs), as well as a small single-copy (SSC) and a large single-copy (LSC) region. The IR region measured 26,371 bp, while the SSC and LSC regions were 17,729 bp and 85,277 bp in length, respectively. A total of 137 genes were identified, including 85 protein-coding genes, 38 tRNA genes, eight rRNA genes, and six pseudogenes. Phylogenic analysis revealed T. xianjuensis shared a clade with T. formosana Baker 1879 and T. macropoda Miq. 1867, with a support rate of 100%. The assembly and analysis of T. xianjuensis chloroplast genome provided an insight into further studies on the conservation genetics of this endangered species.

Three new species of Trimmatothelopsis (Acarosporales, Acarosporaceae) from southwestern North America

The discovery and study of three new species of Trimmatothelopsis from Southwestern North America, T.californica, T.mexicana, and T.novomexicana, adds not only to the diversity of the genus and family but generated new insights into the occurrence of two ascus types in the genus and the variety of conidiogenous cells and conidia. Trimmatothelopsis now includes 15 species with a mainly Holarctic distribution (Asia, Europe, North America) and one species in Australia. A key is supplied to the genus. An overview of the genus Trimmatothelopsis is given, including differentiation from other genera of Acarosporaceae. The monotypic genus Thelocarpella is considered to be a synonym of Trimmatothelopsis. The new combination Trimmatothelopsiswirthii is proposed. The ascus type is shown to be variable in the genus with species with two types being intermixed with each other in our phylogeny.

Phenotypic plasticity and genetic diversity shed light on endemism of rare Boechera perstellata and its potential vulnerability to climate warming

The rapid pace of contemporary environmental change puts many species at risk, especially rare species constrained by limited capacity to adapt or migrate due to low genetic diversity and/or fitness. But the ability to acclimate can provide another way to persist through change. We compared the capacity of rare Boechera perstellata (Braun's rockcress) and widespread B. laevigata to acclimate to change. We investigated the phenotypic plasticity of growth, biomass allocation, and leaf morphology of individuals of B. perstellata and B. laevigata propagated from seed collected from several populations throughout their ranges in a growth chamber experiment to assess their capacity to acclimate. Concurrently, we assessed the genetic diversity of sampled populations using 17 microsatellite loci to assess evolutionary potential. Plasticity was limited in both rare B. perstellata and widespread B. laevigata, but differences in the plasticity of root traits between species suggest that B. perstellata may have less capacity to acclimate to change. In contrast to its widespread congener, B. perstellata exhibited no plasticity in response to temperature and weaker plastic responses to water availability. As expected, B. perstellata also had lower levels of observed heterozygosity than B. laevigata at the species level, but population-level trends in diversity measures were inconsistent due to high heterogeneity among B. laevigata populations. Overall, the ability of phenotypic plasticity to broadly explain the rarity of B. perstellata versus commonness of B. laevigata is limited. However, some contextual aspects of our plasticity findings compared with its relatively low genetic variability may shed light on the narrow range and habitat associations of B. perstellata and suggest its vulnerability to climate warming due to acclimatory and evolutionary constraints.

Substrate Heterogeneity as a Trigger for Species Diversity in Marine Benthic Assemblages

Many studies show that habitat complexity or habitat diversity plays a major role in biodiversity throughout different spatial scales: as structural heterogeneity increases, so does the number of available (micro-) habitats for the potential species inventory. The capability of housing species (even rare species) increases rapidly with increasing habitat heterogeneity. However, habitat complexity is not easy to measure in marine sublittoral sediments. In our study, we came up with a proposal to estimate sublittoral benthic habitat complexity using standard underwater video techniques. This tool was subsequently used to investigate the effect of habitat complexity on species richness in comparison to other environmental parameters in a marine protected area situated in the Fehmarn Belt, a narrow strait in the southwestern Baltic Sea. Our results show that species richness is significantly higher in heterogeneous substrates throughout all considered sediment types. Congruently, the presence of rare species increases with structural complexity. Our findings highlight the importance of the availability of microhabitats for benthic biodiversity as well as of the study area for regional ecosystem functioning.

Algae obscura: The potential of rare species as model systems

Model organism research has provided invaluable knowledge about foundational biological principles. However, most of these studies have focused on species that are in high abundance, easy to cultivate in the lab, and represent only a small fraction of extant biodiversity. Here, we present three examples of rare algae with unusual features that we refer to as "algae obscura." The Cyanidiophyceae (Rhodophyta), Glaucophyta, and Paulinella (rhizarian) lineages have all transitioned out of obscurity to become models for fundamental evolutionary research. Insights have been gained into the prevalence and importance of eukaryotic horizontal gene transfer, early Earth microbial community dynamics, primary plastid endosymbiosis, and the origin of Archaeplastida. By reviewing the research that has come from the exploration of these organisms, we demonstrate that underappreciated algae have the potential to help us formulate, refine, and substantiate core hypotheses and that such organisms should be considered when establishing future model systems.

Current State of Rare and Endangered Barbels of the Genus Luciobarbus Heckel, 1843 in the Aral-Syrdarya Basin (Kazakhstan) and Prospects for Their Conservation (A Review)

The current status of the barbels inhabiting the Kazakhstan section of the Syrdarya River needs special study, as has been noted since the second half of the 20th century. Stocks of commercial fish valuable in the past as barbels in the Aral-Syrdarya basin are now catastrophically reduced as a result of anthropogenic impact on the ichthyofauna and natural environment of the Aral Sea region. The study of the condition; abundance and distribution range is necessary to determine measures for their restoration in natural habitats and their breeding in fish farms. Research on the biotechnology of barbel breeding with subsequent acclimatization and reacclimatization of these fish species will not only improve the composition of the ichthyofauna of the Aral-Syrdarya basin, but also preserve the genetic potential of natural populations. At present, the only way to restore the population of the Aral barbel is stocking hatchery reared juveniles in natural environments. Under the current situation, a way forward is seen in the creation of domesticated replacement-broodstocks of barbels. As a result of the influence of anthropogenic factors, the populations of this species have come to almost complete degradation and depletion and require the development and adoption of urgent measures for their conservation and restoration through reintroduction, which is a priority and urgent task for the fisheries of the republic.

Thismiakenyirensis (Thismiaceae), a new species from Taman Negeri Kenyir, Terengganu, Peninsular Malaysia

A new mycoheterotrophic species, Thismiakenyirensis Siti-Munirah & Dome from Peninsular Malaysia, is described and illustrated. Thismiakenyirensis differs from other previously described species in the following characteristics: the flower tube is completely orange, with alternating darker and paler-coloured longitudinal lines on the outer and inner surfaces, the outer tepals are ovate (petaloid), the inner tepals are narrowly lanceolate, each ending with a long appendage. According to the IUCN Red List categories and criteria, T.kenyirensis is provisionally classified as Least Concern.

Testing the passive sampling hypothesis: The role of dispersal in shaping microbial species-area relationship

Dispersal is one of the key processes determining biodiversity. The passive sampling hypothesis, which emphasizes dispersal processes, suggests that larger habitats receive more species from the species pool as the main mechanism leading to more species in larger habitats than in smaller habitats (i.e., species-area relationships). However, the specific mechanisms by which dispersion shapes biodiversity still need to be discovered due to the difficulties of quantifying dispersal and the influence of multiple factors. Solving the above problem with a designed experiment is necessary to test the passive sampling hypothesis. This study designed a passive sampling experiment using sterile filter paper to quantify the microbial diffusion process, excluding the effects of pure sampling effects, habitat heterogeneity, and extinction processes. The results of high-throughput sequencing showed that a larger filter paper could receive more colonists, and the passive sampling hypothesis of SAR was confirmed. Dispersal shaped SAR by increasing species richness, especially rare species, and increasing the species replacement rate between habitats. These two processes are the mechanisms by which dispersal shapes biodiversity patterns. Compared with the results of this study, the commonly used mathematical model of passive sampling was able to predict the richness of non-rare species accurately but underestimated the richness of rare species. Underestimating rare species by mathematical models of passive sampling is more severe in small habitats. These findings provide new insights into the study of dispersal processes and the mechanism of species-area relationships.

Tropical forest loss impoverishes arboreal mammal assemblages by increasing tree canopy openness

Landscape-scale deforestation poses a major threat to global biodiversity, not only because it limits habitat availability, but also because it can drive the degradation of the remaining habitat. However, the multiple pathways by which deforestation directly and indirectly affects wildlife remain poorly understood, especially for elusive forest-dependent species such as arboreal mammals. Using structural equation models, we assessed the direct and indirect effects of landscape forest loss on arboreal mammal assemblages in the Lacandona rainforest, Mexico. We placed camera traps in 100 canopy trees, and assessed the direct effect of forest cover and their indirect effects via changes in tree basal area and canopy openness on the abundance and diversity (i.e., species richness and exponential of Shannon entropy) of arboreal mammals. We found that forest loss had negative indirect effects on mammal richness through the increase of tree canopy openness. This could be related to the fact that canopy openness is usually inversely related to resource availability and canopy connectivity for arboreal mammals. Furthermore, independently of forest loss, the abundance and richness of arboreal mammals was positively related to tree basal area, which is typically higher in old-growth forests. Thus, our findings suggest that arboreal mammals generally prefer old-growth vegetation with relatively low canopy openness and high tree basal area. However, unexpectedly, forest loss was directly and positively related to the abundance and richness of mammals, probably due to a crowding effect, a reasonable possibility given the relatively short history (~40 years) of deforestation in the study region. Conversely, the Shannon diversity was not affected by the predictors we evaluated, suggesting that rare mammals (not the common species) are the ones most affected by these changes. All in all, our findings emphasize that conservation measures ought to focus on increasing forest cover in the landscape, and preventing the loss of large trees in the remaining forest patches.

Rarity begets rarity: Social and environmental drivers of rare organisms in cities

Cities are sometimes characterized as homogenous with species assemblages composed of abundant, generalist species having similar ecological functions. Under this assumption, rare species, or species observed infrequently, would have especially high conservation value in cities for their potential to increase functional diversity. Management to increase the number of rare species in cities could be an important conservation strategy in a rapidly urbanizing world. However, most studies of species rarity define rarity in relatively pristine environments where human management and disturbance is minimized. We know little about what species are rare, how many species are rare, and what management practices promote rare species in urban environments. Here, we identified which plants and species of birds and bees that control pests and pollinate crops are rare in urban gardens and assessed how social, biophysical factors, and cross-taxonomic comparisons influence rare species richness. We found overwhelming numbers of rare species, with more than 50% of plants observed classified as rare. Our results highlight the importance of women, older individuals, and gardeners who live closer to garden sites in increasing the number of rare plants within urban areas. Fewer rare plants were found in older gardens and gardens with more bare soil. There were more rare bird species in larger gardens and more rare bee species for which canopy cover was higher. We also found that in some cases, rarity begets rarity, with positive correlations found between the number of rare plants and bee species and between bee and bird species. Overall, our results suggest that urban gardens include a high number of species existing at low frequency and that social and biophysical factors promoting rare, planned biodiversity can cascade down to promote rare, associated biodiversity.

A revision of the North American genus Proctorus (Coleoptera, Curculionidae, Ellescini) with descriptions of two new species

The rarely collected North American endemic genus Proctorus (Coleoptera, Curculionidae, Ellescini) has hitherto contained two described species, P.armatus LeConte, 1876 and P.decipiens (LeConte, 1876). Here, Proctorus is revised and two new species, namely P.emarginatus sp. nov. and P.truncatus sp. nov., are described. Lectotypes for P.armatus and P.decipiens are designated from known syntypes. All four species in the genus are associated with Salicaceae, but, in addition to differences in external and genital morphology, there is also evidence of differing host plant usage between the species. A photographic key to the four species is provided to facilitate identification.

Community‐level phylogenetic diversity does not differ between rare and common lineages across tallgrass prairies in the northern Great Plains

Niche differentiation has served as one explanation for species coexistence, and phylogenetic relatedness provides a means to approximate how ecologically similar species are to each other. To explore the contribution of rare species to community phylogenetic diversity, we sampled 21 plant communities across the Prairie Coteau ecoregion, an area of high conservation concern. We used breakpoint analysis through the iterative addition of less abundant species to the phylogenetic tree for each community to assess the contribution of rare species to community phylogenetic diversity. We also quantify the phylogenetic signal of abundance using Blomberg's K statistic and calculated the phylogenetic similarity between rare and common species using a phylogenetic beta‐diversity metric (D_nn). To estimate the phylogenetic structuring of these prairie communities, we calculated two common metrics that capture evolutionary relatedness at different scales (MPD and MNTD). Additionally, we examine the correlation between Faith's PD, MPD, and MNTD and species richness. We found rare species do not generally contribute higher levels of phylogenetic diversity than common species. Eight communities had significant breakpoints, with only four communities having an increasing trend for the rarest species. The phylogenetic signal for abundance was low but significant in only four communities, and communities had lower phylogenetic diversity than expected from the regional species pool. Finally, the strength of the correlation between species richness and phylogenetic diversity was mixed. Our results indicate niche differentiation does not explain the persistence of rare species in tallgrass prairies, as they were more closely related than expected from random, suggesting high functional redundancy between rare and common species. This is promising for the long‐term resilience of this ecosystem, but only insofar as enough species remain in the system. With ongoing biodiversity loss, it is essential that we understand the role rare species play in their communities.

Eco-evolutionary causes and consequences of rarity in plants: a meta-analysis

Species differ dramatically in their prevalence in the natural world, with many species characterized as rare due to restricted geographic distribution, low local abundance and/or habitat specialization. We investigated the ecoevolutionary causes and consequences of rarity with phylogenetically controlled metaanalyses of population genetic diversity, fitness and functional traits in rare and common congeneric plant species. Our syntheses included 252 rare species and 267 common congeners reported in 153 peer-reviewed articles published from 1978 to 2020 and one manuscript in press. Rare species have reduced population genetic diversity, depressed fitness and smaller reproductive structures than common congeners. Rare species also could suffer from inbreeding depression and reduced fertilization efficiency. By limiting their capacity to adapt and migrate, these characteristics could influence contemporary patterns of rarity and increase the susceptibility of rare species to rapid environmental change. We recommend that future studies present more nuanced data on the extent of rarity in focal species, expose rare and common species to ecologically relevant treatments, including reciprocal transplants, and conduct quantitative genetic and population genomic analyses across a greater array of systems. This research could elucidate the processes that contribute to rarity and generate robust predictions of extinction risks under global change.

An Extended dataset of occurrences of species listed in Resolution 6 of the Bern Convention from Ukraine

Background

The dataset includes georeferenced occurrences of species listed in Annex I of Resolution 6 of the Bern Convention and, partly, in the Red Data Book of Ukraine. The dataset was compiled within the work of NGO "Ukrainian Nature Conservation Group" aimed to prepare a Shadow list of Emerald Network (European network Areas of Special Conservation Interest) in Ukraine - newly proposed territories aimed at conservation of particular species and habitats mentioned in Resolution 4 and 6 of the Bern Convention. The list was prepared in 2017-2020 for expanding the already existing Emerald Network of Ukraine. Based on actual registrations of flora and fauna collected and gathered by scientists and naturalists in a form of dataset, which is described in the following paper.

New information

This dataset provides information about 29,938 occurrences of species from the territory of Ukraine listed in Annex I of Resolution 6 of the Bern Convention, as well as in the Red Data Book of Ukraine. This is the largest public dataset on occurrences of rare and endangered species from Ukraine till now. Data presented here laid the foundations for the proposal of 106 approved Emerald Network sites (2019), as well as for 148 Emerald Network sites that were nominated in 2020. New insights on the endemic species Centaureapseudoleucolepis Kleopow is provided, which was previously considered to be extinct, according to the IUCN Red List.

Sampling and modelling rare species: Conceptual guidelines for the neglected majority

Biodiversity conservation faces a methodological conundrum: Biodiversity measurement often relies on species, most of which are rare at various scales, especially prone to extinction under global change, but also the most challenging to sample and model. Predicting the distribution change of rare species using conventional species distribution models is challenging because rare species are hardly captured by most survey systems. When enough data are available, predictions are usually spatially biased towards locations where the species is most likely to occur, violating the assumptions of many modelling frameworks. Workflows to predict and eventually map rare species distributions imply important trade-offs between data quantity, quality, representativeness and model complexity that need to be considered prior to survey and analysis. Our opinion is that study designs need to carefully integrate the different steps, from species sampling to modelling, in accordance with the different types of rarity and available data in order to improve our capacity for sound assessment and prediction of rare species distribution. In this article, we summarize and comment on how different categories of species rarity lead to different types of occurrence and distribution data depending on choices made during the survey process, namely the spatial distribution of samples (where to sample) and the sampling protocol in each selected location (how to sample). We then clarify which species distribution models are suitable depending on the different types of distribution data (how to model). Among others, for most rarity forms, we highlight the insights from systematic species-targeted sampling coupled with hierarchical models that allow correcting for overdispersion and spatial and sampling sources of bias. Our article provides scientists and practitioners with a much-needed guide through the ever-increasing diversity of methodological developments to improve the prediction of rare species distribution depending on rarity type and available data.

Database of fish fauna in a highly urbanised river (Tsurumi River Basin, Kanagawa, Japan)

Background

Urbanisation has facilitated changes in the hydrological cycle, sediment dynamics and habitat loss and it has had a tremendous impact on river ecosystems. Moreover, the invasion of non-native species reduces the number of native species with the progress of urbanisation, thereby resulting in the homogenisation of fish fauna and significant decrease in diversity. However, the effects of urbanisation on fish fauna vary depending on the region, degree of urbanisation and number of years since the construction of the city. Hence, it is necessary to collect information on how fish fauna changes due to urbanisation in different regions. The target site of the present study is the Tsurumi River, of which approximately 85% of the basin is urbanised and many of the river channels have been affected by straightening and concrete channelling. Monitoring of biota has been conducted mainly in downstream areas; however, data on fish fauna in upstream areas and tributaries of the river, which have been substantially affected by urbanisation, are lacking.

New information

Surveys were conducted at 71 sites in the Tsurumi River Basin during summers and winters, focusing on river channels that have been straightened or converted to concrete channels due to urbanisation. As a result of this investigation, 10 families, 28 species and 9,335 individuals were collected. Some of the fish collected included rare species, such as Tanakialanceolata, Lefuaechigonia and Pseudobagrustokiensis, indicating that, even in rivers that have been severely impacted by human activities, there are still rare indigenous species living there, albeit in limited numbers. In addition, Misgurnus sp. (clade B2), Micropterussalmoides, Lepomismacrochirus and Poeciliareticulata were confirmed to be non-native species. Misgurnus sp. (clade B2) was widespread; however, populations of carnivorous non-native alien species were small. The data are all accessible from the document "database_fish_urban_tsurumi" (https://ipt.pensoft.net/manage/resource?r=database_fish_urban_tsurumi).

Rare Species-Driven Diversity-Ecosystem Multifunctionality Relationships are Promoted by Stochastic Community Assembly

The relative functional importance of rare and abundant species in driving relationships between biodiversity and ecosystem functions (BEF) remains unknown. Here, we investigated the functional roles of rare and abundant species diversity (multitrophic soil organism groups) on multifunctionality derived from 16 ecosystem functions in 228 agricultural fields relating to soil and crop health. The results revealed that the diversity of rare species, rather than of abundant species, was positively related to multifunctionality. Abundant taxa tended to maintain a larger number of functions than rare taxa, while rare subcommunity contributed more phylotypes supporting to the single ecosystem functions. Community assembly processes were closely related to the ecosystem functional performance of soil biodiversity, only observed in rare subcommunity. Higher relative contributions of stochastic assembly processes promoted the positive effects of diversity of rare taxa on multifunctionality, while reducing their diversity and multifunctionality overall. Our results highlight the importance of rare species for ecosystem multifunctionality and elucidate the linkage between ecological assembly processes and BEF relationships.

Many bee species, including rare species, are important for function of entire plant-pollinator networks

It is important to understand how biodiversity, including that of rare species, affects ecosystem function. Here, we consider this question with regard to pollination. Studies of pollination function have typically focused on pollination of single plant species, or average pollination across plants, and typically find that pollination depends on a few common species. Here, we used data from 11 plant-bee visitation networks in New Jersey, USA, to ask whether the number of functionally important bee species changes as we consider function separately for each plant species in increasingly diverse plant communities. Using rarefaction analysis, we found the number of important bee species increased with the number of plant species. Overall, 2.5 to 7.6 times more bee species were important at the community scale, relative to the average plant species in the same community. This effect did not asymptote in any of our datasets, suggesting that even greater bee biodiversity is needed in real-world systems. Lastly, on average across plant communities, 25% of bee species that were important at the community scale were also numerically rare within their network, making this study one of the strongest empirical demonstrations to date of the functional importance of rare species.

Anthropogenic fragmentation increases risk of genetic decline in the threatened orchid Platanthera leucophaea

Protecting biodiversity requires an understanding of how anthropogenic changes impact the genetic processes associated with extinction risk. Studies of the genetic changes due to anthropogenic fragmentation have revealed conflicting results. This is likely due to the difficulty in isolating habitat loss and fragmentation, which can have opposing impacts on genetic parameters. The well-studied orchid, Platanthera leucophaea, provides a rich dataset to address this issue, allowing us to examine range-wide genetic changes. Midwestern and Northeastern United States. We sampled 35 populations of P. leucophaea that spanned the species' range and varied in patch composition, degree of patch isolation, and population size. From these populations we measured genetic parameters associated with increased extinction risk. Using this combined dataset, we modeled landscape variables and population metrics against genetic parameters to determine the best predictors of increased extinction risk. All genetic parameters were strongly associated with population size, while development and patch isolation showed an association with genetic diversity and genetic structure. Genetic diversity was lowest in populations with small census sizes, greater urbanization pressures (habitat loss), and small patch area. All populations showed moderate levels of inbreeding, regardless of size. Contrary to expectation, we found that critically small populations had negative inbreeding values, indicating non-random mating not typically observed in wild populations, which we attribute to selection for less inbred individuals. The once widespread orchid, Platanthera leucophaea, has suffered drastic declines and extant populations show changes in the genetic parameters associated with increased extinction risk, especially smaller populations. Due to the important correlation with risk and habitat loss, we advocate continued monitoring of population sizes by resource managers, while the critically small populations may need additional management to reverse genetic declines.

Biodiversity of macrophyte communities and associated aquatic organisms in lakes of the Vologda Region (north-western Russia)

BACKGROUND

This paper provides current data on the biodiversity of boreal lakes of the Vologda Region (north-western Russia), including macrophytes (vascular plants and macroscopic algae) and macrophyte inhabitants (invertebrates and microalgae). The raw data, given in two datasets (Sampling event dataset and an Occurrence dataset) and presented in the form of GBIF-mediated data, were collected from 139 lakes (macrophytes between 2005 and 2021, macrophyte inhabitants between 2014 and 2020). The dataset contains materials on the diversity of vascular plants (Tracheophyta, 3225 occurrences; Bryophyta, 155; Marchantiophyta, 16), macro- and microalgae (Ochrophyta, 546 occurrences; Chlorophyta, 193; Charophyta, 153; Cyanobacteria, 139; Cryptophyta, 86; Myzozoa, 33; Euglenozoa, 27; Rhodophyta, 8; Bigyra, 1) and aquatic invertebrates (Arthropoda, 1408 occurrences; Annelida, 487; Mollusca, 263; Platyhelminthes, 36; Cnidaria, 11). This paper summarises previously unpublished materials in a standardised form.

NEW INFORMATION

The paper summarises the data collected during the long-term phytodiversity studies in a series of lakes of different types (Vologda Region, north-western Russia). Data on algae and invertebrates diversity were obtained in 60 different plant communities of aquatic, semi-aquatic and coastal plants or their combinations. A total of 6787 occurrences were included in the dataset, published in the global biodiversity database (GBIF) for the first time. According to the GBIF taxonomic backbone, the dataset comprised 837 taxa, including 711 lower-rank taxa (species, subspecies, varieties, forms). New records of 47 species rare and protected in the Vologda Region are given: 43 species of plants, three species of animals and one species of Cyanobacteria.

Macrophyte diversity in rivers and streams of the Vologda Region and several other regions of Russia

BACKGROUND

The data paper contains the authors' materials on the diversity of macrophytes, macroscopic plants regardless of their taxonomic position, in rivers and streams of East European Russia and Western Siberia. These data, collected on 247 rivers and 32 streams in 13 administrative regions of the Russian Federation, were provided as an occurrence dataset presented in the form of GBIF-mediated data. The main portion of the data was obtained in water objects of the Vologda Region (5201 occurrences). In addition, occurrences from the Arkhangelsk Region (347 occurrences), Khanty-Mansi Autonomous Okrug (159), Yaroslavl Region (132), Novgorod Region (97), Kostroma Region (41), Republic of Karelia (31), Sverdlovsk Region (29), Komi Republic (28), Orenburg Region (26), Chelyabinsk Region (22), Voronezh Region (22) and Tyumen Region (18) were given. The studies were carried out mainly in the southern and middle taiga and, to a lesser extent, in the northern taiga and the forest-steppe. The analysed watercourses belong to five drainage basins: the Azov Sea, the Baltic Sea, the White Sea, the Caspian Sea and the Kara Sea. The dataset contains materials on the diversity of Plantae (6094 occurrences) and Chromista (59 occurrences). This paper, in a standardised form, summarises mostly unpublished materials on the biodiversity of lotic ecosystems.

NEW INFORMATION

The paper summarises the data obtained in long-term studies of phytodiversity in a range of rivers and streams of East European Russia and, fragmentarily, Western Siberia. A total of 6153 occurrences were included in the dataset. According to the GBIF taxonomic backbone, the dataset comprises 292 taxa, including 280 lower-rank taxa (species, subspecies, varieties) and 12 taxa identified to the genus level. All the occurrences are published openly through the Global Biodiversity Information Facility (GBIF) for the first time. Most of the data were stored in field diaries and, thus, by adding the data in GBIF, we believe that other researchers could benefit from it.

A New Species of Dynamine Hübner, [1919] (Lepidoptera: Nymphalidae: Biblidinae) from the Atlantic Forest in Southeastern Brazil

A new butterfly species, Dynamine sideria Rosa & Freitas sp. nov. (Nymphalidae: Biblidinae), is described from the Atlantic Forest in Southeastern Brazil. The new species is known from only seven adult specimens and three observation records (two from photographs) in five sites, including a large forest reserve, forest fragments on a disturbed landscape, and a backyard in a dense urban site. Illustrations of adults and male genitalia are provided, as well as a distribution map and limited natural history notes.

The rare and enigmatic mayfly Prosopistoma pennigerum (Müller, 1785): Habitat characteristics, recent records from the Volga (Russia) and Vjosa (Albania) rivers, and a proposal for flagship species status

Nymphs of all 29 described Prosopistoma species share a conspicuous synapomorphy: a round mesonotal shield, the carapace. They occur in the Palaearctic (nine species), the Oriental (12 species) and the Afrotropic as well as Australian regions (six and two species, respectively). Relatively little is known about their ecology, but past and extant distribution patterns indicate an association with undisturbed conditions. Prosopistoma pennigerum is a rare European mayfly with conspicuous nymphs. Formerly common in large rivers, it has been extirpated from central Europe over the last century.This study evaluated general habitat characteristics and human pressures for historical and current records of this rare species. Prosopistoma pennigerum is currently known from only three European rivers, all with gravel substrates, naturally dynamic discharge regimes, summer-warm water temperatures, and little human pressure.This study showed that nymphs from the Vjosa and upper Volga rivers, two relatively natural watercourses 2,000 km apart, are morphologically indistinguishable, and show no variation across a ca. 600-bp fragment of the mitochondrial cytochrome c oxidase I gene.Flagship species were first designated in the 1980s, when charismatic species with high habitat requirements such as the Bengal tiger or the giant panda, but also invertebrates are used to communicate conservation and protection needs. We propose that Europe's rarest mayfly P. pennigerum, with its unusual nymphs and remaining populations in naturally dynamic river courses, can serve as a flagship species promoting the preservation of ecological integrity in European rivers.

Occurrences of Threatened Species included in the Third Edition of the Red Data Book of the Komi Republic (Russia)

BACKGROUND

The purpose of the data paper was to introduce into scientific literature the results of scientific work carried out for the third edition of the 'Red Data Book of the Komi Republic'. The article reflects methodological approaches to the formation of a list of rare and in need of protection species and describes the corresponding datasets published in GBIF.

NEW INFORMATION

Information about 7,187 occurrences of 438 rare species and infraspecies included in the third edition of the 'Red Data Book of the Komi Republic' have been published.

A case for multiscale habitat selection studies of small mammals

Habitat information for small mammals typically consists of anecdotal descriptions or infrequent analyses of habitat use, which often are reported erroneously as signifying habitat preference, requirements, or quality. Habitat preferences can be determined only by analysis of habitat selection, a behavioral process that results in the disproportionate use of one resource over other available resources and occurs in a hierarchical manner across different environmental scales. North American chipmunks (Neotamias and Tamias) are a prime example of the lack of studies on habitat selection for small mammal species. We used the Organ Mountains Colorado chipmunk (N. quadrivittatus australis) as a case study to determine whether previous descriptions of habitat in the literature were upheld in a multiscale habitat selection context. We tracked VHF radiocollared chipmunks and collected habitat information at used and available locations to analyze habitat selection at three scales: second order (i.e., home range), third order (i.e., within home range), and microhabitat scales. Mean home range was 2.55 ha ± 1.55 SD and did not differ between sexes. At the second and third order, N. q. australis avoided a coniferous forest land cover type and favored particular areas of arroyos (gullies) that were relatively steep-sided and greener and contained montane scrub land cover type. At the microhabitat scale, chipmunks selected areas that had greater woody plant diversity, rock ground cover, and ground cover of coarse woody debris. We concluded that habitat selection by N. q. australis fundamentally was different from descriptions of habitat in the literature that described N. quadrivittatus as primarily associated with coniferous forests. We suggest that arroyos, which are unique and rare on the landscape, function as climate refugia for these chipmunks because they create a cool, wet microclimate. Our findings demonstrate the importance of conducting multiscale habitat selection studies for small mammals to ensure that defensible and enduring habitat information is available to support appropriate conservation and management actions.

Microhabitats associated with solar energy development alter demography of two desert annuals

Political and economic initiatives intended to increase energy production while reducing carbon emissions are driving demand for solar energy. Consequently, desert regions are now targeted for development of large-scale photovoltaic solar energy facilities. Where vegetation communities are left intact or restored within facilities, ground-mounted infrastructure may have negative impacts on desert-adapted plants because it creates novel rainfall runoff and shade conditions. We used experimental solar arrays in the Mojave Desert to test how these altered conditions affect population dynamics for a closely related pair of native annual plants: rare Eriophyllum mohavense and common E. wallacei. We estimated aboveground demographic rates (seedling emergence, survivorship, and fecundity) over 7 yr and used seed bank survival rates from a concurrent study to build matrix models of population growth in three experimental microhabitats. In drier years, shade tended to reduce survival of the common species, but increase survival of the rare species. In a wet year, runoff from panels tended to increase seed output for both species. Population growth projections from microhabitat-specific matrix models showed stronger effects of microhabitat under wetter conditions, and relatively little effect under dry conditions (lack of rainfall was an overwhelming constraint). Performance patterns across microhabitats in the wettest year differed between rare and common species. Projected growth of E. mohavense was substantially reduced in shade, mediated by negative effects on aboveground demographic rates. Hence, the rare species were more susceptible to negative effects of panel infrastructure in wet years that are critical to seed bank replenishment. Our results suggest that altered shade and water runoff regimes associated with energy infrastructure will have differential effects on demographic transitions across annual species and drive population-level processes that determine local abundance, resilience, and persistence.

Microhabitats associated with solar energy development alter demography of two desert annuals

Political and economic initiatives intended to increase energy production while reducing carbon emissions are driving demand for solar energy. Consequently, desert regions are now targeted for development of large-scale photovoltaic solar energy facilities. Where vegetation communities are left intact or restored within facilities, ground-mounted infrastructure may have negative impacts on desert-adapted plants because it creates novel rainfall runoff and shade conditions. We used experimental solar arrays in the Mojave Desert to test how these altered conditions affect population dynamics for a closely related pair of native annual plants: rare Eriophyllum mohavense and common E. wallacei. We estimated aboveground demographic rates (seedling emergence, survivorship, and fecundity) over 7 yr and used seed bank survival rates from a concurrent study to build matrix models of population growth in three experimental microhabitats. In drier years, shade tended to reduce survival of the common species, but increase survival of the rare species. In a wet year, runoff from panels tended to increase seed output for both species. Population growth projections from microhabitat-specific matrix models showed stronger effects of microhabitat under wetter conditions, and relatively little effect under dry conditions (lack of rainfall was an overwhelming constraint). Performance patterns across microhabitats in the wettest year differed between rare and common species. Projected growth of E. mohavense was substantially reduced in shade, mediated by negative effects on aboveground demographic rates. Hence, the rare species were more susceptible to negative effects of panel infrastructure in wet years that are critical to seed bank replenishment. Our results suggest that altered shade and water runoff regimes associated with energy infrastructure will have differential effects on demographic transitions across annual species and drive population-level processes that determine local abundance, resilience, and persistence.

A new method for broad-scale modeling and projection of plant assemblages under climatic, biotic, and environmental cofiltering

There is increasing interest in broad-scale analysis, modeling, and prediction of the distribution and composition of plant species assemblages under climatic, environmental, and biotic filtering, particularly for conservation purposes. We devised a method (broad-scale analysis & modeling of plant assemblages under climatic-biotic-environmental co-filtering, BAM-PACC) for reliably predicting the impact of climate change on arbitrarily large assemblages of plant communities, while also considering competing biotic and abiotic factors. When applied to a large set of plant communities in the Swiss Alps, BAM-PACC explained presences/absences of 175 plant species in 608 plots with >87% cross-validated accuracy, predicted decreases in α, β, and γ diversity by 2040 under both moderate and extreme climate scenarios, and identified plant species likely to be favored/disfavored by climate change. BAM-PACC also revealed the importance of topography and soil in determining the distribution of plant species and their response to climate change, and showed the overriding importance of temperature extremes rather than averages. BAM-PACC was able to address a number of challenging research problems, such as scaling to large numbers of species, exploiting species relationships, dealing with species rarity, and overwhelming proportion of absences in the presence/absence matrix. By handling hundreds/thousands of plants and plots simultaneously over large areas, BAM-PACC can help broad-scale conservation of plant species under climate change, as it allows species that require urgent conservation planning and policies (assisted migration, seed conservation, ex-situ conservation) to be detected and prioritized. BAM-PACC can also increase the practicality of assisted colonization of plant species, by helping to prevent ill-advised introduction of plant species with limited future survival probability in a certain area. This article is protected by copyright. All rights reserved.

Integrative Taxonomic, Ecological and Genotyping Study of Charophyte Populations from the Egyptian Western-Desert Oases and Sinai Peninsula

Present-day information available on the charophyte macroalgae in Egypt, including their phylogenetic affinities, remains largely incomplete. In this study, nine charophyte populations were collected from different aquatic biotopes across the Egyptian Western-Desert Oases and Sinai Peninsula. All populations were investigated using an integrative polyphasic approach including phylogenetic analyses inferred from the chloroplast-encoded gene (rbcL) and the internal transcribed spacer (ITS1) regions, in parallel with morphotaxonomic assignment, ultrastructure of the oospore walls, and autecology. The specimens identified belonged to the genera Chara, Nitella, and Tolypella, with predominance of the first genus to which five species were assigned though they presented some interesting aberrant taxonomic features: C. aspera, C. contraria, C. globata, C. tomentosa, and C. vulgaris. Based on our integrative study, the globally rare species C. globata was reported for the second time for the whole African continent. The genus Nitella was only represented by N. flagellifera, and based on the available literature, it is a new record for North Africa. Noteworthy, an interesting Tolypella sp., morphologically very similar to T. glomerata, was collected and characterized and finally designated with the working name 'Tolypella sp. PBA-1704 from a desert, freshwater wetland', mainly based on its concatenated rbcL+ITS1 phylogenetic position. This study not only improved our understanding on the diversity, biogeography and autecological preferences of charophytes in Egypt, but it also broadened our knowledge on this vulnerable algal group in North Africa, emphasizing the need of more in-depth research work in the future, particularly in the less-impacted desert habitats.

Potamophylax coronavirus sp. n. (Trichoptera: Limnephilidae), a new species from Bjeshkët e Nemuna National Park in the Republic of Kosovo, with molecular and ecological notes

Background

The Western Balkans are an important hotspot of caddisfly diversity in Europe, with several microscale endemics, many of which were discovered during the recent years. The genus Potamophylax Wallengren, 1891 likely originated and diversified in Europe, with the Balkan Peninsula being one of the most important diversity hotspots.

New information

In this paper, we describe the new species Potamophylax coronavirus sp. n. from Bjeshkët e Nemuna National Park in the Republic of Kosovo. The new species belongs to the Potamophylax winneguthi species group and is morphologically most similar to Potamophylax juliani Kumanski, 1999, currently known only from Bulgaria and Potamophylax winneguthi Klapalek, 1902, known from Bosnia and Herzegovina and Serbia. The male of the new species differs from its most similar congeners mainly in exhibiting: (1) elongated subrectangular superior appendages in lateral view; (2) hardly acuminate, almost rounded apex of intermediate appendages; (3) differently shaped, irregular and higher inferior appendages; (4) narrow spinate area, roughly rectangular in dorsal view, slightly wider at the base and (5) different paramere shape and/or spine pattern. The new species also differs by its considerably smaller size and association with open, high altitude eucrenal zones.The uncorrected interspecific pairwise distance between P. coronavirus and other species of the P. winneguthi species group is on par with those amongst other recognised species in the group, as well as with the yet ambiguously identified taxa from the Sharr, Rila and Bajgorë Mountains.The new species is most probably a microendemic of Bjeshkët e Nemuna, thus highlighting further this area as an important hotspot of caddisfly biodiversity in Europe.

The Assessment and the Within-Plant Variation of the Morpho-Physiological Traits and VOCs Profile in Endemic and Rare Salvia ceratophylloides Ard. (Lamiaceae)

Salvia ceratophylloides (Ard.) is an endemic and rare plant species recently rediscovered as very few individuals at two different Southern Italy sites. The study of within-plant variation is fundamental to understand the plant adaptation to the local conditions, especially in rare species, and consequently to preserve plant biodiversity. Here, we reported the variation of the morpho-ecophysiological and metabolic traits between the sessile and petiolate leaf of S. ceratophylloides plants at two different sites for understanding the adaptation strategies for surviving in these habitats. The S. ceratophylloides individuals exhibited different net photosynthetic rate, maximum quantum yield, light intensity for the saturation of the photosynthetic machinery, stomatal conductance, transpiration rate, leaf area, fractal dimension, and some volatile organic compounds (VOCs) between the different leaf types. This within-plant morpho-physiological and metabolic variation was dependent on the site. These results provide empirical evidence of sharply within-plant variation of the morpho-physiological traits and VOCs profiles in S. ceratophylloides, explaining the adaptation to the local conditions.

Sampling Efforts for Estimating Fish Species Richness in Western USA River Sites

Fish species richness is an indicator of river ecological condition but it is particularly difficult to estimate in large unwadeable rapidly flowing rivers. Intensive multi-gear sampling is time consuming, logistically complex and expensive. However, insufficient sampling effort underestimates species richness and yields inaccurate data about the ecological condition of river sites. We raft-electrofished 10 river sites in 10 different ecoregions and six western USA states for distances equal to 300 times their mean wetted channel widths (MCWs) to estimate the effort needed to approach asymptotes in fish species richness. To collect 90% of the observed fish species at the sites, we found that an average of 150 MCWs (ranging 80-210 MCWs) were needed, with the number of MCWs increasing in rivers with a higher proportion of spatially rare species. Frequently, the second or third additional 100 MCWs produced only one or two additional singletons or doubletons (species occurring only once or twice at a site). Before initiating sampling programs for adequately estimating species richness, we recommend assessing sampling effort, particularly if rare or uncommon species are expected or desired.

Distribution Patterns of Grasshoppers and Their Kin over the Eurasian Steppes

Simple Summary

The steppe zone is the huge area in temperate Eurasia where different grasslands form the main type of vegetation. The main part of this life zone has been transformed by human activity and used for crop cultivation (mainly wheat) and livestock. Regional and local transformations and/or climate changes can result in some shifts in species and population distribution of Orthoptera. Over this area, the climatic conditions and the dominated grasslands are suitable for numerous grasshoppers and their relatives, especially the graminivorous ones. The general level of their diversity is usually high. Many species are very abundant and may become important pests. However, there are also many rare species. The main aims of this paper are to reveal general patterns of Orthoptera distribution in the Eurasian steppes, to evaluate long-term trends of changes in distribution of taxa and populations, and to estimate the potential for population changes relative to human activity and global warming trends.

Abstract

The main aims of this paper are to reveal general patterns of Orthoptera distribution in the Eurasian steppes, to evaluate long-term trends of changes in distribution of taxa and populations, and to estimate the potential for population changes relative to human activity and global warming trends. The main publications concerning diversity and distribution of these insects over the steppes are analyzed. The fauna of the Eurasian steppes includes more than 440 species of Orthoptera. The general distribution of grasshoppers and their kin in the Eurasian steppes reflects their common associations with different grasslands. The species richness increases from the relatively cold forest-steppes to the semi-deserts with their warm summer. There are some endemic or subendemic taxa, including the tribe Onconotini (Tettigoniidae). The populations’ distribution of Orthoptera is also analyzed. The populations of native Orthoptera extend through all the herbaceous landscapes. Under these conditions, the interrelating of colonies of each species may result in great abundance. The population distribution of three species locusts (Locusta migratoria, Calliptamus italicus, Dociostaurus maroccanus) is also discussed. Some notable changes of their populations’ distribution and dynamics are characterized. The situation with rare Orthoptera is estimated. Retrospective and prospective of the steppe fauna of Orthoptera are discussed.

Bovine Teat Cistern Microbiota Composition and Richness Are Associated With the Immune and Microbial Responses During Transition to Once-Daily Milking

The relationship between microbiota and health has been widely reported in humans and animals. We established a link between teat cistern microbiota composition and bovine mastitis, an inflammatory disease often due to bacterial infections. To further decipher the relationships between teat cistern microbiota and immune and microbial responses, a switch from twice- to once-daily milking (ODM) in 31 initially healthy quarters of dairy cows was used to trigger an udder perturbation. In this study, a temporal relationship was reported between initial teat cistern microbiota composition and richness, the immune response to ODM, and mastitis development. Quarters with a low initial microbiota richness and taxonomic markers such as Bacteroidetes and Proteobacteria were associated with a higher rate of mastitis during ODM. Quarters with a higher richness and taxonomic markers such as Firmicutes, including the Lachnospiraceae family, and genera such as Bifidobacterium and Corynebacterium displayed early inflammation following transition to ODM but without developing mastitis (no infection). Short-term compositional shifts of microbiota indicates that microbiotas with a higher initial richness were more strongly altered by transition to ODM, with notably the disappearance of rare OTUs. Microbiota modifications were associated with an early innate immune system stimulation, which, in turn, may have contributed to the prevention of mastitis development.

Pternopetalum paucifoliolatum (Apiaceae), a new Critically Endangered species from Sichuan, China

Pternopetalum paucifoliolatum, a new species from Sixigou Scenic Area, Emeishan City, Sichuan Province, is proposed and described. Diagnostic morphological characters, full description, detailed illustrations, and a distribution map are provided. The new species is similar to P. porphyronotum in possessing the 1-pinnate leaves and the abaxially purple-red leaflets, but differs from the latter by shorter stature, fewer leaflets ((1-) 3-7) and rays (5-8), the leaflet margin white-ciliate. The new species, which is assessed as Critically Endangered (CR), was only found on limestone cliffs. We also provide a new key to the species of Pternopetalum.

A new maximum size for the family Nomeidae and the third record of a longfin cigarfish, Cubiceps paradoxus (Stromateoidei: Nomeidae) from California, USA

We report the largest specimen from the stromateoid family Nomeidae. The specimen, measuring 1283 mm total length unpreserved, was caught on hook and line from shore in Port Hueneme, California, USA in June 2019. Despite scavenging damage, the specimen was identified as a longfin cigarfish, Cubiceps paradoxus, using morphological characters and molecular techniques. This is the third record of C. paradoxus from California. We also provide an account of a previously unreported C. paradoxus collected off the US-Mexico Border in 1999 that was examined but not preserved.

Visualizing connectivity of ecological and evolutionary concepts-An exploration of research on plant species rarity

Understanding the ecological and evolutionary factors that influence species rarity has important theoretical and applied implications, yet the reasons why some species are rare while others are common remain unresolved. As a novel exploration of scientific knowledge, we used network analysis conceptually to visualize the foci of a comprehensive base of >800 studies on plant species rarity within the context of ecology and evolution. In doing so, we highlight existing research strengths that could substantiate novel syntheses and gaps that could inspire new research. Our results reveal strong integrated foci on population dynamics with other ecological concepts. In contrast, despite the potential for ecological and evolutionary processes to interact, few studies explored the interplay of environmental factors and microevolutionary patterns. The cellular and molecular biology, physiology, and plasticity of rare plant species within both ecological and evolutionary contexts similarly provide avenues for impactful future investigations.

Simulated Photovoltaic Solar Panels Alter the Seed Bank Survival of Two Desert Annual Plant Species

Seed bank survival underpins plant population persistence but studies on seed bank trait-environment interactions are few. Changes in environmental conditions relevant to seed banks occur in desert ecosystems owing to solar energy development. We developed a conceptual model of seed bank survival to complement methodologies using in-situ seed bank packets. Using this framework, we quantified the seed bank survival of two closely related annual desert plant species, one rare (Eriophyllum mohavense) and one common (Eriophyllum wallacei), and the seed bank-environment interactions of these two species in the Mojave Desert within a system that emulates microhabitat variation associated with solar energy development. We tracked 4860 seeds buried across 540 seed packets and found, averaged across both species, that seed bank survival was 21% and 6% for the first and second growing seasons, respectively. After two growing seasons, the rare annual had a significantly greater seed bank survival (10%) than the common annual (2%). Seed bank survival across both species was significantly greater in shade (10%) microhabitats compared to runoff (5%) and control microhabitats (3%). Our study proffers insight into this early life-stage across rare and common congeners and their environmental interactions using a novel conceptual framework for seed bank survival.

Direct and indirect effect of cannibalism and intraguild predation in the two sibling Harmonia ladybird beetles

In this study, we focused on the direct (i.e., predation) and indirect (i.e., potential threat from coexisting with a larger individual) effects of cannibalism and intraguild predation (IGP) during larval stages of two sibling ladybird beetles. These effects play an important role in the coexistence of the generalist-common Harmonia axyridis and specialist-rare H. yedoensis (Coleoptera: Coccinellidae). Direct predation effect of cannibalism and IGP was asymmetric in the two sibling ladybird beetles; the fourth instar larvae of H. axyridis were better intraguild predators than cannibals, while the reverse was true in the larvae of H. yedoensis. Neither cannibalism nor IGP significantly affected female body weight in either species. Larval H. axyridis surviving exposure to cannibalism or IGP had a reduced number of ovarioles as adults, whereas adult H. yedoensis ovarioles were not affected. For the indirect effects, longer developmental times in males and females and a lower total number of ovarioles in females were detected in H. axyridis. In H. yedoensis, shorter developmental time of males, lighter adult weight and fewer total ovarioles in females were observed. Olfactometer choice experiments clarified that the fourth instar larvae of H. axyridis avoided the first instar conspecific larvae, while those of H. yedoensis were attracted to the odors from H. axyridis and conspecifics. Thus, H. axyridis has an avoidance mechanism only for cannibalism but not for IGP, whereas H. yedoensis does not have any avoidance mechanism. These different behaviors in the direct and indirect effects of cannibalism and IGP observed in the laboratory may play important roles in the coexistence of generalist-common H. axyridis and specialist-rare H. yedoensis in natural conditions, compensating for the large handicap of H. yedoensis at reproductive interference from H. axyridis.

Trait-based climate vulnerability of native rodents in southwestern Mexico

AIM

Incorporate species' trait information together with climate projections for associated habitat to assess the potential vulnerability of rodent taxa to climate change.

LOCATION

Oaxaca State, Mexico.

METHODS

We used a trait-based approach together with climate exposure models to evaluate the vulnerability of rodent species to projected climate conditions in the study region. Vulnerability was estimated based on three factors: (a) Level of climatic exposure that species are projected to experience across their current statewide range; (b) inherent species-specific sensitivity to stochastic events; and (c) species' capacity to cope with climate change effects. We defined species as inherently sensitive if they had any of the following: restricted geographic distribution in Mexico; narrow altitudinal range; low dispersal ability; or long generation length.

RESULTS

Vulnerability varied depending on the climate change scenario applied. Under the MPI general circulation model and current emissions trends, by 2099, all species evaluated were projected to have some level of threat (vulnerable for at least one factor), with 4 out of 55 species vulnerable for all three factors, 29 for two factors, and 22 for one factor. Six out of ten rodent species endemic to Oaxaca were vulnerable for two or more factors. We found that species with narrow and restricted-range distributions combined with low adaptive capacity were projected to be particularly vulnerable.

MAIN CONCLUSIONS

By including species-specific trait information in climate exposure assessments, researchers can contextualize and enhance their understanding about how climate change is likely to affect individual taxa in an area of interest. As such, studies like this one provide more relevant threat assessment information than exposure analyses alone and serve as a starting point for considering how climatic changes interact with an array of other variables to affect native species across their range.

The chloroplast genome of the pincushion cactus Mammilllaria haageana subsp. san-a ngelensis, a Mexican endangered species

The genus Mammillaria occupies diverse habitats and exhibits diverse growth patterns and a large range of morphologies. Most of the species of this genus are used as ornamental plants and are subject to mass habitat loss. Due to these factors, they are being submitted to selective pressure that might affect conservational efforts and management plans. We obtained the 133 gene chloroplast genome as part of the project of sequencing the complete genome of pincushion cactus, including 88 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. The phylogenetic tree indicates the pincushion cactus is a sister species of M. supertexta and M. huitzilopochtli.

Multifunctionality of biocrusts is positively predicted by network topologies consistent with interspecies facilitation

The potential of biodiversity loss to impair the delivery of ecosystem services has motived ecologists to better understand the relationship between biodiversity and ecosystem functioning. Although increasing evidence underlines the collective contribution of different biodiversity components on the simultaneous performance of multiple functions (multifunctionality), we know little about the trade‐offs between individual diversity effects and the extent to which they determine multifunctionality differentially. Here, at a subcontinental scale of 62 dryland sites, we show in phototrophic microbiota of biological soil crusts (biocrusts) that, whereas richness alone is unable to guarantee the maxima of multifunctional performance, interspecies facilitation and compositional identity are particularly stronger but often neglected predictors. The inconsistent effects of different biodiversity components imply that soil multifunctionality can be lost despite certain species remaining present. Moreover, we reveal a significant empirical association between species functional importance and its topological feature in co‐occurrence networks, indicating a functional signal of species interaction. Nevertheless, abundant species tend to isolate and merely interact within small topological structures, but rare species were tightly connected in complicated network modules. Our findings suggest that abundant and rare species of soil phototrophs exhibit distinct functional relevance. These results give a comprehensive view of how soil constructive species drive multifunctionality in biocrusts and ultimately promote a deeper understanding of the consequences of biodiversity loss in real‐world ecosystems.

Decoding diversity in a coral reef fish species complex with restricted range using metagenomic sequencing of gut contents

AIM

Identification of the processes that generate and maintain species diversity within the same region can provide insight into biogeographic patterns at broader spatiotemporal scales. Hawkfishes in the genus Paracirrhites are a unique taxon to explore with respect to niche differentiation, exhibiting diagnostic differences in coloration, and an apparent center of distribution outside of the Indo-Malay-Philippine (IMP) biodiversity hotspot for coral reef fishes. Our aim is to use next-generation sequencing methods to leverage samples of a taxon at their center of maximum diversity to explore phylogenetic relationships and a possible mechanism of coexistence.

LOCATION

Flint Island, Southern Line Islands, Republic of Kiribati.

METHODS

A comprehensive review of museum records, the primary literature, and unpublished field survey records was undertaken to determine ranges for four "arc-eye" hawkfish species in the Paracirrhites species complex and a potential hybrid. Fish from four Paracirrhites species were collected from Flint Island in the Southern Line Islands, Republic of Kiribati. Hindgut contents were sequenced, and subsequent metagenomic analyses were used to assess the phylogenetic relatedness of the host fish, the microbiome community structure, and prey remains for each species.

RESULTS

Phylogenetic analyses conducted with recovered mitochondrial genomes revealed clustering of P. bicolor with P. arcatus and P. xanthus with P. nisus, which were unexpected on the basis of previous morphological work in this species complex. Differences in taxonomic composition of gut microbial communities and presumed prey remains indicate likely separation of foraging niches.

MAIN CONCLUSIONS

Our findings point toward previously unidentified relationships in this cryptic species complex at its proposed center of distribution. The three species endemic to the Polynesian province (P. nisus, P. xanthus, and P. bicolor) cluster separately from the more broadly distributed P. arcatus on the basis of relative abundance of metazoan sequences in the gut (presumed prey remains). Discordance between gut microbial communities and phylogeny of the host fish further reinforce the hypothesis of niche separation.

Phyllodiaptomus (Phyllodiaptomus) roietensis, a new diaptomid copepod (Copepoda, Calanoida) from temporary waters in Thailand and Cambodia, with a key to the species

Phyllodiaptomus (Phyllodiaptomus) roietensissp. nov. was collected from temporary water bodies in Roi Et and Nakhon Ratchasima provinces in northeastern Thailand and Kampong Thom Province in central Cambodia. The new species is closely related to Phyllodiaptomus (P.) surinensis Sanoamuang & Yindee, 2001 in that it shares common morphological characters in the males: urosomites 2-3, P5 intercoxal sclerite, right P5 Exp-2, and left P5 Exp. Minor differences on the right antennule, right caudal ramus, P5 basis and Enp exist. The females differ in their Pdg 5, genital double-somite, and P5. An updated key to the species of the genus Phyllodiaptomus Kiefer, 1936 is provided.

Elevated precipitation alters the community structure of spring ephemerals by changing dominant species density in Central Asia

Global climate change is one of the most pressing conservation challenges; in particular, changes in precipitation regimes have already substantially influenced terrestrial ecosystems. However, the mechanisms influencing precipitation changes on individual plants and the plant communities in desert grasslands have yet to be fully elucidated. We therefore examine the influence of increased precipitation on plant community compositions in the Gurbantunggut Desert, Xinjiang, northwestern China, from 2005 to 2009. We found that growth of all plant species and the community productivities increased markedly with enhanced water input. Cover of ephemeral synusia also significantly increased due to increased precipitation, implying that the role of the ephemeral community for stabilization of sand dunes was strengthened by increased precipitation. The response of plant community compositions to increased precipitation was primarily reflected as changes in plant density, while increased precipitation did not affect plant species richness and the diversity index. Dominant species drove the response of plant density to increasing precipitation during the five-year study period. However, the relative responses of rare species were stronger than those of the dominant species, thereby potentially driving species turnover with long-term increased precipitation. This finding improved our understanding of how increased precipitation drives the changes in plant community composition in desert grasslands and will help to better predict changes in the community composition of ephemerals under future global climate change scenarios.

Rare Species Shift the Structure of Bacterial Communities Across Sphagnum Compartments in a Subalpine Peatland

Sphagnum-associated microbiomes are crucial to Sphagnum growth and peatland ecological functions. However, roles of rare species in bacterial communities across Sphagnum compartments are poorly understood. Here the structures of rare taxa (RT) and conditionally abundant and rare taxa (CART) from Sphagnum palustre peat (SP), S. palustre ectosphere (Ecto) and S. palustre endosphere (Endo) were investigated in the Dajiuhu Peatland, central China. Our results showed that plant compartment effects significantly altered the diversities and structures of bacterial communities. The Observed species and Simpson indices of RT and CART in alpha diversity significantly increased from Endo to SP, with those of Ecto in-between. The variations of community dissimilarities of RT and CART among compartments were consistent with those of whole bacterial communities (WBC). Network analysis indicated a non-random co-occurrence pattern of WBC and all keystone species are affiliated with RT and CART, indicating their important role in sustaining the WBC. Furthermore, the community structures of RT and CART in SP were significantly shaped by water table and total nitrogen content, which coincided with the correlations between WBC and environmental factors. Collectively, our results for the first time confirm the importance of rare species to bacterial communities through structural and predicted functional analyses, which expands our understanding of rare species in Sphagnum-associated microbial communities in subalpine peatlands.

[Rare species in the structure of acid-resistent members of the order Actinomycetales isolated from clinical material.]

The article presents data on the structure of acid-resistant members of the order Actinomycetales and rare species that have been isolated and identified using various methods. The study included strains of non-tuberculous mycobacteria (NTM) isolated from clinical material during examination for tuberculosis in the period from 2016 to 2019. The total number of samples with signs of NTMs growth that were included in the study was 316 samples. Primary isolation on Levenshtein-Jensen, Finn II, and MGIT media and NTMs identification by DNA-hybridization. All strains that were not identified prior to the species and culture, identified as microorganisms with a high G+C content (High GC GR +) were re-identified using a MALDI-ToF Microflex LT mass spectrometer (Bruker®). By the method of DNA-hybridization, 188 strains isolated by NTM were successfully identified to form 58.5% of all selected cultures. Among the selected species, representatives of slowly growing NTMs (M. avium complex, M. gordonae, M. kansasii) predominated, which amounted to 67.0% of all NTM strains identified to the species. Among the cultures for which DNA hybridization failed to carry out acceptable identification, predominantly NTMs were found, among which M. gordonae, M. avium, M. kansasii dominated. A number of NTMs were represented by rare species: M. iranicum and M. pseudoshottsii. Among this group of microorganisms, other acid-resistant aerobic actinomycetes were isolated, including those of potential clinical significance: Gordonia spp., Tsukamurella spp., Rhodococcus spp., Nocardia spp. When identifying cultures containing high concentrations of G+C, the maximum number of microbial associations was revealed, including those consisting of two types of NTMs (M. monacense + M. flavescens, M. avium + M. kansasii), as well as associations of M. gordonae with staphylococci. The same group included rare NTM species: M. fredericbergense, M. szulgai, M. malmoense, M. bohemicum, M. septicum, as well as representatives of the genera Nocardia, Gordonia, Tsukamurella.

High-resolution distribution modeling of a threatened short-range endemic plant informed by edaphic factors

Short-range endemic plants often have edaphic specializations that, with their restricted distributions, expose them to increased risk of anthropogenic extinction.Here, we present a modeling approach to understand habitat suitability for Ricinocarpos brevis R.J.F.Hend. & Mollemans (Euphorbiaceae), a threatened shrub confined to three isolated populations in the semi-arid south-west of Western Australia. The model is a maximum entropy species distribution projection constructed on the basis of physical soil characteristics and geomorphology data at approximately 25 m2 (1 arc-second) resolution.The model predicts the species to occur on shallow, low bulk density soils that are located high in the landscape. The model shows high affinity (72.1% average likelihood of occurrence) for the known populations of R. brevis, as well as identifying likely locations that are not currently known to support the species. There was a strong relationship between the likelihood of R. brevis occurrence and soil moisture content that the model estimated at a depth of 20 cm.We advocate that our approach should be standardized using publicly available data to generate testable hypotheses for the distribution and conservation management of short-range endemic plant species for all of continental Australia.

Distribution of two rare taxa of caddisflies (Trichoptera: Rhyacophilidae, Polycentropodidae) from the Republic of Kosovo

Background

The knowledge about distribution, ecology and species composition of caddisflies of the Balkan Peninsula is still not complete. The ongoing investigations of the last years highlight this area as an important hotspot of caddisfly diversity. Polycentropus ierapetra slovenica has been considered a narrow range endemic of Slovenia and surrounding areas. Rhyacophila aurata, a species known from many parts of Europe, according to the current knowledge, is absent from a large part of the Balkan Peninsula.

New information

In this paper, we present records of these two rare taxa of Trichoptera from the Republic of Kosovo with exact distribution data, based on sampling carried out randomly during 2014 and 2017. Polycentropus ierapetra slovenica was found in several streams in Bjeshkët e Nemuna Mountains and Karadak Mountains. Rhyacophila aurata was found during this investigation at a single locality in Bjeshkët e Nemuna Mountains.The unexpected finding of these two taxa in Kosovo greatly enlarges their known distribution area and makes a contribution towards the better knowledge of distributional patterns of these rare taxa of caddisflies in this part of Europe.

How diverse can rare species be on the margins of genera distribution?

Different genetic patterns have been demonstrated for narrowly distributed taxa, many of them linking rarity to evolutionary history. Quite a few species in young genera are endemics and have several populations that present low variability, sometimes attributed to geographical isolation or dispersion processes. Assessing the genetic diversity and structure of such species may be important for protecting them and understanding their diversification history. In this study, we used microsatellite markers and plastid sequences to characterize the levels of genetic variation and population structure of two endemic and restricted species that grow in isolated areas on the margin of the distribution of their respective genera. Plastid and nuclear diversities were very low and weakly structured in their populations. Evolutionary scenarios for both species are compatible with open-field expansions during the Pleistocene interglacial periods and genetic variability supports founder effects to explain diversification. At present, both species are suffering from habitat loss and changes in the environment can lead these species towards extinction.