Proteomic characterization of Pseudogymnoascus spp. isolates from polar and temperate regions.

Proteomics has been used extensively in the field of mycology, mainly in trying to understand the complex network of protein-protein interactions that has been implicated in the molecular functions of fungi. It is also a useful tool to compare metabolic differences within a genus. Species of Pseudogymnoascus, a genus under the phyla Ascomycota, have been shown to play an important role in the soil environment. They have been found in both polar and temperate regions and are a known producer of many extracellular hydrolases that contribute to soil decomposition. Despite the apparent importance of Pseudogymnoascus spp. in the soil ecosystem, investigations into their molecular functions are still very limited. In the present study, proteomic characterization of six Pseudogymnoascus spp. isolated from three biogeographic regions (the Arctic, Antarctic, and temperate regions) was carried out using tandem mass spectrometry. Prior to proteomic analysis, the optimization for protein extraction was carried out. Trichloroacetic acid­acetone­phenol was found to be the best extraction method to be used for proteomic profiling of Pseudogymnoascus spp. The proteomic analysis identified 2003 proteins that were successfully mapped to the UniProtKB database. The identified proteins were clustered according to their biological processes and molecular functions. The shared proteins found in all Pseudogymnoascus spp. (1201 proteins) showed a significantly close relationship in their basic cellular functions, despite differences in morphological structures. Analysis of Pseudogymnoascus spp. proteome also identified proteins that were unique to each region. However, a high number of these proteins belonged to protein families of similar molecular functions, namely, transferases and hydrolases. Our proteomic data can be used as a reference for Pseudogymnoascus spp. across different global regions and a foundation for future soil ecosystem function research.

Biogeographic survey of soil bacterial communities across Antarctica.

BACKGROUND: Antarctica and its unique biodiversity are increasingly at risk from the effects of global climate change and other human influences. A significant recent element underpinning strategies for Antarctic conservation has been the development of a system of Antarctic Conservation Biogeographic Regions (ACBRs). The datasets supporting this classification are, however, dominated by eukaryotic taxa, with contributions from the bacterial domain restricted to Actinomycetota and Cyanobacteriota. Nevertheless, the ice-free areas of the Antarctic continent and the sub-Antarctic islands are dominated in terms of diversity by bacteria. Our study aims to generate a comprehensive phylogenetic dataset of Antarctic bacteria with wide geographical coverage on the continent and sub-Antarctic islands, to investigate whether bacterial diversity and distribution is reflected in the current ACBRs. RESULTS: Soil bacterial diversity and community composition did not fully conform with the ACBR classification. Although 19% of the variability was explained by this classification, the largest differences in bacterial community composition were between the broader continental and maritime Antarctic regions, where a degree of structural overlapping within continental and maritime bacterial communities was apparent, not fully reflecting the division into separate ACBRs. Strong divergence in soil bacterial community composition was also apparent between the Antarctic/sub-Antarctic islands and the Antarctic mainland. Bacterial communities were partially shaped by bioclimatic conditions, with 28% of dominant genera showing habitat preferences connected to at least one of the bioclimatic variables included in our analyses. These genera were also reported as indicator taxa for the ACBRs. CONCLUSIONS: Overall, our data indicate that the current ACBR subdivision of the Antarctic continent does not fully reflect bacterial distribution and diversity in Antarctica. We observed considerable overlap in the structure of soil bacterial communities within the maritime Antarctic region and within the continental Antarctic region. Our results also suggest that bacterial communities might be impacted by regional climatic and other environmental changes. The dataset developed in this study provides a comprehensive baseline that will provide a valuable tool for biodiversity conservation efforts on the continent. Further studies are clearly required, and we emphasize the need for more extensive campaigns to systematically sample and characterize Antarctic and sub-Antarctic soil microbial communities. Video Abstract.

Applying molecular genetic data at different scales to support conservation assessment of European Habitats Directive listed species: A case study of Eurasian otter in Austria.

Evaluating intraspecific genetic structure and diversity is fundamental to assessing a species' conservation status, but direct incorporation of such information into legal frameworks such as the EU's Habitats Directive is surprisingly rare. How genetic structure aligns with EU member state boundaries or biogeographic regions may be very important in designing management plans or achieving legislative goals. The Eurasian fish otter experienced a sharp population decline during the 20th century but is currently re-expanding in several countries. The species is listed under Annex II and IV of the European Habitats Directive, and member states are obliged to assess the species separately across different biogeographic regions. We genotyped 2492 otter spraints across four provinces in Austria, collected between 2017 and 2021. A total of 384 different genotypes were identified, supporting densities along river habitats from 0.1 to 0.47 otters per river km (mean: 0.306), with a resampling-based simulation supporting limited density overestimation at survey lengths of 20 km or more. Three distinct genetic clusters were revealed, two of them presumably reflecting two relict populations whereas the source of the third cluster is unknown. The geographic extent of the three clusters does not coincide with provincial or biogeographic boundaries, both relevant for assessment and management within existing national or European legislative frameworks. We advocate more consideration of genetic structure in the assessment and conservation management planning of species listed in the European Habitats Directive.

Rapid assessment of plant diversity using MODIS biophysical proxies.

The spectral information derived from satellite data provides important inputs for assessing plant diversity. If a suitable satellite-derived biophysical proxy is applicable to assess and monitor plant diversity of different biogeographic regions will be of interest to policy makers and conservationists. We selected four biogeographic regions of India, i.e., semi-arid, Eastern Ghats, Western Ghats, and Northeast as the test sites on the basis of variations in moisture availability. The flora data collected for the study sites are the extract of the national biodiversity project 'Biodiversity Characterization at Landscape Level'. The available Moderate Resolution Imaging Spectroradiometer (MODIS)-derived biophysical proxies at high temporal frequencies was considered to compare the biophysical proxies: surface reflectance-red and near-infrared, normalized difference vegetation index-NDVI, enhanced vegetation index-EVI, leaf area index-LAI, and fraction of absorbed photosynthetically active radiation-FAPAR at different temporal scales (monthly, post-monsoon, seasonal, annual) in each selected biogeographic regions of India. Generalized linear model (GLM) and multivariate adaptive regression spline (MARS) were utilized to evaluate the relationship between plant diversity and MODIS-derived biophysical proxies. MARS summarized the suitable biophysical proxies at monthly scale in descending order for the total forest area in semi-arid was red, NDVI, and FAPAR; for Eastern Ghats was EVI, FAPAR, and LAI; for Western Ghats was EVI, LAI, and FAPAR; and for Northeast was NDVI, near-infrared, and red. Furthermore, monthly FAPAR commonly found to be the suitable proxy to large scale monitoring of plant diversity in the moisture-varied biogeographic regions of India, except Northeast. Using artificial neural network, the relationship of plant diversity and monthly FAPAR/NDVI were modeled. The correlation between the predicted and reference plant diversity was found to be r = 0.56 for semi-arid, r = 0.52 for Eastern Ghats, r = 0.52 for Western Ghats and r = 0.61 for Northeast at p-value < 0.001. The study affirms that FAPAR is potentially an essential biodiversity variable (EBV) for carrying out rapid/indicative assessment of plant diversity in different biogeographic regions, and thereby, meeting various international commitments dealing with conservation and management measures for biodiversity.

Biogeographic variability in wildfire severity and post-fire vegetation recovery across the European forests via remote sensing-derived spectral metrics.

Wildfires have large-scale and profound effects on forest ecosystems, and they force burned forest areas toward a wide range of post-fire successional trajectories from simple reduction of ecosystem functions to transitions to other stable non-forest states. Fire disturbances represent a key driver of changes in forest structure and composition due to post-fire succession processes, thus contributing to modify ecosystem resilience to subsequent disturbances. Here, we aimed to provide useful insights into wildfire severity and post-fire recovery processes at the European continental scale, contributing to improved description and interpretation of large-scale wildfire spatial patterns and their effects on forest ecosystems in the context of climate change. We analyzed fire severity and short-term post-fire vegetation recovery patterns across the European forests between 2004 and 2015 using Corine Land Cover Forest classes and bioregions, based on MODIS-derived spectral metrics of the relativized burn ratio (RBR), normalized difference vegetation index (NDVI) and relative recovery indicator (RRI). The RBR-based fire severity showed geographic differences and interannual variability in the Boreal bioregion compared to that in other biogeographic regions. The NBR-based RRI showed a slower post-fire vegetation recovery rate with respect to the NDVI, highlighting the differential sensitivities of the analyzed remote sensing-spectral metrics. Moreover, the RRI showed a significant decreasing trend during the observation period, suggesting a growing lag in post-fire vegetation recovery across European forests.

Morphological discreteness of the estuarine croaker Pseudotolithus elongatus (Teleostei: Sciaenidae).

The estuarine croaker (Pseudotolithus elongatus, Sciaenidae) has long-term socio-economic and ecological significance in tropical and subtropical regions of the world, but little has been reported on the population demographics of this species. In this study, a traditional morphometric approach was used to test the hypothesis that island samples are morphologically distinctive from adjoining estuarine waters. The study involved a total number of 612 specimens from four islands (Alligator, Tobacco, Parrot and James) of the lower Cross River, Nigeria as well as from the mouth of the Cross River estuary, sampled from January to July 2020. Each specimen was subjected to morphometric measurements consisting of 14 allometrically modified characters. Results of principal component analysis explained 85.6% of the total variance. The pooled between-groups discriminant function analysis correctly classified 66.0% of individuals into two distinct stocks (Island and Estuary mouth). The present finding demonstrates that the Cross River Islands hold a unit stock of P. elongatus that is morphologically separable from the adjoining estuarine waters. We therefore recommend that the croaker population in Cross River should be managed as separate stocks.

Identification of areas of very high biodiversity value to achieve the EU Biodiversity Strategy for 2030 key commitments.

BACKGROUND: The European Union strives to increase protected areas of the EU terrestrial surface to 30% by year 2030, of which one third should be strictly protected. Designation of the Natura 2000 network, the backbone of nature protection in the EU, was mostly an expert-opinion process with little systematic conservation planning. The designation of the Natura 2000 network in Romania followed the same non-systematic approach, resulting in a suboptimal representation of invertebrates and plants. To help identify areas with very high biodiversity without repeating past planning missteps, we present a reproducible example of spatial prioritization using Romania's current terrestrial Natura 2000 network and coarse-scale terrestrial species occurrence. METHODS: We used 371 terrestrial Natura 2000 Sites of Community Importance (Natura 2000 SCI), designated to protect 164 terrestrial species listed under Annex II of Habitats Directive in Romania in our spatial prioritization analyses (marine Natura 2000 sites and species were excluded). Species occurrences in terrestrial Natura 2000 sites were aggregated at a Universal Traverse Mercator spatial resolution of 1 km2. To identify priority terrestrial Natura 2000 sites for species conservation, and to explore if the Romanian Natura 2000 network sufficiently represents species included in Annex II of Habitats Directive, we used Zonation v4, a decision support software tool for spatial conservation planning. We carried out the analyses nationwide (all Natura 2000 sites) as well as separately for each biogeographic region (i.e., Alpine, Continental, Pannonian, Steppic and Black Sea). RESULTS: The results of spatial prioritization of terrestrial Natura 2000 vary greatly by planning scenario. The performance of national-level planning of top priorities is minimal. On average, when 33% of the landscape of Natura 2000 sites is protected, only 20% of the distribution of species listed in Annex II of Habitats Directive are protected. As a consequence, the representation of species by priority terrestrial Natura 2000 sites is lessened when compared to the initial set of species. When planning by taxonomic group, the top-priority areas include only 10% of invertebrate distribution in Natura 2000. When selecting top-priority areas by biogeographical region, there are significantly fewer gap species than in the national level and by taxa scenarios; thusly, the scenario outperforms the national-level prioritization. The designation of strictly protected areas as required by the EU Biodiversity Strategy for 2030 should be followed by setting clear objectives, including a good representation of species and habitats at the biogeographical region level.

Diagnostic indicators of wild pollinators for biodiversity monitoring in long-term conservation.

For the conservation of wild pollinators, instead of surveying the whole community, one or more indicator species can be used as monitoring targets for long-term conservation. China, the richest country in terms of bumblebee species with 125 species, was selected here to investigate the indicator species of the different biogeographic regions of bumblebees. Four principal biogeographic regions of bumblebee species, i.e., South China, North-Northeast China (North China), the Mongolian Plateau and surrounding mountains (Mongolian Plateau) and the Tibetan Plateau and surrounding mountains (Tibetan Plateau), were revealed by Ward's agglomerative cluster analysis. The role of climatic factors in defining the biogeographic regions was found to be greater than those of topographical factors and their joint effects. We found that 14, 13, 12 and 12 species were associated with the regions of South China, North China, the Mongolian Plateau and the Tibetan Plateau, respectively. In addition, among these species, seven (Bombus atripes, B. bicoloratus, B. breviceps, B. eximius, B. flavescens, B. montivagus and B. trifasciatus), five (B. deuteronymus, B. patagiatus, B. pseudobaicalensis, B. tricornis and B. ussurensis), ten (B. armeniacus, B. confusus, B. cryptarum, B. cullumanus, B. hortorum, B. muscorum, B. ruderarius, B. soroeensis, B. subterraneus and B. terrestris) and four species (B. kashmirensis, B. personatus, B. rufofasciatus and B. waltoni) were identified as important indicator species for South China, North China, the Mongolian Plateau and the Tibetan Plateau, respectively. Furthermore, we identified specific areas for targeted bumblebee diversity monitoring in each region. This study highlights the bioregionalization and the identification of indicator species of bumblebee pollinators for long-term monitoring in conservation.

Biogeographic regions and events of isolation and diversification of the endemic biota of the tropical Andes.

Understanding the spatial and temporal evolution of biota in the tropical Andes is a major challenge, given the region's topographic complexity and high beta diversity. We used a network approach to find biogeographic regions (bioregions) based on high-resolution species distribution models for 151 endemic bird taxa. Then, we used dated molecular phylogenies of 14 genera to reconstruct the area history through a sequence of allopatric speciation processes. We identified 15 biogeographical regions and found 26 events of isolation and diversification within their boundaries that are independently confirmed with disjunct distributions of sister taxa. Furthermore, these events are spatially congruent with six geographical barriers related to warm and/or dry river valleys, discontinuities in elevation, and high peaks separating fauna from different range slopes. The most important barrier is the Marañon River Valley, which limits the boundaries of four bioregions and is congruent with eight phylogenetic distribution breaks, separating the Central and Northern Andes, where the most bioregions are found. We also show that many bioregions have diffuse and overlapping structures, with contact and transition zones that challenge previous conceptions of biogeographical regions as spatially simple in structure. This study found evidence that the drivers of our identified bioregions were processes of Andean uplift and mountain dispersal facilitated by temperature oscillations of the Pleistocene. Therefore, Andean bioregions were not formed from one simple biogeographical event in a certain time frame, but from a combination of vicariance and dispersal events, which occurred in different time periods.

Intraspecific variation and phylogeography of the millipede model organism, the Black Pill Millipede Glomerismarginata (Villers, 1789) (Diplopoda, Glomerida, Glomeridae).

The Black Pill Millipede, Glomerismarginata, is the best studied millipede species and a model organism for Diplopoda. Glomerismarginata is widespread, with numerous colour morphs occurring across its range, especially in the south. This study investigates whether colour morphs might represent cryptic species as well as the haplotype diversity and biogeography of G.marginata. The results of the COI barcoding fragment analysis include 97 G.marginata, as well as 21 specimens from seven potentially related species: G.intermedia Latzel, 1884, G.klugii Brandt, 1833 (G.undulata C.L. Koch, 1844), G.connexa Koch, 1847, G.hexasticha Brandt, 1833, G.maerens Attems, 1927, G.annulata Brandt, 1833 and G.apuana Verhoeff, 1911. The majority of the barcoding data was obtained through the German Barcode of Life project (GBOL). Interspecifically, G.marginata is separated from its congeners by a minimum uncorrected genetic distance of 12.9 %, confirming its monophyly. Uncorrected intraspecific distances of G.marginata are comparable to those of other widespread Glomeris species, varying between 0-4.7%, with the largest genetic distances (>2.5 %) found at the Mediterranean coast. 97 sampled specimens of G.marginata yielded 47 different haplotypes, with identical haplotypes occurring at large distances from one another, and different haplotypes being present in populations occurring in close proximity. The highest number of haplotypes was found in the best-sampled area, western Germany. The English haplotype is identical to northern Spain; specimens from southern Spain are closer to French Mediterranean specimens. Analyses (CHAO1) show that approximately 400 different haplotypes can be expected in G.marginata. To cover all haplotypes, it is projected that up to 6,000 specimens would need to be sequenced, highlighting the impossibility of covering the whole genetic diversity in barcoding attempts of immobile soil arthropod species.

Does the colonization of new biogeographic regions influence the diversification and accumulation of clade richness among the Corvides (Aves: Passeriformes)?

Regional variation in clade richness can be vast, reflecting differences in the dynamics of historical dispersal and diversification among lineages. Although it has been proposed that dispersal into new biogeographic regions may facilitate diversification, to date there has been limited assessment of the importance of this process in the generation, and maintenance, of broad-scale biodiversity gradients. To address this issue, we analytically derive biogeographic regions for a global radiation of passerine birds (the Corvides, c. 790 species) that are highly variable in the geographic and taxonomic distribution of species. Subsequently, we determine rates of historical dispersal between regions, the dynamics of diversification following regional colonization, and spatial variation in the distribution of species that differ in their rates of lineage diversification. The results of these analyses reveal spatiotemporal differences in the build-up of lineages across regions. The number of regions occupied and the rate of transition between regions both predict family richness well, indicating that the accumulation of high clade richness is associated with repeated expansion into new geographic areas. However, only the largest family (the Corvidae) had significantly heightened rates of both speciation and regional transition, implying that repeated regional colonization is not a general mechanism promoting lineage diversification among the Corvides.

Minimal SNP overlap among multiple panels of ancestry informative markers argues for more international collaboration.

The century-old use of genetic markers to determine population relationships has morphed in modern forensics into use of markers to determine the ancestry of an individual from a DNA sample. Researchers have identified sets of SNPs that have frequency differences among populations and many sets of SNPs have been published for the purpose of inferring ancestry. Such inference also requires reference datasets for the particular set of SNPs selected. We have identified 21 largely independent published panels of ancestry informative SNPs (AISNPs) and examined their union of 1397 SNPs. No SNP occurs in more than 6 panels. The 1397 SNPs in 21 panels yield a largely empty matrix that is inhibiting progress on more refined ability to infer ancestry for a forensic sample. The most common set of reference populations is the HGDP set of 52 small population samples totaling a thousand individuals. Only 46 (3%) of the 1397 SNPs occur in three or more panels. We assembled a new dataset for 44 of those SNPs involving 4,559 individuals from 73 populations. Analyses of this dataset provided clear differentiation of only five biogeographic regions: sub-Saharan Africa, Europe and SW Asia, South Asia, East Asia, and the Americas. This is an inadequate level of biogeographic resolution already exceeded by other panels. We conclude that more such AISNP panels are not needed and that the forensic community must collaborate to develop a common set of highly differentiating AISNPs typed on a very large number of population samples. How that can be accomplished will be the subject of future discussion.

Grado de cobertura del muestreo de escarabajos coprófagos (Coleoptera: Scarabaeidae: Scarabaeinae) en Colombia / Estimation of the sampling cover for dung beetles (Coleoptera: Scarabaeinae) in Colombia

The promotion of biodiversity conservation strategies must address the lack of information and the difficulty of identifying knowledge gaps that may facilitate our knowledge of different taxonomic groups. Dung beetles constitute one of those groups, despite having been proposed as an efficient bioindicator of environmental disturbance processes. In this work, we aimed to prepare a diagnosis on the state of knowledge of the subfamily Scarabaeinae, focusing on the cover sampling degree of this group in Colombia, with the purpose of identifying high-priority areas that will allow the completion of a national inventory. The work consisted of a bibliographical compilation using 12 referential databases and the examination of specimens deposited in 26 national collections. A total of 16 940 individuals were examined, finding registers for 232 species from 386 localities. The respective distribution cover maps were presented, and the cover at a national level was 10.62%. A historical analysis demonstrated a proliferation in the number of studies for the last three decades; nevertheless, a great proportion of unpublished works persists, resulting in only 64 sampled localities with published records. The localities with the greatest sampling efforts were RN La Planada, Lloro, AUN Los Estoraques, PNN Tinigua and Mariquita. Registries for all departments were available, and the best sampled ones were Cundinamarca, Antioquia, Valle del Cauca and Boyaca. The ecosystems with the greatest number of publications are the Andean pre mountain humid forest, followed by the Andean mountain humid forest and the Pacific humid forest. Other ecosystems with few studies included mangroves, desert zones, natural savannahs, palm swamps, paramos, flooding forests and agroforestry systems. The biogeographic region with the greatest number of localities was the Andean region, followed by Choco-Magdalenense and Amazonia. Our results showed that high levels of subsampling persist and that some zones lack registries, as in the case of some parks of the national system of protected areas. It is imperative that the sampling cover is extended at a national level, focusing all possible efforts on collecting in those subsampled regions that have high conservation importance, with the main goal of completing the listing of species and their distribution. Rev. Biol. Trop. 63 (1): 97-125. Epub 2015 March 01.

Una de las principales limitantes para generar estrategias para la conservación, es la falta de información y la dificultad para identificar vacíos de conocimiento, que faciliten el entendimiento de un grupo taxonómico. En este trabajo desarrollamos el diagnóstico sobre el grado de cobertura del muestreo de escarabajos coprófagos en Colombia. Se recopiló la bibliografía, utilizando 12 bases de datos y se revisaron 16 940 especímenes depositados en 26 colecciones. Se encontraron 232 especies, en 386 localidades, con un porcentaje de cobertura del 10.62%. Se evidencia en los últimos años un incremento en el número de estudios, sin embargo solo 64 localidades tienen publicaciones. Se encontraron registros para todos los departamentos, siendo los mejor muestreados: Cundinamarca, Antioquia, Valle del Cauca y Boyacá. Los ecosistemas con mayor número de publicaciones son el bosque húmedo premontano Andino, el bosque húmedo montano Andino y el bosque húmedo del Pacífico. Sin embargo, existen muchos ecosistemas con muy pocos estudios como los manglares, zonas desérticas, savanas naturales, morichales, páramos, bosques inundables y sistemas agrícolas. La región biogeográfica con mayor número de localidades es la Andina, seguida del Chocó-Magdalenense y la Amazonía. A nivel general, persiste un alto nivel de submuestreo. Se evidencia la necesidad de ampliar la cobertura del muestreo a nivel nacional, enfocando los esfuerzos en aquellas áreas submuestreadas con importancia a nivel de conservación.

Global biogeography of the ectomycorrhizal /sebacina lineage (Fungi, Sebacinales) as revealed from comparative phylogenetic analyses.

Compared with plants and animals, large-scale biogeographic patterns of microbes including fungi are poorly understood. By the use of a comparative phylogenetic approach and ancestral state reconstructions, we addressed the global biogeography, rate of evolution and evolutionary origin of the widely distributed ectomycorrhizal (EcM) /sebacina lineage that forms a large proportion of the Sebacinales order. We downloaded all publicly available internal transcribed spacer (ITS) sequences and metadata and supplemented sequence information from three genes to construct dated phylogenies and test biogeographic hypotheses. The /sebacina lineage evolved 45-57 Myr ago that groups it with relatively young EcM taxa in other studies. The most parsimonious origin for /sebacina is inferred to be North American temperate coniferous forests. Among biogeographic traits, region and biome exhibited stronger phylogenetic signal than host family. Consistent with the resource availability (environmental energy) hypothesis, the ITS region is evolving at a faster rate in tropical than nontropical regions. Most biogeographic regions exhibited substantial phylogenetic clustering suggesting a strong impact of dispersal limitation over a large geographic scale. In northern Holarctic regions, however, phylogenetic distances and phylogenetic grouping of isolates indicate multiple recent dispersal events.