True Species Research Articles

Orthoptera assemblages of the relict meadows of the Szernye marsh area (West Ukraine: Transcarpathia)

Orthoptera assemblages were sampled between 2012 and 2014 on six grasslands in marginal part of the former Szernye Marsh (Bereg Lowland, Transcarpathia, West Ukraine). 24 species in 1306 individuals were observed which is about the half of the Orthoptera species known from the Bereg Lowland. The bulk of the assemblages is formed by generalist chortobiont species (62.5%), while thamnobionts, connected with tall forb and/or shrubby vegetation, also reach a relatively high frequency (29.1%). According to the biogeographical composition, the Euro-Siberian species were predominating (58.3%), combined with only scarce presence of West Palearctic and Mediterranean species. The multivariate analysis did not show any clear subdivision according to the a priori vegetation types with the exception of the xeric habitats. This assemblage type were characterised by a low species number (7–12) and very high frequency of one or at least two dominant species which were common in all types of studied habitats. Although their subdominant species differed from the other two assemlage types but they could not be referred as true character species. Thus the studied xeric habitats are not such true xeric grasslands as the sandy and saline grasslands of the Pannonian lowland. The main natural value of the area is preseved by semi-natural humide and transitional habitat types, which can be conserved by yearly alternating mowing and preserving the mosaic structure with some corridors among them.

Mangrove floristics, forest structure and mapping of Neil Island (Andaman and Nicobar Islands, India) with emphasis on the diversity of Rhizophora species and the significance of small island mangroves

Abstract Mangroves in small islands are critical resources for the stability of the island and the livelihood of local coastal communities. However, scientific inventories of mangroves in small islands are rare due to their limited distribution. Considering this, the present study was conducted during 2014–2015 to determine the species composition, biomass, vegetative carbon stock and spatial distribution of mangroves at Neil Island, one of the small islands of the Andaman and Nicobar Islands, India. The spatial locations of different species of mangroves identified from our extensive field surveys were compared with high-resolution images, and the coverage of mangroves (genus level distribution) was interpreted entirely based on the elements of tone and texture. The results show that the mangroves of Neil Island consist of 17 true mangrove species belonging to 12 genera in eight families. The co-existence of all three Indo-West Pacific mangrove species of the genus Rhizophora (Rhizophora apiculata, Rhizophora mucronata and Rhizophora stylosa), and their hybrids (Rhizophora × annamalayana, Rhizophora × lamarckii and Rhizophora × mohanii) shows that this island is a unique place for studying the hybridization and speciation of Rhizophora, a worldwide dominant mangrove genus. Rhizophora mucronata was found to be the dominant species in terms of density, basal area and biomass estimated from forest structural assessments using the quadrat method. The mean density and basal area were 1162 trees ha−1 and 28 m2 ha−1, respectively. The mean above-ground biomass was 271 Mg ha−1, while the mean below-ground biomass was 104 Mg ha−1. The total mean biomass of Neil Island mangroves was 375 Mg ha−1 and its corresponding vegetative carbon stock was 171 Mg C ha−1. The present study provides a practical approach to species-level mapping and assessment to gain site-specific knowledge of the mangroves of Neil Island. Since mangroves are vital for small islands such as Neil Island to cope with rising sea level and increases in natural calamities, the baseline scientific information provided by this study will be beneficial for Integrated Island Management.

First record of non-migratory Blue-gray Gnatcatcher (Polioptila caerulea) as a host to the Bronzed Cowbird (Molothrus aeneus) in Mexico

We report the first record of Bronzed Cowbird (Molothrus aeneus) brood parasitism on a sedentary tropical population of the Blue-gray Gnatcatcher (Polioptila caerulea), which probably represents the subspecies P. c. deppei. Our observations represent the 46th known true host species parasitized by this cowbird species, the 104th host and victim, and the 3rd known brood parasite for the family Polioptilidae. “Victims” are all species parasitized by cowbirds and “hosts” are those species that hatch, feed, and successfully raise cowbirds. Our assignment of these records to the true host list are based on feeding behavior observations at a nest in Veracruz, Mexico. We provide additional information on nest characteristics of an understudied gnatcatcher population.

Hydroalkylation of Alkenes with 1,3-Diketones via Gold(III) or Silver(I) Catalysis: Divergent Mechanistic Pathways Revealed by a DFT-Based Investigation

Density functional theory calculations were used to investigate the mechanisms of established hydroalkylation reactions of styrenes with 1,3-diketones that are promoted by either AuCl3/AgOTf or AgOTf catalyst systems. In the former case, our studies led us to propose an original mechanism that is initiated by the generation of highly electrophilic Au(OTf)3, which then coordinates the enol tautomer of the 1,3-diketone substrate. The ensuing highly Bronsted acidic π-complex serves to protonate the styrene to generate a relatively low-energy benzylic carbocation. Notably, this suggests that this benzylic carbocation represents the true catalytic species in the reaction, and thus, the role of the gold complex is solely to generate this active catalyst. AuCl3 alone does not serve as a good initiator for this process because it is not electrophilic enough to generate the relatively low-energy benzylic carbocation. Our investigation of the hydroalkylation facilitated by the slightly electron-deficient AgOTf catalyst revealed that an alternative mechanism predominates. Specifically, it is more likely that the reaction proceeds via a demetallation process directly mediated by the silver catalyst. We found a clear trend indicating that the electron deficiency of the metal center dictates which of these two mechanistic scenarios occurs. This article discusses these two mechanistic pathways in detail, providing key information for the experimental development of hydroalkylation processes.

Mechanistic Understanding of Water Oxidation in the Presence of a Copper Complex by In Situ Electrochemical Liquid Transmission Electron Microscopy.

The design of molecular oxygen-evolution reaction (OER) catalysts requires fundamental mechanistic studies on their widely unknown mechanisms of action. To this end, copper complexes keep attracting interest as good catalysts for the OER, and metal complexes with TMC (TMC = 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane) stand out as active OER catalysts. A mononuclear copper complex, [Cu(TMC)(H2O)](NO3)2 (TMC = 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane), combined both key features and was previously reported to be one of the most active copper-complex-based catalysts for electrocatalytic OER in neutral aqueous solutions. However, the functionalities and mechanisms of the catalyst are still not fully understood and need to be clarified with advanced analytical studies to enable further informed molecular catalyst design on a larger scale. Herein, the role of nanosized Cu oxide particles, ions, or clusters in the electrochemical OER with a mononuclear copper(II) complex with TMC was investigated by operando methods, including in situ vis-spectroelectrochemistry, in situ electrochemical liquid transmission electron microscopy (EC-LTEM), and extended X-ray absorption fine structure (EXAFS) analysis. These combined experiments showed that Cu oxide-based nanoparticles, rather than a molecular structure, are formed at a significantly lower potential than required for OER and are candidates for being the true OER catalysts. Our results indicate that for the OER in the presence of a homogeneous metal complex-based (pre)catalyst, careful analyses and new in situ protocols for ruling out the participation of metal oxides or clusters are critical for catalyst development. This approach could be a roadmap for progress in the field of sustainable catalysis via informed molecular catalyst design. Our combined approach of in situ TEM monitoring and a wide range of complementary spectroscopic techniques will open up new perspectives to track the transformation pathways and true active species for a wide range of molecular catalysts.

Re-Description of Sillago malabarica, Silver Whiting from Southern Indian Waters

Sillaginids possess similar taxonomic characters, which make the specific identification difficult, and many true species may be hidden in the synonymy of wide-ranging species. There are currently 36 valid species of sand whitings in the family Sillaginidae. Thirteen valid species are reported from Indian waters and six species are reported from the Arabian Sea. Investigations into the sillaginid diversity off the west coast of India revealed the presence of a species from the Arabian seawhich, on examination, proved to be very similar to the types of Sciaena malabarica. Based on conventional taxonomic analysis and DNA barcoding, we therefore raise Sillago malabarica (new combination) from the synonymy of S. sihama and re-describe it here. Distinctive characteristics of the species include XI-XII spines in the first dorsal fin; I, 21–24 rays in the 2nd dorsal fin; 3–4/7–8 gill rakers on 1st gill arch, Head length 25.2–30.4; Snout length 39.4%–46.8% HL; post-orbital length 34%–37.5% HL, 34 total vertebrae (abdominal: 13, haemal: 4 and caudal: 17); single sharp spine on the opercular edge; swim-bladder with eight or nine lateral processes extending from entire lateral surface of main body of swim bladder; golden silvery body, dorsal and anal fins hyaline, with yellow tips and the absence of a mid-lateral streak or dark bands. Apart from re described species S. malabarica, original S. sihama is also recorded from Indian waters, in our studies.

Integrated Approach for Species Identification and Quality Analysis for Labisia pumila Using DNA Barcoding and HPLC.

Labisia pumila is a precious herb in Southeast Asia that is traditionally used as a health supplement and has been extensively commercialized due to its claimed therapeutic properties in boosting a healthy female reproductive system. Indigenous people used these plants by boiling the leaves; however, in recent years it has been marketed as powdered or capsuled products. Accordingly, accuracy in determination of the authenticity of these modern herbal products has faced great challenges. Lack of authenticity is a public health risk because incorrectly used herbal species can cause adverse effects. Hence, any measures that may aid product authentication would be beneficial. Given the widespread use of Labisia herbal products, the current study focuses on authenticity testing via an integral approach of DNA barcoding and qualitative analysis using HPLC. This study successfully generated DNA reference barcodes (ITS2 and rbcL) for L. pumila var. alata and pumila. The DNA barcode that was generated was then used to identify species of Labisia pumila in herbal medicinal products, while HPLC was utilized to determine their quality. The findings through the synergistic approach (DNA barcode and HPLC) implemented in this study indicate the importance of both methods in providing the strong evidence required for the identification of true species and to examine the authenticity of such herbal medicinal products.

Effect of Anthropogenic Factors on the Ecosystem of the Yenisei River Anabranch within the City of Krasnoyarsk

In recent decades, freshwater ecosystems have regularly experienced blooms of green algae (green tides), causing environmental and economic damage. Blooms of green alga Spirogyra sp. occur in the ‘Abakanskaya’ anabranch of the Yenisei River in summer months. The anabranch is influenced by several anthropogenic factors: construction of a dam in the upper reaches; heated water discharge from a thermal power plant; fish farming. The aim of this study was to assess the impact of anthropogenic factors on the ecosystem of the Abakanskaya anabranch and to identify the main factors favoring Spirogyra sp. blooms. Samples were taken in May-September 2018-2019 at four sites: 1 – upstream of the dam (control), 2 – downstream of the dam, 3 – near the point of heated water discharge, 4 – downstream of the fish farm. Physical and chemical parameters, biomass and species composition of phytoplankton, phytoperiphyton, zooplankton, zoobenthos, and higher water plants, gross primary production (GPP), nitrogen content in biomass of periphyton, higher plants, and zoobenthos were studied. The main factor that caused changes in the community was that there was no water flow in the anabranch because of the low capacity of the dam drainage pipes. While upstream of the dam most ecosystem features were within the limits typical for this part of the Yenisei River, downstream of the dam, the system seemed to change from lotic to lentic: percentage of motile forms of phytoplankton, biomass of zooplankton, percentage of true zooplankton species, taxon number and taxonomic diversity of zooplankton and zoobenthos became higher; phytoperiphyton primary production rose (because of Spirogyra sp. bloom); higher water plants thrived. The other investigated factors, namely, thermal, nutrient, and organic pollution evidently produced combined effect on the ecosystem because of the absence of water flow, and their specific effects were not obvious

Most Genomic Loci Misrepresent the Phylogeny of an Avian Radiation Because of Ancient Gene Flow.

Phylogenetic trees based on genome-wide sequence data may not always represent the true evolutionary history for a variety of reasons. One process that can lead to incorrect reconstruction of species phylogenies is gene flow, especially if interspecific gene flow has affected large parts of the genome. We investigated phylogenetic relationships within a clade comprising eight species of passerine birds (Phylloscopidae, Phylloscopus, leaf warblers) using one de novo genome assembly and 78 resequenced genomes. On the basis of hypothesis-exclusion trials based on D-statistics, phylogenetic network analysis, and demographic inference analysis, we identified ancient gene flow affecting large parts of the genome between one species and the ancestral lineage of a sister species pair. This ancient gene flow consistently caused erroneous reconstruction of the phylogeny when using large amounts of genome-wide sequence data. In contrast, the true relationships were captured when smaller parts of the genome were analyzed, showing that the “winner-takes-all democratic majority tree” is not necessarily the true species tree. Under this condition, smaller amounts of data may sometimes avoid the effects of gene flow due to stochastic sampling, as hidden reticulation histories are more likely to emerge from the use of larger data sets, especially whole-genome data sets. In addition, we also found that genomic regions affected by ancient gene flow generally exhibited higher genomic differentiation but a lower recombination rate and nucleotide diversity. Our study highlights the importance of considering reticulation in phylogenetic reconstructions in the genomic era.[Bifurcation; introgression; recombination; reticulation; Phylloscopus.]

Two new species of emTypton/em Costa, 1844 from tropical American waters, withtaxonomic notes on emT. tortugae/em McClendon, 1911 and a new record of br /emT. granulosus/em Ayón-Parente, Hendrickx amp; Galvan-Villa, 2015 (Decapoda: Caridea: Palaemonidae).

Two new species of the palaemonid shrimp genus Typton Costa, 1844 are described based on material from Panama and Mexico. Both species are closely related to T. tortugae McClendon, 1911, a species originally described from the Dry Tortugas, off southern Florida, USA, and later scarcely recorded from other western Atlantic localities, from Bermuda to Mexico and Brazil. Some clarification and additional illustrations are provided for the type material of T. tortugae. Typton jonkayei sp. nov., is described based on material from fouling-encrusting communities dominated by sponges, growing on submerged roots of the red mangrove, Rhizhophora mangle L., in Bocas del Toro, Caribbean coast of Panama. This new species differs from T. tortugae in several morphological details, for instance, on the minor and major chelipeds (second pereiopods), telson, uropod, frontal margin and ambulatory pereiopods. Typton cousteaui sp. nov. is described based on a single ovigerous female dredged in the southern Gulf of California off Baja California Sur, Mexico, previously reported as T. tortugae. This new taxon seems to represent a true cryptic species with no significant morphological divergence from the allopatrically isolated T. tortugae, except for slight morphometric differences. In addition, T. granulosus Ayón-Parente, Hendrickx Galvan-Villa, 2015 is recorded from the Pacific coast of Panama, based on material collected in the Coiba Archipelago. Some taxonomic, distributional and ecological remarks are provided for T. granulosus and the closely related T. serratus Holthuis, 1951.

PRELIMINARY CHECKLIST OF FRESHWATER FISHES OF ULU PAIP ECO-PARK FOREST, KEDAH, PENINSULAR MALAYSIA

This report is the first on freshwater fishes of Ulu Paip Eco-Park Forest, Kedah, which aims to document the fish species richness in this recreational forest. All species were collected from the main stream, Sungai Karangan, and its unnamed tributaries. In total, 20 species of fishes from 10 families were recorded. Cyprinidae is the most dominant family with six species followed by Danionidae with three species. Other families contribute at least one species each. Most of the species recorded here are commonly found in the northern part of Peninsular Malaysia. Further studies should be expected to record more species and the utilization of various sampling gear such as electro fishing technique would be able to recordthe true species richness of fishes in this area.

New Permian radiolarians from east Asia and the quantitative reconstruction of their evolutionary and ecological significances

The biostratigraphically important Permian radiolarian genera Pseudoalbaillella sensu stricto and Follicucullus (Follicucullidae, Polycystinea) are discriminated by morphological gaps in their wings and segmentation. Previous statistical analyses demonstrated that Longtanella fills morphological gaps between these two genera. Longtanella has long been regarded as a junior synonym of Parafollicucullus, and only a few species have been described. Herein several true Longtanella species are recognized from South China, and eight new species and five indeterminate species are described and illustrated to prove the validity of the genus Longtanella. In addition, a new genus, Parafollicucullinoides gen. nov., is described. Their palaeogeographic distributions and living environments are explored by applying correspondence analysis (CA), with occurrence datasets of selected fusulinacean genera from the Japanese Islands, China and Sundaland. CA results indicate that Longtanella was present to a limited extent in warmer conditions in the fusulinacean Province B and C during Kungurian–Roadian time, and possibly lived above the thermocline and below the deepest limit of fusulinaceans. The Pseudoalbaillella and the Follicucullus group preferred open ocean conditions, living below the thermocline and distributed not only in the ‘Equatorial Warm Water Province’, but also the northern peri-Gondwana Cool Water Province and the southern North Cool Water Province.

The Roles of Protein Structure, Taxon Sampling, and Model Complexity in Phylogenomics: A Case Study Focused on Early Animal Divergences

Despite the long history of using protein sequences to infer the tree of life, the potential for different parts of protein structures to retain historical signal remains unclear. We propose that it might be possible to improve analyses of phylogenomic datasets by incorporating information about protein structure. We test this idea using the position of the root of Metazoa (animals) as a model system. We examined the distribution of “strongly decisive” sites (alignment positions that support a specific tree topology) in a dataset comprising >1500 proteins and almost 100 taxa. The proportion of each class of strongly decisive sites in different structural environments was very sensitive to the model used to analyze the data when a limited number of taxa were used but they were stable when taxa were added. As long as enough taxa were analyzed, sites in all structural environments supported the same topology regardless of whether standard tree searches or decisive sites were used to select the optimal tree. However, the use of decisive sites revealed a difference between the support for minority topologies for sites in different structural environments: buried sites and sites in sheet and coil environments exhibited equal support for the minority topologies, whereas solvent-exposed and helix sites had unequal numbers of sites, supporting the minority topologies. This suggests that the relatively slowly evolving buried, sheet, and coil sites are giving an accurate picture of the true species tree and the amount of conflict among gene trees. Taken as a whole, this study indicates that phylogenetic analyses using sites in different structural environments can yield different topologies for the deepest branches in the animal tree of life and that analyzing larger numbers of taxa eliminates this conflict. More broadly, our results highlight the desirability of incorporating information about protein structure into phylogenomic analyses.

Developmental validation of Oxford Nanopore Technology MinION sequence data and the NGSpeciesID bioinformatic pipeline for forensic genetic species identification

Species identification of non-human biological evidence through DNA nucleotide sequencing is routinely used for forensic genetic analysis to support law enforcement. The gold standard for forensic genetics is conventional Sanger sequencing; however, this is gradually being replaced by high-throughput sequencing (HTS) approaches which can generate millions of individual reads in a single experiment. HTS sequencing, which now dominates molecular biology research, has already been demonstrated for use in a number of forensic genetic analysis applications, including species identification. However, the generation of HTS data to date requires expensive equipment and is cost-effective only when large numbers of samples are analysed simultaneously. The Oxford Nanopore Technologies (ONT) MinION™ is an affordable and small footprint DNA sequencing device with the potential to quickly deliver reliable and cost effective data. However, there has been no formal validation of forensic species identification using high-throughput (deep read) sequence data from the MinION making it currently impractical for many wildlife forensic end-users. Here, we present a MinION deep read sequence data validation study for species identification. First, we tested whether the clustering-based bioinformatics pipeline NGSpeciesID can be used to generate an accurate consensus sequence for species identification. Second, we systematically evaluated the read variation distribution around the generated consensus sequences to understand what confidence we have in the accuracy of the resulting consensus sequence and to determine how to interpret individual sample results. Finally, we investigated the impact of differences between the MinION consensus and Sanger control sequences on correct species identification to understand the ability and accuracy of the MinION consensus sequence to differentiate the true species from the next most similar species. This validation study establishes that ONT MinION sequence data used in conjunction with the NGSpeciesID pipeline can produce consensus DNA sequences of sufficient accuracy for forensic genetic species identification.

True bugs (Heteroptera) of the Pannonic salt steppes and salt marshes in Serbia and their conservation status in the Pannonian countries

Summary Inland saline grasslands and wetlands of the Pannonian Region are areas of great conservation importance since they are the only habitats known for numerous Eurasian steppe species. Characteristic vegetation of halophytes accommodates unique communities of true bugs with several saline habitat specialists. These saline specialists and some rare steppe species are highly threatened and listed in the red lists of several Pannonian countries. Serbian data on true bug fauna from saline habitats are scarce, and the last known work on these insects was done by Géza Horváth more than a century ago. Our study aims to explore the richness of the true bug fauna of saline habitats with the presence of saline specialists in Northern Serbia. We also aim to highlight the species of potential conservation importance. In total, 231 species of true bugs species are recorded from saline habitats of the Pannonian Serbia. For the first time Agramma (Agramma) ruficorne (Germar, 1835), Chlamydatus (Chlamydatus) saltitans (Fallén, 1807), Emblethis brachynotus Horváth, 1897, Lygaeosoma anatolicum Seidenstücker, 1960, Geotomus punctulatus (Costa, 1847) and Phimodera flori Fieber, 1863 are mentioned here from our country. After several decades, seven species are rediscovered – Chartoscirta cocksii (Curtis, 1835), Acalypta gracilis (Fieber, 1844), Aoploscelis bivirgata (Costa, 1853), Compsidolon (Apsinthophylus) pumilum (Jakovlev, 1876), Conostethus hungaricus Wagner, 1941, Criocoris sulcicornis (Kirschbaum, 1856) and Crypsinus angustatus (Baerensprung, 1859) – previously, the most recent records of the latter four species were provided by Horváth in the late nineteenth century. After five years of systematic research of the Pannonic salt steppes and salt marshes, we could say that this unique group of habitats is one of the best-studied for true bugs in our country. However, to give a solid foundation for future red lists of true bugs of Serbia, other parts of the country also need to be explored thoroughly. Besides saline specialists, the red list should consider and prioritize species with rare records in Serbia.

Addressing the "Paradox of the Plankton": Using Metabarcoding to Explore Zooplankton Diversity Patterns Across Chemical Conditions in the Salish Sea

Traditional taxonomic analysis of zooplankton is time consuming, expensive, and unable to resolve the true species diversity of a community due to a lack of diagnostic morphological characters for many taxa. This is especially true for early life stages, undescribed, and cryptic species. This limitation has led to a dramatic under-estimation of the incredible diversity of life that inhabits the ocean, hindering our understanding of the environmental conditions that structure communities. Multi-gene metabarcode high-throughput sequencing (HTS) analyses entailing field sampling and bioinformatics offer new means to rapidly and accurately characterize the species identities, diversity, and composition of entire communities. We use multiple diagnostic Illumina MiSeq HTS metabarcode assays (for mitochondrial COI, 16SRNA, and 12SRNA gene regions) and a custom bioinformatics pipeline to analyze communities of invertebrates and fishes from zooplankton net tows collected concurrently with environmental chemistry data across Puget Sound in the southern Salish Sea. We compare results among sites for spring and autumn seasons, as a prelude to multi-year analyses. Findings show considerable divergence in species composition and diversity among sites and season, reflecting differences in salinity, pH, and proximity to the ocean. This approach has great potential for wide-spread use in monitoring programs to assess the diversity of marine plankton communities in conjunction with changing conditions, including ocean acidification, hypoxia, and global temperature rise.

An Optimised Surface Structure for Passive, Unidirectional Fluid Transport Bioinspired by True Bugs

Some true bug species use droplet-shaped, open-capillary structures for passive, unidirectional fluid transport on their body surface in order to spread a defensive fluid to protect themselves against enemies. In this paper we investigated if the shape of the structures found on bugs (bug-structure) could be optimised with regard to better performance in unidirectional fluid transportation. Furthermore, to use this kind of surface structure in technical applications where fluid surface interaction occurs, it is necessary to adapt the structure geometry to the contact angle between fluid and surface. Based on the principal of operation of the droplet-shaped structures, we optimised the structure shape for better performance in targeted fluid flow and increase in flexibility in design of the structure geometry. To adapt the structure geometry and the structure spacing to the contact angle, we implemented an equilibrium simulation of the, the structure surrounding, fluid. In order to verify the functionality of the optimised structure, we designed and manufactured a prototype. By testing this prototype with pure water used as fluid, the functionality of the optimised structure and the simulation could be proved. This kind of structure may be used on technical surfaces where targeted fluid transport is needed, e.g. evacuation of condensate in order to prevent the surface from mold growth, microfluidics, lab-on-a-chip applications and on microneedles for efficient drug/vaccine coating.

New and rare for the Belarusian fauna True Bug species (Insecta: Hemiptera: Heteroptera) from the parks of Brest Region

New and rare for the Belarusian fauna True Bug species (Insecta: Hemiptera: Heteroptera) from the parks of Brest Region

Comparing sample bias correction methods for species distribution modeling using virtual species

AbstractA key assumption in species distribution modeling (SDM) with presence‐background (PB) methods is that sampling of occurrence localities is unbiased and that any sampling bias is proportional to the background distribution of environmental covariates. This assumption is rarely met when SDM practitioners rely on federated museum records from natural history collections for geo‐located occurrences due to inherent sampling bias found in these collections. We use a simulation approach to explore the effectiveness of three methods developed to account for sampling bias in SDM with PB frameworks. Two of the methods rely on careful filtering of observation data—geographic thinning (G‐Filter) and environmental thinning (E‐Filter)—while a third, FactorBiasOut, creates selection weights for background data to bias locations toward areas where the observation dataset was sampled. While these methods have been assessed previously, evaluation has emphasized spatial predictions of habitat potential. Here, we dig deeper into the effectiveness of these methods by exploring how sampling bias not only affects predictions of habitat potential, but also our understanding of niche characteristics such as which explanatory variables and response curves best represent species–environment relationships. We simulate 100 virtual species ranging from generalist to specialist in their habitat preferences and introduce geographic and environmental bias at three intensity levels to measure the effectiveness of each correction method to (1) predict true probability of occurrence across a study area, (2) recover true species–environment relationships, and (3) identify true explanatory variables. We find that the FactorBiasOut most often showed the greatest improvement in recreating known distributions but did no better at correctly identifying environmental covariates or recreating species–environment relationships than G‐Filter or E‐Filter methods. Narrow niche species are most problematic for biased calibration datasets, such that correction methods can, in some cases, make predictions worse.

Impacts of harvesting intensity on tree taxonomic diversity, structural diversity, population structure, and stability in a West African mangrove forest

Understanding the impacts of wood harvesting intensity on the diversity and structure of ecosystems such as mangroves is essential for defining actions for their sustainable management. We compared tree taxonomic diversity, structural diversity and dominance patterns, density, growth characteristics, size class distribution-SCD and stand stability in West African mangroves subject to low vs. high wood harvesting intensity. Data on tree species identity, total height, diameter (dbh), and conditions (logged, topped or pruned) were collected from ten mangrove sites per harvesting intensity. We found seven species of which two true mangroves species (Rhizophora racemosa and Avicennia germinans) that were dominant across all sites. As expected, there were significantly 3–4, 3–7, and 2–4 times more logged, topped and pruned trees respectively in high-harvesting sites than in low-harvesting sites. Taxonomic diversity was less affected than structural diversity (dbh and height-based diversity metrics). Tree density was significantly 1.3–5 times higher in low-harvesting sites than in high-harvesting sites for the whole stand and each of the dominant species. Total regeneration density was also low in high-harvesting sites. However, regeneration density was relatively higher in high-harvesting sites for R. racemosa contrary to A. germinans. Trees were also significantly smaller and shorter in high-harvesting sites. The SCD indicated inverse J-shaped distributions, irrespective of the harvesting intensity and showed that tree harvesting targeted mostly dbh classes 10–30 cm. The density of this class was 2.6–6.2 times lower in high-harvesting sites. This study provides important information on impacts of wood harvesting in a marginally studied mangroves’ area.