Composition and spatio-temporal dynamics of aquatic bird community in humid areas of Alto Parana Atlantic Forest / Composição e dinâmica espaço-temporal da comunidade de aves aquáticas em áreas úmidas da Floresta Atlântica do Alto Paraná

Abstract The northwestern portion of the Upper Paraná Atlantic Forest ecoregion is one of the most disturbed and fragmented areas in the Atlantic Forest, and little is known about the local avifauna. In this study, we have described the composition and diversity of the aquatic avifauna of this region and analyzed the patterns of similarity with respect to the seasonal as well as spatial distribution. We used the line transect sampling technique in six distinct humid areas (including lentic and lotic water bodies) during the dry and rainy seasons of 2012 and 2013. A total of 52 species of waterfowl were recorded. The species richness of the studied areas was surprisingly distinct; only seven waterfowl species, namely Cairina moschata (Linnaeus, 1758), Tigrisoma lineatum (Boddaert, 1783), Rosthramus sociabilis (Vieillot, 1817), Aramus guarauna (Linnaeus, 1766), Vanellus chilensis (Molina, 1782), Jacana jacana (Linnaeus, 1766), and Arundinicola leucocephala (Linnaeus, 1764), were common to these six studied areas. This indicated that the other bird species that were observed might be habitat selective. Moreover, the analysis of the composition of birds in the two seasons (dry and rainy) combined with their spatial distributions showed significant dissimilarities between the areas with lotic (river and constructed wetland) and lentic (lagoons) characteristics. Nevertheless, despite the small extent and low total richness of the entire study area, it was found to be home to 1/3 of all freshwater aquatic birds documented in the state of São Paulo, with the record of 5 migratory species and 11 new species added to the northwest of the state. The heterogeneity of local aquatic environments, habitat selection combined with seasonality, and the absence of other humid locations in the surroundings can explain the diversity and distribution of these birds in the water bodies of this uninvestigated Atlantic Forest ecoregion.

Resumo A porção noroeste da ecorregião Floresta Atlântica do Alto Paraná é uma das mais alteradas e fragmentadas da Mata Atlântica, da qual pouco se sabe sobre a avifauna local. Nosso objetivo foi descrever a diversidade e composição da avifauna aquática, bem como analisar os padrões de similaridade quanto a distribuição temporal e espacial destas aves nesta ecorregião. Utilizamos a transecção linear para amostragem em seis áreas úmidas (corpos d'água lênticos e lóticos), nos períodos de seca e chuva entre 2012 e 2013. Registramos 52 espécies de aves aquáticas e as riquezas das áreas mostraram-se distintas, pois apenas Cairina moschata (Linnaeus, 1758), Tigrisoma lineatum (Boddaert, 1783), Rosthramus sociabilis (Vieillot, 1817), Aramus guarauna (Linnaeus, 1766), Vanellus chilensis (Molina, 1782), Jacana jacana (Linnaeus, 1766), and Arundinicola leucocephala (Linnaeus, 1764) foram comuns às seis áreas, o que indica seleção de habitat. Quando analisada a composição das aves nos dois períodos aliada à distribuição espacial, encontramos dissimilaridades temporais acentuadas entre os ambientes com características lóticas (rio e aterro) e lênticas (lagoas). Isto mostra que, além das diferentes épocas sazonais, é necessário analisar separadamente os diferentes tipos de áreas úmidas. Por fim, apesar da extensão pequena e baixa riqueza total, a área amostrada abrigou 1/3 das aves aquáticas de água doce para o estado de São Paulo, cinco espécies migratórias e 11 novas espécies para o noroeste do estado. A heterogeneidade de ambientes aquáticos locais, forte seleção de habitat aliada à sazonalidade e ausência de outros locais úmidos em seu entorno, explicam a diversidade e distribuição destas aves estreitamente relacionadas aos corpos d'água desta desconhecida ecorregião da Mata Atlântica.

Insects associated to ephemeral pools in Huentelauquén (29ºS Coquimbo Region, Chile) / Insetos associados a lagoas temporárias em Huentelauquén (29ºS Região de Coquimbo, Chile)

Abstract In northern central Chile, ephemeral pools constitute shallow isolated water bodies with a favourable habitat for fauna adapted to seasonal changes. Based on the limited knowledge about the fauna—particularly insects—associated to these ecosystems, the objective of this study was to characterize the richness, composition, structure and similarity of the insect communities associated with ephemeral pools in Huentelauquén (29º S, Coquimbo Region, Chile). By using pitfall traps, 10,762 individuals were captured, represented by 7 orders, 27 families, and 51 species. Coleoptera and Hymenoptera were the best represented orders, with Neuroptera, Orthoptera and Plecoptera being poorly represented groups. The non-parametric estimators evaluated showed wealth values above those observed for all the studied pools, and their accumulation curves suggest the existence of an incomplete species inventory in the studied community. Additionally, the hierarchical and ordering analysis showed groupings of pools located in the northwest and southeast of Huentelauquén. Preliminarily we found a negative correlation between the area of the pools and the richness (species) and abundance of insects. Additional studies (on other arthropod groups and other seasons of the year) could provide a better understanding of the local processes of extinction and colonization of the species inhabiting these fragile coastal environments.

Resumo No norte central do Chile, lagoas efêmeras constituem corpos de água isolados e pouco profundos, com um habitat favorável para a fauna adaptada as mudanças sazonais que as zonas úmidas estão sujeitas. Com relação a estes ecossistemas, sabe-se pouco sobre sua fauna, principalmente a de insetos. O objetivo do presente estudo foi caracterizar a riqueza, composição, estrutura e similaridade das comunidades de insetos que habitam as lagoas temporárias de Huentelauquén (29º S, Região de Coquimbo, Chile). Usando armadilhas de interceptação, se capturou um total de 10.762 indivíduos, pertencentes a 7 ordens, 27 famílias e 51 espécies. Coleoptera e Hymenoptera foram as ordens mais representativas, enquanto Neuroptera, Orthoptera e Plecoptera foram grupos pouco representativos. Os estimadores não paramétricos avaliados mostraram valores de riqueza superiores ao observados para todas as lagoas estudadas, e suas curvas de acumulação parecem indicar que o inventario da comunidade estudada está incompleto. A análise hierárquica e de ordenamento revelou agrupamentos de lagoas correspondentes a zona nordeste e sudeste de Huentelauquén. Preliminarmente encontramos uma correlação negativa entre a área de lagoas efêmeras e a riqueza (espécies) e abundância de insetos. É necessário realizar estudos adicionais (sobre outros grupos de artrópodes e em outras estações do ano) para melhor compreensão dos processos locais de extinção e colonização das espécies que habitam estes frágeis ambientes costeiros estudados.

Impacts of mining on local fauna of wildlife in District Mardan & District Mohmand Khyber Pakhtunkhwa Pakistan / Impactos da mineração na fauna local da vida selvagem nos Distritos de Mardan e de Mohmand, Khyber Pakhtunkhwa, Paquistão

Abstract Mining is vital for human sustenance and a crucial sector in the state economy. However, its impacts on the environment and biodiversity cannot be underestimated. Which are potent to the attract government's attention. Environment and wildlife are subject to the harmful impacts of mining and its related activities. In this study, districts, namely Mardan and Mohmand have been targeted with respect to mining impacts. The assessment was carried out on wildlife adversely affected by the mining sector. The fauna has been keenly observed to bring the calculated risks and threat perception of the regional wildlife. Total 9 species of mammals, 21 species of birds, were recorded in District Mardan. While in District Mohmand 2 species of mammals, 9 species of birds, and 4 species of reptiles were studied. The Study explored that mining primarily responsible for land degradation. Which lead to food and agriculture losses. Several other factors like blasting, pollution, hunting, deforestation, habitat loss was also observed. Deforestation surfaced one of the major causes for extinction of fauna in the said region. preemptive measures are needed to seize the man-made catastrophe.

Resumo A mineração é vital para o sustento humano e um setor crucial na economia do Estado. No entanto, seus impactos sobre o meio ambiente e a biodiversidade não podem ser subestimados, visto serem potentes para atrair a atenção do governo. O meio ambiente e a vida selvagem estão sujeitos aos impactos prejudiciais da mineração e de suas atividades relacionadas. Neste estudo, os distritos, nomeadamente Mardan e Mohmand, foram selecionados ​​no que diz respeito aos impactos da mineração. A avaliação foi realizada em animais selvagens afetados negativamente pelo setor de mineração. A fauna tem sido observada atentamente para trazer os riscos calculados e a percepção de ameaça à vida selvagem regional. Um total de nove espécies de mamíferos, 21 espécies de pássaros, foi registrado no Distrito Mardan. Enquanto no Distrito Mohmand, duas espécies de mamíferos, nove espécies de pássaros e quatro espécies de répteis foram estudadas. O estudo explorou essa mineração que é principalmente responsável pela degradação do solo, acarretando perdas de alimentos e na agricultura. Vários outros fatores como explosões, poluição, caça, desmatamento, perda de habitat também foram observados. O desmatamento veio à tona como uma das principais causas de extinção da fauna da região, e tem-se que medidas preventivas são necessárias para dimensionar a catástrofe provocada pelo homem.

Benthic community ecology for Algerian river Seybouse / Ecologia da comunidade bêntica para o rio Seybouse da Argélia

Abstract The Seybouse is the second largest river basin in Algeria, hosting an important biodiversity and providing various ecosystem services. This watershed is highly influenced by agricultural and industrial activities, which threaten its biodiversity and ecosystem integrity. The use of benthic macroinvertebrates as biological indicators has a long tradition in developed countries and integrated into all assessments of the ecological quality of river systems. However, the macroinvertebrates of many North African regions are still not well studied, including those of the Seybouse river. The aim of this study is to assess the inventory and ecological role of benthic macroinvertebrates in inland waters of the Seybouse River and determine the impact of pollution on their spatial distributions. We sampled the benthic macrofauna of Wadi Seybouse and its affluents using regular surveys in three sites, of which one was in the upper Seybouse Bouhamdane in Medjez Amar and two in the middle Seybouse. Between December 2019 and May 2020, 10 physico-chemical parameters (pH, EC, OD, water speed, NO3, Salinity, NO2, MES, turbidity, depth) were measured in order to establish a health state diagnosis of these aquatic ecosystems. The complementary biological approach by the analysis of populations of macroinvertebrates identified 7482 individuals and 40 taxa divided into five classes: Crustaceans which were the most dominant, insects with the main orders (Ephemeroptera, Diptera, Trichoptera, Heteroptera and Odonata), Molluscs, Nematodes and Annelids. The physico-chemical analyzes and the application of the organic pollution indices indicated a strong to excessive pollution for all sites, especially in Seybouse upstream

Resumo O Seybouse é um rio no nordeste da Argélia, é o segundo maior rio, tem uma área de captação de cerca de 6.500 km2 que acolhe cerca de 1,5 milhões de habitantes. Importantes atividades agrícolas e industriais são desenvolvidas nesta bacia hidrográfica. O uso de macroinvertebrados bentônicos como indicadores biológicos tem uma longa tradição em países desenvolvidos e está integrado em todas as avaliações da qualidade ecológica dos sistemas fluviais. O objetivo deste estudo foi revisar o inventário e o papel ecológico dos macroinvertebrados bentônicos nas águas interiores do rio Seybouse e determinar o impacto da poluição em suas distribuições. Resultados semelhantes foram relatados para outros países e rios argelinos. Este estudo enfoca a macrofauna bentônica de Wadi Seybouse e seus afluentes. Foram prospectados 03 locais, um no alto Seybousse Bouhamdane em Medjez Amar e dois no meio Seybousse Salah Salah Salah e Oued Zimba. Entre dezembro de 2019 e maio de 2020, dez parâmetros físico-químicos (pH, CE, DO, velocidade da água, NO3, Salinidade, NO2, MES, turbidez, deth) foram medidos para estabelecer um diagnóstico do estado de saúde desses ecossistemas aquáticos. A abordagem biológica complementar pela análise de populações de macroinvertebrados identificou 7.482 indivíduos e 40 táxons divididos em cinco classes: Crustáceos que são os mais dominantes, Insetos com as ordens principais (Ephemeroptera, Diptera, Trichoptera, Heteroptera e Odonata), Moluscos, Nematóides e Anelídeos. As análises físico-químicas e a aplicação dos índices de poluição orgânica, indicaram uma poluição forte a excessiva para todos os locais especialmente Salah Salah Salah.

Diversity of culturable endophytic fungi vary through time in Manihot esculenta Crantz / A diversidade de fungos endofíticos cultiváveis ​​varia ao longo do tempo em Manihot esculenta Crantz

Abstract Endophytic fungi are a ubiquituos group that colonize all plant species on earth. Studies comparing the location of endophytic fungi within the leaves and the sampling time in Manihot esculenta Crantz (cassava) are limited. In this study, mature leaves of M. esculenta from Panama were collected in order to compare the cultivable diversity of endophytic fungi and to determine their distribution within the leaves. A total of one hundred sixty endophytes belonging to 97 species representing 13 genera and 8 morphospecies determined as mycelia sterilia that containing 63 isolates were isolated. Cladosporium, Nigrospora, Periconia, and mycelia sterilia 1 and 3 were the most predominant isolated endophytes. We detected that endophytes varied across the sampling time, but not amongst locations within leaves. The endophytes composition across sampling and the location of endophytes within leaf was similar, except for Periconia and mycelia sterilia 3 and 7. The data generated in this study contribute to the knowledge on the biodiversity of endophytic fungi in Panama, and establish the bases for future research focused on understanding the function of endophytes in M. esculenta crops.

Resumo Os fungos endofíticos são um grupo ubiquituo que colonizam todas as espécies de plantas na terra. Os estudos que comparam a localização dos fungos endofíticos dentro das folhas de Manihot esculenta Crantz (mandioca) e o tempo de amostragem são muito escassos. Neste estudo, folhas maduras de M. esculenta foram coletadas do Panamá com a finalidade de comparar a diversidade cultivável de endófitos e determinar sua distribuição dentro das folhas. Um total de 170 endófitos foram isolados de 97 espécies que representam 13 gêneros e 8 morfoespécies determinadas como micélios esterilizados contendo 63 isolados. Os fungos Cladosporium, Nigrospora, Periconia e mycelia sterilia 1 e 3 foram os isolados mais predominantes. Também detectamos que os endófitos variaram ao longo do tempo de amostragem, mas não entre os locais dentro das folhas. A composição de endófitos na amostragem e localização de endófitos dentro da folha foi semelhante, exceto para Periconia e mycelia sterilia 3 e 7. Os dados gerados neste estudo contribuem para o conhecimento da biodiversidade de fungos endofíticos no Panamá e estabelecem as bases para pesquisas sobre o entendimento da função de endófitos em culturas de M. esculenta.

Biodiversity, distributions and isolation of microplastics pollution in finfish species in the Panjkora River at Lower and Upper Dir districts of Khyber Pakhtunkhwa province of Pakistan / Biodiversidade, distribuição e isolamento de poluições por microplásticos em espécies de peixes no rio Panjkora nos distritos de Lower e Upper Dir da província de Khyber Pakhtunkhwa do Paquistão

The basic aim of this study was aimed to determine the ichthyofaunal diversity of River Panjkora in both upper and lower Dir districts in Khyber Pakhtunkhwa province of Pakistan.Fish samples were collected by using fishnets from March to September 2020. A total of 724 specimens were collected and classified into 5 families, 14 genera, and 18 species. The overall results revealed that most fish fauna of river Panjkora contains 8 species of family Cyprinidae (56.49%) followed by 4 species of Nemacheilidae (24.44%), 2 species of Channidae (10.63%), and Sisoridae (7.04%), and 1 species of Mastacembelidae (1.38%), respectively. Among all kinds of fish species, Schizothorax plagiostomus (16.57%) was highly dominated and followed by Carassius auratus (11.87%) and Racoma labiata (9.66%) and were reported as highly abundant, especially during April, May, and June. The least abundant species were Glyptothorax punjabensis, Glyptothorax sufii, and Mastacembelus armatus, that constituting 2.48%, 2.20%, and 1.38% of the total fish samples. The Overall Simpson's diversity (1-D= 0.919) and Simpson's Reciprocal index values (1/D= 12.3876), and Shannon's index (H= 2.68) were indicating that river Panjkora contains a quite rich and diverse group of fish species. The highest microplastics observed in site 7 compared to other study area. Conservation steps should be taken as a top priority to protect and conserve the marine environment and natural heritage from further loss, extinction and stop or minimize losses incurred through irresponsible fishery practices

O objetivo básico deste estudo foi determinar a diversidade ictiofaunística do rio Panjkora nos distritos de Lower e Upper de Dir, na província de Khyber Pakhtunkhwa, no Paquistão. Amostras de peixes foram coletadas com redes de arrasto de março a setembro de 2020. Foram coletados 724 espécimes, classificados em 5 famílias, 14 gêneros e 18 espécies. Os resultados gerais revelaram que a maioria da ictiofauna do rio Panjkora contém 8 espécies da família Cyprinidae (56,49%), seguidas por 4 espécies de Nemacheilidae (24,44%), 2 espécies de Channidae (10,63%) e Sisoridae (7,04%) e 1 espécie de Mastacembelidae (1,38%). Entre todas as espécies de peixes, Schizothorax plagiostomus (16,57%) foi altamente predominante, seguida por Carassius auratus (11,87%) e Racoma labiata (9,66%), e elas foram relatadas como altamente abundantes, especialmente nos meses de abril, maio e junho. As espécies menos abundantes foram Glyptothorax punjabensis, Glyptothorax sufii e Mastacembelus armatus, que constituíram 2,48%, 2,20% e 1,38%, respectivamente, do total de peixes amostrados. O índice de diversidade de Simpson (1-D = 0,919), o índice recíproco de Simpson (1/D = 12,3876) e o índice de Shannon (H = 2,68) indicaram que o rio Panjkora contém um grupo bastante rico e diversificado de espécies de peixes. Os microplásticos mais altos foram observados no local 7 em comparação com outra área de estudo. Medidas de conservação devem ser tomadas como prioridade máxima para proteger e conservar o ambiente marinho e o patrimônio natural de novas perdas e extinção e para parar ou minimizar as perdas ocorridas por práticas de pesca irresponsáveis.

Grasshopper (Orthoptera: Acridomorpha) diversity in response to fallow-land use in southern Cameroon with recommendations for land management.

The sensitivity of grasshoppers to disturbance makes them useful bioindicators for land management. The current study compared the grasshopper communities of three fallow-lands at different levels of human pressure: heavily used land (Ongot), moderately used land (Zamakoe), and least-used land (Ngutadjap). Grasshoppers were sampled by nets, pitfall traps, and box quadrats. Their species composition was analyzed using species-richness, abundance, abundance distribution-model, occurrence, and diversity indexes. Species number was not very different between localities. However, the opening up of forests by human activities offers suitable environment for the development or proliferation of the pest grasshopper populations such as Zonocerus variegatus (Linnaeus, 1758), Eyprepocnemis plorans (Charpentier, 1825), and Catantops sylvestrisJago, 1984, which are adapted to the very common Asteraceae found in fallow lands. Native forest species [such as Mazaea granulosa Stål, 1876, Holopercna gerstaeckeri (Bolívar, 1890), Digentia fasciataRamme, 1929] were, generally absent or rare and were collected in only forest/fallow-land ecotones. Low abundance and low occurrence of ecotone species fitted the log-normal abundance distribution model. The grasshopper communities of the less degraded localities were quite similar, but different from the Ongot community. Forest management by reforestation, reduction of slash-and-burn agriculture, and wood cutting, would restore the original grasshopper assemblages and general environmental health.

Distinctive origin and evolution of endemic thistle of Korean volcanic island: Structural organization and phylogenetic relationships with complete chloroplast genome.

Unlike other Cirsium in Korea, Cirsium nipponicum (Island thistle) is distributed only on Ulleung Island, a volcanic island off the east coast of the Korean Peninsula, and a unique thistle with none or very small thorns. Although many researchers have questioned the origin and evolution of C. nipponicum, there is not much genomic information to estimate it. We thus assembled the complete chloroplast of C. nipponicum and reconstructed the phylogenetic relationships within the genus Cirsium. The chloroplast genome was 152,586 bp, encoding 133 genes consisting of 8 rRNA genes, 37 tRNA genes, and 88 protein-coding genes. We found 833 polymorphic sites and eight highly variable regions in chloroplast genomes of six Cirsium species by calculating nucleotide diversity, as well as 18 specific variable regions distinguished C. nipponicum from other Cirsium. As a result of phylogenetic analysis, C. nipponicum was closer to C. arvense and C. vulgare than native Cirsium in Korea: C. rhinoceros and C. japonicum. These results indicate that C. nipponicum is likely introduced through the north Eurasian root, not the mainland, and evolved independently in Ulleung Island. This study contributes to further understanding the evolutionary process and the biodiversity conservation of C. nipponicum on Ulleung Island.

Highly accurate long reads are crucial for realizing the potential of biodiversity genomics.

BACKGROUND: Generating the most contiguous, accurate genome assemblies given available sequencing technologies is a long-standing challenge in genome science. With the rise of long-read sequencing, assembly challenges have shifted from merely increasing contiguity to correctly assembling complex, repetitive regions of interest, ideally in a phased manner. At present, researchers largely choose between two types of long read data: longer, but less accurate sequences, or highly accurate, but shorter reads (i.e., >Q20 or 99% accurate). To better understand how these types of long-read data as well as scale of data (i.e., mean length and sequencing depth) influence genome assembly outcomes, we compared genome assemblies for a caddisfly, Hesperophylax magnus, generated with longer, but less accurate, Oxford Nanopore (ONT) R9.4.1 and highly accurate PacBio HiFi (HiFi) data. Next, we expanded this comparison to consider the influence of highly accurate long-read sequence data on genome assemblies across 6750 plant and animal genomes. For this broader comparison, we used HiFi data as a surrogate for highly accurate long-reads broadly as we could identify when they were used from GenBank metadata. RESULTS: HiFi reads outperformed ONT reads in all assembly metrics tested for the caddisfly data set and allowed for accurate assembly of the repetitive ~ 20 Kb H-fibroin gene. Across plants and animals, genome assemblies that incorporated HiFi reads were also more contiguous. For plants, the average HiFi assembly was 501% more contiguous (mean contig N50 = 20.5 Mb) than those generated with any other long-read data (mean contig N50 = 4.1 Mb). For animals, HiFi assemblies were 226% more contiguous (mean contig N50 = 20.9 Mb) versus other long-read assemblies (mean contig N50 = 9.3 Mb). In plants, we also found limited evidence that HiFi may offer a unique solution for overcoming genomic complexity that scales with assembly size. CONCLUSIONS: Highly accurate long-reads generated with HiFi or analogous technologies represent a key tool for maximizing genome assembly quality for a wide swath of plants and animals. This finding is particularly important when resources only allow for one type of sequencing data to be generated. Ultimately, to realize the promise of biodiversity genomics, we call for greater uptake of highly accurate long-reads in future studies.

Mapping of Phragmites in estuarine wetlands using high-resolution aerial imagery.

Phragmites australis is a widespread invasive plant species in the USA that greatly impacts estuarine wetlands by creating dense patches and outcompeting other plants. The invasion of Phragmites into wetland ecosystems is known to decrease biodiversity, destroy the habitat of threatened and endangered bird species, and alter biogeochemistry. While the impact of Phragmites is known, the spatial extent of this species is challenging to document due to its fragmented occurrence. Using high-resolution imagery from the National Agriculture Imagery Program (NAIP) from 2017, we evaluated a geospatial method of mapping the spatial extent of Phragmites across the state of DE. Normalized difference vegetation index (NDVI) and principal component analysis (PCA) bands are generated from the NAIP data and used as inputs in a random forest classifier to achieve a high overall accuracy for the Phragmites classification of around 95%. The classified gridded dataset has a spatial resolution of 1 m and documents the spatial distribution of Phragmites throughout the state's estuarine wetlands (around 11%). Such detailed classification could aid in monitoring the spread of this invasive species over space and time and would inform the decision-making process for landscape managers.

A validated protocol for eDNA-based monitoring of within-species genetic diversity in a pond-breeding amphibian.

In light of the dramatic decline in amphibian biodiversity, new cost-efficient tools to rapidly monitor species abundance and population genetic diversity in space and time are urgently needed. It has been amply demonstrated that the use of environmental DNA (eDNA) for single-species detection and characterization of community composition can increase the precision of amphibian monitoring compared to traditional (observational) approaches. However, it has been suggested that the efficiency and accuracy of the eDNA approach could be further improved by more timely sampling; in addition, the quality of genetic diversity data derived from the same DNA has been confirmed in other vertebrate taxa, but not amphibians. Given the availability of previous tissue-based genetic data, here we use the common frog Rana temporaria Linnaeus, 1758 as our target species and an improved eDNA protocol to: (i) investigate differences in species detection between three developmental stages in various freshwater environments; and (ii) study the diversity of mitochondrial DNA (mtDNA) haplotypes detected in eDNA (water) samples, by amplifying a specific fragment of the COI gene (331 base pairs, bp) commonly used as a barcode. Our protocol proved to be a reliable tool for monitoring population genetic diversity of this species, and could be a valuable addition to amphibian conservation and wetland management.

Effects of light and noise pollution on avian communities of European cities are correlated with the species' diet.

Urbanization affects avian community composition in European cities, increasing biotic homogenization. Anthropic pollution (such as light at night and noise) is among the most important drivers shaping bird use in urban areas, where bird species are mainly attracted by urban greenery. In this study, we collected data on 127 breeding bird species at 1349 point counts distributed along a gradient of urbanization in fourteen different European cities. The main aim was to explore the effects of anthropic pollution and city characteristics, on shaping the avian communities, regarding species' diet composition. The green cover of urban areas increased the number of insectivorous and omnivorous bird species, while slightly decreasing the overall diet heterogeneity of the avian communities. The green heterogeneity-a measure of evenness considering the relative coverage of grass, shrubs and trees-was positively correlated with the richness of granivorous, insectivorous, and omnivorous species, increasing the level of diet heterogeneity in the assemblages. Additionally, the effects of light pollution on avian communities were associated with the species' diet. Overall, light pollution negatively affected insectivorous and omnivorous bird species while not affecting granivorous species. The noise pollution, in contrast, was not significantly associated with changes in species assemblages. Our results offer some tips to urban planners, managers, and ecologists, in the challenge of producing more eco-friendly cities for the future.

Bioinformatic and Statistical Analysis of Microbiome Data.

Since advances in next-generation sequencing (NGS) technique enabled to investigate uncultured microbiota and their genomes in unbiased manner, many microbiome researches have been reporting strong evidences for close links of microbiome to human health and disease. Bioinformatic and statistical analysis of NGS-based microbiome data are essential components in those microbiome researches to explore the complex composition of microbial community and understand the functions of community members in relation to host and environment. This chapter introduces bioinformatic analysis methods that generate taxonomy and functional feature count table along with phylogenetic tree from raw NGS microbiome data and then introduce statistical methods and machine learning approaches for analyzing the outputs of the bioinformatic analysis to infer the biodiversity of a microbial community and unravel host-microbiome association. Understanding the advantages and limitations of the analysis methods will help readers use the methods correctly in microbiome data analysis and may give a new opportunity to develop new analytic techniques for microbiome research.

Predicting of the current and future geographical distribution of Laurus nobilis L. under the effects of climate change.

Today, climate change affects all living things on earth. It also leads to serious losses in terms of biodiversity, ecosystem services, and human welfare. In this context, Laurus nobilis L. is a very important species for Turkey, and the Mediterranean countries. This research aimed to simulate the current distribution of the suitable habitat for L. nobilis in Turkey and to predict its possible range shifts in future climate scenarios. To predict the geographical distribution of L. nobilis, the study used the maximum-entropy algorithm-based MaxEnt 3.4.1 with seven bioclimatic variables created using the Community Climate System Model 4.0 (CCSM4) and the prediction models RCP4.5-8.5 for the years 2050-2070. The results indicated that the most important bioclimatic variables that shape the distribution of L. nobilis are BIO11-mean temperature of coldest quarter, and BIO7-annual temperature range. Two climate change scenarios predicted that the geographical distribution of L. nobilis would increase slightly and then decrease in the future. However, the spatial change analysis showed that the general geographical distribution area of L. nobilis did not change significantly, but the "moderate," "high," and "very high" suitable habitats changed towards "low" suitable habitats. These changes were particularly effective in Turkey's Mediterranean region, which shows that climate change is instrumental in determining the future of the Mediterranean ecosystem. Therefore, suitability mapping and change analysis of potential future bioclimatic habitats can help in planning for land use, conservation, and ecological restoration of L. nobilis.

Land-use diversity predicts regional bird taxonomic and functional richness worldwide.

Unveiling the processes that shape biodiversity patterns is a cornerstone of ecology. Land-use diversity (i.e., the variety of land-use categories within an area) is often considered an important environmental factor that promotes species richness at landscape and regional scales by increasing beta-diversity. Still, the role of land-use diversity in structuring global taxonomic and functional richness is unknown. Here, we examine the hypothesis that regional species taxonomic and functional richness is explained by global patterns of land-use diversity by analyzing distribution and trait data for all extant birds. We found strong support for our hypothesis. Land-use diversity predicted bird taxonomic and functional richness in almost all biogeographic realms, even after accounting for the effect of net primary productivity (i.e., a proxy of resource availability and habitat heterogeneity). This link was particularly consistent with functional richness compared to taxonomic richness. In the Palearctic and Afrotropic realms, a saturation effect was evident, suggesting a non-linear relationship between land-use diversity and biodiversity. Our results reveal that land-use diversity is a key environmental factor associated with several facets of bird regional diversity, widening our understanding of key large-scale predictors of biodiversity patterns. These results can contribute to policies aimed at minimizing regional biodiversity loss.

Application and Comparison of Different Models for Quantifying the Aquatic Community in a Dam-Controlled River.

In order to develop a better model for quantifying aquatic community using environmental factors that are easy to get, we construct quantitative aquatic community models that utilize the different relationships between water environmental impact factors and aquatic biodiversity as follows: a multi-factor linear-based (MLE) model and a black box-based 'Genetic algorithm-BP artificial neural networks' (GA-BP) model. A comparison of the model efficiency and their outputs is conducted by applying the models to real-life cases, referring to the 49 groups of seasonal data observed over seven field sampling campaigns in Shaying River, China, and then performing model to reproduce the seasonal and inter-annual variation of the water ecological characteristics in the Huaidian (HD) site over 10 years. The results show that (1) the MLE and GA-BP models constructed in this paper are effective in quantifying aquatic communities in dam-controlled rivers; and (2) the performance of GA-BP models based on black-box relationships in predicting the aquatic community is better, more stable, and reliable; (3) reproducing the seasonal and inter-annual aquatic biodiversity in the HD site of Shaying River shows that the seasonal variation of species diversity for phytoplankton, zooplankton, and zoobenthos are inconsistent, and the inter-annual levels of diversity are low due to the negative impact of dam control. Our models can be used as a tool for aquatic community prediction and can become a contribution to showing how quantitative models in other dam-controlled rivers to assisting in dam management strategies.

The Relationship between Landscape Construction and Bird Diversity: A Bibliometric Analysis.

Urbanization development is the main cause of drastic habitat changes and biodiversity loss, and urban green space construction is one of the effective ways to mitigate biodiversity decay. The proper construction of urban green space landscapes can maintain or increase the resources provided by urban biodiversity, especially bird diversity. This paper is based on 4112 papers published in this research area between 2002 and 2022, and CiteSpace was used to conduct a bibliometric analysis of the research area in terms of the number of articles published, the country or region of publication, core authors, and academic development. The paper systematically reviews the hotspots, history, and frontiers of research on landscape architecture and bird diversity. At the same time, the relationship between landscape construction and bird diversity is discussed in the context of landscape features, vegetation characteristics, and human behavioral activities. The results revealed: (1) research on the association between landscape camping and bird diversity received high priority from 2002 to 2022. Moreover, this research area has become a mature discipline. (2) Throughout the research history, there are four research hotspots (fundamental research on bird communities, influencing factors related to changes in bird community characteristics, research on bird activity rhythms, and ecological and ornamental values of birds), four development stages (2002-2004, 2005-2009, 2010-2015, and 2016-2022), and several research frontiers. (3) Our aim was to reasonably consider the activity characteristics of birds in future landscape construction, and to thoroughly study the landscape construction strategies and management principles for the harmonious coexistence of humans and birds.

Unraveling the Bombus terrestris Hemolymph, an Indicator of the Immune Response to Microbial Infections, through Complementary Mass Spectrometry Approaches.

Pollinators, including Bombus terrestris, are crucial for maintaining biodiversity in ecosystems and for agriculture. Deciphering their immune response under stress conditions is a key issue for protecting these populations. To assess this metric, we analyzed the B. terrestris hemolymph as an indicator of their immune status. Hemolymph analysis was carried out using mass spectrometry, MALDI molecular mass fingerprinting was used for its effectiveness in assessing the immune status, and high-resolution mass spectrometry was used to measure the impact of experimental bacterial infections on the "hemoproteome". By infecting with three different types of bacteria, we observed that B. terrestris reacts in a specific way to bacterial attacks. Indeed, bacteria impact survival and stimulate an immune response in infected individuals, visible through changes in the molecular composition of their hemolymph. The characterization and label-free quantification of proteins involved in specific signaling pathways in bumble bees by bottom-up proteomics revealed differences in protein expression between the non-experimentally infected and the infected bees. Our results highlight the alteration of pathways involved in immune and defense reactions, stress, and energetic metabolism. Lastly, we developed molecular signatures reflecting the health status of B. terrestris to pave the way for diagnosis/prognosis tools in response to environmental stress.