Miguel Briones-Salas, Gabriela E. Medina-Cruz, Cintia Natalia Martin-Regalado
Urbanization is one of the leading causes of habitat loss, which has increased significantly in tropical regions in recent years, leading to the loss of species, their ecological functions, and evolutionary history. To determine the effect of urbanization on the diversity of bat communities in urban and suburban environments, we analyzed the α and β taxonomic, functional, and phylogenetic diversities at four sites along urbanization gradients surrounding a rapidly expanding city (Oaxaca City) in southern Mexico. We recorded bats using conventional techniques such as mist nets and acoustic monitoring. We calculated the diversity of bats in four sites with different urbanization conditions: urban (1), suburban (1), and rural (2). To assess the degree of total differentiation and components of bat turnover and nestedness between sites, we calculated the β taxonomic, functional, and phylogenetic diversities. A total of 33 bat species were recorded. The highest taxonomic and functional diversity was observed in the Center of Oaxaca (the site with the highest level of urbanization). In contrast, the highest phylogenetic diversity was found in the West (the site with the lowest level of urbanization). The total β taxonomic diversity was higher than the functional and phylogenetic diversity. Regarding the contributions of turnover and nestedness, turnover made a more significant contribution than nestedness to the taxonomic and phylogenetic β diversity. In contrast, functional nestedness contributed more to the functional β diversity than turnover. Tadarida brasiliensis, Desmodus rotundus, Sturnira hondurensis, and S. parvidens were recorded in all three urbanization conditions. In the most urbanized site, four Myotis species were recorded: M. fortidens, M. keaysi, M. thysanodes, and M. velifer. We suggest that the analysis of different dimensions of diversity is essential and should be considered to strengthen conservation strategies; moreover, we suggest the preservation of native vegetation mosaics and water bodies within the city to maintain bat diversity.
城市化是栖息地丧失的主要原因之一，近年来热带地区的城市化程度显著增加，导致物种、其生态功能和进化历史的丧失。为了确定城市化对城市和郊区环境中蝙蝠群落多样性的影响，我们分析了墨西哥南部一个快速扩张的城市（瓦哈卡市）周围沿城市化梯度的四个地点的α和β分类、功能和系统发育多样性。我们使用雾网和声学监测等传统技术记录蝙蝠。我们计算了四个不同城市化条件地点的蝙蝠多样性：城市（1）、郊区（1）和农村（2）。为了评估不同地点之间蝙蝠更替和嵌套的总体分化程度和组成部分，我们计算了β分类、功能和系统发育多样性。共记录了 33 种蝙蝠。瓦哈卡中心（城市化程度最高的地点）的分类和功能多样性最高。相比之下，西部（城市化水平最低的地区）的系统发育多样性最高。总的β分类多样性高于功能多样性和系统发育多样性。就更替和嵌套度的贡献而言，更替比嵌套度对分类学和系统发生学 β 多样性的贡献更大。相比之下，功能嵌套性对功能β多样性的贡献大于周转率。在所有三种城市化条件下，都记录到了 Tadarida brasiliensis、Desmodus rotundus、Sturnira hondurensis 和 S. parvidens。在城市化程度最高的地点，记录到四种麝类：M. fortidens、M. keaysi、M. thysanodes 和 M. velifer。我们建议，对多样性的不同维度进行分析至关重要，应考虑加强保护策略；此外，我们还建议保护城市中的原生植被和水体，以保持蝙蝠的多样性。
{"title":"Taxonomic, Functional, and Phylogenetic Diversity of Bats in Urban and Suburban Environments in Southern México","authors":"Miguel Briones-Salas, Gabriela E. Medina-Cruz, Cintia Natalia Martin-Regalado","doi":"10.3390/d16090527","DOIUrl":"https://doi.org/10.3390/d16090527","url":null,"abstract":"Urbanization is one of the leading causes of habitat loss, which has increased significantly in tropical regions in recent years, leading to the loss of species, their ecological functions, and evolutionary history. To determine the effect of urbanization on the diversity of bat communities in urban and suburban environments, we analyzed the α and β taxonomic, functional, and phylogenetic diversities at four sites along urbanization gradients surrounding a rapidly expanding city (Oaxaca City) in southern Mexico. We recorded bats using conventional techniques such as mist nets and acoustic monitoring. We calculated the diversity of bats in four sites with different urbanization conditions: urban (1), suburban (1), and rural (2). To assess the degree of total differentiation and components of bat turnover and nestedness between sites, we calculated the β taxonomic, functional, and phylogenetic diversities. A total of 33 bat species were recorded. The highest taxonomic and functional diversity was observed in the Center of Oaxaca (the site with the highest level of urbanization). In contrast, the highest phylogenetic diversity was found in the West (the site with the lowest level of urbanization). The total β taxonomic diversity was higher than the functional and phylogenetic diversity. Regarding the contributions of turnover and nestedness, turnover made a more significant contribution than nestedness to the taxonomic and phylogenetic β diversity. In contrast, functional nestedness contributed more to the functional β diversity than turnover. Tadarida brasiliensis, Desmodus rotundus, Sturnira hondurensis, and S. parvidens were recorded in all three urbanization conditions. In the most urbanized site, four Myotis species were recorded: M. fortidens, M. keaysi, M. thysanodes, and M. velifer. We suggest that the analysis of different dimensions of diversity is essential and should be considered to strengthen conservation strategies; moreover, we suggest the preservation of native vegetation mosaics and water bodies within the city to maintain bat diversity.","PeriodicalId":501149,"journal":{"name":"Diversity","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142198500","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Francesco Zangaro, Maurizio Pinna, Valeria Specchia
Non-indigenous species (NIS) introduction notoriously threatens the Mediterranean Sea. In addition, Mediterranean coastal lagoons play a crucial role as nurseries for marine species, which new NIS arrivals can threaten. Therefore, monitoring and early warning of NIS presence is essential in preserving biodiversity. An innovative technique for rapid and accurate species identification and biodiversity screening is the application of environmental DNA (eDNA) metabarcoding. In this research, different Penaeidae (Arthropoda, Crustacea, Decapoda) NIS specimens were collected from a Mediterranean coastal lagoon after an early warning about a potentially invasive NIS arising from next-generation sequencing data. DNA barcoding of the DNA extracted from tissue samples and amplified with specifically designed primer pairs led to the recognition of Penaeus aztecus in this NATURA 2000 protected ecosystem for the first time. DNA barcoding from DNA isolated from the water where the living specimens were stored further validated the possibility of identifying P. aztecus starting from eDNA. This approach demonstrated the validity of environmental DNA analysis in the early screening of potentially invasive NIS presence in Mediterranean protected areas and ecosystems. This work describes an applicative example of the efficacy in improving the biomonitoring of lagoon ecosystems using molecular tools and it represents a guideline for the validation of eDNA metabarcoding data for the presence of potentially invasive species.
非本地物种（NIS）的引入对地中海造成了严重威胁。此外，地中海沿岸泻湖作为海洋物种的哺育地发挥着至关重要的作用，而新的 NIS 的到来可能会威胁到这些物种。因此，监测和预警 NIS 的存在对保护生物多样性至关重要。应用环境 DNA（eDNA）代谢编码是快速准确识别物种和筛选生物多样性的一项创新技术。在这项研究中，在下一代测序数据发出潜在入侵 NIS 的预警后，从地中海沿岸泻湖采集了不同的 Penaeidae（节肢动物门、甲壳动物门、十足目）NIS 标本。从组织样本中提取的 DNA 经专门设计的引物对扩增后进行 DNA 条形编码，首次在该 NATURA 2000 保护生态系统中识别出 Penaeus aztecus。从存放活体标本的水中分离出的 DNA 条形码进一步验证了从 eDNA 开始识别 P. aztecus 的可能性。这种方法证明了环境 DNA 分析在早期筛选地中海保护区和生态系统中可能存在的入侵 NIS 方面的有效性。这项工作描述了利用分子工具改进泻湖生态系统生物监测的一个应用实例，为验证 eDNA 代谢编码数据是否存在潜在入侵物种提供了指导。
{"title":"Environmental DNA as Early Warning for Alien Species in Mediterranean Coastal Lagoons: Implications for Conservation and Management","authors":"Francesco Zangaro, Maurizio Pinna, Valeria Specchia","doi":"10.3390/d16090525","DOIUrl":"https://doi.org/10.3390/d16090525","url":null,"abstract":"Non-indigenous species (NIS) introduction notoriously threatens the Mediterranean Sea. In addition, Mediterranean coastal lagoons play a crucial role as nurseries for marine species, which new NIS arrivals can threaten. Therefore, monitoring and early warning of NIS presence is essential in preserving biodiversity. An innovative technique for rapid and accurate species identification and biodiversity screening is the application of environmental DNA (eDNA) metabarcoding. In this research, different Penaeidae (Arthropoda, Crustacea, Decapoda) NIS specimens were collected from a Mediterranean coastal lagoon after an early warning about a potentially invasive NIS arising from next-generation sequencing data. DNA barcoding of the DNA extracted from tissue samples and amplified with specifically designed primer pairs led to the recognition of Penaeus aztecus in this NATURA 2000 protected ecosystem for the first time. DNA barcoding from DNA isolated from the water where the living specimens were stored further validated the possibility of identifying P. aztecus starting from eDNA. This approach demonstrated the validity of environmental DNA analysis in the early screening of potentially invasive NIS presence in Mediterranean protected areas and ecosystems. This work describes an applicative example of the efficacy in improving the biomonitoring of lagoon ecosystems using molecular tools and it represents a guideline for the validation of eDNA metabarcoding data for the presence of potentially invasive species.","PeriodicalId":501149,"journal":{"name":"Diversity","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142198650","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nicholas R. Longrich, Angel Alejandro Ramirez Velasco, Jim Kirkland, Andrés Eduardo Bermúdez Torres, Claudia Inés Serrano-Brañas
The Late Cretaceous of Western North America (Laramidia) supported a diverse dinosaur fauna, with duckbilled dinosaurs (Hadrosauridae) being among the most speciose and abundant members of this assemblage. Historically, collecting and preservational biases have meant that dinosaurs from Mexico and the American Southwest are poorly known compared to those of the northern Great Plains. However, evidence increasingly suggests that distinct species and clades inhabited southern Laramidia. Here, a new kritosaurin hadrosaurid, represented by the anterior part of a skull, is reported from the late Campanian of the Cerro del Pueblo Formation, ~72.5 Ma, in Coahuila, Mexico. The Cerro del Pueblo Formation kritosaur was originally considered to represent the same species as a saurolophine from the Olmos Formation of Sabinas, but the Sabinas hadrosaur is now considered a distinct taxon. More recently, the Cerro del Pueblo Formation kritosaur has been referred to Kritosaurus navajovius. We show it represents a new species related to Gryposaurus. The new species is distinguished by its large size, the shape of the premaxillary nasal process, the strongly downturned dentary, and massive denticles on the premaxilla’s palatal surface, supporting recognition of a new taxon, Coahuilasaurus lipani. The dinosaur assemblage of the Cerro del Pueblo Formation shows higher diversity than the contemporaneous fauna of the Horseshoe Canyon Formation in Alberta. Furthermore, Kritosaurini, Lambeosaurini, and Parasaurolophini all persist into the latest Campanian in southern Laramidia after disappearing from northern Laramidia. These patterns suggest declining herbivore diversity seen at high latitudes may be a local, rather than global phenomenon, perhaps driven by cooling at high latitudes in the Late Campanian and Maastrichtian.
北美洲西部的晚白垩世（Laramidia）拥有多种多样的恐龙动物群，其中鸭嘴龙（Hadrosauridae）是这一动物群中种类最多、数量最大的成员。从历史上看，由于采集和保存上的偏差，墨西哥和美国西南部的恐龙与大平原北部的恐龙相比鲜为人知。然而，越来越多的证据表明，拉拉米迪亚南部栖息着独特的物种和支系。本文报告了墨西哥科阿韦拉州Cerro del Pueblo地层坎盆纪晚期（约72.5Ma）的一种新的克利龙类剑龙，其头骨的前半部分为代表。塞罗德尔普韦布洛地层的克利龙最初被认为与萨比纳斯奥尔莫斯地层的栉龙代表同一物种，但萨比纳斯栉龙现在被认为是一个独立的类群。最近，Cerro del Pueblo Formation 的剑龙被称为 Kritosaurus navajovius。我们证明它是与蝼蛄龙有关的一个新物种。该新种的特点是体型巨大、前颌鼻突的形状、强烈下翘的齿槽以及前颌腭面上的巨大齿列，从而支持了新类群 Coahuilasaurus lipani 的认定。Cerro del Pueblo地层的恐龙组合比阿尔伯塔省马蹄峡谷地层的同期动物群显示出更高的多样性。此外，Kritosaurini、Lambeosaurini和Parasaurolophini在拉腊米迪亚北部消失后，在拉腊米迪亚南部一直持续到坎盆纪晚期。这些模式表明，在高纬度地区出现的食草动物多样性下降可能是一种局部现象，而不是全球性现象，其原因可能是在晚钟元世和马斯特里赫特世的高纬度地区出现了降温。
{"title":"Coahuilasaurus lipani, a New Kritosaurin Hadrosaurid from the Upper Campanian Cerro Del Pueblo Formation, Northern Mexico","authors":"Nicholas R. Longrich, Angel Alejandro Ramirez Velasco, Jim Kirkland, Andrés Eduardo Bermúdez Torres, Claudia Inés Serrano-Brañas","doi":"10.3390/d16090531","DOIUrl":"https://doi.org/10.3390/d16090531","url":null,"abstract":"The Late Cretaceous of Western North America (Laramidia) supported a diverse dinosaur fauna, with duckbilled dinosaurs (Hadrosauridae) being among the most speciose and abundant members of this assemblage. Historically, collecting and preservational biases have meant that dinosaurs from Mexico and the American Southwest are poorly known compared to those of the northern Great Plains. However, evidence increasingly suggests that distinct species and clades inhabited southern Laramidia. Here, a new kritosaurin hadrosaurid, represented by the anterior part of a skull, is reported from the late Campanian of the Cerro del Pueblo Formation, ~72.5 Ma, in Coahuila, Mexico. The Cerro del Pueblo Formation kritosaur was originally considered to represent the same species as a saurolophine from the Olmos Formation of Sabinas, but the Sabinas hadrosaur is now considered a distinct taxon. More recently, the Cerro del Pueblo Formation kritosaur has been referred to Kritosaurus navajovius. We show it represents a new species related to Gryposaurus. The new species is distinguished by its large size, the shape of the premaxillary nasal process, the strongly downturned dentary, and massive denticles on the premaxilla’s palatal surface, supporting recognition of a new taxon, Coahuilasaurus lipani. The dinosaur assemblage of the Cerro del Pueblo Formation shows higher diversity than the contemporaneous fauna of the Horseshoe Canyon Formation in Alberta. Furthermore, Kritosaurini, Lambeosaurini, and Parasaurolophini all persist into the latest Campanian in southern Laramidia after disappearing from northern Laramidia. These patterns suggest declining herbivore diversity seen at high latitudes may be a local, rather than global phenomenon, perhaps driven by cooling at high latitudes in the Late Campanian and Maastrichtian.","PeriodicalId":501149,"journal":{"name":"Diversity","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142198659","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Miroslav Macek, Jaroslav Vrba, Josef Hejzlar, Klára Řeháková, Jiří Jarošík, Michal Šorf, Karel Šimek
The perception of the importance of ciliate in freshwater has changed dramatically since the “microbial loop” conceptualisation, reflecting methodological attempts. The data from two decades (1994–2018) on the surface (0–3 m) ciliate assemblage in the Slapy reservoir (Vltava River, Czech Republic) during two different nutrient-load defined periods were analysed. We grouped the identified, quantified, and biomass-evaluated ciliates in the quantitative protargol-impregnated preparations according to their feeding behaviour. The sampling median and interquartile range data of the ciliates were plotted; the modelled water age, nutrients, bacteria, heterotrophic nanoflagellates, and Rhodomonas spp. were applied as the main explanatory background variables. We validated the differences between the periods, engaging multivariate analyses. The picoplankton-filtering species dominated the assemblages in an annual mean (halteriids and minute strobilidiids followed by peritrichs). Algae hunting urotrichs, Balanion planctonicum, and nanoplankton filtering tintinnids were significant before the spring phytoplankton peak when a maximum of ciliate biomass reflected mixotrophic nanoplankton filtering pelagostrombidiids. Only there did ciliate biomass tightly follow their quantified prey. Heterotrophic and mixotrophic Askenasia and Lagynophrya were typical raptorial/flagellate-hunting cilates; only Mesodinium spp. reached the maximum during autumn. The observed oligotrophication of the reservoir increased the ciliate assemblage biomass in the surface layer during stratification in concordance with the Plankton Ecology Group (PEG) model.
{"title":"Two-Decade Changes in the Ciliate Assemblage Feeding Pattern Reflect the Reservoir Nutrient Load","authors":"Miroslav Macek, Jaroslav Vrba, Josef Hejzlar, Klára Řeháková, Jiří Jarošík, Michal Šorf, Karel Šimek","doi":"10.3390/d16090534","DOIUrl":"https://doi.org/10.3390/d16090534","url":null,"abstract":"The perception of the importance of ciliate in freshwater has changed dramatically since the “microbial loop” conceptualisation, reflecting methodological attempts. The data from two decades (1994–2018) on the surface (0–3 m) ciliate assemblage in the Slapy reservoir (Vltava River, Czech Republic) during two different nutrient-load defined periods were analysed. We grouped the identified, quantified, and biomass-evaluated ciliates in the quantitative protargol-impregnated preparations according to their feeding behaviour. The sampling median and interquartile range data of the ciliates were plotted; the modelled water age, nutrients, bacteria, heterotrophic nanoflagellates, and Rhodomonas spp. were applied as the main explanatory background variables. We validated the differences between the periods, engaging multivariate analyses. The picoplankton-filtering species dominated the assemblages in an annual mean (halteriids and minute strobilidiids followed by peritrichs). Algae hunting urotrichs, Balanion planctonicum, and nanoplankton filtering tintinnids were significant before the spring phytoplankton peak when a maximum of ciliate biomass reflected mixotrophic nanoplankton filtering pelagostrombidiids. Only there did ciliate biomass tightly follow their quantified prey. Heterotrophic and mixotrophic Askenasia and Lagynophrya were typical raptorial/flagellate-hunting cilates; only Mesodinium spp. reached the maximum during autumn. The observed oligotrophication of the reservoir increased the ciliate assemblage biomass in the surface layer during stratification in concordance with the Plankton Ecology Group (PEG) model.","PeriodicalId":501149,"journal":{"name":"Diversity","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142198654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Martina Canessa, Egidio Trainito, Giorgio Bavestrello
The occurrence and abundance of Astrospartus mediterraneus (Risso, 1826) have significantly increased in the last three decades in several areas of the Mediterranean Sea. In the Tavolara–Punta Coda Cavallo Marine Protected Area (NE Sardinia, Tyrrhenian Sea, Mediterranean Sea), 60 specimens were observed mainly on the granitic shoals of the Tavolara Channel, an area characterized by very intense currents and high sedimentation. The basket stars were mainly found living as epibionts of gorgonians (Eunicella verrucosa, Paramuricea clavata and Leptogorgia sarmentosa) and massive sponges (Spongia officinalis, S. lamella, Sarcotragus foetidus). We also documented 21 small specimens (3–20 mm in diameter of the oral disc) observed in June 2024 between 27 and 52 m depth on E. verrucosa and P. clavata colonies. The bimodal size-frequency distribution of these specimens suggested that, probably, specimens belong to two different reproductive events occurring in spring 2023 and 2024.
{"title":"Recruitment of the Basket Star Astrospartus mediterraneus (Risso, 1826) (Ophiuroidea, Gorgonocephalidae)","authors":"Martina Canessa, Egidio Trainito, Giorgio Bavestrello","doi":"10.3390/d16090528","DOIUrl":"https://doi.org/10.3390/d16090528","url":null,"abstract":"The occurrence and abundance of Astrospartus mediterraneus (Risso, 1826) have significantly increased in the last three decades in several areas of the Mediterranean Sea. In the Tavolara–Punta Coda Cavallo Marine Protected Area (NE Sardinia, Tyrrhenian Sea, Mediterranean Sea), 60 specimens were observed mainly on the granitic shoals of the Tavolara Channel, an area characterized by very intense currents and high sedimentation. The basket stars were mainly found living as epibionts of gorgonians (Eunicella verrucosa, Paramuricea clavata and Leptogorgia sarmentosa) and massive sponges (Spongia officinalis, S. lamella, Sarcotragus foetidus). We also documented 21 small specimens (3–20 mm in diameter of the oral disc) observed in June 2024 between 27 and 52 m depth on E. verrucosa and P. clavata colonies. The bimodal size-frequency distribution of these specimens suggested that, probably, specimens belong to two different reproductive events occurring in spring 2023 and 2024.","PeriodicalId":501149,"journal":{"name":"Diversity","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142198653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The pale chub Zacco platypus (Cypriniformes; Xenocyprididae; Jordan & Evermann, 1902) is widely distributed across freshwater ecosystems in East Asia and has been recognized as a potential model fish species for ecotoxicology and environmental monitoring. Here, a high-quality de novo genome assembly of Z. platypus was constructed through the integration of a combination of long-read Pacific Bioscience (PacBio) sequencing, short-read Illumina sequencing, and Hi-C sequencing technologies. Z. platypus has the smallest genome size compared to other species belonging to the order Cypriniformes. The assembled genome encompasses 41.45% repeat sequences. As shown in other fish, a positive correlation was observed between genome size and the composition of transposable elements (TE) in the genome. Among TEs, a relatively higher rate of DNA transposon was observed, which is a common pattern in the members of the order Cypriniformes. Functional annotation was processed using four representative databases, identifying a core set of 12,907 genes shared among them. Orthologous gene family analysis revealed that Z. platypus has experienced more gene family contraction rather than expansion compared to other Cypriniformes species. Among the uniquely expanded gene families in Z. platypus, detoxification and stress-related gene families were identified, suggesting that this species could represent a promising model for ecotoxicology and environmental monitoring. Taken together, the Z. platypus genome assembly will provide valuable data for omics-based health assessments in aquatic ecosystems, offering further insights into the environmental and ecological facets within this species.
{"title":"Annotation and Characterization of the Zacco platypus Genome","authors":"Sang-Eun Nam, Dae-Yeul Bae, Jae-Sung Rhee","doi":"10.3390/d16090529","DOIUrl":"https://doi.org/10.3390/d16090529","url":null,"abstract":"The pale chub Zacco platypus (Cypriniformes; Xenocyprididae; Jordan & Evermann, 1902) is widely distributed across freshwater ecosystems in East Asia and has been recognized as a potential model fish species for ecotoxicology and environmental monitoring. Here, a high-quality de novo genome assembly of Z. platypus was constructed through the integration of a combination of long-read Pacific Bioscience (PacBio) sequencing, short-read Illumina sequencing, and Hi-C sequencing technologies. Z. platypus has the smallest genome size compared to other species belonging to the order Cypriniformes. The assembled genome encompasses 41.45% repeat sequences. As shown in other fish, a positive correlation was observed between genome size and the composition of transposable elements (TE) in the genome. Among TEs, a relatively higher rate of DNA transposon was observed, which is a common pattern in the members of the order Cypriniformes. Functional annotation was processed using four representative databases, identifying a core set of 12,907 genes shared among them. Orthologous gene family analysis revealed that Z. platypus has experienced more gene family contraction rather than expansion compared to other Cypriniformes species. Among the uniquely expanded gene families in Z. platypus, detoxification and stress-related gene families were identified, suggesting that this species could represent a promising model for ecotoxicology and environmental monitoring. Taken together, the Z. platypus genome assembly will provide valuable data for omics-based health assessments in aquatic ecosystems, offering further insights into the environmental and ecological facets within this species.","PeriodicalId":501149,"journal":{"name":"Diversity","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142198656","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Natalia E. Gogoleva, Marina A. Nasyrova, Alexander S. Balkin, Olga Ya. Chervyatsova, Lyudmila Yu. Kuzmina, Elena I. Shagimardanova, Yuri V. Gogolev, Andrey O. Plotnikov
Karst caves, formed by the erosion of soluble carbonate rocks, provide unique ecosystems characterized by stable temperatures and high humidity. These conditions support diverse microbial communities, including wall microbial fouling, aquatic biofilms, and planktonic communities. This study discloses the taxonomic diversity of protists in aquatic biotopes of Shulgan-Tash Cave, a culturally significant site and popular tourist destination, by 18S rRNA gene metabarcoding. Our findings reveal the rich protist communities in the cave’s aquatic biotopes, with the highest diversity observed in Blue Lake at the cave entrance. In contrast, Distant Lake in the depth of the cave was inhabited by specific communities of plankton, mats, and pool fingers, which exhibited lower richness and evenness, and were adapted to extreme conditions (cold, darkness, and limited nutrients). High-rank taxa including Opisthokonta, Stramenopiles, and Rhizaria dominated all biotopes, aligning with observations from other subterranean environments. Specific communities of biotopes inside the cave featured distinct dominant taxa: amoeboid stramenopile (Synchromophyceae) and flagellates (Choanoflagellatea and Sandona) in mats; flagellates (Choanoflagellatea, Bicoecaceae, Ancyromonadida) and amoeboid protists (Filasterea) in pool fingers; flagellates (Ochromonadales, Glissomonadida, Synchromophyceae), fungi-like protists (Peronosporomycetes), and fungi (Ustilaginomycotina) in plankton. The specificity of the communities was supported by LEfSe analysis, which revealed enriched or differentially abundant protist taxa in each type of biotope. The predominance of Choanoflagellatea in the communities of cave mats and pool fingers, as well as the predominance of Synchromophyceae in the cave mats, appears to be a unique feature of Shulgan-Tash Cave. The cold-tolerant yeast Malassezia recorded in other caves was present in both plankton and biofilm communities, suggesting its resilience to low temperatures. However, no potentially harmful fungi were detected, positioning this research as a baseline for future monitoring. Our results emphasize the need for ongoing surveillance and conservation efforts to protect the fragile ecosystems of Shulgan-Tash Cave from human-induced disturbances and microbial invasions.
{"title":"Flourishing in Darkness: Protist Communities of Water Sites in Shulgan-Tash Cave (Southern Urals, Russia)","authors":"Natalia E. Gogoleva, Marina A. Nasyrova, Alexander S. Balkin, Olga Ya. Chervyatsova, Lyudmila Yu. Kuzmina, Elena I. Shagimardanova, Yuri V. Gogolev, Andrey O. Plotnikov","doi":"10.3390/d16090526","DOIUrl":"https://doi.org/10.3390/d16090526","url":null,"abstract":"Karst caves, formed by the erosion of soluble carbonate rocks, provide unique ecosystems characterized by stable temperatures and high humidity. These conditions support diverse microbial communities, including wall microbial fouling, aquatic biofilms, and planktonic communities. This study discloses the taxonomic diversity of protists in aquatic biotopes of Shulgan-Tash Cave, a culturally significant site and popular tourist destination, by 18S rRNA gene metabarcoding. Our findings reveal the rich protist communities in the cave’s aquatic biotopes, with the highest diversity observed in Blue Lake at the cave entrance. In contrast, Distant Lake in the depth of the cave was inhabited by specific communities of plankton, mats, and pool fingers, which exhibited lower richness and evenness, and were adapted to extreme conditions (cold, darkness, and limited nutrients). High-rank taxa including Opisthokonta, Stramenopiles, and Rhizaria dominated all biotopes, aligning with observations from other subterranean environments. Specific communities of biotopes inside the cave featured distinct dominant taxa: amoeboid stramenopile (Synchromophyceae) and flagellates (Choanoflagellatea and Sandona) in mats; flagellates (Choanoflagellatea, Bicoecaceae, Ancyromonadida) and amoeboid protists (Filasterea) in pool fingers; flagellates (Ochromonadales, Glissomonadida, Synchromophyceae), fungi-like protists (Peronosporomycetes), and fungi (Ustilaginomycotina) in plankton. The specificity of the communities was supported by LEfSe analysis, which revealed enriched or differentially abundant protist taxa in each type of biotope. The predominance of Choanoflagellatea in the communities of cave mats and pool fingers, as well as the predominance of Synchromophyceae in the cave mats, appears to be a unique feature of Shulgan-Tash Cave. The cold-tolerant yeast Malassezia recorded in other caves was present in both plankton and biofilm communities, suggesting its resilience to low temperatures. However, no potentially harmful fungi were detected, positioning this research as a baseline for future monitoring. Our results emphasize the need for ongoing surveillance and conservation efforts to protect the fragile ecosystems of Shulgan-Tash Cave from human-induced disturbances and microbial invasions.","PeriodicalId":501149,"journal":{"name":"Diversity","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142198652","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Alan H. Fielding, David Anderson, Catherine Barlow, Stuart Benn, Charlotte J. Chandler, Robin Reid, Ruth Tingay, Ewan D. Weston, D. Philip Whitfield
Satellite tracking allows for novel investigations into golden eagle home range characteristics. Understanding home range characteristics is important for conservation and for assessing the potential impact of landscape changes from forest planting, wind farms, etc. Small sample sizes, inconsistent definitions and methods restricted several previous studies. Our study involved 69 resident tagged eagles with over one year of data across five Scottish regions. Home range size was estimated from 95% isopleth contours extracted from Utilisation Distributions. Above a small threshold, estimated range size was not affected by the number of records but at least one year of data is required, largely because of the breeding and non-breeding seasonal differences. There were no significant range size differences between birds tagged as range holders and those previously tagged as nestlings. Across four regions, with considerable intra-regional variation, planar 95% isopleths did not differ (medians, km2): Argyll 58.9, Northwest Highlands 61.7, Northeast Highlands 89.3, South of Scotland 91.9. Ranges in the isolated Outer Hebrides region were exceptionally small, at 24.0 km2. Estimated range area was usually reduced to 70–80% of the planar area when restricted to usable habitat, as estimated by the Golden Eagle Topography (GET) model. Applying measures of known unsuitable habitat (closed-canopy commercial forest and wind turbines) further reduced usable open land. Loss of otherwise suitable habitat was substantially due to commercial forest. Larger ranges had larger extents of suitable habitat (according to GET), with no apparent optimum of preferred GET habitat. Range size was not different across a year between the sexes. Breeding ranges were smaller, and females’ breeding ranges were much smaller than those of males, but larger than males’ ranges in the non-breeding season. Breeding attempt duration was probably also influential. Our study provides novel insights into golden eagle home range characteristics and can guide further research and practical applications.
{"title":"The Characteristics and Variation of the Golden Eagle Aquila chrysaetos Home Range","authors":"Alan H. Fielding, David Anderson, Catherine Barlow, Stuart Benn, Charlotte J. Chandler, Robin Reid, Ruth Tingay, Ewan D. Weston, D. Philip Whitfield","doi":"10.3390/d16090523","DOIUrl":"https://doi.org/10.3390/d16090523","url":null,"abstract":"Satellite tracking allows for novel investigations into golden eagle home range characteristics. Understanding home range characteristics is important for conservation and for assessing the potential impact of landscape changes from forest planting, wind farms, etc. Small sample sizes, inconsistent definitions and methods restricted several previous studies. Our study involved 69 resident tagged eagles with over one year of data across five Scottish regions. Home range size was estimated from 95% isopleth contours extracted from Utilisation Distributions. Above a small threshold, estimated range size was not affected by the number of records but at least one year of data is required, largely because of the breeding and non-breeding seasonal differences. There were no significant range size differences between birds tagged as range holders and those previously tagged as nestlings. Across four regions, with considerable intra-regional variation, planar 95% isopleths did not differ (medians, km2): Argyll 58.9, Northwest Highlands 61.7, Northeast Highlands 89.3, South of Scotland 91.9. Ranges in the isolated Outer Hebrides region were exceptionally small, at 24.0 km2. Estimated range area was usually reduced to 70–80% of the planar area when restricted to usable habitat, as estimated by the Golden Eagle Topography (GET) model. Applying measures of known unsuitable habitat (closed-canopy commercial forest and wind turbines) further reduced usable open land. Loss of otherwise suitable habitat was substantially due to commercial forest. Larger ranges had larger extents of suitable habitat (according to GET), with no apparent optimum of preferred GET habitat. Range size was not different across a year between the sexes. Breeding ranges were smaller, and females’ breeding ranges were much smaller than those of males, but larger than males’ ranges in the non-breeding season. Breeding attempt duration was probably also influential. Our study provides novel insights into golden eagle home range characteristics and can guide further research and practical applications.","PeriodicalId":501149,"journal":{"name":"Diversity","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142198658","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jeļena Oreha, Aleksandra Morozova, Alberts Garkajs, Muza Kirjušina, Inese Gavarāne, Vladimir G. Kostousov, Mihails Pupins, Nataļja Škute
The European eel (Anguilla anguilla (L.)) is a unique catadromous euryhaline fish and the only anguillid eel species classified as ‘critically endangered’. The Baltic Lakeland area contains naturally recruited and introduced eels. There is great uncertainty regarding a baseline for the location and number of naturally dispersed eels in the region. Little is known about the genetic structure of the European eel populations in Baltic countries. The estimation of population genetic structure is important for the efficient management of naturally recruited and introduced eels. Two mitochondrial regions were used to investigate the genetic structure within and between eel samples from 11 waterbodies. In this study, new, unique, and widely distributed haplotypes were revealed. The studied eel population in the Baltic Lakeland shows high genetic diversity, which is possibly a result of intensive restocking programs. Sequences characterized for Anguilla rostrata were revealed in both mitochondrial regions. Understanding the genetic structure of eel populations worldwide is crucial for conservation efforts. Eel restocking in waterbodies where natural migration is restricted contributes to diversity loss for the world gene pool of eels.
{"title":"Genetic Diversity and Distribution of Haplotypes of Freshwater Eel in Baltic Lakeland Based on Mitochondrial DNA D-Loop and Cytochrome b Sequence Variation","authors":"Jeļena Oreha, Aleksandra Morozova, Alberts Garkajs, Muza Kirjušina, Inese Gavarāne, Vladimir G. Kostousov, Mihails Pupins, Nataļja Škute","doi":"10.3390/d16090522","DOIUrl":"https://doi.org/10.3390/d16090522","url":null,"abstract":"The European eel (Anguilla anguilla (L.)) is a unique catadromous euryhaline fish and the only anguillid eel species classified as ‘critically endangered’. The Baltic Lakeland area contains naturally recruited and introduced eels. There is great uncertainty regarding a baseline for the location and number of naturally dispersed eels in the region. Little is known about the genetic structure of the European eel populations in Baltic countries. The estimation of population genetic structure is important for the efficient management of naturally recruited and introduced eels. Two mitochondrial regions were used to investigate the genetic structure within and between eel samples from 11 waterbodies. In this study, new, unique, and widely distributed haplotypes were revealed. The studied eel population in the Baltic Lakeland shows high genetic diversity, which is possibly a result of intensive restocking programs. Sequences characterized for Anguilla rostrata were revealed in both mitochondrial regions. Understanding the genetic structure of eel populations worldwide is crucial for conservation efforts. Eel restocking in waterbodies where natural migration is restricted contributes to diversity loss for the world gene pool of eels.","PeriodicalId":501149,"journal":{"name":"Diversity","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142198651","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xiaojing Song, Fen Hu, Min Xu, Yi Zhang, Yan Jin, Xiaodi Gao, Zunlei Liu, Jianzhong Ling, Shengfa Li, Jiahua Cheng
Nursery habitats play a significant role in completing fish life cycles, and they are now recognized as essential habitats. Monthly variations in nursery ground distributions of Larimichthys polyactis were investigated in the southern Yellow Sea in 2019. Bayesian hierarchical models with integrated nested Laplace approximation were utilized to model the preferential nursery habitats of L. polyactis larvae. The study analyzed the spatial and temporal distributions of the larvae and juveniles based on three environmental variables: sea surface temperature, sea surface salinity, and depth. Additionally, this study examined the utilization of habitats by different fish life stages and ontogenetic shifts. A total of 3240 individuals were collected from April to June, with the peak occurring in May (0.05 ind./m3), and the distribution areas varied between different months. The prediction of the model reveals the ecological adaptability of L. polyactis to temperature variations. The optimal temperature for L. polyactis density ranges from 12.5 °C to 16.5 °C in April and 16.5 °C to 17.5 °C in May, demonstrating a broad temperature tolerance for L. polyactis survival. In addition, there are variations in distribution patterns among different developmental stages. Larimichthys polyactis spawn in the inshore and nearshore waters, and after hatching, larvae in the pre-flexion stage tend to remain aggregated near the spawning beds. However, larvae in the advanced development stage (post-flexion) and juveniles move towards the sandy ridge habitats along the coast and start to migrate offshore in June. This study provides valuable insights for the effective management of fishery resources in the area and can be utilized to identify marine areas with specific habitat features that require conservation.
{"title":"Spatiotemporal Distribution and Dispersal Pattern of Early Life Stages of the Small Yellow Croaker (Larimichthys Polyactis) in the Southern Yellow Sea","authors":"Xiaojing Song, Fen Hu, Min Xu, Yi Zhang, Yan Jin, Xiaodi Gao, Zunlei Liu, Jianzhong Ling, Shengfa Li, Jiahua Cheng","doi":"10.3390/d16090521","DOIUrl":"https://doi.org/10.3390/d16090521","url":null,"abstract":"Nursery habitats play a significant role in completing fish life cycles, and they are now recognized as essential habitats. Monthly variations in nursery ground distributions of Larimichthys polyactis were investigated in the southern Yellow Sea in 2019. Bayesian hierarchical models with integrated nested Laplace approximation were utilized to model the preferential nursery habitats of L. polyactis larvae. The study analyzed the spatial and temporal distributions of the larvae and juveniles based on three environmental variables: sea surface temperature, sea surface salinity, and depth. Additionally, this study examined the utilization of habitats by different fish life stages and ontogenetic shifts. A total of 3240 individuals were collected from April to June, with the peak occurring in May (0.05 ind./m3), and the distribution areas varied between different months. The prediction of the model reveals the ecological adaptability of L. polyactis to temperature variations. The optimal temperature for L. polyactis density ranges from 12.5 °C to 16.5 °C in April and 16.5 °C to 17.5 °C in May, demonstrating a broad temperature tolerance for L. polyactis survival. In addition, there are variations in distribution patterns among different developmental stages. Larimichthys polyactis spawn in the inshore and nearshore waters, and after hatching, larvae in the pre-flexion stage tend to remain aggregated near the spawning beds. However, larvae in the advanced development stage (post-flexion) and juveniles move towards the sandy ridge habitats along the coast and start to migrate offshore in June. This study provides valuable insights for the effective management of fishery resources in the area and can be utilized to identify marine areas with specific habitat features that require conservation.","PeriodicalId":501149,"journal":{"name":"Diversity","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142198536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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