Phylogenetic interpretations and ecological potentials of the Mesomycetozoea (Ichthyosporea)

The Mesomycetozoea (Ichthyosporea) includes a group of fungus-like microorganisms which diverged near the animal fungus divide and is basal to the animal lineage in the Opisthokont supergroup. The composition of species within this group has changed considerably since it was reviewed by Mendoza et al. in 2002. There have been many additions to the group as a result of phylogenetic sequencing, and new species have been discovered following examination of digestive tracts of arthropods and other groups of invertebrates. Furthermore, ecological surveys and environmental sampling have revealed a high diversity of Mesomycetozoean phylotypes in marine, freshwater and terrestrial environments. Initially considered a group comprising mainly fish parasites, the Mesomycetozoea are now known to live in association with a wide range of host organisms including invertebrates, fish, amphibians, birds and mammals. Here we review the Mesomycetozoea and examine the broad spectrum of its ecology in the light of recent research based on sequence data, cultivation and in vivo studies.     

Ithomiini Butterflies (Lepidoptera: Nymphalidae) of Antioquia, Colombia

Colombia is one of the most biodiverse countries on the planet. However, economic and scientific investment in completing inventories of its biodiversity has been relatively poor in comparison with other Neotropical countries. Butterflies are the best studied group of invertebrates, with the highest proportion of known to expected species. More than 3,200 species of butterflies have been recorded in Colombia, although the study of the still many unexplored areas will presumably increase this number. This work provides a list of Ithomiini butterflies collected in the department of Antioquia and estimates the total number of species present, based on revision of entomological collections, records in the literature and field work performed between 2003 and 2011. The list includes 99 species and 32 genera, representing 27% of all Ithomiini species. We report 50 species of Ithomiini not formerly listed from Antioquia, and found the highest diversity of ithomiine species to be at middle elevations (900–1,800 m). The mean value of the Chao2 estimator for number of species in Antioquia is 115 species, which is close to a predicted total of 109 based on known distributions of other Ithomiini not yet recorded from the department. Nine species are potentially of particular conservation importance because of their restricted distributions, and we present range maps for each species. We also highlight areas in Antioquia with a lack of biodiversity knowledge to be targeted in future studies. This paper contributes to mapping the distribution of the Lepidoptera of Antioquia department in particular and of Colombia in general.     

中国生物物种编目进展与展望

发现并描述地球上的生物物种, 建立可靠的生物分类系统, 编制权威且具有时效性的生物物种名录, 实现生物物种多样性信息的数字化和共享, 对于生物多样性科学研究、资源管理、科学决策和社会经济发展都有重要意义。在全球和区域层面, 生物物种编目工作越来越被重视, 也取得了一些可喜的进展。为反映中国生物物种编目工作近些年取得的成绩, 本文联合各相关类群的专家, 分别总结了脊椎动物、昆虫和其他无脊椎动物、植物、菌物等主要类群的物种编目进展情况, 并就将来如何更好地促进生物编目工作的开展提出了展望。现有数据显示, 中国已记录哺乳动物698种, 鸟类1,450种, 爬行类586种, 两栖类611种, 淡水鱼类1,591种, 高等植物38,493种(其中维管植物35,379种), 菌物约27,900种, 但尚无全面的包括所有昆虫和无脊椎动物的物种名录。近10年, 中国新增维管植物5个新科、86个新属、2,090个新种、374个新记录; 新增菌物新物种4,679个, 隶属于36纲140目438科1,372属。     

Spineless and overlooked: DNA metabarcoding of autonomous reef monitoring structures reveals intra- and interspecific genetic diversity in Mediterranean invertebrates

The ability to gather genetic information using DNA metabarcoding of bulk samples obtained directly from the environment is crucial to determine biodiversity baselines and understand population dynamics in the marine realm. While DNA metabarcoding is effective in evaluating biodiversity at community level, genetic patterns within species are often concealed in metabarcoding studies and overlooked for marine invertebrates. In the present study, we implement recently developed bioinformatics tools to investigate intraspecific genetic variability for invertebrate taxa in the Mediterranean Sea. Using metabarcoding samples from Autonomous Reef Monitoring Structures (ARMS) deployed in three locations, we present haplotypes and diversity estimates for 145 unique species. While overall genetic diversity was low, we identified several species with high diversity records and potential cryptic lineages. Further, we emphasize the spatial scale of genetic variability, which was observed from locations to individual sampling units (ARMS). We carried out a population genetic analysis of several important yet understudied species, which highlights the current knowledge gap concerning intraspecific genetic patterns for the target taxa in the Mediterranean basin. Our approach considerably enhances biodiversity monitoring of charismatic and understudied Mediterranean species, which can be incorporated into ARMS surveys.     

Biodiversity associated with an irrigated rice agro-ecosystem in Sri Lanka

Irrigated rice fields are temporary wetland agro-ecosystems, managed with a variable degree of intensity. A survey was carried out in Sri Lanka to document the overall biodiversity associated with this unique agro-ecosystem, using a combination of sampling techniques to document different groups of fauna and flora. The total number of biota recorded and identified from the rice field ecosystem during the entire study period consisted of 494 species of invertebrates belonging to 10 phyla and 103 species of vertebrates, while the flora included 89 species of macrophytes, 39 genera of microphytes and 3 species of macrofungi. Of the total species documented, 15 species of invertebrates and one weed species are new records to Sri Lanka. Arthropods were the dominant group of invertebrates (405 species), of which 55 species were rice pest insects, and 200 species were natural enemies of pest insects. The fauna and flora recorded from the rice field were observed to follow a uniform pattern of seasonal colonization and succession during successive rice cultivation cycles. The biodiversity of the irrigated rice agro-ecosystem interests both agroecologists and conservation biologists. Therefore, the integrated efforts of these two groups can result in the formulation of strategies based on biodiversity as an organizing principal in the sustainable management of the rice field agro-ecosystem.     

An assessment of the use of volunteers for terrestrial invertebrate biodiversity surveys

Species’ distributions, assemblage patterns and the processes influencing these are poorly understood, and urgently require study. Use of volunteers to collect data is becoming increasingly common in biodiversity research. We assess the effectiveness of volunteers sampling terrestrial savanna invertebrates in comparison to experienced researchers, and examine the potential contribution of volunteers to terrestrial invertebrate surveys. There were relatively few differences in the diversity sampled by 54 Earthwatch Institute volunteers when compared to expert researchers. The major difference was in the results from the less spatially constrained method, where experience (microhabitat selection) most affected results, and experienced researchers performed better both quantitatively (more species sampled) and qualitatively (more unique and rare species). For the more constrained and less subjective methods, our training enabled the volunteers to quickly equal the experienced experts. Volunteers’ experience in invertebrate research influenced both the researchers’ perceptions of volunteers’ capacity and the actual performance of the volunteers. This suggests that appropriate training for the methods used can help to improve volunteers’ success with the sampling. We demonstrated that volunteers collect valid data; for the most part they sample invertebrates as effectively as a trained researcher, and that using volunteers has enormous direct benefits in terms of volume of work accomplished. For invertebrate studies using volunteers, we recommend that the subjectivity of the method be minimised, that experience is compensated for by increasing volunteer effort (two volunteers = one researcher), and that there is close management of volunteers in the field to ensure ongoing data quality. Volunteers provide a valuable resource to researchers carrying out biodiversity surveys, but using volunteers to carry out a scientifically sound project is not an easy option, and should only be implemented when volunteers would make a meaningful contribution and enable an otherwise impossible project.     

Lepidoptera research in Puerto Rico: Reconnecting with historical legacies to guide future priorities

The Caribbean archipelago of Puerto Rico supports a diverse flora and fauna and is located in a region characterized by complex socio-economic and environmental change. The diversity of entomofauna across Puerto Rico has received considerable attention in wide-scale research over the last century, with particular emphasis on the order Lepidoptera as the subject of substantial taxonomic and ecological surveys. However, much of this work is incomplete, outdated, or has been obscured in gray literature. Thus, our primary objectives were to contextualize the role of past research in the current understanding of Puerto Rican Lepidoptera and to outline an agenda for future research. Specifically, we provide an overview of taxonomic, ecological, agricultural, and conservation Lepidoptera research in Puerto Rico and highlight key studies and historical datasets. We found that, despite a strong taxonomic legacy, native moth taxonomy remains poorly understood, except for a few major pests. Further, much of the recent Lepidoptera research has focused on short-term evaluations of agricultural pests, necessitated by immediate economic needs. The current ecological status of Lepidoptera on the islands is unknown. Therefore, prioritizing ecological research could provide timely insight for understanding changing Lepidoptera diversity and distribution and for conserving this biologically and economically significant group. Greater emphasis on long-term monitoring and digitization of museum collections would be particularly useful for quantifying past and forecasting future impacts of global change. Abstract in Spanish is available with online material.     

Local scale processes drive long‐term change in biodiversity of sandy beach ecosystems

Evaluating impacts to biodiversity requires ecologically informed comparisons over sufficient time spans. The vulnerability of coastal ecosystems to anthropogenic and climate change‐related impacts makes them potentially valuable indicators of biodiversity change. To evaluate multidecadal change in biodiversity, we compared results from intertidal surveys of 13 sandy beaches conducted in the 1970s and 2009–11 along 500 km of coast (California, USA). Using a novel extrapolation approach to adjust species richness for sampling effort allowed us to address data gaps and has promise for application to other data‐limited biodiversity comparisons. Long‐term changes in species richness varied in direction and magnitude among beaches and with human impacts but showed no regional patterns. Observed long‐term changes in richness differed markedly among functional groups of intertidal invertebrates. At the majority (77%) of beaches, changes in richness were most evident for wrack‐associated invertebrates suggesting they have disproportionate vulnerability to impacts. Reduced diversity of this group was consistent with long‐term habitat loss from erosion and sea level rise at one beach. Wrack‐associated species richness declined over time at impacted beaches (beach fill and grooming), despite observed increases in overall intertidal richness. In contrast richness of these taxa increased at more than half (53%) of the beaches including two beaches recovering from decades of off‐road vehicle impacts. Over more than three decades, our results suggest that local scale processes exerted a stronger influence on intertidal biodiversity on beaches than regional processes and highlight the role of human impacts for local spatial scales. Our results illustrate how comparisons of overall biodiversity may mask ecologically important changes and stress the value of evaluating biodiversity change in the context of functional groups. The long‐term loss of wrack‐associated species, a key component of sandy beach ecosystems, documented here represents a significant threat to the biodiversity and function of coastal ecosystems.     

Old and new records of turbellarians from the central areas of Spain

From the point of view of its biodiversity, the Iberian Peninsula is one of the most interesting areas. Its special geographical location and geological history have created a high degree of diversity within the invertebrates groups in general, and within the ecological group of the Turbellaria in particular. In the present work, old and new records of turbellarian species from the central areas of the Iberian Peninsula are presented. Data on their biology and distribution within the freshwater habitats, mainly limnic, are also provided. This study is mainly based on the project Fauna Iberica III. This revised version was published online in July 2006 with corrections to the Cover Date.     

The amphibians and reptiles of Luzon Island,Philippines, VIII: the herpetofauna of Cagayan and Isabela Provinces,northern Sierra Madre Mountain Range

We provide the first report on the herpetological biodiversity (amphibians and reptiles) of the northern Sierra Madre Mountain Range (Cagayan and Isabela provinces), northeast Luzon Island, Philippines. New data from extensive previously unpublished surveys in the Municipalities of Gonzaga, Gattaran, Lasam, Santa Ana, and Baggao (Cagayan Province), as well as fieldwork in the Municipalities of Cabagan, San Mariano, and Palanan (Isabela Province), combined with all available historical museum records, suggest this region is quite diverse. Our new data indicate that at least 101 species are present (29 amphibians, 30 lizards, 35 snakes, two freshwater turtles, three marine turtles, and two crocodilians) and now represented with well-documented records and/or voucher specimens, confirmed in institutional biodiversity repositories. A high percentage of Philippine endemic species constitute the local fauna (approximately 70%). The results of this and other recent studies signify that the herpetological diversity of the northern Philippines is far more diverse than previously imagined. Thirty-eight percent of our recorded species are associated with unresolved taxonomic issues (suspected new species or species complexes in need of taxonomic partitioning). This suggests that despite past and present efforts to comprehensively characterize the fauna, the herpetological biodiversity of the northern Philippines is still substantially underestimated and warranting of further study.     

中国半翅目昆虫多样性和地理分布数据集

全球生物多样性逐渐丧失已成为最严重的环境问题之一, 探究各地生物多样性资源及形成机制是生态学和生物地理学领域关注的重要科学问题。生物多样性数据的整合和共享可以为相关研究的开展提供科学依据。昆虫是地球上多样性最高的生物类群, 但是由于目前关于昆虫多样性数据的整理不足, 相关研究较为缺乏。为了促进昆虫类群的多样性数据整理和共享工作的发展, 本研究选取昆虫纲中重要且多样的半翅目作为对象, 通过广泛的数据检索和收集, 系统整理了截至2017年已发表的中国半翅目昆虫的多样性及地理分布信息。数据集中共收集了102科2,090属7,822种半翅目昆虫的分类信息及其39,298条地理分布记录。该数据集可以为今后开展生物多样性格局、生物区系演化和害虫防治等方面的研究工作提供帮助。     

Diversity of the order Lepidoptera (Hesperioidea and Papilionoidea) from Corrientes city, Argentina

Urbanization is one of the most important threats for biodiversity. Among many different organisms, butterflies are useful indicators of environment diversity and quality. The aim of this study was to investigate the Lepidoptera from Corrientes city. Random samplings were performed at two sites: a native forest situated in Santa Catalina district and an urban area, Parque Mitre. The captures were carried out using entomological nets, at four seasons between January to October 2007. A total of 1 114 butterflies, represented by six families: Hesperiidae, Lycaenidae, Nymphalidae, Papilionidae, Pieridae and Riodinidae and 18 subfamilies were recorded. Fifty-nine genera and 75 species were identified; Anartia jatrophae jatrophae was the most abundant species at both localities. This species and Urbanus procne, Phoebis sennae marcellina, Pyrgus orcus and Dryas iulia alcionea were, among other seven, captured at all months. Highest values of abundance were registered during the warmest seasons. Santa Catalina presented the largest abundance (n = 701), richness (S = 74) and diversity (H' = 3.87). A total of 413 individuals and 52 species were identified at Parque Mitre, and Shannon diversity index was 3.58. The obtained data reveals a high species richness and similarity at both sites.     

土壤动物的分子分类预测策略评估

土壤动物类群包含庞大的生物多样性, 由于传统的形态学鉴定技术很难满足该类群多样性调查和监测的巨大需求, 基于DNA等遗传物质的分子层面的鉴定技术(分子分类预测)逐渐登上舞台。然而, 分子分类预测能否在参考分子序列严重匮乏的土壤动物分类研究中实现有效鉴定、如何利用分子分类预测更为准确高效地获取土壤动物的分类信息, 是当下分子分类预测在土壤动物应用中的两大难题。为探究这两大难题, 本文基于宏条形码技术, 对5款常用的分子分类预测软件(VSEARCH、HS-BLASTN、EPA-NG、RAPPAS和APPLES; 前两款基于相似度算法, 其余基于系统发育位置算法)进行了准确性(科和属阶元)、运行速度和内存占用等性能的比较和评估。其中, 预测准确性的评估基于4类土壤动物(弹尾纲, 蜱螨亚纲, 环带纲和色矛纲)和3种分子标记(COI、16S和18S)展开。结果表明: EPA-NG在大部分场合下准确性最高, 尤其是在使用COI标记时, 准确性远高于其他工具。VSEARCH和HS-BLASTN准确性也较高, 基于16S和18S标记时, 它们的准确性和EPA-NG相当。此外, VSEARCH在所有软件中运行速度最快且内存占用最小, 这使得它在16S和18S的应用中比EPA-NG更具竞争力。RAPPAS和APPLES具有较低的假阳性, 但假阴性很高, 相对保守的算法使得它们无法将一些物种鉴定到低阶元。总体来说, 即使是在参考数据库缺少目标物种且小部分物种在分类上存在界定争议的前提下, 5款分子分类预测软件都能极为准确地将土壤动物预测至科级阶元, 因此分子分类预测在土壤动物应用中前景远大。COI标记在土壤动物科、属和种阶元上的覆盖度最广且能有效实现分子鉴定, 在目前最适合作为土壤动物尤其是土壤节肢动物的分子标记。在应用COI标记且参考数据库规模不大时, EPA-NG是分子分类预测的最佳选择; 而在应用16S、18S标记或参考数据库规模较大时, 更推荐使用VSEARCH。     

Checklist of the ants (Hymenoptera,Formicidae) of the Solomon Islands and a new survey of Makira Island

The intent of this paper is to facilitate future research of the Solomon Islands ant fauna by providing the first comprehensively researched species inventory in over 75 years. The species list presented here includes the names of all ant species recorded from the islands that are available in the literature together with specimen records from several museum collections and new records from our 2008 Makira field expedition. All the names of described species presented are valid in accordance with the most recent Formicidae classification. In total, the checklist is composed of 237 species and subspecies (including 30 morphospecies) in 59 genera representing nine subfamilies. We report that the recent field expedition added 67 new species records to Makira and 28 new species records to the Solomon Islands. Our research recovered species occurrence records for 32 individual islands and five island groups. The five islands with the highest number of recorded species are: Makira (142 spp.), Guadalcanal (107 spp.), Malaita (70 spp.), Santa Isabel (68 spp.), and Rennell (66 spp.). Based on our results, we discuss the taxonomic composition of the archipelago’s ant fauna, which islands are most in need of additional sampling, and the importance of establishing biodiversity baselines before environmental threats such as the invasive ant Wasmannia auropunctata cause irrevocable harm to the native biodiversity.     

基于在线数据库的鳞翅目刺蛾科昆虫物种多样性及其全球分布格局

鳞翅目刺蛾科昆虫在全球范围内广泛分布, 是重要经济林、行道林的主要害虫。本研究通过对在线数据库中刺蛾科昆虫分布数据进行整理分析, 阐明其在全球范围内的物种多样性及分布格局, 并初步探讨造成其物种分布不均的原因, 从而为物种多样性保护及害虫防治提供科学依据。通过检索生物条形码数据库(Barcode of Life Data System V4, BOLD V4)和全球生物多样性信息数据库(Global Biodiversity Information Facility, GBIF)中记录的标本信息, 并结合部分地区鳞翅目昆虫名录及野外采集样本数据, 对刺蛾科昆虫的分布信息进行汇总分析并绘制分布图。统计得到具有明确地理坐标的刺蛾科昆虫分布信息61,947条, 共187属637种。结果表明, 在世界动物地理区系尺度上, 东洋区刺蛾科昆虫物种多样性最高, 共72属, 古北区31属, 澳新区及新热带区均为27属, 非洲热带区22属, 新北区19属。在国家尺度上, 中国存在刺蛾科昆虫123种, 越南116种, 其次为哥斯达黎加(75种)和澳大利亚(69种)。中低纬度地区具有较高的刺蛾科昆虫物种多样性和丰富度, 这有可能与该地区的气候历史条件及丰富的寄主植物资源有关。     

Systematic and evolutionary insights derived from mtDNA COI barcode diversity in the Decapoda (Crustacea: Malacostraca)

Background

Decapods are the most recognizable of all crustaceans and comprise a dominant group of benthic invertebrates of the continental shelf and slope, including many species of economic importance. Of the 17635 morphologically described Decapoda species, only 5.4% are represented by COI barcode region sequences. It therefore remains a challenge to compile regional databases that identify and analyse the extent and patterns of decapod diversity throughout the world.

Methodology/Principal Findings

We contributed 101 decapod species from the North East Atlantic, the Gulf of Cadiz and the Mediterranean Sea, of which 81 species represent novel COI records. Within the newly-generated dataset, 3.6% of the species barcodes conflicted with the assigned morphological taxonomic identification, highlighting both the apparent taxonomic ambiguity among certain groups, and the need for an accelerated and independent taxonomic approach. Using the combined COI barcode projects from the Barcode of Life Database, we provide the most comprehensive COI data set so far examined for the Order (1572 sequences of 528 species, 213 genera, and 67 families). Patterns within families show a general predicted molecular hierarchy, but the scale of divergence at each taxonomic level appears to vary extensively between families. The range values of mean K2P distance observed were: within species 0.285% to 1.375%, within genus 6.376% to 20.924% and within family 11.392% to 25.617%. Nucleotide composition varied greatly across decapods, ranging from 30.8 % to 49.4 % GC content.

Conclusions/Significance

Decapod biological diversity was quantified by identifying putative cryptic species allowing a rapid assessment of taxon diversity in groups that have until now received limited morphological and systematic examination. We highlight taxonomic groups or species with unusual nucleotide composition or evolutionary rates. Such data are relevant to strategies for conservation of existing decapod biodiversity, as well as elucidating the mechanisms and constraints shaping the patterns observed.