Impacts of taxonomic inertia for the conservation of African ungulate diversity: an overview

We review the state of African ungulate taxonomy over the last 120 years, with an emphasis on the introduction of the polytypic species concept and the discipline's general neglect since the middle of the 20th century. We single out negative consequences of ‘orthodox’ taxonomy, highlighting numerous cases of neglect of threatened lineages, unsound translocations that led to lineage introgression, and cases of maladaptation to local conditions including parasitic infections. Additionally, several captive breeding programmes have been hampered by chromosome rearrangements caused by involuntary lineage mixing. We advocate that specimen‐based taxonomy should regain its keystone role in mammal research and conservation biology, with its scientific values augmented with genomic evidence. While integration with molecular biology, ecology and behaviour is needed for a full understanding of ungulate alpha diversity, we stress that morphological diversity has been neglected despite its tremendous practical importance for some groups of ‘utilizers’ such as trophy hunters, wildlife tourists and conservationists. We conclude that there is no evidence that purported ‘taxonomic inflation’ has adverse effects on ungulate conservation: rather, it is taxonomic inertia that has such adverse effects. We stress that sound science, founded on robust taxonomy, should underpin effective sustainable management (hunting, ranching, captive breeding and reintroduction programmes) of this unique African natural resource.     

基于生物学物种定义探讨物种形成理论与验证的研究进展

物种形成是进化生物学研究的一个永恒主题, 由于生物群体进化是连续和动态的, 物种界限变得难于界定。本文首先讨论了3种地理物种形成模式(同域、邻域及异域), 并分析了近期报道的研究证据。其次, 评述了合子后生殖隔离机制的分子遗传基础和应用群体基因组数据分析的证据, 包括BDMI模型(Bateson-Dobzhansky-Muller incompatibility)、QTLs (quantitative trait loci)、霍尔丹法则及大X染色体效应。最后, 探讨了交配系统作为合子前隔离机制之一与物种形成的关系, 认为近交或自交通过扩大种群遗传结构分化, 增强不同交配系统的种群间不对称基因渐渗, 或种群间无基因渐渗等途径, 促进新物种形成。已知植物交配系统的演化更倾向于从异交(或自交不亲和)向自交(或近交亲和)方式, 花性状和基因组的分化推动形成所谓的自交综合征, 研究交配系统驱动或强化物种形成模式对认识植物物种形成机制有重要意义。     

Research in zoos: a growth area in conservation

Despite early menageries being the source of much useful biological information on anatomy and taxonomy, it is only more recently that the potential for research in zoos has been recongnized. Collections of captive animals are unique and irreplaceable resources for conservation; but without research in zoological parks, progress in conservation science would diminish. There is a flow of information from zoo researchers to field scientists that assists in providing new insights into species biology. Reciprocally, data collected in the field enhance efforts in captive breeding. This paper summarizes the new research initiatives undertaken in zoos, e.g., in the fields of reproductive and genetic technologies, and highlights their significance for conservation and management of threatened species. It is evident that zoo research has a vital role in linking in situ and ex situ conservation. This role needs to be expanded and developed to meet the challenge posed by expanding human and declining wildlife populations and ecosystems.     

New proposals for naming lower-ranked taxa within the frame of the International Code of Zoological Nomenclature

The recent multiplication of cladistic hypotheses for many zoological groups poses a challenge to zoological nomenclature following the International Code of Zoological Nomenclature: in order to account for these hypotheses, we will need many more ranks than currently allowed in this system, especially in lower taxonomy (around the ranks genus and species). The current Code allows the use of as many ranks as necessary in the family-series of nomina (except above superfamily), but forbids the use of more than a few ranks in the genus and species-series. It is here argued that this limitation has no theoretical background, does not respect the freedom of taxonomic thoughts or actions, and is harmful to zoological taxonomy in two respects at least: (1) it does not allow to express in detail hypothesized cladistic relationships among taxa at lower taxonomic levels (genus and species); (2) it does not allow to point taxonomically to low-level differentiation between populations of the same species, although this would be useful in some cases for conservation biology purposes. It is here proposed to modify the rules of the Code in order to allow use by taxonomists of an indeterminate number of ranks in all nominal-series. Such an 'expanded nomenclatural system' would be highly flexible and likely to be easily adapted to any new finding or hypothesis regarding cladistic relationships between taxa, at genus and species level and below. This system could be useful for phylogeographic analysis and in conservation biology. In zoological nomenclature, whereas robustness of nomina is necessary, the same does not hold for nomenclatural ranks, as the latter are arbitrary and carry no special biological, evolutionary or other information, except concerning the mutual relationships between taxa in the taxonomic hierarchy. Compared to the Phylocode project, the new system is equally unambiguous within the frame of a given taxonomic frame, but it provides more explicit and informative nomina for non-specialist users, and is more economic in terms of number of nomina needed to account for a given hierarchy. These ideas are exemplified by a comparative study of three possible nomenclatures for the taxonomy recently proposed by Hillis and Wilcox (2005) for American frogs traditionally referred to the genus Rana.     

519. Paralophia Epiphytica

Summary.  A new genus Paralophia ( Orchidaceae ) is established for two Madagascan species formerly assigned to Eulophia as E. epiphytica and E. palmicola . The history, taxonomy, habitat, conservation biology and cultivation of the recently described Paralophia epiphytica from Madagascar are discussed.     

中国重要海洋动物遗传多样性的研究进展

海洋动物遗传多样性的研究不仅可以揭示物种的起源与进化历史,而且为遗传资源的保存、海水养殖动物育种和遗传改良及整个海洋生态环境的修复和稳定等工作提供理论依据.本文概述了近十几年来我国重要海洋动物(主要包括鱼类、虾蟹类和贝类)遗传多样性研究所取得的成果,具体阐述其在种质鉴定、系统进化、群体遗传结构分析和良种培育等方面的应用,以期进一步推动海洋动物遗传多样性研究,加快优良种质的培育,促进海水养殖业的健康发展,实现海洋生物资源的合理开发和可持续利用.     

Fireflies as a catalyst for science education

The study of fireflies makes an ideal subject for introducing students of all ages to the world of science, conservation biology, field studies and the importance of observation and understanding connections in the natural world.The synchronous fireflies, Photinus carolinus of the Great Smoky Mountains National Park's Elkmont Historic District can be used as a basis for classroom and field activities in subjects as diverse as conservation biology, economics, geography, ecology, governmental policy, zoology, history, taxonomy and animal behavior.Having been fascinated with the synchronous fireflies for over two decades, I will use the life cycle of the Elkmont Phontinus carolinus found in the Great Smoky Mountains National Park as an example.     

571. DENDROSERIS LITORALIS

Summary.  The taxonomy, pollination biology, conservation status, cultivation requirements of Dendroseris litoralis are discussed. A colour plate and line drawings are provided for this critically endangered plant from Juan Fernández Island, also known as Robinson Crusoe Island. The media interest generated by this plant is commented on.     

地花菌属的研究概况和进展

地花菌属（Albatrellus Gray）是多孔菌类中具有突出特征和特殊地位的一个属,有极高的系统学和分类学研究价值,但专门的针对性研究很少。综述了地花菌属在分类学、系统学、牛态习性、经济价值、保护生物学等方面的研究概况和进展,并对该属的深入研究提出了针对性的建议。     

A Position Paper on the Electronic Publication of Nematode Taxonomic Manuscripts

Several nematode species have now attained ‘model organism’ status, yet there remain many niches in basic biological inquiry for which nematodes would be ideal model systems of study. However, furthering the model system approach is hindered by lack of information on nematode biodiversity. The shortage of taxonomic resources to inventory and characterize biodiversity hinders research programs in invasion biology, ecosystem functioning, conservation biology, and many others. The disproportion between numbers of species to be described and numbers of available taxonomic specialists is greater for Nematoda than for any other metazoan phylum. A partial solution to the taxonomic impediment is the adoption of recent advances in electronic publishing. Electronic publishing has the potential to increase the rate at which taxonomic papers are published, the breadth of their distribution, and the type, quantity, quality, and accessibility of data. We propose that the Journal of Nematology implement the advantageous aspects of electronic publication as a means to help ameliorate the limitations of an underdeveloped taxonomy and empower the nematological disciplines currently hindered by it.     

Bioinformatics, genomics and evolution of non-flagellar type-III secretion systems: a Darwinian perspective

We review the biology of non-flagellar type-III secretion systems from a Darwinian perspective, highlighting the themes of evolution, conservation, variation and decay. The presence of these systems in environmental organisms such as Myxococcus, Desulfovibrio and Verrucomicrobium hints at roles beyond virulence. We review newly discovered sequence homologies (e.g., YopN/TyeA and SepL). We discuss synapomorphies that might be useful in formulating a taxonomy of type-III secretion. The problem of information overload is likely to be ameliorated by launch of a web site devoted to the comparative biology of type-III secretion ().     

Considering evolutionary processes in the use of single-locus genetic data for conservation,with examples from the Lepidoptera

The increasing popularity of molecular taxonomy will undoubtedly have a major impact on the practice of conservation biology. The appeal of such approaches is undeniable since they will clearly be an asset in rapid biological assessments of poorly known taxa or unexplored areas, and for discovery of cryptic biodiversity. However, as an approach for diagnosing units for conservation, some caution is warranted. The essential issue is that mitochondrial DNA variation is unlikely to be causally related to, and thus correlated with, ecologically important components of fitness. This is true for DNA barcoding, molecular taxonomy in general, or any technique that relies on variation at a single, presumed neutral locus. Given that natural selection operates on a time scale that is often much more rapid than the rates of mutation and allele frequency changes due to genetic drift, neutral genetic variation at a single locus can be a poor predictor of adaptive variation within or among species. Furthermore, reticulate processes, such as introgressive hybridization, may also constrain the utility of molecular taxonomy to accurately detect significant units for conservation. A survey of published genetic data from the Lepidoptera indicates that these problems may be more prevalent than previously suspected. Molecular approaches must be used with caution for conservation genetics which is best accomplished using large sample sizes over extensive geography in addition to data from multiple loci. Matthew L. Forister, Chris C. Nice and James A. Fordyce contributed equally to this paper.     

Darwin Medal presentation: Corals-seeking the big picture

Recipients of Darwin Medals from the International Society of Reef Studies are requested to write an overview of the work that led to their award. This account is a personal perspective of thirty-five years work on corals. The fields of taxonomy, biogeography, palaeontology, molecular biology, and evolution are presented in an historical context. Emphasis is given to the changing relevance of these fields to today’s world of information technology and the ever-increasing conservation needs.     

野生蜜蜂及其传粉作用的研究现状

传粉是维持与提升生物多样性的重要生态过程。膜翅目蜜蜂总科昆虫是自然界中最重要的传粉者, 但对野生蜜蜂的研究一直以来非常薄弱, 如野生蜜蜂类群的资源调查、种类的准确鉴别、营巢生物学与传粉生物学研究等方面。目前, 生物多样性与保护生物学方面的工作越来越多地涉及野生蜜蜂与植物的相互关系, 地方植物区系与农林作物的传粉生物学基础研究与应用项目也引起重视。本文综述了国内外野生蜜蜂的研究现状, 期望从分类学、营巢生物学与传粉生物学等方面推动野生蜜蜂传粉在农林业生产实践中的应用。     

Phylogeny,taxonomy, genetics and global heritage ranks of an imperilled,freshwater snail genus Lithasia (Pleuroceridae)

Numerous aquatic species are threatened with extinction from habitat elimination or modification. One particularly imperilled group is the freshwater gastropod family Pleuroceridae. Pleurocerids reach their greatest diversity in the southeastern United States, and many species are currently considered extinct, endangered or threatened. One issue hindering efforts to implement conservation management plans for imperilled pleurocerid species is that the taxonomy is in an abysmal state. The taxonomy of pleurocerids is currently based on late 19th- and early 20th-century studies, which used a typological or morphospecies concept. Most biologists today doubt the validity of many of the currently recognized species; however, this does not stop them from assigning conservation ranks in an attempt to determine which species are imperilled or currently stable. We conducted a phylogenetic analysis of the pleurocerid genus Lithasia using morphological and mitochondrial DNA sequence (mtDNA) data in an attempt to delimit species boundaries and test previous taxonomic schemes. We found that the current taxonomy of Lithasia does not reflect species diversity adequately within the genus, with two new undescribed species being discovered. The conservation status ranks of the new, undescribed species are imperilled and would have been overlooked had we relied on the conventional taxonomy. Additionally, the undescribed species' conservation ranks that were previously apparently secure became vulnerable due to being inappropriately assigned as members of formerly widely distributed species instead of the imperilled status they warrant and vice versa, as some taxa that were considered imperilled are now thought to be modestly stable. Our study suggests that conservation ranks should be considered suspect at best in taxonomically poorly known groups until the taxa are reviewed using modern systematic methods.     

Fishery,biology, aquaculture and conservation of the threatened Asian Sun catfish

We summarize the research on Asian Sun catfish, Horabagrus brachysoma (Günther), an endemic and threatened freshwater catfish from Western Ghats of India, and provide a comprehensive review of its taxonomy, distribution, biology, population, conservation and aquaculture. Although described in 1864, the taxonomy of H. brachysoma, particularly its familial affinities, continues to be in flux. The species, originally described from the erstwhile ‘state of Cochin’ in present day Kerala State, India, has a current distribution ranging from southern Kerala (8°N) to southern Maharashtra (16°N), where they are found in lowland westward-flowing rivers, as well as natural freshwater lakes and backwaters. As a much relished food fish, H. brachysoma is exploited throughout its range, predominantly through an unmanaged artisanal fishery. Although there are no scientific estimates of either the status or trends in overall population of this endemic catfish, anecdotal evidence and fisher-knowledge suggests drastic declines of several local populations. The fishery for H. brachysoma in the Periyar and Achenkovil rivers in the State of Kerala has been documented to be unsustainable. As a result of an overall population decline of 35 % due to overharvest and habitat loss, H. brachysoma is assessed as ‘Vulnerable’ on the IUCN Red List of Threatened Species?. Primary research on various aspects of feeding, reproductive biology and demography has generated a wealth of information on the species, but this knowledge is yet to be utilized for the development and implementation of in situ conservation or management plans. In view of its high consumer demand, efficient biological and eco-physiological characteristics, as well as the availability of a captive breeding technology, H. brachysoma is considered an emerging species for small-scale aquaculture. Priorities for scientific research to address knowledge-gaps, as well as strategies for effective conservation of this threatened freshwater catfish are discussed.     

种质资源保存的战略问题和面临的挑战

植物种质资源保存,特别是种子库保存是各种迁地保护措施中最为经济有效的方法。通过对成千上万个物种的有效保存,种子库为减缓物种的灭绝和气候变化对生物多样性的影响发挥了特别关键的作用。本文较为详细地介绍了“中国西南野生生物种质资源库”的立项背景和最新进展,同时介绍了世界上其它几个主要的植物迁地保存设施,特别是英国皇家植物园的“千年种子库”。结合“全球植物保护策略”讨论了中国植物濒危状况,估计我国受威胁的物种比例达20—25％,甚至更高。本文还简要讨论了种子保存中的一些科学问题,包括超低温保存,并强调了植物分类学和种子生物学的学科建设在植物种质资源保护中的重要意义。     

Delimitation despite discordance: Evaluating the species limits of a confounding species complex in the face of mitonuclear discordance

The delimitation of species is an essential pursuit of biology, and proper taxonomies are crucial for the assessment and conservation management of organismal diversity. However, delimiting species can be hindered by a number of factors including highly conserved morphologies (e.g., cryptic species), differences in criteria of species concepts, lineages being in the early stages of the speciation or divergence process, and discordance between gene topologies (e.g., mitonuclear discordance). Here we use a taxonomically confounded species complex of toads in Central America that exhibits extensive mitonuclear discordance to test delimitation hypotheses. Our investigation integrates mitochondrial sequences, nuclear SNPs, morphology, and macroecological data to determine which taxonomy best explains the divergence and evolutionary relationships among these toads. We found that a three species taxonomy following the distributions of the nuclear SNP haplotypes offers the best explanation of the species in this complex based off of the integrated data types. Due to the taxonomic instability of this group, we also discuss conservation concerns in the face of improper taxonomic delimitation. Our study provides an empirical and integrative hypothesis testing framework to assess species delimitation hypotheses in the face of cryptic morphology and mitonuclear discordance and highlights the importance that a stable taxonomy has over conservation‐related actions.     

新一代植物志：iFlora

进入21世纪,随着分子生物学及计算机信息等技术的快速发展,人们认知自然的手段和方式发生了根本性的变化。在现有电子植物志（eFlora）的基础上,融入新一代测序技术、DNA条形码数据、地理信息数据和计算机信息技术等新元素的新一代植物志（iFlora）应运而生。iFlora是通过系列关键技术的集成和攻关,构建便捷、准确识别植物和掌握相关数字化信息的新一代植物志（或智能装备）,它将极大地促进植物分类学和系统发育、演化生物学、生态学、生物地理学和保护生物学等相关学科的发展,有效地服务于生物多样性保护和生物资源可持续利用、国家生态安全和社会公共教育等,并进一步提升公众对生物多样性的认识。iFlora的实施,将为培育和拓展物种识别圈（taxasphere）和生物文化圈（bioliterate world）做出应有的贡献,并可能成为引领国际植物学发展新的生长点。     

The Next-Generation Flora iFlora

The 21st century has witnessed a rapid development in technologies of molecular biology and computer informatics. Fundamental changes have taken place in means and methods in which humans take cognition of the world. Based on the currently available eFlora and combining this with elements of next generation sequencing techniques, DNA sequence data, geographical information system data and computer information technology, the next-generation Flora (iFlora) is bursting. Through a series of key technological innovations and integrations, the main objective of iFlora is to construct the next-generation Flora, which will fulfill the function of accurately and rapidly identifying species and acquiring species related digital information. iFlora will greatly advance the development of plant taxonomy, phylogenetics, evolutionary biology, ecology, biogeography, conservation biology and other related disciplines. Furthermore, iFlora will be a valuable tool for biodiversity conservation and sustainable utilization of biological resources, ecological security, public education and services, and will profoundly promote public understanding of biodiversity. The application of iFlora will tremendously nurture and boost the taxasphere and bioliterate world, and will be a new focal point that may reshape modern botany at the global and regional levels.