On the nature of the species problem and the four meanings of 'species'

Present-day thought on the notion of species is troubled by a mistaken understanding of the nature of the issue: while the species problem is commonly understood as concerning the epistemology and ontology of one single scientific concept, I argue that in fact there are multiple distinct concepts at stake. An approach to the species problem is presented that interprets the term 'species' as the placeholder for four distinct scientific concepts, each having its own role in biological theory, and an explanation is given of the concepts involved. To illustrate how these concepts are commonly conflated, two widely accepted ideas on species are criticized: species individualism and species pluralism. I argue that by failing to distinguish between the four concepts and their particular roles in contemporary biological theory, these ideas stand in the way of a final resolution of the species problem.     

Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent

Gene trees are evolutionary trees representing the ancestry of genes sampled from multiple populations. Species trees represent populations of individuals—each with many genes—splitting into new populations or species. The coalescent process, which models ancestry of gene copies within populations, is often used to model the probability distribution of gene trees given a fixed species tree. This multispecies coalescent model provides a framework for phylogeneticists to infer species trees from gene trees using maximum likelihood or Bayesian approaches. Because the coalescent models a branching process over time, all trees are typically assumed to be rooted in this setting. Often, however, gene trees inferred by traditional phylogenetic methods are unrooted. We investigate probabilities of unrooted gene trees under the multispecies coalescent model. We show that when there are four species with one gene sampled per species, the distribution of unrooted gene tree topologies identifies the unrooted species tree topology and some, but not all, information in the species tree edges (branch lengths). The location of the root on the species tree is not identifiable in this situation. However, for 5 or more species with one gene sampled per species, we show that the distribution of unrooted gene tree topologies identifies the rooted species tree topology and all its internal branch lengths. The length of any pendant branch leading to a leaf of the species tree is also identifiable for any species from which more than one gene is sampled.     

Cryptic species as a window into the paradigm shift of the species concept

The species concept is the cornerstone of biodiversity science, and any paradigm shift in the delimitation of species affects many research fields. Many biologists now are embracing a new “species” paradigm as separately evolving populations using different delimitation criteria. Individual criteria can emerge during different periods of speciation; some may never evolve. As such, a paradigm shift in the species concept relates to this inherent heterogeneity in the speciation process and species category—which is fundamentally overlooked in biodiversity research. Cryptic species fall within this paradigm shift: they are continuously being reported from diverse animal phyla but are poorly considered in current tests of ecological and evolutionary theory. The aim of this review is to integrate cryptic species in biodiversity science. In the first section, we address that the absence of morphological diversification is an evolutionary phenomenon, a “process” counterpart to the long‐studied mechanisms of morphological diversification. In the next section regarding taxonomy, we show that molecular delimitation of cryptic species is heavily biased towards distance‐based methods. We also stress the importance of formally naming of cryptic species for better integration into research fields that use species as units of analysis. Finally, we show that incorporating cryptic species leads to novel insights regarding biodiversity patterns and processes, including large‐scale biodiversity assessments, geographic variation in species distribution and species coexistence. It is time for incorporating multicriteria species approaches aiming to understand speciation across space and taxa, thus allowing integration into biodiversity conservation while accommodating for species uncertainty.     

Studies on the helminth parasites of freshwater fishes of the Sudan

2419 freshwater fishes from the Sudan were examined for helminth parasites and found to harbour one monogenean species, 15 species of adult digenetic trematodes, three species of larval trematodes, 16 species of adult cestodes, 13 species of adult nematodes, two species of larval nematodes and three species of acanthocephalans. Four species of adults and four species of larval worms are recorded for the first time in the Sudan and 30 new hosts are listed. The intensity of infestation of each species, the host-specificity and the variations in the infestation of fishes are discussed. The helminth fauna of the Sudan is compared with that of other African countries.     

Patterns in the geographic ranges of the world's woodpeckers

We used data on the world's woodpeckers to test for patterns in the geographic distributions of a single group of closely related species. The frequency distribution of woodpecker geographic range sizes is approximately lognormal. Most variation in range sizes is explained by differences between species within genera; that is, range size seems to be an evolutionarily labile trait. The largest woodpecker ranges are found in Eurasia, both when absolute differences are compared and when range size is measured as a proportion of estimated available habitat. Notably, there is a negative relationship between the mean range sizes attained by species in a genus or tribe in South America and the mean ranges attained by species in the same tribe or genus in North America. Large-bodied species tend to be more widely distributed and to live at higher latitudes, but both tendencies disappear if the taxonomic relatedness of species is controlled for. Species living at high latitudes also tend to be more widely distributed. This relationship seems largely due to the effect of North American woodpeckers, which show it even when the taxonomic relatedness of species is controlled. Small continents generally have more woodpecker species than do large ones. Woodpecker geographic range sizes are smaller the more woodpecker species inhabit an area. Species show less overlap in their geographic ranges with species of similar than with species of dissimilar body size. The implications of these results for our understanding of patterns in geographic range sizes are discussed.     

Branches in the lines of descent: Charles Darwin and the evolution of the species concept

Charles Darwin introduced a novel idea into the concept of species, namely that species are branches in the lines of descent (segments of population lineages). In addition to this novel evolutionary component, Darwin's species concept also retained an older taxonomic component, namely the view that the species category is a taxonomic rank; moreover, he adopted amount of difference as a criterion for ranking lineages as species. Subsequent biologists retained both components of Darwin's species concept, although they replaced Darwin's ranking criterion with ranking criteria that either are more objectively defined or relate more directly to the biological bases of lineage separation and divergence. Numerous alternative ranking criteria were proposed, resulting in a proliferation of species definitions and a controversy concerning the concept of species. That controversy can be resolved by distinguishing more explicitly between the theoretical concept of species and the operational criteria that are used to apply the concept in practice. By viewing the various alternative ranking criteria as operational indicators of lineage separation rather than necessary properties of species, the conflicts among competing species concepts are eliminated, resulting in a unified concept of species. A brief examination of the history of biology reveals that an important shift related to the unified species concept has been emerging ever since Darwin reformulated the concept of species with an evolutionary basis. The species category is effectively being decoupled from the hierarchy of taxonomic ranks and transferred to the hierarchy of biological organization. Published 2011. This article is a US Government work and is in the public domain in the USA. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103 , 19–35.     

Marine species in the algal flora of the Anzali Swamp (Iran)

The composition of marine species in the algal flora of the Anzali Swamp, which is situated parallel to the Caspian Sea coast, is examined. Sampling was carried out at seven stations. A total of 74 species with 89 infraspecific taxa were identified: Cyanophyta, 20 species; Cryptophyta, 2 species; Bacillariophyta, 51 species (66 infraspecific taxa); and Chlorophyta, 1 species.     

Genetic Evidence for the Allodiploid Origin of the Moss Species Polytrichum longisetum

Abstract: Fixed heterozygous banding patterns observed for 4 allozyme and 12 microsatellite loci, in combination with a chromosome number of 14, show that Polytrichum longisetum is an allodiploid species. Comparison of these banding patterns with those of related Polytrichaceae species suggest that Polytrichum formosum, or an ancestor taxon of this species, is one of the haploid progenitors of P. longisetum. The second progenitor species of P. longisetum could not be designated in this study as it was not among the examined possible progenitor species. DNA sequence data for two microsatellite loci, however, suggest that the second progenitor species should possibly be more closely related to P. formosum than any of the other haploid possible progenitor species examined in this study. As the current systematic literature does not mention the existence of such a species, this could indicate that the second progenitor species is already extinct.     

Drosophila auraria复合种Period基因Thr-Gly区段的初步研究

测定了金色果蝇复合种（Drosophila auraria species complex）5个姐妹种（sibling species）和D.rufa的period(per)基因的Thr-Gly区段序列。该区段序列分析表明：DNA序列的碱其组成拥有果蝇其他基因的共同特点;颠换数多于转换数,两两种种间的颠换率与转换率的总比值为2～5,密码子第3位的颠换与转换的比值为2.5～5;同义替换/异义替换（Ks/Ka）值远大于10,且有的物种间根本不存在非同义突变,低的Ka值说明该复合种的per基因Thr-Gly区段在进化过程中可能承受着较强的选择压力。运用所得的核苷酸序列构建Drosophila auraria复合种的系统发育树,为澄清该类群的系统演化关系提供了新的线索。     

A Preliminary Investigation on the Status of the Wildlife Trade in Guangxi,China

1IntroductionWildlifetradeisamain~mpetustoutilizewildlife.Thechangeinspeciesandvolumein-volvedinthewildlifetrademayreflectconservationstatus,dynamicsandexploitedlevelofwildliferesources.Thestudyonwildlifetradeisthetheoriticalbasisonwhichproposalsastolimittradeonrareorendangeredspeciescanbemade,andwithwhichfuturemonitoringofthetradecanbecompared.Theresultalsocanbeusedtoevaluateconservationeffectsofprotectionmeasuresandlawsforbiodiversityconservation.Itisofgreatsignificanceinguid-ingsustainable…     

浅析物种概念的演变历史

本文是一篇关于物种概念演变的简述。生物学家用不同的方法或标准划分物种, 就形成了不同的物种概念, 如生物学物种、形态学物种、生态学物种、进化物种、系统发生或支序物种, 或它们的组合, 等等。它们都揭示了物种属性的特定侧面, 都是不同物种客观存在的真实反映, 但都无法令所有人满意。对真核生物来说, 无论它们在形态上的差别有多大, 生殖隔离(不能产生可育的后代)应该是两个群体能否真正分化成不同物种的关键, 这种隔离机制可以是地理的、行为的或其他方式; 而生殖隔离总会伴随着一些形态或遗传上的变化, 虽然这些特征可能与生殖隔离本身并无多大关系, 但往往成为分类学家或分子进化生物学家区分种的依据,对已经灭绝的化石物种来说, 生殖隔离的物种划分方式就无能为力了。如何准确定义一个物种依然充满着矛盾, 因为基于生殖隔离的物种概念不实用, 而实用的物种概念(如形态学物种)又被认为是人为的。     

Molecular analysis of the phylogenetic relationships among the diploid aegilops species of the section Sitopsis

RAPD analysis was used to study the intraspecific variation and phylogenetic relationships of S-genome diploid Aegilops species regarded as potential donors of the B genome of cultivated wheat. In total, 21 DNA specimens from six S-genome diploid species were examined. On a dendrogram, Ae. speltoides and Ae. aucheri formed the most isolated cluster. Among the other species, Ae. searsii was the most distant while Ae. longissima and Ae. sharonensis were the closest species. The maximum difference between individual accessions within one species was approximately the same (0.18-0.22) in Ae. bicornis, Ae. longissima. Ae. sharonensis, and Ae. searsii. The difference between the clusters of questionable species Ae. speltoides and Ae. aucheri corresponded to the intraspecific level; the difference between closely related Ae. longissima and Ae. sharonensis corresponded to the interspecific level. The section Sitopsis of the genus Aegilops includes six diploid species containing the S genome, which is regarded as an ancestor of the B genome of cultivated wheat. The species of the section are thought to be closest to the genus Triticum. Note that the taxonomic status of some forms of the section Sitopsis is questionable. For instance, Ae. speltoides and Ae. aucheri are variously considered as individual species or as a single species, Ae. speltoides. The situation with Ae. longissima and Ae. sharonensis is similar. Thus, although the group includes only diploid species and is well studied morphologically, its phylogeny and taxonomy are still questionable.     

Biogeographical indices of the freshwater fish spatial distribution in the upper reaches of the Yangtze River

The spatial distribution of freshwater fish species (Total species and Unique species) in the upper reaches of the Yangtze River was studied, focusing on the spatial distribution of geographic ranges. Two biogeographical indices: environmental resistance (R₅₀), anisotropy (A₅₀) and a fractal dimension method were used to identify the relationship between them and spatial distribution of freshwater fish. R₅₀ quantifies the loss of biotic resemblance occurring from any point in the map to the rest of the study area. A₅₀ quantifies the extent to which the perimeter: area ratio of the geographical ranges of all species whose distributions overlap at any particular location depart from the perimeter of area ratio of a circle. We concluded that the western of the study area is populated by a large number of total and unique species, the eastern part with the total species richness, the middle regions populated by small number of unique species, the mid-west region populated by small number of total species, and the mid-eastern region populated by a large number of total species. We also analyzed how topology affects the spatial arrangement of species, species density has strong curvilinear correlation (species density increases with increased of fractal dimension), the species density in the tributaries is lower than that in mainstream. The results and methods used give us detailed information about the spatial distribution of species, so as to illuminate the species distribution and change by the human activities.     

Does the species/area relationship account for the density/area relationship?

The best-known macroecological generalisation is the species/area relationship: larger areas contain more species. It has also been observed that the estimated densities of individual species is lower when they are censused over a larger area. Let us call this the density/area relationship. Numerous explanations for the density/area relationship have been proposed – including the idea that the relationship is artefactual. One possible explanation is that it is a necessary consequence of the species/area relationship – after all, if a larger area is to contain more species then the average abundance of individual species must decline. We study a data set that allows us to study both relationships simultaneously. We conclude that the density/area relationship observed for the individual species in this study is consistent with the species/area relationship explanation: in other words, the densities of individual species decline, quantitatively, in the manner required to fit more species into communities with larger areas. We conclude that whatever explains the species/area relationship also explains the density/area relationship and discuss, in particular, the habitat heterogeneity hypothesis.     

Zoogeographical analysis of the hoverfly fauna (Diptera, Syrphidae) of the northwestern Caucasus

The hoverfly fauna of the northwestern Caucasus comprises 257 species of 72 genera. They possess 32 types of ranges that could be united into 11 groups of ranges. Widespread species from the basis of the hoverfly fauna in the region: species with narrower ranges, those distributed in more than one zoogeographical region, and those distributed in more than one dominion, constitute 12.9%, 63.1%, and 24% of the fauna, respectively. The hoverfly fauna of the northwestern Caucasus is composed of nemoral species common for Europe and Mediterranean basin, and also by species widespread in the Palaearctic (92.9%). Autochthomous species constitute 5.5%, and species of the eastern Palaearctic origin, 1.6%. Hoverfly species with zoophagous larvae are the most widespread. The fraction of such species is low among species with narrowly local ranges (12.5%) and high among species with ranges including more than one dominion. Phytophagous species are wider represented among hoverflies with narrowly local ranges (44.7%) than among flies with interdominion ranges (8%). Ranges of dendrobiontic saprophagous species are determined by the presence of arboreal vegetation and no widespread polytopic hoverflies are found in this group. The distribution of mycetophagous species, commensals, and terrestrial saprophagous species is determined by the presence of fungi, ranges of some hymenopterans, and the presence of decaying plant remnants.     

基于贝叶斯权重估计方法估计浙江省古田山国家级自然保护区两栖爬行动物多样性

传统的两栖爬行动物多样性调查方法在进行野外实验时,常遇到抽样限制的问题,一些稀有物种可能无法在个体样本中被发现,由于存在相对较大的物种缺失,导致不同的研究结果差距较大,较难反映真实的物种多样性.因此,基于有限的调查和监测数据尽可能准确地估计生物多样性极其重要.本文于2017—2020年的每年秋季,采用视觉遇见法调查了4...     

澜沧江糯扎渡季雨林厚皮树+家麻树群落的研究

根据5个20m×25m样地的调查资料,对分布于澜沧江糯扎渡河岸山地,以厚皮树、家麻树为优势种的季雨林群落进行了分析研究,结果显示:(1)该群落乔木层以落叶成分厚皮树和家麻树为优势种,层间以常绿的大型木质藤本云南翅子藤为特征;(2)在群落2500m2样地内,共计维管束植物72种,隶属于38科65属;其中有乔木25种,草本植物25种,灌木10种和层间藤本植物12种;(3)综合5个样地后计算所得群落乔木层树种丰富度为25种,Shannon-Wiener指数为2.9010,Pielou均匀度指数为0.9012,Simpson指数为0.9346,在群落中,随着乔木径级的增大,个体数和种数逐渐减小;(4)该群落主要以高位芽植物为主,并以中高位芽植物为优势,占所统计总种数的35.8%;(5)该群落中落叶种类占总种数的62.5%,中叶占47.2%,小叶占41.7%,单叶占69.4%,纸质叶占61.1%,全缘叶占56.9%;(6)该群落的物种数/样地面积关系曲线显示在取样面积1000m2时开始趋于平缓,意味着该取样面积可以考虑作为群落最小取样面积。     

A review of the alien and expansive species of freshwater cyanobacteria and algae in the Czech Republic

The invasion and spread of non-native species of many different kinds of organisms is of increasing interest to researchers. Invasions by microscopic organisms, however, are poorly understood, and their impact on the environment is probably underestimated. We collected available data on non-native and invasive/expansive algae and cyanobacteria in the Czech Republic; we mapped their distribution and assessed their impact on local species and other real or potential risks resulting from their spread. The list of alien species in the Czech Republic contains 10 species of cyanobacteria, 9 species of Bacillariophyceae, 1 species of Dinophyta, 1 species of Ulvophyceae, 2 species of Chlorophyceae, and 1 species complex of Zygnematopyceae. The literature on the worldwide occurrence of these taxa is also reviewed.     

The cladistic solution to the species problem

The correct explanation of why species, in evolutionary theory, are individuals and not classes is the cladistic species concept. The cladistic species concept defines species as the group of organisms between two speciation events, or between one speciation event and one extinction event, or (for living species) that are descended from a speciation event. It is a theoretical concept, and therefore has the virtue of distinguishing clearly the theoretical nature of species from the practical criteria by which species may be recognized at any one time. Ecological or biological (reproductive) criteria may help in the practical recognition of species. Ecological and biological species concepts are also needed to explain why cladistic species exist as distinct lineages, and to explain what exactly takes place during a speciation event. The ecological and biological species concepts work only as sub-theories of the cladistic species concept and if taken by themselves independently of cladism they are liable to blunder. The biological species concept neither provides a better explanation of species indivudualism than the ecological species concept, nor, taken by itself, can the biological species concept even be reconciled with species individualism. Taking the individuality of species seriously requires subordinating the biological, to the cladistic, species concept.     

Aeolid opisthobranch molluscs (Glaucidae) from the Indian Ocean and the south-west Pacific

Eight aeolid opisthobranch molluscs of the subfamilies Facelininae, Favorininae, and Herviellinae are reported from Tanzanian waters, and two species from Northwestern India. New records from Queensland, Australia greatly extend the range of two species reported from Tanzania. Phidiana militaris (Alder & Hancock) and P. indica (Bergh) are shown to be distinct and a species from New Zealand, originally identified as P. militaris , is shown to be new. P. bourailli (Risbec), previously reported only from New Caledonia, is described from Tanzania, as is a new species of Phidiana. Favorinus japonicus Baba is reported from Tanzania, the first published record outside Japan, a new species of Godiva is described from Tanzania and Queensland, and three new species of Sakuraeolis are described, one from India and two from Tanzania. A new species of Herviella is described from Tanzania.