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.     

黄土丘陵沟壑区潜在抗侵蚀植物分析

基于对黄土丘陵沟壑区延河流域多年(2003—2014年)植被调查资料的整理分析,根据抗侵蚀植物定义及Braun-Blanquet植物社会学方法,筛选该区潜在的抗侵蚀植物,阐明不同抗侵蚀植物的分布特征及其生存繁衍能力。结果表明:1)共筛选出潜在的抗侵蚀植物42种,分属18科33属,禾本科、豆科、菊科、蔷薇科物种最多,占总物种数的66%。2)42种植物中85%的物种生活型为高位芽、地上芽和地面芽植物,76%的物种生长型为灌木/小灌木和多年生草本,78%的物种水分生态类型为旱生和中生;结合该流域的气候条件及42种植物的分布范围,可将其分成广幅种、中幅种、窄幅种3种类型。3)55%的物种最大盖度超过50%,可成为群落的建群种或单优种;其它最大盖度小于50%的物种多成为群落的共优种,这些物种具有较高的盖度和地上生物量,表明植物能适应该区侵蚀环境且长势较好。4)42种植物几乎都具有土壤种子库和幼苗库,60%的物种具有植冠种子库;除一年生植物,其他植物均可进行营养繁殖,表明潜在的抗侵蚀植物均能维持自身的生存繁衍。5)42种植物中有13种为主杆型植物,其较大的冠幅能够保护基部土壤;8种疏丛型植物具较强的保护土体和拦截沉积物能力;6种聚丛型和7种簇丛型植物能有效拦截沉积物。总之,只占研究区记录的总物种数13%的潜在抗侵蚀植物具有种子库和幼苗库,多年生植物以营养生殖为主,能维持自身的生存繁衍;由于植冠对其下土壤的保护和植物基部茎对沉积物的拦截,在植物基部能形成土堆,可有效控制土壤侵蚀。     

Effect of species richness and relative abundance on the shape of the species accumulation curve

Abstract We explain how species accumulation curves are influenced by species richness (total number of species), relative abundance and diversity using computer‐generated simulations. Species richness defines the boundary of the horizontal asymptote value for a species accumulation curve, and the shape of the curve is influenced by both relative abundance and diversity. Simulations with a high proportion of rare species and a few abundant species have a species accumulation curve with a low ‘shoulder’ (inflection point on the ordinate axis) and a long upward slope to the asymptote. Simulations with a high proportion of relatively abundant species have a steeply rising initial slope to the species accumulation curve and plateau early. Diversity (as measured by Simpson's and Shannon–Weaver indices) for simulations is positively correlated with the initial slope of the species accumulation curve. Species accumulation curves cross when one simulation has a high proportion of both rare and abundant species compared with another that has a more even distribution of abundance among species.     

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.     

Assessing the risk of freshwater fish introductions into the Iberian Peninsula

1. Preventing the introduction of species likely to become invaders is the best management option to deal with biological invasions. A data set consisting of native, introduced and species not currently present in Iberian Peninsula (n = 167 species) was used to identify freshwater fish species that are likely to be introduced and become successful invaders in the near future. 2. Principal component analysis (PCA) of species traits was used to determine species likely to be introduced, assuming that the traits of species introduced in the future will resemble those of previously introduced species. The likelihood of introduction was calculated as the proportion of neighbour species (in the space defined by the PCA) that have been introduced to the Iberian Peninsula and, together with metrics related to different stages of invasion, was used to construct a region‐specific risk index (Iberian risk index). 3. Introduced species had higher index values compared with native species or species currently absent from the region. The Iberian risk index was positively related to the results of an independent risk analysis for freshwater fish as well as to the geographical spread of species previously introduced to the Iberian Peninsula. 4. Iberian risk index values were used to establish a cut‐off value for estimating the probability of a successful invasion. This threshold value was used to construct a list of 20 species to be included in a ‘watch list’ to prevent freshwater fish invasions in the Iberian Peninsula.     

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.     

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.     

Dynamics of core and occasional species in the marine plankton: tintinnid ciliates in the north-west Mediterranean Sea

Aim To assess short‐term variability in the community composition and community structure of tintinnid ciliates, herbivores of the microzooplankton. Location North‐west Mediterranean Sea. Methods We sampled on 18 dates over a 4‐week period in 2004 at an open‐water site. Species were classified as ‘core species’, found on every date, or ‘occasional species’, absent on one or more dates. Species abundance distributions of the entire community, and separately the core and occasional species, were compared with geometric, log‐series and log‐normal distributions. Core and occasional species were compared in terms of the shell or lorica oral diameter (LOD), analogous to gape size. Results We found 11 core and 49 occasional species. Diversity metrics were stable compared with shifts in abundances. Core species accounted for the majority of individuals in all samples. On each date, 9–22 occasional species, representing 10–15% of the population, were found. Species richness of the occasionals was positively related to population size. The identities of the occasional species found were unrelated to the time between sampling. The species abundance distribution of the occasional population was best fit by a log‐series distribution, while that of the core species was best fit by a log‐normal distribution. The species abundance distribution of the entire community was best fit by a log‐series distribution. Most of the occasional species had LODs distinct from that of a core species and occupied size classes left empty by the core population. However, the most abundant and frequent of the occasional species had a LOD similar to that of a core species. Main conclusions Among tintinnids, which are planktonic protists, occasional species have a species abundance distribution pattern distinct from that of core species. Occasional species appeared to be composed of two groups, one of relatively abundant species and similar to core species, and a second group of ephemeral species with morphologies distinct from core species. The existence of two categories of occasional or rare species may be common: (1) those similar to, and thus perhaps able to replace, dominant species in the absence of a change in the environment; and (2) those distinct from dominant species and requiring different conditions to prosper.     

A Reconsideration of the Reproductive Biology of the Atlantic Forest in the Volta Velha Reserve

Published species lists that include breeding system designations of vascular plants are rare in the primary literature and, thus, can be potentially valuable sources of information for comparative studies. The published list for vascular plants in the Volta Velha Reserve suffered from a number of errors, notably applying the designation of monoecious to all species with imperfect flowers. Here, I reconsider the breeding systems for 97 woody vascular plant species. The majority of species initially categorized as monoecious are found to be hermaphroditic. I then examine the relationship between breeding system and numbers of individuals in a 1 ha plot. The mean number of individuals was marginally higher in dioecious than hermaphroditic and monoecious species combined. Furthermore, although only 28% of the species were characterized as possessing a dioecious breeding system, 42% of the individuals encountered belonged to a dioecious species. These results suggest that dioecious species can, at least under certain circumstances, overcome the reductions in the number of seed-bearing individuals and mate assurance that accompany possessing spatially segregated sexes.     

Hydromedusae of the Mediterranean Sea

Mediterranean hydromedusae can be classified in several categories: common species, widely distributed throughout the Mediterranean and rare species reported from the Pacific, Indian or Atlantic Oceans; seasonal species comprising cold-season species with a boreal affinity and warm-season species with a hot to temperate affinity; neritic and mid-ocean species; surface species and meso-, infra-, and bathypelagic species. Holoplanktonic species are known to be associated with stable hydrological conditions (offshore waters, deep waters, summer and winter homothermy), whereas meroplanktonic species are more likely to be found in more disturbed hydrological conditions (coastal waters, surface waters, spring and autumn periods of temperature fluctuation). A general pattern of medusa distribution is established based upon comparative study throughout the Mediterranean.     

Resolving the taxonomy of the Polysiphonia scopulorum complex and the Bryocladia lineage (Rhodomelaceae,Rhodophyta)

Cryptic diversity is common among marine macroalgae, with molecular tools leading to the discovery of many new species. To assign names to these morphologically similar species, the type and synonyms have to be examined, and if appropriate, new species must be described. The turf-forming red alga Polysiphonia scopulorum was originally described from Rottnest Island, Australia, and subsequently widely reported in tropical and temperate coasts based on morphological identifications. A recent study of molecular species delineation revealed a complex of 12 species in Australia, South Africa, and Europe. These species are placed in a taxonomically unresolved lineage of the tribe Polysiphonieae. The aim of this study was to resolve the genus- and species-level taxonomy of this complex and related species using molecular and morphological information. Three morphologically indistinguishable species of the complex were found at the type locality of P. scopulorum, preventing a straightforward assignment of the name to any of the molecular lineages. Therefore, we propose a molecularly characterized epitype. Polysiphonia caespitosa is reinstated for the only species found in its type locality in South Africa. We describe seven new species. Only one species of the complex can be morphologically recognized, with the other eight species indistinguishable based on morphometric analysis. The studied complex, together with another seven species currently placed in Polysiphonia and two Bryocladia species, formed a clade distinct from Polysiphonia sensu stricto. Based on observations of Bryocladia cervicornis (the generitype), we describe our seven new species in the genus Bryocladia and transfer another nine species from Polysiphonia to Bryocladia.     

On the centrality and uniqueness of species from the network perspective

Identifying important species for maintaining ecosystem functions is a challenge in ecology. Since species are components of food webs, one way to conceptualize and quantify species importance is from a network perspective. The importance of a species can be quantified by measuring the centrality of its position in a food web, because a central node may have greater influence on others in the network. A species may also be important because it has a unique network position, such that its loss cannot be easily compensated. Therefore, for a food web to be robust, we hypothesize that central species must be functionally redundant in terms of their network position. In this paper, we test our hypothesis by analysing the Prince William Sound ecosystem. We found that species centrality and uniqueness are negatively correlated, and such an observation is also carried over to other food webs.     

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.     

The functional trait space of tree species is influenced by the species richness of the canopy and the type of forest

Analysing how species modify their trait expression along a diversity gradient brings insight about the role that intraspecific variability plays over species interactions, e.g. competition versus complementarity. Here, we evaluated the functional trait space of nine tree species dominant in three types of European forests (a continental‐Mediterranean, a mountainous mixed temperate and a boreal) growing in communities with different species richness in the canopy, including pure stands. We compiled whole‐plant and leaf traits in 1719 individuals, and used them to quantify species trait hypervolumes in communities with different tree species richness. We investigated changes along the species richness gradient to disentangle species responses to the neighbouring environment, in terms of hypervolume size (trait variance), shape (trait relative importance) and centroid translation (shifts of mean trait values) using null models. Our main results showed differences in trait variance and shifts of mean values along the tree diversity gradient, with shorter trees but with larger crowns in mixed stands. We found constrained functional spaces (trait convergence) in pure stands, suggesting an important intraspecific competition, and expanded functional spaces (trait divergence) in two‐species admixtures, suggesting competition release due to interspecific complementarity. Nevertheless, further responses to increasing species richness were different for each forest type, waning species complementarity in sites with limiting conditions for growth. Our results demonstrate that tree species phenotypes respond to the species richness in the canopy in European forests, boosting species complementarity at low level of canopy diversity and with a site‐specific pattern at greater level of species richness. These outcomes evidence the limitation of functional diversity measures based only on traits from pure stands or general trait database values.     

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。     

Applying the dark diversity concept to plants at the European scale

Large‐scale biodiversity maps are essential to macroecology. However, between‐region comparisons can be more useful if patterns of observed species richness are supplemented by variations in dark diversity – the absent portion of the species pool. We aim to quantify and map plant diversity across Europe by using a measure that accounts for both observed and dark diversity. To do this we need to delimit suitable species pools, and evaluate the potential and limitation of a large‐scale dataset. We used Atlas Florae Europaeae (ca 20% of European plant species mapped within 50 × 50 km grid cells) and defined for each grid cell several species pools by applying various geographical and environmental filters: geographic species pool (number of species within 500 km radius), biogeographic species pool (additionally incorporating species distribution patterns, i.e. dispersion fields), site‐specific species pool (additionally integrating environmental preferences of species based on species co‐occurrence). We integrated dark diversity and observed diversity at a relative scale to calculate the completeness of site diversity: logistic expression of observed and dark diversity. We tested whether our results are robust against regional variation in data availability. We used independent regional databases to test if Atlas Florae Europaeae is a representative subset of total species richness. Environmental filtering was the most influential determinant of species pool size with more species filtered out in southern Europe. Both observed and dark diversity adhered to the well‐known latitudinal gradient, but completeness of site diversity varied throughout Europe with no latitudinal trend. Dark diversity patterns were fairly insensitive to variations in regional sampling intensity. Atlas Florae Europaeae represented well the total variation in plant diversity. In summary, dark diversity and completeness of site diversity add valuable information to broad‐scale diversity patterns since observed diversity is expressed at a relative scale.     

Exploring the relationship between land cover and the distribution of water beetle species (Coleoptera) at the regional scale

The advent of remote-sensed satellite land cover data has provided the opportunity to assess the relationship between invertebrate species distributions and individual land cover types. Water beetle species occur in habitats within specific land cover types and the relationship between the distribution of water beetle species and land covers at the regional scale was investigated using records of 154 species from 1018 sites in north-east England. The land covers of tilled land and urban in the lowlands and of shrub heath and heath grassland in the upland areas proved to be most important in explaining the distribution of species. There were both positive and negative associations between some species and other covers such as woodland and the coast. However, a considerable number of species, generally those with a large number of records, showed no strong relationships with any land cover types. The integration of water beetle species recording data and remote-sensed land cover data as a basis for predicting and monitoring both species distribution and environmental change is discussed.     

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.     

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...     

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.