AN AMPLIFICATION OF THE PHYLOGENETIC SPECIES CONCEPT

Abstract— The goal of a phylogenetic species concept is to reveal the smallest units that are analysable by cladistic methods and interpretable as the result of phylogenctic history. We define species as the smallest aggregation of populations (sexual) or lineagcs (asexual) diagnosable by a unique combination of character states in comparable individuals (semaphoronts). A character state is an inherited attribute distributed among all comparable individuals (semaphoronts) of the same historical population, clade, or terminal lineage. This definition of species is character-based and pattern oriented. Evolutionary explanations of phylogenetic species are consistent with contemporary explanations of processes of speciation, but require only the assumption of nested hierarchical pattern. We discuss the compatibility of the phylogenetic species concept with various biological needs for species and justify its use at the exclusion of alternative species concepts.     

A new model for the continuum concept

A reformulation of the continuum concept is presented after considering the implications of the community/continuum controversy and current niche theory. Community is a spatial concept dependent on landscape pattern while the continuum is an environmental concept referring to an abstract space. When applying niche theory to plants, the mechanisms of competition are ill-defined and the assumption of bell-shaped response curves for species unrealistic.Eight testable propositions on the pattern of response of vegetation to environmental gradients are presented 1. Environmental gradients are of two types. a) resource gradients or b) direct physiological gradients. 2. The fundamental niche response of species to resource gradients is a series of similar nested response curves. 3. The fundamental niche response of species to direct gradients is a series of separate, independent, overlapping response curves. 4. Species fundamental response curves are such that they have a relative performance advantage in some part of the environmental space. 5. The shape of the realized niche is variable even bimodal but predictable from the fundamental response given the other species present. Propositions 6–8 describe the response shapes of emergent community properties to environmental gradient; species richness is bimodal, dominance trimodal and standing crop unimodal. Detailed comparisons of these propositions are made with the alternative theories of Ellenberg, Gauch and Whittaker, Grime, and Tilman. These theories are incomplete lacking several generally accepted properties of plants and vegetation.     

The Species Problem in Plant Taxonomy in China

Nooteboom (1992) and Peter Raven (pers. comm. ) have pointed out that Chinese taxonomists often hold a narrow species concept and that this may due to the small volum of collections, especially type specimens, available to them which led to the unadequate study on the variability of the species. Raven remarked that “this leads me to believe that the actual concept of species used in plant systematics in China tends to be fairly typological”. What they said are by no means unreasonable. Indeed, the taxonomical status of a considerable number of species in the Chinese flora is probably open to question. New species based on a single character or solely on vegetative characters are of frequent occurrence. Evidences from a very limited number of researches on the patterns of plant variation heretofore available in China have shown that some “species” are, in fact, ecological races ( Clinopodium ), geographical races (Cunninghamia & Indigofera ), or taxa with topoclinal variation (Lespedeza & Rhododendron ). Species based on plasticity of phenotype variation have been or still regarded as “good species” ( Rorippa ). Segregates of an interspecific hybrid with diverse leaf characters have been given different species names ( Ilex ). The originally complicated situation in taxonomy of an agamic complex becomes even more complicated after the publication of additional new species (Malus). A careful analysis of a species with rather complicated patterns of variation leads to the combination of 25 specific names, of which 10 were published in the 80’s by Chinese taxonomists ( Clematoclethra ). Examples of these kinds will greatly increase with the broadening of research work at the species level. Orthodox plant taxonomy is based largely or solely on morphological characters. The exomorphic characters have the practical advantage that they are relatively easy to observe and to record. The taxonomical species concept can meet the needs of general purpose classification. But the notion that the taxonomical species concept is a solely intuitive judgement or preference of an individual worker and one could hardly say what is right and what is wrong is quite problematical. The species category today is much more capable of objective interpretation than ever before. A correct species concept stems from a correct and thorough understanding of the nature of variation pattern of plants and its taxonomical value. Hence, as a herbarium taxonomist, the first thing is to study as many collections as possible. Secondly, the incorporation of evidence from other sources whenever possible is highly desirable. These evidences,if they are not very useful as taxonomical criteria, are frequently of great significanee in contributing to a better understanding or interpretation of the variation pattern of a given taxon. The taxonomist might find the discontinuities he seeks better expressed in either the phenotypic or the genetic variation. A logical application of these two sorts of criteri-a would lead to a more rational classification at the specific level in a great many genera.     

ISLAND BIOGEOGRAPHY AND PALAEOBIOLOGY: IN SEARCH FOR EVOLUTIONARY EQUILIBRIA

1. The concept of evolutionary equilibrium has been derived from the theory of island biogeography via an ecological rationale for increase in species extinction rate and decrease in speciation rate with increasing diversity of the system.
2. This concept is theoretically plausible at the species level and at a regional scale but, in spite of several empirical tests in the fossil record, it has thus far remained unsupported by empirical evidence. In order to test it conclusively, one has to analyze not only the pattern of species number through time but also its relationship to speciation and species extinction rates; independent evidence for perturbations must also be available.
3. The concept of evolutionary equilibrium at the global scale must be extrapolated over higher levels of taxonomic hierarchy, for reliable species-level data are unavailable at this scale. A theoretical justification for this concept cannot, then, be derived from the theory of island biogeography.
4. The rates of family extinction and origination in the Phanerozoic show no evidence for diversity-dependence, which undermines most quantitative models of biotic diversification based on the concept of global evolutionary equilibrium. Rigorous testing of these models cannot be done at the present state of knowledge because of the uncertainty about the empirical pattern (sampling and taxonomic biases, absolute time scale).     

Molecular phylogeny of the Puerto Rican Lepidocyrtus and Pseudosinella (Hexapoda: Collembola), a validation of Yoshii's "color pattern species"

Color pattern was one of the most important characters used to diagnose species in the genus Lepidocyrtus until the introduction of chaetotaxy to Collembola taxonomy. Chaetotaxy confirmed most species diagnoses based only on color patterns, but a number of populations with distinct pigmentation patterns have been found to be identical in all other morphological characters. The absence of individuals showing intermediate color patterns prompted Yoshii to suggest that, despite chaetotaxic identity, populations with distinct color forms represent valid species (implying reproductive isolation and therefore biological species) in what he designated as "color pattern species." In Puerto Rico Lepidocyrtus biphasis, L. dispar, and L. caprilesi show a remarkable variation in pigmentation and as a group include 11 different color forms. Here I present a phylogenetic analysis of the cytochrome oxidase I gene (COI) in 17 species of Lepidocyrtus and Pseudosinella, including 11 species and 10 color forms of Puerto Rican Lepidocyrtus, to test Yoshii's color pattern species concept. The analysis shows large genetic distances between species defined based on morphology alone (morphospecies) and between most color variants within morphospecies. The most often used calibration for the COI molecular clock (2.3% sequence divergence per million years) suggests that morphospecies diverged between 20 and 25 million years before present while color forms within morphospecies diverged between 8 and 19 million years ago. This indicates that changes in climate and sea levels during the Pleistocene were irrelevant to the speciation process in the Puerto Rican Lepidocyrtus. Examination of the genetic variation, phylogenetic relationships, and collection data in light of the biological and phylogenetic species concepts supports the hypothesis that most populations of morphospecies differing only in color pattern are distinct species, thus validating Yoshii's color pattern species concept. As a result it is suggested that morphological characters traditionally used in species diagnoses are very conservative indicators of genetic divergence, that the diversity of springtails has been greatly underestimated, and that studies concerned with identifying factors promoting speciation in Collembola could be misled if they do not include analysis of mitochondrial markers.     

Absence of temporal pattern in courtship signals suggests loss of species recognition in gecko lizards

According to the concept of ritualization, acquisition of signal function (i.e., species recognition) leads to formalization of specific signal structure (i.e., species-specific pattern). By contrast, loss of species recognition may result in specific pattern collapse of the signal, from a temporally regular pattern to an irregular form. Several studies have reported the loss of species recognition driven by release from selective pressure against hybridization under isolation from close relatives, but no study has reported collapse of a regular signal pattern that serves in species recognition. In nocturnal lizards of the genus Gekko, several species pairs hybridize when brought together, whereas other species pairs never hybridize, despite being sympatric. I investigated the relationship between the existence of natural hybridization, courtship call similarity and species recognition ability in eight species of Gekko. I found that males of all eight species court using calls, and four of these species have species-specific regular patterns in the courtship calls, whereas the other four have no temporal patterns. In playback experiments, females of the species-specific pattern call species discriminated species by the call. On the other hand, in the patternless call species, females did not discriminate species by the call, suggesting that natural hybridization has resulted from the loss of species recognition ability in the patternless call species. In insular Gekko isolated from congeners, acoustic species recognition might have been lost, followed by pattern collapse of the courtship calls. This unique example of the signal pattern collapse would provide a key to answer basic questions concerning the causes and consequences of signal evolution.     

Population systematics of Russell's viper: a multivariate study

A multivariate analysis of the population systematics of Russell's viper, based on scalation and colour pattern characters, reveals that the populations of this viper constitute two well-defined taxa: a western form, comprising all populations from the Indian subcontinent, and an eastern form, comprising all populations from east of the Bay of Bengal. The two forms could be considered either as subspecies of one species, or as two separate species, depending on the species concept used. Within the western form, there is no clear pattern of geographic variation. Within the eastern form, the populations from the Lesser Sunda Islands are clearly divergent from the populations of mainland Asia and Java. The conventionally recognized subspecies of Vipera russelli fail to portray this pattern of geographic variation. There is no clear relationship between the pattern of geographic variation in morphology and the pattern of geographic variation in the clinical effects of the venom in human bite victims: some populations with considerable differences in venom effects are equally distinct morphologically, whereas other populations with equally strong venom differences are morphologically very similar. The distribution of Russell's viper can be attributed to Pleistocene changes in climate and sea level, coupled with the viper's ecological requirements, which appear to include a seasonally dry climate.     

COMPARATIVE ANATOMY OF THE ASPIDIACEAE. I. STELAR PATTERN DEVELOPMENT IN YOUNG SPOROPHYTES OF TECTARIA

Vascular tissue development in young sporophytes of seven species of Tectaria is described. Special emphasis is placed on stelar-pattern ontogeny, the transition region between the primary root and the shoot, and changes in the nodal pattern associated with the sequential production of leaves. The changes in stelar pattern which occur prior to the production of the 8th leaf can be placed in three general categories. In the simplest category, development progresses from a protostele to a siphonostele with a unilacunar one-trace nodal pattern. Species in a second category pass through the one trace per gap pattern to a siphonostele with a unilacunar two-trace nodal pattern. The most complex category includes two species in which by the 3rd or 4th leaf a dictyostele with a unilacunar two-trace nodal pattern is established. The significance of this pattern variation in young Tectaria sporophytes of equivalent stages in relation to taxonomic problems in the Aspidiaceae is discussed. In addition, the occurrence of a unilacunar one-trace nodal pattern in these and other species of leptosporangiate ferns is related to the standard concept that a unilacunar two-trace nodal pattern is basic in the ferns.     

Concepts of taxonomy and concepts of biodiversity: the problem of interaction

There is, or there should be, an interaction between concepts of taxonomy and biodiversity. On the one hand, taxonomy develops some general and particular classificatory paradigms, which own diversity is to be taken into account to understand the nature of variety of natural kinds. On the other hand, analysis of the properties of biodiversity may put forward nontrivial problems for taxonomy that cannot be deduced directly from its own statements. From the point view of taxonomy, it is argued that the current concept of biodiversity based entirely on the species concept is deeply rooted in reductionistic view of nature. It is outdated epistemologically and should be replaced by the modern taxonomic concept of the hierarchical phylogenetic pattern. Operationally, the latter presumes a possibility for each species to be assigned a certain "phylogenetic weight", according to its phylogenetic uniqueness. From the point view of biodiversity, it is argued that the global biodiversity is a three component entity, as it includes, in addition to phylogenetic and ecological hierarchies, a biomorphic hierarchy, as well. This calls for taxonomy to elaborate the general principles of classification of biomorphs.     

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.     

The mid-domain effect and diversity gradients: is there anything to learn?

The mid-domain effect (MDE) has been proposed as a null model for diversity gradients and an explanation for observed patterns. Here we respond to a recent defense of the concept, explaining that it cannot represent a viable model in either real or null worlds. First, the MDE misrepresents the nature of species ranges. There is also an internal logical inconsistency underlying the MDE because the range size frequency distribution, necessary to generate a hump-shaped pattern under randomization, cannot exist in the absence of environmental gradients and is generated by the ecological and historical processes that the MDE claims to exclude.     

Refugial debate: on small sites according to their function and capacity

The occurrence and location of long-term refugia determine the current patterns of biodiversity on Earth. The importance of the refugial debate is certain to increase in response to observed and expected species extinctions caused by climate change. Small areas where species survive outside their core range are important, as unique natural phenomena and model systems for observing the response of species to climate change. They can play a crucial role as potential sources for species recovery in the future or can act as progenitors of a new species. While most authors believe that sites connected with only long-term isolation should be included into the refugium concept, this approach can result in the loss of linkage between the ecological and evolutionary processes taking place during different phases of the species range dynamics. Moreover, the papers often interpret the nature of described phenomena in different ways. In response, the conceptual scheme given in our letter summarises the patterns which occur during species range shift. It proposes an equivalent scheme for small refugial sites according to their function and capacity, based on the relict species concept. This approach and proposed terminology is tested on the example of two plant species with different pattern of the long term range dynamics. Our paper highlights the importance of sites harboring ‘trailing-edge’ young relicts for the future long-term persistence of the species (as old relicts) under unfavorable regional conditions. By considering the age gradients of small refugial sites it is possible to reveal community interactions, species traits or genes that drive the responses of biota to climate changes.     

Trends in aquatic macrophyte species turnover in Northern Ireland — which factors determine the spatial distribution of local species turnover?

Aim The study examined qualitative predictions of ecological theories in relation to the spatial distribution of species turnover of aquatic macrophytes, through the following parameters: (1) distance between lakes (2) chemical conditions of the lakes (3) chemical differences between the lakes, and (4) the lake size. Location 562 lakes dispersed throughout Northern Ireland were analysed. Methods To obtain species turnover estimates independent of richness, the average distance between focal lakes and their five nearest neighbours in ordination space (DCA) was standardized by the species richness in a Generalized Additive Model (GAM). The relationships between species turnover and ecological (chemical condition, chemical difference, distance between lakes, and lake‐size) and geographical parameters (latitude, longitude, and altitude) were analysed using GAM. Results The results indicate that the pattern in species turnover is a combination of the chemical conditions and the distance between the lakes, including the interaction term. The effects of chemical heterogeneity and lake size parameters were both positive but weak. In general, increased distance and decreased ionic concentration contribute to increased turnover. The influence of distance on species turnover is strongest at low and high altitude, and at mid‐elevation the species turnover is mainly driven by the chemical conditions. Towards the north there is an increasing influence of distance, whereas in the south the chemical conditions have their strongest influence. Conclusions There is a need for components from several established ecological theories to explain the spatial trends in species turnover within Northern Ireland. Central theories in this particular study are the population/metapopulation dynamics, the continuum concept, and the species‐pool concept.     

An evolutionary explanation of the aggregation model of species coexistence

In ecology, the 'aggregation model of coexistence' provides a powerful concept to explain the unexpectedly high species richness of insects on ephemeral resources like dung pats, fruits, etc. It suggests that females aggregate their eggs across resource patches, which leads to an increased intraspecific competition within occupied patches and a relatively large number of patches that remain unoccupied. This provides competitor-free patches for heterospecifics, facilitating species coexistence. At first glance, deliberately causing competition among the females' own offspring and leaving resources to heterospecific competitors seems altruistic and incompatible with individual fitness maximization, raising the question of how natural selection operates in favour of egg aggregation on ephemeral resource patches. Allee effects that lead to fitness maxima at intermediate egg densities have been suggested, but not yet detected. Using drosophilid flies on decaying fruits as a study system, we demonstrate a hump-shaped relationship between egg density and individual survival probability, with maximum survivorship at intermediate densities. This pattern clearly selects for egg aggregation and resolves the possible conflict between the ecological concept of species coexistence on ephemeral resources and evolutionary theory.     

边缘幸存空间──一个新概念的提出

通过对物种及其生存空间的研究,提出了边缘幸存空间这一新的概念─—物种生存空间之外,居群不能稳定地延续,而生物个体可以存在的空间。还讨论了边缘幸存空间的存在特点及明确了几种在地层中识别边缘幸存空间的方法。最后,以这一概念为基础,讨论了西藏白垩纪赛诺曼期Ｂｉｓｃｕｔｕｍｅｌｌｉｐｔｉｃｕｍ的发现及其意义。     

Reconciling evolutionary theory and taxonomic practice

The notion of evolution is a notion of change; yet, biologists customarily define each species as if it were a static class. One approach to this supposed disconnect between evolutionary theories and taxonomic practices would be to change those practices. Instead, the author claims this alleged disparity is a misreading. For the most part, it disappears under a proposed modified essentialist species concept involving unique species‐specific developmental suites. Each suite specific to a natural species is envisioned as a number of dispositional alternatives expressed distributively among the organisms in that species. There is support for this species concept in recent work in comparative genomics and developmental genetics. The concept is compatible with intraspecific variation and gradual evolution, and unifies practice and theory. It leads to an extended model of speciation and to an observational protocol for testing the concept and model.     

Patterns of plant species turnover along grazing gradients

Questions: How are plant species distributed along grazing gradients? What is the shape of species richness patterns? How can we test for the existence of potential discontinuities in species turnover pattern? Location: Semi‐deserts in the eastern Caucasus, Azerbaijan, Gobustan district. Methods: We studied the distribution of vascular plant species along transects 900‐m long, perpendicular to five farms, and estimated grazing intensity as current livestock units per distance. We modelled species response curves with Huismann–Olff–Fresco (HOF) models and calculated species turnover by accumulating the first derivatives of all response curves. To test for potential discontinuities in changes of vegetation composition along the grazing gradient, we introduce a new null model based on the individualistic continuum concept that uses permutations of the observed pattern of species responses. Results: Most species show a sigmoidal negative response to grazing intensity, while a few species respond with a unimodal pattern. The monotonic decrease in species richness with increasing grazing intensity marks a process of overgrazing that leads to the complete extirpation of plant species. Although the species turnover pattern shows a clear peak, it does not deviate significantly from the null model of individualistic continuous changes. Conclusions: Our approach offers a method for differentiating between transition zones and continuous shifts in species composition along ecological gradients. It also provides a valuable tool for rangeland management to test state‐and‐transition concepts and gives deeper insights into ecological processes affected by grazing.     

Extinction debt in fragmented grasslands: paid or not?

Fragmentation of grasslands and forests is considered a major threat to biodiversity. In the case of plants, the effect of fragmentation or landscape context is still unclear and published results are divergent. One explanation for this divergence is the slow response of long‐lived plants, creating an extinction debt. However, this has not been empirically confirmed. In this study, data were compiled from broad‐scale studies of grasslands from throughout the world that relate plant diversity to fragmentation effects. Only seven studies from northern Europe, out of a total 61, gave any information on actual habitat fragmentation in time and space. In landscapes with >10% grassland remaining, present‐day species richness was related to past landscape or habitat pattern. In landscapes with <10% grassland remaining, in contrast, plant species richness was more related to contemporary landscape or habitat pattern. Studies from landscapes with >10% grassland remaining supported the concept of an extinction debt, while studies from more fragmented landscapes did not provide any evidence of an extinction debt. In order to make generalisations about historical legacies on species diversity in grasslands it is important to consider a range of highly transformed landscapes, and not only landscapes with a high amount of grassland remaining.     

紫距淫羊藿的地理分布新记录及形态描述

淫羊藿属依据少量栽培个体命名的类群普遍存在,往往缺乏足够的野外调查和形态性状统计,对其性状变异幅度、变异式样和分类价值研究不够。紫距淫羊藿(Epimedium epsteinii)由Stearn于1997年依据引种个体命名,为掌握其资源分布及形态性状变异,该研究基于居群概念,对淫羊藿属分布区展开调查,在各分布区选择一个居群(30个体/居群)于花期进行形态观察、统计和描述。结果表明:紫距淫羊藿以往被认为狭域分布于湖南天平山,该研究调查发现广东省和湖北省均有分布,为新分布记录。此两处新分布分别位于天平山的南部和北部,将其自然分布区显著扩大。基于居群观测的形态变异较原描述更广泛。6个主要数量性状(株高、序轴长、小花数、叶长、叶宽和根茎)和花部颜色在居群间和个体间均呈现丰富的变异。生物种的分布范围并非完全连续,而是由若干个多少间断的居群组成,任何一个居群都存在不同程度的连续性变异,要更好地认识各物种,就应当足够重视这些居群系统。紫距淫羊藿的新分布记录对淫羊藿属的资源利用、扩散机制和系统地理学研究具有重要意义。