The notion of homology in current comparative biology

Current notions on homology, and its recognition, causation, and explanation are reviewed in this report. The focus is primarily on concepts because the formulation of precise definitions of homology has contributed little to our understanding of the issue. Different aspects or concepts of homology have been contrasted, currently the most important ones being the distinction between systematic and biological concepts. The systematic concept of homology focuses on common ancestry and on taxa; the biological concept tries to explain patterns of conservatism in evolution by shared developmental constraints. Similarity or correspondence is generally accepted as a primary criterion in the delimitation of homologues, albeit that this criterion is not without practical and theoretical problems. Apart from similarity, the biological concept of homology also stresses developmental individuality of putative homologous structures. Structural and positional aspects of homology can be separated, with positional homology acquiring an independent status. Similarity, topographic relationships, and ontogenetic development cannot be tests of homology. Within the cladistic paradigm, the most decisive test of homology is that of congruence; proponents of the biological-homology concept have been less concerned with test implications. Adopting a hierarchical view of nature suggests that characters have to be homologized at their appropriate level of organization. A taxic or systematic approach to homology has precedence over a transformational or biological approach. Nevertheless, pattern analysis and process explanations are not independent of each other.     

Der Artbegriff in Zoologie,Phylogenetik und Biostratigraphie

The cladistic species concept, as advocated recently by Bonde (1977), Willmann (1985), and others, operates with a “time-bio-species” whose temporal boundaries are defined by successive speciation events. Phyletic lineages without speciations would then correspond to one single species, even if far reaching morphologic changes occur. On the other hand, speciations would be obligatory species boundaries, even if one daughter species is perfectly identical with the parent species. SIMPSON (1951) has already criticized such a procedure as both undesirable and impractical. But objections of this kind have always been ruled out by cladists pretending that purity of theory could not be sacrificed for the sake of mere practical difficulties. A critical reappraisal of the theoretical foundations of the time-bio-species concept shows, however, that the main argument is logically untenable: Speciation means appearance of reproductive isolation within a population. From this “emoment” on there are two biospecies where formerly there was only one. Nothing more than this rather meagre statement results from the biospecies concept, which - as everybody agrees - applies only to synchronous populations and does not allow to define temporal species boundaries. It is therefore impossible to say which one of the two daughter species is new, or if perhaps both of them are new, i. e. whether the parent species survives speciation or not. A decision would only be possible on the base of additional operative criteria allowing to define species boundaries between allochronous populations. Criteria of this kind have never been proposed by cladists. The cladistic species concept is indeed based on an arbitrary decision and the time-bio-species is a purely conventional unit. It should only be used if there are compelling practical and methodological reasons. But, as to the practical aspect, SIMPSON?S (1951) objections are still entirely valid. We may even add that speciation is rather a slow process. Clear-cut boundaries at speciation events exist only in cladograms. One theoretical argument against the use of morphologically defined chronospecies was always that b i ospecies cannot be defined by morphology. This is true, but has nothing to do with the problem of temporal species boundaries. The basic unit of Recent taxonomy is, of course, the biospecies, but this is no longer true for cladistic analysis, even if it starts from Recent faunas. Cladistic analysis depends on synapomorphies, i. e. on morphological characters in a broad sense. Biospecies can only be used as starting point, if they are morphologically distinguishable. But mostly analysis starts from monophyletic groups of several biospecies where monophyly is inferred from morphology. Cladistic analysis does not reconstruct the succession of speciations but of morphogenetic events. This is not a simple technical problem which may be neglected in “pure” theory, but one of methodology. In scientific research the nature of the respective basic unit should agree with the method employed. It makes no sense to work with a species concept that cannot be tested empirically. There has been much debate as to whether or not different species concepts should be used in paleontology and in neontology. But the question is put in the wrong way. As long as only synchronous populations are studied, the biospecies concept should also be used in paleontology. Fossil ostracodes and foraminifera show that dimorphic species can be recognized with the help of Recent homologues. But in phylogenetics we are forced to use an arbitrarily defined conventional basic unit of taxonomy having a temporal dimension. Only the morphologically defined chronospecies allows to describe evolutionary change adequately. On this base biostratigraphy has produced many valuable results, thus proving the efficiency of the concept.     

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。     

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.     

Defining and measuring ecological specialization

1.  Ecological specialization is one of the main concepts in ecology and conservation. However, this concept has become highly context-dependent and is now obscured by the great variability of existing definitions and methods used to characterize ecological specialization.
2.  In this study, we clarify this concept by reviewing the strengths and limitations of different approaches commonly used to define and measure ecological specialization. We first show that ecological specialization can either be considered as reflecting species' requirements or species' impacts. We then explain how specialization depends on species-specific characteristics and on local and contingent environmental constraints. We further show why and how ecological specialization should be scaled across spatial and temporal scales, and from individuals to communities.
3.  We then illustrate how this review can be used as a practical toolbox to classify widely used metrics of ecological specialization in applied ecology, depending on the question being addressed, the method used, and the data available.
4.   Synthesis and applications . Clarifying ecological specialization is useful to make explicit connections between several fields of ecology using the niche concept. Defining this concept and its practical metrics is also a crucial step to better formulate predictions of scientific interest in ecology and conservation. Finally, understanding the different facets of ecological specialization should facilitate to investigate the causes and consequences of biotic homogenization and to derive relevant indicators of biodiversity responses to land-use changes.     

Species concepts and the recognition of ancestors

Whether or not ancestral species can be recognised depends on the species concept adopted. A “metaspecies”; is a species that completely lacks autapomorphies, and which might (or might not) be ancestral to other species. Such taxa have been identified among both living and fossil organisms. Under the most commonly‐used species concepts (biological, evolutionary, phenetic, phylogenetic, ecological, recognition and cohesion), “metaspecies”; can be assumed to be ancestral. Even if the known members of a metaspecies are not ancestral to anything, parsimony dictates that the (as yet unknown) ancestral lineage is identical to the metaspecies and, under these species concepts, assignable to the same species. Only the cladistic and monophyletic species concepts would deny “metaspecies”; ancestral status, but these species concepts are problematical and have never been used by practising systematists.     

Species: the concept, category and taxon

The term species by itself is vague because it refers to the species concept, the species category and the species taxon, all of which are distinct although related to one another. The species concept is not primarily a part of systematics, but has always been an integral part of basic biological theory, It is based on evolutionary theory and applies only to sexually reproducing organisms. The species concept and the phyletic lineage concept are quite distinct although they are related to one another. The important aspect of the species concept is lack of gene flow between different species, and hence the defining criterion of the species is genetic isolation. The species concept is often considered as non‐dimensional, both in time and space. Species possess three different major properties, namely genetic isolation, reproductive isolation and ecological isolation; these properties evolve at different times and under the effect of different causes during the speciation process. Speciation requires an external isolating barrier during the initial allopatric phase in which genetic isolation evolves and must reach 100% efficiency. The subsequent sympatric phase of speciation occurs after the disappearance of the external isolating barrier when members of the two newly evolved species can interact with one another and exert mutual selective demands on one another. Much of the reproductive and ecological isolation evolves during this secondary sympatric phase. The species category is a rank in the taxonomic hierarchy and serves as the basis on which the diversity of organisms is described; it is not the same as the species concept. The species category applied to all organisms, sexually and asexually reproducing. The species taxon is the practical application of the species category in systematics with the recognition of species taxa requiring many arbitrary decisions. No single set of rules exist by which the species category can be applied to all organisms. Recognition of species taxa in asexually reproducing organisms is based on amount of variation and gaps in the variation of phenotypic features associated with ecological attributes of these organisms as compared with similar attributes in sympatric species taxa of sexually reproducing organisms. Species taxa are multidimensional in that they exist over space–time and often have fuzzy borders. Because recognition of species taxa, including those in sexually reproducing organisms, depends on many arbitrary decisions especially when dealing with broad geographical and temporal ranges, species taxa cannot be used as the foundation for developing and testing theoretical concepts in evolutionary theory which can only be done with the non‐dimensional species concept.     

为什么在物种概念上难以达成共识?

生物学家通常认为物种是生命多样性的基本单位。然而, 尽管近一个世纪以来生物学家们不断地讨论物种概念问题, 但到目前为止仍然难以形成共识。大多数生物学家关注如何定义物种主要是因为它有非常重要的实践意义, 所以, 不同学者提出的物种概念在很大程度上是基于实践应用上的可操作性, 并且其视角难免受其专业见地以及对形成新物种的进化过程的认识所影响。物种代表了进化过程的一个阶段, 而且不同的“物种”可能处于物种形成这个进化过程的不同阶段。鉴于“定义”实际上是一种类似协议的约定或界定, 任何定义都是一种带有局限性的概括, 因此我们可能很难建立一个与分类实践中千变万化的情况都能完全匹配协调的物种定义。已经提出来的那些物种概念或定义都有其合理性, 但是也没有一个是完美无缺的。认识到这一点很重要, 否则就可能会因为固执地坚持某一特定的物种概念而在物种界定和进化研究中自觉或不自觉地引入错误甚至制造混乱。     

THE BIOLOGY OF SPECIATION

Since Darwin published the “Origin,” great progress has been made in our understanding of speciation mechanisms. The early investigations by Mayr and Dobzhansky linked Darwin's view of speciation by adaptive divergence to the evolution of reproductive isolation, and thus provided a framework for studying the origin of species. However, major controversies and questions remain, including: When is speciation nonecological? Under what conditions does geographic isolation constitute a reproductive isolating barrier? and How do we estimate the “importance” of different isolating barriers? Here, we address these questions, providing historical background and offering some new perspectives. A topic of great recent interest is the role of ecology in speciation. “Ecological speciation” is defined as the case in which divergent selection leads to reproductive isolation, with speciation under uniform selection, polyploid speciation, and speciation by genetic drift defined as “nonecological.” We review these proposed cases of nonecological speciation and conclude that speciation by uniform selection and polyploidy normally involve ecological processes. Furthermore, because selection can impart reproductive isolation both directly through traits under selection and indirectly through pleiotropy and linkage, it is much more effective in producing isolation than genetic drift. We thus argue that natural selection is a ubiquitous part of speciation, and given the many ways in which stochastic and deterministic factors may interact during divergence, we question whether the ecological speciation concept is useful. We also suggest that geographic isolation caused by adaptation to different habitats plays a major, and largely neglected, role in speciation. We thus provide a framework for incorporating geographic isolation into the biological species concept (BSC) by separating ecological from historical processes that govern species distributions, allowing for an estimate of geographic isolation based upon genetic differences between taxa. Finally, we suggest that the individual and relative contributions of all potential barriers be estimated for species pairs that have recently achieved species status under the criteria of the BSC. Only in this way will it be possible to distinguish those barriers that have actually contributed to speciation from those that have accumulated after speciation is complete. We conclude that ecological adaptation is the major driver of reproductive isolation, and that the term “biology of speciation,” as proposed by Mayr, remains an accurate and useful characterization of the diversity of speciation mechanisms.     

What is speciation and how should we study it?

To understand speciation, we first need to know what species are. Yet debates over species concepts have seemed endless, with little obvious relevance to the study of speciation. Recently, there has been progress in resolving these debates, favoring a lineage-based, evolutionary species concept. This progress calls for reconsideration of the study of speciation. Traditional speciation research based on the biological species concept has led to great advances in understanding how nonallopatric speciation occurs and how species diverge and remain separate from each other. However, this research has neglected the question of how new species arise in the first place for the most common geographic mode (allopatric). A new and very different research program is needed to understand the ecological and evolutionary processes that split an ancestral species into new allopatric lineages. This research program will connect speciation to many other fundamental questions in evolutionary biology, ecology, biogeography, and conservation biology.     

Understanding processes at the origin of species flocks with a focus on the marine Antarctic fauna

Species flocks (SFs) fascinate evolutionary biologists who wonder whether such striking diversification can be driven by normal evolutionary processes. Multiple definitions of SFs have hindered the study of their origins. Previous studies identified a monophyletic taxon as a SF if it displays high speciosity in an area in which it is endemic (criterion 1), high ecological diversity among species (criterion 2), and if it dominates the habitat in terms of biomass (criterion 3); we used these criteria in our analyses. Our starting hypothesis is that normal evolutionary processes may provide a sufficient explanation for most SFs. We thus clearly separate each criterion and identify which biological (intrinsic) and environmental (extrinsic) traits are most favourable to their realization. The first part focuses on evolutionary processes. We highlight that some popular putative causes of SFs, such as key innovations or ecological speciation, are neither necessary nor sufficient to fulfill some or all of the three criteria. Initial differentiation mechanisms are diverse and difficult to identify a posteriori because a primary differentiation of one type (genetic, ecological or geographical) often promotes other types of differentiation. Furthermore, the criteria are not independent: positive feedbacks between speciosity and ecological diversity among species are expected whatever the initial cause of differentiation, and ecological diversity should enhance habitat dominance at the clade level. We then identify intrinsic and extrinsic factors that favour each criterion. Low dispersal emerges as a convincing driver of speciosity. Except for a genomic architecture favouring ecological speciation, for which assessment is difficult, high effective population sizes are the single intrinsic factor that directly enhances speciosity, ecological diversity and habitat dominance. No extrinsic factor appeared to enhance all criteria simultaneously but a combination of factors (insularity, fragmentation and environmental stability) may favour the three criteria, although the effect is indirect for habitat dominance. We then apply this analytical framework to Antarctic marine environments by analysing data from 18 speciose clades belonging to echinoderms (five unrelated clades), notothenioid fishes (five clades) and peracarid crustaceans (eight clades). Antarctic shelf environments and history appear favourable to endemicity and speciosity, but not to ecological specialization. Two main patterns are distinguished among taxa. (i) In echinoderms, many brooding, species‐rich and endemic clades are reported, but without remarkable ecological diversity or habitat dominance. In these taxa, loss of the larval stage is probably a consequence of past Antarctic environmental factors, and brooding is suggested to be responsible for enhanced allopatric speciation (via dispersal limitation). (ii) In notothenioids and peracarids, many clades fulfill all three SF criteria. This could result from unusual features in fish and crustaceans: chromosome instability and key innovations (antifreeze proteins) in notothenioids, ecological opportunity in peracarids, and a genomic architecture favouring ecological speciation in both groups. Therefore, the data do not support our starting point that normal evolutionary factors or processes drive SFs because in these two groups uncommon intrinsic features or ecological opportunity provide the best explanation. The utility of the three‐criterion SF concept is therefore questioned and guidelines are given for future studies.     

A commentary on Ridley's cladistic solution to the species problem

The cladistic species concept proposed by Ridley (1989) rests on an undefined notion of speciation and its meaning is thus indeterminate. If the cladistic concept is made determinate through the definition of speciation, then it reduces to a form of whatever species concept is implicit in the definition of speciation and fails to be a truly alternative species concept. The cladistic formalism advocated by Ridley is designed to ensure that species are monophyletic, that they are objectively real entities, and that they are individuals. It is argued that species need not be monophyletic in order to be real entities, and that ancestor-descendant relations are not the only relations that confer individuality on entities. The species problem is recast in terms of a futile quest for a definition of that single kind of entity to which the term species should uniquely apply.     

Ephemeral ecological speciation and the latitudinal biodiversity gradient

The richness of biodiversity in the tropics compared to high‐latitude parts of the world forms one of the most globally conspicuous patterns in biology, and yet few hypotheses aim to explain this phenomenon in terms of explicit microevolutionary mechanisms of speciation and extinction. We link population genetic processes of selection and adaptation to speciation and extinction by way of their interaction with environmental factors to drive global scale macroecological patterns. High‐latitude regions are both cradle and grave with respect to species diversification. In particular, we point to a conceptual equivalence of “environmental harshness” and “hard selection” as eco‐evolutionary drivers of local adaptation and ecological speciation. By describing how ecological speciation likely occurs more readily at high latitudes, with such nascent species especially prone to extinction by fusion, we derive the ephemeral ecological speciation hypothesis as an integrative mechanistic explanation for latitudinal gradients in species turnover and the net accumulation of biodiversity.     

Speciation in fungi

In this review on fungal speciation, we first contrast the issues of species definition and species criteria and show that by distinguishing the two concepts the approaches to studying the speciation can be clarified. We then review recent developments in the understanding of modes of speciation in fungi. Allopatric speciation raises no theoretical problem and numerous fungal examples exist from nature. We explain the theoretical difficulties raised by sympatric speciation, review the most recent models, and provide some natural examples consistent with speciation in sympatry. We describe the nature of prezygotic and postzygotic reproductive isolation in fungi and examine their evolution as functions of temporal and of the geographical distributions. We then review the theory and evidence for roles of cospeciation, host shifts, hybridization, karyotypic rearrangement, and epigenetic mechanisms in fungal speciation. Finally, we review the available data on the genetics of speciation in fungi and address the issue of speciation in asexual species.     

Try Tri again? Resolving species boundaries in the Lomatium triternatum (Apiaceae) complex

Species boundaries have traditionally been delimited by applying phenotypic characters to a morphological species concept. With an increased understanding of the complexities of speciation as a process, species concepts have proliferated while at the same time, the ability to gather greater numbers and types of molecular characters has expanded the means by which species can be delimited. Phylogenetic studies of molecular data provide an opportunity to identify reciprocally monophyletic groupsand have led to the identification of cryptic or nearly cryptic species in which subtle differences in phenotypes or ecological niches can be uncovered only after monophyletic groups have been identified. Here, we investigate evolutionary relationships among a group of species in the Lomatium triternatum complex using molecular phylogenetic analyses for all samples, and ecological parameters for two of the 38 species included in this study. The results indicate that there are more reciprocally monophyletic groups in this complex than had been estimated using phenotypic data alone. The ecological data show a clear differentiation for the one pair of sister species where ecological sampling was available, implying that divergence within this group may have resulted from environmental selection for soil preferences that have been strong enough to result in speciation.     

结构稳定性: 概念、方法和应用

群落内物种间相互作用的结构是高度组织化的。群落结构对多物种共存的影响机制是群落生态学的核心科学问题之一。目前生态学界在这一问题上存在多种不同的观点。一个可能的原因是, 由于环境因子的复杂性, 大部分研究忽略了环境因子对群落结构和物种共存的重要影响。在这一背景下, 近期发展起来的结构稳定性理论系统地联系了群落结构、环境因子和物种共存, 并在此基础上建立了一个和经验数据紧密结合的理论框架。本文首先简要回顾了当前关于群落结构研究的争鸣, 然后介绍了结构稳定性的理论框架和计算方法, 最后详细介绍了结构稳定性理论在不同生态群落和不同生态学问题中的应用。在全球气候变化的背景下, 结构稳定性理论提供了一种新的视角来理解群落层面的生物多样性维持机制。     

The debate about the biological species concept - a review

The importance of the species concept in biology has led to a continuing debate about the definition of species. This paper summarizes the recent literature in relation to the ‘biological species concept’ (MAYR 1942). Among the general attributes demanded, possible limitations of the universality and applicability of a species definition are discussed. Three different areas of criticism of the biological species concept are considered: 1. The impracticability of the criterion of reproductive isolation. The demand for more practical criteria is rejected, because reproductive isolation is seen as the factor that produces and maintains species as discrete entities in nature. 2. The inapplicability to non-bisexual organisms. A brief survey of modes of uniparental reproduction and their relative importance suggests that obligatory apomicts are of little evolutionary significance. 3. The inapplicability to multidimensional situations. Despite practical difficulties, the biological species concept is held to apply to organisms separated in space. The impossibility to delimit species in time by reproductive isolation is recognized. Out of two ways to divide continuous evolutionary lineages in time, the phylogenetic approach, which considers only speciation events (cladogenesis), is preferred as it is more objective. A list of recently published alternative definitions of species, none of which is found acceptable, is given. It is concluded that the biological species concept needs not be changed or dismissed on the basis of the discussed criticisms.     

Mutation‐order divergence by sexual selection: diversification of sexual signals in similar environments as a first step in speciation

The origin of species remains a central question, and recent research focuses on the role of ecological differences in promoting speciation. Ecological differences create opportunities for divergent selection (i.e. ‘ecological’ speciation), a Darwinian hypothesis that hardly requires justification. In contrast, ‘mutation‐order’ speciation proposes that, instead of adapting to different environments, populations find different ways to adapt to similar environments, implying that speciation does not require ecological differences. This distinction is critical as it provides an alternative hypothesis to the prevailing view that ecological differences drive speciation. Speciation by sexual selection lies at the centre of debates about the importance of ecological differences in promoting speciation; here, we present verbal and mathematical models of mutation‐order divergence by sexual selection. We develop three general cases and provide a two‐locus population genetic model for each. Results indicate that alternative secondary sexual traits can fix in populations that initially experience similar natural and sexual selection and that divergent traits and preferences can remain stable in the face of low gene flow. This stable divergence can facilitate subsequent divergence that completes or reinforces speciation. We argue that a mutation‐order process could explain widespread diversity in secondary sexual traits among closely related, allopatric species.     

扩散生态学及其意义

扩散研究是生态学研究中的一个热点领域 ,而扩散生态学则是生物学领域一门新的分支学科。本文综述了扩散生态学研究的一些基本理论问题 ,包括扩散的定义、扩散生态学的研究内容及其与生物学其它分支学科的关系 ,并阐述了研究扩散的重要意义。扩散生态学的研究内容十分广泛 ,既涉及所有生物 (从微生物到脊椎动物 )的生态学 (如复合种群、群落、生态系统多样性、复杂性和稳定性 )和进化 (如种化 )等理论问题 ,又涉及物种保护、生物多样性保育、有害生物 (包括外来物种 )的控制、流行病防范、环境保护和人口管理等应用问题。因此 ,研究生物的扩散具有十分重要的理论和实践意义。     

The causes of species richness patterns across space, time, and clades and the role of "ecological limits"

A major goal of research in ecology and evolution is to explain why species richness varies across habitats, regions, and clades. Recent reviews have argued that species richness patterns among regions and clades may be explained by "ecological limits" on diversity over time, which are said to offer an alternative explanation to those invoking speciation and extinction (diversification) and time. Further, it has been proposed that this hypothesis is best supported by failure to find a positive relationship between time (e.g., clade age) and species richness. Here, I critically review the evidence for these claims, and propose how we might better study the ecological and evolutionary origins of species richness patterns. In fact, ecological limits can only influence species richness in clades by influencing speciation and extinction, and so this new "alternative paradigm" is simply one facet of the traditional idea that ecology influences diversification. The only direct evidence for strict ecological limits on richness (i.e., constant diversity over time) is from the fossil record, but many studies cited as supporting this pattern do not, and there is evidence for increasing richness over time. Negative evidence for a relationship between clade age and richness among extant clades is not positive evidence for constant diversity over time, and many recent analyses finding no age-diversity relationship were biased to reach this conclusion. More comprehensive analyses strongly support a positive age-richness relationship. There is abundant evidence that both time and ecological influences on diversification rates are important drivers of both large-scale and small-scale species richness patterns. The major challenge for future studies is to understand the ecological and evolutionary mechanisms underpinning the relationships between time, dispersal, diversification, and species richness patterns.