Species concepts and species delimitation

The issue of species delimitation has long been confused with that of species conceptualization, leading to a half century of controversy concerning both the definition of the species category and methods for inferring the boundaries and numbers of species. Alternative species concepts agree in treating existence as a separately evolving metapopulation lineage as the primary defining property of the species category, but they disagree in adopting different properties acquired by lineages during the course of divergence (e.g., intrinsic reproductive isolation, diagnosability, monophyly) as secondary defining properties (secondary species criteria). A unified species concept can be achieved by treating existence as a separately evolving metapopulation lineage as the only necessary property of species and the former secondary species criteria as different lines of evidence (operational criteria) relevant to assessing lineage separation. This unified concept of species has several consequences for species delimitation, including the following: First, the issues of species conceptualization and species delimitation are clearly separated; the former secondary species criteria are no longer considered relevant to species conceptualization but only to species delimitation. Second, all of the properties formerly treated as secondary species criteria are relevant to species delimitation to the extent that they provide evidence of lineage separation. Third, the presence of any one of the properties (if appropriately interpreted) is evidence for the existence of a species, though more properties and thus more lines of evidence are associated with a higher degree of corroboration. Fourth, and perhaps most significantly, a unified species concept shifts emphasis away from the traditional species criteria, encouraging biologists to develop new methods of species delimitation that are not tied to those properties.     

物种概念及其界定

半世纪以来,物种概念的定义备受关注,不同研究方向的生物学家提出24种不同或至少有分歧的物种概念,根据其不同的物种概念,物种的界定和物种的数量会出现很大的差异。人们普遍认同:物种是进化分离的微居群谱系,但把谱系分离过程中获得的特征如生殖隔离、可鉴定性、单系统发生等视为鉴定物种次级特征却有不同的声音。该文提出统一的物种概念,把谱系进化分离作为物种界定的唯一而又必要的特征,把谱系分离过程中获得的次级特征作为界定谱系分离的证据。鉴于此,物种概念间的分歧就会化解。其一,物种概念化与物种界定明显分开,不再混淆;其二,谱系的次级特征只与物种界定有关,在某种程度上为谱系分离提供证据;第三,若能把合理解释的任何一个特征作为某物种客观存在的证据,这样更多的特征更能确定谱系分离;最后最重要的是,统一物种概念使我们解放思想,扬弃传统的物种界定标准,探求物种界定的新思路。     

Microbiology and the species problem

This paper examines the species problem in microbiology and its implications for the species problem more generally. Given the different meanings of ‘species’ in microbiology, the use of ‘species’ in biology is more multifarious and problematic than commonly recognized. So much so, that recent work in microbial systematics casts doubt on the existence of a prokaryote species category in nature. It also casts doubt on the existence of a general species category for all of life (one that includes both prokaryotes and eukaryotes). Prokaryote biology also undermines recent attempts to save the species category, such as the suggestion that species are metapopulation lineages and the idea that ‘species’ is a family resemblance concept.     

The competitive dynamics of metapopulations subject to the Allee-like effect

It is well recognized that individuals of many species can benefit from the presence of conspecifics, a concept broadly referred to as the Allee effect. At the metapopulation level, there is an analogous but essentially different phenomenon called the Allee-like effect that leads to metapopulation extinction thresholds at low habitat occupancy. But so far not adequate attention has been paid to this phenomenon. In this paper, the Allee-like effect is introduced into a metapopulation model of one species and also that of a three-state two-species competitive system. Phase plane analysis is used to investigate the dynamics of these models. We demonstrate that the Allee-like effect alone could lead to multiple stable states in three-state two-species competitive systems at the metapopulation level, and the number of stable states decrease as the Allee-like effect becomes more severe. Severe Allee-like effects may make coexistence impossible and may even lead to the extinction of both species even if their initial habitat occupancies are high and suitable habitats are enough. It is especially noticeable that depending on their initial conditions one species may exclude the other one that subjects to a weaker Allee-like effect than the former, while the second species always excludes the first one when both species are assumed to be in the absence of the Allee-like effect. We also investigate the habitat destructive effect on the Allee-like system mentioned above. Research indicates that the existence of the Allee-like effect makes a metapopulation more susceptible to habitat destruction. All in all, the Allee-like effect is probably a destabilizing factor that, together with habitat destruction, would affect the continuous existence of species. These conclusions may have important implications for conservation and metacommunity organization.     

The species concept as an emergent property of population biology

Resurgent interest in the genetics of population divergence and speciation coincides with recent critical evaluation of species concepts and proposals for species delimitation. An important result of these parallel trends is a slight but important conceptual shift in focus away from species diagnoses based on prior species concepts or definitions, and toward analyses of the processes acting on lineages of metapopulations that eventually lead to differences recognizable as species taxa. An advantage of this approach is that it identifies quantitative metapopulation differences in continuous variables, rather than discrete entities that do or do not conform to a prior species concept, and species taxa are recognized as an emergent property of population-level processes. The tension between species concepts and diagnosis versus emergent recognition of species taxa is at least as old as Darwin, and is unlikely to be resolved soon in favor of either view, because the products of both approaches (discrete utilitarian taxon names for species, process-based understanding of the origins of differentiated metapopulations) continue to have important applications.     

Mystery of mysteries: Darwin and the species problem

Darwin offered an intriguing answer to the species problem. He doubted the existence of the species category as a real category in nature, but he did not doubt the existence of those taxa called “species”. And despite his scepticism of the species category, Darwin continued using the word “species”. Many have said that Darwin did not understand the nature of species. Yet his answer to the species problem is both theoretically sound and practical. On the theoretical side, Darwin’s answer is confirmed by contemporary biology, and it offers a more satisfactory answer to the species problem than recent attempts to save the species category. On the practical side, Darwin’s answer frees us from the search for the correct theoretical definition of “species”. But at the same time it does not require that we banish the word “species” from biology as some recent sceptics of the species category advocate. © The Willi Hennig Society 2010.     

Disturbances allow coexistence of competing species

We give the first mathematically rigorous proof that disturbances allow competing species to coexist. This work provides a mathematical framework to explain the existence of fugitive species and the role played by disturbances in increasing or decreasing the biodiversity of ecosystems. We study modifications of the metapopulation model for patchy environments proposed by Caswell and Cohen (1990, 1991). For the one- and two-species models we give necessary and sufficient conditions on the parameters for the existence of a non-trivial equilibrium solution, which is shown to be always globally stable.     

Is the F(ST) a good predictor of extinction?

The organization of neutral genetic variation has long been used as a diagnostic tool to infer demographic properties of populations, and recently it has been shown that this information can also be used to estimate the magnitude of genetic deterioration in small or fragmented populations. A further step of this research is to assess whether neutral genetic indicators can serve to predict and compare the viabilities of endangered species. I use modeling to explore how ecological metapopulation settings are related to neutral genetic indicators (such as the fixation index [F(ST)]), changes in genetic load, and metapopulation viability. The analysis indicates that genetic indicators are generally strongly and consistently correlated with the genetic load, population size and structure, and time of extinction but identifies two potential limitations for their use in viability assessments. First, the regime of environmental perturbations is not accurately reflected by neutral indicators, so that their predictive power may be reduced in variable environments. Second, many species are threatened by recent human-induced changes of their habitat configuration. In most cases, genetic indicators may not have reached their equilibrium value in the altered habitat, which limits their ability to compare species with heterogeneous histories and life-history traits.     

Retrospective coalescent methods and the reconstruction of metapopulation histories in the sea

Phylogeographic analyses are a key interface between ecological and evolutionary ways of knowing because such analyses integrate the cumulative effects of demographic (ecological) processes over geological (evolutionary) time scales. Newly developed coalescent methods allow evolutionary ecologists to overcome some limitations associated with inferring population history from classic methods such as Wright’s F _ST. Here we briefly contrast classic and coalescent methods for looking backward in time through a population genetic lens, focusing on the key advantages of the isolation-with-migration (IM) class of coalescent methods for distinguishing ancient connectedness from actual recurrent contemporary gene flow as causes of genetic similarity or differentiation among populations. Making this critical distinction can lead to the discovery of otherwise obscured histories underlying conventional patterns of spatial variation. We illustrate the importance of these insights using analyses of Pacific fishes, snails, and sea stars in which population sizes and divergence times are more important than rates of contemporary gene flow as determinants of population genetic differentiation. We then extend the IM method to genetic data from two model metapopulation species (California abalone, Australian damselfish). The analyses show the potential use of non-equilibrium IM methods for differentiating among metapopulation models that make different predictions about population parameters and have different implications for the design of marine protected areas and other conservation goals. At face value, the results largely rule out classic metapopulation dynamics (dominated by extinction and colonization rather than connectivity via ongoing recurrent gene flow) but, at the same time, do not strongly support a modern marine metapopulation dynamic (ecologically significant connectivity between demes). However, the results also highlight the need for much more data (i.e., loci) sampled on different spatial scales in order to determine whether metapopulation dynamics might exist on smaller scales than are typically sampled by most phylogeographers and landscape geneticists.     

PHYLOGENETIC SYSTEMATICS AND THE SPECIES PROBLEM

Abstract— A tension has arisen over the primacy of interbreeding versus monophyly in defining the species category. Manifestations of this tension include unnecessary restriction of the concept of monophyly as well as inappropriate attribution of "species" properties, to "higher taxa", and vice versa. Distinctions between systems (wholes) deriving their existence from different underlying. processes have been obscured by failure to acknowledge different interpretations of the concept of individuality. We identify interbreeding (resulting in populations) and evolutionary descent (resulting in monophyletic groups) as two processes of interest to phylogenetic systematists, and explore the relations between the systems resulting from these processes. In the case of sexual reproduction, populations of interbreeding organisms (regardless of whether they are monophyletic) exist as cohesive wholes and play a special role in phylogenetic systematics, being the least inclusive entities appropriate for use as terminal units in phylogenetic analysis of organismal relationships. Both sexual and asexual organisms form monophyletic groups. Accepting the reality and significance of both interbreeding and monophyly emphasizes that a conscious decision must be made regarding which phenomenon should be used to define the species category. Examination of species concepts that focus either on interbreeding or on common descent leads us to conclude that several alternatives are acceptable from the standpoint of phylogenetic systematics but that no one species concept can meet the needs of all comparative biologists.     

Alternative causes for range limits: a metapopulation perspective

All species have limited distributions at broad geographical scales. At local scales, the distribution of many species is influenced by the interplay of the three factors of habitat availability, local extinctions and colonization dynamics. We use the standard Levins metapopulation model to illustrate how gradients in these three factors can generate species' range limits. We suggest that the three routes to range limits have radically different evolutionary implications. Because the Levins model makes simplifying assumptions about the spatial coupling of local populations, we present numerical studies of spatially explicit metapopulation models that complement the analytical model. The three routes to range limits give rise to distinct spatiotemporal patterns. Range limits in one species can also arise because of environmental gradients impinging upon other species. We briefly discuss a predator–prey example, which illustrates indirect routes to range limits in a metacommunity context.     

Long-term dynamics in a metapopulation of the American pika

A 20-yr study of a metapopulation of the American pika revealed a regional decline in occupancy in one part of a large network of habitat patches. We analyze the possible causes of this decline using a spatially realistic metapopulation model, the incidence function model. The pika metapopulation is the best-known mammalian example of a classical metapopulation with significant population turnover, and it satisfies closely the assumptions of the incidence function model, which was parameterized with data on patch occupancy. The model-predicted incidences of patch occupancy are consistent with observed incidences, and the model predicts well the observed turnover rate between four metapopulation censuses. According to model predictions, the part of the metapopulation where the decline has been observed is relatively unstable and prone to large oscillations in patch occupancy, whereas the other part of the metapopulation is predicted to be persistent. These results demonstrate how extinction-colonization dynamics may produce spatially correlated patterns of patch occupancy without any spatially correlated processes in local dynamics or extinction rate. The unstable part of the metapopulation gives an empirical example of multiple quasi equilibria in metapopulation dynamics. Phenomena similar to those observed here may cause fluctuations in species' range limits.     

A metapopulation perspective on genetic diversity and differentiation in partially self-fertilizing plants

Abstract.— Partial self-fertilization is common in higher plants. Mating system variation is known to have important consequences for how genetic variation is distributed within and among populations. Selfing is known to reduce effective population size, and inbreeding species are therefore expected to have lower levels of genetic variation than comparable out crossing taxa. However, several recent empirical studies have shown that reductions in genetic diversity within populations of inbreeding species are far greater than the expected reductions based on the reduced effective population size. Two different processes have been argued to cause these patterns, selective sweeps (or hitchhiking) and background selection. Both are expected to be most effective in reducing genetic variation in regions of low recombination rates. Selfing is known to reduce the effective recombination rate, and inbreeding taxa are thus thought to be particularly vulnerable to the effects of hitchhiking or background selection. Here I propose a third explanation for the lower-than-expected levels of genetic diversity within populations of selfing species; recurrent extinctions and recolonizations of local populations, also known as metapopulation dynamics. I show that selfing in a metapopulation setting can result in large reductions in genetic diversity within populations, far greater than expected based the lower effective population size inbreeding species is expected to have. The reason for this depends on an interaction between selfing and pollen migration.     

生境破坏的模式对集合种群动态和续存的影响

构建了空间关联的集合种群模型,该模型不但包含了种群的空间结构信息,而且引入了破坏生境的全局密度和局部密度两个指标,它们描述了破坏生境的模式.模型揭示了破坏生境的空间分布格局复杂地影响了集合种群的动态和续存,破坏和未破坏生境斑块的均匀混合不利于集合种群的增长和续存,而生境类型聚集分布可以促进集合种群的快速增长和长期续存;对于两种斑块类型相对均匀混合的生境来说,均匀场假设可能会高估集合种群的续存,对于相对斑块类型高度聚集的生境,均匀场假设可能会低估集合种群的续存;物种的迁移范围也会影响集合种群的续存,迁移范围越大的物种越容易抵御生境的破坏而免遭灭绝.这意味着在生物保护中不能仅仅考虑生境的恢复和斑块质量的改善,生境结构的构建也是很重要的,加强生境斑块之间的连通性也有利于物种的长期续存.     

Support for a metapopulation structure among mammals

• 1 The metapopulation metaphor is increasingly used to explain the spatial dynamics of animal populations. However, metapopulation structure is difficult to identify in long‐lived species that are widely distributed in stochastic environments, where they can resist extinctions. The literature on mammals may not provide supporting evidence for classic metapopulation dynamics, which call for the availability of discrete habitat patches, asynchrony in local population dynamics, evidence for extinction and colonization processes, and dispersal between local populations.
• 2 Empirical evidence for metapopulation structure among mammals may exist when applying more lenient criteria. To meet these criteria, mammals should live in landscapes as discrete local breeding populations, and their demography should be asynchronous.
• 3 We examined the literature for empirical evidence in support of the classical criteria set by Hanski (1999 ), and for the more lenient subset of criteria proposed by Elmhagen & Angerbjörn (2001 ). We suggest circumstances where metapopulation theory could be important in understanding population processes in mammals of different body sizes.
• 4 The patchy distribution of large (>100 kg) mammals and dispersal often motivate inferences in support of a metapopulation structure. Published studies seldom address the full suite of classical criteria. However, studies on small mammals are more likely to record classic metapopulation criteria than those on large mammals. The slow turnover rate that is typical for medium‐sized and large mammals apparently makes it difficult to identify a metapopulation structure during studies of short duration.
• 5 To identify a metapopulation structure, studies should combine the criteria set by Hanski (1999 ) and Elmhagen & Angerbjörn (2001 ). Mammals frequently live in fragmented landscapes, and processes involved in the maintenance of a metapopulation structure should be considered in conservation planning and management.

     

Increased coupling between subpopulations in a spatially structured environment can lead to population outbreaks

Destruction and fragmentation of habitats is widely considered as a major threat to biological diversity. A theoretical framework aimed at understanding and predicting species responses to these destructive processes is still lacking, however. In this paper, the species dynamics in a spatially structured, two-habitat, patchy environment is considered subject to changes in individual migration intensity, i.e. coupling between the habitats. The subpopulation dynamics inside each habitat is assumed to be bistable but with different parameter values. By using space-discrete/continuous metapopulation dynamic models and computer simulations, we show that there can be two principally different regimes of metapopulation dynamics. With increasing intensity in the interplay between subpopulations, the total abundance can either gradually decrease or experience a sudden burst-like increase. This result is shown to be robust to the choice of mathematical models (discrete or continuous). Particularly, both the "self-excitation" and "self-inhibition" regimes of the metapopulation system are robust to variation in habitat size; however, when one of the habitats is much smaller than the other, the "self-excitation" regime can give way to the "self-inhibition" regime and vice versa.     

Colonization and extinction dynamics of an annual plant metapopulation in an urban environment

The metapopulation framework considers that the spatiotemporal distribution of organisms results from a balance between the colonization and extinction of populations in a suitable and discrete habitat network. Recent spatially realistic metapopulation models have allowed patch dynamics to be investigated in natural populations but such models have rarely been applied to plants. Using a simple urban fragmented population system in which favourable habitat can be easily mapped, we studied patch dynamics in the annual plant Crepis sancta (Asteraceae). Using stochastic patch occupancy models (SPOMs) and multi‐year occupancy data we dissected extinction and colonization patterns in our system. Overall, our data were consistent with two distinct metapopulation scenarios. A metapopulation (sensu stricto) dynamic in which colonization occurs over a short distance and extinction is lowered by nearby occupied patches (rescue effect) was found in a set of patches close to the city centre, while a propagule rain model in which colonization occurs from a large external population was most consistent with data from other networks. Overall, the study highlights the importance of external seed sources in urban patch dynamics. Our analysis emphasizes the fact that plant distributions are governed not only by habitat properties but also by the intrinsic properties of colonization and dispersal of species. The metapopulation approach provides a valuable tool for understanding how colonization and extinction shape occupancy patterns in highly fragmented plant populations. Finally, this study points to the potential utility of more complex plant metapopulation models than traditionally used for analysing ecological and evolutionary processes in natural metapopulations.     

Patchy population structure in a short-distance migrant: evidence from genetic and demographic data

Species often occur in subdivided populations as a consequence of spatial heterogeneity of the habitat. To describe the spatial organization of subpopulations, existing theory proposes three main population models: patchy population, metapopulation and isolated populations. These models differ in their predicted levels of connectivity among subpopulations, and in the risk that a subpopulation will go extinct. However, spatially discrete subpopulations are commonly considered to be organized as metapopulations, even though explicit tests of metapopulation assumptions are rare. Here, we test predictions of the three models on the basis of demographic and genetic data, a combined approach so far surprisingly little used in mobile organisms. From 2002 to 2005, we studied nine subpopulations of the wetland-restricted reed bunting ( Emberiza schoeniclus ) in the southeastern part of the Canton Zurich (Switzerland), from which local declines of this species have been reported. Here, wetlands are as small as 2.7 ha and separated through intensively used agricultural landscapes. Demographic data consisted of dispersal of colour-banded individuals among subpopulations, immigration rates and extinction-/recolonization dynamics. Genetic data were based on the distribution of genetic variability and gene flow among subpopulations derived from the analysis of nine microsatellite loci. Both demographic and genetic data revealed that the patchy population model best described the spatial organization of reed bunting subpopulations. High levels of dispersal among subpopulations, high immigration into the patchy population, and genetic admixture suggested little risk of extinction of both subpopulations and the entire patchy population. This study exemplifies the idea that spatially discrete subpopulations may be organized in ways other than a metapopulation, and hence has implications for the conservation of subpopulations and species.     

BIODIVERSITY RESEARCH: When is a species really extinct? Testing extinction inference from a sighting record to inform conservation assessment

Aim The global extinction of a species typically represents the end point in a series of population extinctions, during which unique evolutionary history is lost at every stage. Insight into the process of extinction can provide the means to identify species at high risk, but the number of extinctions being identified languishes far behind true totals. More proactive ways of inferring extinction from limited data are required. Location Historic sightings, collections and specimen data from Australia and Asia. Method We used a technique called optimal linear estimation to analyse the sightings record of mammal and bird species of varying ecology, life history and population demography. The mammal species chosen were all considered regionally extinct in the literature, while the bird species chosen had all been highlighted as candidates for the new IUCN Red List category flag: Critically Endangered (Possibly Extinct). Results Nine of the ten mammal species were predicted to be probably extinct, but only two with 95% certainty. Seven of the ten bird species were predicted to be probably extinct, four with 95% certainty. Main conclusions Superficially, determining whether a species is extinct might seem a simple task, whereby we either find a species extant, or it is extinct. In reality, however, the task is much more complex. Techniques such as optimal linear estimation, in combination with other data sources, and knowledge of recording effort, may prove useful in inferring extinction across a variety of taxa but should not be used in isolation.     

Pattern does not equal process: what does patch occupancy really tell us about metapopulation dynamics?

Patch occupancy surveys are commonly used to parameterize metapopulation models. If isolation predicts patch occupancy, this is generally attributed to a balance between distance-dependent recolonization and spatially independent extinctions. We investigated whether similar patterns could also be generated by a process of spatially correlated extinctions following a unique colonization event (analogous to nonequilibrium processes in island biogeography). We simulated effects of spatially correlated extinctions on patterns of patch occupancy among pikas (Ochotona princeps) at Bodie, California, using randomly located extinction disks to represent the likely effects of predation. Our simulations produced similar patterns to those cited as evidence of balanced metapopulation dynamics. Simulations using a variety of disk sizes and patch configurations confirmed that our results are potentially applicable to a broad range of species and sites. Analyses of the observed patterns of patch occupancy at Bodie revealed little evidence of rescue effects and strong evidence that most recolonizations are ephemeral in nature. Persistence will be overestimated if static or declining patterns of patch occupancy are mistakenly attributed to dynamically stable metapopulation processes. Consequently, simple patch occupancy surveys should not be considered as substitutes for detailed experimental tests of hypothesized population processes, particularly when conservation concerns are involved.