Species monophyly

In biological systematics, as well as in the philosophy of biology, species and higher taxa are individuated through their unique evolutionary origin. This is taken by some authors to mean that monophyly is a (relational) property not only of higher taxa, but also of species. A species is said to originate through speciation, and to go extinct when it splits into two daughter species (or through terminal extinction). Its unique evolutionary origin is said to bestow identity on a species through time and change, and to render species names rigid designators. Species names are thus believed to function just like names of supraspecific taxa. However, large parts of the Web of Life are composed of species that do not have a unique evolutionary origin from a single population, lineage or stem-species. Further, monophyly is an ambiguous concept if it is defined simply in terms of 'unique evolutionary origin'. Disambiguating the concept by defining a monophyletic taxon as 'a taxon that includes the ancestor and all, and only, its descendant' renders monophyly inapplicable to species. At the heart of the problem lies a fundamental distinction between species and monophyletic taxa, where species form mutually exclusive reticulated systems, while higher taxa form inclusive hierarchical systems. Examples are given both at the species level and below to illustrate the problems that result from the application of the monophyly criterion to species. The conclusion is that the concepts of exclusivity and monophyly should be treated as non-overlapping: exclusivity marks out a species synchronistically, i.e. in the present time. Monophyly marks out clades (groups of species) diachronistically, i.e. within an historical dimension.     

Comparing Species Assemblages Via Species Accumulation Curves

Summary Comparing species assemblages given incidence‐based data is of importance in ecological studies, often done by a visual inspection of estimated species accumulation curves or by an ad hoc use of 95% pointwise confidence bands of these curves. It is shown that comparing species assemblages is a challenging problem. A χ² test is proposed. An adjustment using an eigenvalue decomposition is proposed to overcome computational difficulties. The bootstrap method is also suggested to approximate the distribution of the proposed test statistic. The eigenvalue adjusted (Eva) χ² test and the Eva‐bootstrap test are assessed by a simulation study. Both the Eva‐χ² and the Eva‐bootstrap tests are applied to a study that involves two woody seedling species assemblages.     

Species orthogonalization

We discuss the general formation of complementary behaviors, functions and forms in biological species competing for resources. We call orthogonalization the related processes on macro and micro-level of a self-organized formation of correlations in the species properties. Orthogonalization processes could be, for example, easily observed in sympatric speciation, as we show in numerical studies carried out with a new population equation. As a practical result, we find that the number of species is proportional to the effective richness of resources and depends on their history.     

Species and paleoanthropology

The biotic world is self-evidently “packaged” into units, of which the most basic is the species. It is necessary to develop an accurate understanding of what species are and how they are to be identified before we can proceed to more complex analyses of the evolutionary histories and relationships of extinct and extant taxa at all levels of the systematic hierarchy. In this article, we review the major species concepts current today among paleoanthropologists, and examine the limitations of their applicability to practical studies of extant and extinct faunas. The primary such limitation for paleoanthropologists is the fact that all major species definitions stress reproductive continuity (whether by exclusionary or inclusionary mechanisms), a quality that is inferential at best among forms known only as fossils (and, in many cases, in the extant fauna as well). The only reliable signal as to species status in the fossil record is morphology, yet speciation carries with it no specifiable quantity of morphological innovation. Some groups with autapomorphies are not species, and some species do not bear autapomorphies. How, then, are we to recognize species in the hominid and other fossil records? Noting that osteodental differences among congeneric primate species tend to be subtle, and that when consistent identifiable “morphs” can be found at least as many species are present, we recommend equating morphs based on several characters with species—realizing that only one or two distinctive characters may not make a morph. In this way, our views of the phylogenetic histories of higher taxa may be oversimplified, but their essential patterns will not be distorted.     

The Importance of Species Traits for Species Distribution on Oceanic Islands

Understanding species'' ability to colonize new habitats is a key knowledge allowing us to predict species'' survival in the changing landscapes. However, most studies exploring this topic observe distribution of species in landscapes which are under strong human influence being fragmented only recently and ignore the fact that the species distribution in these landscapes is far from equilibrium. Oceanic islands seem more appropriate systems for studying the relationship between species traits and its distribution as they are fragmented without human contribution and as they remained unchanged for a long evolutionary time. In our study we compared the values of dispersal as well as persistence traits among 18 species pairs from the Canary Islands differing in their distribution within the archipelago. The data were analyzed both with and without phylogenetic correction. The results demonstrate that no dispersal trait alone can explain the distribution of the species in the system. They, however, also suggest that species with better dispersal compared to their close relatives are better colonizers. Similarly, abundance of species in the archipelago seems to be an important predictor of species colonization ability only when comparing closely related species. This implies that analyses including phylogenetic correction may provide different insights than analyses without such a correction and both types of analyses should be combined to understand the importance of various plant traits for species colonization ability.     

物种与物种多样性

本文首先讨论生物物种的科学概念和生物学本质，分析物种客观存在的自然属性和物种概念的局限性，认为物种的生物学属性和物种多样性的科学属性之间有着本质联系。物种多样性研究的实质是研究生物物种的生物学多样性。度量物种多样性程度有多种方法，但物种数目是物种多样性程度最直接、也是最基本的表达，估计物种多样性数目是当前国际上物种多样性研究的核心与热点内容。物种多样性产生的根源是物种形成，物种绝灭速率是维持物种多样性的关键因素。本文简要总结了物种形成与绝灭的基本模式和机制，通过分析生物地理区系与物种多样性研究的密切关系，说明物种的区系成份分析是物种多样性大尺度格局研究的重要内容。     

Shoot-Level Flammability of Species Mixtures is Driven by the Most Flammable Species: Implications for Vegetation-Fire Feedbacks Favouring Invasive Species

Invasive species can cause shifts in vegetation composition and fire regimes by initiating positive vegetation-fire feedbacks. To understand the mechanisms underpinning these shifts, we need to determine how invasive species interact with other species when burned in combination and thus how they may influence net flammability in the communities they invade. Previous studies using litter and ground fuels suggest that flammability of a species mixture is nonadditive and is driven largely by the more-flammable species. However, this nonadditivity has not been investigated in the context of plant invasions nor for canopy fuels. Using whole shoots, we measured the flammability of indigenous-invasive species pairs for six New Zealand indigenous and four globally invasive plant species, along with single-species control burns. Our integrated measure of flammability was clearly nonadditive, and the more-flammable species per pairing had the stronger influence on flammability in 83% of combinations. The degree of nonadditivity was significantly positively correlated with the flammability difference between the species in a pairing. The strength of nonadditivity differed among individual flammability components. Ignitability and combustibility were strongly determined by the more-flammable species per pair, yet both species contributed more equally to consumability and sustainability. Our results suggest mechanisms by which invasive species entrain positive vegetation-fire feedbacks that alter ecosystem flammability, enhancing their invasion. Of the species tested, Hakea sericea and Ulex europaeus are those most likely to increase the flammability of New Zealand ecosystems and should be priorities for management.     

山东省的长肢林蛙种组物种

前人报道天津和山东有日本林蛙的分布,但也有学者表示怀疑。本文报道采集于山东徂徕山的该类物种。从成体量度和蝌蚪唇踟式来看,与现报道的镇海林蛙和峨眉林蛙有一定差异。该物种体型大小与峨眉林蛙相近似,唇齿式为1：2-2／111     

Species concept and speciation

Defining and recognizing a species has been a controversial issue for a long time. To determine the variation and the limitation between species, many concepts have been proposed. When a taxonomist study a particular taxa, he/she must adopted a species concept and provide a species limitation to define this taxa. In this paper some of species concepts are discussed starting from the typological species concepts to the phylogenetic concept. Positive and negative aspects of these concepts are represented in addition to their application.     

Invasive Species and Evolution

Invasive species are a major threat to modern ecosystems and cause billions of dollars in economic damage annually. The long-term impacts of species invasions are difficult to assess on ecological timescales available to biologists, but the fossil record provides analogues that allow investigation of the long-term impacts of species invasions. Two case studies of ancient invasions, the Late Devonian Biodiversity Crisis (~375?million years ago) and the Late Ordovician Richmondian Invasion (~446?million years ago), provide insight into the effect of invasive species on extinction, speciation, and ecosystem structuring. During both intervals, invasive species are characterized by broad ecological tolerances, broad geographic ranges, and higher-than-average survival potential through the crisis interval. Among the native species, narrowly adapted ecological specialists are more likely to become extinct, while broadly-adapted generalist species persisted through the invasion interval by modifying aspects of their ecological niche through niche evolution. In addition, formation of new species practically stopped during the invasion intervals due to reduced opportunities for geographic isolation and speciation. The results of these impacts produced post-invasion biotas with less diversity, greater biotic homogenization between regions, and a lack of new species forming. Conservation efforts to eradicate invasive species may help mitigate these outcomes in the current biodiversity crisis.     

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.     

Host Specificity of Pathogenic Pythium Species: Implications for Tree Species Diversity

In the Janzen–Connell hypothesis, host-specific natural enemies enhance species diversity and influence the structure of plant communities. This study tests the explicit assumption of host specificity for soil pathogens of the genus Pythium that cause damping-off disease of germinating seeds and seedlings. We isolated Pythium spp. from soil of a tropical forest in Panama. Then, in an inoculation experiment, we determined the pathogenicity of 75 tropical isolates of unknown pathogenicity and seven pathogenic temperate isolates of Pythium on seeds and/or seedlings of eight tropical tree species. Only three tropical isolates, one identified as P. ultimum and two as P. aphanidermatum , were pathogenic. Tropical pathogenic isolates were pathogenic on 4–6 of eight tree species. Temperate isolates were pathogenic on 0–4 of eight species, indicating that some tropical tree species are susceptible to novel isolates of Pythium . No tree species was susceptible to all isolates and two species were not susceptible to any isolate. Collectively, these results indicate that these Pythium isolates vary widely in their pathogenicity, causing differential mortality of potential host species; likewise, the tree species vary in their susceptibility to a given Pythium isolate. These differences in pathogenicity and susceptibility indicate some support for the Janzen–Connell assumption of host specificity. While they are not restricted to a single species, their intermediate level of specificity suggests that Pythium spp. have the potential to have some effect on forest community structure and diversity.     

不同稀有种处理对双向指示种分析分类结果影响的比较

为探讨不同稀有种处理对TWINSPAN分类结果的影响,以北京小龙门林场华北落叶松林调查数据为例,采用2×2列联表比较了剔除频度＜5%、盖度＜5%的稀有种前后TWINSPAN分类结果的异同,同时结合引入的DBI重点对比了最佳分类等级的吻合性。结果表明：(1)在相同的分类终止原则下,剔除稀有种前后的最大分类结果分别分为12、11个群落类型;(2)基于结合系数r,剔除稀有种前后TWINSPAN在低分类等级的结果差异较大,随着分类等级的增加,二者的吻合度增大,表明稀有种对低分类等级的结果影响较为明显;(3)引入的DBI适用于确定TWINSPAN分类的最佳分类等级,尽管剔除稀有种前后的最佳分类等级不同,但分类结果的吻合度较高。因此,在TWINSPAN分类应用中,建议引入DBI指数辅助确定最佳分类等级,同时取低分类等级结果时必须做删除稀有种处理。     

Species as a Process

Species are generally considered to be the basic units of evolution, and hence to constitute spatio-temporally bounded entities. In addition, it has been argued that species also instantiate a natural kind. Evolution is fundamentally about change. The question then is how species can remain the same through evolutionary change. Proponents of the species qua individuals thesis individuate species through their unique evolutionary origin. Individuals, or spatio-temporally located particulars in general, can be bodies, objects, events, or processes, or a combination of these. It is here argued that species are best understood as open or closed, causally integrated processual systems that also instantiate an historically conditioned homeostatic property cluster natural kind.     

Effects of Species Richness on Resident and Target Species Components in a Prairie Restoration

The ecological role of biodiversity in achieving successful restoration has been little explored in restoration ecology. We tested the prediction that we are more likely to create persistent, species‐rich plant communities by increasing the number of species sown, and, to some degree, by varying functional group representation, in experimental prairie plantings. There were 12 treatments consisting of 1‐, 2‐, 3‐, 4‐, 8‐, 12‐, and 16‐species mixtures of native perennials representing four functional groups (C₄ grasses, C₃ grasses, nitrogen‐fixing species, and late‐flowering composites) that predominate within Central Plains tallgrass prairies. In 2000, species were seeded into square plots (6 × 6 m), with five replicates per treatment, on former agricultural land. Annually, we measured total species richness and evenness, target species richness and cover, and richness and cover of resident species (i.e., those emerging from the seed bank). Both target species richness and rate of establishment of target communities were highest in the most species‐rich mixtures, but there was no additional benefit for treatments that contained more than eight species. Richness of resident species did not vary with target species richness; however, cover by resident species was lower in the higher target species treatments. Our results, indicating that establishment of species‐rich prairie mimics can be enhanced by starting with larger numbers of species at the outset, have implications for grassland restoration in which community biodiversity creation and maintenance are key goals.     

Species delimitation and geography

Despite the importance of the geographical arrangement of populations for the inference of species boundaries, only a few approaches that integrate spatial information into species delimitation have thus far been developed. Persistent differentiation of sympatric groups of individuals is the best criterion for species status. Species delimitation becomes more prone to error if allopatric metapopulations are considered because it is often difficult to assess whether observed differences between allopatric metapopulations would be sufficient to prevent the fusion of these metapopulations upon contact. We propose a novel approach for testing the hypothesis that the multilocus genetic distances between individuals or populations belonging to two different candidate species are not larger than expected based on their geographical distances and the relationship of genetic and geographical distances within the candidate species. A rejection of this null hypothesis is an argument for classifying the two studied candidate species as distinct species. Case studies show that the proposed tests are suitable to distinguish between intra‐ and interspecific differentiation. The regression approach proposed here is more appropriate for testing species hypotheses with regard to isolation by distance than (partial) Mantel tests. Our tests assume a linear relationship between genetic and (transformed) geographical distances. This assumption can be compromised by a high genetic variability within populations as found in a case study with microsatellite markers.     

The Species Delimitation Uncertainty Principle

If, as Einstein said, "it is the theory which decides what we can observe," then "the species problem" could be solved by simply improving our theoretical definition of what a species is. However, because delimiting species entails predicting the historical fate of evolutionary lineages, species appear to behave according to the Heisenberg Uncertainty Principle, which states that the most philosophically satisfying definitions of species are the least operational, and as species concepts are modified to become more operational they tend to lose their philosophical integrity. Can species be delimited operationally without losing their philosophical rigor? To mitigate the contingent properties of species that tend to make them difficult for us to delimit, I advocate a set of operations that takes into account the prospective nature of delimiting species. Given the fundamental role of species in studies of evolution and biodiversity, I also suggest that species delimitation proceed within the context of explicit hypothesis testing, like other scientific endeavors. The real challenge is not so much the inherent fallibility of predicting the future but rather adequately sampling and interpreting the evidence available to us in the present.     

Species Delimitation and Analysis of Cryptic Species Diversity in the XXI Century

The potentials and limitations of different approaches to revealing species boundaries and describing cryptic species are discussed. Both the traditional methods of species delimitation, mostly based on morphological analysis, and the approaches using molecular markers are considered. Besides, the prospects of species identification using digital image recognition and machine learning are briefly considered. It is concluded that molecular markers provide very important material for species delimitation; the value of these data increases manifold if they can be compared with information on morphology, geographic distribution, and ecological preferences of the studied taxa. In many cases, only a practicing taxonomist who knows his or her group thoroughly can correctly interpret the molecular data and incorporate them into the existing knowledge system in order to make a taxonomic decision.

     

Edge Effects on Species Composition and Exotic Species Abundance in the North Carolina Piedmont

Edges between forest and non-forest habitats often have significant effects on forest microclimate and resource availability, with corresponding effects on species composition and abundance. Exotic species are often increased in abundance near forest edges. This increase in abundance could be either because of the increase in resource availability near edges, or because of increased dispersal into forest edges. We measured species composition and a set of geospatial variables on transects at 66 edges in the North Carolina Piedmont in an attempt to distinguish between these two factors. Mantel tests show that species composition is significantly different in forest edges than in the forest interior, but that this effect only penetrates about 5 m into the forest. Indicator species analysis finds several species that are indicative of edge communities, including trumpet vine (Campsis radicans), two drought-tolerant oak species (Quercus stellata and Q. falcata), a serviceberry (Amelanchier arboreum), and a common exotic species, tree-of-heaven (Ailanthus altissima). Poisson regression techniques showed that in both the seedling and tree strata of the forest, exotic species increased in abundance on flat sites with a high potential seed source. Mapping predicted exotic species abundance onto the landscape. We find that large-scale variation in exotic species abundance is due mostly to variation in potential seed sources, while small-scale variation relates more to edaphic factors. Our results stress that both dispersal and environmental filters are important for determining exotic species abundance, but potentially the filters operate at different spatial scales.