Distinguishing species

Given two organisms, how can one distinguish whether they belong to the same species or not? This might be straightforward for two divergent organisms, but can be extremely difficult and laborious for closely related ones. A molecular marker giving a clear distinction would therefore be of immense benefit. The internal transcribed spacer 2 (ITS2) has been widely used for low-level phylogenetic analyses. Case studies revealed that a compensatory base change (CBC) in the helix II or helix III ITS2 secondary structure between two organisms correlated with sexual incompatibility. We analyzed more than 1300 closely related species to test whether this correlation is generally applicable. In 93%, where a CBC was found between organisms classified within the same genus, they belong to different species. Thus, a CBC in an ITS2 sequence-structure alignment is a sufficient condition to distinguish even closely related species.     

Helminth species diversity of mammals: parasite species richness is a host species attribute

Studies investigating parasite diversity have shown substantial geographical variation in parasite species richness. Most of these studies have, however, adopted a local scale approach, which may have masked more general patterns. Recent studies have shown that ectoparasite species richness in mammals seems highly repeatable among populations of the same mammal host species at a regional scale. In light of these new studies we have reinvestigated the case of parasitic helminths by using a large data set of parasites from mammal populations in 3 continents. We collected homogeneous data and demonstrated that helminth species richness is highly repeatable in mammals at a regional scale. Our results highlight the strong influence of host identity in parasite species richness and call for future research linking helminth species found in a given host to its ecology, immune defences and potential energetic trade-offs.     

Population dynamics of species with gynogenetic sibling species

Models are formulated for the population dynamics of a monoecious or dioecious species with an all-female parthenogenetic sibling species which is also gynogenetic. Continuous, deterministic reproduction and mortality, a stationary age distribution, random mating, and limited sexual competence for all individuals are posited. It is also supposed that in the dioecious case males do not distinguish between true and gynogenetic females. Similarly, hermaphrodites do not differentiate hermaphrodites and gynogens. The model implies that extinction is highly likely in the dioecious situation, but much less so in the monoecious one. Empirical evidence is reviewed and related to the assumptions and conclusions.     

Phylogenetic species recognition and species concepts in fungi

The operational species concept, i.e., the one used to recognize species, is contrasted to the theoretical species concept. A phylogenetic approach to recognize fungal species based on concordance of multiple gene genealogies is compared to those based on morphology and reproductive behavior. Examples where Phylogenetic Species Recognition has been applied to fungi are reviewed and concerns regarding Phylogenetic Species Recognition are discussed.     

Predicting species establishment using absent species and functional neighborhoods

Species establishment within a community depends on their interactions with the local environment and resident community. Such environmental and biotic filtering is frequently inferred from functional trait and phylogenetic patterns within communities; these patterns may also predict which additional species can establish. However, differentiating between environmental and biotic filtering can be challenging, which may complicate establishment predictions. Creating a habitat‐specific species pool by identifying which absent species within the region can establish in the focal habitat allows us to isolate biotic filtering by modeling dissimilarity between the observed and biotically excluded species able to pass environmental filters. Similarly, modeling the dissimilarity between the habitat‐specific species pool and the environmentally excluded species within the region can isolate local environmental filters. Combined, these models identify potentially successful phenotypes and why certain phenotypes were unsuccessful. Here, we present a framework that uses the functional dissimilarity among these groups in logistic models to predict establishment of additional species. This approach can use multivariate trait distances and phylogenetic information, but is most powerful when using individual traits and their interactions. It also requires an appropriate distance‐based dissimilarity measure, yet the two most commonly used indices, nearest neighbor (one species) and mean pairwise (all species) distances, may inaccurately predict establishment. By iteratively increasing the number of species used to measure dissimilarity, a functional neighborhood can be chosen that maximizes the detection of underlying trait patterns. We tested this framework using two seed addition experiments in calcareous grasslands. Although the functional neighborhood size that best fits the community's trait structure depended on the type of filtering considered, selecting these functional neighborhood sizes allowed our framework to predict up to 50% of the variation in actual establishment from seed. These results indicate that the proposed framework may be a powerful tool for studying and predicting species establishment.     

Finding unknown species in the genomes of extant species

Although many species have gone extinct, their genetic components might exist in extant species because of ancient hybridization. Via advances in genome sequencing and development of modern population genetics, one can find the legacy of unknown or extinct species in the context of available genomes from extant species. Such discovery can be used as a strategy to search for hidden species or fossils in conservation biology and archeology, gain novel insight into complex evolutionary history, and provide the new sources of genetic variation for breeding and trait improvement in agriculture.     

Exotic species richness and native species endemism increase the impact of exotic species on islands

Aim Exotic species pose one of the most significant threats to biodiversity, especially on islands. The impacts of exotic species vary in severity among islands, yet little is known about what makes some islands more susceptible than others. Here we determine which characteristics of an island influence how severely exotic species affect its native biota. Location We studied 65 islands and archipelagos from around the world, ranging from latitude 65° N to 54° S. Methods We compiled a global database of 10 island characteristics for 65 islands and determined the relative importance of each characteristic in predicting the impact of exotic species using multivariate modelling and hierarchical partitioning. We defined the impact of exotic species as the number of bird, amphibian and mammal (BAM) species listed by the International Union for Conservation of Nature (IUCN) as threatened by exotics, relative to the total number of BAM species on that island. Results We found that the impact of exotic species is more severe on islands with more exotic species and a greater proportion of native species that are endemic. Unexpectedly, the level of anthropogenic disturbance did not influence an island's susceptibility to the impacts of exotic species. Main conclusions By coupling our results with studies on the introduction and establishment of exotic species, we conclude that colonization pressure, or invasion opportunities, influences all stages of the invasion process. However, species endemism, the other important factor determining the impact of exotic species, is not known to contribute to introduction and establishment success on islands. This demonstrates that different factors correlate with the initial stages of the invasion process and the subsequent impacts of those invaders, highlighting the importance of studying the impacts of exotic species directly. Our study helps identify islands that are at risk of impact by exotics and where investment should focus on preventing further invasions.     

Confronting species distribution model predictions with species functional traits

Species distribution models are valuable tools in studies of biogeography, ecology, and climate change and have been used to inform conservation and ecosystem management. However, species distribution models typically incorporate only climatic variables and species presence data. Model development or validation rarely considers functional components of species traits or other types of biological data. We implemented a species distribution model (Maxent) to predict global climate habitat suitability for Grass Carp (Ctenopharyngodon idella). We then tested the relationship between the degree of climate habitat suitability predicted by Maxent and the individual growth rates of both wild (N = 17) and stocked (N = 51) Grass Carp populations using correlation analysis. The Grass Carp Maxent model accurately reflected the global occurrence data (AUC = 0.904). Observations of Grass Carp growth rate covered six continents and ranged from 0.19 to 20.1 g day⁻¹. Species distribution model predictions were correlated (r = 0.5, 95% CI (0.03, 0.79)) with observed growth rates for wild Grass Carp populations but were not correlated (r = −0.26, 95% CI (−0.5, 0.012)) with stocked populations. Further, a review of the literature indicates that the few studies for other species that have previously assessed the relationship between the degree of predicted climate habitat suitability and species functional traits have also discovered significant relationships. Thus, species distribution models may provide inferences beyond just where a species may occur, providing a useful tool to understand the linkage between species distributions and underlying biological mechanisms.     

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。     

Dominant species maintain ecosystem function with non-random species loss

Loss of species caused by widespread stressors, such as drought and fragmentation, is likely to be non‐random depending on species abundance in the community. We experimentally reduced the number of rare and uncommon plant species while independently reducing only the abundance of dominant grass species in intact, native grassland. This allowed us to simulate a non‐random pattern of species loss, based on species abundances, from communities shaped by natural ecological interactions and characterized by uneven species abundance distributions. Over two growing seasons, total above‐ground net primary productivity (ANPP) declined with reductions in abundance of the dominant species but was unaffected by a threefold decline in richness of less common species. In contrast, productivity of the remaining rare and uncommon species decreased with declining richness, in part due to loss of complementary interactions among these species. However, increased production of the dominant grasses offset the negative effects of species loss. We conclude that the dominant species, as controllers of ecosystem function, can provide short‐term resistance to reductions in ecosystem function when species loss is nonrandom. However, the concurrent loss of complementary interactions among rare and uncommon species, the most diverse component of communities, may contribute to additional species loss and portends erosion of ecosystem function in the long term.     

On the measurement of species diversity incorporating species differences

When pairwise differences (relatedness) between species are numerically given, the average of the species differences weighted by relative frequencies can be used as a species diversity index. This paper first theoretically develops the indices of this type, then applies them to forestry data. As examples of diversity indices, this paper explores the taxonomic diversity and the newly introduced amino acid diversity, which is a modification of the nucleotide diversity in genetics. The first, mathematical part shows that both indices can be decomposed into three inner factors; evenness of relative frequencies (=the Simpson index), the simple average over species differences regardless of relative frequencies, and the taxonomic or genetic balance in relative frequencies. The taxonomic diversity has another decomposition: the sum over the Simpson indices at all the taxonomic levels. The second part examines the effects of different forest management techniques on diversity. It is shown that a thinning operation for promoting survival of specific desirable species also contributed to increasing the taxonomic diversity. If we calculated only conventional indices that do not incorporate species relatedness, we would simply conclude that the thinning did not significantly affect the diversity. The theoretical developments of the first part complement the result, leading us to a better interpretation about contrasting vegetation structures. The mathematical results also reveal that the amino acid diversity involves redundant species, which is undesirable when measuring diversity; hence, this index is used to demonstrates crucial points when we introduce species relatedness. The results suggest further possibilities of applying diversity indices incorporating species differences to a variety of ecological studies.     

Protein-protein interactions more conserved within species than across species

Experimental high-throughput studies of protein-protein interactions are beginning to provide enough data for comprehensive computational studies. Today, about ten large data sets, each with thousands of interacting pairs, coarsely sample the interactions in fly, human, worm, and yeast. Another about 55,000 pairs of interacting proteins have been identified by more careful, detailed biochemical experiments. Most interactions are experimentally observed in prokaryotes and simple eukaryotes; very few interactions are observed in higher eukaryotes such as mammals. It is commonly assumed that pathways in mammals can be inferred through homology to model organisms, e.g. the experimental observation that two yeast proteins interact is transferred to infer that the two corresponding proteins in human also interact. Two pairs for which the interaction is conserved are often described as interologs. The goal of this investigation was a large-scale comprehensive analysis of such inferences, i.e. of the evolutionary conservation of interologs. Here, we introduced a novel score for measuring the overlap between protein-protein interaction data sets. This measure appeared to reflect the overall quality of the data and was the basis for our two surprising results from our large-scale analysis. Firstly, homology-based inferences of physical protein-protein interactions appeared far less successful than expected. In fact, such inferences were accurate only for extremely high levels of sequence similarity. Secondly, and most surprisingly, the identification of interacting partners through sequence similarity was significantly more reliable for protein pairs within the same organism than for pairs between species. Our analysis underlined that the discrepancies between different datasets are large, even when using the same type of experiment on the same organism. This reality considerably constrains the power of homology-based transfer of interactions. In particular, the experimental probing of interactions in distant model organisms has to be undertaken with some caution. More comprehensive images of protein-protein networks will require the combination of many high-throughput methods, including in silico inferences and predictions. http://www.rostlab.org/results/2006/ppi_homology/     

The bacterial species dilemma and the genomic-phylogenetic species concept

The number of species of Bacteria and Archaea (ca 5000) is surprisingly small considering their early evolution, genetic diversity and residence in all ecosystems. The bacterial species definition accounts in part for the small number of named species. The primary procedures required to identify new species of Bacteria and Archaea are DNA-DNA hybridization and phenotypic characterization. Recently, 16S rRNA gene sequencing and phylogenetic analysis have been applied to bacterial taxonomy. Although 16S phylogeny is arguably excellent for classification of Bacteria and Archaea from the Domain level down to the family or genus, it lacks resolution below that level. Newer approaches, including multilocus sequence analysis, and genome sequence and microarray analyses, promise to provide necessary information to better understand bacterial speciation. Indeed, recent data using these approaches, while meagre, support the view that speciation processes may occur at the subspecies level within ecological niches (ecovars) and owing to biogeography (geovars). A major dilemma for bacterial taxonomists is how to incorporate this new information into the present hierarchical system for classification of Bacteria and Archaea without causing undesirable confusion and contention. This author proposes the genomic-phylogenetic species concept (GPSC) for the taxonomy of prokaryotes. The aim is twofold. First, the GPSC would provide a conceptual and testable framework for bacterial taxonomy. Second, the GPSC would replace the burdensome requirement for DNA hybridization presently needed to describe new species. Furthermore, the GPSC is consistent with the present treatment at higher taxonomic levels.