Measurement of biological information with applications from genes to landscapes

Biological diversity is quantified for reasons ranging from primer design, to bioprospecting, and community ecology. As a common index for all levels, we suggest Shannon's (S)H, already used in information theory and biodiversity of ecological communities. Since Lewontin's first use of this index to describe human genetic variation, it has been used for variation of viruses, splice-junctions, and informativeness of pedigrees. However, until now there has been no theory to predict expected values of this index under given genetic and demographic conditions. We present a new null theory for (S)H at the genetic level, and show that this index has advantages including (i) independence of measures at each hierarchical level of organization; (ii) robust estimation of genetic exchange over a wide range of conditions; (iii) ability to incorporate information on population size; and (iv) explicit relationship to standard statistical tests. Utilization of this index in conjunction with other existing indices offers powerful insights into genetic processes. Our genetic theory is also extendible to the ecological community level, and thus can aid the comparison and integration of diversity at the genetic and community levels, including the need for measures of community diversity that incorporate the genetic differentiation between species.     

Background and Overview of Comparative Genomics

Comparative genomics---the cross-referencing of information on genome organization between species---provides an additional dimension to the Human Genome Project and can derive much information from it for the benefit of animal health and animal breeding. Arrangements of genes and other DNA sequences may be determined by a variety of genetic and physical techniques, at resolutions from the gross cytological level to the level of the single base pair. Gross arrangements and rearrangements can also be charted by comparative chromosome painting. Genome organization may then be compared across mammal---and other vertebrate---species. Genetic mapping is well advanced in several livestock species as well as rodent model species, and outline maps are available for at least 30 mammal species in eight orders. At the time of this writing, maps are being rapidly constructed for chicken and fish species. Comparisons, even over vast evolutionary time scales, show that the mammal genome---indeed, the vertebrate genome---has been highly conserved. Thus, information about location and function of genes is directly transferable across species and should greatly accelerate the search for genes that specify inherited diseases in domestic mammals and humans as well as genes that specify economically important traits.     

Fine-scale community and genetic structure are tightly linked in species-rich grasslands

Recent evidence indicates that grassland community structure and species diversity are influenced by genetic variation within species. We review what is known regarding the impact of intraspecific diversity on grassland community structure, using an ancient limestone pasture as a focal example. Two genotype-dependent effects appear to modify community structure in this system. First, the abundance of individual constituent species can depend upon the combined influence of direct genetic effects stemming from individuals within the population. Second, the outcome of localized interspecific interactions occurring within the community can depend on the genotypes of participating individuals (indicating indirect genetic effects). Only genotypic interactions are thought to be capable of allowing the long-term coexistence of both genotypes and species. We discuss the implications of these effects for the maintenance of diversity in grasslands. Next, we present new observations indicating that losses of genotypic diversity from each of two species can be predicted by the abundance of other coexisting species within experimental grassland communities. These results suggest genotype-specific responses to abundance in other coexisting species. We conclude that both direct and indirect genetic effects are likely to shape community structure and species coexistence in grasslands, implying tight linkage between fine-scale genetic and community structure.     

生物群落多样性的测度方法 V.生物群落物种数目的估计方法

群落的物种数目,即物种丰富度,是最古老、同时也是最基本的一个多样性概念,从对它的估计中可以得到关于物种灭绝速率方面的信息,这对生物多样性保护是非常重要的。已经提出了很多方法来估计群落中的物种数目,这些方法可以分为两大类,即基于理论抽样的方法和基于数据分析的方法。前者包括经典估计方法和贝叶斯估计方法;后者包括对数正态分布的积分方法、再抽样方法和种－面积曲线的外推方法。发现：（１）有些方法适用于动物群落,如大多数基于理论抽样的方法;有些方法则适用于植物群落,如大多数基于数据分析的方法;（２）这些方法还没有经过全面而系统地比较;（３）还没有一个普遍认为比较好的方法。因此,建议采用野外调查与模拟研究相结合的方法对各种估计方法进行系统地评价。     

Strategies for the conservation of endangered freshwater pearl mussels (<Emphasis Type="Italic">Margaritifera margaritifera</Emphasis> L.): a synthesis of Conservation Genetics and Ecology

Freshwater pearl mussels (Margartifera margaritifera L.) are among the most critically threatened freshwater bivalves worldwide. The pearl mussel simultaneously fulfils criteria of indicator, flagship, keystone and umbrella species and can thus be considered an ideal target species for the process conservation of aquatic ecosystem functioning. The development of conservation strategies for freshwater pearl mussels and for other bivalve species faces many challenges, including the selection of priority populations for conservation and strategic decisions on habitat restoration and/or captive breeding. This article summarises the current information about the species’ systematics and phylogeny, its distribution and status as well as about its life history strategy and genetic population structure. Based on this information, integrative conservation strategies for freshwater mollusc species which combine genetic and ecological information are discussed. Holistic conservation strategies for pearl mussels require the integration of Conservation Genetics and Conservation Ecology actions at various spatial scales, from the individual and population level to global biodiversity conservation strategies. The availability of high resolution genetic markers for the species and the knowledge of the critical stages in the life cycle, particularly of the most sensitive post-parasitic phase, are important prerequisites for conservation. Effective adaptive conservation management also requires an evaluation of previous actions and management decisions. As with other freshwater bivalves, an integrative conservation approach that identifies and sustains ecological processes and evolutionary lineages is urgently needed to protect and manage freshwater pearl mussel diversity. Such research is important for the conservation of free-living populations, as well as for artificial culturing and breeding techniques, which have recently been or which are currently being established for freshwater pearl mussels in several countries.     

TriMEDB: A database to integrate transcribed markers and facilitate genetic studies of the tribe Triticeae

Background  

The recent rapid accumulation of sequence resources of various crop species ensures an improvement in the genetics approach, including quantitative trait loci (QTL) analysis as well as the holistic population analysis and association mapping of natural variations. Because the tribe Triticeae includes important cereals such as wheat and barley, integration of information on the genetic markers in these crops should effectively accelerate map-based genetic studies on Triticeae species and lead to the discovery of key loci involved in plant productivity, which can contribute to sustainable food production. Therefore, informatics applications and a semantic knowledgebase of genome-wide markers are required for the integration of information on and further development of genetic markers in wheat and barley in order to advance conventional marker-assisted genetic analyses and population genomics of Triticeae species.     

EXPERIMENTAL STUDIES OF COMMUNITY EVOLUTION II: THE ECOLOGICAL BASIS OF THE RESPONSE TO COMMUNITY SELECTION

Community selection, defined as the differential proliferation and/or extinction of communities, can bring about a response that may be qualitatively different from the response to selection acting at lower levels. This is because community selection can result in genetic changes in all of the species within the community by acting on the interaction among species. In the experiment presented here, a series of one generation assays were performed on the coevolved communities of two species of flour beetles, Tribolium castaneum and T. confusum, discussed by Goodnight (1990). Two community assays and one single-species assay were performed. Taken together, these provide insights into the genetic basis of the response to community selection. The first community assay involved measuring the selected traits on the original coevolved communities that had been subjected to community selection. This assay indicated that all of the selection treatments resulted in a significant response to selection in the original coevolved communities. The single-species assay involved separating the coevolved communities into their constituent single-species populations and again measuring the selected traits on these populations. None of the single-species populations exhibited a significant response to selection; thus the responses to community selection observed in the first community assay are expressed only in a community context. The second community assay again involved separating the coevolved communities into their constituent single-species populations; however, in this assay a competitor of the opposite species that had never been exposed to community selection was added to each population to form a “reconstructed” community. The results of this assay were that for two traits, emigration rate in T. castaneum and emigration rate in T. confusum, the genetic identity of the competing species did not affect the response to selection. This indicates that the competing species was acting like a nonevolving part of the environment. For the other two traits measured, population size in T. castaneum and population size in T. confusum, the results were very different. For these traits there was no detectable response to selection in the reconstructed communities. This indicates that for these traits the response to selection cannot be attributed to a genetic change in either species independently of the other species in the community. Rather it resides in the interaction between the two species.     

Alarm communication networks as a driver of community structure in African savannah herbivores

Social information networks have the potential to shape the spatial structure of ecological communities by promoting the formation of mixed‐species groups. However, what actually drives social affinity between species in the wild will depend on the characteristics of the species available to group. Here we first present an agent‐based model that predicts trait‐related survival benefits from mixed‐species group formation in a multi‐species community and we then test the model predictions in a community‐wide field study of African savannah herbivores using multi‐layered network analysis. We reveal benefits from information transfer about predators as a key determinant of mixed‐species group formation, and that dilution benefits alone are not enough to explain patterns in interspecific sociality. The findings highlight the limitations of classical ecological approaches focusing only on direct trophic interactions when analysing community structure and suggest that declines in species occupying central social network positions, such as key informants, can have significant repercussions throughout communities.     

Effects of vicariant barriers, habitat stability, population isolation and environmental features on species divergence in the south-western Australian coastal reptile community

Identifying explicit hypotheses regarding the factors determining genetic structuring within species can be difficult, especially in species distributed in historically dynamic regions. To contend with these challenges, we use a framework that combines species distribution models, environmental data and multi-locus genetic data to generate and explore phylogeographic hypotheses for reptile species occupying the coastal sand-dune and sand-plain habitats of the south-western Australian biodiversity hotspot, a community which has both a high diversity of endemics and has varied dramatically in spatial extent over time. We use hierarchical amova, summary statistic and distance-based analyses to explicitly test specific phylogeographic hypotheses. Namely, we test if biogeographic vicariance across barriers, habitat stability, population isolation along a linear habitat or fragmentation across different environments can explain genetic divergence within five co-distributed squamate reptile species. Our results show that patterns of genetic variation reflect complex and species-specific interactions related to the spatial distribution of habitats present currently and during repeated glacial minima, as opposed to being associated with historical factors such as habitat stability between glacial and inter-glacial periods or vicariant barriers. We suggest that the large impact of habitat characteristics over time (i.e. relative levels of habitat connectivity, climatic gradients and spatial heterogeneity of soil types) reflects the ecological restrictions of the sand-dune and sand-plain reptile communities and may explain the lack of concordance across taxa. The study demonstrates the general utility of the approach for assemblage-level, as well as single species, phylogeographic study, including its usefulness for exploring biologically informed hypotheses about what factors have influenced patterns of genetic variation.     

Analysis of biodiversity across levels of biological organization: a problem of defining traits

Biodiversity is a term that comprises the appearance, structure and function of all levels of biological organization, including genes, species and ecosystems. The vast majority of measures of biodiversity (usually termed ‘diversity indices’) considers only number, proportion and distribution of species which belong to a specified group and exist in a defined area or ecosystem. Genetic diversity as a part of biodiversity within species (or populations) was either not regarded in this respect or was treated (by geneticists) as a separate entity of diversity quantified with separate measures. Little attention has been given to the integration of both types of diversity, within and among species, in a single measurement (termed ‘transspecific’ diversity). In order to attain this integration on a general basis, an operational trait concept is developed which allows the determination of variation in traits observable in members not only of the same species but also of different species. The concept rests on methods of investigation that can be adapted to a broader range of organisms without modification of their characteristics. Once a trait is specified on this basis, any meaningful measure of diversity can be applied to assess biodiversity across levels of biological organization. The utility of the concept is demonstrated by application to the results of an earlier study on associations between species and genetic diversity in a forest tree community. Attributes of isozymes which are visible in electrophoresis are used as a transspecific genetic trait.     

Using community and population approaches to understand how contemporary and historical factors have shaped species distribution in river ecosystems

Aim To examine how the employment of both community‐ and population‐level approaches can provide a wider view of the importance of contemporary and historical factors on current species distribution. We posit that community ecology should provide more information about contemporary factors, whereas population genetics should provide better information about historical factors. Location Rivers of the western Mediterranean Basin, including four subregions differing in geological history: the Iberian Plate, Transitional, Betic and Rif. Methods For a community‐level approach, Trichoptera richness and community composition were compared between subregions using species accumulation curves and a correspondence analysis. For a population‐level approach, the mtDNA cytochrome C oxidase subunit I (COI) gene of specimens of the Trichoptera midstream‐lowland species Chimarra marginata (L.) was sequenced and analysed using phylogeographical methods. Results The community approach revealed that historical events had more influence on headwater communities than contemporary ecological factors, whereas historical events had negligible influence on midstream‐lowland communities. In midstream‐lowland sites, however, the population approach showed that the genetic structure of C. marginata differed significantly between subregions and revealed patterns of historical gene migration. In terms of species richness, the Rif subregion had the lowest value per basin due to local climatic features and isolation. Main conclusions Both community‐ and population‐level approaches yielded information about the effects of historical factors on species distribution. However, the importance of historical events on current Trichoptera communities depends on the river zonation. Unlike headwater sites, midstream‐lowland sites showed signs of historical events at the population level but not at the community level at the scale used, indicating that both approaches should be employed together in biogeographical studies. Lack of detection of historical events at the community level does not necessarily mean that they are negligible. Most likely, the organizational level used is not appropriate. We also stress the importance of implementing conservation measures for rivers in the western Mediterranean, especially under future scenarios of climate change and human disturbances in the Mediterranean Basin.     

Measuring the contribution of evolution to community trait structure in freshwater zooplankton

There are currently few predictions about when evolutionary processes are likely to play an important role in structuring community features. Determining predictors that indicate when evolution is expected to impact ecological processes in natural landscapes can help researchers identify eco-evolutionary ‘hotspots', where eco-evolutionary interactions are more likely to occur. Using data collected from a survey in freshwater cladoceran communities, landscape population genetic data and phenotypic trait data measured in a common garden, we applied a Bayesian linear model to assess whether the impact of local trait evolution in the keystone species Daphnia magna on cladoceran community trait values could be predicted by population genetic properties (within-population genetic diversity, genetic distance among populations), ecological properties (Simpson's diversity, phenotypic divergence) or environmental divergence. We found that the impact of local trait evolution varied among communities. Moreover, community diversity and phenotypic divergence were found to be better predictors of the contribution of evolution to community trait values than environmental features or genetic properties of the evolving species. Our results thus indicate the importance of ecological context for the impact of evolution on community features. Our study also demonstrates one way to detect signatures of eco-evolutionary interactions in communities inhabiting heterogeneous landscapes using survey data of contemporary ecological and evolutionary structure.     

An integrated species distribution modelling framework for heterogeneous biodiversity data

Most knowledge about species and habitats is in-homogeneously distributed, with biases existing in space, time and taxonomic and functional knowledge. Yet, controversially the total amount of biodiversity data has never been greater. A key challenge is thus how to make effective use of the various sources of biodiversity data in an integrated manner. Particularly for widely used modelling approaches, such as species distribution models (SDMs), the need for integration is urgent, if spatial and temporal predictions are to be accurate enough in addressing global challenges.Here, I present a modelling framework that brings together several ideas and methodological advances for creating integrated species distribution models (iSDM). The ibis.iSDM R-package is a set of modular convenience functions that allows the integration of different data sources, such as presence-only, community survey, expert ranges or species habitat preferences, in a single model or ensemble of models. Further it supports convenient parameter transformations and tuning, data preparation helpers and allows the creation of spatial-temporal projections and scenarios. Ecological constraints such as projection limits, dispersal, connectivity or adaptability can be added in a modular fashion thus helping to prevent unrealistic estimates of species distribution changes.The ibis.iSDM R-package makes use of a series of methodological advances and is aimed to be a vehicle for creating more realistic and constrained spatial predictions. Besides providing convenience functions for a range of different statistical models as well as an increasing number of wrappers for mechanistic modules, ibis.iSDM also introduces several innovative concepts such as sequential or weighted integration, or thresholding by prediction uncertainty. The overall framework will be continued to be improved and further functionalities be added.     

Bio-Ontology and text: bridging the modeling gap

MOTIVATION: Natural language processing (NLP) techniques are increasingly being used in biology to automate the capture of new biological discoveries in text, which are being reported at a rapid rate. Yet, information represented in NLP data structures is classically very different from information organized with ontologies as found in model organisms or genetic databases. To facilitate the computational reuse and integration of information buried in unstructured text with that of genetic databases, we propose and evaluate a translational schema that represents a comprehensive set of phenotypic and genetic entities, as well as their closely related biomedical entities and relations as expressed in natural language. In addition, the schema connects different scales of biological information, and provides mappings from the textual information to existing ontologies, which are essential in biology for integration, organization, dissemination and knowledge management of heterogeneous phenotypic information. A common comprehensive representation for otherwise heterogeneous phenotypic and genetic datasets, such as the one proposed, is critical for advancing systems biology because it enables acquisition and reuse of unprecedented volumes of diverse types of knowledge and information from text. RESULTS: A novel representational schema, PGschema, was developed that enables translation of phenotypic, genetic and their closely related information found in textual narratives to a well-defined data structure comprising phenotypic and genetic concepts from established ontologies along with modifiers and relationships. Evaluation for coverage of a selected set of entities showed that 90% of the information could be represented (95% confidence interval: 86-93%; n = 268). Moreover, PGschema can be expressed automatically in an XML format using natural language techniques to process the text. To our knowledge, we are providing the first evaluation of a translational schema for NLP that contains declarative knowledge about genes and their associated biomedical data (e.g. phenotypes). AVAILABILITY: http://zellig.cpmc.columbia.edu/PGschema     

Relative importance of tree genetics and microhabitat on macrofungal biodiversity on coarse woody debris

Understanding the contribution of genetic variation within foundation species to community-level pattern and diversity represents the cornerstone of the developing field of community genetics. We assessed the relative importance of intraspecific genetic variation, spatial variation within a forest and microhabitat variation on a macrofungal decay community developing on logs of the Australian forest tree, Eucalyptus globulus. Uniform logs were harvested from trees from eight geographic races of E. globulus growing in a 15-year-old genetic trial. Logs were placed as designed grids within a native E. globulus forest and after 3 years of natural colonisation the presence of 62 macrofungal taxa were recorded from eight microhabitats on each log. The key factor found to drive macrofungal distribution and biodiversity on structurally uniform coarse woody debris was log-microhabitat, explaining 42% of the total variation in richness. Differences between log-microhabitats appeared to be due to variation in aspect, substrate (bark vs wood) and area/time of exposure to colonisation. This findings demonstrates the importance of considering fine-scale (within substrate) variation in the conservation and management of macrofungal biodiversity, an area that has received little previous attention. While a number of recent studies have demonstrated that the genetics of foundation tree species can influence dependent communities, this was not found to be the case for the early log decay community associated with E. globulus. Despite genetic variation in wood and bark properties existing within this species, there was no significant effect of tree genetics on macrofungal community richness or composition. This finding highlights the variation that may exist among guilds of organisms in their response to genetic variation within foundation species, an important consideration in a promising new area of research.     

The constancy of the G matrix through species divergence and the effects of quantitative genetic constraints on phenotypic evolution: a case study in crickets

Long-term phenotypic evolution can be modeled using the response-to-selection equation of quantitative genetics, which incorporates information about genetic constraints (the G matrix). However, little is known about the evolution of G and about its long-term importance in constraining phenotypic evolution. We first investigated the degree of conservation of the G matrix across three species of crickets and qualitatively compared the pattern of variation of G to the phylogeny of the group. Second, we investigated the effect of G on phenotypic evolution by comparing the direction of greatest quantitative genetic variation within species (g(max)) to the direction of phenotypic divergence between species (Delta(z)). Each species, Gryllus veletis, G. firmus, and G. pennsylvanicus, was reared in the laboratory using a full-sib breeding design to extract quantitative genetic information. Five morphological traits related to size were measured. G matrices were compared using three statistical approaches: the T method, the Flury hierarchy, and the MANOVA method. Results revealed that the differences between matrices were small and mostly caused by differences in the magnitude of the genetic variation, not by differences in principal component structure. This suggested that the G matrix structure of this group of species was preserved, despite significant phenotypic divergence across species. The small observed differences in G matrices across species were qualitatively consistent with genetic distances, whereas ecological information did not provide a good prediction of G matrix variation. The comparison of g(max) and Delta(z) revealed that the angle between these two vectors was small in two of three species comparisons, whereas the larger angle corresponding to the third species comparison was caused in large part by one of the five traits. This suggests that multivariate phenotypic divergence occurred mostly in a direction predicted by the direction of greatest genetic variation, although it was not possible to demonstrate the causal relationship from G to Delta(z). Overall, this study provided some support for the validity of the predictive power of quantitative genetics over evolutionary time scales.     

The relative of species pools in determining plant species richness: an alternative explanation of species coexistence?

Explanations of the pattern of species have traditionally relied on small-scale, local processes occurring in ecological time. Differences in species richness have associated with different mechanisms avoiding competition, such as spatiotemporal heterogeneity (weaker competitors may find a more favourable place or time) or environmental stress (competition is assumed to be less intensive under difficult conditions). More recently, large-scale process have been taken into account, raising such questions as: which plant species may potentially grow in a certain community? Are evolutionary processes and species dispersal responsible for the differences between communities? The species-pool theory attempts to answer these general questions, and information about species pools is needed for the design of experiments where the number of species in a community is manipulated.     

Eavesdropping on heterospecific alarm calls: from mechanisms to consequences

Animals often gather information from other species by eavesdropping on signals intended for others. We review the extent, benefits, mechanisms, and ecological and evolutionary consequences of eavesdropping on other species' alarm calls. Eavesdropping has been shown experimentally in about 70 vertebrate species, and can entail closely or distantly related species. The benefits of eavesdropping include prompting immediate anti‐predator responses, indirect enhancement of foraging or changed habitat use, and learning about predators. Eavesdropping on heterospecifics can provide more eyes looking for danger, complementary information to that from conspecifics, and potentially information at reduced cost. The response to heterospecific calls can be unlearned or learned. Unlearned responses occur when heterospecific calls have acoustic features similar to that used to recognize conspecific calls, or acoustic properties such as harsh sounds that prompt attention and may allow recognition or facilitate learning. Learning to recognize heterospecific alarm calls is probably essential to allow recognition of the diversity of alarm calls, but the evidence is largely indirect. The value of eavesdropping on different species is affected by problems of signal interception and the relevance of heterospecific alarm calls to the listener. These constraints on eavesdropping will affect how information flows among species and thus affect community function. Some species are ‘keystone’ information producers, while others largely seek information, and these differences probably affect the formation and function of mixed‐species groups. Eavesdroppers might also integrate alarm calls from multiple species to extract relevant and reliable information. Eavesdropping appears to set the stage for the evolution of interspecific deception and communication, and potentially affects communication within species. Overall, we now know that eavesdropping on heterospecific alarm calls is an important source of information for many species across the globe, and there are ample opportunities for research on mechanisms, fitness consequences and implications for community function and signalling evolution.     

History matters: ecometrics and integrative climate change biology

Climate change research is increasingly focusing on the dynamics among species, ecosystems and climates. Better data about the historical behaviours of these dynamics are urgently needed. Such data are already available from ecology, archaeology, palaeontology and geology, but their integration into climate change research is hampered by differences in their temporal and geographical scales. One productive way to unite data across scales is the study of functional morphological traits, which can form a common denominator for studying interactions between species and climate across taxa, across ecosystems, across space and through time-an approach we call 'ecometrics'. The sampling methods that have become established in palaeontology to standardize over different scales can be synthesized with tools from community ecology and climate change biology to improve our understanding of the dynamics among species, ecosystems, climates and earth systems over time. Developing these approaches into an integrative climate change biology will help enrich our understanding of the changes our modern world is undergoing.     

The effect of species models on estimates of within-lineage variation in integration

Species may be modeled as comprised of individuals, populations or a virtual code. A virtual code can be understood as general potential that appears as actualization within specific environmental, both internal and external, contexts. These general potentials form a capacity to network that allows potentials to be expressed and offers robustness through its interconnections. In the present work, the degree of within-lineage variation in integration was not strongly model-dependent. However, the relationships among model-dependent estimates of such variation and within-lineage phyletic variation were not equal. The strongest relationship was between within-lineage variation in integration, when species were modeled as a virtual code, and within-lineage phyletic variation. The second strongest, and only other statistically significant relationship, was between variation in integration when species were modeled as a virtual code and as a collection of populations. The last result argues for a strong ontogenetic and micro-environmental effect on the expression of features in an individual. If species were a virtual code they would evolve by incorporation of all attributes, ontogenetic, environmental and genetic into that code until it becomes unstable and bifurcates. Species as a virtual code, an approach that explicitly incorporates developmental change into evolution, is a non-material representation of species as a complex information system, incorporating, if we refer to mathematical analysis, both the real and the imaginary. If one wished to stress the material, this study could be seen as empirical documentation of species as information systems.