Evaluating management options for aquatic invasive species: concepts and methods

In analyses that attempt to estimate the costs of species invasions, it has been typical to report the costs of management and/or to multiply per-unit costs by the number affected to arrive at a total. These estimates are of limited value for most policy questions. We start our discussion by recognizing that biological pollutants such as aquatic invasive species are like conventional pollutants in important ways and appeal to the well-developed literature on conventional pollution to guide our thinking into how best to conceptualize the problem. We use a standard pollution control framework to identify the margins over which costs and benefits should be estimated to guide wise decision-making. We then use examples from the literature to illustrate how transactions in related markets can be used to estimate the benefits of management. The roles of adaptation, mitigation, and species population growth have particular relevance and are highlighted. In the final section of the paper, we think through the conditions under which investing in genetic biocontrol methods would be economically justified.     

The unholy trinity: taxonomy, species delimitation and DNA barcoding

Recent excitement over the development of an initiative to generate DNA sequences for all named species on the planet has in our opinion generated two major areas of contention as to how this 'DNA barcoding' initiative should proceed. It is critical that these two issues are clarified and resolved, before the use of DNA as a tool for taxonomy and species delimitation can be universalized. The first issue concerns how DNA data are to be used in the context of this initiative; this is the DNA barcode reader problem (or barcoder problem). Currently, many of the published studies under this initiative have used tree building methods and more precisely distance approaches to the construction of the trees that are used to place certain DNA sequences into a taxonomic context. The second problem involves the reaction of the taxonomic community to the directives of the 'DNA barcoding' initiative. This issue is extremely important in that the classical taxonomic approach and the DNA approach will need to be reconciled in order for the 'DNA barcoding' initiative to proceed with any kind of community acceptance. In fact, we feel that DNA barcoding is a misnomer. Our preference is for the title of the London meetings--Barcoding Life. In this paper we discuss these two concerns generated around the DNA barcoding initiative and attempt to present a phylogenetic systematic framework for an improved barcoder as well as a taxonomic framework for interweaving classical taxonomy with the goals of 'DNA barcoding'.     

Integrating Homo sapiens into ecological models: Imperatives of climate change

In the opening lecture at a 2013 Banff International Research Station (BIRS) workshop on the impact of climate change on biological invasions and population distributions, Henri Berestycki (École des Hautes Études en Sciences Sociales) asked a crucial question: Can a species keep pace with a changing climate? “Species” in this context was generally understood to be all living things on Earth (except humans). But mounting scientific evidence suggests that it is time to pose the parallel question: Can Homo sapiens keep pace with a changing climate? Furthermore, should we merely “keep pace”, or should we strive to get ahead and then do our utmost to stop any further climate change?In this paper we document the very real potential for climate change to have devastating consequences before the end of this century. The urgency of the situation calls for concerted action by anyone who understands the problem, and mathematical ecologists are uniquely trained to contribute to such efforts. We ask modellers to deliberately incorporate the species H. sapiens into their modelling work, and offer suggestions as to how this might be done. Ultimately modellers must seek ways to provide guidance to citizens and policy-makers as we all wrestle with the most important existential threat of our time.     

Conflict over sex allocation drives conflict over reproductive allocation in perennial social insect colonies

Queen-worker conflict in the social Hymenoptera has become a cornerstone of sex-ratio theory. Extending that theory to conflict over life-history decisions, however, has proven controversial. Pamilo first proposed that queen-worker conflict over reproductive allocation should be important in perennial, social insect colonies, but Bourke and Chan have questioned the generality of that claim. Here, we reexamine this problem for the simplest case of a monogynous and monandrous hymenopteran society by relaxing assumptions of Pamilo's model. In populations with monomorphic sex ratios, queens and workers agree on allocation to growth versus reproduction. However, variation in sex allocation across colonies can induce queen-worker conflict over reproductive allocation; the former is a necessary condition for the latter. We explore how conflict over reproductive allocation depends on the population-wide sex ratio, the survivorship probabilities for existing colonies, and the likelihood of establishing new colonies. We then test our theory for two ant species, each with two years of data. We find considerable support for our contention of queen-worker conflict over reproductive allocation and suggest how future studies should be structured to explore this conflict further.     

Predicting phenology by integrating ecology,evolution and climate science

Forecasting how species and ecosystems will respond to climate change has been a major aim of ecology in recent years. Much of this research has focused on phenology – the timing of life‐history events. Phenology has well‐demonstrated links to climate, from genetic to landscape scales; yet our ability to explain and predict variation in phenology across species, habitats and time remains poor. Here, we outline how merging approaches from ecology, climate science and evolutionary biology can advance research on phenological responses to climate variability. Using insight into seasonal and interannual climate variability combined with niche theory and community phylogenetics, we develop a predictive approach for species’ reponses to changing climate. Our approach predicts that species occupying higher latitudes or the early growing season should be most sensitive to climate and have the most phylogenetically conserved phenologies. We further predict that temperate species will respond to climate change by shifting in time, while tropical species will respond by shifting space, or by evolving. Although we focus here on plant phenology, our approach is broadly applicable to ecological research of plant responses to climate variability.     

The importance of data mining for conservation science: a case study on the wolverine

Assessing the scale of ecological changes that have occurred since the onset of the Anthropocene is challenging. One major problem is that of shifting baselines, whereby the norms we set for judging the state of species, populations, or ecosystems change over time due to incomplete information. Here we show how data mining can be used to fill some of the information gaps fueling shifting baselines. We used as example an elusive species, the wolverine (Gulo gulo), given that information gaps are so prevailing for such species. We applied the concept of data mining to search documents hosted on publicly accessible online repositories and found information about the historical occurrence of wolverines that allowed us to revise their historical range in eastern North America. We found 12 historical accounts attesting the presence of wolverines in various parts of the Maritime Provinces of Canada, of which 11 were new to contemporary science. According to our results, the eastern limit of the historical range of the wolverine should be extended to include the current jurisdictions of New Brunswick and Nova Scotia. Biological change is the central paradigm of species status assessments. We show that online repositories of public domain literature can now be critical sources of information to assess biological change, including in the case of elusive species. Data mining constitutes a productive tool to uncover useful knowledge hidden in a sea of digitized historical information, and should thus allow researchers and conservationists to more effectively mitigate the problem of shifting baselines.     

Conceptualizing communities as natural entities: a philosophical argument with basic and applied implications

Recent work has suggested that conservation efforts such as restoration ecology and invasive species eradication are largely value-driven pursuits. Concurrently, changes to global climate are forcing ecologists to consider if and how collections of species will migrate, and whether or not we should be assisting such movements. Herein, we propose a philosophical framework which addresses these issues by utilizing ecological and evolutionary interrelationships to delineate individual ecological communities. Specifically, our Evolutionary Community Concept (ECC) recognizes unique collections of species that interact and have co-evolved in a given geographic area. We argue this concept has implications for a number of contemporary global conservation issues. Specifically, our framework allows us to establish a biological and science-driven context for making decisions regarding the restoration of systems and the removal of exotic species. The ECC also has implications for how we view shifts in species assemblages due to climate change and it advances our understanding of various ecological concepts, such as resilience.     

Orthology relations, symbolic ultrametrics, and cographs

Orthology detection is an important problem in comparative and evolutionary genomics and, consequently, a variety of orthology detection methods have been devised in recent years. Although many of these methods are dependent on generating gene and/or species trees, it has been shown that orthology can be estimated at acceptable levels of accuracy without having to infer gene trees and/or reconciling gene trees with species trees. Thus, it is of interest to understand how much information about the gene tree, the species tree, and their reconciliation is already contained in the orthology relation on the underlying set of genes. Here we shall show that a result by Böcker and Dress concerning symbolic ultrametrics, and subsequent algorithmic results by Semple and Steel for processing these structures can throw a considerable amount of light on this problem. More specifically, building upon these authors’ results, we present some new characterizations for symbolic ultrametrics and new algorithms for recovering the associated trees, with an emphasis on how these algorithms could be potentially extended to deal with arbitrary orthology relations. In so doing we shall also show that, somewhat surprisingly, symbolic ultrametrics are very closely related to cographs, graphs that do not contain an induced path on any subset of four vertices. We conclude with a discussion on how our results might be applied in practice to orthology detection.     

Identifying ecological drivers of interspecific variation in song complexity in songbirds (Passeriformes,Passeri)

A diversity of selective pressures and stochastic processes have likely created substantial variation in song structure, creating difficulties in quantifying the influence of specific ecological factors. This problem is further compounded by differences in study taxa and methods of data analysis between studies. Large comparative studies offer the potential to mitigate some of these methodological difficulties by maximizing the power of statistical analyses and minimizing the probability of misidentifying the magnitude and direction of relationships between independent and dependent variables. In this study, we quantified song complexity for 367 species of globally distributed songbirds (Passeriformes, Passeri). We quantified eight individual acoustic variables that have previously been linked to audio complexity which we analyzed independently, and after applying multivariate statistics to the variables. We used Bayesian linear mixed effect models to test multiple hypotheses regarding song complexity: that it should be greater in open habitats, in migratory species, for sexually monomorphic species, at higher latitudes and altitudes, and that it should co‐vary with clutch size characteristics. Our results challenge perceptions of the effect of habitat structure on song complexity; for instance, counter to expectation, we found songs in closed environments to have reduced syllable diversity. Additionally, our results suggest song complexity may not be ubiquitously a means of communicating male quality, with no significant difference between recordings from monomorphic and dimorphic species. By estimating song complexity in multiple ways, and quantifying these over large taxonomic and spatial scales, we are able to gain a more nuanced understanding of how song complexity is potentially affected by a range of biotic and abiotic factors. Our results also suggest that caution is required when making generalized statements about the relative influence of different factors on song complexity; more densely‐sampled, group‐specific studies are necessary complements to this taxonomically broad analysis.     

What became of Hystrix?

Hystrix Moench was a perennial genus of the Triticeae. Its members differed from those of other genera in the tribe in lacking glumes. The type species is H. patulaMoench, a North American taxon. When it became accepted that H. patula should be included in Elymus, Hystrix could not be used as a generic name. The problem became how to treat the other species that had been included in Hystrix. Hystrix patula, like many other species of Elymus, has the StH genomic composition but H. coreana (Honda) Ohwi, H. californica (Bol.) Kuntze, H. duthiei (Stapf) Bor ssp. duthiei, and H. duthiei ssp. longearistata have the NsXm genomic composition that is associated with Leymus. Using genomic in situ hybridization analysis, we showed that H. komarovii (Roshev.) Ohwi has an NsE^e genomic composition, a combination not known from any other species. Hystrix sibirica (Trautv.) Kuntze and H. duthiei ssp. japonica are included in Leymus on morphological grounds. The status of H. kunlunensis K. S. Hao is not clear. In this paper, we summarize our results and those of others concerning what is now known and the problems that remain concerning the species that used to be included in Hystrix.     

How many species of flowering plants are there?

We estimate the probable number of flowering plants. First, we apply a model that explicitly incorporates taxonomic effort over time to estimate the number of as-yet-unknown species. Second, we ask taxonomic experts their opinions on how many species are likely to be missing, on a family-by-family basis. The results are broadly comparable. We show that the current number of species should grow by between 10 and 20 per cent. There are, however, interesting discrepancies between expert and model estimates for some families, suggesting that our model does not always completely capture patterns of taxonomic activity. The as-yet-unknown species are probably similar to those taxonomists have described recently—overwhelmingly rare and local, and disproportionately in biodiversity hotspots, where there are high levels of habitat destruction.     

The interaction between plant competition and disease

It is well documented that pathogens can affect the survival, reproduction, and growth of individual plants. Drawing together insights from diverse studies in ecology and agriculture, we evaluate the evidence for pathogens affecting competitive interactions between plants of both the same and different species. Our objective is to explore the potential ecological and evolutionary consequences of such interactions. First, we address how disease interacts with intraspecific competition and present a simple graphical model suggesting that diverse outcomes should be expected. We conclude that the presence of pathogens may have either large or minimal effects on population dynamics depending on many factors including the density-dependent compensatory ability of healthy plants and spatial patterns of infection. Second, we consider how disease can alter competitive abilities of genotypes, and thus may affect the genetic composition of populations. These genetic processes feed back on population dynamics given trade-offs between disease resistance and other fitness components. Third, we examine how the effect of disease on interspecific plant interactions may have potentially far-reaching effects on community composition. A host-specific pathogen, for example, may alter a competitive hierarchy that exists between host and non-host species. Generalist pathogens can also induce indirect competitive interactions between host species. We conclude by highlighting lacunae in our current understanding and suggest that future studies should (1) examine a broader taxonomic range of pathogens since work to date has largely focused on fungal pathogens; (2) increase the use of field competition studies; (3) follow interactions for multiple generations; (4) characterize density-dependent processes; and (5) quantify pathogen, as well as plant, population and community dynamics.     

A consensus tree approach for reconstructing human evolutionary history and detecting population substructure

The random accumulation of variations in the human genome over time implicitly encodes a history of how human populations have arisen, dispersed, and intermixed since we emerged as a species. Reconstructing that history is a challenging computational and statistical problem but has important applications both to basic research and to the discovery of genotype-phenotype correlations. We present a novel approach to inferring human evolutionary history from genetic variation data. We use the idea of consensus trees, a technique generally used to reconcile species trees from divergent gene trees, adapting it to the problem of finding robust relationships within a set of intraspecies phylogenies derived from local regions of the genome. Validation on both simulated and real data shows the method to be effective in recapitulating known true structure of the data closely matching our best current understanding of human evolutionary history. Additional comparison with results of leading methods for the problem of population substructure assignment verifies that our method provides comparable accuracy in identifying meaningful population subgroups in addition to inferring relationships among them. The consensus tree approach thus provides a promising new model for the robust inference of substructure and ancestry from large-scale genetic variation data.     

Evolutionary ecology of inducible morphological plasticity in predator–prey interaction: toward the practical links with population ecology

The outcome of species interactions is often strongly influenced by variation in the functional traits of the individuals participating. A rather large body of work demonstrates that inducible morphological plasticity in predators and prey can both influence and be influenced by species interaction strength, with important consequences for individual fitness. Much of the past research in this area has focused on the ecological and evolutionary significance of trait plasticity by studying single predator–prey pairs and testing the performance of individuals having induced and noninduced phenotypes. This research has thus been critical in improving our understanding of the adaptive value of trait plasticity and its widespread occurrence across species and community types. More recently, researchers have expanded this foundation by examining how the complexity of organismal design and community-level properties can shape plasticity in functional traits. In addition, researchers have begun to merge evolutionary and ecological perspectives by linking trait plasticity to community dynamics, with particular attention on trait-mediated indirect interactions. Here, we review recent studies on inducible morphological plasticity in predators and their prey with an emphasis on internal and external constraints and how the nature of predator–prey interactions influences the expression of inducible phenotypes. In particular, we focus on multiple-trait plasticity, flexibility and modification of inducible plasticity, and reciprocal plasticity between predator and prey. Based on our arguments on these issues, we propose future research directions that should better integrate evolutionary and population studies and thus improve our understanding of the role of phenotypic plasticity in predator–prey population and community dynamics.     

Credit Assignment during Movement Reinforcement Learning

We often need to learn how to move based on a single performance measure that reflects the overall success of our movements. However, movements have many properties, such as their trajectories, speeds and timing of end-points, thus the brain needs to decide which properties of movements should be improved; it needs to solve the credit assignment problem. Currently, little is known about how humans solve credit assignment problems in the context of reinforcement learning. Here we tested how human participants solve such problems during a trajectory-learning task. Without an explicitly-defined target movement, participants made hand reaches and received monetary rewards as feedback on a trial-by-trial basis. The curvature and direction of the attempted reach trajectories determined the monetary rewards received in a manner that can be manipulated experimentally. Based on the history of action-reward pairs, participants quickly solved the credit assignment problem and learned the implicit payoff function. A Bayesian credit-assignment model with built-in forgetting accurately predicts their trial-by-trial learning.     

Anthropogenic impacts on tropical forest biodiversity: a network structure and ecosystem functioning perspective

Huge areas of diverse tropical forest are lost or degraded every year with dramatic consequences for biodiversity. Deforestation and fragmentation, over-exploitation, invasive species and climate change are the main drivers of tropical forest biodiversity loss. Most studies investigating these threats have focused on changes in species richness or species diversity. However, if we are to understand the absolute and long-term effects of anthropogenic impacts on tropical forests, we should also consider the interactions between species, how those species are organized in networks, and the function that those species perform. I discuss our current knowledge of network structure and ecosystem functioning, highlighting empirical examples of their response to anthropogenic impacts. I consider the future prospects for tropical forest biodiversity, focusing on biodiversity and ecosystem functioning in secondary forest. Finally, I propose directions for future research to help us better understand the effects of anthropogenic impacts on tropical forest biodiversity.