Klaas Hartmann

The global diversity of birds in space and time

Current global patterns of biodiversity result from processes that operate over both space and time and thus require an integrated macroecological and macroevolutionary perspective. Molecular time trees have advanced our understanding of the tempo and mode of diversification and have identified remarkable adaptive radiations across the tree of life. However, incomplete joint phylogenetic and geographic sampling has limited broad-scale inference. Thus, the relative prevalence of rapid radiations and the importance of their geographic settings in shaping global biodiversity patterns remain unclear. Here we present, analyse and map the first complete dated phylogeny of all 9,993 extant species of birds, a widely studied group showing many unique adaptations. We find that birds have undergone a strong increase in diversification rate from about 50 million years ago to the near present. This acceleration is due to a number of significant rate increases, both within songbirds and within other young and mostly temperate radiations including the waterfowl, gulls and woodpeckers. Importantly, species characterized with very high past diversification rates are interspersed throughout the avian tree and across geographic space. Geographically, the major differences in diversification rates are hemispheric rather than latitudinal, with bird assemblages in Asia, North America and southern South America containing a disproportionate number of species from recent rapid radiations. The contribution of rapidly radiating lineages to both temporal diversification dynamics and spatial distributions of species diversity illustrates the benefits of an inclusive geographical and taxonomical perspective. Overall, whereas constituent clades may exhibit slowdowns, the adaptive zone into which modern birds have diversified since the Cretaceous may still offer opportunities for diversification.

Evolutionarily distinctive species often capture more phylogenetic diversity than expected

Evolutionary distinctiveness measures of how evolutionarily isolated a species is relative to other members of its clade. Recently, distinctiveness metrics that explicitly incorporate time have been proposed for conservation prioritization. However, we found that such measures differ qualitatively in how well they capture the total amount of evolution (termed phylogenetic diversity, or PD) represented by a set of species. We used simulation and simple graph theory to explore this relationship with reference to phylogenetic tree shape. Overall, the distinctiveness measures capture more PD on more unbalanced trees and on trees with many splits near the present. The rank order of performance was robust across tree shapes, with apportioning measures performing best and node-based measures performing worst. A sample of 50 ultrametric trees from the literature showed the same patterns. Taken together, this suggests that distinctiveness metrics may be a useful addition to other measures of value for conservation prioritization of species. The simplest measure, the age of a species, performed surprisingly well, suggesting that new measures that focus on tree shape near the tips may provide a transparent alternative to more complicated full-tree approaches.

Sampling Trees from Evolutionary Models

A wide range of evolutionary models for species-level (and higher) diversification have been developed. These models can be used to test evolutionary hypotheses and provide comparisons with phylogenetic trees constructed from real data. To carry out these tests and comparisons, it is often necessary to sample, or simulate, trees from the evolutionary models. Sampling trees from these models is more complicated than it may appear at first glance, necessitating careful consideration and mathematical rigor. Seemingly straightforward sampling methods may produce trees that have systematically biased shapes or branch lengths. This is particularly problematic as there is no simple method for determining whether the sampled trees are appropriate. In this paper, we show why a commonly used simple sampling approach (SSA)-simulating trees forward in time until n species are first reached-should only be applied to the simplest pure birth model, the Yule model. We provide an alternative general sampling approach (GSA) that can be applied to most other models. Furthermore, we introduce the constant-rate birth-death model sampling approach, which samples trees very efficiently from a widely used class of models. We explore the bias produced by SSA and identify situations in which this bias is particularly pronounced. We show that using SSA can lead to erroneous conclusions: When using the inappropriate SSA, the variance of a gradually evolving trait does not correlate with the age of the tree; when the correct GSA is used, the trait variance correlates with tree age. The algorithms presented here are available in the Perl Bio::Phylo package, as a stand-alone program TreeSample, and in the R TreeSim package.

Marine foods sourced from farther as their use of global ocean primary production increases

The growing human population must be fed, but historic land-based systems struggle to meet expanding demand. Marine production supports some of the worlds poorest people but increasingly provides for the needs of the affluent, either directly by fishing or via fodder-based feeds for marine and terrestrial farming. Here we show the expanding footprint of humans to utilize global ocean productivity to feed themselves. Our results illustrate how incrementally each year, marine foods are sourced farther from where they are consumed and moreover, require an increasing proportion of the oceans primary productivity that underpins all marine life. Though mariculture supports increased consumption of seafood, it continues to require feeds based on fully exploited wild stocks. Here we examine the oceans ability to meet our future demands to 2100 and find that even with mariculture supplementing near-static wild catches our growing needs are unlikely to be met without significant changes.

PASTIS: an R package to facilitate phylogenetic assembly with soft taxonomic inferences

Phylogenetic trees that include all member lineages are necessary for many questions in macroevolution, biogeography and conservation. Currently, producing such trees when genetic data or phenotypic characters for some tips are missing generally involves assigning missing species to the root of theirmost exclusive clade, essentially grafting them onto existing and static topologies as polytomies. 2. We describe an R package, ‘PASTIS’, that enables a two-stage Bayesian method usingMrBayes version 3.2 (or higher) to incorporate lineages lacking genetic data at the tree inference stage. The inputs include a consensus topology, a set of taxonomic statements (e.g. placing species in genera and aligning some genera with each other or placing subspecies within species) and user-defined priors on edge lengths and topologies. PASTIS produces input files for execution inMrBayes that will produce a posterior distribution of complete ultrametric trees that captures uncertainty under a homogeneous birth-death prior model of diversification and placement constraints. If the age distribution of a focal node is known (e.g. from fossils), the ultrametric tree distribution can be converted to a set of dated trees.We also provide functions to visualize the placement ofmissing taxa in the posterior distribution. 3. The PASTIS approach is not limited to the level of species and could equally be applied to higher or lower levels of organization (e.g. accounting for all recognized subspecies or populations within a species) given an appropriate choice of priors on branching times.

BIO::Phylo-phyloinformatic analysis using perl

BackgroundPhyloinformatic analyses involve large amounts of data and metadata of complex structure. Collecting, processing, analyzing, visualizing and summarizing these data and metadata should be done in steps that can be automated and reproduced. This requires flexible, modular toolkits that can represent, manipulate and persist phylogenetic data and metadata as objects with programmable interfaces.ResultsThis paper presents Bio::Phylo, a Perl5 toolkit for phyloinformatic analysis. It implements classes and methods that are compatible with the well-known BioPerl toolkit, but is independent from it (making it easy to install) and features a richer API and a data model that is better able to manage the complex relationships between different fundamental data and metadata objects in phylogenetics. It supports commonly used file formats for phylogenetic data including the novel NeXML standard, which allows rich annotations of phylogenetic data to be stored and shared. Bio::Phylo can interact with BioPerl, thereby giving access to the file formats that BioPerl supports. Many methods for data simulation, transformation and manipulation, the analysis of tree shape, and tree visualization are provided.ConclusionsBio::Phylo is composed of 59 richly documented Perl5 modules. It has been deployed successfully on a variety of computer architectures (including various Linux distributions, Mac OS X versions, Windows, Cygwin and UNIX-like systems). It is available as open source (GPL) software from http://search.cpan.org/dist/Bio-Phylo

Stochastic properties of generalised Yule models, with biodiversity applications

The Yule model is a widely used speciation model in evolutionary biology. Despite its simplicity many aspects of the Yule model have not been explored mathematically. In this paper, we formalise two analytic approaches for obtaining probability densities of individual branch lengths of phylogenetic trees generated by the Yule model. These methods are flexible and permit various aspects of the trees produced by Yule models to be investigated. One of our methods is applicable to a broader class of evolutionary processes, namely the Bellman–Harris models. Our methods have many practical applications including biodiversity and conservation related problems. In this setting the methods can be used to characterise the expected rate of biodiversity loss for Yule trees, as well as the expected gain of including the phylogeny in conservation management. We briefly explore these applications.

Age-dependent speciation can explain the shape of empirical phylogenies

Tens of thousands of phylogenetic trees, describing the evolutionary relationships between hundreds of thousands of taxa, are readily obtainable from various databases. From such trees, inferences can be made about the underlying macroevolutionary processes, yet remarkably these processes are still poorly understood. Simple and widely used evolutionary null models are problematic: Empirical trees show very different imbalance between the sizes of the daughter clades of ancestral taxa compared to what models predict. Obtaining a simple evolutionary model that is both biologically plausible and produces the imbalance seen in empirical trees is a challenging problem, to which none of the existing models provide a satisfying answer. Here we propose a simple, biologically plausible macroevolutionary model in which the rate of speciation decreases with species age, whereas extinction rates can vary quite generally. We show that this model provides a remarkable fit to the thousands of trees stored in the online database TreeBase. The biological motivation for the identified age-dependent speciation process may be that recently evolved taxa often colonize new regions or niches and may initially experience little competition. These new taxa are thus more likely to give rise to further new taxa than a taxon that has remained largely unchanged and is, therefore, well adapted to its niche. We show that age-dependent speciation may also be the result of different within-species populations following the same laws of lineage splitting to produce new species. As the fit of our model to the tree database shows, this simple biological motivation provides an explanation for a long standing problem in macroevolution.

Benthic habitat mapping with autonomous underwater vehicles

We provide an outline of an autonomous benthic habitat mapping algorithm. This algorithm enables real-time on-board classification of images gathered by an autonomous underwater vehicle (AUV), with the ability to classify aquatic vegetation at a resolution approaching the species level. The algorithm is generic with respect to both the classification task and the imaging equipment being used. For example, it may be used to detect objects rather than habitat types using hyperspectral rather than visible light cameras.

When is spillover from marine reserves likely to benefit fisheries

The net movement of individuals from marine reserves (also known as no-take marine protected areas) to the remaining fishing grounds is known as spillover and is frequently used to promote reserves to fishers on the grounds that it will benefit fisheries. Here we consider how mismanaged a fishery must be before spillover from a reserve is able to provide a net benefit for a fishery. For our model fishery, density of the species being harvested becomes higher in the reserve than in the fished area but the reduction in the density and yield of the fished area was such that the net effect of the closure was negative, except when the fishery was mismanaged. The extent to which effort had to exceed traditional management targets before reserves led to a spillover benefit varied with rates of growth and movement of the model species. In general, for well-managed fisheries, the loss of yield from the use of reserves was less for species with greater movement and slower growth. The spillover benefit became more pronounced with increasing mis-management of the stocks remaining available to the fishery. This model-based result is consistent with the literature of field-based research where a spillover benefit from reserves has only been detected when the fishery is highly depleted, often where traditional fisheries management controls are absent. We conclude that reserves in jurisdictions with well-managed fisheries are unlikely to provide a net spillover benefit.