Computing the Skewness of the Phylogenetic Mean Pairwise Distance in Linear Time

The phylogenetic Mean Pairwise Distance (MPD) is one of the most popular measures for computing the phylogenetic distance between a given group of species. More specifically, for a phylogenetic tree T and for a set of species R represented by a subset of the leaf nodes of T, the MPD of R is equal to the average cost of all possible simple paths in T that connect pairs of nodes in R. Among other phylogenetic measures, the MPD is used as a tool for deciding if the species of a given group R are closely related. To do this, it is important to compute not only the value of the MPD for this group but also the expectation, the variance, and the skewness of this metric. Although efficient algorithms have been developed for computing the expectation and the variance the MPD, there has been no approach so far for computing the skewness of this measure. In the present work we describe how to compute the skewness of the MPD on a tree T optimally, in Theta(n) time; here n is the size of the tree T. So far this is the first result that leads to an exact, let alone efficient, computation of the skewness for any popular phylogenetic distance measure. Moreover, we show how we can compute in Theta(n) time several interesting quantities in T that can be possibly used as building blocks for computing efficiently the skewness of other phylogenetic measures.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Examining neotropical primate community structure at regional and local scales : insights from taxonomic and phylogenetic approaches

Understanding mechanisms underlying distribution of biodiversity remains a central issue in ecology. I integrate ecological and phylogenetic information at multiple spatial scales to better understand neotropical primate distribution and community structure. I investigate the variation within species ranges in relation to species richness and patterns of species relatedness. Results suggest positive associations among species throughout their distributions, whereby species tend to present higher richness within their ranges than average richness for the entire taxon. However, comparing empirical distributions to a null model of range cohesion suggests mechanisms other than dispersal are setting a limit to the number of species capable of co-occurring throughout a species’ range. These differences in species associations across geographic ranges generate variation in local community composition. I analyzed the relative contribution of ecological, historical and spatial processes in determining taxonomic and phylogenetic community structure across 74 sites throughout the Neotropics. Spatial predictors explained most of the independent variation for taxonomic and phylogenetic metrics, suggesting spatial processes, such as dispersal limitation, are important determinants of community structure. Most of the contribution of environmental predictors was associated with spatial processes, evincing importance of environmental and spatial gradients in determining change in community structure. While the overall contributions of predictors were similar for taxonomic and phylogenetic metrics, analyses of phylogenetic metrics independently presented complex relationships. At local communities, niche differentiation is expected to allow species coexistence. However, these differences may reflect evolutionary constraints of species, rather than active selection. I investigated niche overlap and presence of niche conservatism for primate species at three communities. For the niche characteristics measured by my study, I found no significant differences in niches of closely related species within sites. However, when comparing niches across sites, significant differences were registered between populations of the same species or closely related species. These findings suggest ecological differentiation may be acting at large spatial scales promoting niche differentiation, while at local scales phylogenetic constraints may be a stronger driver of community structure. Overall, these results represent valuable insights regarding our understanding of mechanisms responsible for generating and maintaining community structure for a highly diverse tropical mammal radiation

Discriminative Measures for Comparison of Phylogenetic Trees

In this paper we introduce and study three new measures for efficient discriminative comparison of phylogenetic trees. The NNI navigation dissimilarity $d_{nav}$ counts the steps along a “combing” of the Nearest Neighbor Interchange (NNI) graph of binary hierarchies, providing an efficient approximation to the (NP-hard) NNI distance in terms of “edit length”. At the same time, a closed form formula for $d_{nav}$ presents it as a weighted count of pairwise incompatibilities between clusters, lending it the character of an edge dissimilarity measure as well. A relaxation of this formula to a simple count yields another measure on all trees — the crossing dissimilarity $d_{CM}$. Both dissimilarities are symmetric and positive definite (vanish only between identical trees) on binary hierarchies but they fail to satisfy the triangle inequality. Nevertheless, both are bounded below by the widely used Robinson–Foulds metric and bounded above by a closely related true metric, the cluster-cardinality metric $d_{CC}$. We show that each of the three proposed new dissimilarities is computable in time O($n^2$) in the number of leaves $n$, and conclude the paper with a brief numerical exploration of the distribution over tree space of these dissimilarities in comparison with the Robinson–Foulds metric and the more recently introduced matching-split distance. For more information: Kod*La

Evolution and ecology of two iconic Australian clades: the Meliphagidae (birds) and the Hakeinae (plants)

The first part of this dissertation explores the evolution of two iconic groups of species through Australian climate space: the Meliphagidae, or honeyeaters, which are primarily nectar-feeding birds, and the Hakeinae, a section of the plant family Proteaceae. Both groups are inferred to have had their origins in Gondwanan rainforests that were widespread across Australia 45 million years ago and then diversified into more arid environments as the continent’s climate became more arid. Accordingly, dry environments are inhabited by closely related (phylogenetically clustered) sets of species, although, in contrast to the honeyeaters, Hakeinae communities are characterized by more localized diversification. The impressive and rapid Hakeinae diversification may have been driven by specialization onto a variety of highly weathered, nutrient-poor soil types on the ancient Australian landmass. The second part of this dissertation reviews a variety of methods to assess the phylogenetic structure of communities, such as local assemblages of honeyeaters and Hakeinae. Many published methods were found to be redundant, and some of the truly unique approaches do not measure what they purport to. Accordingly, only a small subset of phylogenetic community structure methods have merit. In the third part of the dissertation, observations on foraging by 74 of 75 Australian honeyeater species are used to explore patterns of community assembly. Australian honeyeater communities reflect both stochastic and deterministic processes. Co-occurring species exhibit substantial overlap in foraging niche space, in contrast to predictions from assembly theory based on competition. At the same time, species tend to occupy characteristic portions of niche space and available niche space is smaller in the arid regions of the continent. Within this smaller available niche space, arid-zone species tend to be more widely separated in niche space than species in more mesic environments

Climate, host phylogeny and the connectivity of host communities govern regional parasite assembly

Aim Identifying barriers that govern parasite community assembly and parasite invasion risk is critical to understand how shifting host ranges impact disease emergence. We studied regional variation in the phylogenetic compositions of bird species and their blood parasites (Plasmodium and Haemoproteus spp.) to identify barriers that shape parasite community assembly. Location Australasia and Oceania Methods We used a dataset of parasite infections from >10,000 host individuals sampled across 29 bioregions. Hierarchical models and matrix regressions were used to assess the relative influences of interspecies (host community connectivity and local phylogenetic distinctiveness), climate and geographic barriers on parasite local distinctiveness and composition. Results Parasites were more locally distinct (co-occurred with distantly related parasites) when infecting locally distinct hosts, but less distinct (co-occurred with closely related parasites) in areas with increased host diversity and community connectivity (a proxy for parasite dispersal potential). Turnover and the phylogenetic symmetry of parasite communities were jointly driven by host turnover, climate similarity and geographic distance. Main conclusions Interspecies barriers linked to host phylogeny and dispersal shape parasite assembly, perhaps by limiting parasite establishment or local diversification. Infecting hosts that co-occur with few related species decreases a parasite’s likelihood of encountering related competitors, perhaps increasing invasion potential but decreasing diversification opportunity. While climate partially constrains parasite distributions, future host range expansions that spread distinct parasites and diminish barriers to host shifting will likely be key drivers of parasite invasions

A Statistical Social Network Model for Consumption Data in Food Webs

We adapt existing statistical modeling techniques for social networks to study consumption data observed in trophic food webs. These data describe the feeding volume (non-negative) among organisms grouped into nodes, called trophic species, that form the food web. Model complexity arises due to the extensive amount of zeros in the data, as each node in the web is predator/prey to only a small number of other trophic species. Many of the zeros are regarded as structural (non-random) in the context of feeding behavior. The presence of basal prey and top predator nodes (those who never consume and those who are never consumed, with probability 1) creates additional complexity to the statistical modeling. We develop a special statistical social network model to account for such network features. The model is applied to two empirical food webs; focus is on the web for which the population size of seals is of concern to various commercial fisheries.Comment: On 2013-09-05, a revised version entitled "A Statistical Social Network Model for Consumption Data in Trophic Food Webs" was accepted for publication in the upcoming Special Issue "Statistical Methods for Ecology" in the journal Statistical Methodolog

Landscape Genetics, Phylogeography, and Demographic History of a Pollinator Longhorn Beetle (Typocerus v. Velutinus)

One of the central problems in contemporary ecology and conservation biology is the drastic change of landscapes induced by anthropogenic activities, resulting in habitat loss and fragmentation. For many wild living species, local extinctions of fragmented populations are common and re-colonization is critical for regional survival. Thus, habitat fragmentation in the landscape is a major threat to biodiversity, of which insects are a major proportion. Understanding the link between patterns, processes and population genetic continuity in the landscape is crucial for conserving genetic diversity within species. This is important for species persistence, for ecosystem functioning, and for future evolution. Herein, I use a newly introduced landscape gradient paradigm with surface metrology metrics, phylogeography, and landscape genetics to evaluate the influence of contemporary events (e.g. habitat fragmentation in the landscape) and pre-historic events (e.g. Quaternary glaciation) on the demography and population genetic structure of a pollinator longhorn beetle [Typocerus v. velutinus (Olivier)] in Indiana, USA and Canada. Landsat 7 ETM+ imagery products provide researchers in many fields with a large amount of remotely sensed data that serves many applications. However, a malfunction of the scan line corrector (SLC) onboard Landsat 7 causes substantial data gaps and data are available only as is, in the SLC-off mode. These data gaps may form an obstacle in using Landsat 7 ETM+ in many research disciplines. Several methods have been proposed to fix data gaps in Landsat 7 ETM+ imagery. These methods yield reliable results, but require sophisticated analyses and intensive computations and are still accompanied by some caveats. In the second chapter of this dissertation I demonstrate a spatial replacement method that is based on a simple neighborhood interpolation (SNI) approach. The results suggest that SNI provides an easily applicable, relatively quick and potentially reliable correction for the missing data patterns in Landsat 7 ETM+ data. I demonstrate the efficiency of the technique for two color bands across Indiana, USA. I tested the corrected imagery in calculating the normalized difference vegetation index (NDVI). Measuring habitat connectivity in complex landscapes is a major focus of landscape ecology and conservation research. Most studies use a binary landscape or patch mosaic model for describing spatial heterogeneity and understanding pattern-process relationships. While the value of a landscape gradient approach is recognized, applications of the newly proposed three-dimensional surface metrics remain extremely under-used. In the third chapter, I created a surface habitat quality from several GIS layers and applied surface metrics to measure connectivity between 67 locations in Indiana, USA that were surveyed for one group of ecosystem service providers, flower longhorn beetles (Cerambycidae: Lepturinae). The results demonstrated great potential of surface metrics of connectivity to explain the differences of lepturine assemblages among the 2211 studied landscapes. Surface kurtosis and its interaction with geographic distance were among the most important metrics. This approach provided unique information about the landscape through four configuration metrics. There were some uniform trends of the responses of many species to some of surface metrics, however some species responded differently to other metrics. I suggest that surface metrics of connectivity applied to a habitat surface map created with insight into species requirements is a valuable approach for understanding the spatial dynamics of species, guilds, and ecosystem services. Historical geological processes have shaped the contemporary distribution of genetic variation in many species. However, there have been few empirical appraisals of cerambycid phylogeography despite of their economic importance and the fact that many geological processes (e.g., glaciations) should have had pronounced impacts on these insects as well as other taxa. In chapter four, I aimed to quantify phylogeographic effects on the contemporary gene pool of Typocerus v. velutinus. The beetle was collected from sites that were glaciated and unglaciated during the Pleistocene to determine genetic structure within and among populations from the US and Canada, to elucidate phylogenetic relationships among demes, and to determine divergence times between populations. A total of 451 beetles were sampled from 14 sites and sequenced at a mitochondrial DNA (mtDNA) gene. Maximum likelihood and Bayesian approaches were applied to analyze the mtDNA genealogy and to reconstruct phylogenetic trees whereas Bayesian skyline analyses were used to estimate divergence time. A total of sixteen haplotypes revealed weak geographical population structuring among most populations, but statistical tests identified significant differences between the Canadian and US populations. As a result of post-glacial recolonization, the US populations appear to have experienced demographic expansion while the Canadian population was influenced by a bottleneck. The results suggest that Canadian population diverged from more southern populations around the time of last glacial maximum (~17,500 ybp). Understanding the underling patterns and processes in the landscape that are affecting the population genetic structure and population connectivity is a major discipline in landscape genetics research. A vast number of these studies have implemented categorical approaches in analyzing both landscape and genetic data. In chapter five, I adopted a landscape gradient model and used the surface metrics of connectivity to model the genetic continuity between populations of the beetle (Typocerus v. velutinus) that was collected at 17 sites across a fragmentation gradient from Indiana, USA. I tested the hypothesis that landscape structure and habitat connectivity facilitate beetle movement and thus gene flow between the beetle populations against a null model of isolation by distance (IBD). I used next-generation sequencing and developed 10 polymorphic microsatellite loci and genotyped the population. Genetic dissimilarities between sites were calculated using RST and the population genetic structure was assessed using both non-spatial and spatial explicit Bayesian techniques. The connectivity in 137 landscapes was measured using surface topology metrics. The results indicated that panmixia was not evident with the beetle population. The source of genetic variation was mainly within rather than among populations. The surface metrics were found to significantly explain the variance in genetic dissimilarities between beetle populations 30 times better than IBD. I concluded that surface metrics of connectivity is a powerful extension in landscape genetics tools and need more attention especially to understand the configuration metrics. This approach might yield insightful applications in conservation management