Beyond similarity: A network approach for identifying and delimiting biogeographical regions

Biogeographical regions (geographically distinct assemblages of species and communities) constitute a cornerstone for ecology, biogeography, evolution and conservation biology. Species turnover measures are often used to quantify biodiversity patterns, but algorithms based on similarity and clustering are highly sensitive to common biases and intricacies of species distribution data. Here we apply a community detection approach from network theory that incorporates complex, higher order presence-absence patterns. We demonstrate the performance of the method by applying it to all amphibian species in the world (c. 6,100 species), all vascular plant species of the USA (c. 17,600), and a hypothetical dataset containing a zone of biotic transition. In comparison with current methods, our approach tackles the challenges posed by transition zones and succeeds in identifying a larger number of commonly recognised biogeographical regions. This method constitutes an important advance towards objective, data derived identification and delimitation of the world's biogeographical regions.Comment: 5 figures and 1 supporting figur

Retracing Micro-Epidemics of Chagas Disease Using Epicenter Regression

Vector-borne transmission of Chagas disease has become an urban problem in the city of Arequipa, Peru, yet the debilitating symptoms that can occur in the chronic stage of the disease are rarely seen in hospitals in the city. The lack of obvious clinical disease in Arequipa has led to speculation that the local strain of the etiologic agent, Trypanosoma cruzi, has low chronic pathogenicity. The long asymptomatic period of Chagas disease leads us to an alternative hypothesis for the absence of clinical cases in Arequipa: transmission in the city may be so recent that most infected individuals have yet to progress to late stage disease. Here we describe a new method, epicenter regression, that allows us to infer the spatial and temporal history of disease transmission from a snapshot of a population's infection status. We show that in a community of Arequipa, transmission of T. cruzi by the insect vector Triatoma infestans occurred as a series of focal micro-epidemics, the oldest of which began only around 20 years ago. These micro-epidemics infected nearly 5% of the community before transmission of the parasite was disrupted through insecticide application in 2004. Most extant human infections in our study community arose over a brief period of time immediately prior to vector control. According to our findings, the symptoms of chronic Chagas disease are expected to be absent, even if the strain is pathogenic in the chronic phase of disease, given the long asymptomatic period of the disease and short history of intense transmission. Traducción al español disponible en Alternative Language Text S1/A Spanish translation of this article is available in Alternative Language Text S

Retracing Micro-Epidemics of Chagas Disease Using Epicenter Regression

Vector-borne transmission of Chagas disease has become an urban problem in the city of Arequipa, Peru, yet the debilitating symptoms that can occur in the chronic stage of the disease are rarely seen in hospitals in the city. The lack of obvious clinical disease in Arequipa has led to speculation that the local strain of the etiologic agent, Trypanosoma cruzi, has low chronic pathogenicity. The long asymptomatic period of Chagas disease leads us to an alternative hypothesis for the absence of clinical cases in Arequipa: transmission in the city may be so recent that most infected individuals have yet to progress to late stage disease. Here we describe a new method, epicenter regression, that allows us to infer the spatial and temporal history of disease transmission from a snapshot of a population\u27s infection status. We show that in a community of Arequipa, transmission of T. cruzi by the insect vector Triatoma infestans occurred as a series of focal micro-epidemics, the oldest of which began only around 20 years ago. These micro-epidemics infected nearly 5% of the community before transmission of the parasite was disrupted through insecticide application in 2004. Most extant human infections in our study community arose over a brief period of time immediately prior to vector control. According to our findings, the symptoms of chronic Chagas disease are expected to be absent, even if the strain is pathogenic in the chronic phase of disease, given the long asymptomatic period of the disease and short history of intense transmission

Nodal dynamics, not degree distributions, determine the structural controllability of complex networks

Structural controllability has been proposed as an analytical framework for making predictions regarding the control of complex networks across myriad disciplines in the physical and life sciences (Liu et al., Nature:473(7346):167-173, 2011). Although the integration of control theory and network analysis is important, we argue that the application of the structural controllability framework to most if not all real-world networks leads to the conclusion that a single control input, applied to the power dominating set (PDS), is all that is needed for structural controllability. This result is consistent with the well-known fact that controllability and its dual observability are generic properties of systems. We argue that more important than issues of structural controllability are the questions of whether a system is almost uncontrollable, whether it is almost unobservable, and whether it possesses almost pole-zero cancellations.Comment: 1 Figures, 6 page

Spatial bias in the marine fossil record.

Inference of past and present global biodiversity requires enough global data to distinguish biological pattern from sampling artifact. Pertinently, many studies have exposed correlated relationships between richness and sampling in the fossil record, and methods to circumvent these biases have been proposed. Yet, these studies often ignore paleobiogeography, which is undeniably a critical component of ancient global diversity. Alarmingly, our global analysis of 481,613 marine fossils spread throughout the Phanerozoic reveals that where localities are and how intensively they have been sampled almost completely determines empirical spatial patterns of richness, suggesting no separation of biological pattern from sampling pattern. To overcome this, we analyze diversity using occurrence records drawn from two discrete paleolatitudinal bands which cover the bulk of the fossil data. After correcting the data for sampling bias, we find that these two bands have similar patterns of richness despite markedly different spatial coverage. Our findings suggest that i) long-term diversity trends result from large-scale tectonic evolution of the planet, ii) short-term diversity trends are region-specific, and iii) paleodiversity studies must constrain their analyses to well-sampled regions to uncover patterns not driven by sampling

Patterns of richness and sampling proxies through the Phanerozoic.

<p>A) Distribution of genus richness across paleolatitude strips. B) Distribution of total equal area grid cells with at least one fossil locality recorded in the PaleoDB across paleolatitude strips. C) Distribution of faunal lists with collection IDs in the PaleoDB across paleolatitude strips. D) The percentage variation of richness in each paleolatitude strips explained by geographic coverage and sampling intensity in each of those paleolatitude strips. Note that the sampling proxies are not rendundant; parts of the Phanerozoic lack geographic coverage but have high sampling intensity and vice versa. Each interval is shaded by the color of the model with the lowest AIC score.</p

500,000 meter equal area gridding scheme for geographic coverage measure superimposed on a geographic map of the present day.

<p>This measure is equal to the number of equal area cells in a paleolatitude strip with fossil occurrences of our target taxa.</p

Diversity and sampling bias in latitude strips.

<p>A–B) Number of grid cells with sampled fossils for each time bin within two fixed paleolatiutudinal belts (temperate and equatorial). A gradual increase in sampled grid cells is evident in the temperate strip (A), while no such pattern is evident in the equatorial strip (B). C–D) Mean richness per sampled grid cell reveals no obvious pattern for faunas in the two paleolatitudinal belts. E–F) Null model that assumes biodiversity is driven purely by sampling (black) compared with observed genus richness (red). The null model explains the overall signal in the data, but select portions of the Phanerozoic deviate from the expectation. G–H) Plots show the difference between empirical richness and the expectation of the null model. Dashed bars indicate 99% confidence intervals for the null model. Overall, we find that the temperate and tropical faunas have similar trajectories despite markedly different trends in spatial sampling pattern over time.</p

Spatial shifts in fossil occurrences through the Phanerozoic.

<p>A) The median latitude of fossil occurrences steadily rises through the Phanerozoic, but is punctuated by short-term noise and contractions and expansions of geographic coverage. Error bars indicate 25th and 75th quantiles, while the red line is a moving average across five points. B) The Mann-Whitney U test statistic plotted for each interval. A higher test-statistic corresponds to a more severe change in latitude. All transitions are statistically significant but vary in their effect size.</p

The distribution of genus richness across latitudes plotted for key intervals.

<p>A) For the last three Cenozoic time intervals (Cenozoic 4–6), Cenozoic 6 has more equitable sampling across latitudes than its predecessors. B) The Permo-Carboniferous boundary reflects a weakness in geographic coverage that biases estimates of global diversity inferred by subsampling.</p