Knowledge of the spatial organization of the gut microbiota is important for understanding the physical and molecular interactions among its members. These interactions are thought to influence ...microbial succession, community stability, syntrophic relationships, and resiliency in the face of perturbations. The complexity and dynamism of the gut microbiota pose considerable challenges for quantitative analysis of its spatial organization. Here, we illustrate an approach for addressing this challenge, using (i) a model, defined 15-member consortium of phylogenetically diverse, sequenced human gut bacterial strains introduced into adult gnotobiotic mice fed a polysaccharide-rich diet, and (ii) in situ hybridization and spectral imaging analysis methods that allow simultaneous detection of multiple bacterial strains at multiple spatial scales. Differences in the binding affinities of strains for substrates such as mucus or food particles, combined with more rapid replication in a preferred microhabitat, could, in principle, lead to localized clonally expanded aggregates composed of one or a few taxa. However, our results reveal a colonic community that is mixed at micrometer scales, with distinct spatial distributions of some taxa relative to one another, notably at the border between the mucosa and the lumen. Our data suggest that lumen and mucosa in the proximal colon should be conceptualized not as stratified compartments but as components of an incompletely mixed bioreactor. Employing the experimental approaches described should allow direct tests of whether and how specified host and microbial factors influence the nature and functional contributions of “microscale” mixing to the dynamic operations of the microbiota in health and disease.
The Hawaiian silversword alliance (Asteraceae) is an iconic adaptive radiation. However, like many island plant lineages, no fossils have been assigned to the clade. As a result, the clade’s age and ...diversification rate are not known precisely, making it difficult to test biogeographic hypotheses about the radiation. In lieu of fossils, paleogeographically structured biogeographic processes may inform species divergence times; for example, an island must first exist for a clade to radiate upon it. We date the silversword clade and test biogeographic hypotheses about its radiation across the Hawaiian Archipelago by modeling interactions between species relationships, molecular evolution, biogeographic scenarios, divergence times, and island origination times using the Bayesian phylogenetic framework, RevBayes. The ancestor of living silverswords most likely colonized the modern Hawaiian Islands once from the mainland approximately 5.1 Ma, with the most recent common ancestor of extant silversword lineages first appearing approximately 3.5 Ma. Applying an event-based test of the progression rule of island biogeography, we found strong evidence that the dispersal process favors old-to-young directionality, but strong evidence for diversification continuing unabated into later phases of island ontogeny, particularly for Kaua‘i. This work serves as a general example for how diversification studies benefit from incorporating biogeographic and paleogeographic components.
In a recent survey of populations of the Korean torrent catfish
, a distinctive species was discovered from the Geum River and its tributaries flowing into the western coast of Korea, and here ...described as a new species,
It is distinguishable from other congeners by a combination of the following characters: I, 8 pectoral fin-rays; 52-56 caudal-fin rays; a relatively short occiput to dorsal-fin origin distance (6.9-9.8% SL); a short pelvic-fin insertion to anal-fin origin distance (11.9-17.3% SL); a long dorsal-fin base (10.6-13.5% SL); 8-9 gill rakers; 5-8 serrations on the pectoral fin; the body and fins are dark yellow, the margins of the dorsal, anal, and caudal fins are dark brown, but the outermost rim is faintly yellow. Analysis of the cytb gene also confirmed that
is a monophyletic lineage distinct from other congeners.
Aim
The equilibrium theory of island biogeography predicts the positive species–area relationship and the negative species–isolation relationship, resulting in higher species richness on large and ...close islands. Unlike species richness, soundscape diversity integrates sound from various sources (e.g. biophony, geophony and anthrophony). However, how soundscape diversity varies with island area and isolation still needs to be tested. Here, we explored the island biogeography of bird soundscapes and the determinants of island attributes in shaping bird diversity and soundscape diversity.
Location
Thousand Island Lake, Zhejiang, China.
Taxon
Birds.
Methods
We recorded avian soundscapes by audio recorders and censused bird diversity by line transects on 20 land‐bridge islands. We calculated four acoustic indices (acoustic complexity index, bioacoustic index, acoustic evenness index and acoustic entropy index) to assess acoustic richness, evenness and heterogeneity to explore the soundscape diversity of birds. We used multiple linear regressions, spatial autoregressions and piecewise structural equation models to examine the relationships between bird richness and acoustic diversity, and island attributes.
Results
We found positive diversity–area relationships for avian soundscapes. Larger islands had more vocal species and higher habitat diversity, which led to an increment in the richness and unevenness of avian soundscapes on large islands. Acoustic evenness decreased with increasing isolation (distance to the mainland).
Main Conclusions
Soundscapes on large islands are more diverse than those on small islands. Rich acoustic assemblages and heterogeneous habitats promote increased soundscape diversity on islands. Conversely, the lack of vocal contributors, resulting in a decrement in the communication of acoustic signals, can create a lower soundscape diversity on small and remote islands. Our study emphasizes the necessity of examining both species and habitat diversity in island biogeography for better understanding the underlying mechanisms determining biological soundscapes on islands.
The latitudinal diversity gradient (LDG) is one of the most widely studied patterns in ecology, yet no consensus has been reached about its underlying causes. We argue that the reasons for this are ...the verbal nature of existing hypotheses, the failure to mechanistically link interacting ecological and evolutionary processes to the LDG, and the fact that empirical patterns are often consistent with multiple explanations. To address this issue, we synthesize current LDG hypotheses, uncovering their eco-evolutionary mechanisms, hidden assumptions, and commonalities. Furthermore, we propose mechanistic eco-evolutionary modeling and an inferential approach that makes use of geographic, phylogenetic, and trait-based patterns to assess the relative importance of different processes for generating the LDG.
The latitudinal diversity gradient (LDG) is one of the most widely debated patterns in ecology and evolution, associated with hundreds of papers, dozens of hypotheses, and disagreements about its underlying processes.
The lack of agreement stems from: (i) the verbal nature of existing hypotheses, (ii) the failure to mechanistically integrate all relevant ecological and evolutionary processes to the LDG, and (iii) the degree to which many empirical patterns are consistent with multiple LDG explanations.
We show how mapping LDG hypotheses to a set of key ecological and evolutionary processes leads to a better understanding of the internal logic of those hypotheses. The codification of those processes within a mechanistic eco-evolutionary model is essential for contrasting support for hypotheses and for understanding the relative importance of the processes themselves.
Aim
To test whether the species richness of understorey insectivorous birds on forest islands induced by a major hydroelectric dam is best explained by either the island biogeography theory (IBT) or ...the habitat amount hypothesis (HAH). Given the low dispersal ability of the focal species group and the hostile water matrix, we predict that the species richness will be predominantly driven by an island effect as posited by the IBT, rather than a sample area effect as posited by the HAH.
Location
Forest islands within the Balbina Hydroelectric Reservoir, central Brazilian Amazonia.
Taxon
Birds.
Methods
We mist‐netted birds at 33 forest islands (0.63–1,699 ha), totalling 874 individuals of 59 species. The size of the local landscape used to calculate the habitat amount was determined by a multi‐scale analysis in which buffers around mist‐net lines ranged from 50 to 2,000 m. We applied four tests to examine whether the species richness on forest islands is predominantly driven by either an island effect (island size) or a sample area effect (habitat amount).
Results
From the four tests applied, one was consistent with an island effect, two were regarded as inappropriate to test the HAH, and one could not be adequately addressed due to island size being highly correlated with habitat amount in the local landscape (200‐m buffer).
Main conclusions
Some of the proposed ways of testing the HAH may lead to misleading conclusions. The relative importance of island size in determining the species richness of understorey insectivorous birds on forest islands is higher than that of surrounding habitat amount, thereby providing stronger support for IBT. We propose a conceptual framework, based on the degree of matrix permeability and species dispersal ability, to determine to what extent a patch‐ or landscape‐centric worldview in landscape ecology provides the most appropriate framework to assess the effects of habitat fragmentation on biodiversity.
Conservation practitioners have long recognized ecological connectivity as a global priority for preserving biodiversity and ecosystem function. In the early years of conservation science, ecologists ...extended principles of island biogeography to assess connectivity based on source patch proximity and other metrics derived from binary maps of habitat. From 2006 to 2008, the late Brad McRae introduced circuit theory as an alternative approach to model gene flow and the dispersal or movement routes of organisms. He posited concepts and metrics from electrical circuit theory as a robust way to quantify movement across multiple possible paths in a landscape, not just a single least‐cost path or corridor. Circuit theory offers many theoretical, conceptual, and practical linkages to conservation science. We reviewed 459 recent studies citing circuit theory or the open‐source software Circuitscape. We focused on applications of circuit theory to the science and practice of connectivity conservation, including topics in landscape and population genetics, movement and dispersal paths of organisms, anthropogenic barriers to connectivity, fire behavior, water flow, and ecosystem services. Circuit theory is likely to have an effect on conservation science and practitioners through improved insights into landscape dynamics, animal movement, and habitat‐use studies and through the development of new software tools for data analysis and visualization. The influence of circuit theory on conservation comes from the theoretical basis and elegance of the approach and the powerful collaborations and active user community that have emerged. Circuit theory provides a springboard for ecological understanding and will remain an important conservation tool for researchers and practitioners around the globe.
Aplicaciones de la Teoría de Circuitos a la Conservación y a la Ciencia de la Conectividad
Resumen
Quienes practican la conservación han reconocido durante mucho tiempo que la conectividad ecológica es una prioridad mundial para la preservación de la biodiversidad y el funcionamiento del ecosistema. Durante los primeros años de la ciencia de la conservación los ecólogos difundieron los principios de la biografía de islas para evaluar la conectividad con base en la proximidad entre el origen y el fragmento, así como otras medidas derivadas de los mapas binarios de los hábitats. Entre 2006 y 2008 el fallecido Brad McRae introdujo la teoría de circuitos como una estrategia alternativa para modelar el flujo génico y la dispersión o las rutas de movimiento de los organismos. McRae propuso conceptos y medidas de la teoría de circuitos eléctricos como una manera robusta para cuantificar el movimiento a lo largo de múltiples caminos posibles en un paisaje, no solamente a lo largo de un camino o corredor de menor costo. La teoría de circuitos ofrece muchos enlaces teóricos, conceptuales y prácticos con la ciencia de la conservación. Revisamos 459 estudios recientes que citan la teoría de circuitos o el software de fuente abierta Circuitscape. Nos enfocamos en las aplicaciones de la teoría de circuitos a la ciencia y a la práctica de la conservación de la conectividad, incluyendo temas como la genética poblacional y del paisaje, movimiento y caminos de dispersión de los organismos, barreras antropogénicas de la conectividad, comportamiento ante incendios, flujo del agua, y servicios ambientales. La teoría de circuitos probablemente tenga un efecto sobre la ciencia de la conservación y quienes la practican por medio de una percepción mejorada de las dinámicas del paisaje, el movimiento animal, y los estudios de uso de hábitat, y por medio del desarrollo de nuevas herramientas de software para el análisis de datos y su visualización. La influencia de la teoría de circuitos sobre la conservación viene de la base teórica y la elegancia de la estrategia y de las colaboraciones fuertes y la comunidad activa de usuarios que han surgido recientemente. La teoría de circuitos proporciona un trampolín para el entendimiento ecológico y seguirá siendo una importante herramienta de conservación para los investigadores y practicantes en todo el mundo.
摘要
保护实践者长期以来一直将生态连接度视为保护生物多样性和生态系统功能的当务之急。在保护科学发展早期, 生态学家将岛屿生物地理学的原理进行扩展, 基于源斑块邻近度和其它来自二元生境图的指标来评估连接度。2006 年到2008 年, 已故的Brad McRae 引入了电路理论, 作为模拟基因流和生物体扩散或移动路径的新方法。他用电路理论中的概念和指标开发了一种稳健的方法来量化景观中多种可能的移动路径, 而这不只是一条最低成本的路径或廊道。电路理论为保护科学提供了许多理论、概念和实践方面的联系。我们综述了近期引用电路理论或是开源软件Circuitscape的459 项研究, 重点关注电路理论在连接度保护科学与实践中的应用, 包括景观和种群遗传学、生物体运动和扩散路径、连接度的人为障碍、火灾、水流和生态系统服务等问题。电路理论通过帮助理解景观动力学、动物移动和生境利用研究, 以及开发新的数据分析和可视化软件工具, 影响着保护科学和实践者。电路理论对保护的影响来自于该方法的理论基础和优雅性, 以及现已出现的强大的合作队伍和活跃的用户群体。电路理论为生态学理解提供了跳板, 并将继续作为全球研究人员和实践者的重要保护工具。翻译: 胡怡思; 审校: 聂永刚
Article impact statement: Uses of circuit theory to understand connectivity have had a durable and global impact on conservation science and practice.
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