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Results for “Ecology, Evolution, and Systematics”

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Concurrent speciation in the eastern woodland salamanders (Genus Plethodon):DNA sequences of the complete albumin nuclear and partialmitochondrial 12s genes

Salamanders of the North American plethodontid genus Plethodon are important model organisms in a variety of studies that depend on a phylogenetic framework (e.g., chemical communication, ecological competition, life histories, hybridization, and speciation), and consequently their systematics has been intensively investigated over several decades. Nevertheless, we lack a synthesis of relationships among the species. In the analyses reported here we use new DNA sequence data from the complete nuclear albumin gene (1818 bp) and the 12s mitochondrial gene (355 bp), as well as published data for four other genes (Wiens et al., 2006), up to a total of 6989 bp, to infer relationships. We relate these results to past systematic work based on morphology, allozymes, and DNA sequences. Although basal relationships show a strong consensus across studies, many terminal relationships remain in flux despite substantial sequencing and other molecular and morphological studies. This systematic instability appears to be a consequence of contemporaneous bursts of speciation in the late Miocene and Pliocene, yielding many closely related extant species in each of the four eastern species groups. Therefore we conclude that many relationships are likely to remain poorly resolved in the face of additional sequencing efforts. On the other hand, the current classification of the 45 eastern species into four species groups is supported. The Plethodon cinereus group (10 species) is the sister group to the clade comprising the other three groups, but these latter groups (Plethodon glutinosus [28 species], Plethodon welleri [5 species], and Plethodon wehrlei [2 species]) probably diverged from each other at approximately the same time.

Molecular Phylogenetics and Evolution↗

A roadmap for sampling and scaling biological nitrogen fixation in terrestrial ecosystems

Accurately quantifying rates and patterns of biological nitrogen fixation (BNF) in terrestrial ecosystems is essential to characterize ecological and biogeochemical interactions, identify mechanistic controls, improve BNF representation in conceptual and numerical modelling, and forecast nitrogen limitation constraints on future carbon (C) cycling. While many resources address the technical advantages and limitations of different methods for measuring BNF, less systematic consideration has been given to the broader decisions involved in planning studies, interpreting data, and extrapolating results. Here, we present a conceptual and practical road map to study design, study execution, data analysis and scaling, outlining key considerations at each step. We address issues including defining N‐fixing niches of interest, identifying important sources of temporal and spatial heterogeneity, designing a sampling scheme (including method selection, measurement conditions, replication, and consideration of hotspots and hot moments), and approaches to analysing, scaling and reporting BNF. We also review the comparability of estimates derived using different approaches in the literature, and provide sample R code for simulating symbiotic BNF data frames and upscaling. Improving and standardizing study design at each of these stages will improve the accuracy and interpretability of data, define limits of extrapolation, and facilitate broader use of BNF data for downstream applications. We highlight aspects—such as quantifying scales of heterogeneity, statistical approaches for dealing with non‐normality, and consideration of rates versus ecological significance—that are ripe for further development.

Methods in Ecology and Evolution↗

A systematic review of avian influenza virus transmission models: Gaps and opportunities

Highly pathogenic avian influenza virus (HPAIV) increasingly threatens wild birds, poultry, non-human mammals and humans, yet gaps and opportunities in avian influenza virus (AIV) transmission modelling have not been comprehensively synthesized. We reviewed 182 articles published through 2025, categorized dimensions, including modelling approaches, data, host types, biological levels, spatial scales, temporal scales and model objectives, examined associations among these dimensions, and synthesized author-stated limitations and recommendations. Statistical and mechanistic models dominated. Model data centred on population dynamics and demography, disease surveillance, host epidemiology and competence, meteorology and land use and land cover. Most studies focused on poultry or wild birds at regional spatial scales, seasonal/annual and multi-year temporal scales, population or multi-population levels, and were retrospective. Machine learning and decision- making models were less common. Immunity, behaviour and life history, community composition, morphology, viral genetics and viral persistence received less attention. Non-human mammals, individual and community biological levels, local and broader spatial scales, daily temporal scales and prospective modelling were also less frequently modelled. The authors frequently reported limitations related to data availability, surveillance sampling and reporting bias, and model simplification, while commonly recommending improved data quality and greater model complexity and realism.

Methods in Ecology and Evolution↗

Developing a temporal database of urban development for the Baltimore/Washington region

The U.S. Geological Survey (USGS), the University of Maryland Baltimore County (UMBC), and the U.S. Bureau of the Census are working together as a multiagency, multidisciplinary team in developing a temporal database that documents the growth of the Baltimore-Washington metropolitan region. This database consists of urban development, principal transportation, shoreline, and population density change. The urban development theme, considered a primary data layer in the study of urban land transformation resulting from human impact on the land, is the focus of this paper. The Baltimore-Washington Spatial Dynamics and Human Impacts Study builds on earlier research efforts that mapped urban land use change for the San Francisco Bay area (Acevedo and Bell, 1994; Bell and others, 1995; Kirtland and others, 1994). In developing a temporal database (Acevedo and others, in press), the team participants hope to provide data that can be used to study patterns of urban growth; assess ecological, environmental, and climatic impacts of urban change; and model and predict future urbanization patterns and impacts (Clarke and others, 1996). Both the San Francisco and Baltimore-Washington regions were selected because of the rapid urban growth and resulting impacts on their ecosystems. The Chesapeake Bay region in particular has undergone extensive environmental agitation due to the hydrologic problems that have arisen from the increase in impermeable surfaces and structures, that is buildings and pavement that physically cover the soil. Because of the inability of water to percolate into the ground, little purification occurs by filtration. Water runs over paved surfaces and quickly washes high levels of toxins directly into the water system. Toxins like gasoline, oil, and fertilizer have dramatically affected the local streams, rivers, and the bay. ABSTRACT The U.S. Geological Survey, the University of Maryland Baltimore County, and the U.S. Bureau of the Census are developing a temporal database to study urban development in the Baltimore-Washington region. The primary data layer, the extent of urban or built-up areas, was compiled using a geographic information system and historical maps, remotely sensed data, digital land use data, and census information from a variety of sources. Urban land use change has been documented by the Baltimore-Washington Spatial Dynamics & Human Impact Study Team for the last 200 years. The methods, definitions, and collection criteria used to define urban or built-up areas were developed by a multi-disciplinary team that also ensures consistency in collection techniques and documentation methods for subsequent application in other regions. Animation techniques were used to visualize the database and to document the evolution of the region's urban landscape. The database is an important tool to urban and regional planners, ecologists, and global change researchers for measuring trends in urban sprawl, analyzing patterns of water pollution, understanding the impacts of development on ecosystems, and developing predictive modeling techniques to better forecast areas of urban growth. This paper describes the techniques used to map the extent of urban areas for Phase I and does not discuss Phase II in detail because the work is still in progress. In this study, urban development is defined as areas of intensive use, with much of the land covered by structures. The built-up areas are characterized by the existence of a systematic street pattern, and the relative concentration of buildings and associated intensive use areas, such as parking lots. Using this definition, urban development does not refer to political boundaries and may include incorporated or unincorporated areas as well as military reservations. ABSTRACT The U.S. Geological Survey, the University of Maryland Baltimore County, and the U.S. Bureau of the Census are developing a temporal database to study urban development in the Baltimore-Washington region. The primary data layer, the extent of urban or built-up areas, was compiled using a geographic information system and historical maps, remotely sensed data, digital land use data, and census information from a variety of sources. Urban land use change has been documented by the Baltimore-Washington Spatial Dynamics & Human Impact Study Team for the last 200 years. The methods, definitions, and collection criteria used to define urban or built-up areas were developed by a multi-disciplinary team that also ensures consistency in collection techniques and documentation methods for subsequent application in other regions. Animation techniques were used to visualize the database and to document the evolution of the region's urban landscape. The database is an important tool to urban and regional planners, ecologists, and global change researchers for measuring trends in urban sprawl, analyzing patterns of water pollution, understanding the impacts of development on ecosystems, and developing predictive modeling techniques to better forecast areas of urban growth. To build the urban component of the temporal database, a multidisciplinary team was assembled and a phased approach initiated. Expanding on procedures developed for the San Francisco Regional Study (Bell and others, 1995), the team developed data definitions, a classification scheme, compilation criteria, mapping specifications, guidelines for source materials, and metadata specifications to support development of a logically consistent dataset. Extensive documentation procedures were established to ensure consistency in data collection, and for subsequent application to other regions. Phase II was the implementation of the regional mapping effort. ABSTRACT The U.S. Geological Survey, the University of Maryland Baltimore County, and the U.S. Bureau of the Census are developing a temporal database to study urban development in the Baltimore-Washington region. The primary data layer, the extent of urban or built-up areas, was compiled using a geographic information system and historical maps, remotely sensed data, digital land use data, and census information from a variety of sources. Urban land use change has been documented by the Baltimore-Washington Spatial Dynamics & Human Impact Study Team for the last 200 years. The methods, definitions, and collection criteria used to define urban or built-up areas were developed by a multi-disciplinary team that also ensures consistency in collection techniques and documentation methods for subsequent application in other regions. Animation techniques were used to visualize the database and to document the evolution of the region's urban landscape. The database is an important tool to urban and regional planners, ecologists, and global change researchers for measuring trends in urban sprawl, analyzing patterns of water pollution, understanding the impacts of development on ecosystems, and developing predictive modeling techniques to better forecast areas of urban growth. The study area for Phase I consisted of an approximate area of 15- by 15-minute segment centered around the city of Baltimore (fig. 1). Phase I was used as a prototype for the technique development and integration that the multiagency collaborative effort would require. The regional study, Phase II, encompassed a 2-degree square centered on Washington, D.C. With more than 7 million people spread across 39 counties, the Baltimore-Washington region is one the Nation's fastest growing metropolitan areas. The two cities are rapidly merging into one.

Maryland↗