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1. North-East Pacific: Interactions on intertidal hard substrata and alteration by human impacts

   https://doi.org/10.1017/9781108235792.011  

   Fenberg, P. ; Menge, B.a. ( January 2019 , Interactions in the Marine Benthos: Global Patterns and Processes)

   The flora and fauna of the rocky intertidal zone are among the most biologically diverse on the planet – not in terms of species richness, but of the diversity and density of higher taxonomic categories. All of the major animal phyla can be found in the rocky intertidal, sometimes with representatives of each inhabiting a single rock or boulder. In addition to this phylogenetic diversity, the rocky intertidal may be one of the most ancient of habitats because it is a necessary and continual result of celestial mechanics set in motion prior to the diversification of life. When advising readers to ‘. . . look from the tide pool to the stars and then back to the tide pool again’, Steinbeck and Ricketts (1951) seemed to underline this point while advocating for a holistic approach to ecological research. A few years earlier, Ricketts and Calvin set out to comprehensively document what was then known about the ecology of the north-eastern Pacific (NEP) rocky intertidal in their classic book, Between Pacific Tides (Ricketts et al., 1985). Since the first edition of Between Pacific Tides (1939), the NEP has become widely recognised as an ideal natural laboratory for experimental ecologists and as a platform for more observationally focussed ecologists seeking to understand macroecological and biogeographical patterns. It is, of course, outside the scope of this chapter to attempt a comprehensive review of this extensive research. Rather, we focus on a couple of broad topics that are central to our current understanding of fundamental ecological, evolutionary and conservation topics that have benefitted from NEP rocky intertidal case studies. The first half of the chapter deals with recent work on the biotic and abiotic factors influencing patterns of range wide abundance and distribution of species, and how such patterns are being affected by human impacts. The second half reviews the latest research on the role of direct and indirect human impacts on topdown and bottom-up control of rocky intertidal community structure and functioning. 

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2. Linking Biodiversity Data Using Evolutionary History

   https://doi.org/10.3897/biss.3.36207  

   McTavish, Emily Jane ( June 2019 , Biodiversity Information Science and Standards)

   All life on earth is linked by a shared evolutionary history. Even before Darwin developed the theory of evolution, Linnaeus categorized types of organisms based on their shared traits. We now know these traits derived from these species’ shared ancestry. This evolutionary history provides a natural framework to harness the enormous quantities of biological data being generated today. The Open Tree of Life project is a collaboration developing tools to curate and share evolutionary estimates (phylogenies) covering the entire tree of life (Hinchliff et al. 2015, McTavish et al. 2017). The tree is viewable at https://tree.opentreeoflife.org, and the data is all freely available online. The taxon identifiers used in the Open Tree unified taxonomy (Rees and Cranston 2017) are mapped to identifiers across biological informatics databases, including the Global Biodiversity Information Facility (GBIF), NCBI, and others. Linking these identifiers allows researchers to easily unify data from across these different resources (Fig. 1). Leveraging a unified evolutionary framework across the diversity of life provides new avenues for integrative wide scale research. Downstream tools, such as R packages developed by the R OpenSci foundation (rotl, rgbif) (Michonneau et al. 2016, Chamberlain 2017) and others tools (Revell 2012), make accessing and combining this information straightforward for students as well as researchers (e.g. https://mctavishlab.github.io/BIO144/labs/rotl-rgbif.html). Figure 1. Example linking phylogenetic relationships accessed from the Open Tree of Life with specimen location data from Global Biodiversity Information Facility. For example, a recent publication by Santorelli et al. 2018 linked evolutionary information from Open Tree with species locality data gathered from a local field study as well as GBIF species location records to test a river-barrier hypothesis in the Amazon. By combining these data, the authors were able test a widely held biogeographic hypothesis across 1952 species in 14 taxonomic groups, and found that a river that had been postulated to drive endemism, was in fact not a barrier to gene flow. However, data provenance and taxonomic name reconciliation remain key hurdles to applying data from these large digital biodiversity and evolution community resources to answering biological questions. In the Amazonian river analysis, while they leveraged use of GBIF records as a secondary check on their species records, they relied on their an intensive local field study for their major conclusions, and preferred taxon specific phylogenetic resources over Open Tree where they were available (Santorelli et al. 2018). When Li et al. 2018 assessed large scale phylogenetic approaches, including Open Tree, for measuring community diversity, they found that synthesis phylogenies were less resolved than purpose-built phylogenies, but also found that these synthetic phylogenies were sufficient for community level phylogenetic diversity analyses. Nonetheless, data quality concerns have limited adoption of analyses data from centralized resources (McTavish et al. 2017). Taxonomic name recognition and reconciliation across databases also remains a hurdle for large scale analyses, despite several ongoing efforts to improve taxonomic interoperability and unify taxonomies, such at Catalogue of Life + (Bánki et al. 2018). In order to support innovative science, large scale digital data resources need to facilitate data linkage between resources, and address researchers' data quality and provenance concerns. I will present the model that the Open Tree of Life is using to provide evolutionary data at the scale of the entire tree of life, while maintaining traceable provenance to the publications and taxonomies these evolutionary relationships are inferred from. I will discuss the hurdles to adoption of these large scale resources by researchers, as well as the opportunities for new research avenues provided by the connections between evolutionary inferences and biodiversity digital databases. 

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3. Reproductive isolation is a heuristic, not a measure: a commentary on Westram et al., 2022

   https://doi.org/10.1111/jeb.14052  

   Mallet, James ; Mullen, Sean P. ( September 2022 , Journal of Evolutionary Biology)

   Abstract Reproductive isolation is the heuristic basis of the biological species concept, but what is it? Westram et al. (this issue) propose that it is a measurable quantity, “barrier strength,” that prevents gene flow among populations. However, their attempt to make the concept of reproductive isolation more scientific is unlikely to satisfy the diverse opinions of all evolutionary biologists. There are many different opinions about the nature of species, even under the biological species concept. Complete reproductive isolation, where gene flow is effectively zero, is regarded by some biologists as an important end point of speciation. Others, including Westram et al., argue for a more nuanced approach, and they also suggest that reproductive isolation may differ in different parts of the genome due to variation in genetic linkage to divergently selected loci. In contrast to both these approaches, we favour as a key criterion of speciation the stable coexistence of divergent populations in sympatry. Obviously, such populations must be reproductively isolated in some sense, but neither the fraction of the genome that is exchanged, nor measures of overall barrier strength acting on neutral variation will yield very precise predictions as to species status. Although an overall measure of reproductive isolation is virtually unattainable for these reasons, its early generation components, such as assortative mating, divergent selection, or hybrid inviability and sterility are readily measurable and remain informative. For example, we can make the prediction that to remain divergent in sympatry, almost all sexual species will require strong assortative mating, as well as some sort of ecological or intrinsic selection against hybrids and introgressed variants. 

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4. The phylogeny and systematics of Xiphosura

   https://doi.org/10.7717/peerj.10431  

   Lamsdell, James C. ( January 2020 , PeerJ)

   null (Ed.)

   Xiphosurans are aquatic chelicerates with a fossil record extending into the Early Ordovician and known from a total of 88 described species, four of which are extant. Known for their apparent morphological conservatism, for which they have gained notoriety as supposed ‘living fossils’, recent analyses have demonstrated xiphosurans to have an ecologically diverse evolutionary history, with several groups moving into non-marine environments and developing morphologies markedly different from those of the modern species. The combination of their long evolutionary and complex ecological history along with their paradoxical patterns of morphological stasis in some clades and experimentation among others has resulted in Xiphosura being of particular interest for macroevolutionary study. Phylogenetic analyses have shown the current taxonomic framework for Xiphosura—set out in the Treatise of Invertebrate Paleontology in 1955—to be outdated and in need of revision, with several common genera such as Paleolimulus Dunbar, 1923 and Limulitella Størmer, 1952 acting as wastebasket taxa. Here, an expanded xiphosuran phylogeny is presented, comprising 58 xiphosuran species as part of a 158 taxon chelicerate matrix coded for 259 characters. Analysing the matrix under both Bayesian inference and parsimony optimisation criteria retrieves a concordant tree topology that forms the basis of a genus-level systematic revision of xiphosuran taxonomy. The genera Euproops Meek, 1867, Belinurus König, 1820, Paleolimulus , Limulitella , and Limulus are demonstrated to be non-monophyletic and the previously synonymized genera Koenigiella Raymond, 1944 and Prestwichianella Cockerell, 1905 are shown to be valid. In addition, nine new genera ( Andersoniella gen. nov. , Macrobelinurus gen. nov. , and Parabelinurus gen. nov. in Belinurina; Norilimulus gen. nov. in Paleolimulidae; Batracholimulus gen. nov. and Boeotiaspis gen. nov. in Austrolimulidae; and Allolimulus gen. nov., Keuperlimulus gen. nov., and Volanalimulus gen. nov. in Limulidae) are erected to accommodate xiphosuran species not encompassed by existing genera. One new species, Volanalimulus madagascarensis gen. et sp. nov., is also described. Three putative xiphosuran genera— Elleria Raymond, 1944, Archeolimulus Chlupáč, 1963, and Drabovaspis Chlupáč, 1963—are determined to be non-xiphosuran arthropods and as such are removed from Xiphosura. The priority of Belinurus König, 1820 over Bellinurus Pictet, 1846 is also confirmed. This work is critical for facilitating the study of the xiphosuran fossil record and is the first step in resolving longstanding questions regarding the geographic distribution of the modern horseshoe crab species and whether they truly represent ‘living fossils’. Understanding the long evolutionary history of Xiphosura is vital for interpreting how the modern species may respond to environmental change and in guiding conservation efforts. 

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5. Geographic Variation in Salt Marsh Structure and Function for Nekton: a Guide to Finding Commonality Across Multiple Scales

   https://doi.org/10.1007/s12237-020-00894-y  

   Ziegler, Shelby L. ; Baker, Ronald ; Crosby, Sarah C. ; Colombano, Denise D. ; Barbeau, Myriam A. ; Cebrian, Just ; Connolly, Rod M. ; Deegan, Linda A. ; Gilby, Ben L. ; Mallick, Debbrota ; et al ( January 2021 , Estuaries and Coasts)

   null (Ed.)

   Coastal salt marshes are distributed widely across the globe and are considered essential habitat for many fish and crustacean species. Yet, the literature on fishery support by salt marshes has largely been based on a few geographically distinct model systems, and as a result, inadequately captures the hierarchical nature of salt marsh pattern, process, and variation across space and time. A better understanding of geographic variation and drivers of commonalities and differences across salt marsh systems is essential to informing future management practices. Here, we address the key drivers of geographic variation in salt marshes: hydroperiod, seascape configuration, geomorphology, climatic region, sediment supply and riverine input, salinity, vegetation composition, and human activities. Future efforts to manage, conserve, and restore these habitats will require consideration of how environmental drivers within marshes affect the overall structure and subsequent function for fisheries species. We propose a future research agenda that provides both the consistent collection and reporting of sources of variation in small-scale studies and collaborative networks running parallel studies across large scales and geographically distinct locations to provide analogous information for data poor locations. These comparisons are needed to identify and prioritize restoration or conservation efforts, identify sources of variation among regions, and best manage fisheries and food resources across the globe. Introduction Understanding the drivers of geographic variation in the condition and composition of habitats is crucial to our capacity to generalize management plans across space and time and to clarify and perhaps challenge assumptions of functional equivalence among sites. Broadly defined wetland types such as salt marshes are often assumed to provide similar functions throughout their global range, such as providing nursery habitat for fishery species. However, a growing body of evidence suggests substantial geographic variation in the functioning of salt marsh and other coastal ecosystems (Bradley et al. 2020; Whalen et al. 2020). Variation in ecological patterns and processes within habitat types can alter community structure and dynamics. Local-scale patterns and processes (e.g., patch [10s of meters], local [100s of meters]) can be influenced by processes that occur at larger spatial scales (e.g., regional [kms], global), thereby causing geographic differences in the function and ecosystem service delivery of a given habitat type. Salt marshes (which include vegetated platform, interconnected tidal creeks, fringing mudflats, ponds, and pools) are widely distributed (Fig. 1) and function as valuable nursery habitats by providing key resources for many estuarine species that transition to marine or aquatic habitats as adults (Beck et al. 2001; Minello et al. 2003; Sheaves et al. 2015). However, factors that underlie variability in the delivery of ecological functions are still inadequately understood. Previous studies have explored geographic variation in the function of salt marshes for fish and mobile crustaceans (“nekton”; e.g., Minello et al. 2012, Baker et al. 2013). However, field studies that compare multiple sites across a geographical gradient are typically limited in duration and scale. In addition, the explanatory variables (e.g., elevation, flooding duration, plant structure) collected by smaller scale studies are often inconsistent and therefore limit generalizations across sites. 

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