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1. Bayesian analyses detect a history of both vicariance and geodispersal in Neotropical freshwater fishes

   https://doi.org/10.1111/jbi.13207  

   Machado, Carolina Barros ; Galetti, Jr, Pedro Manoel ; Carnaval, Ana Carolina ( March 2018 , Journal of Biogeography)

   Among the main biogeographical hypotheses explaining the remarkable diversity of fishes in the Neotropics is the “palaeogeographical hypothesis”, focusing on vicariance, and the “hydrogeological hypothesis”, focusing on geodispersal. Yet while reflecting different processes, they may result in similar biogeographical patterns. We employed a model‐based Bayesian approach to test these alternative hypotheses and determine which shaped the phylogeographical patterns observed in a group of Neotropical fishes.

   South America.

   Salminus.

   We used mitochondrial and nuclear markers to infer phylogenetic relationships and estimate divergence times amongSalminusspecies, associating the results with known geological events. We then employed approximate Bayesian computation (ABC) to explore changes in population size over time, asking whether vicariance or geodispersal events best explain the phylogeographical signature observed in the data. Because geodispersal captures a few individuals from a parental population, which can then expand and lead to a new lineage, we expect to find genetic signatures of a founder event following population expansion under this scenario, but not under vicariance.

   The analyses suggest that the diversification process inSalminusbegan in Upper Miocene, andABCindicates that it involved both vicariance and geodispersal events: while a vicariance event better explains the phylogeographical structure withinS. brasiliensisand the genetic patterns of differentiation betweenS. sp. Amazon andS. sp. Araguaia, geodispersal appears to have been the most important event structuring lineages ofSalminus hilarii.

   Both vicariance and geodispersal signatures were detected in our biological model, inferring a complex yet realistic demographic history ofSalminuslineages. The correspondence between theABCresults and traditional phylogeographical interpretations provide further confidence in the models drawn and tested. This study reinforces the value of applying anABCframework in phylogeographical studies, particularly for those interested in testing alternative and biologically plausible processes underlying similar biogeographical patterns.

    

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2. Neutral processes and species sorting in benthic microalgal community assembly: effects of tidal resuspension

   https://doi.org/10.1111/jpy.12445  

   Plante, Craig J. ; Fleer, Virginia ; Jones, Martin L. ; Mock, ed., T. ( August 2016 , Journal of Phycology)

   Benthic microalgae (BMA) provide vital food resources for heterotrophs and stabilize sediments with their extracellular secretions. A central goal in ecology is to understand how processes such as species interactions and dispersal, contribute to observed patterns of species abundance and distribution. Our objectives were to assess the effects of sediment resuspension on microalgal community structure. We tested whether taxa‐abundance distributions could be predicted using neutral community models (NCMs) and also specific hypotheses about passive migration: (i) As migration decreases in sediment patches,BMAα‐diversity will decrease, and (ii) As migration decreases,BMAcommunity dissimilarity (β‐diversity) will increase. Co‐occurrence indices (checkerboard score and variance ratio) were also computed to test for deterministic factors, such as competition and niche differentiation, in shaping communities. Two intertidal sites (mudflat and sand bar) differing in resuspension regime were sampled throughout the tidal cycle. Fluorometry and denaturing gradient gel electrophoresis were utilized to investigate diatom community structure. Observed taxa‐abundances fit those predicted fromNCMs reasonably well (R²of 0.68–0.93), although comparisons of observed local communities to artificial randomly assembled communities rejected the null hypothesis that diatom communities were assembled solely by stochastic processes. No co‐occurrence tests indicated a significant role for competitive exclusion or niche partitioning in microalgal community assembly. In general, predictions about relationships between migration and species diversity were supported for local community dynamics.BMAat low tide (lowest migration) exhibited reduced α‐diversity as compared to periods of immersion at both mudflat and sand bar sites. β‐diversity was higher during low tide emersion on the mudflat, but did not differ temporally at the sand bar site. In between‐site metacommunity comparisons, low‐ and high‐resuspension sites exhibited distinct community compositions while the low‐energy mudflats contained higher microalgal biomass and greater α‐diversity. To our knowledge this is the first study to test the relevance of neutral processes in structuring marine microalgal communities. Our results demonstrate a prominent role for stochastic factors in structuring localBMAcommunity assembly, although unidentified nonrandom processes also appear to play some role. High passive migration, in particular, appears to help maintain species diversity and structure communities in both sand and muddy habitats.

    

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3. A global analysis of bats using automated comparative phylogeography uncovers a surprising impact of Pleistocene glaciation

   https://doi.org/10.1111/jbi.13382  

   Carstens, Bryan C. ; Morales, Ariadna E. ; Field, Kathryn ; Pelletier, Tara A. ( June 2018 , Journal of Biogeography)

   Our work seeks to understand the global demographical response of bat species to the climate change that occurred at the Last Glacial Maximum (LGM).

   All continents except Antarctica.

   MitochondrialDNAsequences were sampled from bat species throughout the planet where we could associate a georeferenced sample with a givenDNAsequence. Our investigation estimates the historical demographical response using over 12,000 samples from >300 nominal species of bats. CustomPythonand R scripts were written to aggregate sequence data from GenBank, locality information fromGBIF, and to associate these records to individual samples. We conducted approximate Bayesian computation to calculate the posterior probability of demographical bottleneck and expansion responses to the end of the Pleistocene, and then collected organismal trait data to identify traits that were associated with either demographical response. We also used R to estimate current and end‐Pleistocene species distribution models (SDM) for species where >10 georeferenced samples were available.

   Analysis of the genetic data indicate that some temperate insectivores responded to the end of the Pleistocene by undergoing a demographical expansion. However, the neotropical family Phyllostomidae experienced the most dramatic response, with many of its species undergoing demographical bottlenecks. Larger bats, and those with shorter forewings, were more likely to undergo a demographical bottleneck. In contrast with the results of the genetic data analysis, the automated SDMs all predicted range expansion since the LGM.

   Historical populations of Neotropical bats that rely on Angiosperms for resources (i.e., pollen, nectar, fruit) were negatively influenced by the climate change that occurred at the end of the Pleistocene. Our work highlights the utility of incorporating exploratory trait‐based analyses in phylogeography. It serves as an example of automated big data phylogeography, and suggests that repurposed data can lead to new insights about global biodiversity.

    

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4. Testing Darwin's Naturalization Conundrum using phylogenetic relationships: Generalizable patterns across disparate communities?

   https://doi.org/10.1111/ddi.12861  

   Ng, Julienne ; Weaver, William N. ; Laport, Robert G. ; Holmgren, ed., Milena ( December 2018 , Diversity and Distributions)

   Alternative hypotheses of Darwin's Naturalization Conundrum (DNC) predict that the non‐native species that successfully establish within a community are those either more closely or more distantly related to the resident native species. Despite the increasing number of studies using phylogenetic data to testDNCand evaluate community assembly, it remains unknown whether phylogenetic relationships alone can be used to predict invasion susceptibility across communities differing environmentally and in disturbance history. In this study, we evaluate whether phylogenetic structure of diverse native communities predicts the occurrence of non‐native species and offers insight into community assembly.

   Eastern United States of America.

   We examine multiple communities across a north–south transect of the eastern United States to test whether non‐native species richness and abundance are associated with phylogenetic diversity measures of the native community. We also test whether non‐native species are consistently closely or distantly related to native species using two approaches differing in phylogenetic scale and whether this differs with ecologically successful species.

   Our analyses did not unambiguously resolveDNC. Non‐native species richness and abundance decreased with increasing native species phylogenetic diversity. Within some communities, non‐native species were significantly more closely related to native species than expected by chance, and tended to be more often closely related to a native species than that native species was to other native relatives. When considering species abundance, only one community showed that ecologically successful non‐native species were closely related to resident species.

   Phylogenetic relationships can reveal important details about community assembly in diverse ecological settings. However, given the multifaceted nature of community assembly, phylogenetic metrics alone have limited utility as a general predictive tool for community invasion. Our study highlights a need to incorporate additional types of data to better understand why some communities are more susceptible to non‐native species establishment.

    

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5. Late Pleistocene range expansion of North American topminnows accompanied by admixture and introgression

   https://doi.org/10.1111/jbi.13597  

   Duvernell, David D. ; Westhafer, Eric ; Schaefer, Jacob F. ( June 2019 , Journal of Biogeography)

   We used genome‐scale sampling to assess the phylogeography of a group of topminnows in theFundulus notatusspecies complex. Two of the species have undergone extensive range expansions resulting in broadly overlapping distributions, and sympatry within drainages has provided opportunities for hybridization and introgression. We assessed the timing and pattern of range expansion in the context of late Pleistocene–Holocene drainage events and evaluated the evidence for introgressive hybridization between species.

   Central and southern United States including drainages of the Gulf of Mexico Coastal Plain and portions of the Mississippi River drainage in and around the Central Highlands.

   Topminnows, GenusFundulus, subgenusZygonectes—Fundulus notatus, Fundulus olivaceus, Fundulus euryzonus.

   We sampled members of theF. notatusspecies complex throughout their respective ranges, including numerous drainage systems where species co‐occur. We collected genome‐wide single nucleotide polymorphisms (SNPs) using the genotype‐by‐sequencing (GBS) method and subjected data to population genetic analyses to infer the population histories of both species, including explicit tests for admixture and introgression. The methods employed includedSTRUCTURE, principal coordinates analysis, TreeMix and approximate Bayesian computation.

   Genetic data are presented for 749 individuals sampled from 14F. notatus, 20F. olivaceusand 2F. euryzonuspopulations. Members of the species complex differed in phylogeographic structure, withF. notatusexhibiting geographic clusters corresponding to Pleistocene coastal drainages andF. olivaceuscomparatively lacking in phylogeographic structure. Evidence for interspecific introgression varied by drainage.

   Populations ofF. notatusandF. olivaceusexhibited contrasting patterns of lineage diversity among coastal drainages, indicating interspecific differences in their Pleistocene southern refugia. Phylogeographic patterns in both species indicated that range expansions into the northern limits of contemporary distributions coincided with and continued subsequent to the Last Glacial Maximum. There was evidence of introgression between species in some, but not all drainages where the species co‐occur, in a pattern that is correlated with previous estimates of hybridization rates.

    

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