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1. Seagrass‐associated fungal communities follow Wallace's line, but host genotype does not structure fungal community

   https://doi.org/10.1111/jbi.13168  

   Wainwright, Benjamin J. ; Zahn, Geoffrey L. ; Arlyza, Irma S. ; Amend, Anthony S. ( February 2018 , Journal of Biogeography)

   To test whether or not fungal communities associated with the widespread seagrass,Syringodium isoetifoliumcan be differentiated on either side of Wallace's line, a boundary line separating Asian and Australasian fauna. Additionally, we examine whether host multilocus genotype predicts fungal community composition.

   A total of 77 samples were collected from 14 sampling sites spanning the Indonesian archipelago.

   We sequenced the fungalITS1 gene using Illumia MiSeq technology and used a clustering‐free Divisive Amplicon Denoising Algorithm to infer ribosomal sequence variants. Data were analysed via non‐metric multidimensional scaling, Mantel tests and permutational multivariate analysis of variance. Binary and quantitative null models were used to determine whether results significantly deviated from random. Host genotype was determined by genotyping at 18 microsatellite loci and standard genetic analysis was performed in the R packageAPE.

   Significant differences in fungal community composition were detected on either side of Wallace's line (p = <.001R² = .040). A significant distance decay of similarity pattern was observed between ribosomal sequence variants and geographical distance (p = .001R² = .227) and several fungal ribosomal sequence variants were significantly associated with sampling sites found either east or west of Wallace's line.

   Fungi are generally considered to have excellent dispersal potentials and marine fungi have the potential to disperse far and wide in an environment that has no obvious barriers to dispersal. Despite this assumed excellent dispersal potential, we show that fungal communities on either side of Wallace's line are significantly different from one another. We speculate that limited dispersal and differences in habitat type are responsible for the observed pattern. Work examining biogeographical patterns in marine fungi is still in its infancy and further research is required to fully understand marine fungal biogeography.

    

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2. Geographic cline analysis as a tool for studying genome‐wide variation: a case study of pollinator‐mediated divergence in a monkeyflower

   https://doi.org/10.1111/mec.13645  

   Stankowski, Sean ; Sobel, James M. ; Streisfeld, Matthew A. ( June 2016 , Molecular Ecology)

   A major goal of speciation research is to reveal the genomic signatures that accompany the speciation process. Genome scans are routinely used to explore genome‐wide variation and identify highly differentiated loci that may contribute to ecological divergence, but they do not incorporate spatial, phenotypic or environmental data that might enhance outlier detection. Geographic cline analysis provides a potential framework for integrating diverse forms of data in a spatially explicit framework, but has not been used to study genome‐wide patterns of divergence. Aided by a first‐draft genome assembly, we combined anF_CTscan and geographic cline analysis to characterize patterns of genome‐wide divergence between divergent pollination ecotypes ofMimulus aurantiacus.F_CTanalysis of 58 872SNPs generated viaRAD‐seq revealed little ecotypic differentiation (meanF_CT = 0.041), although a small number of loci were moderately‐to‐highly diverged. Consistent with our previous results from the geneMaMyb2, which contributes to differences in flower colour, 130 loci have cline shapes that recapitulate the spatial pattern of trait divergence, suggesting that they may reside in or near the genomic regions that contribute to pollinator isolation. In the narrow hybrid zone between the ecotypes, extensive admixture among individuals and low linkage disequilibrium between markers indicate that most outlier loci are scattered throughout the genome, rather than being restricted to one or a few divergent regions. In addition to revealing the genomic consequences of ecological divergence in this system, we discuss how geographic cline analysis is a powerful but under‐utilized framework for studying genome‐wide patterns of divergence.

    

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3. Distance, elevation and environment as drivers of diversity and divergence in bumble bees across latitude and altitude

   https://doi.org/10.1111/mec.14735  

   Jackson, Jason M. ; Pimsler, Meaghan L. ; Oyen, Kennan Jeannet ; Koch‐Uhuad, Jonathan B. ; Herndon, James D. ; Strange, James P. ; Dillon, Michael E. ; Lozier, Jeffrey D. ( June 2018 , Molecular Ecology)

   Identifying drivers of dispersal limitation and genetic differentiation is a key goal in biogeography. We examine patterns of population connectivity and genetic diversity using restriction site‐associatedDNAsequencing (RADseq) in two bumble bee species,Bombus vosnesenskiiandBombus bifarius,across latitude and altitude in mountain ranges from California, Oregon and Washington, U.S.A.Bombus vosnesenskii, which occurs across a broader elevational range at most latitudes, exhibits little population structure whileB. bifarius, which occupies a relatively narrow higher elevation niche across most latitudes, exhibits much stronger population differentiation, although gene flow in both species is best explained by isolation with environmental niche resistance. A relationship between elevational habitat breadth and genetic diversity is also apparent, withB. vosnesenskiiexhibiting relatively consistent levels of genetic diversity across its range, whileB. bifariushas reduced genetic diversity at low latitudes, where it is restricted to high‐elevation habitat. The results of this study highlight the importance of the intersect between elevational range and habitat suitability in influencing population connectivity and suggest that future climate warming will have a fragmenting effect even on populations that are presently well connected, as they track their thermal niches upward in montane systems.

    

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4. Population genomics of divergence among extreme and intermediate color forms in a polymorphic insect

   https://doi.org/10.1002/ece3.1928  

   Lozier, Jeffrey D. ; Jackson, Jason M. ; Dillon, Michael E. ; Strange, James P. ( January 2016 , Ecology and Evolution)

   Geographic variation in insect coloration is among the most intriguing examples of rapid phenotypic evolution and provides opportunities to study mechanisms of phenotypic change and diversification in closely related lineages. The bumble beeBombus bifariuscomprises two geographically disparate color groups characterized by red‐banded and black‐banded abdominal pigmentation, but with a range of spatially and phenotypically intermediate populations across western North America. Microsatellite analyses have revealed thatB. bifariusin the USA are structured into two major groups concordant with geography and color pattern, but also suggest ongoing gene flow among regional populations. In this study, we better resolve the relationships among major color groups to better understand evolutionary mechanisms promoting and maintaining such polymorphism. We analyze >90,000 and >25,000 single‐nucleotide polymorphisms derived from transcriptome (RNAseq) and double digest restriction site associatedDNAsequencing (ddRAD), respectively, in representative samples from spatial and color pattern extremes inB. bifariusas well as phenotypic and geographic intermediates. Both ddRADandRNAseq data illustrate substantial genome‐wide differentiation of the red‐banded (eastern) color form from both black‐banded (western) and intermediate (central) phenotypes and negligible differentiation among the latter populations, with no obvious admixture among bees from the two major lineages. Results thus indicate much stronger background differentiation amongB. bifariuslineages than expected, highlighting potential challenges for revealing loci underlying color polymorphism from population genetic data alone. These findings will have significance for resolving taxonomic confusion in this species and in future efforts to investigate color‐pattern evolution inB. bifariusand other polymorphic bumble bee species.

    

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5. Gene flow, divergent selection and resistance to introgression in two species of morning glories ( Ipomoea )

   https://doi.org/10.1111/mec.14945  

   Rifkin, Joanna L. ; Castillo, Allan S. ; Liao, Irene T. ; Rausher, Mark D. ( April 2019 , Molecular Ecology)

   Gene flow is thought to impede genetic divergence and speciation by homogenizing genomes. Recent theory and research suggest that sufficiently strong divergent selection can overpower gene flow, leading to loci that are highly differentiated compared to others. However, there are also alternative explanations for this pattern. Independent evidence that loci in highly differentiated regions are under divergent selection would allow these explanations to be distinguished, but such evidence is scarce. Here, we present multiple lines of evidence that many of the highly divergentSNPs in a pair of sister morning glory species,Ipomoea cordatotrilobaandI. lacunosa, are the result of divergent selection in the face of gene flow. We analysed aSNPdata set across the genome to assess the amount of gene flow, resistance to introgression and patterns of selection on loci resistant to introgression. We show that differentiation between the two species is much lower in sympatry than in allopatry, consistent with interspecific gene flow in sympatry. Gene flow appears to be substantially greater fromI. lacunosatoI. cordatotrilobathan in the reverse direction, resulting in sympatric and allopatricI. cordatotrilobabeing substantially more different than sympatric and allopatricI. lacunosa. ManySNPs highly differentiated in allopatry have experienced divergent selection, and, despite gene flow in sympatry, resist homogenization in sympatry. Finally, five out of eight floral and inflorescence characteristics measured exhibit asymmetric convergence in sympatry. Consistent with the pattern of gene flow,I. cordatotrilobatraits become much more like those ofI. lacunosathan the reverse. Our investigation reveals the complex interplay between selection and gene flow that can occur during the early stages of speciation.

    

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