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1. Reproductive isolation and environmental adaptation shape the phylogeography of mountain pine beetle ( Dendroctonus ponderosae )

   https://doi.org/10.1111/mec.14342  

   Dowle, Eddy J. ; Bracewell, Ryan R. ; Pfrender, Michael E. ; Mock, Karen E. ; Bentz, Barbara J. ; Ragland, Gregory J. ( November 2017 , Molecular Ecology)

   Chromosomal rearrangement can be an important mechanism driving population differentiation and incipient speciation. In the mountain pine beetle (MPB,Dendroctonus ponderosae), deletions on the Y chromosome that are polymorphic among populations are associated with reproductive incompatibility. Here, we usedRADsequencing across the entireMPBrange in western North America to reveal the extent of the phylogeographic differences between Y haplotypes compared to autosomal and X‐linked loci. Clustering and geneflow analyses revealed three distinct Y haplogroups geographically positioned within and on either side of the Great Basin Desert. Despite close geographic proximity between populations on the boundaries of each Y haplogroup, there was extremely low Y haplogroup mixing among populations, and gene flow on the autosomes was reduced across Y haplogroup boundaries. These results are consistent with a previous study suggesting that independent degradation of a recently evolved neo‐Y chromosome in previously isolated populations causes male sterility or inviability among Y haplotype lineages. Phylogeographic results supported historic contraction ofMPBinto three separate Pleistocene glacial refugia followed by postglacial range expansion and secondary contact. Distinct sets ofSNPs were statistically associated with environmental data among the most genetically distinct sets of geographic populations. This finding suggests that the process of adaptation to local climatic conditions is influenced by population genetic structure, with evidence for largely independent evolution in the most genetically isolated Y haplogroup.

    

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2. Amphibian‐killing chytrid in B razil comprises both locally endemic and globally expanding populations

   https://doi.org/10.1111/mec.13599  

   Jenkinson, T. S. ; Betancourt Román, C. M. ; Lambertini, C. ; Valencia‐Aguilar, A. ; Rodriguez, D. ; Nunes‐de‐Almeida, C. H. L. ; Ruggeri, J. ; Belasen, A. M. ; da Silva Leite, D. ; Zamudio, K. R. ; et al ( March 2016 , Molecular Ecology)

   Chytridiomycosis, caused by the fungusBatrachochytrium dendrobatidis(Bd), is the emerging infectious disease implicated in recent population declines and extinctions of amphibian species worldwide.Bdstrains from regions of disease‐associated amphibian decline to date have all belonged to a single, hypervirulent clonal genotype (Bd‐GPL). However, earlier studies in the Atlantic Forest of southeastern Brazil detected a novel, putatively enzootic lineage (Bd‐Brazil), and indicated hybridization betweenBd‐GPLandBd‐Brazil. Here, we characterize the spatial distribution and population history of these sympatric lineages in the Brazilian Atlantic Forest. To investigate the genetic structure ofBdin this region, we collected and genotypedBdstrains along a 2400‐km transect of the Atlantic Forest.Bd‐Brazil genotypes were restricted to a narrow geographic range in the southern Atlantic Forest, whileBd‐GPLstrains were widespread and largely geographically unstructured.Bdpopulation genetics in this region support the hypothesis that the recently discovered Brazilian lineage is enzootic in the Atlantic Forest of Brazil and thatBd‐GPLis a more recently expanded invasive. We collected additional hybrid isolates that demonstrate the recurrence of hybridization between panzootic and enzootic lineages, thereby confirming the existence of a hybrid zone in the Serra da Graciosa mountain range of Paraná State. Our field observations suggest thatBd‐GPLmay be more infective towards native Brazilian amphibians, and potentially more effective at dispersing across a fragmented landscape. We also provide further evidence of pathogen translocations mediated by the Brazilian ranaculture industry with implications for regulations and policies on global amphibian trade.

    

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3. 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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4. Africanization of a feral honey bee ( Apis mellifera ) population in S outh T exas: does a decade make a difference?

   https://doi.org/10.1002/ece3.1974  

   Rangel, Juliana ; Giresi, Melissa ; Pinto, Maria Alice ; Baum, Kristen A. ; Rubink, William L. ; Coulson, Robert N. ; Johnston, John Spencer ( March 2016 , Ecology and Evolution)

   The arrival to theUnitedStates of theAfricanized honey bee, a hybrid betweenEuropean subspecies and theAfrican subspeciesApis mellifera scutellata, is a remarkable model for the study of biological invasions. This immigration has created an opportunity to study the dynamics of secondary contact of honey bee subspecies fromAfrican andEuropean lineages in a feral population inSouthTexas. An 11‐year survey of this population (1991–2001) showed that mitochondrial haplotype frequencies changed drastically over time from a resident population of eastern and western European maternal ancestry, to a population dominated by theAfrican haplotype. A subsequent study of the nuclear genome showed that theAfricanization process included bidirectional gene flow between European and Africanized honey bees, giving rise to a new panmictic mixture ofA. m. scutellata‐and European‐derived genes. In this study, we examined gene flow patterns in the same population 23 years after the first hybridization event occurred. We found 28 active colonies inhabiting 92 tree cavities surveyed in a 5.14 km²area, resulting in a colony density of 5.4 colonies/km². Of these 28 colonies, 25 were ofA. m. scutellatamaternal ancestry, and three were of western European maternal ancestry. No colonies of eastern European maternal ancestry were detected, although they were present in the earlier samples. NuclearDNArevealed little change in the introgression ofA. m. scutellata‐derived genes into the population compared to previous surveys. Our results suggest this feral population remains an admixed swarm with continued low levels of European ancestry and a greater presence of African‐derived mitochondrial genetic composition.

    

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5. Phylogeography of the widespread creek chub Semotilus atromaculatus (Cypriniformes: Leuciscidae)

   https://doi.org/10.1111/jfb.13778  

   Schönhuth, Susana ; Gagne, Roderick B. ; Alda, Fernando ; Neely, David A. ; Mayden, Richard L. ; Blum, Michael J. ( November 2018 , Journal of Fish Biology)

   The extent and nature of genetic differentiation inSemotilus atromaculatus, one of the most abundant and widespread leuciscids in North America, were evaluated based on mitochondrial (mt) and nuclear DNA sequence variation. Phylogenetic relationships were first inferred based on a fragment of the cytochrome b (cytb) region and the nuclear introns7gene forS. atromaculatusand all other congeners as well as representative species from all other genera in the creek chub–plagopterin clade. The phylogeography of major haplogroups ofS. atromaculatuswas also assessed according to variation in a fragment of the mitochondrialcytbregion from 567 individuals across its range. All analyses identifiedS. thoreauianus,S. lumbeeandS. corporalisas reciprocally monophyletic groups. Analyses of nuclear sequence variation resolvedS. atromaculatusas a single clade, whereS. thoreauianusandS. lumbeewere recovered as the sister group toS. atromaculatus, andS. corporaliswas resolved as sister to all other species in the genus. Analyses of mtDNA sequence variation recoveredS. atromaculatusas three well supported and differentiated monophyletic groups, with a widespread genetically homogeneous lineage extending across most of the current range of the species; a more geographically restricted and geographically structured lineage in the southern Appalachians, sister group toS. lumbee; and a geographically restricted lineage was identified from two Gulf Slope basins. Evidence of complex mito‐nuclear discordance and phylogeographic differentiation withinS. atromaculatusillustrates that further analysis of widespread species is warranted to understand North American freshwater fish diversity and distributions.

    

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