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1. Identification and Expression Analyses of the Nitrate Transporter Gene ( NRT2 ) Family Among Skeletonema species (Bacillariophyceae)

   https://doi.org/10.1111/jpy.12896  

   Kang, Lee‐Kuo ; Rynearson, Tatiana A. ; Kroth, ed., P. ( August 2019 , Journal of Phycology)

   High‐affinity nitrate transporters are considered to be the major transporter system for nitrate uptake in diatoms. In the diatom genusSkeletonema, three forms of genes encoding high‐affinity nitrate transporters (NRT2) were newly identified from transcriptomes generated as part of the marine microbial eukaryote transcriptome sequencing project. To examine the expression of each form ofNRT2under different nitrogen environments, laboratory experiments were conducted under nitrate‐sufficient, ammonium‐sufficient, and nitrate‐limited conditions using three ecologically importantSkeletonemaspecies:S. dohrnii,S. menzelii,andS. marinoi. Primers were developed for eachNRT2form and species and Q‐RT‐PCRwas performed. For eachNRT2form, the threeSkeletonemaspecies had similar transcriptional patterns. The transcript levels ofNRT2:1were significantly elevated under nitrogen‐limited conditions, but strongly repressed in the presence of ammonium. The transcript levels ofNRT2:2were also repressed by ammonium, but increased 5‐ to 10‐fold under nitrate‐sufficient and nitrogen‐limited conditions. Finally, the transcript levels ofNRT2:3did not vary significantly under various nitrogen conditions, and behaved more like a constitutively expressed gene. Based on the observed transcript variation amongNRT2forms, we propose a revised model describing nitrate uptake kinetics regulated by multiple forms of nitrate transporter genes in response to various nitrogen conditions inSkeletonema. The differentialNRT2transcriptional responses among species suggest that species‐specific adaptive strategies exist within this genus to cope with environmental changes.

    

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2. Phylogenetic diversity in freshwater‐dwelling Isochrysidales haptophytes with implications for alkenone production

   https://doi.org/10.1111/gbi.12330  

   Richter, Nora ; Longo, William M. ; George, Sarabeth ; Shipunova, Anna ; Huang, Yongsong ; Amaral‐Zettler, Linda ( February 2019 , Geobiology)

   Members of the order Isochrysidales are unique among haptophyte lineages in being the exclusive producers of alkenones, long‐chain ketones that are commonly used for paleotemperature reconstructions. Alkenone‐producing haptophytes are divided into three major groups based largely on molecular ecological data: Group I is found in freshwater lakes, GroupIIcommonly occurs in brackish and coastal marine environments, and GroupIIIconsists of open ocean species. Each group has distinct alkenone distributions; however, only GroupsIIandIIIIsochrysidales currently have cultured representatives. The uncultured Group I Isochrysidales are distinguished geochemically by the presence of tri‐unsaturated alkenone isomers (C_37:3bMe, C_38:3bEt, C_38:3bMe, C_39:3bEt) present in water column and sediment samples, yet their genetic diversity, morphology, and environmental controls are largely unknown. Using small‐subunit (SSU) ribosomalRNA(rRNA) marker gene amplicon high‐throughput sequencing of environmental water column and sediment samples, we show that Group I is monophyletic with high phylogenetic diversity and contains a well‐supported clade separating the previously described “EV” clade from the “Greenland” clade. We infer the first partial large‐subunit (LSU)rRNAgene Group I sequence phylogeny, which uncovered additional well‐supported clades embedded within Group I. Relative to GroupII, Group I revealed higher levels of genetic diversity despite conservation of alkenone signatures and a closer evolutionary relationship with GroupIII. In Group I, the presence of the tri‐unsaturated alkenone isomers appears to be conserved, which is not the case for GroupII. This suggests differing environmental influences on Group I andIIand perhaps uncovers evolutionary constraints on alkenone biosynthesis.

    

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3. Phylogeographic patterns of a lower intertidal isopod in the Gulf of California and the Caribbean and comparison with other intertidal isopods

   https://doi.org/10.1002/ece3.2599  

   Hurtado, Luis A. ; Mateos, Mariana ; Liu, Shuang ( December 2016 , Ecology and Evolution)

   A growing body of knowledge on the diversity and evolution of intertidal isopods across different regions worldwide has enhanced our understanding on biological diversification at the poorly studied, yet vast, sea–land interface. High genetic divergences among numerous allopatric lineages have been identified within presumed single broadly distributed species.Excirolana mayanais an intertidal isopod that is commonly found in sandy beaches throughout the Gulf of California. Its distribution in the Pacific extends from this basin to Colombia and in the Atlantic from Florida to Venezuela. Despite its broad distribution and ecological importance, its evolutionary history has been largely neglected. Herein, we examined phylogeographic patterns ofE. mayanain the Gulf of California and the Caribbean, based on maximum‐likelihood and Bayesian phylogenetic analyses ofDNAsequences from four mitochondrial genes (16SrDNA, 12SrDNA, cytochrome oxidase I gene, and cytochrome b gene). We compared the phylogeographic patterns ofE. mayanawith those of the coastal isopodsLigiaandExcirolana braziliensis(Gulf of California and Caribbean) andTylos(Gulf of California). We found highly divergent lineages in both, the Gulf of California and Caribbean, suggesting the presence of multiple species. We identified two instances of Atlantic–Pacific divergences. Some geographical structuring among the major clades found in the Caribbean is observed. Haplotypes from the Gulf of California form a monophyletic group sister to a lineage found in Venezuela. Phylogeographic patterns ofE. mayanain the Gulf of California differ from those observed inLigiaandTylosin this region. Nonetheless, several clades ofE. mayanahave similar distributions to clades of these two other isopod taxa. The high levels of cryptic diversity detected inE. mayanaalso pose challenges for the conservation of this isopod and its fragile environment, the sandy shores.

    

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4. Mixed ancestry and admixture in Kauai's feral chickens: invasion of domestic genes into ancient Red Junglefowl reservoirs

   https://doi.org/10.1111/mec.13096  

   Gering, E. ; Johnsson, M. ; Willis, P. ; Getty, T. ; Wright, D. ( March 2015 , Molecular Ecology)

   A major goal of invasion genetics is to determine how establishment histories shape non‐native organisms' genotypes and phenotypes. While domesticated species commonly escape cultivation to invade feral habitats, few studies have examined how this process shapes feral gene pools and traits. We collected genomic and phenotypic data from feral chickens (Gallus gallus) on the Hawaiian island of Kauai to (i) ascertain their origins and (ii) measure standing variation in feral genomes, morphology and behaviour. Mitochondrial phylogenies (D‐loop & whole Mt genome) revealed two divergent clades within our samples. The rare clade also contains sequences from Red Junglefowl (the domestic chicken's progenitor) and ancientDNAsequences from Kauai that predate European contact. This lineage appears to have been dispersed into the east Pacific by ancient Polynesian colonists. The more prevalent MtDNAclade occurs worldwide and includes domesticated breeds developed recently in Europe that are farmed within Hawaii. We hypothesize this lineage originates from recently feralized livestock and found supporting evidence for increasedG. gallusdensity on Kauai within the last few decades.SNPs obtained from whole‐genome sequencing were consistent with historic admixture between Kauai's divergent(G. gallus)lineages. Additionally, analyses of plumage, skin colour and vocalizations revealed that Kauai birds' behaviours and morphologies overlap with those of domestic chickens and Red Junglefowl, suggesting hybrid origins. Together, our data support the hypotheses that (i) Kauai's feralG. gallusdescend from recent invasion(s) of domestic chickens into an ancient Red Junglefowl reservoir and (ii) feral chickens exhibit greater phenotypic diversity than candidate source populations. These findings complicate management objectives for Pacific feral chickens, while highlighting the potential of this and other feral systems for evolutionary studies of invasions.

    

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5. Genomic landscape of the global oak phylogeny

   https://doi.org/10.1111/nph.16162  

   Hipp, Andrew L. ; Manos, Paul S. ; Hahn, Marlene ; Avishai, Michael ; Bodénès, Cathérine ; Cavender‐Bares, Jeannine ; Crowl, Andrew A. ; Deng, Min ; Denk, Thomas ; Fitz‐Gibbon, Sorel ; et al ( October 2019 , New Phytologist)

   The tree of life is highly reticulate, with the history of population divergence emerging from populations of gene phylogenies that reflect histories of introgression, lineage sorting and divergence. In this study, we investigate global patterns of oak diversity and test the hypothesis that there are regions of the oak genome that are broadly informative about phylogeny.

   We utilize fossil data and restriction‐site associatedDNAsequencing (RAD‐seq) for 632 individuals representing nearly 250Quercusspecies to infer a time‐calibrated phylogeny of the world's oaks. We use a reversible‐jump Markov chain Monte Carlo method to reconstruct shifts in lineage diversification rates, accounting for among‐clade sampling biases. We then map the > 20 000RAD‐seq loci back to an annotated oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny.

   Oak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification, probably in response to climatic transitions or ecological opportunity.

   The strong support for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome.

    

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