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1. Evolutionary trajectories of duplicated FT homologues and their roles in soybean domestication

   https://doi.org/10.1111/tpj.13521  

   Wu, Faqiang ; Sedivy, Eric J. ; Price, William Brian ; Haider, Waseem ; Hanzawa, Yoshie ( April 2017 , The Plant Journal)

   To clarify the molecular bases of flowering time evolution in crop domestication, here we investigate the evolutionary fates of a set of four recently duplicated genes in soybean:FT2a,FT2b,FT2candFT2dthat are homologues of the floral inducerFLOWERING LOCUST(FT). WhileFT2amaintained the flowering inducer function, other genes went through contrasting evolutionary paths.FT2bevolved attenuated expression potentially associated with a transposon insertion in the upstream intergenic region, whileFT2candFT2dobtained a transposon insertion and structural rearrangement, respectively. In contrast toFT2bandFT2dwhose mutational events occurred before the separation ofG. maxandG. soja, the evolution ofFT2cis aG. maxlineage specific event. TheFT2callele carrying a transposon insertion is nearly fixed in soybean landraces and differentiates domesticated soybean from wild soybean, indicating that this allele spread at the early stage of soybean domestication. The domesticated allele causes later flowering than the wild allele under short day and exhibits a signature of selection. These findings suggest thatFT2cmay have underpinned the evolution of photoperiodic flowering regulation in soybean domestication and highlight the evolutionary dynamics of this agronomically important gene family.

    

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2. Cultivated sunflower ( Helianthus annuus L.) has lower tolerance of moderate drought stress than its con‐specific wild relative, but the underlying traits remain elusive

   https://doi.org/10.1002/pld3.581  

   Tran, Vivian H. ; Nolting, Kristen M. ; Donovan, Lisa A. ; Temme, Andries A. ( April 2024 , Plant Direct)

   Cultivated crops are generally expected to have less abiotic stress tolerance than their wild relatives. However, this assumption is not well supported by empirical literature and may depend on the type of stress and how it is imposed, as well as the measure of tolerance being used. Here, we investigated whether wild and cultivated accessions ofHelianthus annuusdiffered in stress tolerance assessed as proportional decline in biomass due to drought and whether wild and cultivated accessions differed in trait responses to drought and trait associations with tolerance. In a greenhouse study,H. annuusaccessions in the two domestication classes (eight cultivated and eight wild accessions) received two treatments: a well‐watered control and a moderate drought implemented as a dry down followed by maintenance at a predetermined soil moisture level with automated irrigation. Treatments were imposed at the seedling stage, and plants were harvested after 2 weeks of treatment. The proportional biomass decline in response to drought was 24% for cultivatedH. annuusaccessions but was not significant for the wild accessions. Thus, using the metric of proportional biomass decline, the cultivated accessions had less drought tolerance. Among accessions, there was no tradeoff between drought tolerance and vigor assessed as biomass in the control treatment. In a multivariate analysis, wild and cultivated accessions did not differ from each other or in response to drought for a subset of morphological, physiological, and allocational traits. Analyzed individually, traits varied in response to drought in wild and/or cultivated accessions, including declines in specific leaf area, leaf theoretical maximum stomatal conductance (g_smax), and stomatal pore length, but there was no treatment response for stomatal density, succulence, or the ability to osmotically adjust. Focusing on traits associations with tolerance, plasticity in g_smaxwas the most interesting because its association with tolerance differed by domestication class (although the effects were relatively weak) and thus might contribute to lower tolerance of cultivated sunflower. OurH. annuusresults support the expectation that stress tolerance is lower in crops than wild relatives under some conditions. However, determining the key traits that underpin differences in moderate drought tolerance between wild and cultivatedH. annuusremains elusive.

    

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3. A comparative assessment of SNP and microsatellite markers for assigning parentage in a socially monogamous bird

   https://doi.org/10.1111/1755-0998.12589  

   Kaiser, Sara_A ; Taylor, Scott_A ; Chen, Nancy ; Sillett, T_Scott ; Bondra, Eliana_R ; Webster, Michael_S ( August 2016 , Molecular Ecology Resources)

   Single‐nucleotide polymorphisms (SNPs) are preferred over microsatellite markers in many evolutionary studies, but have only recently been applied to studies of parentage. Evaluations ofSNPs and microsatellites for assigning parentage have mostly focused on special cases that require a relatively large number of heterozygous loci, such as species with low genetic diversity or with complex social structures. We developed 120SNPmarkers from a transcriptome assembled usingRNA‐sequencing of a songbird with the most common avian mating system—social monogamy. We compared the effectiveness of 97 novelSNPs and six previously described microsatellites for assigning paternity in the black‐throated blue warbler,Setophaga caerulescens. We show that the full panel of 97SNPs (meanH_o = 0.19) was as powerful for assigning paternity as the panel of multiallelic microsatellites (meanH_o = 0.86). Paternity assignments using the two marker types were in agreement for 92% of the offspring. Filtering individual samples by a 50% call rate andSNPs by a 75% call rate maximized the number of offspring assigned with 95% confidence usingSNPs. We also found that the 40 most heterozygousSNPs (meanH_o = 0.37) had similar power to assign paternity as the full panel of 97SNPs. These findings demonstrate that a relatively small number of variableSNPs can be effective for parentage analyses in a socially monogamous species. We suggest that the development ofSNPmarkers is advantageous for studies that require high‐throughput genotyping or that plan to address a range of ecological and evolutionary questions.

    

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4. Do relaxed selection and habitat temperature facilitate biased mitogenomic introgression in a narrowly endemic fish?

   https://doi.org/10.1002/ece3.2121  

   Hulsey, Christopher Darrin ; Bell, Katherine L. ; García‐de‐León, Francisco J. ; Nice, Chris C. ; Meyer, Axel ( April 2016 , Ecology and Evolution)

   Introgression might be exceptionally common during the evolution of narrowly endemic species. For instance, in the springs of the small and isolatedCuatroCiénegasValley, the mitogenome of the cichlid fishHerichthys cyanoguttatuscould be rapidly introgressing into populations of the trophically polymorphicH. minckleyi. We used a combination of genetic and environmental data to examine the factors associated with this mitochondrial introgression. A reduced representation library of over 6220 single nucleotide polymorphisms (SNPs) from the nuclear genome showed that mitochondrial introgression intoH. minckleyiis biased relative to the amount of nuclear introgression.SNPassignment probabilities also indicated that cichlids with more hybrid ancestry are not more commonly female providing no support for asymmetric backcrossing or hybrid‐induced sex‐ratio distortion in generating the bias in mitochondrial introgression. Smaller effective population size inH. minckleyiinferred from theSNPs coupled with sequences of all 13 mitochondrial proteins suggests that relaxed selection on the mitogenome could be facilitating the introgression of “H. cyanoguttatus” haplotypes. Additionally, we showed that springs with colder temperatures had greater amounts of mitochondrial introgression fromH. cyanoguttatus. Relaxed selection inH. minckleyicoupled with temperature‐related molecular adaptation could be facilitating mitogenomic introgression intoH. minckleyi.

    

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5. Tangled banks: A landscape genomic evaluation of Wallace's Riverine barrier hypothesis for three Amazon plant species

   https://doi.org/10.1111/mec.14948  

   Nazareno, Alison G. ; Dick, Christopher W. ; Lohmann, Lúcia G. ( February 2019 , Molecular Ecology)

   Wallace's Riverine Barrier hypothesis is one of the earliest biogeographic explanations for Amazon speciation, but it has rarely been tested in plants. In this study, we used three woody Amazonian plant species to evaluate Wallace's Hypothesis using tools of landscape genomics. We generated unlinked single‐nucleotide polymorphism (SNP) data from the nuclear genomes of 234 individuals (78 for each plant species) across 13 sampling sites along the Rio Branco, Brazil, forAmphirrhox longifolia(8,075SNPs),Psychotria lupulina(9,501SNPs) andPassiflora spinosa(14,536SNPs). Although significantly different migration rates were estimated between species, the population structure data do not support the hypothesis that the Rio Branco—an allopatric barrier for primates and birds—is a significant genetic barrier forAmphirrhox longifolia,Passiflora spinosaorPsychotria lupulina. Overall, we demonstrated that medium‐sized rivers in the Amazon Basin, such as the Rio Branco, are permeable barriers to gene flow for animal‐dispersed and animal‐pollinated plant species.

    

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