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1. Population genomic analysis of mango ( Mangifera indica ) suggests a complex history of domestication

   https://doi.org/10.1111/nph.15731  

   Warschefsky, Emily J. ; von Wettberg, Eric J. B. ( March 2019 , New Phytologist)

   Humans have domesticated diverse species from across the plant kingdom, yet much of our foundational knowledge of domestication has come from studies investigating relatively few of the most important annual food crops. Here, we examine the impacts of domestication on genetic diversity in a tropical perennial fruit species, mango (Mangifera indica).

   We used restriction site associatedDNAsequencing to generate genomic single nucleotide polymorphism (SNP) data from 106 mango cultivars from seven geographical regions along with 52 samples of closely related species and unidentified cultivars to identify centers of mango genetic diversity and examine how post‐domestication dispersal shaped the geographical distribution of diversity.

   We identify two gene pools of cultivated mango, representing Indian and Southeast Asian germplasm. We found no significant genetic bottleneck associated with the introduction of mango into new regions of the world. By contrast, we show that mango populations in introduced regions have elevated levels of diversity.

   Our results suggest that mango has a more complex history of domestication than previously supposed, perhaps including multiple domestication events, hybridization and regional selection. Our work has direct implications for mango breeding and genebank management, and also builds on recent efforts to understand how woody perennial crops respond to domestication.

    

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2. 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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3. Conservation genetic assessment of the paleback darter, Etheostoma pallididorsum , a narrowly distributed endemic in the Ouachita Highlands, Arkansas, USA

   https://doi.org/10.1002/aqc.3510  

   McCall, Brittany L. ; Fluker, Brook L. ( March 2021 , Aquatic Conservation: Marine and Freshwater Ecosystems)

   The paleback darter,Etheostoma pallididorsum, is considered imperilled and has recently been petitioned for listing under the Endangered Species Act. Previous allozyme‐based studies found evidence of a small effective population size, warranting conservation concern. The objective of this study was to assess the population dynamics and the phylogeographical history of the paleback darter, using a multilocus microsatellite approach and mitochondrial DNA.

   The predictions of this study were that: paleback darter populations will exhibit low genetic diversity and minimal gene flow; population structure will correspond to the river systems from which the samples are derived; reservoir dams impounding the reaches between the Caddo and Ouachita rivers would serve as effective barriers to gene flow; and the Caddo and Ouachita rivers are reciprocally monophyletic.

   Microsatellite DNA loci revealed significant structure among sampled localities (globalF_st= 0.17,P< 0.001), with evidence of two distinct populations representing the Caddo and Ouachita rivers. However, Bayesian phylogeographical analyses resulted in three distinct clades: Caddo River, Ouachita River, and Mazarn Creek. Divergence from the most recent ancestor shared among the river drainages was estimated at 60 Kya. Population genetic diversity was relatively low (H_e= 0.65; mean alleles per locus,A= 6.26), but was comparable with the population genetic diversity found in the close relatives slackwater darter,Etheostoma boschungi(H_e= 0.65;A= 6.74), and Tuscumbia darter,Etheostoma tuscumbia(H_e= 0.57;A= 5.53).

   These results have conservation implications for paleback darter populations and can be informative for other headwater specialist species. Like other headwater species with population structuring and relatively low genetic diversity, the persistence of paleback darter populations is likely to be tied to the persistence and connectivity of local breeding and non‐breeding habitat. These results do not raise conservation concern for a population decline; however, the restricted distribution and endemic status of the species still renders paleback darter populations vulnerable to extirpation or extinction.

    

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4. 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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5. 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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