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1. The multiple fates of gene duplications: Deletion, hypofunctionalization, subfunctionalization, neofunctionalization, dosage balance constraints, and neutral variation

   https://doi.org/10.1093/plcell/koac076  

   Birchler, James A. ; Yang, Hua ( March 2022 , The Plant Cell)

   Gene duplications have long been recognized as a contributor to the evolution of genes with new functions. Multiple copies of genes can result from tandem duplication, from transposition to new chromosomes, or from whole-genome duplication (polyploidy). The most common fate is that one member of the pair is deleted to return the gene to the singleton state. Other paths involve the reduced expression of both copies (hypofunctionalization) that are held in duplicate to maintain sufficient quantity of function. The two copies can split functions (subfunctionalization) or can diverge to generate a new function (neofunctionalization). Retention of duplicates resulting from doubling of the whole genome occurs for genes involved with multicomponent interactions such as transcription factors and signal transduction components. In contrast, these classes of genes are underrepresented in small segmental duplications. This complementary pattern suggests that the balance of interactors affects the fate of the duplicate pair. We discuss the different mechanisms that maintain duplicated genes, which may change over time and intersect.

    

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2. Cryptic diversity in the Mexican highlands: Thousands of UCE loci help illuminate phylogenetic relationships, species limits and divergence times of montane rattlesnakes (Viperidae: Crotalus )

   https://doi.org/10.1111/1755-0998.12970  

   Blair, Christopher ; Bryson, Jr, Robert W. ; Linkem, Charles W. ; Lazcano, David ; Klicka, John ; McCormack, John E. ( December 2018 , Molecular Ecology Resources)

   With the continued adoption of genome‐scale data in evolutionary biology comes the challenge of adequately harnessing the information to make accurate phylogenetic inferences. Coalescent‐based methods of species tree inference have become common, and concatenation has been shown in simulation to perform well, particularly when levels of incomplete lineage sorting are low. However, simulation conditions are often overly simplistic, leaving empiricists with uncertainty regarding analytical tools. We use a large ultraconserved element data set (>3,000 loci) from rattlesnakes of theCrotalus triseriatusgroup to delimit lineages and estimate species trees using concatenation and several coalescent‐based methods. Unpartitioned and partitioned maximum likelihood and Bayesian analysis of the concatenated matrix yield a topology identical to coalescent analysis of a subset of the data inbpp. ASTRAL analysis on a subset of the more variable loci also results in a tree consistent with concatenation andbpp, whereas theSVDquartetsphylogeny differs at additional nodes. The size of the concatenated matrix has a strong effect on species tree inference usingSVDquartets, warranting additional investigation on optimal data characteristics for this method. Species delimitation analyses suggest up to 16 unique lineages may be present within theC. triseriatusgroup, with divergences occurring during the Neogene and Quaternary. Network analyses suggest hybridization within the group is relatively rare. Altogether, our results reaffirm the Mexican highlands as a biodiversity hotspot and suggest that coalescent‐based species tree inference on data subsets can provide a strongly supported species tree consistent with concatenation of all loci with a large amount of missing data.

    

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3. Demographic history inference and the polyploid continuum

   https://doi.org/10.1093/genetics/iyad107  

   Blischak, Paul D. ; Sajan, Mathews ; Barker, Michael S. ; Gutenkunst, Ryan N. ; Gravel, ed., S. ( June 2023 , GENETICS)

   Polyploidy is an important generator of evolutionary novelty across diverse groups in the Tree of Life, including many crops. However, the impact of whole-genome duplication depends on the mode of formation: doubling within a single lineage (autopolyploidy) versus doubling after hybridization between two different lineages (allopolyploidy). Researchers have historically treated these two scenarios as completely separate cases based on patterns of chromosome pairing, but these cases represent ideals on a continuum of chromosomal interactions among duplicated genomes. Understanding the history of polyploid species thus demands quantitative inferences of demographic history and rates of exchange between subgenomes. To meet this need, we developed diffusion models for genetic variation in polyploids with subgenomes that cannot be bioinformatically separated and with potentially variable inheritance patterns, implementing them in the dadi software. We validated our models using forward SLiM simulations and found that our inference approach is able to accurately infer evolutionary parameters (timing, bottleneck size) involved with the formation of auto- and allotetraploids, as well as exchange rates in segmental allotetraploids. We then applied our models to empirical data for allotetraploid shepherd’s purse (Capsella bursa-pastoris), finding evidence for allelic exchange between the subgenomes. Taken together, our model provides a foundation for demographic modeling in polyploids using diffusion equations, which will help increase our understanding of the impact of demography and selection in polyploid lineages.

    

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4. Neighborhood diversity simultaneously increased and decreased susceptibility to contrasting herbivores in an early stage forest diversity experiment

   https://doi.org/10.1111/1365-2745.13097  

   Grossman, Jake J. ; Cavender‐Bares, Jeannine ; Reich, Peter B. ; Montgomery, Rebecca A. ; Hobbie, Sarah E. ; Shefferson, ed., Richard ( December 2018 , Journal of Ecology)

   Forest structure and diversity can regulate tree vulnerability to damage by insects and pathogens. Past work suggests that trees with diverse neighbours should experience less leaf herbivory and less damage from specialist herbivores and diseases, and that the effect of neighbourhood diversity should be strongest at small spatial scales.

   In an early stage temperate tree diversity experiment, we monitored damage from leaf removing herbivores, specialist (gallers and leaf miners) herbivores, and two specialist fungal diseases (maple leaf anthracnose and cedar apple gall rust) over 3 years. The experimental design included treatments that varied independently in phylogenetic and functional diversity and we made our analyses across four spatial scales (1–16 m²).

   Neighborhood diversity simultaneously increased leaf removal for some species, decreased it for others, and had no effect on yet others. Height apparency—the difference between a focal plant’s height and its neighbours’—was the best single predictor of leaf removal across species and spatial scales, but the strength and direction of its effect were also species‐specific.

   Specialist pathogens and fungal foliar diseases showed signs of associational resistance and susceptibility. Oaks (Quercusspp.) were more resistant to leaf miners and maples were more resistant to anthracnose when surrounded by diverse neighbours (associational resistance). In contrast, birches (Betula papyrifera) were more susceptible to leaf miners and eastern red cedars (Juniperus virginiana) were more susceptible to cedar apple gall rust (Gymnosporangium juniperi‐virginianae) infection in diverse environments (associational susceptibility).

   Herbivore and pathogen damage was better predicted by community structure and diversity at small spatial scales (1 and 4 m²) than large scales (9 and 16 m²), suggesting a characteristic spatial scale for these biodiversity‐ecosystem functioning effects.

   Synthesis.Humans control forest diversity through selective harvesting and planting in natural stands and plantations. Our experimental demonstration of the role of local community structure and diversity in suppressing some forms of pest and pathogen damage to trees suggests that forest management can be most effective when diversity is considered at small spatial scales and the underlying biology of particular pests, pathogens, and hosts is taken into account. Pictured here: the “galls” formed by cedar apple gall rust (Gymnosporangium juniperae‐virginiae) on eastern red cedar (Juniperus virginiana) in early spring release wind‐dispersed teleospores. Junipers showed associational susceptibility: greater susceptibility to gall rust with more diverse neighbours.

    

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5. A test of adaptive divergence in a newly discovered host association of the soapberry bug Jadera haematoloma on Mexican buckeye, Ungnadia speciosa

   https://doi.org/10.1111/eea.13118  

   Comerford, Mattheau S. ; Carroll, Scott P. ; Egan, Scott P. ( November 2021 , Entomologia Experimentalis et Applicata)

   Host races represent an important step in the speciation process of phytophagous insects as they reflect the maintenance of genetically divergent host‐associated populations in the face of appreciable gene flow. The red‐shouldered soapberry bug,Jadera haematoloma(Herrich‐Schäffer) (Hemiptera: Rhopalidae), is an oligophagous seed predator with a history of host race evolution on plant associations in the (soapberry) family Sapindaceae. Soapberry bugs are a model group for understanding rapid ecological adaptation to their hosts, and hence good candidates for investigating evolutionary divergence in host associations over short timescales. Here, we describe the recent discovery of Mexican buckeye,Ungnadia speciosaEndl., as a host ofJ. haematolomain a region of the Chihuahuan desert including west Texas and southeastern New Mexico, USA. This host differs fromJ. haematoloma’s previously recorded hosts in the Sapindaceae in seed chemistry, ecology, and phylogeny. The tendency toward rapid, host‐associated adaptations by populations ofJ. haematolomaand the unique biology of the newly discoveredUngnadiahost create the opportunity for potential host race formation, as it overlaps geographically with two previously recorded host plants in this region – the native western soapberry tree,Sapindus saponariavar.drummondii(Hook & Arn.), and the non‐native goldenrain tree,Koelreuteria paniculataLaxm. We explore the possibility of host race formation onUngnadia‐associated insects by testing for host‐associated differentiation in morphology and feeding behaviors. We find evidence of differentiation in the length of the mouth parts, which is an ecologically relevant feeding trait between host plant species with larger or smaller seed capsules. This divergence is maintained in the face of potential gene flow by reproductive isolation in the form of habitat isolation, which we detect in host preference trials. Together, our results demonstrate that soapberry bugs associated with this newly discovered host exhibit morphological and behavioral traits consistent with host race formation, but additional work is required to confirm its state along the speciation continuum.

    

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