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1. Morphological Analysis of Size and Shape ( MASS ): An integrative software program for morphometric analyses of leaves

   https://doi.org/10.1002/aps3.11288  

   Chuanromanee, Tya S. ; Cohen, James I. ; Ryan, Gillian L. ( September 2019 , Applications in Plant Sciences)

   Morphometric analysis is a common approach for comparing and categorizing botanical samples; however, completing a suite of analyses using existing tools may require a multi‐stage, multi‐program process. To facilitate streamlined analysis within a single program, Morphological Analysis of Size and Shape (MASS) for leaves was developed. Its utility is demonstrated using exemplar leaf samples fromAcer saccharum,Malus domestica, andLithospermum.

   Exemplar samples were obtained from across a single tree (Acer saccharum), three trees in the same species (Malus domestica), and online, digitized herbarium specimens (Lithospermum).MASSwas used to complete simple geometric measurements of samples, such as length and area, as well as geometric morphological analyses including elliptical Fourier and Procrustes analyses. Principal component analysis (PCA) of data was also completed within the same program.

   MASSis capable of making desired measurements and analyzing traditional morphometric data as well as landmark and outline data.

   UsingMASS, differences were observed among leaves of the three studied taxa, but only inMalus domesticawere differences statistically significant or correlated with other morphological features. In the future,MASScould be applied for analysis of other two‐dimensional organs and structures.MASSis available for download athttps://github.com/gillianlynnryan/MASS.

    

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2. Transposable elements contribute to dynamic genome content in maize

   https://doi.org/10.1111/tpj.14489  

   Anderson, Sarah N. ; Stitzer, Michelle C. ; Brohammer, Alex B. ; Zhou, Peng ; Noshay, Jaclyn M. ; O'Connor, Christine H. ; Hirsch, Cory D. ; Ross‐Ibarra, Jeffrey ; Hirsch, Candice N. ; Springer, Nathan M. ( September 2019 , The Plant Journal)

   Transposable elements (TEs) are ubiquitous components of eukaryotic genomes and can create variation in genome organization and content. Most maize genomes are composed ofTEs. We developed an approach to define shared and variableTEinsertions across genome assemblies and applied this method to four maize genomes (B73, W22, Mo17 andPH207) with uniform structural annotations ofTEs. Among these genomes we identified approximately 400 000TEs that are polymorphic, encompassing 1.6 Gb of variableTEsequence. These polymorphicTEs include a combination of recent transposition events as well as deletions of olderTEs. There are examples of polymorphicTEs within each of the superfamilies ofTEs and they are found distributed across the genome, including in regions of recent shared ancestry among individuals. There are many examples of polymorphicTEs within or near maize genes. In addition, there are 2380 gene annotations in the B73 genome that are located within variableTEs, providing evidence for the role ofTEs in contributing to the substantial differences in annotated gene content among these genotypes.TEs are highly variable in our survey of four temperate maize genomes, highlighting the major contribution ofTEs in driving variation in genome organization and gene content.

   This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available athttps://github.com/SNAnderson/maizeTE_variation;https://mcstitzer.github.io/maize_TEs.

    

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3. Microhaplotypes provide increased power from short‐read DNA sequences for relationship inference

   https://doi.org/10.1111/1755-0998.12737  

   Baetscher, Diana S. ; Clemento, Anthony J. ; Ng, Thomas C. ; Anderson, Eric C. ; Garza, John C. ( December 2017 , Molecular Ecology Resources)

   The accelerating rate at whichDNAsequence data are now generated by high‐throughput sequencing instruments provides both opportunities and challenges for population genetic and ecological investigations of animals and plants. We show here how the common practice of calling genotypes from a singleSNPper sequenced region ignores substantial additional information in the phased short‐read sequences that are provided by these sequencing instruments. We target sequenced regions with multipleSNPs in kelp rockfish (Sebastes atrovirens) to determine “microhaplotypes” and then call these microhaplotypes as alleles at each locus. We then demonstrate how these multi‐allelic marker data from such loci dramatically increase power for relationship inference. The microhaplotype approach decreases false‐positive rates by several orders of magnitude, relative to calling bi‐allelicSNPs, for two challenging analytical procedures, full‐sibling and single parent–offspring pair identification. We also show how the identification of half‐sibling pairs requires so much data that physical linkage becomes a consideration, and that most published studies that attempt to do so are dramatically underpowered. The advent of phased short‐readDNAsequence data, in conjunction with emerging analytical tools for their analysis, promises to improve efficiency by reducing the number of loci necessary for a particular level of statistical confidence, thereby lowering the cost of data collection and reducing the degree of physical linkage amongst markers used for relationship estimation. Such advances will facilitate collaborative research and management for migratory and other widespread species.

    

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4. Extreme copy number variation at a tRNA ligase gene affecting phenology and fitness in yellow monkeyflowers

   https://doi.org/10.1111/mec.14904  

   Nelson, Thomas C. ; Monnahan, Patrick J. ; McIntosh, Mariah K. ; Anderson, Kayli ; MacArthur‐Waltz, Evan ; Finseth, Findley R. ; Kelly, John K. ; Fishman, Lila ( December 2018 , Molecular Ecology)

   Copy number variation (CNV) is a major part of the genetic diversity segregating within populations, but remains poorly understood relative to single nucleotide variation. Here, we report on atRNAligase gene (Migut.N02091;RLG1a) exhibiting unprecedented, and fitness‐relevant,CNVwithin an annual population of the yellow monkeyflowerMimulus guttatus.RLG1a variation was associated with multiple traits in pooled population sequencing (PoolSeq) scans of phenotypic and phenological cohorts. Resequencing of inbred lines revealed intermediate‐frequency three‐copy variants ofRLG1a (trip+;5/35 = 14%), andtrip+lines exhibited elevatedRLG1a expression under multiple conditions.trip+carriers, in addition to being over‐represented in late‐flowering and large‐flowered PoolSeq populations, flowered later under stressful conditions in a greenhouse experiment (p < 0.05). In wild population samples, we discovered an additional rareRLG1a variant (high+) that carries 250–300 copies ofRLG1a totalling ~5.7 Mb (20–40% of a chromosome). In the progeny of ahigh+carrier, Mendelian segregation of diagnostic alleles andqPCR‐based copy counts indicate thathigh+is a single tandem array unlinked to the single‐copyRLG1a locus. In the wild,high+carriers had highest fitness in two particularly dry and/or hot years (2015 and 2017; bothp < 0.01), while single‐copy individuals were twice as fecund as eitherCNVtype in a lush year (2016:p < 0.005). Our results demonstrate fluctuating selection onCNVs affecting phenological traits in a wild population, suggest that planttRNAligases mediate stress‐responsive life‐history traits, and introduce a novel system for investigating the molecular mechanisms of gene amplification.

    

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5. 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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