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1. REMIX: Efficient Range Query for LSM-trees

   Wenshao Zhong, Chen Chen (January 2021, 19th USENIX Conference on File and Storage Technologies)

   null (Ed.)
2. Pathways of tundra encroachment by trees and tall shrubs in the western Brooks Range of Alaska

   https://doi.org/10.1111/ecog.05015  

   Terskaia, Anna; Dial, Roman J.; Sullivan, Patrick F. (February 2020, Ecography)
3. Aridity drives coordinated trait shifts but not decreased trait variance across the geographic range of eight Australian trees

   https://doi.org/10.1111/nph.16795  

   Anderegg, Leander D. L.; Loy, Xingwen; Markham, Ian P.; Elmer, Christina M.; Hovenden, Mark J.; HilleRisLambers, Janneke; Mayfield, Margaret M. (August 2020, New Phytologist)

   Summary Large intraspecific functional trait variation strongly impacts many aspects of communities and ecosystems, and is the medium upon which evolution works. Yet intraspecific trait variation is inconsistent and hard to predict across traits, species and locations.We measured within‐species variation in leaf mass per area (LMA), leaf dry matter content (LDMC), branch wood density (WD), and allocation to stem area vs leaf area in branches (branch Huber value (HV)) across the aridity range of seven Australian eucalypts and a co‐occurringAcaciaspecies to explore how traits and their variances change with aridity.Within species, we found consistent increases in LMA, LDMC and WD and HV with increasing aridity, resulting in consistent trait coordination across leaves and branches. However, this coordination only emerged across sites with large climate differences. Unlike trait means, patterns of trait variance with aridity were mixed across populations and species. Only LDMC showed constrained trait variation in more xeric species and drier populations that could indicate limits to plasticity or heritable trait variation.Our results highlight that climate can drive consistent within‐species trait patterns, but that patterns might often be obscured by the complex nature of morphological traits, sampling incomplete species ranges or sampling confounded stress gradients. 

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4. Phylogenetic trees

   https://doi.org/10.2140/jsag.2021.11.1  

   Hector Banos, Nathaniel Bushek (January 2021, The journal of software for algebra and geometry)

   null (Ed.)

   We introduce the package PhylogeneticTrees for Macaulay2, which allows users to compute phylogenetic invariants for group-based tree models. We provide some background information on phylogenetic algebraic geometry and show how the package PhylogeneticTrees can be used to calculate a generating set for a phylogenetic ideal as well as a lower bound for its dimension. Finally, we show how methods within the package can be used to compute a generating set for the join of any two ideals. 

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5. Completing gene trees without species trees in sub-quadratic time

   https://doi.org/10.1093/bioinformatics/btab875  

   Mai, Uyen; Mirarab, Siavash; Schwartz, ed., Russell (January 2022, Bioinformatics)

   Abstract MotivationAs genome-wide reconstruction of phylogenetic trees becomes more widespread, limitations of available data are being appreciated more than ever before. One issue is that phylogenomic datasets are riddled with missing data, and gene trees, in particular, almost always lack representatives from some species otherwise available in the dataset. Since many downstream applications of gene trees require or can benefit from access to complete gene trees, it will be beneficial to algorithmically complete gene trees. Also, gene trees are often unrooted, and rooting them is useful for downstream applications. While completing and rooting a gene tree with respect to a given species tree has been studied, those problems are not studied in depth when we lack such a reference species tree. ResultsWe study completion of gene trees without a need for a reference species tree. We formulate an optimization problem to complete the gene trees while minimizing their quartet distance to the given set of gene trees. We extend a seminal algorithm by Brodal et al. to solve this problem in quasi-linear time. In simulated studies and on a large empirical data, we show that completion of gene trees using other gene trees is relatively accurate and, unlike the case where a species tree is available, is unbiased. Availability and implementationOur method, tripVote, is available at https://github.com/uym2/tripVote. Supplementary informationSupplementary data are available at Bioinformatics online. 

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