Journal of Systematics and Evolution

Understanding evolutionary relationships in hyperdiverse plant groups remains a major challenge in systematics. The orchid genus Bulbophyllum, the second largest genus of flowering plants, represents an exceptional example of phylogenetic and morphological complexity. Relationships, particularly within the species-rich Asian clade, have remained poorly resolved due to extensive morphological variation and limited resolution in previous phylogenetic studies. Here, we reconstructed phylogenetic relationships using 63 plastid genes from 355 specimens representing 322 species and 65 of the 97 recognised sections of Bulbophyllum. Our analyses confirmed that the genus comprises five major evolutionary lineages comprised of species predominantly from Australasia, Madagascar, Continental Africa, Neotropics, and Asia. We provide the first robust phylogenetic evidence for a dichotomous split within the Asian clade into two well-supported lineages: the Asian-Malesian clade and the Malesian-Papuasian clade, with the latter containing a strongly supported Papuasian subclade. Additionally, this study supports the monophyly of several currently recognised sections while clarifying relationships in previously problematic groups. This study provides the most comprehensive plastid-based phylogenomic framework for Bulbophyllum to date and establishes a foundation for future taxonomic revision and integrative analyses of diversification and trait evolution within this hyperdiverse genus.

Although genetic diversity is a fundamental component of biodiversity, we lack data for a majority of species, particularly in biodiversity hotspots such as tropical forests. We present a comparative genetic dataset of 19 tropical tree species (including one palm) from the Caribbean island of Puerto Rico and neighboring islands (Hispanola and the US Virgin Islands). Using a reduced-representation sequencing technique (SLAF-seq), we identified species-specific single-nucleotide polymorphism (SNP) datasets with 24,413 to 433,637 high-quality SNPs per species. The focal species represent a range of life-history and climate associations, which may be relevant to their genetic structure. Therefore, we also include complementary information on species functional traits (wood density, leaf thickness, specific leaf area, maximum height, and seed dry mass), as well as geographic distributions and climatic associations from species distribution models.

The remarkable diversity of life on Earth results from evolutionary processes functioning across different spatial and temporal scales. Species diversification occurs through various mechanisms and at widely varying rates, but identifying the conditions that trigger bursts of diversification over short timescales remains a central challenge in evolutionary biology. This difficulty is more pronounced when incomplete lineage sorting (ILS), hybridization, and ongoing gene flow obscure evolutionary relationships and complicate species delimitation. In this study, we investigated the evolutionary history and species boundaries within a group of recently diverged Petunia lineages shaped by pervasive gene flow. We integrated phylogenomic, population genetic, and species delimitation approaches to reconstruct lineage relationships and assess whether these lineages represent distinct species or stages along a speciation continuum. By applying methods that account for both ILS and gene flow, we revealed that most lineages are not fully independent evolutionary units but rather occupy intermediate positions along this continuum. Gene flow played a crucial role during diversification, blurring species boundaries and generating reticulate evolutionary patterns. Our findings demonstrate that traditional phylogenetic trees may oversimplify relationships in such systems, while phylogenetic networks offer a more accurate representation of evolutionary history. Comprehensive and integrative analyses, such as those employed here, are essential for capturing these complex dynamics. Ultimately, only four lineages could be confidently recognized as distinct species, whereas the remaining represent cases of ongoing divergence. These results emphasize the need to refine species delimitation frameworks for systems characterized by recent divergence and extensive reticulation.

We present a genome assembly from a specimen of Quercus canariensis (Fagaceae; Fagales; Magnoliopsida). The assembly was generated using PacBio HiFi long reads with an approximate sequencing depth of 39X and scaffolded using a reference-guided approach. The genome sequence has a total length of 816.0 megabases for haplotype 1 and 804.8 megabases for haplotype 2. The two haplotypes are each resolved into 12 chromosomal pseudomolecules, with only 3.48% and 1.36% of sequences remaining unplaced in haplotypes 1 and 2, respectively. Assembly completeness is supported by BUSCO scores of 98.3% and 98.2% complete genes for haplotypes 1 and 2, respectively. Structural annotation identified 51,882 and 46,482 protein-coding genes in haplotypes 1 and 2, respectively. This genome assembly provides the first chromosome-scale reference genome for Q. canariensis, laying the base for future genomic and evolutionary studies in this understudied species of the hybridizing white oak species complex. TaxonomyLineage cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fagales; Fagaceae; Quercus EBI:txid568684 Quercus canariensis Willd. 1809 (Willdenow)

Phylogenetic trees represent the evolutionary histories of taxa and support tasks such as clustering and Tree of Life reconstruction. Many established comparison methods, including the Robinson-Foulds (RF) distance, assume identical taxon sets. A methodological gap remains for trees with distinct but overlapping taxa. Existing approaches either prune non-common leaves, which can discard information, or complete both trees such that they share the same taxa. Completion is more comprehensive, but current methods typically ignore branch lengths, which are essential for identifying evolutionary patterns. This paper introduces k-Nearest Common Leaves (k-NCL), an algorithm for completing rooted phylogenetic trees defined on different but overlapping taxa. The method uses branch lengths and topological characteristics and does not rely on a specific distance measure. The k-NCL algorithm is designed to preserve evolutionary relationships in the trees under comparison. The running time is O(n2), where n is the size of the union of the two leaf sets. Additional properties include preservation of original distances and topology, symmetry, and uniqueness of the completion. Implemented in Python, k-NCL is evaluated on biological datasets of amphibians, birds, mammals, and sharks. Experimental results show that RF combined with k-NCL improves phylogenetic tree clustering performance compared to the RF(+) tree completion approach. Availability and implementationAn open-source implementation of k-NCL in Python and the datasets used in this study are available at https://github.com/tahiri-lab/KNCL.

The combination of target capture sequencing (TCS) with low-coverage whole genome sequencing (lcWGS), an approach known as Hyb-Seq, has allowed the integration of natural history collections into the genomics revolution, transforming biodiversity research. To implement Hyb-Seq, a collection of genomic targets, often nuclear orthologs, is needed to design probes for TCS. In flowering plants, the universal Angiosperms353 probe set has been proven resolutive at multiple evolutionary scales, with caveats. Malpighiales is known to be one of the most challenging flowering plant orders to resolve. Within this order, the clusioid clade ([~]2.2K species, 94 genera, five families) is no exception. To resolve phylogenetic relationships in this recalcitrant clade, we design a custom probe set, the Clusioids626 kit, composed of 39,936 120-mer probes targeting 626 nuclear orthologs ([~]6.6M nucleotides). This probe set includes all Angiosperms353 targets and 273 clusioid-specific ones, carefully chosen taking copy-number, length evenness, and phylo-informativeness into account. We test our probe set on 70 accessions representing all families and tribes in the clusioid clade. On average, 50.4% of TCS reads mapped to our targets, recovering a median of [~]600 orthologs. Relationships for all clusioid families are fully resolved for our nuclear targets. Additionally, 105 plastid coding DNA sequences were retrieved from the lcWGS fraction. A strong cyto-nuclear conflict was detected. The Clusioids626 kit performs better than the universal Angiosperms353 enrichment panel alone. Our kit design workflow can be extended into other lineages for which a universal probe set exists but more resolution is needed.

Renowned for its aromatic fruits and economic importance, the genus Vanilla poses longstanding taxonomic and phylogenetic challenges. Despite recent molecular studies, a comprehensive species tree is lacking, and the evolutionary processes and historical patterns shaping the genus remain poorly understood. We present a new, comprehensive phylogenomic framework for Vanilla, based on 349 low-copy nuclear genes and 76 plastid loci from the Angiosperms353 probe set, which we used to infer evolutionary relationships, assess cyto-nuclear and gene-species tree discordance, and thoroughly investigate its historical distribution and diversification. Sampling 43% of the genus, our framework resolves phylogenetic uncertainties, clarifies major clades, confirms prior hypotheses, and reveals novel placements, including V. planifolia and Vanilla subg. Gondwana. Discordances are primarily driven by incomplete lineage sorting, particularly in the vanillin-producing clade, with evidence of both ancient and recent hybridization, including a natural hybrid from the Yucatan Peninsula. Biogeographic analyses indicate a Guiana Shield origin ([~]30 Mya), Amazonia as a major diversification source, the Andes as a permeable barrier, and Central America as the main diversification sink. This study provides a robust evolutionary framework for Vanilla, supporting taxonomic revisions, comparative trait analyses, and a deeper understanding of the processes shaping this economically and biologically important orchid genus.

If youve ever complained about a species name thats a mouthful--say, the soldier fly Parastratiosphecomyia stratiosphecomyioides or the myxobacterium Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis--youre in very good company. But could the readability of binomial scientific names cause more than complaints? Could it influence how much species are studied and talked about? We examined a random sample of 3,019 species names spanning 29 phyla/divisions. We tested whether name length and reading difficulty are associated with species representation in the scientific literature (measured via literature mentions) and their visibility to the public (measured via Wikipedia pageviews). Both species name traits showed significant negative relationships with literature mentions and Wikipedia reads. Increasing name length from 10 to 30 characters is associated with a 66% decrease in expected mentions and a 65% decrease in Wikipedia reads, while shifting from the most to the least readable name in the dataset corresponds to 53% and 76% decreases. These patterns are consistent with something familiar: the fickleness of human attention, responding to features of the world that are far from rational. While creativity in naming is a cherished part of taxonomy, a touch of orthographic restraint may ultimately benefit both science and the species themselves--especially among understudied uncharismatic taxa.

Characterized by the earliest use of pottery, the Jomon culture was a unique Neolithic culture that spread throughout the Japanese Archipelago. Previous archaeological evidence suggests that Jomon hunter-gatherers colonized the southernmost islands, the Ryukyu Archipelago, by approximately 7,000 years before present (YBP). However, genetic characteristics of the Ryukyu Jomon population and its contribution to the modern population have not been elucidated yet. In this study, we newly sequenced 273 modern and 25 ancient (6,700-900 YBP) whole genomes collected across the Ryukyu Archipelago. Our analysis demonstrated a genetic differentiation between the Hondo (Japanese mainland) and Ryukyu Jomon, dating back to [~]6,900 YBP. After the divergence from the Hondo Jomon, the Ryukyu Jomon experienced severe bottlenecks, with an effective population size of [~]2,000. Admixture between the Ryukyu Jomon and migrants from the historic Hondo population occurred [~]1,000 YBP, which corresponds to the widespread adoption of iron tools and agriculture in the Central Ryukyus. Different demographic histories between modern Hondo and Ryukyu populations resulted in different rates of Jomon ancestry in these populations. By providing a new perspective on the peopling of the Ryukyu Archipelago, this study significantly enhances our understanding of cultural transitions in the region.

In their recent study entitled "Ancient DNA reveals the co-existence of domestic horses, donkeys and their hybrids in the prehistorical northwestern China", Li and colleagues (2026) report the genetic identification of three horses, three donkeys and four first-generation hinny hybrids dating to 400-160 BCE from the Mazongshan jade mining site in northwestern China. While a re-analysis of their ancient DNA sequence data confirms the horse and donkey identifications, it indicates that the four putative hinny specimens were, in fact, donkeys. This revision removes the primary evidence originally shown for the presence of hinnies at this site. Therefore, new data from the Mazongshan bone assemblage are required to support the proposed role of hinny hybrids as integral components of trans-regional trade networks during the Late Warring States and Early Han periods.

Integrating taxonomic data from various sources presents a significant challenge in the study of biodiversity research, due to non-standardized nomenclature and evolving species classifications. Discrepancies between major repositories like the Global Biodiversity Information Facility (GBIF) and the National Center for Biotechnology Information (NCBI), as well as citizen science platforms such as iNaturalist, lead to fragmented and sometimes inaccurate biological data. We present TaxonMatch, a tool designed to address these challenges. TaxonMatch aligns taxonomic names, resolves synonymy, and corrects typographical and structural inconsistencies across databases. We show how it can be used to build a common backbone arthropod taxonomy over NCBI, GBIF and iNaturalist, to find the closest molecular data to a given fossil, and to identify IUCN endangered species with molecular data. TaxonMatch provides a cohesive taxonomic framework and a consistent taxonomic backbone, and can be applied to any taxonomic source. The tool is available at https://github.com/MoultDB/TaxonMatch.

Ancestral state reconstruction is a classical problem of broad relevance in phylogenetics. Likelihood-based methods for reconstructing ancestral states under discrete character models, such as Markov models, have proven extremely useful, but only work so long as the assumed model yields a tractable likelihood function. Unfortunately, extending a simple but tractable phylogenetic model to possess new, but biologically realistic, properties often results in an intractable likelihood, preventing its use in standard modeling tasks, including ancestral state reconstruction. The rapid advancement of deep learning offers a potential alternative to likelihood-based inference of ancestral states, particularly for models with intractable likelihoods. In this study, we modify the phylogenetic deep learning software O_SCPLOWPHYDDLEC_SCPLOW to conduct ancestral state reconstruction. We evaluate O_SCPLOWPHYDDLEC_SCPLOWs performance under various methodological and modeling conditions, while comparing to Bayesian inference when possible. For simple models and small trees, its performance resembles the performance of Bayesian inference, but worsens as tree size increases. While O_SCPLOWPHYDDLEC_SCPLOW still performs adequately for more complex models, such as speciation and extinction models, the estimates differ more from Bayesian inference in comparison with simpler models. Lastly, we use O_SCPLOWPHYDDLEC_SCPLOW to infer ancestral states for two empirical datasets, one of the ancestral ranges of a subclade of the genus Liolaemus and ancestral locations for sequences from the 2014 Sierra Leone Ebola virus disease outbreak.

Understanding the phylogenetic relationships among eukaryotic lineages is essential for tracing the evolution of key phenotypic traits and inferring the nature of the Last Eukaryotic Common Ancestor. While phylogenomic analyses have clustered eukaryotic taxa into several well-supported major supergroups, the relationships among them remain largely uncertain. Phylogenetic signal erosion over deep time and limited available taxon sampling are among the possible causes. However, most previous studies rely on variations of the same core protein dataset, hence containing the same potential systematic biases. Here, we reconstructed the eukaryotic Tree of Life using a largely independent, marker-rich dataset derived from highly conserved Benchmarking Universal Single-Copy Orthologs. Unlike previous collections, our 277-marker supermatrix minimizes ribosomal protein representation and shares less than 25% overlap with previous datasets. State-of-the-art analyses of this dataset confirm most eukaryotic supergroups previously observed, but suggest different positions for some lineages. Notably, Telonemia clusters with Haptophyta rather than SAR (Stramenopiles-Alveolata-Rhizaria), and Ancyromonadida and Malawimonadida form a monophyletic group at the base of the Opimoda. Our results highlight the importance of analyzing independent phylogenomic datasets and support the hypothesis that extant eukaryotic diversity encompasses a small number of high-rank, supergroup lineages.

Text AbstractIn this study, we characterized the genetic structure and reconstructed the demographic history of cactus wrens (Campylorhynchus brunneicapillus), an endemic species of desert regions of North America, that shows a clear phenotypic and genotypic variation. We evaluated the effects of historical climate change on the structure and population dynamics of desert species using genomic data through genotyping by sequencing (GBS) and applied a population structure analysis (FST and ADMIXTURE), revealing two genetically differentiated groups: one continental and another peninsular in Baja California. Subsequently, we implemented the MSMC2 coalescent model on data divided into autosomal regions and the Z sex chromosome to estimate changes in effective population size (Ne) through evolutionary time. Additionally, we developed ecological niche models (ENMs) projected to the Last Glacial Maximum (LGM), Last Interglacial (LIG), Present times, and Future (2060 - 2080). Results indicate that both populations maintained moderated Nes before the LGM, experienced severe bottlenecks (Ne [~] 102-103), followed by a sustained expansion. However, recovery was limited to the Z chromosome of the peninsular population. These findings reveal how glaciations and interglacials shaped the evolutionary history of desert species and provide genomic evidence of the splitting of C. affinis from C. brunneicapillus. Article summaryThis research examines how climate changes shaped genetic diversity of cactus wrens across North American warm deserts. Using coalescent methods, researchers tracked effective population size changes over 100,000 years, using ecological niche modeling they predicted habitat suitability across climate periods. Results showed that continental and peninsular populations experienced bottlenecks during the Last Glacial Maximum, followed by demographic recovery on warm periods. However, the sex chromosome (Z) revealed male-biased demographic patterns in peninsular populations. Future projections indicated habitat suitability reductions for peninsular populations, highlighting conservation concerns. These findings demonstrate that past climate shaped genetic diversity of cactus wrens.

Astyanax Baird & Girard, 1854 is a widely distributed and species-rich genus of Acestrorhamphidae, whose abundant populations in Neotropical basins play a crucial ecological role at the trophic level. Taxonomic uncertainties persist within the genus, as seen in Astyanax sp. (formerly designated as A. fasciatus) from the Magdalena basin in Colombia. Concerns about its genetic status are heightened due to ecological threats posed by hydroelectric dams, from habitat loss to river connectivity. We isolated and characterized 17 microsatellite loci to assess the population genetics of this species in a broad sample from the middle and lower sections of the Cauca River, now interrupted by the Ituango dam. Furthermore, a multidisciplinary approach integrating phylogenetic analyses of mitochondrial (COI) and nuclear (rag2) markers with geometric morphometric analyses was employed to evaluate potential cryptic diversity within Astyanax sp. Microsatellites revealed two genetic groups in the studied area, strongly supported as distinct lineages by phylogenetic analyses. Unexpectedly, one of these lineages of Astyanax sp. was recovered in an unresolved clade with samples of A. microlepis and allopatric samples of A. viejita from the Maracaibo Lake basin. Each genetic group showed high genetic diversity, but also evidence of recent bottleneck events and significant-high values of inbreeding. Morphometric analyses provided evidence of significant phenotypic differentiation among A. microlepis, Astyanax sp. 1 (Asp1), and Astyanax sp. 2 (Asp2). Morphological patterns ranged from the robust profile of A. microlepis to the streamlined shape of Astyanax sp. 2 (Asp2), with Astyanax sp. 1 (Asp1) displaying intermediate traits and localized differences in head length and fin placement. Statistical support from permutation tests and a high overall classification accuracy (95.65%) underscore the existence of distinct morphospecies, suggesting that phenotypic differentiation is well-established, despite the complex evolutionary history of the group. This study suggests the presence of cryptic diversity within Astyanax sp. and provides valuable genetic information for the conservation and management of their populations in the Magdalena basin.

Primarily inhabiting the harsh, high-altitude environment of the Qiangtang National Nature Reserve exceeding 5,000 meters above the sea (m.a.s.l.), the golden wild yak is critically endangered, with fewer than 300 individuals remaining in the world, a situation exacerbated by the significant challenges of conducting research and conservation of their genetic resources. Somatic cell nuclear transfer (SCNT) can be an effective method for their preservation, but facing several obstacles in this context, including the hypoxic stress at high altitude that impairs embryonic development due to in vitro manipulation, and constraints of long-distance embryo transport. In the present study, the ear tissue was collected from a childhood male golden wild yak at Xizang Geye Wildlife Rescue Station (4800 m.a.s.l.) and send to Institute of Animal Science at Beijing to derive fibroblast cells. Using fibroblast cells of the golden wild yak as nuclear donors, and bovine oocytes from a local slaughterhouse at Beijing as recipients, the interspecific SCNT (iSCNT) embryos were generated and in vitro developed to blastocysts. To maintain the embryonic viability after long-distance transportation from Beijing to Xizang, iSCNT blastocysts were subjected to cryopreservation by vitrification method. Thawing of vitrified iSCNT blastocysts were completed at Xizang Dangxiong Yak Breeding Innovation Base (4200 m.a.s.l.), and transferred into the uterine horn of domestic yaks. 257 days after blastocyst transfer, a cloned golden wild yak was successfully harvested on January 10, 2026. This work demonstrates, for the first time, that interspecies somatic cell nuclear transfer can successfully produce a cloned offspring under extreme conditions, spanning 4800 m.a.s.l. donor origin, long-distance vitrified embryo transportation, and high-altitude blastocyst transfer at 4200 m.a.s.l., establishing a viable strategy for conserving critically endangered high-altitude species.

Angiogenesis, the process by which new blood vessels form from existing vasculature, is fundamental to tissue repair and regeneration but also underlies pathological conditions such as cancer progression. Targeting angiogenesis has thus become a promising approach for developing novel cancer therapeutics. While various phytochemicals have demonstrated anti-angiogenic effects, the role of 2-5(H)-Furanone, a naturally occurring lactone found in various plants and marine sources with diverse biological activities, remains insufficiently explored. In this study, we systematically evaluate the anti-angiogenic potential of 2-5(H)-Furanone using Human Umbilical Vein Endothelial Cells (HUVECs) as an in vitro model and zebrafish embryos as an in vivo model. Experimental findings demonstrated that treatment of HUVECs with increasing concentrations of 2-5(H)-Furanone led to significant, dose-dependent reductions in proliferation, invasion, migration, and tube formation. Analyses of gene expression revealed marked downregulation of key pro-angiogenic mediators, VEGF, and HIF-1. Complementing these in vitro results, in vivo studies in zebrafish embryos showed robust, dose-dependent inhibition of intersegmental vessel (ISV) formation, accompanied by suppression of critical angiogenesis-related genes. Molecular docking further supported these observations by indicating stable binding of 2-5(H)-Furanone to major angiogenic targets, including VEGFR2, MMP2, HIF-1, and PIK3CA. Collectively, our data demonstrate that 2-5(H)-Furanone potently inhibits angiogenesis, as evidenced in both HUVEC and zebrafish models, through functional and molecular mechanisms. These findings support the further development of 2-5(H)-Furanone as a promising anti-angiogenic therapy candidate.

Trees accumulate somatic mutations throughout their long lifespan, resulting in genetic mosaicism among branches. While recent genomic studies quantified these mutations, they were largely limited to describing static patterns of variation. In this study, we developed a mathematical model to infer the dynamic processes of somatic mutation accumulation from snapshot genomic data obtained from four tropical trees (Dipterocarpaceae), which dominate tropical rain forests in Southeast Asia. Our model focus on genetic differences between shoot apical meristems (SAMs) at branch tips and explicitly incorporate stem cell dynamics within SAMs during shoot elongation and branching, enabling us to quantify somatic genetic drift arising from stem cell lineage replacement. By comparing model predictions with empirical data from Dipterocarpaceae trees, we estimated key parameters governing stem cell dynamics and somatic mutation rates. Our results indicate that both shoot elongation and branching involve replacement of stem cell lineages, leading to a moderate degree of somatic genetic drift. Accounting for stem cell dynamics resulted in slightly lower mutation rate estimates than previous approaches that ignored these processes. Using the estimated parameters, we further performed stochastic simulations to predict patterns of somatic mutations, including features not directly observed in the sampled trees, such as occasional deviations of somatic mutation phylogenies from physical architecture. Together, our modeling framework provides insights into how genetic mosaicism is shaped within tropical trees and reveals the stem cell dynamics underlying their long-term growth and accumulation of somatic mutations. (236 words) Highlights- We built mathematical models to predict the genetic differences between branch tips by somatic mutations. - The model considers the varying dynamics of stem cells in shoot meristem during shoot elongation and branching. - We compared the model prediction with empirical data from tropical trees, Dipterocarpaceae, and estimated the dynamics of stem cells and mutation rate. - Somatic mutation dynamics were shaped by somatic genetic drift arising from stem cell lineage replacement during shoot elongation and branching. - Accounting for stem cell dynamics led to slightly smaller estimates of mutation rates compared with previous estimates that ignored the dynamics. - Our models offer insights into how genetic variability is shaped in the tropical trees and the stem cell dynamics underlying their long-term growth.

Climate change is reshaping the adaptive landscape of forest ecosystems, demanding more efficient strategies to identify and deploy resilient tree genotypes. Genomic prediction offers a powerful framework to accelerate selection for complex physiological traits underlying climate adaptability in long-lived species such as sessile oak (Quercus petraea (Matt.) Liebl.). Here, we conducted genomic prediction for three key physiological traits carbon isotope composition, nitrogen isotope composition, and the carbon-to-nitrogen content ratio (C/N ratio) measured in 746 trees genotyped with dense genome-wide markers ([~]580,000 SNPs). High genomic heritabilities were estimated across traits, with within-year prediction accuracies (Pearsons r between genomic estimated values and observed phenotypes) reaching 0.77. Notably, across-year and across-provenance predictions remained substantial (0.41 < r < 0.82), with predictability declining with increasing genetic distance (FST) between training and test provenances for nitrogen isotope composition and C/N ratio. In addition, GWAS-guided SNP preselection increased heritability capture by [~]15% relative to random SNP subsets. And, the pronounced provenance-by-environment interactions observed indicated substantial phenotypic plasticity in these traits. These results demonstrate the strong potential of applying genomic prediction to foliar physiological traits as polygenic predictors for climate adaptation in plants, support provenance-aware breeding to improve forest establishment, and provide practical strategies for deploying genomic prediction in long-lived species.

AO_SCPLOWBSTRACTC_SCPLOWA new Bayesian measure of phylogenetic information content is introduced based on geodesic distances in treespace. The measure is based on the relative variance of phylogenetic trees sampled from the posterior distribution compared to the prior distribution. This ratio is expected to equal 1 if there is no information in the data about phylogeny and 0 if there is complete information. Trees can be scaled to have the same mean tree length to avoid dominance by edge length information and focus on topological information. The method scales well, requiring only that a valid sample can be obtained from both prior and posterior distributions. We show how dissonance (information conflict) among data sets can also be estimated. Both simulated and empirical examples are provided to illustrate that the new approach produces sensible and intuitive results.