Biology subjects

Landis, J. B.

Publications and source records attributed to Landis, J. B..

At least 19 recordsLinked to original sources

bioRxiv2026

Morphological evolution and phylogeny are unlinked in Hawaiian Doryopteris (Cheilanthoideae: Pteridaceae)

Premise of the study: Doryopteris J.Sm. is a genus of dry-adapted ferns found widely across the southern hemisphere and the tropics. In the Hawaiian Islands, the genus is represented by four endemic species and one putative hybrid. Two of the endemic species (D. decora and D. decipiens) are widespread across all major islands, while two (D. angelica and D. takeuchii) are federally and state-listed endangered single-island endemics.We aimed to resolve the evolutionary relationships and biogeographic history of Hawaiian Doryopteris. Methods: We used a target-capture approach and the GoFlag 408 flagellate land plant probe set to sequence more than 400 nuclear loci for 40 Hawaiian and 29 non-Hawaiian individuals in Doryopteris and the related genera Lytoneuron and Ormopteris. After processing the sequences into alignments and single nucleotide polymorphism sites, we performed phylogenetic inference and population-level principal component analyses. Key results: We infer that Hawaiian Doryopteris are monophyletic and are nested within the pantropical species D. concolor. Within Hawai'i, clades and clusters of individuals correspond to geographical, geological, and climatological factors, more so than species identifications, with a few exceptions. We posit that Hawaiian Doryopteris represents an incipient radiation at the very earliest stages of divergence, and that budding speciation has led to non-monophyly of several taxa. Conclusions Our inference using genome-wide sequencing data sheds light on the complex evolutionary history of Hawaiian Doryopteris. Overall, the phylogeny of Hawaiian Doryopteris shows strong links with geographical, geological, and climatological processes and little with morphological evolution.

evolutionary biology↗

bioRxiv2026

BLink-seq delivers population-scale haplotypes without long reads: a scalable framework for non-model genomics

Information about segregating haplotypes and structural variation (SV) can be extremely rich for a variety of applications in population genomics but remains largely inaccessible for many non-model species. Of the available methods, linked-read sequencing is especially promising for its low cost and scalability, but its adoption remains limited. One existing linked-read method is Haplotagging, which barcodes sequencing reads to reconstruct long molecules that encode haplotype information, with the potential to generate phased whole-genome data and detect structural variants. In this study, we present BLink-seq, a novel Haplotagging method that is compatible with standard short-read next-generation sequencing platforms, is locally reproducible with low-cost reagents, and is scalable for high-throughput sample processing. We optimized library preparation parameters, explored their relationship to linked-read library metrics, and validated phasing performance and structural variant detection in two evolutionary extremes: an experimental Drosophila melanogaster cross of inbred lines carrying known inversions, and four Atlantic silverside (Menidia menidia) parent-offspring trios sourced from highly outbred, wild-caught populations. We then applied our protocol to a cohort of 376 silversides to demonstrate its scalability and potential for SV detection and genotype imputation. Using BLink-seq, we generated chromosome-scale phased blocks and identified known inversions in both validation datasets. We discovered previously uncharacterized structural complexity within a known adaptive inversion on silverside chromosome 11, demonstrating that linked-read data can refine our understanding of SV architecture beyond what short reads alone can resolve. Finally, we provide a user guide for researchers interested in using BLink-seq.

genomics↗

bioRxiv2026

Genomic sampling and population structure of farmer-maintained varieties reveal previously uncharacterized diversity of Theobroma cacao L. in Costa Rica

Understanding crop genetic diversity is essential for conservation and breeding, yet farmer-maintained germplasm remains largely underrepresented in genomic studies. Theobroma cacao L. has a complex domestication history and extensive global diversity, and cacao currently cultivated in Central America, particularly in Costa Rica, has been understudied compared to South American and Mexican cultivars despite cultural and historical importance. In this study, we investigate the genetic diversity of cacao from farmer-managed systems across Costa Rica to search for Criollo germplasm and identify and characterize any unique local genetic groups. Ninety-four trees were sampled from 17 farms across four regions of the country and sequenced using whole genome resequencing. Farmer materials were analyzed alongside 166 previously characterized reference accessions representing major cacao genetic groups. Population structure analyses, phylogenetic reconstruction, and network approaches revealed that Costa Rican cacao encompasses multiple known genetic groups, including Criollo-derived lineages, while also harboring locally distinct diversity not fully represented in current global reference collections. Analyses revealed close kinship between many accessions with no clear geographic patterns corresponding to the observed population differentiation, reflecting the effects of farmers in creating dominant patterns of gene flow through seed-saving, clonal propagation, and sharing genotypes among farms. Heterozygosity levels varied substantially among individuals, consistent with a mixture of highly inbred Criollo trees and more heterozygous, admixed genotypes. We find that farmer-managed cacao systems are reservoirs of genetic diversity, including possibly rare or historically important lineages, underscoring the value of these farming systems for effective conservation and management of genomic resources for cacao resilience and improvement.

genomics↗

bioRxiv2025

Diversity of the dwarf palmetto: A phylogeographic analysis of the North American coastal plain and investigation of stem polymorphism in Sabal minor (Jacq.) Pers.

Premise of the studySabal minor is considered one of two cold tolerant palm species, inhabiting riparian zones in temperate and subtropical North America. Ecologically it is often overlooked due to its short compact underground stem that makes it appear stemless, or acaulescent. However, across the central US Gulf Coast S. minor is polymorphic for trunk type, with some individuals identified as caulescent, bearing an above-ground trunk that can reach up to two meters in height. MethodsWe adopt a population genomics approach to characterize the genetic diversity of S. minor and to identify whether the caulescent and acaulescent forms of this temperate palm represent phenotypic variation within a single species. Key resultsThe caulescent and acaulescent forms are not reciprocally monophyletic, suggesting these two forms are phenotypic variants of a single species, S. minor s.l. Genetic clustering does not correspond to stem phenotype but rather reflects five discrete biogeographic clusters that span the native range. These geographic clusters indicate phylogeographic breaks along the Tombigbee River with a history that appears to be influenced by the delta of the Mississippi River. Two ecologically divergent populations, one in White Lake and another in Central Texas, show high genetic differentiation from surrounding populations indicating the presence of ecological barriers to gene flow. ConclusionsPopulation genetic structure of S. minor does not reflect stem morphotype (caulescence or acaulescence) supporting the current taxonomic recognition of one polymorphic species rather than two. However, populations of S. minor show genetic structuring corresponding to known phylogeographic barriers illustrating the dynamic roles regional landscape features played in shaping contemporary S. minor.

evolutionary biology↗

bioRxiv2025

AVITI library prep miniaturization and combining with Illumina data for phylogenomic and population genomic analyses

Recent advancements in next generation sequencing approaches allow for expansion of evolutionary research into the discovery of genetic patterns and processes underlying diversification across scales. The increased popularity of the Element Bioscience AVITI platform, partially due to the high sequencing accuracy and low cost of reagents, is becoming a viable alternative approach for generating massive amounts of comparative sequencing data across diverse organismal lineages. Using a data set of five accessions from the monocot genus Costus, we tested miniaturization conditions for generating robust, cost-effective libraries and made comparisons of data generated by AVITI and Illumina sequencing platforms to investigate the potential for combining data for population genomic and phylogenomic analyses. Our results show that the AVITI and Illumina data sets are highly congruent in terms of inferring overlapping SNPs, with only a small fraction picked up by only one of the two platforms. The rates of duplication in miniaturized libraries were much higher than in full volume libraries and in the Illumina libraries, resulting in missing SNPs and less sequence coverage when volumes are reduced. For all generated libraries, most downstream evolutionary analyses, including clustering algorithms (such as PCA) and phylogenetic inference, yielded similar results. However, Structure analyses were less consistent across datasets, with data from the most miniaturized libraries being assigned to the wrong clusters. The AVITI platform should be seen as a cost-effective approach for generating genomic data for comparison across taxonomic lineages, even for ongoing projects where Illumina data already exists.

evolutionary biology↗

bioRxiv2024

Ectopic cambia in Japanese wisteria (Wisteria floribunda) vines are associated with the expression of conserved KNOX genes

Secondary growth is a conserved mechanism that gives rise to vascular tissues produced via a single vascular cambium. Molecular mechanisms underlying this process are characterized mostly in model species bearing typical vascular architecture, while the genetics underlying ecologically-important atypical vascular architectures remain unexplored. We use developmental anatomy, comparative transcriptomics, and molecular evolutionary analyses to address this knowledge gap, investigating how multiple ectopic cambia (EC) form in the woody vine Japanese wisteria. Anatomical studies show EC in Japanese wisteria arise from cortical parenchyma, while cambium-specific transcriptome comparisons reveal that genes acting as regulators of typical cambium development in model species are likewise associated with atypical EC development. Gene trees of KNOX proteins indicate duplication events may contribute to EC formation, including a Fabaceae-specific duplication of KNAT6 detected as under positive selection. These findings reveal insights into the genetics of EC formation, advancing our understanding of the development of complex vascular traits.

plant biology↗

bioRxiv2024

Target enrichment phylogenomics and biogeographic analyses unravel rapid radiation and reticulate evolution between Hainan-South China mainland -Vietnam in Section Nintooa (Lonicera, Caprifoliaceae)

The South China mainland and nearby islands are biodiversity hotspots. Section Nintooa, widely distributed across mainland China, Vietnam, and Hainan Island, exhibits a typical disjunct distribution pattern. However, the origins of the flora of Hainan Island and the phylogenetic relationships within Section Nintooa remain contentious. In this study, we collected 81 samples encompassing all recognized species of Section Nintooa, along with samples from other sections of Lonicera. We reconstructed the phylogenetic relationships using 491 orthologous nuclear genes and complete plastomes generated by target enrichment and genome skimming sequencing. Our nuclear gene-based species and concatenated trees support the monophyly of Section Nintooa. The species tree indicates that the Vietnamese and Hainan populations form sister clades. However, the plastome results indicate that Section Nintooa is polyphyletic, with subsection Volubilis forming a monophyletic group and subsection Calcaratae forming a sister clade with other members of subgenus Chamaecerasus. Our hybridization network analysis reveals extensive gene flow within Section Nintooa, whereas subsection Calcaratae shows no gene flow with subsection Volubilis, leaving the origin of Calcaratae unclear. Lonicera species from Hainan Island exhibit unstable phylogenetic positions and underwent a rapid radiation during the Miocene. Biogeographical results indicate that populations from Vietnam and Hainan both originated from mainland China. Overall, our findings enhance the understanding of the evolutionary diversification history of Lonicera.

plant biology↗

bioRxiv2024

nQuack: An R package for predicting ploidal level from sequence data using site-based heterozygosity

PremiseTraditional methods of ploidal level estimation are tedious; leveraging sequence data for cytotype estimation is an ideal alternative. Multiple statistical approaches to leverage DNA sequence data for ploidy prediction based on site-based heterozygosity have been developed. However, these approaches may require high-coverage sequence data, use improper probability distributions, or have additional statistical shortcomings that limit inference abilities. We introduce nQuack, an open-source R package, that addresses the main shortcomings of current methods. Methods and ResultsnQuack performs model selection for improved ploidy predictions. Here, we implement expected maximization algorithms with normal, beta, and beta-binomial distributions. Using extensive computer simulations that account for variability in sequencing depth, as well as real data sets, we demonstrate the utility and limitations of nQuack. ConclusionInferring ploidal level based on site-based heterozygosity alone is discouraged due to the low accuracy of pattern-based inference.

bioinformatics↗

bioRxiv2023

Natural selection drives emergent genetic homogeneity in a century-scale experiment with barley

Direct observation is central to our understanding of the process of adaptation, but evolution is rarely documented in a large, multicellular organism for more than a few generations. Here, we observe genetic and phenotypic evolution across a century-scale competition experiment, barley composite cross II (CCII). CCII was founded in 1929 with tens of thousands of unique genotypes and has been adapted to local conditions in Davis, CA, USA for 58 generations. We find that natural selection has massively reduced genetic diversity leading to a single clonal lineage constituting most of the population by generation F50. Selection favored alleles originating from similar climates to that of Davis, and targeted genes regulating reproductive development, including some of the most well-characterized barley diversification loci, Vrs1, HvCEN, and Ppd-H1. We chronicle the dynamic evolution of reproductive timing in the population and uncover how parallel molecular pathways are targeted by stabilizing selection to optimize this trait. Our findings point to selection as the predominant force shaping genomic variation in one of the worlds oldest ongoing biological experiments. One-Sentence SummaryWholesale genetic restructuring of an experimental population is a consequence of rapid environmental adaptation.

genetics↗

bioRxiv2023

Comparative phylogenomic analyses of SNP versus full locus datasets: insights and recommendations for researchers

PremiseIn phylogenomic analyses, no consensus exists on whether using single nucleotide polymorphisms (SNPs) or including flanking regions (full locus) is best, nor how strictly missing data should be filtered. Moreover, empirical evidence on whether SNP-only trees are suitable for downstream phylogenetic comparative methods such as divergence time estimation and ancestral state reconstructions is lacking. MethodsUsing GBS data from 22 taxa of Glycine, we addressed the effects of SNP vs. locus usage and filtering stringency on phylogenomic inference and phylogenetic comparative methods. We compared branch length, node support, and divergence time estimation across eight datasets with varying amounts of missing data and total size. ResultsOur results reveal five aspects of phylogenomic data usage: 1. tree topology is largely congruent regardless of data type or filtering parameters; 2. filtering missing data too strictly reduces the confidence in some relationships; 3. absolute branch lengths vary by two orders of magnitude between datasets; 4. data type and branch length variation have little effect on divergence time estimation; 5. phylograms significantly alter the estimation of ancestral states. DiscussionWhen conducting phylogenomic analyses we recommend not to filter datasets too strictly to minimize the risk of misleading topologies, low support, and inaccurate divergence times.

evolutionary biology↗

bioRxiv2023

Pleistocene glaciation advances the younger temporal dimension of species diversification in a major biodiversity hotspot

O_LIThe expansive Himalayan-Hengduan Mountains (HM) and Qinghai-Tibet Plateau (QTP) form a biodiversity hotspot imperiled by global change. The species diversity, resulting from myriad factors led to plant diversification from 10 million years ago till now. However, despite understanding speciation timing better, a lack of in-depth population-level studies and a dearth of organismal sampling among closely related species and populations leaves an incomplete view of diversification trends and biotic influences. C_LIO_LIWe delve into the complex factors influencing diversification through genomic and eco-morphological analysis within the Stellera chamaejasme L. complex, known for its significant floral diversity. C_LIO_LIOur results uncover four cryptic species, indicating a more recent and younger diversification period ([~]2.67-0.9 Mya), driven by Pleistocene glaciation and a complex set of interacting biotic factors. These factors prompted allopatric speciation and advocated cyclical warming-cooling episodes along latitudinal and altitudinal gradients throughout the Pleistocene. C_LIO_LIThe study emphasizes the existence of cryptic species within these mountains, broadening our understanding of species diversification to more recent than previously recognized. This novel perspective may reshape evolutionary paradigms in plant science. Additionally, it also brings to light concerns over future warmings possible impacts on alpine species distribution and speciation, underlining the urgency for increased conservation efforts. C_LI

evolutionary biology↗

bioRxiv2022

Genomic underpinnings of convergent adaptation to high altitudes for alpine plants

Evolutionary convergence is one of the most striking examples of adaptation driven by natural selection. However, genomic evidence for convergent adaptation to extreme environments remains scarce. The Himalaya-Hengduan Mountains represent the worlds most species-rich temperate alpine biota, providing an ideal "natural laboratory" for studying convergent adaptation to high altitudes. Here, we generate reference genomes for two alpine plants, Saussurea obvallata (Asteraceae) and Rheum alexandrae (Polygonaceae), with 37,938 and 61,463 annotated protein-coding genes. By integrating an additional five alpine genomes, we investigate genomic signatures of convergent adaptation to the hostile environments of high altitudes. We show that alpine genomes tend to mitigate their genetic load by contracting genes functioning in the immune system to survive such harsh environments with few pathogens present. We detect signatures of convergent positive selection on a set of genes involved in reproduction and development and reveal that molecular convergence has acted on genes involved in self-incompatibility, cell wall modification, DNA repair and stress resistance, which underlie adaptation to extremely cold, high UV radiation and hypoxia environments. Using gene expression profiles, we further demonstrate that genes associated with cuticular wax and flavonoid biosynthetic pathways exhibit higher expression levels in leafy bracts, shedding lights on the genetic mechanisms of the adaptive greenhouse morphology. Our integrative data provide genomic insights into the convergent evolution at higher-taxonomic levels, aiding in deep understanding of genetic adaptation to complex environments.

evolutionary biology↗

bioRxiv2022

Target sequence capture data shed light on the deeper evolutionary relationship on the subgenus Chamaecerasus of Lonicera (Caprifoliaceae)

The genus Lonicera L. is widely distributed and is well-known for its high species richness and morphological diversity. Previous studies have suggested that many sections of Lonicera are not monophyletic and phylogenetic relationships within the genus are still poorly known. In this study, we sampled 37 accessions of Lonicera, covering four sections of subgenus Chamaecerasus plus six outgroup taxa to recover the main clades of Lonicera based on sequences of nuclear loci generated by target enrichment and cpDNA from genome skimming. We found extensive cytonuclear discordance across the subgenus. Both nuclear and plastid phylogenetic analyses supported subgenus Chamaecerasus sister to subgenus Lonicera. Within subgenus Chamaecerasus, sections Isika and Niatoon were polyphyletic. Based on the nuclear and chloroplast phylogenies we propose to merge Lonicera korolkowii into section Coeloxylosteum and Lonicera caerulea into section Nintooa. In addition, Lonicera is estimated to have originated in the late Miocene (19.84 Ma). The stem age of section Nintooa was estimated to be 17.97 Ma (95% HPD: 13.31- 22.89). The stem age of subgenus Lonicera was estimated to be 16.35 Ma (95% HPD: 9.33- 45.15). Ancestral area reconstruction analyses indicate that Lonicera originated in the Qinghai Tibet Plateau (QTP) and Asia, with subsequent dispersal into other areas. The aridification of the Asian interior possibly promoted the rapid radiation of Lonicera within this region, and the uplift of the QTP appears to have triggered the dispersal and recent rapid diversification of the genus in the QTP and adjacent regions. Overall, this study provides new insights into the taxonomically complex lineages of Lonicera at the section level and the process of speciation.

evolutionary biology↗

bioRxiv2022

Genomic analyses provide new insights into the evolutionary history and reproduction of the Paleogene relictual Kingdonia (Circaeasteraceae, Ranunculales)

Asexual lineages are perceived to be short-lived on evolutionary timescales due to accumulation of deleterious mutations. Hence reports for exceptional cases of putative ancient asexual species usually raise doubts about whether such species are recently derived or engage in some undocumented sexual reproduction. However, there have been few studies to solve the mystery. The monotypic Kingdonia dating to the early Eocene, contains only K. uniflora that has no known definitive evidence for sexual reproduction nor records for having closely related congeneric sexual species, seeming to have persisted under strict asexuality for long periods of time. In this study, we use population genomic analyses to test for reproduction mode and infer the evolutionary process and mechanisms facilitating the survival of the species. Our results indicate the presence of three differentiating genetic lineages within the species and support that asexual reproduction in K. uniflora indicated by high allelic heterozygosity had occurred prior to the lineage differentiation ([~]0.5 mya). We also detected DNA recombination events in some populations, in line with occurrence of unseen and unevenly distributed sexual reproduction among populations. However the observation of high linkage disequilibrium, relatively high ratio of{pi} N/{pi}S (nonsynonymous versus synonymous nucleotide diversity), together with high allelic heterozygosity suggest the sexual reproduction is infrequent. Furthermore, we found that genes containing SNPs with elevated Fst values are significantly enriched in functions associated with seed development, suggesting differentiation in genes regulating seed development is likely to be the key reason of the uneven distribution of sexual reproduction in K. uniflora. Evidence from our study supports predominate asexual reproduction in K. uniflora, but unseen sexual reproduction must have played a key role to ensure the long-term survival of the lineage in general. Uneven distribution of sexual reproduction in the species may be a key factor underlying the observed genetic differentiation between populations. This study provides novel insights into the reproduction and evolution of Kingdonia, a relict lineage evolved in the Paleogene and known for asexual reproduction, and demonstrate the power of data from population genome sequencing in resolving long-standing evolutionary questions.

genomics↗

bioRxiv2021

Towards a global perspective for Salvia L: Phylogeny, diversification, and floral evolution

Premise of this studySalvia is the most species-rich genus in Lamiaceae, encompassing approximately 1000 species distributed all over the world. We sought a new evolutionary perspective for Salvia by employing macroevolutionary analyses to address the tempo and mode of diversification. To study the association of floral traits with speciation and extinction, we modeled and explored the evolution of corolla length and the lever-mechanism pollination system across our Salvia phylogeny. MethodsWe reconstructed a multigene phylogeny for 366 species of Salvia in the broad sense including all major recognized lineages and numerous species from Iran, a region previously overlooked in studies of the genus. Our phylogenetic data in combination with divergence time estimates were used to examine the evolution of corolla length, woody vs. herbaceous habit, and presence vs. absence of a lever mechanism. We investigated the timing and dependence of Salvia diversification related to corolla length evolution through a disparity test and BAMM analysis. A HiSSE model was used to evaluate the dependency of diversification on the lever-mechanism pollination system in Salvia. Key ResultsBased on recent investigations and classifications, Salvia is monophyletic and comprises [~]1000 species. Our inclusion, for the first time, of a comprehensive sampling for Iranian species of Salvia provides higher phylogenetic resolution for southwestern Asian species than obtained in previous studies. A medium corolla length (15-18mm) was reconstructed as the ancestral state for Salvia with multiple shifts to shorter and longer corollas. Macroevolutionary model analyses indicate that corolla length disparity is high throughout Salvia evolution, significantly different from expectations under a Brownian motion model during the last 28 million years of evolution. Our analyses show evidence of a higher diversification rate of corolla length for some Andean species of Salvia compared to other members of the genus. Based on our tests of diversification models, we reject the hypothesis of a direct effect of the lever mechanism on Salvia diversification. ConclusionsUsing a broader species sampling than previous studies, we obtained a well- resolved phylogeny for southwest Asian species of Salvia. Corolla length is an adaptive trait throughout the Salvia phylogeny with a higher rate of diversification in the South American clade. Our results suggest caution in considering the lever-mechanism pollination system as one of the main drivers of speciation in Salvia.

plant biology↗

bioRxiv2021

Hybridization and introgression are prevalent in Southern European Erysimum (Brassicaceae) species

Background and AimsHybridization is a common and important force in plant evolution. One of its outcomes is introgression - the transfer of small genomic regions from one taxon to another by hybridization and repeated backcrossing. This process is believed to be common in glacial refugia, where range expansions and contractions can lead to cycles of sympatry and isolation, creating conditions for extensive hybridization and introgression. Polyploidization is another genome-wide process with a major influence on plant evolution. Both hybridization and polyploidization can have complex effects on plant evolution. However, these effects are often difficult to understand in recently evolved species complexes. MethodsWe combined flow cytometry, transcriptomic and genomic analyses, and pollen-tube growth assays to investigate the consequences of polyploidization, hybridization, and introgression on the recent evolution of several Erysimum (Brassicaceae) species from the South of the Iberian Peninsula, a well-known glacial refugium. This species complex differentiated in the last 2Myr, and its evolution has been hypothesized to be determined mainly by polyploidization, interspecific hybridization, and introgression. Key ResultsOur results support a scenario of widespread hybridization involving both extant and "ghost" taxa. Several taxa studied here, most notably those with purple corollas, are polyploids, likely of allopolyploid origin. Moreover, hybridization in this group might be an ongoing phenomenon, as prezygotic barriers appeared weak in many cases. ConclusionsThe evolution of Erysimum spp. has been determined by hybridization to a large extent. The adaptive value of such genomic exchanges remains unclear, but our results indicate the importance of hybridization for plant diversification across evolutionary scales.

evolutionary biology↗

bioRxiv2021

Measuring hidden phenotype: Quantifying the shape of barley seeds using the Euler Characteristic Transform

Shape plays a fundamental role in biology. Traditional phenotypic analysis methods measure some features but fail to measure the information embedded in shape comprehensively. To extract, compare, and analyze this information embedded in a robust and concise way, we turn to Topological Data Analysis (TDA), specifically the Euler Characteristic Transform. TDA measures shape comprehensively using mathematical representations based on algebraic topology features. To study its use, we compute both traditional and topological shape descriptors to quantify the morphology of 3121 barley seeds scanned with X-ray Computed Tomography (CT) technology at 127 micron resolution. The Euler Characteristic Transform measures shape by analyzing topological features of an object at thresholds across a number of directional axes. A Kruskal-Wallis analysis of the information encoded by the topological signature reveals that the Euler Characteristic Transform picks up successfully the shape of the crease and bottom of the seeds. Moreover, while traditional shape descriptors can cluster the seeds based on their accession, topological shape descriptors can cluster them further based on their panicle. We then successfully train a support vector machine (SVM) to classify 28 different accessions of barley based exclusively on the shape of their grains. We observe that combining both traditional and topological descriptors classifies barley seeds better than using just traditional descriptors alone. This improvement suggests that TDA is thus a powerful complement to traditional morphometrics to comprehensively describe a multitude of "hidden" shape nuances which are otherwise not detected.

plant biology↗

bioRxiv2021

Insights into the drivers of radiating diversification in biodiversity hotspots using Saussurea (Asteraceae) as a case

O_LIThe Qinghai-Tibet Plateau (QTP) encompasses areas with a remarkably high degree of biodiversity, harboring exceptional species-rich radiations. How these radiations formed by interacting with geology, climate and ecology remains seldom examined. C_LIO_LIWe investigate the roles of abiotic (environmental) and biotic (species-intrinsic) factors in driving radiating diversification of Saussurea (Asteraceae) by deploying a number of time-dependent, paleoenvironment-dependent and trait-dependent models, as well as ecological distribution data. C_LIO_LIWe show that three main clades of Saussurea begin to diversify in the Miocene almost simultaneously, with increasing diversification rates toward the present and negative dependence to paleotemperature. Acceleration in diversification rates are correlated with adaptive traits, as well climate lability, niche breadth and species range. C_LIO_LIWe conclude that fluctuation of paleoclimate along with complex QTP environments provided opportunities for increased diversification rates of Saussurea with diverse adaptive traits, highlighting the importance of combinations of clade-specific traits and ecological niches in driving rapid radiation. C_LI

evolutionary biology↗