Biology subjects

Eiserhardt, W. L.

Publications and source records attributed to Eiserhardt, W. L..

12 recordsLinked to original sources

bioRxiv2026

A large phylogenetic tree for euphyllophytes

PremiseMolecular datasets for estimating phylogenetic trees increasingly include more species and gene regions. Often trees are constructed using backbone phylogenies, subtrees, and other techniques to address the challenges of large dataset size. Currently, there is no established approach to integrate these rapidly expanding datasets. MethodsWe generated a phylogenetic tree (and 1,000 bootstrap trees) with divergence times that span euphyllophytes. To do this, we integrated taxonomically broad dated backbone phylogenies with species-level trees generated from phylogenetic analysis of individual clades. Datasets for species-level trees were assembled using PyPHLAWD. ResultsThe resulting dated phylogenetic tree includes: 121,641 angiosperm species; 1,026 gymnosperms; and 5,603 ferns. This is the largest euphyllophyte phylogenetic tree constructed to date. Topological uncertainty spikes at the start of the Cretaceous and gradually increases during the Cenozoic. Uncertainty in age estimates gradually increases in the Cenozoic but increases dramatically in the most recent 5 Myrs. DiscussionThis dated phylogenetic framework can underpin evolutionary studies spanning euphyllophytes, and enable the integration of insights from the recent to the distant past. Our approach also enables the tree to be easily updated in the future to reflect future increases in data availability, and systematic and taxonomic advances within specific clades.

plant biology↗

bioRxiv2024

The Arabidopsis thaliana core splicing factor PORCUPINE/SmE1 requires intron-mediated expression

Plants are prone to genome duplications and tend to preserve multiple gene copies. This is also the case for the genes encoding the Sm proteins of Arabidopsis thaliana (L). The Sm proteins are best known for their roles in RNA processing such as pre-mRNA splicing and nonsense-mediated mRNA decay. In this study, we have taken a closer look at the phylogeny and differential regulation of the SmE-coding genes found in A. thaliana, PCP/SmE1, best known for its cold-sensitive phenotype, and its paralog, PCPL/SmE2. The phylogeny of the PCP homologs in the green lineage shows that SmE duplications happened multiple times independently in different plant clades and that the duplication that gave rise to PCP and PCPL occurred only in the Brassicaceae family. Our analysis revealed that A. thaliana PCP and PCPL proteins, which only differ in two amino acids, exhibit a very high level of functional conservation and are able to perform the same function in the cell. However, our results indicate that PCP is the prevailing copy of the two SmE genes in A. thaliana as it is more highly expressed and that the main difference between PCP and PCPL resides in their transcriptional regulation, which is strongly linked to intronic sequences.

plant biology↗

bioRxiv2024

Early Cretaceous Origin and Evolutionary History of Palms (Arecaceae) inferred from 1,033 Nuclear Genes and a New Synthesis of Fossil Evidence

AO_SCPLOWBSTRACTC_SCPLOWTropical rainforests are home to almost half of all known plant diversity, yet a shortfall in tropical plant phylogenetic hypotheses is hindering our understanding of how rainforests have formed and adapted to past global changes. Phylogenetic and historical biogeographic evidence from key rainforest lineages, including palms (Arecaceae), are required to illuminate the history of these ecosystems. However, our current understanding of the palm tree of life is based on uneven sampling of data from the plastid and nuclear genome, and numerous palm genera and palm fossils have been described or revised over the past decade, casting doubt on many palm relationships, ages and ancestral ranges inferred in previous studies. Here, we infer the phylogenetic relationships of all palm genera based on data from 1,033 nuclear genes generated using target sequence capture. Our palm tree of life is highly resolved and supported. Remaining areas of ambiguity reflect the complex dynamics of palm evolution, including many rapid diversification events in subfamily Arecoideae and putative cases of ancient reticulation throughout the family. We review the phylogenetic placement and age of hundreds of palm fossils and use a vetted selection to estimate divergence times and ancestral ranges for all palm genera. We show that the family is older than previously thought, likely first diversifying in the Early Cretaceous in Laurasia, and that three quarters of the genera had originated by the Oligocene. The early spread of palms across the world involved at least 40 long-distance dispersals across oceanic gaps. Dispersals away from northern latitudes vastly outnumber dispersals into these latitudes, consistent with the ancient affinity of palms for megathermal climates, and suggesting that global cooling during the Oligocene was a major constraint on early palm distribution. Our dated phylogenomic tree and curated fossil dataset provide a new foundation for evolutionary studies on palms, opening the door to deeper research on the rainforest biome in which they thrive.

evolutionary biology↗

bioRxiv2023

Occurrence-based diversity estimation reveals macroecological and conservation knowledge gaps for global woody plants

Incomplete sampling of species geographic distributions has challenged biogeographers for many years to precisely quantify global-scale biodiversity patterns. After correcting for the spatial inequality of sample completeness, we generated a global species diversity map for woody angiosperms (82,974 species, 13,959,780 occurrence records). The estimated diversity demonstrated non-linear latitudinal and longitudinal patterns that were potentially related to region-specific biogeographic factors including current climate, paleoclimate, and topographical factors, while energy availability was the most important predictor at a global level. We identified the areas with potentially high species richness and rarity, but poorly explored, unprotected, and threatened by deforestation: they are distributed mostly at low latitudes across central South America, central Africa, subtropical China, and Indomalayan islands. These priority areas for botanical exploration would help to efficiently fill spatial knowledge gaps for better describing the status of biodiversity and improve the effectiveness of the protected area network for global woody plant conservation. TeaserBias-corrected diversity map based on occurrence records sheds new light on global macroecology and conservation of woody angiosperms.

ecology↗

bioRxiv2023

Genomic signatures of past megafrugivore-mediated dispersal in Malagasy palms

O_LISeed dispersal is a key process in the generation and maintenance of genetic diversity and genetic differentiation of plant populations in tropical ecosystems. During the Last Quaternary, most seed-dispersing megafauna was lost globally, but whether this has caused dispersal limitation, loss of genetic diversity, and increased genetic differentiation between plant populations with large, megafaunal fruits (i.e., > 4 cm - megafruits) remains unclear. C_LIO_LIHere, we assessed whether megafrugivore extinctions in Madagascar (e.g., giant lemurs, elephant birds) have affected the genetic diversity and genetic differentiation of four animal-dispersed Malagasy palm (Arecaceae) species with large (Borassus madagascariensis), medium-sized (Hyphaene coriacea, Bismarckia nobilis), and small (Chrysalidocarpus madagascariensis) fruits. We integrated double-digest restriction-site-associated DNA sequencing (ddRAD) of 167 individuals from 25 populations with (past) distribution ranges for extinct and extant seed-dispersing animal species, climate and human impact data, and applied linear mixed-effects models to explore the drivers of variation in genetic diversity and genetic differentiation across Malagasy palm populations. C_LIO_LIWe detected higher genetic diversity in species with megafruits than in the species with small fruits, and genetic differentiation was lowest for the human-used medium-sized megafruit species. Furthermore, we found that a higher number of shared extinct megafrugivore species between palm population pairs was associated with less genetic differentiation, indicating higher gene flow, whereas no relationship with extant frugivores - that are not able to swallow and disperse the seeds - was found. Finally, genetic diversity decreased with road density, whereas genetic differentiation decreased with increasing human population density, but only for populations with megafruits. C_LIO_LIOur results suggest that the legacy of megafrugivores regularly achieving long dispersal distances is still reflected in the genetic diversity and genetic differentiation of palms that were formerly dispersed by such large animals. Furthermore, high genetic diversity and low genetic differentiation were possibly maintained after the megafauna extinctions through human-mediated dispersal, long generation times, and long lifespans of these palms. Our study illustrates how integrating genetics with ecological data on species interactions, climate, and human impact, provides novel insights into the consequences of megafauna extinctions for plants with megafruits. C_LI

evolutionary biology↗

bioRxiv2022

Socioeconomics and biogeography jointly drive geographic biases in our knowledge of plant traits: a global assessment of the Raunkiaerian shortfall in plants

The traits of plants determine how they interact with each other and their environment, constituting key knowledge for diverse fields. The lack of comprehensive knowledge of plant traits (the "Raunkiaerian shortfall") poses a major, cross-disciplinary, barrier to scientific advancement. Spatial biases in trait coverage may also lead to erroneous conclusions affecting ecosystem management and conservation planning. Thus, there is an urgent need to assess the spatial completeness of plant trait data, understand drivers of geographic biases, and to identify solutions for filling regional gaps. Here, we leverage a comprehensive set of regional species checklists for vascular plants and trait data for 2,027 traits and 128,929 plant species from the TRY database to assess trait data completeness across the globe. We show that trait data availability in TRY is associated with socioeconomic and biological factors influencing sampling likelihood: trait completeness was positively associated with mean species range size, research expenditure, and human population density and negatively associated with endemism and vascular plant species richness. Integration of a second, regional trait database (AusTraits) more than doubled trait completeness for the continent covered, indicating that the creation and integration of regional databases can rapidly expand trait completeness. Plain Language SummaryThe traits of plants determine how they interact with each other and their environment. Our knowledge of plant traits is incomplete, limiting scientific advancement as well as our ability to manage ecosystems and plan conservation actions. We show that there are large biases in trait data availability which are associated with both biological factors (range size, endemism, species richness) and socioeconomic factors (research expenditure, human population density). We also show how regionally-focused efforts can help rapidly expand trait data availability.

ecology↗

bioRxiv2021

A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life

The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. This paper (i) documents our methods, (ii) describes our first data release and (iii) presents a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic dataset for angiosperms to date, comprising 3,099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96%) and 2,333 genera (17%). Using the multi-species coalescent, we inferred a "first pass" angiosperm tree of life from the data, which totalled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns. The tree is strongly supported and highly congruent with existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated dataset, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer. This major milestone towards a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardised nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the worlds natural history collections.

evolutionary biology↗

bioRxiv2020

Quaternary climate change explains global patterns of tree beta-diversity

Both historical and contemporary environmental conditions determine present biodiversity patterns, but their relative importance is not well understood. One way to disentangle their relative effects is to assess how different dimensions of beta-diversity relate to past climatic changes, i.e., taxonomic, phylogenetic and functional compositional dissimilarity, and their components generated by replacement of species, lineages and traits (turnover) and richness changes (nestedness). Here, we quantify global patterns of each of these aspects of beta-diversity among neighboring sites for angiosperm trees using the most extensive global database of tree species-distributions (43,635 species). We found that temperature change since the Last Glacial Maximum (LGM) was the major influence on both turnover and nestedness components of beta-diversity, with a negative correlation to turnover and a positive correlation to nestedness. Moreover, phylogenetic and functional nestedness was higher than expected from taxonomic beta-diversity in regions that experienced large temperature changes since the LGM. This pattern reflects relatively greater losses of phylogenetic and functional diversity in species-poor assemblages, possibly caused by phylogenetically and functionally selective species extinction and recolonization during glacial-interglacial oscillations. Our results send a strong warning that rapid anthropogenic climate change is likely to result in a long-lasting phylogenetic and functional compositional simplification, potentially impairing forest ecosystem functioning.

ecology↗

bioRxiv2020

Paleoclimate and current climate collectively shape the phylogenetic and functional diversity of trees worldwide

Trees are of vital importance for ecosystem functioning and services at local to global scales, yet we still lack a detailed overview of the global patterns of tree diversity and the underlying drivers, particularly the imprint of paleoclimate. Here, we present the high-resolution (110 km) worldwide mapping of tree species richness, functional and phylogenetic diversities based on [~]7 million quality-assessed occurrences for 46,752 tree species (80.5% of the estimated total number of tree species), and subsequent assessments of the influence of paleo-climate legacies on these patterns. All three tree diversity dimensions exhibited the expected latitudinal decline. Contemporary climate emerged as the strongest driver of all diversity patterns, with Pleistocene and deeper-time (>107 years) paleoclimate as important co-determinants, and, notably, with past cold and drought stress being linked to reduced current diversity. These findings demonstrate that tree diversity is affected by paleoclimate millions of years back in time and highlight the potential for tree diversity losses from future climate change.

ecology↗

bioRxiv2020

Half of the world's tree biodiversity is unprotected and is increasingly threatened by human activities

Although trees are key to ecosystem functioning, many forests and tree species across the globe face strong threats. Preserving areas of high biodiversity is a core priority for conservation; however, different dimensions of biodiversity and varied conservation targets make it difficult to respond effectively to this challenge. Here, we (i) identify priority areas for global tree conservation using comprehensive coverage of tree diversity based on taxonomy, phylogeny, and functional traits; and (ii) compare these findings to existing protected areas and global biodiversity conservation frameworks. We find that ca. 51% of the top-priority areas for tree biodiversity are located in current protected areas. The remaining half top-priority areas are subject to moderate to high human pressures, indicating conservation actions are needed to mitigate these human impacts. Our findings emphasize the effectiveness of using tree conservation priority areas for future global conservation planning.

ecology↗

bioRxiv2020

The Demographic History of Micro-endemics: Have Rare Species Always Been Rare?

Extinction has increased as human activities impact ecosystems. Conservation assessments for the IUCN red list are a fundamental tool in aiding the prevention of further extinction, yet, relatively few species have been thoroughly assessed. To increase the efficiency of assessments, novel approaches are needed to highlight threatened species that are currently data deficient. Many Madagascan plant species currently have extremely narrow ranges, but this may not have always been the case. To assess this, we used high-throughput DNA sequencing for 2-5 individuals of each species - reflecting the paucity of samples available for rare species. We estimated effective population size (Ne) for each species and compared this to census population (Nc) sizes when known. In each case, Ne was an order of magnitude larger than Nc - a signature of rapid, recent population decline. We then estimated the demographic history of each species, tracking changes in Ne over time. Five out of ten species displayed significant population declines towards the present (68-90% decreases). Our results for palm trees indicate that it is possible to predict extinction risk, particularly in the most threatened species. We performed simulations to show that our approach has the power to detect population decline during the Anthropocene, but performs less well when less data is used. Similar declines to those in palms were observed in data deficient species or those assessed as of least concern. These analyses reveal that Madagascars narrow endemics were not always rare, having experienced rapid decline in their recent history. Our approach offers the opportunity to target species in need of conservation assessment with little prior information, particularly in regions where human modification of the environment has been rapid. SummaryCurrent IUCN conservation assessment methods are reliant on observed declines in species population and range sizes over the last one hundred years, but for the majority of species this information is not available. We used a population genetic approach to reveal historical demographic decline in the rare endemic flora of Madagascar. These results show that it is possible to predict extinction risk from demographic patterns inferred from genetic data and that destructive human influence is likely to have resulted in the very high frequency of narrow endemics present on the island. Our approach will act as an important tool for rapidly assessing the threatened status of poorly known species in need of further study and conservation, particularly for tropical flora and fauna.

evolutionary biology↗

bioRxiv2018

A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-medoids Clustering

Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the cost associated with developing targeted sequencing approaches is preliminary data needed for identifying orthologous loci for probe design. In plants, identifying orthologous loci has proven difficult due to a large number of whole-genome duplication events, especially in the angiosperms (flowering plants). We used multiple sequence alignments from over 600 angiosperms for 353 putatively single-copy protein-coding genes to design a set of targeted sequencing probes for phylogenetic studies of any angiosperm lineage. To maximize the phylogenetic potential of the probes while minimizing the cost of production, we introduce a k-medoids clustering approach to identify the minimum number of sequences necessary to represent each coding sequence in the final probe set. Using this method, five to 15 representative sequences were selected per orthologous locus, representing the sequence diversity of angiosperms more efficiently than if probes were designed using available sequenced genomes alone. To test our approximately 80,000 probes, we hybridized libraries from 42 species spanning all higher-order lineages of angiosperms, with a focus on taxa not present in the sequence alignments used to design the probes. Out of a possible 353 coding sequences, we recovered an average of 283 per species and at least 100 in all species. Differences among taxa in sequence recovery could not be explained by relatedness to the representative taxa selected for probe design, suggesting that there is no phylogenetic bias in the probe set. Our probe set, which targeted 260 kbp of coding sequence, achieved a median recovery of 137 kbp per taxon in coding regions, a maximum recovery of 250 kbp, and an additional median of 212 kbp per taxon in flanking non-coding regions across all species. These results suggest that the Angiosperms353 probe set described here is effective for any group of flowering plants and would be useful for phylogenetic studies from the species level to higher-order lineages, including all angiosperms.

evolutionary biology↗