Biology subjects

McTavish, E. J.

Publications and source records attributed to McTavish, E. J..

9 recordsLinked to original sources

bioRxiv2026

clootl: an R package for accessing and manipulating a complete, versioned avian phylogeny

Birds are frequently used as a focal taxon for evolutionary and ecological studies. Thousands of papers a year are published using birds as study systems. Hundreds more are published clarifying the evolutionary relationships among clades or regionally circumscribed sets of bird species. Up to date phylogenies are essential for informing and guiding avian studies, controlling for the expectation of shared trait evolution, and for science communication, among other applications. However, employing up to date phylogenies to address these questions has proven challenging for a number of reasons. First, individually published phylogenies are often hard to access in a usable manner. For example, sequences are usually made available, and an image of the phylogeny is published, but the actual phylogeny data product is often not digitally available. Second, published phylogenies often do not include all taxa of interest or have branch lengths in units of time. Third, taxonomic mismatches between phylogenies and existing datasets can complicate analyses. We address these issues by sharing an R package, clootl, that wraps together a new, complete, dated bird phylogeny with easy to use tools to extract trees for taxa of interest and sample over uncertainty. The phylogeny incorporates information from more than 300 individually published bird phylogenies. The R package includes tools to help appropriately cite these input studies. This software will enable users to smoothly integrate accurate evolutionary information into any analyses on birds.

evolutionary biology↗

bioRxiv2026

Assembling a fully-dated complete tree of life

Time-scaled phylogenetic trees summarising evolutionary relationships are fundamental to many analyses in biology, from diversification rate estimation to conservation prioritisation. The most comprehensive available summary of these relationships, the Open Tree of Life, synthesises information from over two thousand studies into a supertree covering the full range of global biodiversity, but its use in downstream analyses is limited by the lack of divergence times. Previous work has mapped dates from Open Trees database of trees to certain nodes in the supertree, but for the majority of nodes no date is available. While algorithms exist to interpolate missing dates in a tree, we found that their time and memory requirements scaled quadratically with the number of nodes, which made it computationally infeasible to run them on the entire tree. In this work, we describe novel date interpolation algorithms that scale linearly with the number of nodes. These enabled us to produce a distribution of fully-dated trees containing 2.3 million extant described species, greatly expanding the scope of feasible phylogenetic analyses. We illustrate the utility of these trees by computing the most robust estimate yet of the phylogenetic diversity of the complete tree of life, incorporating both topological and temporal uncertainty.

evolutionary biology↗

bioRxiv2025

Phylogenetic Diversity Across the Complete Tree of Life

In the face of rapid biodiversity loss, many approaches have been developed to measure biodiversity in ways that go beyond species richness. One prominent example is Phylogenetic Diversity (PD), which, on a dated phylogenetic tree, measures evolutionary history by summing the branch lengths measured in time required to connect a set of species. PD may also capture other biodiversity measures by proxy such as the richness of biological features and their potential benefits for humanity, known as future options. The total global PD is known for some well-studied groups, such as most vertebrates, but PD estimates are lacking for the majority of the tree of life. Here, we characterize the distribution of PD across the complete tree of life with over 2.2 million species. To do this we use data from the Open Tree of Life and a smoothing method to interpolate between nodes without date information. We estimate that the PD represented by all described species together is between 30 and 33 trillion years (95% confidence interval). We characterize the distribution of evolutionary distinctiveness, a measure of the fair share of PD captured by individual species, across all life and within selected clades. This Evolutionary Distinctiveness metric has previously been used as the basis for conservation prioritization schemes such as EDGE (Evolutionary Distinct and Globally Endangered) which synthesizes phylogenetic tree data with extinction risk data from the IUCN Red List of threatened species. We use our results to estimate EDGE scores for over 130,000 species. We also estimate the amount of threatened phylogenetic diversity across the complete tree of life. We hope this work will pave the way for more complete and automated analyses of PD, Evolutionary Distinctiveness, threatened evolutionary history, and EDGE scores across the complete tree of life.

evolutionary biology↗

bioRxiv2024

A complete and dynamic tree of birds

We present a complete, time-scaled, evolutionary tree of the worlds bird species. This tree unites phylogenetic estimates for 9,239 species from 262 studies published between 1990 and 2024, using the Open Tree synthesis algorithm. The remaining species are placed in the tree based on curated taxonomic information. The tips of this complete tree are aligned to the species in the Clements Taxonomy used by eBird and other resources, and cross-mapped to other taxonomic systems including the Open Tree of Life (Open Tree), National Center for Biotechnology Information (NCBI), and Global Biodiversity Information Facility (GBIF). The total number of named bird species varies between 10,824 and 11,017 across the taxonomy versions we applied (v2021, v2022 and v2023). We share complete trees for each taxonomy version. The procedure, software and data-stores we used to generate this tree are public and reproducible. The tree presented here is Aves v1.2 and can be easily updated with new phylogenetic information as new estimates are published. We demonstrate the types of large scale analyses this data resource enables by linking geographic data with the phylogeny to calculate the regional phylogenetic diversity of birds across the world. We will release updated versions of the phylogenetic synthesis and taxonomic translation tables annually. The procedure we describe here can be applied to developing complete phylogenetic estimates for any taxonomic group of interest. Significance statementBirds are charismatic - well loved, and highly studied. Many new phylogenies elucidating avian birds evolutionary relationships are published every year. We have united phylogenetic estimates from hundreds of studies to create a complete evolutionary tree of all birds. While a variety of resources aggregate huge collections of trait, behavior and location data for birds, previously the barriers to linking data between these data resources and bird evolutionary history have limited the opportunities to do exciting large scale analyses. We have bridged that gap, and developed a system that allows us to easily update our understanding of bird evolution as new estimates are generated. We share a workflow and the software needed to create a complete evolutionary tree for any group.

evolutionary biology↗

bioRxiv2022

Leveraging shared ancestral variation to detect local introgression

Introgression is a common evolutionary phenomenon that results in shared genetic material across non-sister taxa. Existing statistical methods such as Pattersons D statistic can detect introgression by measuring an excess of shared derived alleles between populations. The D statistic is effective to detect genome-wide patterns of introgression but can give spurious inferences of introgression when applied to local regions. We propose a new statistic, D+, that leverages both shared ancestral and derived alleles to infer local introgressed regions. Incorporating both shared derived and ancestral alleles increases the number of informative sites per region, improving our ability to identify local introgression. We use a coalescent framework to derive the expected value of this statistic as a function of different demographic parameters under an instantaneous admixture model and use coalescent simulations to compute the power and precision of D+. While the power of D and D+ is comparable, D+ has better precision than D. We apply D+ to empirical data from the 1000 Genome Project and Heliconius butterflies to infer local targets of introgression in humans and in butterflies.

evolutionary biology↗

bioRxiv2020

OpenTree: A Python package for Accessing andAnalyzing data from the Open Tree of Life

The Open Tree of Life project constructs a comprehensive, dynamic and digitally-available tree of life by synthesizing published phylogenetic trees along with taxonomic data. Open Tree of Life provides web-service application programming interfaces (APIs) to make the tree estimate, unified taxonomy, and input phylogenetic data available to anyone. Here, we describe the python package opentree, which provides a user friendly python wrapper for these APIs and a set of scripts and tutorials for straightforward downstream data analyses. We demonstrate the utility of these tools by generating an estimate of the phylogenetic relationships of all bird families, and by capturing a phylogenetic estimate for all taxa observed at the University of California Merced Vernal Pools and Grassland Reserve.

bioinformatics↗

bioRxiv2020

Physcraper: A Python package for continual update of evolutionary estimates using the Open Tree of Life

O_LIPhylogenies are a key part of research in many areas of biology. Tools that automate some parts of the process of phylogenetic reconstruction, mainly molecular character matrix assembly, have been developed for the advantage of both specialists in the field of phylogenetics and nonspecialists. However, interpretation of results, comparison with previously available phylogenetic hypotheses, and selection of one phylogeny for downstream analyses and discussion still impose difficulties to one that is not a specialist either on phylogenetic methods or on a particular group of study. C_LIO_LIPhyscraper is a command-line Python program that automates the update of published phylogenies by adding public DNA sequences to underlying alignments of previously published phylogenies. It also provides a framework for straightforward comparison of published phylogenies with their updated versions, by leveraging upon tools from the Open Tree of Life project to link taxonomic information across databases. C_LIO_LIPhyscraper can be used by the nonspecialist, as a tool to generate phylogenetic hypotheses based on publicly available expert phylogenetic knowledge. Phylogeneticists and taxonomic group specialists will find it useful as a tool to facilitate molecular dataset gathering and comparison of alternative phylogenetic hypotheses (topologies). C_LIO_LIThe Physcraper workflow demonstrates the benefits of doing open science for phylogenetics, encour-aging researchers to strive for better sharing practices. Physcraper can be used with any OS and is released under an open-source license. Detailed instructions for installation and use are available at https://physcraper.readthedocs. C_LI

bioinformatics↗

bioRxiv2020

Color polymorphism is a driver of diversification in the lizard family Lacertidae

Color polymorphism - two or more heritable color phenotypes maintained within a single breeding population - is an extreme type of intra-specific diversity widespread across the tree of life but rarely studied in a comparative framework. Color polymorphism is thought to be an engine for speciation, where morph loss or divergence between distinct color morphs within a species results in the rapid evolution of new lineages, and thus, color polymorphic lineages are expected to display elevated diversification rates. Lizards of the family Lacertidae have evolved multiple lineages with color polymorphism, but lack of a complete and robust phylogeny for the group has made comparative analysis difficult. Here, we produce a comprehensive species-level phylogeny of the lizard family Lacertidae to reconstruct the evolutionary history of color polymorphism and test if color polymorphism has been a driver of diversification. Accounting for phylogenetic uncertainty, we estimate an ancient macroevolutionary origin of color polymorphism within the Lacertini tribe (subfamily Lacertinae). Color polymorphism most likely evolved several times in the Lacertidae and has been lost at a much faster rate than gained. Evolutionary transitions to color polymorphism are associated with shifts in increased net diversification rate in this family of lizards. Taken together, our empirical results support long-standing theoretical expectations that color polymorphism is a driver of diversification.

evolutionary biology↗

bioRxiv2020

A Biodiversity Composition Map of California Derived from Environmental DNA Metabarcoding and Earth Observation

Unique ecosystems globally are under threat from ongoing anthropogenic environmental change. Effective conservation management requires more thorough biodiversity surveys that can reveal system-level patterns and that can be applied rapidly across space and time. We offer a way to use environmental DNA, community science and remote sensing together as methods to reduce the discrepancy between the magnitude of change and historical approaches to measure it. Taking advantages of modern ecological models, we integrate environmental DNA and Earth observations to evaluate regional biodiversity patterns for a snapshot of time, and provide critical community-level characterization. We collected 278 samples in Spring 2017 from coastal, shrub and lowland forest sites in California, a large-scale biodiversity hotspot. We applied gradient forest to model 915 family occurrences and community composition together with environmental variables and multi-scalar habitat classifications to produce a statewide biodiversity-based map. 16,118 taxonomic entries recovered were associated with environmental variables to test their predictive strength on alpha, beta, and zeta diversity. Local habitat classification was diagnostic of community composition, illuminating a characteristic of biodiversity hotspots. Using gradient forest models, environmental variables predicted 35% of the variance in eDNA patterns at the family level, with elevation, sand percentage, and greenness (NDVI32) as the top predictors. This predictive power was higher than we found in published literature at global scale. In addition to this indication of substantial environmental filtering, we also found a positive relationship between environmentally predicted families and their numbers of biotic interactions. In aggregate, these analyses showed that strong eDNA community-environment correlation is a general characteristic of temperate ecosystems, and may explain why communities easily destabilize under disturbances. Our study provides the first example of integrating citizen science based eDNA with biodiversity mapping across the tree of life, with promises to produce large scale, high resolution assessments that promote a more comprehensive and predictive understanding of the factors that influence biodiversity and enhance its maintenance.

ecology↗