Nicholas Matzke

Nicholas Matzke
Australian National University | ANU · Division of Evolution, Ecology and Genetics

PhD

About

105
Publications
108,727
Reads
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10,424
Citations
Introduction
RESEARCH INTEREST: Integrating Ecological and Historical Biogeography, using Statistical Phylogenetics For my work and CV, please see: http://phylo.wikidot.com/nicholas-j-matzke Note: there are too many redundant "academic profile" sites, including this one. The only things I can keep up-to-date are my CV (above) and Google Scholar. Go to Scholar to see the latest: https://scholar.google.com/citations?user=YR6Ql3QAAAAJ&hl=en
Additional affiliations
August 2007 - August 2013
University of California, Berkeley
Position
  • Graduate Student Researcher and Instructor
September 2000 - May 2003
University of California, Santa Barbara
Position
  • PhD Student

Publications

Publications (105)
Article
Statistical model comparison has become common in historical biogeography, enabled by the R package BioGeoBEARS, which implements several models in a common framework, allowing models to be compared with standard likelihood‐based methods of statistical model comparison. Ree and Sanmartín (Journal of Biogeography, 45, 741–749, 2018) critiqued the co...
Article
Ribosomal DNA genes (rDNA) encode the major ribosomal RNAs and in eukaryotes typically form tandem repeat arrays. Species have characteristic rDNA copy numbers, but there is substantial intra-species variation in copy number that results from frequent rDNA recombination. Copy number differences can have phenotypic consequences, however difficulties...
Article
The role of whole-genome duplication (WGD) in facilitating shifts into novel biomes remains unknown. Focusing on two diverse woody plant groups in New Zealand, Coprosma (Rubiaceae) and Veronica (Plantaginaceae), we investigate how biome occupancy varies with ploidy level, and test the hypothesis that WGD increases the rate of biome shifting. Ploidy...
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Evolutionary models account for either population- or species-level processes, but usually not both. We introduce a new model, the FBD-MSC, which makes it possible for the first time to integrate both the genealogical and fossilization phenomena, by means of the multispecies coalescent (MSC) and the fossilized birth-death (FBD) processes. Using thi...
Article
We report evidence further supporting homology between proteins in the F1FO‐ATP synthetase and the bacterial flagellar motor (BFM). BFM proteins FliH, FliI, and FliJ have been hypothesized to be homologous to FO‐b + F1‐δ, F1‐α/β, and F1‐γ, with similar structure and interactions. We conduct a further test by constructing a gene order dataset, exami...
Article
The ability of lineages to disperse over evolutionary timescales may be influenced by the gain or loss of traits after adaptation to new ecological conditions. For example, rails (Aves: Rallidae) have many cases of flightless insular endemic species that presumably evolved after flying ancestors dispersed over large ocean barriers and became isolat...
Preprint
Full-text available
Ribosomal DNA genes (rDNA) encode the major ribosomal RNAs (rRNA) and in eukaryotic genomes are typically present as one or more arrays of tandem repeats. Species have characteristic rDNA copy numbers, ranging from tens to thousands of copies, with the number thought to be redundant for rRNA production. However, the tandem rDNA repeats are prone to...
Article
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The ENMTools software package was introduced in 2008 as a platform for making measurements on environmental niche models (ENMs, frequently referred to as species distribution models or SDMs), and for using those measurements in the context of newly developed Monte Carlo tests to evaluate hypotheses regarding niche evolution. Additional functionalit...
Preprint
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Evidence of homology between proteins in the ATP synthetase and the bacterial flagellar motor (BFM) has been accumulating since the 1980s. Specifically, the BFM's Type 3 Secretion System (T3SS) export apparatus FliH, FliI, and FliJ are considered homologous to F O -b + F 1 -δ, F 1 -α/β, and F 1 -γ, and have similar structure and interactions. We re...
Article
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The bacterial flagellar motor (BFM) is a nanomachine that rotates the flagellum to propel many known bacteria. The BFM is powered by ion transit across the cell membrane through the stator complex, a membrane protein. Different bacteria use various ions to run their BFM, but the majority of BFMs are powered by either proton (H ⁺ ) or sodium (Na ⁺ )...
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Echinoderms make up a substantial component of Ordovician marine invertebrates, yet their speciation and dispersal history as inferred within a rigorous phylogenetic and statistical framework is lacking. We use biogeographic stochastic mapping (BSM; implemented in the R package BioGeoBEARS) to infer ancestral area relationships and the number and t...
Article
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Species distribution models are used across evolution, ecology, conservation and epidemiology to make critical decisions and study biological phenomena, often in cases where experimental approaches are intractable. Choices regarding optimal models, methods and data are typically made based on discrimination accuracy: a model's ability to predict su...
Preprint
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Aim Species distribution models are used across evolution, ecology, conservation, and epidemiology to make critical decisions and study biological phenomena, often in cases where experimental approaches are intractable. Choices regarding optimal models, methods, and data are typically made based on discrimination accuracy: a model’s ability to pred...
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The importance of long-distance dispersal (LDD) in shaping geographical distributions has been debated since the nineteenth century. In terrestrial vertebrates, LDD events across large water bodies are considered highly improbable, but organismal traits affecting dispersal capacity are generally not taken into account. Here, we focus on a recent li...
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The bacterial flagellar motor (BFM) powers the rotation that propels swimming bacteria. Rotational torque is generated by harnessing the flow of ions through ion channels known as stators which couple the energy from the ion gradient across the inner membrane to rotation of the rotor. Here we used error‐prone PCR to introduce single point mutations...
Article
Aim Almost half of the extant species of Crocodylia (nine genera, sensu Benton & Clark) belong to the genus Crocodylus, which originated in the Miocene. Today, this genus has a circumtropical distribution, with representatives found in Asia, Oceania, Africa and the Neotropics. However, its geographical origin and the historical events behind its ra...
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The ability of lineages to disperse long distances over evolutionary timescales may be influenced by the gain or loss of traits adapted to enhance local, ecological dispersal. For example, some species in the southern conifer sister families Podocarpaceae and Araucariaceae have fleshy cones that encourage bird dispersal, but it is unknown how this...
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Are different fruit colours related to large‐scale patterns of dispersal, distribution and diversification? Here, we investigate this question for the first time, using phylogenetic approaches in the tribe Gaultherieae (Ericaceae). We test relationships between fruit colour and (a) biogeographic dispersal, (b) elevational and latitudinal species di...
Preprint
The bacterial flagellar motor (BFM) is a molecular complex which powers the rotation of the filament that propels swimming bacteria. Rotational torque is generated by harnessing the flow of ions through ion channels known as stators which couple the energy from the ion gradient across the inner membrane to rotation of the rotor. Here we use error-p...
Article
Fossil tip‐dating allows for the inclusion of morphological data in divergence time estimates based on both extant and extinct taxa. Neoselachii have a cartilaginous skeleton, which is less prone to fossilization compared to skeletons of Osteichthyans. Therefore, the majority of the neoselachian fossil record is comprised of single teeth, which fos...
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Non‐equilibrium dynamics and non‐neutral processes, such as trait‐dependent dispersal, are often missing from quantitative island biogeography models despite their potential explanatory value. One of the most influential non‐equilibrium models is the taxon cycle, but it has been difficult to test its validity as a general biogeographical framework....
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Ecological opportunity is a powerful driver of evolutionary diversification, and predicts rapid lineage and phenotypic diversification following colonisation of competitor‐free habitats. Alternatively, topographic or environmental heterogeneity could be key to generating and sustaining diversity. We explore these hypotheses in a widespread lineage...
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Tip-dating, where fossils are included as dated terminal taxa in Bayesian dating inference, is an increasingly popular method. Data for these studies often come from morphological character matrices originally developed for non-dated, and usually parsimony, analyses. In parsimony, only shared derived characters (synapomorphies) provide grouping inf...
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Abstract Allopolyploidy has played an important role in the evolution of the flowering plants. Genome mergers are often accompanied by significant and rapid alterations of genome size and structure via chromosomal rearrangements and altered dynamics of tandem and dispersed repetitive DNA families. Recent developments in sequencing technologies and...
Preprint
Bayesian methods can be used to accurately estimate species tree topologies, times and other parameters, but only when the models of evolution which are available and utilized sufficiently account for the underlying evolutionary processes. Multispecies coalescent (MSC) models have been shown to accurately account for the evolution of genes within s...
Article
Mexican dry environments are widespread and characterized by a rich flora and fauna in terms of both overall species diversity and endemism, but the factors that have shaped this diversity remain unclear. In this study, we evaluated hypotheses concerning the biogeographical origin and evolutionary history of Florestina (Asteraceae) in Mexican dry e...
Article
The Middle to Late Ordovician was a time of profound biotic diversification, paleoecological change, and major climate shifts. Yet studies examining speciation mechanisms and drivers of dispersal are lacking. In this study, we use Bayesian phylogenetics and maximum likelihood analyses in the R package BioGeoBEARS to reanalyze ten published data matr...
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The Andean mountains of South America are the most species-rich biodiversity hotspot worldwide with c. 15% of the world’s plant species, in only 1% of the world’s land surface. Orchids are a key element of the Andean flora, and one of the most prominent components of the Neotropical epiphyte diversity, yet very little is known about their origin an...
Preprint
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• The Andean mountains of South America are the most species-rich biodiversity hotspot worldwide with about 15% of the world’s plant species, in only 1% of the world’s land surface. Orchids are a key element of the Andean flora, and one of the most prominent components of the Neotropical epiphyte diversity, yet very little is known about their orig...
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Estimating divergence times on phylogenies is critical in paleontological and neontological studies. Chronostratigraphically-constrained fossils are the only direct evidence of absolute timing of species divergence. Strict temporal calibration of fossil-only phylogenies provides minimum divergence estimates, and various methods have been proposed t...
Article
Statistical historical biogeographic methods rely on models that represent various biogeographic processes. Until recently model selection in this domain was not widely used, and the impact of differential model selection on inferring biogeographic scenarios was not well understood. Focusing on Neotropical weevils in the Exophthalmus genus complex...
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The tomato family Solanaceae is distributed on all major continents except Antarctica and has its centre of diversity in South America. Its worldwide distribution suggests multiple long-distance dispersals within and between the New and Old Worlds. Here, we apply maximum likelihood (ML) methods and newly developed biogeographical stochastic mapping...
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Tip-dating methods are becoming popular alternatives to traditional node calibration approaches for building time-scaled phylogenetic trees, but questions remain about their application to empirical datasets. We compared the performance of the most popular methods against a dated tree of fossil Canidae derived from previously published monographs....
Preprint
Full-text available
Tip-dating methods are becoming popular alternatives to traditional node calibration approaches for building time-scaled phylogenetic trees, but questions remain about their application to empirical datasets. We compared the performance of the most popular methods against a dated tree of fossil Canidae derived from previously published monographs....
Article
The rise of oxygen ca. 2.3 billion years ago (Ga) is the most distinct environmental transition in Earth history. This event was enabled by the evolution of oxygenic photosynthesis in the ancestors of Cyanobacteria. However, long-standing questions concern the evolutionary timing of this metabolism, with conflicting answers spanning more than one b...
Article
Dated phylogenies of fossil taxa allow palaeobiologists to estimate the timing of major divergences and placement of extinct lineages, and to test macroevolutionary hypotheses. Recently developed Bayesian 'tip-dating' methods simultaneously infer and date the branching relationships among fossil taxa, and infer putative ancestral relationships. Usi...
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True frogs of the genus Rana are widely used as model organisms in studies of development, genetics, physiology, ecology, behavior, and evolution. Comparative studies among the more than 100 species of Rana rely on an understanding of the evolutionary history and patterns of diversification of the group. We estimate a well-resolved, time-calibrated...
Article
Statistical historical biogeographical methods rely on the use of models that assume various biogeographic processes. Until recently model selection remains an explored topic and the impacts of using different models on inferring biogeographic history are poorly understood. Focusing on the Neotropical weevils in the Exophthalmus genus complex (Inse...
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To examine the role of geological history, connectivity and distance in shaping the biogeographical structure of North American desert clades that are restricted to habitat islands (sand dunes and relictual aquatic habitats), using statistical model choice on old and new probabilistic biogeographical models. North America, Mojave, Sonoran and Chihu...
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A phylogeny identifies ancestors of modern creationist legislation.
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The phylogenetic relationships of several hominin species remain controversial. Two methodological issues contribute to the uncertainty-use of partial, inconsistent datasets and reliance on phylogenetic methods that are ill-suited to testing competing hypotheses. Here, we report a study designed to overcome these issues. We first compiled a superma...
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High-resolution imagery is lacking for much of the West Indies, impeding accurate intertidal habitat assessments and conservation planning. The West Indian topsnail, which inhabits rocky shores, is an important, regional fishery. It was overfished to extinction in Bermuda but reintroduced in 1982. In this study, we estimate potential population siz...
Article
We address several central concerns of conservation paleobiology, namely, the inference of geographic ranges of ancestral and ancient species, the changes in geographic range under climate change, and the associated question of inferring the environmental preferences of ancestral lineages and how they have evolved over geological time. We will show...
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Founder-event speciation, where a rare jump dispersal event founds a new genetically isolated lineage, has long been considered crucial by many historical biogeographers, but its importance is disputed within the vicariance school. Probabilistic modeling of geographic range evolution creates the potential to test different biogeographical models ag...
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Climate refugia, locations where taxa survive periods of regionally adverse climate, are thought to be critical for maintaining biodiversity through the glacial–interglacial climate changes of the Quaternary. A critical research need is to better integrate and reconcile the three major lines of evidence used to infer the existence of past refugia –...
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It is often suggested that horizontal gene transfer is so ubiquitous in microbes that the concept of a phylogenetic tree representing the pattern of vertical inheritance is oversimplified or even positively misleading. "Universal proteins" have been used to infer the organismal phylogeny, but have been criticized as being only the "tree of one perc...
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Historical biogeography has been characterized by a large diversity of methods and unresolved debates about which processes, such as dispersal or vicariance, are most important for explaining distributions. A new R package, BioGeoBEARS, implements many models in a common likelihood framework, so that standard statistical model selection procedures...
Thesis
Full-text available
Historical biogeography has a diversity of methods for inferring ancestral geographic ranges on phylogenies, but many of the methods have conflicting assumptions, and there is no common statistical framework by which to judge which models are preferable. Probabilistic modeling of geographic range evolution, pioneered by Ree and Smith (2008, Systema...
Article
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Chloroplasts and mitochondria descended from bacterial ancestors, but the dating of these primary endosymbiosis events remains very uncertain, despite their importance for our understanding of the evolution of both bacteria and eukaryotes. All phylogenetic dating in the Proterozoic and before is difficult: Significant debates surround potential fos...