Allan Larson

Bio: Allan Larson is an academic researcher from Washington University in St. Louis. The author has contributed to research in topics: Phylogenetic tree & Monophyly. The author has an hindex of 58, co-authored 83 publications receiving 11615 citations. Previous affiliations of Allan Larson include Avila University & University of California, Berkeley.

Genetic variation increases during biological invasion by a Cuban lizard

Abstract: A genetic paradox1,2 exists in invasion biology: how do introduced populations, whose genetic variation has probably been depleted by population bottlenecks, persist and adapt to new conditions? Lessons from conservation genetics show that reduced genetic variation due to genetic drift and founder effects limits the ability of a population to adapt, and small population size increases the risk of extinction1,3,4. Nonetheless, many introduced species experiencing these same conditions during initial introductions persist, expand their ranges, evolve rapidly and become invasive. To address this issue, we studied the brown anole, a worldwide invasive lizard. Genetic analyses indicate that at least eight introductions have occurred in Florida from across this lizard's native range, blending genetic variation from different geographic source populations and producing populations that contain substantially more, not less, genetic variation than native populations. Moreover, recently introduced brown anole populations around the world originate from Florida, and some have maintained these elevated levels of genetic variation. Here we show that one key to invasion success may be the occurrence of multiple introductions that transform among-population variation in native ranges to within-population variation in introduced areas. Furthermore, these genetically variable populations may be particularly potent sources for introductions elsewhere. The growing problem of invasive species introductions brings considerable economic and biological costs5,6. If these costs are to be mitigated, a greater understanding of the causes, progression and consequences of biological invasions is needed7.

Contingency and Determinism in Replicated Adaptive Radiations of Island Lizards

Abstract: The vagaries of history lead to the prediction that repeated instances of evolutionary diversification will lead to disparate outcomes even if starting conditions are similar. We tested this proposition by examining the evolutionary radiation of Anolis lizards on the four islands of the Greater Antilles. Morphometric analyses indicate that the same set of habitat specialists, termed ecomorphs, occurs on all four islands. Although these similar assemblages could result from a single evolutionary origin of each ecomorph, followed by dispersal or vicariance, phylogenetic analysis indicates that the ecomorphs originated independently on each island. Thus, adaptive radiation in similar environments can overcome historical contingencies to produce strikingly similar evolutionary outcomes.

Tempo and Mode of Evolutionary Radiation in Iguanian Lizards

Abstract: Identification of general properties of evolutionary radiations has been hindered by the lack of a general statistical and phylogenetic approach applicable across diverse taxa. We present a comparative analytical framework for examining phylogenetic patterns of diversification and morphological disparity with data from four iguanian-lizard taxa that exhibit substantially different patterns of evolution. Taxa whose diversification occurred disproportionately early in their evolutionary history partition more of their morphological disparity among, rather than within, subclades. This inverse relationship between timing of diversification and morphological disparity within subclades may be a general feature that transcends the historically contingent properties of different evolutionary radiations.

Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome.

Abstract: Two novel mitochondrial gene arrangements are identified in an agamid lizard and a ranid frog. Statistical tests incorporating phylogeny indicate a link between novel vertebrate mitochondrial gene orders and movement of the origin of light-strand replication. A mechanism involving errors in light-strand replication and tandem duplication of genes is proposed for rearrangement of vertebrate mitochondrial genes. A second mechanism involving small direct repeats also is identified. These mechanisms implicate gene order as a reliable phylogenetic character. Shifts in gene order define major lineages without evidence of parallelism or reversal. The loss of the origin of light-strand replication from its typical vertebrate position evolves in parallel and, therefore, is a less reliable phylogenetic character. Gene junctions also evolve in parallel. Sequencing across multigenic regions, in particular transfer RNA genes, should be a major focus of future systematic studies to locate novel gene orders and to provide a better understanding of the evolution of the vertebrate mitochondrial genome.

Molecular Phylogenetics of Squamata: The Position of Snakes, Amphisbaenians, and Dibamids, and the Root of the Squamate Tree

Abstract: Squamate reptiles (snakes, lizards, and amphisbaenians) serve as model systems for evolutionary studies of a variety of morphological and behavioral traits, and phylogeny is crucial to many generalizations derived from such studies. Specifically, the traditional dichotomy between Iguania (anoles, iguanas, chameleons, etc.) and Scleroglossa (skinks, geckos, snakes, etc.) has been correlated with major evolutionary shifts within Squamata. We present a molecular phylogenetic study of 69 squamate species using approximately 4600 (2876 parsimony-informative) base pairs (bp) of DNA sequence data from the nuclear genes RAG-1(approximately 2750 bp) and c-mos(approximately 360 bp) and the mitochondrial ND2 region (approximately 1500 bp), sampling all major clades and most major subclades. Under our hypothesis, species previously placed in Iguania, Anguimorpha, and almost all recognized squamate families form strongly supported monophyletic groups. However, species previously placed in Scleroglossa, Varanoidea, and several other higher taxa do not form monophyletic groups. Iguania, the traditional sister group of Scleroglossa, is actually highly nested within Scleroglossa. This unconventional rooting does not seem to be due to long-branch attraction, base composition biases among taxa, or convergence caused by similar selective forces acting on nonsister taxa. Studies of functional tongue morphology and feeding mode have contrasted the similar states found in Sphenodon(the nearest outgroup to squamates) and Iguania with those of Scleroglossa, but our findings suggest that similar states in Sphenodonand Iguania result from homoplasy. Snakes, amphisbaenians, and dibamid lizards, limbless forms whose phylogenetic positions historically have been impossible to place with confidence, are not grouped together and appear to have evolved this condition independently. Amphisbaenians are the sister group of lacertids, and dibamid lizards diverged early in squamate evolutionary history. Snakes are grouped with iguanians, lacertiforms, and anguimorphs, but are not nested within anguimorphs.

The Theory of Island Biogeography

Abstract: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

Testing for phylogenetic signal in comparative data: behavioral traits are more labile.

Abstract: The primary rationale for the use of phylogenetically based statistical methods is that phylogenetic signal, the tendency for related species to resemble each other, is ubiquitous. Whether this assertion is true for a given trait in a given lineage is an empirical question, but general tools for detecting and quantifying phylogenetic signal are inadequately developed. We present new methods for continuous-valued characters that can be implemented with either phylogenetically independent contrasts or generalized least-squares models. First, a simple randomization procedure allows one to test the null hypothesis of no pattern of similarity among relatives. The test demonstrates correct Type I error rate at a nominal α = 0.05 and good power (0.8) for simulated datasets with 20 or more species. Second, we derive a descriptive statistic, K, which allows valid comparisons of the amount of phylogenetic signal across traits and trees. Third, we provide two biologically motivated branch-length transformat...

Phylogenies and Community Ecology

Abstract: ▪ Abstract As better phylogenetic hypotheses become available for many groups of organisms, studies in community ecology can be informed by knowledge of the evolutionary relationships among coexisting species. We note three primary approaches to integrating phylogenetic information into studies of community organization: 1. examining the phylogenetic structure of community assemblages, 2. exploring the phylogenetic basis of community niche structure, and 3. adding a community context to studies of trait evolution and biogeography. We recognize a common pattern of phylogenetic conservatism in ecological character and highlight the challenges of using phylogenies of partial lineages. We also review phylogenetic approaches to three emergent properties of communities: species diversity, relative abundance distributions, and range sizes. Methodological advances in phylogenetic supertree construction, character reconstruction, null models for community assembly and character evolution, and metrics of community ...

Animal mitochondrial genomes

Abstract: Animal mitochondrial DNA is a small, extrachromosomal genome, typically ~16 kb in size. With few exceptions, all animal mitochondrial genomes contain the same 37 genes: two for rRNAs, 13 for proteins and 22 for tRNAs. The products of these genes, along with RNAs and proteins imported from the cytoplasm, endow mitochondria with their own systems for DNA replication, transcription, mRNA processing and translation of proteins. The study of these genomes as they function in mitochondrial systems—‘mitochondrial genomics’— serves as a model for genome evolution. Furthermore, the comparison of animal mitochondrial gene arrangements has become a very powerful means for inferring ancient evolutionary relationships, since rearrangements appear to be unique, generally rare events that are unlikely to arise independently in separate evolutionary lineages. Complete mitochondrial gene arrangements have been published for 58 chordate species and 29 non-chordate species, and partial arrangements for hundreds of other taxa. This review compares and summarizes these gene arrangements and points out some of the questions that may be addressed by comparing mitochondrial systems.