Emily Moriarty Lemmon

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

Although reconstruction of the phylogeny of living birds has progressed tremendously in the last decade, the evolutionary history of Neoaves—a clade that encompasses nearly all living bird species—remains the greatest unresolved challenge in dinosaur systematics. Here we investigate avian phylogeny with an unprecedented scale of data: >390,000 bases of genomic sequence data from each of 198 species of living birds, representing all major avian lineages, and two crocodilian outgroups. Sequence data were collected using anchored hybrid enrichment, yielding 259 nuclear loci with an average length of 1,523 bases for a total data set of over 7.8 × 107 bases. Bayesian and maximum likelihood analyses yielded highly supported and nearly identical phylogenetic trees for all major avian lineages. Five major clades form successive sister groups to the rest of Neoaves: (1) a clade including nightjars, other caprimulgiforms, swifts, and hummingbirds; (2) a clade uniting cuckoos, bustards, and turacos with pigeons, mesites, and sandgrouse; (3) cranes and their relatives; (4) a comprehensive waterbird clade, including all diving, wading, and shorebirds; and (5) a comprehensive landbird clade with the enigmatic hoatzin (Opisthocomus hoazin) as the sister group to the rest. Neither of the two main, recently proposed Neoavian clades—Columbea and Passerea—were supported as monophyletic. The results of our divergence time analyses are congruent with the palaeontological record, supporting a major radiation of crown birds in the wake of the Cretaceous–Palaeogene (K–Pg) mass extinction.

Anchored hybrid enrichment for massively high-throughput phylogenomics

The field of phylogenetics is on the cusp of a major revolution, enabled by new methods of data collection that leverage both genomic resources and recent advances in DNA sequencing. Previous phylogenetic work has required labor-intensive marker development coupled with single-locus polymerase chain reaction and DNA sequencing on clade-by-clade and locus-by-locus basis. Here, we present a new, cost-efficient, and rapid approach to obtaining data from hundreds of loci for potentially hundreds of individuals for deep and shallow phylogenetic studies. Specifically, we designed probes for target enrichment of >500 loci in highly conserved anchor regions of vertebrate genomes (flanked by less conserved regions) from five model species and tested enrichment efficiency in nonmodel species up to 508 million years divergent from the nearest model. We found that hybrid enrichment using conserved probes (anchored enrichment) can recover a large number of unlinked loci that are useful at a diversity of phylogenetic timescales. This new approach has the potential not only to expedite resolution of deep-scale portions of the Tree of Life but also to greatly accelerate resolution of the large number of shallow clades that remain unresolved. The combination of low cost (~1% of the cost of traditional Sanger sequencing and ~3.5% of the cost of high-throughput amplicon sequencing for projects on the scale of 500 loci × 100 individuals) and rapid data collection (~2 weeks of laboratory time) are expected to make this approach tractable even for researchers working on systems with limited or nonexistent genomic resources.

The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference

Abstract Although an increasing number of phylogenetic data sets are incomplete, the effect of ambiguous data on phylogenetic accuracy is not well understood. We use 4-taxon simulations to study the effects of ambiguous data (i.e., missing characters or gaps) in maximum likelihood (ML) and Bayesian frameworks. By introducing ambiguous data in a way that removes confounding factors, we provide the first clear understanding of 1 mechanism by which ambiguous data can mislead phylogenetic analyses. We find that in both ML and Bayesian frameworks, among-site rate variation can interact with ambiguous data to produce misleading estimates of topology and branch lengths. Furthermore, within a Bayesian framework, priors on branch lengths and rate heterogeneity parameters can exacerbate the effects of ambiguous data, resulting in strongly misleading bipartition posterior probabilities. The magnitude and direction of the ambiguous data bias are a function of the number and taxonomic distribution of ambiguous characters, the strength of topological support, and whether or not the model is correctly specified. The results of this study have major implications for all analyses that rely on accurate estimates of topology or branch lengths, including divergence time estimation, ancestral state reconstruction, tree-dependent comparative methods, rate variation analysis, phylogenetic hypothesis testing, and phylogeographic analysis.

When trees grow too long: investigating the causes of highly inaccurate bayesian branch-length estimates.

A surprising number of recent Bayesian phylogenetic analyses contain branch-length estimates that are several orders of magnitude longer than corresponding maximum-likelihood estimates. The levels of divergence implied by such branch lengths are unreasonable for studies using biological data and are known to be false for studies using simulated data. We conducted additional Bayesian analyses and studied approximate-posterior surfaces to investigate the causes underlying these large errors. We manipulated the starting parameter values of the Markov chain Monte Carlo (MCMC) analyses, the moves used by the MCMC analyses, and the prior-probability distribution on branch lengths. We demonstrate that inaccurate branch-length estimates result from either 1) poor mixing of MCMC chains or 2) posterior distributions with excessive weight at long tree lengths. Both effects are caused by a rapid increase in the volume of branch-length space as branches become longer. In the former case, both an MCMC move that scales all branch lengths in the tree simultaneously and the use of overdispersed starting branch lengths allow the chain to accurately sample the posterior distribution and should be used in Bayesian analyses of phylogeny. In the latter case, branch-length priors can have strong effects on resulting inferences and should be carefully chosen to reflect biological expectations. We provide a formula to calculate an exponential rate parameter for the branch-length prior that should eliminate inference of biased branch lengths in many cases. In any phylogenetic analysis, the biological plausibility of branch-length output must be carefully considered.

Geological and climatic forces driving speciation in the continentally distributed trilling chorus frogs (Pseudacris)

Abstract Tertiary geological events and Quaternary climatic fluctuations have been proposed as important factors of speciation in the North American flora and fauna. Few studies, however, have rigorously tested hypotheses regarding the specific factors driving divergence of taxa. Here, we test explicit speciation hypotheses by correlating geologic events with divergence times among species in the continentally distributed trilling chorus frogs (Pseudacris). In particular, we ask whether marine inundation of the Mississippi Embayment, uplift of the Appalachian Mountains, or modification of the ancient Teays-Mahomet River system contributed to speciation. To examine the plausibility of ancient rivers causing divergence, we tested whether modern river systems inhibit gene flow. Additionally, we compared the effects of Quaternary climatic factors (glaciation and aridification) on levels of genetic variation. Divergence time estimates using penalized likelihood and coalescent approaches indicate that the major lineages of chorus frogs diversified during the Tertiary, and also exclude Quaternary climate change as a factor in speciation of chorus frogs. We show the first evidence that inundation of the Mississippi Embayment contributed to speciation. We reject the hypotheses that Cenozoic uplift of the Appalachians and that diversion of the Teays-Mahomet River contributed to speciation in this clade. We find that by reducing gene flow, rivers have the potential to cause divergence of lineages. Finally, we demonstrate that populations in areas affected by Quaternary glaciation and aridification have reduced levels of genetic variation compared to those from more equable regions, suggesting recent colonization.

Diversification of Conspecific Signals in Sympatry: Geographic Overlap Drives Multidimensional Reproductive Character Displacement in Frogs

Theoretical models suggest that geographic overlap with different heterospecific assemblages can promote divergence of mate recognition systems among conspecific populations. Divergence occurs when different traits undergo reproductive character displacement across populations within a contact zone. Here, I tested this hypothesis by assessing patterns of acoustic signal divergence in two- and three-species assemblages of chorus frogs (Pseudacris), focusing in particular on P. feriarum and P. nigrita. In addition, I tested one criterion for reinforcement, by examining the evolution of female P. feriarum preferences in the contact zone. Patterns of signal evolution indicated that in each of the four sympatric populations studied, only the rarer species displaced substantially (P. feriarum in three cases and P. nigrita in one instance). Moreover, the three displaced P. feriarum populations diverged in different signal traits across the contact zone, evolving in directions that increased the energetic cost of calling relative to the allopatric call, and in ways that maximized differences from the particular heterospecific assemblage present. Consistent with reinforcement, divergence of female preferences in sympatry was estimated to reduce their propensity to hybridize by 60%. Together, signal and preference data suggest that interactions between species can promote diversification within species, potentially contributing to reproductive isolation among conspecific populations.

A Likelihood Framework for Estimating Phylogeographic History on a Continuous Landscape

Due to lack of an adequate statistical framework, biologists studying phylogeography are abandoning traditional methods of estimating phylogeographic history in favor of statistical methods designed to test a priori hypotheses. These new methods may, however, have limited descriptive utility. Here, we develop a new statistical framework that can be used to both test a priori hypotheses and estimate phylogeographic history of a gene (and the statistical confidence in that history) in the absence of such hypotheses. The statistical approach concentrates on estimation of geographic locations of the ancestors of a set of sampled organisms. Now we use (2) to derive the likelihood of the ancestral geographic coordinates and the value of the scaled dispersal parameter, given the observed geographic coordinates (assuming known topology and branch lengths). Using a maximum likelihood approach, which is implemented in the new program PhyloMapper, we apply this statistical framework to a 246-taxon mitochondrial genealogy of North American chorus frogs, focusing in detail on one of these species. We demonstrate three lines of evidence for recent northward expansion of the mitochondrion of the coastal clade of Pseudacris feriarum: higher per-generation dispersal distance in the recently colonized region, a noncentral ancestral location, and directional migration. After illustrating one method of accommodating phylogenetic uncertainty, we conclude by discussing how extensions of this framework could function to incorporate a priori ecological and geological information into phylogeographic analyses.

A high-throughput venom-gland transcriptome for the Eastern Diamondback Rattlesnake (Crotalus adamanteus) and evidence for pervasive positive selection across toxin classes

Despite causing considerable human mortality and morbidity, animal toxins represent a valuable source of pharmacologically active macromolecules, a unique system for studying molecular adaptation, and a powerful framework for examining structure-function relationships in proteins. Snake venoms are particularly useful in the latter regard as they consist primarily of a moderate number of proteins and peptides that have been found to belong to just a handful of protein families. As these proteins and peptides are produced in dedicated glands, transcriptome sequencing has proven to be an effective approach to identifying the expressed toxin genes. We generated a venom-gland transcriptome for the Eastern Diamondback Rattlesnake (Crotalus adamanteus) using Roche 454 sequencing technology. In the current work, we focus on transcripts encoding toxins. We identified 40 unique toxin transcripts, 30 of which have full-length coding sequences, and 10 have only partial coding sequences. These toxins account for 24% of the total sequencing reads. We found toxins from 11 previously described families of snake-venom toxins and have discovered two putative, previously undescribed toxin classes. The most diverse and highly expressed toxin classes in the C. adamanteus venom-gland transcriptome are the serine proteinases, metalloproteinases, and C-type lectins. The serine proteinases are the most abundant class, accounting for 35% of the toxin sequencing reads. Metalloproteinases are the most diverse; 11 different forms have been identified. Using our sequences and those available in public databases, we detected positive selection in seven of the eight toxin families for which sufficient sequences were available for the analysis. We find that the vast majority of the genes that contribute directly to this vertebrate trait show evidence for a role for positive selection in their evolutionary history.

Reinforcement in chorus frogs: lifetime fitness estimates including intrinsic natural selection and sexual selection against hybrids.

Maladaptive hybridization is hypothesized to be an important force driving the evolution of reproductive isolation between closely related species. Because the magnitude and direction of selection can vary across a life cycle, an accurate understanding of the ubiquity of reinforcement requires fitness to be estimated across the life cycle, but the literature is surprisingly depauperate of such studies. We present fitness estimates of laboratory‐raised hybrids between the chorus frogs Pseudacris feriarum and Pseudacris nigrita—two species that have undergone reproductive character displacement where they come into secondary contact. By studying viability, mating success, and fertility across the life cycle, we find strong support for reinforcement as the force driving displacement in this system. Specifically, we find hybrid fitness is reduced by 44%. This reduction results from both sexual selection against hybrid males and natural selection on male fertility, but not viability selection. Sexual selection against hybrid males is four times stronger than natural selection. Hybrid female fitness is not reduced, however, suggesting that Haldanes rule may be operating in this system if males are heterogametic. We also found higher variation in hybrid male fertilization success relative to P. feriarum males, suggesting that the hybrid incompatibility genes are polymorphic within one or both of the parent species.

High-throughput identification of informative nuclear loci for shallow-scale phylogenetics and phylogeography.

One of the major challenges for researchers studying phylogeography and shallow-scale phylogenetics is the identification of highly variable and informative nuclear loci for the question of interest. Previous approaches to locus identification have generally required extensive testing of anonymous nuclear loci developed from genomic libraries of the target taxon, testing of loci of unknown utility from other systems, or identification of loci from the nearest model organism with genomic resources. Here, we present a fast and economical approach to generating thousands of variable, single-copy nuclear loci for any system using next-generation sequencing. We performed Illumina paired-end sequencing of three reduced-representation libraries (RRLs) in chorus frogs (Pseudacris) to identify orthologous, single-copy loci across libraries and to estimate sequence divergence at multiple taxonomic levels. We also conducted PCR testing of these loci across the genus Pseudacris and outgroups to determine whether loci developed for phylogeography can be extended to deeper phylogenetic levels. Prior to sequencing, we conducted in silico digestion of the most closely related reference genome (Xenopus tropicalis) to generate expectations for the number of loci and degree of coverage for a particular experimental design. Using the RRL approach, we: (i) identified more than 100,000 single-copy nuclear loci, 6339 of which were obtained for divergent conspecifics and 904 of which were obtained for heterospecifics; (ii) estimated average nuclear sequence divergence at 0.1% between alleles within an individual, 1.1% between conspecific individuals that represent two different clades, and 1.8% between species; and (iii) determined from PCR testing that 53% of the loci successfully amplify within-species and also many amplify to the genus-level and deeper in the phylogeny (16%). Our study effectively identified nuclear loci present in the genome that have levels of sequence divergence on par with mitochondrial loci commonly used in phylogeography. Specifically, we estimated that ~7% of loci in the chorus frog genome are >3% divergent within species; this translates to a prediction of approximately 50,000 single-copy loci in the genome with >3% divergence. Moreover, successful amplification of many loci at deeper phylogenetic levels indicates that the RRL approach represents an efficient method for rapid identification of informative loci for both phylogenetics and phylogeography. We conclude by making recommendations for minimizing the cost and maximizing the efficiency of locus identification for future studies in this field.