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List of works by Alan R. Lemmon

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

scientific article
Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

scientific article published on May 17, 2012
The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference

scientific article
The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics.

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

scientific article
The importance of proper model assumption in bayesian phylogenetics

scientific article published in April 2004
Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics

scientific article
The venom-gland transcriptome of the eastern diamondback rattlesnake (Crotalus adamanteus)

scientific article
A Likelihood Framework for Estimating Phylogeographic History on a Continuous Landscape

scientific article (publication date: 14 August 2008)
A high-throughput venom-gland transcriptome for the Eastern Diamondback Rattlesnake (Crotalus adamanteus) and evidence for pervasive positive selection across toxin classes

scientific article
The metapopulation genetic algorithm: An efficient solution for the problem of large phylogeny estimation

scientific article
Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life

scientific article
A hybrid phylogenetic-phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification

scientific article
Effectiveness of phylogenomic data and coalescent species-tree methods for resolving difficult nodes in the phylogeny of advanced snakes (Serpentes: Caenophidia).

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

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

scientific article published on 20 January 2010
The impact of anchored phylogenomics and taxon sampling on phylogenetic inference in narrow-mouthed frogs (Anura, Microhylidae)

scientific article (publication date: 19 March 2015)
Phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika cichlid fishes

scientific article published in Nature Communications
High-Throughput Identification of Informative Nuclear Loci for Shallow-Scale Phylogenetics and Phylogeography

scientific article published on May 18, 2012
Resolving Rapid Radiations Within Angiosperm Families Using Anchored Phylogenomics

scientific article published on 4 May 2017
Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards

scientific article published on 11 April 2015
Phylogeny-based delimitation of species boundaries and contact zones in the trilling chorus frogs (Pseudacris).

scientific article published on 3 May 2007
Methodological congruence in phylogenomic analyses with morphological support for teiid lizards (Sauria: Teiidae).

scientific article
Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L.

scientific article published on 19 January 2017
Resolving Cypriniformes relationships using an anchored enrichment approach

scientific article
Resolving relationships among the megadiverse butterflies and moths with a novel pipeline for Anchored Phylogenomics

scientific article
Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudoxyrhophiine snakes

scientific article published on October 12, 2015
Phylogenomic data yield new and robust insights into the phylogeny and evolution of weevils

scientific article published on 26 December 2017
A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans

scientific article published on 01 April 2019
Anchored enrichment dataset for true flies (order Diptera) reveals insights into the phylogeny of flower flies (family Syrphidae)

scientific article
The promises and pitfalls of next-generation sequencing data in phylogeography

scientific article published in October 2012
Are 100 enough? Inferring acanthomorph teleost phylogeny using Anchored Hybrid Enrichment

scientific article
Phylogenomic support for evolutionary relationships of New World direct-developing frogs (Anura: Terraranae).

scientific article
A Passerine Bird's evolution corroborates the geologic history of the island of New Guinea

scientific article published in 2011
Quantity, Not Quality: Rapid Adaptation in a Polygenic Trait Proceeded Exclusively through Expression Differentiation

scientific article published on 30 August 2017
Recalcitrant deep and shallow nodes in Aristolochia (Aristolochiaceae) illuminated using anchored hybrid enrichment

scientific article
In the shadows: Phylogenomics and coalescent species delimitation unveil cryptic diversity in a Cerrado endemic lizard (Squamata: Tropidurus).

scientific article
A pilot study applying the plant Anchored Hybrid Enrichment method to New World sages (Salvia subgenus Calosphace; Lamiaceae).

scientific article
New insights on the sister lineage of percomorph fishes with an anchored hybrid enrichment dataset

scientific article
Anchored Hybrid Enrichment-Based Phylogenomics of Leafhoppers and Treehoppers (Hemiptera: Cicadomorpha: Membracoidea)

Selection To Increase Expression, Not Sequence Diversity, Precedes Gene Family Origin and Expansion in Rattlesnake Venom

scientific article published on 5 May 2017
Reinforcement and the genetics of hybrid incompatibilities

scientific article
The phylogeny and biogeography of Hakea (Proteaceae) reveals the role of biome shifts in a continental plant radiation

scientific article
Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes

scientific article published on 25 February 2019
Anchored hybrid enrichment generated nuclear, plastid and mitochondrial markers resolve the Lepanthes horrida (Orchidaceae: Pleurothallidinae) species complex

scientific article published on 21 July 2018
Resolving the psyllid tree of life: phylogenomic analyses of the superfamily Psylloidea (Hemiptera)

Phylogenomics clarifies repeated evolutionary origins of inbreeding and fungus farming in bark beetles (Curculionidae, Scolytinae)

scientific article published on 31 May 2018
Anchored Phylogenomics of Angiosperms I: Assessing the Robustness of Phylogenetic Estimates

article
Diversification in wild populations of the model organism Anolis carolinensis: A genome-wide phylogeographic investigation.

scientific article published on 17 October 2016
Interrogating genomic-scale data for Squamata (lizards, snakes, and amphisbaenians) shows no support for key traditional morphological relationships

scientific article published on 24 September 2019

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