Comparative phylogenomics reveal complex evolution of life history strategies in a clade of bivalves with parasitic larvae (Bivalvia: Unionoida: Ambleminae)

Population structure, genetic diversity, and colonization history of the eastern pondmussel, Sagittunio nasutus , in the Great Lakes drainage

(2020) Mariah W. Scott et al.   AQUATIC CONSERVATION-MARINE AND FRESHWATER ECOSYSTEMS

Unioverse: A phylogenomic resource for reconstructing the evolution of freshwater mussels (Bivalvia, Unionoida)

(2019) John M. Pfeiffer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Integrative taxonomy reveals a new species of freshwater mussel, Potamilus streckersoni sp. nov. (Bivalvia: Unionidae): implications for conservation and management

(2019) Chase H. Smith et al.   SYSTEMATICS AND BIODIVERSITY

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Molecular and morphological data reveal non-monophyly and speciation in imperiled freshwater mussels ( Anodontoides and Strophitus )

(2018) Chase H. Smith et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

Host attraction, brooding phenology, and host specialization on freshwater drum by 4 freshwater mussel species

(2018) Bernard E. Sietman et al.   Freshwater Science

Host attraction, brooding phenology, and host specialization on freshwater drum by 4 freshwater mussel species

(2018) Bernard E. Sietman et al.   Freshwater Science

MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons

(2018) Vincent Ranwez et al.   MOLECULAR BIOLOGY AND EVOLUTION

Integrative taxonomy resolves taxonomic uncertainty for freshwater mussels being considered for protection under the U.S. Endangered Species Act

(2018) Nathan A. Johnson et al.   Scientific Reports

Ecological correlates and phylogenetic signal of host use in North American unionid mussels

(2018) Trevor L. Hewitt et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

Convergent evolution of complex structures for ant–bacterial defensive symbiosis in fungus-farming ants

(2018) Hongjie Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogeny of Mesoamerican freshwater mussels and a revised tribe-level classification of the Ambleminae

(2018) John M. Pfeiffer et al.   ZOOLOGICA SCRIPTA

Molecular phylogeny of the Nearctic and Mesoamerican freshwater mussel genus Megalonaias

(2017) John M. Pfeiffer et al.   HYDROBIOLOGIA

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Resolving Relationships among the Megadiverse Butterflies and Moths with a Novel Pipeline for Anchored Phylogenomics

(2017) Jesse W. Breinholt et al.   SYSTEMATIC BIOLOGY

Long-term genomic coevolution of host-parasite interaction in the natural environment

(2017) Elina Laanto et al.   Nature Communications

Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices

(2016) Olga Chernomor et al.   SYSTEMATIC BIOLOGY

Repeated evolution and the impact of evolutionary history on adaptation

(2015) Terry J. Ord et al.   BMC EVOLUTIONARY BIOLOGY

Generic reclassification and species boundaries in the rediscovered freshwater mussel ‘Quadrula’ mitchelli (Simpson in Dall, 1896)

(2015) John M. Pfeiffer III et al.   CONSERVATION GENETICS

Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection

(2015) Martin D. Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

Coevolution with Bacteriophages Drives Genome-Wide Host Evolution and Constrains the Acquisition of Abiotic-Beneficial Mutations

(2015) Pauline D. Scanlan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular phylogenetic analysis supports a Gondwanan origin of the Hyriidae (Mollusca: Bivalvia: Unionida) and the paraphyly of Australasian taxa

(2015) Daniel L. Graf et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evolution of bilaterally asymmetrical larvae in freshwater mussels (Bivalvia: Unionoida: Unionidae)

(2015) John M. Pfeiffer et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Bridger: a new framework for de novo transcriptome assembly using RNA-seq data

(2015) Zheng Chang et al.   GENOME BIOLOGY

Population Demographics and Life History of the Round Hickorynut (Obovaria subrotunda) in the Duck River, Tennessee

(2014) Chase A Ehlo et al.   AMERICAN MIDLAND NATURALIST

AliView: a fast and lightweight alignment viewer and editor for large datasets

(2014) Anders Larsson   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Selecting optimal partitioning schemes for phylogenomic datasets

(2014) Robert Lanfear et al.   BMC EVOLUTIONARY BIOLOGY

FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies

(2014) Patrick Kück et al.   Frontiers in Zoology

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

High-Throughput Genomic Data in Systematics and Phylogenetics

(2013) Emily Moriarty Lemmon et al.   Annual Review of Ecology Evolution and Systematics

The role of fecundity and reproductive effort in defining life-history strategies of North American freshwater mussels

(2013) Wendell R. Haag   BIOLOGICAL REVIEWS

FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection

(2013) B. Murrell et al.   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mantle Display and Glochidia Release Behaviors of Five Quadruline Freshwater Mussel Species (Bivalvia: Unionidae)

(2012) Bernard E. Sietman et al.   AMERICAN MALACOLOGICAL BULLETIN

Early Life History of the Winged Mapleleaf Mussel (Quadrula fragosa)

(2012) Mark C. Hove et al.   AMERICAN MALACOLOGICAL BULLETIN

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

The probability of genetic parallelism and convergence in natural populations

(2012) G. L. Conte et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

(2012) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC BIOLOGY

Critical linkage of imperiled species: Gulf Sturgeon as host for Purple Bankclimber mussels

(2012) Andrea K. Fritts et al.   Freshwater Science

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Life History and Demographics of the Endangered Birdwing Pearlymussel (Lemiox rimosus) (Bivalvia: Unionidae)

(2010) Jess W. Jones et al.   AMERICAN MIDLAND NATURALIST

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell

(2010) T. Junier et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Partial Migration of Fishes as Exemplified by the Estuarine-Dependent White Perch

(2010) Lisa A. Kerr et al.   FISHERIES

Life history and host fish identification forFusconaia burkeiandPleurobema strodeanum(Bivalvia: Unionidae)

(2009) Megan P. White et al.   AMERICAN MALACOLOGICAL BULLETIN

A hierarchical classification of freshwater mussel diversity in North America

(2009) Wendell R. Haag   JOURNAL OF BIOGEOGRAPHY

Adaptations to host infection and larval parasitism in Unionoida

(2008) M. Christopher Barnhart et al.   JOURNAL OF THE NORTH AMERICAN BENTHOLOGICAL SOCIETY

Determination of fish host use by wild populations of rare freshwater mussels using a molecular identification key to identify glochidia

(2008) Stephen C. Kneeland et al.   JOURNAL OF THE NORTH AMERICAN BENTHOLOGICAL SOCIETY

Is convergence surprising? An examination of the frequency of convergence in simulated datasets

(2008) C. Tristan Stayton   JOURNAL OF THEORETICAL BIOLOGY

Recovering cryptic diversity and ancient drainage patterns in eastern North America: Historical biogeography of the Notropis rubellus species group (Teleostei: Cypriniformes)

(2007) Peter B. Berendzen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A three-genome phylogeny of malaria parasites (Plasmodium and closely related genera): Evolution of life-history traits and host switches

(2007) Ellen S. Martinsen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION