B. C. Faircloth

Testing the mettle of METAL: A comparison of phylogenomic methods using a challenging but well-resolved phylogeny

The paper compares phylogenomic methods using a well-resolved bird species tree, finding that ML concatenation performs best, while METAL shows promise with large datasets.

The AEGEAN-169 clade of bacterioplankton is synonymous with SAR11 subclade V (HIMB59) and metabolically distinct

This paper demonstrates that SAR11 subclade V is synonymous with the AEGEAN-169 clade and shows they have distinct metabolic capabilities compared to SAR11.

Widespread sympatry in a species-rich clade of marine fishes (Carangoidei)

This study generates a phylogeny of marine fishes in the Carangoidei clade using UCEs and finds widespread sympatry among sister species pairs.

An island "endemic" born out of hybridization between introduced lineages

The paper uses genomic data and historical records to determine that Cuban bobwhites originated from hybridization between introduced lineages from southern Mexico and the southeastern USA, arriving in Cuba between the 12th and 20th centuries.

Ecophysiology and genomics of the brackish water adapted SAR11 subclade IIIa

This study presents the most comprehensive pangenomic analysis of SAR11 subclade IIIa, revealing ecological and metabolic differentiation across its subgroups and bridging marine and freshwater adaptations.

Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae)

This study evaluates the effectiveness of historical specimens in resolving subspecies-level phylogenetic relationships in New World quails using ultraconserved elements, finding that while species-level relationships are well-supported, subspecies-level discordance can be mitigated by analyzing subclades.

Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous

This study investigates the morphological expansion of spiny-rayed fishes after the K-Pg extinction, finding a prolonged diversification driven by body elongation and lineage radiation throughout the Cenozoic.

Phylogenomic Species Delimitation In Microendemic Frogs Of The Brazilian Atlantic Forest

This study evaluates species delimitation in microendemic frogs using phylogenomic data, finding that adding more loci has a stronger impact on model support than prioritizing informative loci.

A target enrichment bait set for studying relationships among ostariophysan fishes

The paper designs a bait set to enrich 2,708 ultraconserved nuclear loci from ostariophysan fishes and tests its utility across various phylogenetic scales.

Allele Phasing Greatly Improves the Phylogenetic Utility of Ultraconserved Elements

This paper develops a pipeline to recover allele sequences from sequence capture data and shows that phased allele sequences improve phylogenetic accuracy compared to contig sequences.

Cultivation and genomics of the first freshwater SAR11 (LD12) isolate

The paper isolates and genomes the first freshwater SAR11 (LD12) bacterium, revealing metabolic features and evolutionary adaptations to freshwater environments.

Phylogenomics of montane frogs of the Brazilian Atlantic Forest supports a scenario of isolation in sky islands followed by relative climatic stability

This study uses phylogenomic data to support a scenario of diversification-by-isolation in sky islands of the Brazilian Atlantic Forest due to climatic stability.

Conflicting evolutionary histories of the mitochondrial and nuclear genomes in New World Myotis

The study examines conflicting evolutionary histories between mitochondrial and nuclear genomes in New World Myotis using UCE data and mitochondrial genomes.