Multi-Locus DNA Sequence Phylogeny of Ambystomatid Salamanders

Featuring multi-locus DNA sequence data from a phylogenetic study of the Ambystomatidae family of salamanders. The analysis utilized coalescent-based and concordance-based methods to estimate species trees, robustly resolving many clades while identifying regions of unresolved divergence.

Use Cases

• Estimate species trees using coalescent-based methods that account for incomplete lineage sorting within a locus.
• Assess phylogenetic conflict by comparing results from concordance-based methods that estimate the number of sampled loci supporting a clade.
• Identify disproportionate locus effects by repeating analyses with the removal of individual loci, including mtDNA.
• Resolve deep and shallow clades within Ambystoma, such as the placement of A. gracile and A. talpoideum as a sister clade.

Strengths

• Data from the first multi-locus DNA sequence-based phylogenetic study of the Ambystomatidae family.
• Analysis includes a range of methods, including coalescent-based and concordance-based species-tree estimation.
• Results robustly resolved many deep and relatively shallow clades within the genus Ambystoma.

Limitations

• Intermediate depths of divergence in the ambystomatid species tree remain unresolved, potentially indicating rapid radiation or a hard polytomy.
• The dataset's specific size, format, and granular structure (e.g., row/column counts) are not detailed in the provided input.

Provenance

Source

Dryad

Collection Method

Multi-locus DNA sequence data collection and phylogenetic analysis using coalescent and concordance methods.

Freshness

2020-06-24