Abstract
BackgroundImprovements in sequencing technology now allow easy acquisition of large datasets; however, analyzing these data for phylogenetics can be challenging. We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps of de novo whole genome assembly, multiple genome alignment, and annotation.ResultsFor simulations SISRS is able to identify large numbers of loci containing variable sites with phylogenetic signal. For genomic data from apes, SISRS identified thousands of variable sites, from which we produced an accurate phylogeny. Finally, we used SISRS to identify phylogenetic markers that we used to estimate the phylogeny of placental mammals. We recovered eight phylogenies that resolved the basal relationships among mammals using datasets with different levels of missing data. The three alternate resolutions of the basal relationships are consistent with the major hypotheses for the relationships among mammals, all of which have been supported previously by different molecular datasets.ConclusionsSISRS has the potential to transform phylogenetic research. This method eliminates the need for expensive marker development in many studies by using whole genome shotgun sequence data directly. SISRS is open source and freely available at https://github.com/rachelss/SISRS/releases.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0632-y) contains supplementary material, which is available to authorized users.
Highlights
Improvements in sequencing technology allow easy acquisition of large datasets; analyzing these data for phylogenetics can be challenging
We demonstrate that Site identification from short read sequences (SISRS) provides high quality phylogenetic datasets across a range of simulated and empirical data
The number of potentially informative sites identified using SISRS increased with increased coverage (Fig. 3)
Summary
Improvements in sequencing technology allow easy acquisition of large datasets; analyzing these data for phylogenetics can be challenging. We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps of de novo whole genome assembly, multiple genome alignment, and annotation. Phylogenetic studies relied on tens of loci (at most) from the genome to determine evolutionary relationships [1, 2]. These datasets often had insufficient information to provide strong support for all the relationships of interest [3]. Even given a reference genome, homologous loci may not be recoverable for species distantly related to the reference [13]
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