Thanks to the development of high-throughput sequencing technologies, target enrichment sequencing of nuclear ultraconserved DNA elements (UCEs) now allows routine inference of phylogenetic relationships from thousands of genomic markers. Recently, it has been shown that mitochondrial DNA (mtDNA) is frequently sequenced alongside the targeted loci in such capture experiments. Despite its broad evolutionary interest, mtDNA is rarely assembled and used in conjunction with nuclear markers in capture-based studies. Here, we developed MitoFinder, a user-friendly bioinformatic pipeline, to efficiently assemble and annotate mitogenomic data from hundreds of UCE libraries. As a case study, we used ants (Formicidae) for which 501 UCE libraries have been sequenced whereas only 29 mitogenomes are available. We compared the efficiency of four different assemblers (IDBA-UD, MEGAHIT, MetaSPAdes, and Trinity) for assembling both UCE and mtDNA loci. Using MitoFinder, we show that metagenomic assemblers, in particular MetaSPAdes, are well suited to assemble both UCEs and mtDNA. Mitogenomic signal was successfully extracted from all 501 UCE libraries, allowing us to confirm species identification using CO1 barcoding. Moreover, our automated procedure retrieved 296 cases in which the mitochondrial genome was assembled in a single contig, thus increasing the number of available ant mitogenomes by an order of magnitude. By utilizing the power of metagenomic assemblers, MitoFinder provides an efficient tool to extract complementary mitogenomic data from UCE libraries, allowing testing for potential mitonuclear discordance. Our approach is potentially applicable to other sequence capture methods, transcriptomic data and whole genome shotgun sequencing in diverse taxa. The MitoFinder software is available from GitHub (https://github.com/RemiAllio/MitoFinder).

https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13160

MitoFinder: Efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics

High-throughput genomic sequencing is rapidly changing the field of phylogenetics by decreasing the cost and increasing the quantity and rate of data collection by several orders of magnitude. This deluge of data is exerting tremendous pressure on downstream data-analysis methods providing new opportunities for method development. In this review, we present (a) recent advances in laboratory methods for collection of high-throughput phylogenetic data and (b) challenges and constraints for phylogenetic analysis of these data. We compare the merits of multiple laboratory approaches, compare methods of data analysis, and offer recommendations for the most promising protocols and data-analysis workflows currently available for phylogenetics. We also discuss several strategies for increasing accuracy, with an emphasis on locus selection and proper model choice.

http://anchoredphylogeny.com/download/other_publications/Lemmon%20and%20Lemmon%202013%20AREES.pdf

High-Throughput Genomic Data in Systematics and Phylogenetics

Natural history museum collections provide unique resources for understanding how species respond to environmental change, including the abrupt, anthropogenic climate change of the past century. Ideally, researchers would conduct genome-scale screening of museum specimens to explore the evolutionary consequences of environmental changes, but to date such analyses have been severely limited by the numerous challenges of working with the highly degraded DNA typical of historic samples. Here, we circumvent these challenges by using custom, multiplexed, exon capture to enrich and sequence ~11 000 exons (~4 Mb) from early 20th-century museum skins. We used this approach to test for changes in genomic diversity accompanying a climate-related range retraction in the alpine chipmunks (Tamias alpinus) in the high Sierra Nevada area of California, USA. We developed robust bioinformatic pipelines that rigorously detect and filter out base misincorporations in DNA derived from skins, most of which likely resulted from postmortem damage. Furthermore, to accommodate genotyping uncertainties associated with low-medium coverage data, we applied a recently developed probabilistic method to call single-nucleotide polymorphisms and estimate allele frequencies and the joint site frequency spectrum. Our results show increased genetic subdivision following range retraction, but no change in overall genetic diversity at either nonsynonymous or synonymous sites. This case study showcases the advantages of integrating emerging genomic and statistical tools in museum collection-based population genomic applications. Such technical advances greatly enhance the value of museum collections, even where a pre-existing reference is lacking and points to a broad range of potential applications in evolutionary and conservation biology.

/pdf/unlocking-the-vault-next-generation-museum-population-1tsmbqez2u.pdf

Unlocking the vault: next-generation museum population genomics.

http://www.lucapozzi.me/uploads/6/7/2/4/6724991/pozzi_et_al._2014_mpe.pdf

Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes.

New DNA sequencing technologies are allowing researchers to explore the genomes of the millions of natural history specimens collected prior to the molecular era. Yet, we know little about how well specific next-generation sequencing (NGS) techniques work with the degraded DNA typically extracted from museum specimens. Here, we use one type of NGS approach, sequence capture of ultraconserved elements (UCEs), to collect data from bird museum specimens as old as 120 years. We targeted 5060 UCE loci in 27 western scrub-jays (Aphelocoma californica) representing three evolutionary lineages that could be species, and we collected an average of 3749 UCE loci containing 4460 single nucleotide polymorphisms (SNPs). Despite older specimens producing fewer and shorter loci in general, we collected thousands of markers from even the oldest specimens. More sequencing reads per individual helped to boost the number of UCE loci we recovered from older specimens, but more sequencing was not as successful at increasing the length of loci. We detected contamination in some samples and determined that contamination was more prevalent in older samples that were subject to less sequencing. For the phylogeny generated from concatenated UCE loci, contamination led to incorrect placement of some individuals. In contrast, a species tree constructed from SNPs called within UCE loci correctly placed individuals into three monophyletic groups, perhaps because of the stricter analytical procedures used for SNP calling. This study and other recent studies on the genomics of museum specimens have profound implications for natural history collections, where millions of older specimens should now be considered genomic resources.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.12466

Sequence capture of ultraconserved elements from bird museum specimens

Guenons (tribe Cercopithecini) are one of the most diverse groups of primates. They occupy all of sub-Saharan Africa and show great variation in ecology, behavior, and morphology. This variation led to the description of over 60 species and subspecies. Here, using next-generation DNA sequencing (NGS) in combination with targeted DNA capture, we sequenced 92 mitochondrial genomes from museum-preserved specimens as old as 117 years. We infer evolutionary relationships and estimate divergence times of almost all guenon taxa based on mitochondrial genome sequences. Using this phylogenetic framework, we infer divergence dates and reconstruct ancestral geographic ranges. We conclude that the extraordinary radiation of guenons has been a complex process driven by, among other factors, localized fluctuations of African forest cover. We find incongruences between phylogenetic trees reconstructed from mitochondrial and nuclear DNA sequences, which can be explained by either incomplete lineage sorting or hybridization. Furthermore, having produced the largest mitochondrial DNA data set from museum specimens, we document how NGS technologies can "unlock" museum collections, thereby helping to unravel the tree-of-life. (Museum collection; next-generation DNA sequencing; primate radiation; speciation; target capture.)

/pdf/next-generation-museomics-disentangles-one-of-the-largest-33iskoykf0.pdf

Next-generation museomics disentangles one of the largest primate radiations

Applicability of DNA barcoding to museum specimens of birds from the Democratic Republic of the Congo

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Next-generation museomics disentangles one of the largest primate radiations

Applicability of DNA barcoding to museum specimens of birds from the Democratic Republic of the Congo