Historical DNA (hDNA), obtained from museum and herbarium specimens, has yielded spectacular new insights into the history of organisms. This includes documenting historical genetic erosion and extinction, discovering species new to science, resolving evolutionary relationships, investigating epigenetic effects, and determining origins of infectious diseases. However, the development of best-practices in isolating, processing, and analyzing hDNA remain under-explored, due to the substantial diversity of specimen preparation types, tissue sources, archival ages, and collecting histories. Thus, for hDNA to reach its full potential, and justify the destructive sampling of the rarest specimens, more experimental work using time-series collections, and the development of improved methods to correct for data asymmetries and biases due to DNA degradation are required.

Mining museums for historical DNA: advances and challenges in museomics.

Museum specimens play a crucial role in addressing key questions in systematics, evolution, ecology, and conservation. With the advent of high-throughput sequencing technologies, specimens that have long been the foundation of important biological discoveries can inform new perspectives as sources of genomic data. Despite the many possibilities associated with analyzing DNA from historical specimens, several challenges persist. Using avian systems as a model, we review DNA extraction protocols, sequencing technologies, and capture methods that are helping researchers overcome some of these difficulties. We highlight empirical examples in which researchers have used these technologies to address fundamental questions related to avian conservation and evolution. Increasing accessibility to new sequencing technologies will provide researchers with tools to tap into the wealth of information contained within our valuable natural history collections.

Historical DNA as a tool to address key questions in avian biology and evolution: A review of methods, challenges, applications, and future directions

The typical owl family (Strigidae) comprises 194 species in 28 genera, 14 of which are monotypic. Relationships within and among genera in the typical owls have been challenging to discern because mitochondrial data have produced equivocal results and because many monotypic genera have been omitted from previous molecular analyses. Here, we collected and analyzed DNA sequences of ultraconserved elements (UCEs) from 43 species of typical owls to produce concatenated and multispecies coalescent-based phylogenetic hypotheses for all but one genus in the typical owl family. Our results reveal extensive paraphyly of taxonomic groups across phylogenies inferred using different analytical approaches and suggest the genera Athene, Otus, Asio, Megascops, Bubo, and Strix are paraphyletic, whereas Ninox and Glaucidium are polyphyletic. Secondary analyses of protein-coding mitochondrial genes harvested from off-target sequencing reads and mitochondrial genomes downloaded from GenBank generally support the extent of paraphyly we observe, although some disagreements exist at higher taxonomic levels between our nuclear and mitochondrial phylogenetic hypotheses. Overall, our results demonstrate the importance of taxon sampling for understanding and describing evolutionary relationships in this group, as well as the need for additional sampling, study, and taxonomic revision of typical owl species. Additionally, our findings highlight how both divergence and convergence in morphological characters have obscured our understanding of the evolutionary history of typical owls, particularly those with insular distributions.

Extensive paraphyly in the typical owl family (Strigidae)

Hybridization, introgression, and reciprocal gene flow during speciation, specifically the generation of mitonuclear discordance, are increasingly observed as parts of the speciation process. Genomic approaches provide insight into where, when, and how adaptation operates during and after speciation and can measure historical and modern introgression. Whether adaptive or neutral in origin, hybridization can cause mitonuclear discordance by placing the mitochondrial genome of one species (or population) in the nuclear background of another species. The latter, introgressed species may eventually have its own mtDNA replaced or "captured" by other species across its entire geographical range. Intermediate stages in the capture process should be observable. Two nonsister species of Australasian monarch-flycatchers, Spectacled Monarch (Symposiachrus trivirgatus) mostly of Australia and Indonesia and Spot-winged Monarch (S. guttula) of New Guinea, present an opportunity to observe this process. We analysed thousands of single nucleotide polymorphisms (SNPs) derived from ultraconserved elements of all subspecies of both species. Mitochondrial DNA sequences of Australian populations of S. trivirgatus form two paraphyletic clades, one being sister to and presumably introgressed by S. guttula despite little nuclear signal of introgression. Population genetic analyses (e.g., tests for modern and historical gene flow and selection) support at least one historical gene flow event between S. guttula and Australian S. trivirgatus. We also uncovered introgression from the Maluku Islands subspecies of S. trivirgatus into an island population of S. guttula, resulting in apparent nuclear paraphyly. We find that neutral demographic processes, not adaptive introgression, are the most likely cause of these complex population histories. We suggest that a Pleistocene extinction of S. guttula from mainland Australia resulted from range expansion by S. trivirgatus.

Complex histories of gene flow and a mitochondrial capture event in a nonsister pair of birds.

A long-standing question in biology is how organisms change through time and space in response to their environment. This knowledge is of particular relevance to predicting how organisms might respond to future environmental changes caused by human-induced global change. Usually researchers make inferences about past events based on an understanding of current static genetic patterns, but these are limited in their capacity to inform on underlying past processes. Natural history collections (NHCs) represent a unique and critical source of information to provide temporally deep and spatially broad time-series of samples. By using NHC samples, researchers can directly observe genetic changes over time and space and link those changes with specific ecological/evolutionary events. Until recently, such genetic studies were hindered by the intrinsic challenges of NHC samples (i.e. low yield of highly fragmented DNA). However, recent methodological and technological developments have revolutionized the possibilities in the novel field of NHC genomics. In this Special Feature, we compile a range of studies spanning from methodological aspects to particular case studies which demonstrate the enormous potential of NHC samples for accessing large genomic data sets from the past to advance our knowledge on how populations and species respond to global change at multiple spatial-temporal scales. We also highlight possible limitations, recommendations and a few opportunities for future researchers aiming to study NHC genomics.

Genomics of natural history collections for understanding evolution in the wild

Next-generation sequencing has greatly expanded the utility and value of museum collections by revealing specimens as genomic resources. As the field of museum genomics grows, so does the need for extraction methods that maximize DNA yields. For avian museum specimens, the established method of extracting DNA from toe pads works well for most specimens. However, for some specimens, especially those of birds that are very small or very large, toe pads can be a poor source of DNA. In this study, we apply two DNA extraction methods (phenol-chloroform and silica column) to three different sources of DNA (toe pad, skin punch and bone) from 10 historical avian museum specimens. We show that a modified phenol-chloroform protocol yielded significantly more DNA than a silica column protocol (e.g., Qiagen DNeasy Blood & Tissue Kit) across all tissue types. However, extractions using the silica column protocol contained longer fragments on average than those using the phenol-chloroform protocol, probably as a result of loss of small fragments through the silica column. While toe pads yielded more DNA than skin punches and bone fragments, skin punches proved to be a reliable alternative source of DNA and might be especially appealing when toe pad extractions are impractical. Overall, we found that historical bird museum specimens contain substantial amounts of DNA for genomic studies under most extraction scenarios, but that a phenol-chloroform protocol consistently provides the high quantities of DNA required for most current genomic protocols.

More than skin and bones: Comparing extraction methods and alternative sources of DNA from avian museum specimens.

Hybridization involving introduced species is becoming more common as humans modify landscapes and ecosystems. When two closely related species are introduced to the same area, their niche dynamics will dictate the level of sympatry and potential for hybridization. Amazona parrots offer a rare case where multiple closely related species have established as breeders in Southern California. Red-crowned Parrots (A. viridigenalis) and Lilac-crowned Parrots (A. finschi) are particularly interesting because they are sister species with allopatric native ranges in Mexico. In Southern California, where they established in the 1980s and have since grown in numbers, they appear to occupy the same urban habitat. We sought to test whether introduced Red-crowned and Lilac-crowned parrots have shifted their niches compared to their native ranges, and if so, whether sympatry has led to hybridization. Using broad-scale environmental data collected from weather stations and orbiting satellites, we found that Red- crowned and Lilac-crowned parrots have partially divergent environmental niches in their native ranges, but now occupy the same environmental niche in their introduced range in Southern California. This new niche is largely different from what they experience in their respective home ranges, supporting a niche- shift model of species introduction. Due to this niche shift, the two species now come into contact across Southern California, leading to hybridization. Genomic markers support the existence of some recent hybrids as well as advanced backcrosses resulting from older hybridization events closer to the time of first introduction. Photographs from community scientists included as part of the Free-flying Los Angeles Parrot Project (FLAPP) also document hybrids, but underestimate their frequency compared to genetic data. Despite evidence for ongoing hybridization, the bimodal distribution of ancestry among the introduced population points to the existence of reproductive isolating mechanisms keeping the two species distinct. Further study is needed to understand if reproductive isolating mechanisms result from behavioral factors, such as conspecific flocking preferences, suggested by the community science data, or from genomic incompatibilities built up from a long history of isolation in Mexico. The integrity of these genetic lineages in Southern California carries important conservation implications, as both species are listed as endangered in their native ranges due to trapping for the pet trade and habitat loss.

/pdf/niche-shifts-and-hybridization-in-two-amazona-parrot-sister-4ae9m2ahpa.pdf

Niche shifts and hybridization in two Amazona parrot sister-species introduced to Southern California

This paper has been withdrawn by the authors while evaluating reviewer concerns about interpretation of the genomic data and due to errors found by the authors in the scoring of photos. Therefore, the authors do not wish this work to be cited as a reference for the project. If you have any questions, please contact the corresponding author.

/pdf/niche-shifts-lead-to-hybridization-between-two-amazona-3yc3t59u0z.pdf

Margaret E. Schedl

Papers

More than skin and bones: Comparing extraction methods and alternative sources of DNA from avian museum specimens.

Niche shifts and hybridization in two Amazona parrot sister-species introduced to Southern California

Niche shifts lead to hybridization between two Amazona parrot sister-species introduced to Southern California