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

Testing concordance and conflict in spatial replication of landscape genetics inferences

The degree to which landscape genetics findings can be extrapolated to different areas of a species range is poorly understood. Here, we used a broadly distributed ectothermic lizard (Sceloporus occidentalis, Western Fence lizard) as a model species to evaluate the full role of topography, climate, vegetation, and roads on dispersal and genetic differentiation. We conducted landscape genetics analyses with a total of 119 individuals in five areas within the Sierra Nevada mountain range. Genetic distances calculated from thousands of ddRAD markers were used to optimize landscape resistance surfaces and infer the effects of landscape and topographic features on genetic connectivity. Across study areas, we found a great deal of consistency in the primary environmental gradients impacting genetic connectivity, along with some site-specific differences, and a range in the proportion of genetic variance explained by environmental factors across study sites. High-elevation colder areas were consistently found to be barriers to gene flow, as were areas of high ruggedness and slope. High temperature seasonality and high precipitation during the winter wet season also presented a substantial barrier to gene flow in a majority of study areas. The effect of other landscape variables on genetic differentiation was more idiosyncratic and depended on specific attributes at each site. Across study areas, canyon valleys were always implicated as facilitators to dispersal and key features linking populations and maintaining genetic connectivity, though the relative importance varied in different areas. We emphasize that spatial data layers are complex and multidimensional, and careful consideration of spatial data correlation structure and robust analytic frameworks will be critical to our continued understanding of spatial genetics processes.

GoEnrich: creating high quality genomic DNA resources from limited voucher specimen tissues or museum specimens of at-risk species for conservation-friendly use in the validation of environmental DNA assays

OBJECTIVE

Environmental DNA (eDNA) methods are crucial for monitoring populations, particularly rare and cryptic species. For confident eDNA application, rigorous assay validation is required including specificity testing with genomic DNA (gDNA). However, this critical step is often difficult to achieve as obtaining fresh tissue samples from at-risk species can be difficult, highly limited, or impossible. Natural history museum collections could serve as a valuable and ethical voucher specimen resource for eDNA assay validation. The present study demonstrates the effectiveness of whole genome amplification (WGA) in providing enough gDNA to assemble high quality mitogenomes from which robust targeted eDNA assays can be designed.

RESULTS

Using fresh and historical museum tissue samples from six species spanning fish, birds, and mammals, we successfully developed a WGA method with an average yield of 380 to 1,268 ng gDNA per 20 µL reaction. This gDNA was used for whole genome shotgun sequencing and subsequent assembly of high quality mitogenomes using mtGrasp. These mitogenomes were then used to develop six new robust, targeted quantitative real time polymerase chain reaction-based eDNA assays and 200 ng WGA-enriched yielded satisfactory Cq values and near 100% detection frequencies for all assays tested. This approach offers a cost-effective and non-invasive alternative, streamlining eDNA research processes and aiding in conservation efforts.

Phylogeny and historical biogeography of the swallow family (Hirundinidae) inferred from comparisons of thousands of UCE loci

Swallows (Hirundinidae) are a globally distributed family of passerine birds that exhibit remarkable similarity in body shape but tremendous variation in plumage, sociality, nesting behavior, and migratory strategies. As a result, swallow species have become models for empirical behavioral ecology and evolutionary studies, and variation across the Hirundinidae presents an excellent opportunity for comparative analyses of trait evolution. Exploiting this potential requires a comprehensive and well-resolved phylogenetic tree of the family. To address this need, we estimated swallow phylogeny using genetic data from thousands of ultraconserved element (UCE) loci sampled from nearly all recognized swallow species. Maximum likelihood, coalescent-based, and Bayesian approaches yielded a well-resolved phylogenetic tree to the generic level, with minor disagreement among inferences at the species level, which likely reflect ongoing population genetic processes. The UCE data were particularly useful in helping to resolve deep nodes, which previously confounded phylogenetic reconstruction efforts. Divergence time estimates from the improved swallow tree support a Miocene origin of the family, roughly 13 million years ago, with subsequent diversification of major groups in the late Miocene and Pliocene. Our estimates of historical biogeography support the hypothesis that swallows originated in the Afrotropics and have subsequently expanded across the globe, with major in situ diversification in Africa and a secondary major radiation following colonization of the Neotropics. Initial examination of nesting and sociality indicates that the origin of mud nesting - a relatively rare nest construction phenotype in birds - was a major innovation coincident with the origin of a clade giving rise to over 40% of extant swallow diversity. In contrast, transitions between social and solitary nesting appear less important for explaining patterns of diversification among swallows.

Buffered Lugol's Iodine Preserves DNA Fragment Lengths

Museum collections play a pivotal role in the advancement of biological science by preserving phenotypic and genotypic history and variation. Recently, contrast-enhanced X-ray computed tomography (CT) has aided these advances by allowing improved visualization of internal soft tissues. However, vouchered specimens could be at risk if staining techniques are destructive. For instance, the pH of unbuffered Lugol's iodine (I2KI) may be low enough to damage deoxyribonucleic acid (DNA). The extent of this risk is unknown due to a lack of rigorous evaluation of DNA quality between control and experimental samples. Here, we used formalin-fixed mice to document DNA concentrations and fragment lengths in nonstained, ethanol-preserved controls and 3 iodine-based staining preparations: (1) 1.25% weight-by-volume (wt/vol.) alcoholic iodine (I2E); (2) 3.75% wt/vol. I2KI; and (3) 3.75% wt/vol. buffered I2KI. We tested a null hypothesis of no significant difference in DNA concentrations and fragment lengths between control and treatment samples. We found that DNA concentration decreases because of staining-potentially an effect of measuring intact double-stranded DNA only. Fragment lengths, however, were significantly higher for buffered I2KI and control samples, which were not, themselves, significantly different. Our results implicate buffered I2KI as the appropriate choice for contrast-enhanced CT imaging of museum wet collections to safely maximize their potential for understanding genetic and phenotypic diversity.

Minimally destructive hDNA extraction method for retrospective genetics of pinned historical Lepidoptera specimens

The millions of specimens stored in entomological collections provide a unique opportunity to study historical insect diversity. Current technologies allow to sequence entire genomes of historical specimens and estimate past genetic diversity of present-day endangered species, advancing our understanding of anthropogenic impact on genetic diversity and enabling the implementation of conservation strategies. A limiting challenge is the extraction of historical DNA (hDNA) of adequate quality for sequencing platforms. We tested four hDNA extraction protocols on five body parts of pinned false heath fritillary butterflies, Melitaea diamina, aiming to minimise specimen damage, preserve their scientific value to the collections, and maximise DNA quality and yield for whole-genome re-sequencing. We developed a very effective approach that successfully recovers hDNA appropriate for short-read sequencing from a single leg of pinned specimens using silica-based DNA extraction columns and an extraction buffer that includes SDS, Tris, Proteinase K, EDTA, NaCl, PTB, and DTT. We observed substantial variation in the ratio of nuclear to mitochondrial DNA in extractions from different tissues, indicating that optimal tissue choice depends on project aims and anticipated downstream analyses. We found that sufficient DNA for whole genome re-sequencing can reliably be extracted from a single leg, opening the possibility to monitor changes in genetic diversity maintaining the scientific value of specimens while supporting current and future conservation strategies.

A renewed glance at the Palearctic golden eagle: Genetic variation in space and time

Anthropogenic pressures on nature have been causing population declines for centuries. Intensified persecution of apex predators, like the golden eagle, resulted in population bottlenecks during the 19th and 20th centuries. To study population genetics and demographic history of the golden eagle throughout its distribution, we collected museum samples from previously underrepresented regions, such as Russia and Central Asia. We used 12 microsatellite loci and a fragment of the mitochondrial DNA control region to re-evaluate phylogeography of Eurasian golden eagles and study the impacts of the population bottleneck. Our results revealed a north-south genetic gradient, expressed by the difference between Mediterranean and Holarctic lineages, as well as genetically distinct Northern Europe and Central Asia and Caucasus regions. Furthermore, Northern Europe exhibited the lowest, whereas Central Asia and Caucasus had the highest genetic diversity. Although golden eagles maintained relatively high genetic diversity, we detected genetic signatures of the recent bottleneck, including reduced genetic diversity and a decline in the effective female population size around the year 1975. Our study improves the knowledge of the genetic composition of Eurasian golden eagles and highlights the importance of understanding their historical population dynamics in the face of ongoing and future conservation efforts.

Genetic Load and Adaptive Potential of a Recovered Avian Species that Narrowly Avoided Extinction

High genetic diversity is a good predictor of long-term population viability, yet some species persevere despite having low genetic diversity. Here we study the genomic erosion of the Seychelles paradise flycatcher (Terpsiphone corvina), a species that narrowly avoided extinction after having declined to 28 individuals in the 1960s. The species recovered unassisted to over 250 individuals in the 1990s and was downlisted from Critically Endangered to Vulnerable in the International Union for the Conservation of Nature Red List in 2020. By comparing historical, prebottleneck (130+ years old) and modern genomes, we uncovered a 10-fold loss of genetic diversity. Highly deleterious mutations were partly purged during the bottleneck, but mildly deleterious mutations accumulated. The genome shows signs of historical inbreeding during the bottleneck in the 1960s, but low levels of recent inbreeding after demographic recovery. Computer simulations suggest that the species long-term small Ne reduced the masked genetic load and made the species more resilient to inbreeding and extinction. However, the reduction in genetic diversity due to the chronically small Ne and the severe bottleneck is likely to have reduced the species adaptive potential to face environmental change, which together with a higher load, compromises its long-term population viability. Thus, small ancestral Ne offers short-term bottleneck resilience but hampers long-term adaptability to environmental shifts. In light of rapid global rates of population decline, our work shows that species can continue to suffer the effect of their decline even after recovery, highlighting the importance of considering genomic erosion and computer modeling in conservation assessments.

Minimally Invasive Sampling Methods for Molecular Sexing of Wild and Companion Birds

Birds are highly social and must be paired in order to increase their welfare. Most bird species are monomorphic; therefore, molecular sexing helps provide appropriate welfare for birds. Moreover, early sex determination can be of great value for bird owners. The aim of this study was to demonstrate that sex identification in birds achieved using molecular methods and samples collected via minimally invasive methods is fast, efficient, and accurate. A total of 100 samples (29 paired samples of feathers and oral swabs and 14 tripled samples of feathers, oral swabs, and blood) from 43 birds were included in this study, as follows: wild birds (Falconiformes, Accipitriformes, landfowl-Galliformes, waterfowl-Anseriformes) and companion birds (Passeriformes, Psittaciformes-large-, medium-, and small-sized parrots). Amplification of CHD1-Z and CHD1-W genes was performed via conventional PCR. The results obtained from feathers were compared to those obtained from oral swabs and to those obtained from blood samples, where applicable. The obtained results show that all types of samples can be used for molecular sexing of all studied bird species. To the best of our knowledge, the present study reports, for the first time, molecular sex identification in Red Siskin (Carduelis cucullata) and Goldfinch (Carduelis carduelis major). For higher accuracy, our recommendation is to use minimally invasive samples (oral swabs and feathers) and to test both types of samples for each bird instead of blood samples.

An evaluation of DNA extraction methods on historical and roadkill mammalian specimen

Guidelines identifying appropriate DNA extraction methods for both museum and modern biological samples are scarce or non-existent for mammalian species. Yet, obtaining large-scale genetic material collections are vital for conservation and management purposes. In this study, we evaluated five protocols making use of either spin-column, organic solvents, or magnetic bead-based methods for DNA extraction on skin samples from both modern, traffic-killed (n = 10) and museum (n = 10) samples of European hedgehogs, Ericaneus europaeus. We showed that phenol-chloroform or silica column (NucleoSpin Tissue) protocols yielded the highest amount of DNA with satisfactory purity compared with magnetic bead-based protocols, especially for museum samples. Furthermore, extractions using the silica column protocol appeared to produce longer DNA fragments on average than the other methods tested. Our investigation demonstrates that both commercial extraction kits and phenol-chloroform protocol retrieve acceptable DNA concentrations for downstream processes, from degraded remnants of traffic-killed and museum samples of mammalian specimens. Although all the tested methods could be applied depending on the research questions and laboratory conditions, commercial extraction kits may be preferred due to their effectiveness, safety and the higher quality of the DNA extractions.

An elevational shift facilitated the Mesoamerican diversification of Azure-hooded Jays (Cyanolyca cucullata) during the Great American Biotic Interchange

The Great American Biotic Interchange (GABI) was a key biogeographic event in the history of the Americas. The rising of the Panamanian land bridge ended the isolation of South America and ushered in a period of dispersal, mass extinction, and new community assemblages, which sparked competition, adaptation, and speciation. Diversification across many bird groups, and the elevational zonation of others, ties back to events triggered by the GABI. But the exact timing of these events is still being revealed, with recent studies suggesting a much earlier time window for faunal exchange, perhaps as early as 20 million years ago (Mya). Using a time-calibrated phylogenetic tree, we show that the jay genus Cyanolyca is emblematic of bird dispersal trends, with an early, pre-land bridge dispersal from Mesoamerica to South America 6.3-7.3 Mya, followed by a back-colonization of C. cucullata to Mesoamerica 2.3-4.8 Mya, likely after the land bridge was complete. As Cyanolyca species came into contact in Mesoamerica, they avoided competition due to a prior shift to lower elevation in the ancestor of C. cucullata. This shift allowed C. cucullata to integrate itself into the Mesoamerican highland avifauna, which our time-calibrated phylogeny suggests was already populated by higher-elevation, congeneric dwarf-jays (C. argentigula, C. pumilo, C. mirabilis, and C. nanus). The outcome of these events and fortuitous elevational zonation was that C. cucullata could continue colonizing new highland areas farther north during the Pleistocene. Resultingly, four C. cucullata lineages became isolated in allopatric, highland regions from Panama to Mexico, diverging in genetics, morphology, plumage, and vocalizations. At least two of these lineages are best described as species (C. mitrata and C. cucullata). Continued study will further document the influence of the GABI and help clarify how dispersal and vicariance shaped modern-day species assemblages in the Americas.

Museomics and phylogenomics of lovebirds (Psittaciformes, Psittaculidae, Agapornis) using low-coverage whole-genome sequencing

Natural history collections contain specimens that provide important insights into studies of ecology and evolution. With the advancement of high-throughput sequencing, historical DNA (hDNA) from museum specimens has become a valuable source of genomic data to study the evolutionary history of organisms. Low-coverage whole genome sequencing (WGS) has been increasingly applied to museum specimens for analyzing organelle genomes, but is still uncommon for genotyping the nuclear DNA fraction. In this study, we applied low-coverage WGS to phylogenomic analyses of parrots in the genus Agapornis by including both modern samples and historical specimens of ∼100-year-old. Agapornis are small-sized African and Malagasy parrots with diverse characters. Earlier phylogenetic studies failed to resolve the positions of some key lineages, prohibiting a robust interpretation of the biogeography and evolution of these African parrots. Here, we demonstrated the use of low-coverage WGS for generating both mitochondrial and nuclear genomic data, and evaluated data quality differences between modern and historical samples. Our resolved Agapornis phylogeny indicates the ancestor of Agapornis likely colonized Madagascar from Australasia by trans-oceanic dispersal events before dispersing to the African continent. Genome-wide SNPs also allowed us to identify the parental origins of hybrid Agapornis individuals. This study demonstrates the potential of applying low-coverage WGS to phylogenomics and population genomics analyses and illustrates how including historical museum specimens can address outstanding questions regarding the evolutionary history of contemporary lineages.

Confirmation of the local establishment of alien invasive turtle, Pseudemys peninsularis, in South Korea, using eggshell DNA

Alien invasive species are posing conservation challenges worldwide. Pet trade, one of the many ways, is worsening the situation. Especially, pet turtles have been released into nature due to their longer life span and peoples' religious and traditional beliefs. In addition, unwanted and undesired pets are also released. While information on the successful local establishment and subsequent dispersal into new habitats is required to designate an invasive and ecosystem-disturbing species, alien freshwater turtle nests have always been hard to find and identify in nature. Because one should identify nests by the eggs, which do not always guide properly, as adults abandon the sites quickly. We thought the recent advancement in DNA technology may help improve the situation. We studied Pseudemys peninsularis, one of the most traded freshwater turtle pet species, which has already been reported from a wide range of wild areas in South Korea. Yet, it is not designated as ecosystem-disturbing species due to a lack of adequate information on their local reproduction and establishment. We conducted surveys and found two nests in Jeonpyeongje Neighborhood Park, Maewol-dong, Seo-gu, Gwangju. We developed the methodology for extracting DNA from the eggshells and successfully identified the nests by phylogenetic analysis and verified through egg characteristics and morphological features of artificially hatched juveniles. This was the first successful initiative to extract DNA from freshwater turtle eggshells. We believe it will help future researchers identify the alien invasive turtle nests and develop their control and management policies. In addition, our study also included comparative descriptions and schematic diagrams of the eggs of eight freshwater turtles, including a native and three ecosystem-disturbing species, from South Korea. We urged an immediate designation of P. peninsularis as an ecosystem-disturbing species considering its local establishment, distribution range, and potential negative impact on native ecosystems.

A Comparison of Feathers and Oral Swab Samples as DNA Sources for Molecular Sexing in Companion Birds

The early age determinism of the sex in case of monomorphic birds is very important, because most companion birds have no distinct sexual dimorphic traits. Molecular genetic sexing was proved to be one of the most accurate sex determinations in monomorphic birds. The aim of this study was to compare the results obtained by PCR performed on isolate genomic DNA from paired samples of feathers and oral swabs collected from the same individuals. Samples of oral swabs (n = 101) and feathers (n = 74) were collected from 101 companion birds from four different species (Columba livia domestica, Psittacula krameri, Neophema splendida and Agapornis spp.). The PCR was performed for the amplification of the CHD1W and CHD1Z genes in females and the CHD1Z gene in males. The overall PCR success rate of sex determination was significantly higher from oral swabs than from feathers. The PCR success rate from oral swabs was higher in juveniles and from feathers was significantly higher in adults. The similarity between the oral swab and feathers was obtained in 78.38% of the birds. Oral swabs proved to be a more reliable sample for genetic sex determination in the species tested in this study.

Biogeographic inferences across spatial and evolutionary scales

The field of biogeography unites landscape genetics and phylogeography under a common conceptual framework. Landscape genetics traditionally focuses on recent-time, population-based, spatial genetics processes at small geographical scales, while phylogeography typically investigates deep past, lineage- and species-based processes at large geographical scales. Here, we evaluate the link between landscape genetics and phylogeographical methods using the western fence lizard (Sceloporus occidentalis) as a model species. First, we conducted replicated landscape genetics studies across several geographical scales to investigate how population genetics inferences change depending on the spatial extent of the study area. Then, we carried out a phylogeographical study of population structure at two evolutionary scales informed by inferences derived from landscape genetics results to identify concordance and conflict between these sets of methods. We found significant concordance in landscape genetics processes at all but the largest geographical scale. Phylogeographical results indicate major clades are restricted to distinct river drainages or distinct hydrological regions. At a more recent timescale, we find minor clades are restricted to single river canyons in the majority of cases, while the remainder of river canyons include samples from at most two clades. Overall, the broad-scale pattern implicating stream and river valleys as key features linking populations in the landscape genetics results, and high degree of clade specificity within major topographic subdivisions in the phylogeographical results, is consistent. As landscape genetics and phylogeography share many of the same objectives, synthesizing theory, models and methods between these fields will help bring about a better understanding of ecological and evolutionary processes structuring genetic variation across space and time.

Evolutionary genomics: Insights from the invasive European starlings

Two fundamental questions for evolutionary studies are the speed at which evolution occurs, and the way that this evolution may present itself within an organism's genome. Evolutionary studies on invasive populations are poised to tackle some of these pressing questions, including understanding the mechanisms behind rapid adaptation, and how it facilitates population persistence within a novel environment. Investigation of these questions are assisted through recent developments in experimental, sequencing, and analytical protocols; in particular, the growing accessibility of next generation sequencing has enabled a broader range of taxa to be characterised. In this perspective, we discuss recent genetic findings within the invasive European starlings in Australia, and outline some critical next steps within this research system. Further, we use discoveries within this study system to guide discussion of pressing future research directions more generally within the fields of population and evolutionary genetics, including the use of historic specimens, phenotypic data, non-SNP genetic variants (e.g., structural variants), and pan-genomes. In particular, we emphasise the need for exploratory genomics studies across a range of invasive taxa so we can begin understanding broad mechanisms that underpin rapid adaptation in these systems. Understanding how genetic diversity arises and is maintained in a population, and how this contributes to adaptability, requires a deep understanding of how evolution functions at the molecular level, and is of fundamental importance for the future studies and preservation of biodiversity across the globe.

Genomic investigation refutes record of most diverged avian hybrid

The most diverged avian hybrid that has been documented (Numida meleagris × Penelope superciliaris) was reported in 1957. This identification has yet to be confirmed, and like most contemporary studies of hybridization, the identification was based on phenotype, which can be misleading. In this study, we sequenced the specimen in question and performed analyses to validate the specimen's parentage. We extracted DNA from the specimen in a dedicated ancient DNA facility and performed whole-genome short-read sequencing. We used BLAST to find Galliformes sequences similar to the hybrid specimen reads. We found that the proportion of BLAST hits mapped overwhelmingly to two species, N. meleagris and Gallus gallus. Additionally, we constructed phylogenies using avian orthologs and parsed the species placed as sister to the hybrid. Again, the hybrid specimen was placed as a sister to N. meleagris and G. gallus. Despite not being a hybrid between N. meleagris and P. superciliaris, the hybrid still represents the most diverged avian hybrid confirmed with genetic data. In addition to correcting the "record" of the most diverged avian hybrid, these findings support recent assertions that morphological and behavioral-based identifications of avian hybrids can be error-prone. Consequently, this study serves as a cautionary tale to researchers of hybridization.

Molecular data from the holotype of the enigmatic Bornean Black Shrew, Suncusater Medway, 1965 (Soricidae, Crocidurinae), place it in the genus Palawanosorex

Although Borneo has received more attention from biologists than most other islands in the Malay Archipelago, many questions regarding the systematic relationships of Bornean mammals remain. Using next-generation sequencing technology, we obtained mitochondrial DNA sequences from the holotype of Suncusater, the only known specimen of this shrew. Several shrews collected recently in Sarawak are closely aligned, both morphologically and mitochondrially, with the holotype of S.ater. Phylogenetic analyses of mitochondrial sequences indicate that the S.ater holotype and new Sarawak specimens do not belong to the genus Suncus, but instead are most closely related to Palawanosorexmuscorum. Until now Palawanosorex has been known only from the neighboring Philippine island of Palawan. Additional sequences from nuclear ultra-conserved elements from the new Sarawak specimens strongly support a sister relationship to P.muscorum. We therefore transfer ater to Palawanosorex. The new specimens demonstrate that P.ater is more widespread in northern Borneo than previously recorded. Continued sampling of Bornean mammal diversity and reexamination of type material are critical in understanding the evolutionary history of the biologically rich Malay Archipelago.

Assessing the performance of historical skins and bones for museomics using wolf specimens as a case study

Advances in the field of museomics have promoted a high sampling demand for natural history collections (NHCs), eventually resulting in damage to invaluable resources to understand historical biodiversity. It is thus essential to achieve a consensus about which historical tissues present the best sources of DNA. In this study, we evaluated the performance of different historical tissues from Iberian wolf NHCs in genome-wide assessments. We targeted three tissues—bone (jaw and femur), maxilloturbinal bone, and skin—that have been favored by traditional taxidermy practices for mammalian carnivores. Specifically, we performed shotgun sequencing and target capture enrichment for 100,000 single nucleotide polymorphisms (SNPs) selected from the commercial Canine HD BeadChip across 103 specimens from 1912 to 2005. The performance of the different tissues was assessed using metrics based on endogenous DNA content, uniquely high-quality mapped reads after capture, and enrichment proportions. All samples succeeded as DNA sources, regardless of their collection year or sample type. Skin samples yielded significantly higher amounts of endogenous DNA compared to both bone types, which yielded equivalent amounts. There was no evidence for a direct effect of tissue type on capture efficiency; however, the number of genotyped SNPs was strictly associated with the starting amount of endogenous DNA. Evaluation of genotyping accuracy for distinct minimum read depths across tissue types showed a consistent overall low genotyping error rate (<7%), even at low (3x) coverage. We recommend the use of skins as reliable and minimally destructive sources of endogenous DNA for whole-genome and target enrichment approaches in mammalian carnivores. In addition, we provide a new 100,000 SNP capture array validated for historical DNA (hDNA) compatible to the Canine HD BeadChip for high-quality DNA. The increasing demand for NHCs as DNA sources should encourage the generation of genomic datasets comparable among studies.

Sequence Capture From Historical Museum Specimens: Maximizing Value for Population and Phylogenomic Studies

The application of high-throughput, short-read sequencing to degraded DNA has greatly increased the feasibility of generating genomic data from historical museum specimens. While many published studies report successful sequencing results from historical specimens; in reality, success and quality of sequence data can be highly variable. To examine predictors of sequencing quality, and methodological approaches to improving data accuracy, we generated and analyzed genomic sequence data from 115 historically collected museum specimens up to 180 years old. Data span both population genomic and phylogenomic scales, including historically collected specimens from 34 specimens of four species of Australian rock-wallabies (genus Petrogale) and 92 samples from 79 specimens of Australo-Papuan murine rodents (subfamily Murinae). For historical rodent specimens, where the focus was sampling for phylogenomics, we found that regardless of specimen age, DNA sequence libraries prepared from toe pad or bone subsamples performed significantly better than those taken from the skin (in terms of proportion of reads on target, number of loci captured, and data accuracy). In total, 93% of DNA libraries from toe pad or bone subsamples resulted in reliable data for phylogenetic inference, compared to 63% of skin subsamples. For skin subsamples, proportion of reads on target weakly correlated with collection year. Then using population genomic data from rock-wallaby skins as a test case, we found substantial improvement in final data quality by mapping to a high-quality “closest sister” de novo assembly from fresh tissues, compared to mapping to a sample-specific historical de novo assembly. Choice of mapping approach also affected final estimates of the number of segregating sites and Watterson's θ, both important parameters for population genomic inference. The incorporation of accurate and reliable sequence data from historical specimens has important outcomes for evolutionary studies at both population and phylogenomic scales. By assessing the outcomes of different approaches to specimen subsampling, library preparation and bioinformatic processing, our results provide a framework for increasing sequencing success for irreplaceable historical specimens.

Unlocking inaccessible historical genomes preserved in formalin

Museum specimens represent an unparalleled record of historical genomic data. However, the widespread practice of formalin preservation has thus far impeded genomic analysis of a large proportion of specimens. Limited DNA sequencing from formalin-preserved specimens has yielded low genomic coverage with unpredictable success. We set out to refine sample processing methods and to identify specimen characteristics predictive of sequencing success. With a set of taxonomically diverse specimens collected between 1962 and 2006 and ranging in preservation quality, we compared the efficacy of several end-to-end whole genome sequencing workflows alongside a k-mer-based trimming-free read alignment approach to maximize mapping of endogenous sequence. We recovered complete mitochondrial genomes and up to 3× nuclear genome coverage from formalin-preserved tissues. Hot alkaline lysis coupled with phenol-chloroform extraction out-performed proteinase K digestion in recovering DNA, while library preparation method had little impact on sequencing success. The strongest predictor of DNA yield was overall specimen condition, which additively interacts with preservation conditions to accelerate DNA degradation. Here, we demonstrate a significant advance in capability beyond limited recovery of a small number of loci via PCR or target-capture sequencing. To facilitate strategic selection of suitable specimens for genomic sequencing, we present a decision-making framework that utilizes independent and nondestructive assessment criteria. Sequencing of formalin-preserved specimens will contribute to a greater understanding of temporal trends in genetic adaptation, including those associated with a changing climate. Our work enhances the value of museum collections worldwide by unlocking genomes of specimens that have been disregarded as a valid molecular resource.

Mining museums for historical DNA: advances and challenges in museomics

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.

Uncovering the genomic and metagenomic research potential in old ethanol-preserved snakes

Natural history museum collections worldwide represent a tremendous resource of information on past and present biodiversity. Fish, reptiles, amphibians and many invertebrate collections have often been preserved in ethanol for decades or centuries and our knowledge on the genomic and metagenomic research potential of such material is limited. Here, we use ancient DNA protocols, combined with shotgun sequencing to test the molecular preservation in liver, skin and bone tissue from five old (1842 to 1964) museum specimens of the common garter snake (Thamnophis sirtalis). When mapping reads to a T. sirtalis reference genome, we find that the DNA molecules are highly damaged with short average sequence lengths (38-64 bp) and high C-T deamination, ranging from 9% to 21% at the first position. Despite this, the samples displayed relatively high endogenous DNA content, ranging from 26% to 56%, revealing that genome-scale analyses are indeed possible from all specimens and tissues included here. Of the three tested types of tissue, bone shows marginally but significantly higher DNA quality in these metrics. Though at least one of the snakes had been exposed to formalin, neither the concentration nor the quality of the obtained DNA was affected. Lastly, we demonstrate that these specimens display a diverse and tissue-specific microbial genetic profile, thus offering authentic metagenomic data despite being submerged in ethanol for many years. Our results emphasize that historical museum collections continue to offer an invaluable source of information in the era of genomics.

Genomic library preparation and hybridization capture of formalin-fixed tissues and allozyme supernatant for population genomics and considerations for combining capture- and RADseq-based single nucleotide polymorphism data sets

Until recently many historical museum specimens were largely inaccessible to genomic inquiry, but high-throughput sequencing (HTS) approaches have allowed researchers to successfully sequence genomic DNA from dried and fluid-preserved museum specimens. In addition to preserved specimens, many museums contain large series of allozyme supernatant samples, but the amenability of these samples to HTS has not yet been assessed. Here, we compared the performance of a target-capture approach using alternative sources of genomic DNA from 10 specimens of spring salamanders (Plethodontidae: Gyrinophilus porphyriticus) collected between 1985 and 1990: allozyme supernatants, allozyme homogenate pellets and formalin-fixed tissues. We designed capture probes based on double-digest restriction-site associated sequencing (RADseq) derived loci from frozen blood samples available for seven of the specimens and assessed the success and consistency of capture and RADseq approaches. This study design enabled direct comparisons of data quality and potential biases among the different data sets for phylogenomic and population genomic analyses. We found that in phylogenetic analyses, all enrichment types for a given specimen clustered together. In principal component space all capture-based samples clustered together, but RADseq samples did not cluster with corresponding capture-based samples. Single nucleotide polymorphism calls were on average 18.3% different between enrichment types for a given individual, but these discrepancies were primarily due to differences in heterozygous/homozygous single nucleotide polymorphism calls. We demonstrate that both allozyme supernatant and formalin-fixed samples can be successfully used for population genomic analyses and we discuss ways to identify and reduce biases associated with combining capture and RADseq data.

Current and Forthcoming Approaches for Benchmarking Genetic and Genomic Diversity

The current attrition of biodiversity extends beyond loss of species and unique populations to steady loss of a vast genomic diversity that remains largely undescribed. Yet the accelerating development of new techniques allows us to survey entire genomes ever faster and cheaper, to obtain robust samples from a diversity of sources including degraded DNA and residual DNA in the environment, and to address conservation efforts in new and innovative ways. Here we review recent studies that highlight the importance of carefully considering where to prioritize collection of genetic samples (e.g., organisms in rapidly changing landscapes or along edges of geographic ranges) and what samples to collect and archive (e.g., from individuals of little-known subspecies or populations, even of species not currently considered endangered). Those decisions will provide the sample infrastructure to detect the disappearance of certain genotypes or gene complexes, increases in inbreeding levels, and loss of genomic diversity as environmental conditions change. Obtaining samples from currently endangered, protected, and rare species can be particularly difficult, thus we also focus on studies that use new, non-invasive ways of obtaining genomic samples and analyzing them in these cases where other sampling options are highly constrained. Finally, biological collections archiving such samples face an inherent contradiction: their main goal is to preserve biological material in good shape so it can be used for scientific research for centuries to come, yet the technologies that can make use of such materials are advancing faster than collections can change their standardized practices. Thus, we also discuss current and potential new practices in biological collections that might bolster their usefulness for future biodiversity conservation research.

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

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.

Natural history collections are critical resources for contemporary and future studies of urban evolution

Urban environments are among the fastest changing habitats on the planet, and this change has evolutionary implications for the organisms inhabiting them. Herein, we demonstrate that natural history collections are critical resources for urban evolution studies. The specimens housed in these collections provide great potential for diverse types of urban evolution research, and strategic deposition of specimens and other materials from contemporary studies will determine the resources and research questions available to future urban evolutionary biologists. As natural history collections are windows into the past, they provide a crucial historical timescale for urban evolution research. While the importance of museum collections for research is generally appreciated, their utility in the study of urban evolution has not been explicitly evaluated. Here, we: (a) demonstrate that museum collections can greatly enhance urban evolution studies, (b) review patterns of specimen use and deposition in the urban evolution literature, (c) analyze how urban versus rural and native versus nonnative vertebrate species are being deposited in museum collections, and (d) make recommendations to researchers, museum professionals, scientific journal editors, funding agencies, permitting agencies, and professional societies to improve archiving policies. Our analyses of recent urban evolution studies reveal that museum specimens can be used for diverse research questions, but they are used infrequently. Further, although nearly all studies we analyzed generated resources that could be deposited in natural history collections (e.g., collected specimens), a minority (12%) of studies actually did so. Depositing such resources in collections is crucial to allow the scientific community to verify, replicate, and/or re-visit prior research. Therefore, to ensure that adequate museum resources are available for future urban evolutionary biology research, the research community-from practicing biologists to funding agencies and professional societies-must make adjustments that prioritize the collection and deposition of urban specimens.

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

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.