A paleogenomic perspective on evolution and gene function: new insights from ancient DNA

On Protein Loops, Prior Molecular States and Common Ancestors of Life

The principle of continuity demands the existence of prior molecular states and common ancestors responsible for extant macromolecular structure. Here, we focus on the emergence and evolution of loop prototypes - the elemental architects of protein domain structure. Phylogenomic reconstruction spanning superkingdoms and viruses generated an evolutionary chronology of prototypes with six distinct evolutionary phases defining a most parsimonious evolutionary progression of cellular life. Each phase was marked by strategic prototype accumulation shaping the structures and functions of common ancestors. The last universal common ancestor (LUCA) of cells and viruses and the last universal cellular ancestor (LUCellA) defined stem lines that were structurally and functionally complex. The evolutionary saga highlighted transformative forces. LUCA lacked biosynthetic ribosomal machinery, while the pivotal LUCellA lacked essential DNA biosynthesis and modern transcription. Early proteins therefore relied on RNA for genetic information storage but appeared initially decoupled from it, hinting at transformative shifts of genetic processing. Urancestral loop types suggest advanced folding designs were present at an early evolutionary stage. An exploration of loop geometric properties revealed gradual replacement of prototypes with α-helix and β-strand bracing structures over time, paving the way for the dominance of other loop types. AlphFold2-generated atomic models of prototype accretion described patterns of fold emergence. Our findings favor a ‛processual' model of evolving stem lines aligned with Woese's vision of a communal world. This model prompts discussing the 'problem of ancestors' and the challenges that lie ahead for research in taxonomy, evolution and complexity.

Development of Lasing Silica Microsphere for High-Speed DNA Molecular Detection

Laser and molecular detection techniques that have been used to overcome the limitations of fluorescent DNA labeling have presented new challenges. To address some of these challenges, we developed a DNA laser that uses a solid-state silica microsphere as a ring resonator and a site for DNA-binding reactions, as well as a platform to detect and sequence target DNA molecules. We detected target DNA using laser emission from a DNA-labeling dye and a developed solid-state silica microsphere ring resonator. The microsphere was sensitive; a single base mismatch in the DNA resulted in the absence of an optical signal. As each individual microsphere can be utilized as a parallel DNA analysis chamber, this optical digital detection scheme allows for high-throughput and rapid analysis. More importantly, the solid-state DNA laser is free from deformation, which guarantees stable lasing characteristics, and can be manipulated freely outside the solution. Thus, this promising advanced DNA laser scheme can be implemented on platforms other than optofluidic chips.

Comparison and optimization of protocols and whole-genome capture conditions for ancient DNA samples

Ancient DNA (aDNA) obtained from human remains is typically fragmented and present in relatively low amounts. Here we investigate a set of optimal methods for producing aDNA data by comparing silica-based DNA extraction and aDNA library preparation protocols. We also test the efficiency of whole-genome enrichment (WGC) on ancient human samples by modifying a number of parameter combinations. We find that the Dabney extraction protocol performs significantly better than alternatives. We further observed a positive trend with the BEST library protocol indicating lower clonality. Notably, our results suggest that WGC is effective at retrieving endogenous DNA, particularly from poorly-preserved human samples, by increasing human endogenous proportions by 5x. Thus, aDNA studies will be most likely to benefit from our results.

Evolutionary origin of germline pathogenic variants in human DNA mismatch repair genes

BACKGROUND

Mismatch repair (MMR) system is evolutionarily conserved for genome stability maintenance. Germline pathogenic variants (PVs) in MMR genes that lead to MMR functional deficiency are associated with high cancer risk. Knowing the evolutionary origin of germline PVs in human MMR genes will facilitate understanding the biological base of MMR deficiency in cancer. However, systematic knowledge is lacking to address the issue. In this study, we performed a comprehensive analysis to know the evolutionary origin of human MMR PVs.

METHODS

We retrieved MMR gene variants from the ClinVar database. The genomes of 100 vertebrates were collected from the UCSC genome browser and ancient human sequencing data were obtained through comprehensive data mining. Cross-species conservation analysis was performed based on the phylogenetic relationship among 100 vertebrates. Rescaled ancient sequencing data were used to perform variant calling for archeological analysis.

RESULTS

Using the phylogenetic approach, we traced the 3369 MMR PVs identified in modern humans in 99 non-human vertebrate genomes but found no evidence for cross-species conservation as the source for human MMR PVs. Using the archeological approach, we searched the human MMR PVs in over 5000 ancient human genomes dated from 45,045 to 100 years before present and identified a group of MMR PVs shared between modern and ancient humans mostly within 10,000 years with similar quantitative patterns.

CONCLUSION

Our study reveals that MMR PVs in modern humans were arisen within the recent human evolutionary history.

The Utilization of Reference-Guided Assembly and In Silico Libraries Improves the Draft Genome of Clarias batrachus and Culter alburnus

Long-read sequencing technologies can generate highly contiguous genome assemblies compared to short-read methods. However, their higher cost often poses a significant barrier. To address this, we explore the utilization of mapping-based genome assembly and reference-guided assembly as cost-effective alternative approaches. We assess the efficacy of these approaches in improving the contiguity of Clarias batrachus and Culter alburnus draft genomes. Our findings demonstrate that employing an iterative mapping strategy leads to a reduction in assembly errors. Specifically, after three iterations, the Mismatches per 100 kbp value for the C. batrachus genome decreased from 2447.20 to 2432.67, reaching a minimum of 2422.67 after two iterations. Additionally, the N50 value for the C. batrachus genome increased from 362,143 to 1,315,126 bp, with a maximum of 1,315,403 bp after two iterations. Furthermore, we achieved Mismatches per 100 kbp values of 3.70 for the reference-guided assembly of C. batrachus and 0.34 for C. alburnus. Correspondingly, the N50 value for the C. batrachus and C. alburnus genomes increased from 362,143 bp and 3,686,385 bp to 2,026,888 bp and 43,735,735 bp, respectively. Finally, we successfully utilized the improved C. batrachus and C. alburnus genomes to compare genome studies using the combined approach of Ragout and Ragtag. Through a comprehensive comparative analysis of mapping-based and reference-guided genome assembly methods, we shed light on the specific contributions of reference-guided assembly in reducing assembly errors and improving assembly continuity and integrity. These advancements establish reference-guided assembly and the utilization of in silico libraries as a promising and suitable approach for comparative genomics studies.

Ancient DNA is preserved in fish fossils from tropical lake sediments

Tropical freshwater lakes are well known for their high biodiversity, and particularly the East African Great Lakes are renowned for their adaptive radiation of cichlid fishes. While comparative phylogenetic analyses of extant species flocks have revealed patterns and processes of their diversification, little is known about evolutionary trajectories within lineages, the impacts of environmental drivers, or the scope and nature of now-extinct diversity. Time-structured palaeodata from geologically young fossil records, such as fossil counts and particularly ancient DNA (aDNA) data, would help fill this large knowledge gap. High ambient temperatures can be detrimental to the preservation of DNA, but refined methodology now allows data generation even from very poorly preserved samples. Here, we show for the first time that fish fossils from tropical lake sediments yield endogenous aDNA. Despite generally low endogenous content and high sample dropout, the application of high-throughput sequencing and, in some cases, sequence capture allowed taxonomic assignment and phylogenetic placement of 17% of analysed fish fossils to family or tribe level, including remains which are up to 2700 years old or weigh less than 1 mg. The relationship between aDNA degradation and the thermal age of samples is similar to that described for terrestrial samples from cold environments when adjusted for elevated temperature. Success rates and aDNA preservation differed between the investigated lakes Chala, Kivu and Victoria, possibly caused by differences in bottom water oxygenation. Our study demonstrates that the sediment records of tropical lakes can preserve genetic information on rapidly diversifying fish taxa over time scales of millennia.

Ancient DNA genomics and the renaissance of herbaria

Herbaria are undergoing a renaissance as valuable sources of genomic data for exploring plant evolution, ecology, and diversity. Ancient DNA retrieved from herbarium specimens can provide unprecedented glimpses into past plant communities, their interactions with biotic and abiotic factors, and the genetic changes that have occurred over time. Here, we highlight recent advances in the field of herbarium genomics and discuss the challenges and opportunities of combining data from modern and time-stamped historical specimens. We also describe how integrating herbarium genomics data with other data types can yield substantial insights into the evolutionary and ecological processes that shape plant communities. Herbarium genomic analysis is a tool for understanding plant life and informing conservation efforts in the face of dire environmental challenges.

Simulation-based Benchmarking of Ancient Haplotype Inference for Detecting Population Structure

Paleogenomic data has informed us about the movements, growth, and relationships of ancient populations. It has also given us context for medically relevant adaptations that appear in present-day humans due to introgression from other hominids, and it continues to help us characterize the evolutionary history of humans. However, ancient DNA (aDNA) presents several practical challenges as various factors such as deamination, high fragmentation, environmental contamination of aDNA, and low amounts of recoverable endogenous DNA, make aDNA recovery and analysis more difficult than modern DNA. Most studies with aDNA leverage only SNP data, and only a few studies have made inferences on human demographic history based on haplotype data, possibly because haplotype estimation (or phasing) has not yet been systematically evaluated in the context of aDNA. Here, we evaluate how the unique challenges of aDNA can impact phasing quality. We also develop a software tool that simulates aDNA taking into account the features of aDNA as well as the evolutionary history of the population. We measured phasing error as a function of aDNA quality and demographic history, and found that low phasing error is achievable even for very ancient individuals (~ 400 generations in the past) as long as contamination and read depth are adequate. Our results show that population splits or bottleneck events occurring between the reference and phased populations affect phasing quality, with bottlenecks resulting in the highest average error rates. Finally, we found that using estimated haplotypes, even if not completely accurate, is superior to using the simulated genotype data when reconstructing changes in population structure after population splits between present-day and ancient populations.

CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data

To date, ancient genome analyses have been largely confined to the study of single nucleotide polymorphisms (SNPs). Copy number variants (CNVs) are a major contributor of disease and of evolutionary adaptation, but identifying CNVs in ancient shotgun-sequenced genomes is hampered by typical low genome coverage (<1×) and short fragments (<80 bps), precluding standard CNV detection software to be effectively applied to ancient genomes. Here we present CONGA, tailored for genotyping CNVs at low coverage. Simulations and down-sampling experiments suggest that CONGA can genotype deletions >1 kbps with F-scores >0.75 at ≥1×, and distinguish between heterozygous and homozygous states. We used CONGA to genotype 10,002 outgroup-ascertained deletions across a heterogenous set of 71 ancient human genomes spanning the last 50,000 years, produced using variable experimental protocols. A fraction of these (21/71) display divergent deletion profiles unrelated to their population origin, but attributable to technical factors such as coverage and read length. The majority of the sample (50/71), despite originating from nine different laboratories and having coverages ranging from 0.44×-26× (median 4×) and average read lengths 52-121 bps (median 69), exhibit coherent deletion frequencies. Across these 50 genomes, inter-individual genetic diversity measured using SNPs and CONGA-genotyped deletions are highly correlated. CONGA-genotyped deletions also display purifying selection signatures, as expected. CONGA thus paves the way for systematic CNV analyses in ancient genomes, despite the technical challenges posed by low and variable genome coverage.

A 14,000-year-old genome sheds light on the evolution and extinction of a Pleistocene vulture

The New World Vulture [Coragyps] occidentalis (L. Miller, 1909) is one of many species that were extinct by the end of the Pleistocene. To understand its evolutionary history we sequenced the genome of a 14,000 year old [Coragyps] occidentalis found associated with megaherbivores in the Peruvian Andes. occidentalis has been viewed as the ancestor, or possibly sister, to the extant Black Vulture Coragyps atratus, but genomic data shows occidentalis to be deeply nested within the South American clade of atratus. Coragyps atratus inhabits lowlands, but the fossil record indicates that occidentalis mostly occupied high elevations. Our results suggest that occidentalis evolved from a population of atratus in southwestern South America that colonized the High Andes 300 to 400 kya. The morphological and morphometric differences between occidentalis and atratus may thus be explained by ecological diversification following from the natural selection imposed by this new and extreme, high elevation environment. The sudden evolution of a population with significantly larger body size and different anatomical proportions than atratus thus constitutes an example of punctuated evolution.

14,000 year old DNA reveals the evolutionary dynamics and adaptations of South American vultures.

Fecal Microbiota Transplantation as New Therapeutic Avenue for Human Diseases

The human body is home to a variety of micro-organisms. Most of these microbial communities reside in the gut and are referred to as gut microbiota. Over the last decades, compelling evidence showed that a number of human pathologies are associated with microbiota dysbiosis, thereby suggesting that the reinstatement of physiological microflora balance and composition might ameliorate the clinical symptoms. Among possible microbiota-targeted interventions, pre/pro-biotics supplementations were shown to provide effective results, but the main limitation remains in the limited microbial species available as probiotics. Differently, fecal microbiota transplantation involves the transplantation of a solution of fecal matter from a donor into the intestinal tract of a recipient in order to directly change the recipient's gut microbial composition aiming to confer a health benefit. Firstly used in the 4th century in traditional Chinese medicine, nowadays, it has been exploited so far to treat recurrent Clostridioides difficile infections, but accumulating data coming from a number of clinical trials clearly indicate that fecal microbiota transplantation may also carry the therapeutic potential for a number of other conditions ranging from gastrointestinal to liver diseases, from cancer to inflammatory, infectious, autoimmune diseases and brain disorders, obesity, and metabolic syndrome. In this review, we will summarize the commonly used preparation and delivery methods, comprehensively review the evidence obtained in clinical trials in different human conditions and discuss the variability in the results and the pivotal importance of donor selection. The final aim is to stimulate discussion and open new therapeutic perspectives among experts in the use of fecal microbiota transplantation not only in Clostridioides difficile infection but as one of the first strategies to be used to ameliorate a number of human conditions.

Thirty years of ancient DNA and the faunal biogeography of Aotearoa New Zealand: lessons and future directions

Thirty years ago, DNA sequences were obtained from an extinct Aotearoa New Zealand animal for the first time. Since then, ancient DNA research has provided many - often unexpected - insights into the origins of New Zealand's terrestrial and marine vertebrate fauna. Because recent human activities in New Zealand have caused the decline or extinction of many endemic plant, bird, reptile, and marine mammal species, ancient DNA has been instrumental in reconstructing their identities and origins. However, most ancient DNA studies focusing on New Zealand species have been restricted to vertebrates, with small sample sizes, and/or relatively few genetic markers. This has limited their power to infer fine-scale biogeographic patterns, including (pre)historic distributions and range-shifts driven by past climate and environmental change. Recently, 'next-generation' methodological and technological advances have broadened the range of hypotheses that can feasibly be tested with ancient DNA. These advances represent an exciting opportunity for further exploring New Zealand biogeography using ancient DNA, but their promise has not yet been fully realised. In this review, we summarise the last 30 years of ancient DNA research into New Zealand faunal biogeography and highlight key objectives, challenges, and possibilities for the next 30 years and beyond.

Development and Optimization of a Silica Column-Based Extraction Protocol for Ancient DNA

Rapid and cost-effective retrieval of endogenous DNA from ancient specimens remains a limiting factor in palaeogenomic research. Many methods have been developed to increase ancient DNA yield, but modifications to existing protocols are often based on personal experience rather than systematic testing. Here, we present a new silica column-based extraction protocol, where optimizations were tested in controlled experiments. Using relatively well-preserved permafrost samples, we tested the efficiency of pretreatment of bone and tooth powder with a bleach wash and a predigestion step. We also tested the recovery efficiency of MinElute and QIAquick columns, as well as Vivaspin columns with two molecular weight cut-off values. Finally, we tested the effect of uracil-treatment with two different USER enzyme concentrations. We find that neither bleach wash combined with a predigestion step, nor predigestion by itself, significantly increased sequencing efficiency. Initial results, however, suggest that MinElute columns are more efficient for ancient DNA extractions than QIAquick columns, whereas different molecular weight cut-off values in centrifugal concentrator columns did not have an effect. Uracil treatments are effective at removing DNA damage even at concentrations of 0.15 U/µL (as compared to 0.3 U/µL) of ancient DNA extracts.

Probing the genomic limits of de-extinction in the Christmas Island rat

Three principal methods are under discussion as possible pathways to “true” de-extinction; i.e., back-breeding, cloning, and genetic engineering.^1,2 Of these, while the latter approach is most likely to apply to the largest number of extinct species, its potential is constrained by the degree to which the extinct species genome can be reconstructed. We explore this question using the extinct Christmas Island rat (Rattus macleari) as a model, an endemic rat species that was driven extinct between 1898 and 1908.3, 4, 5 We first re-sequenced its genome to an average of >60× coverage, then mapped it to the reference genomes of different Rattus species. We then explored how evolutionary divergence from the extant reference genome affected the fraction of the Christmas Island rat genome that could be recovered. Our analyses show that even when the extremely high-quality Norway brown rat (R. norvegicus) is used as a reference, nearly 5% of the genome sequence is unrecoverable, with 1,661 genes recovered at lower than 90% completeness, and 26 completely absent. Furthermore, we find the distribution of regions affected is not random, but for example, if 90% completeness is used as the cutoff, genes related to immune response and olfaction are excessively affected. Ultimately, our approach demonstrates the importance of applying similar analyses to candidates for de-extinction through genome editing in order to provide critical baseline information about how representative the edited form would be of the extinct species.

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Evolutionary divergence limits the completeness of extinct species genomes

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The extinct Christmas Island rat was re-sequenced to ca. 60× coverage

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Nevertheless, 4.85% of the Norway brown rat genome remains absent after mapping

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Absences are not random; immune response and olfaction are excessively affected

Museum Genomics

Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth's biodiversity. Museum genomics-genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations-has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of anthropogenic activity on biodiversity. However, leveraging genomics in biological collections has exposed challenges, such as digitizing, integrating, and sharing collections data; updating practices to ensure broadly optimal data extraction from existing and new collections; and modernizing collections practices, infrastructure, and policies to ensure fair, sustainable, and genomically manifold uses of museum collections by increasingly diverse stakeholders. Museum genomics collections are poised to address these challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences.

Ancient Faunal History Revealed by Interdisciplinary Biomolecular Approaches

Starting four decades ago, studies have examined the ecology and evolutionary dynamics of populations and species using short mitochondrial DNA fragments and stable isotopes. Through technological and analytical advances, the methods and biomolecules at our disposal have increased significantly to now include lipids, whole genomes, proteomes, and even epigenomes. At an unprecedented resolution, the study of ancient biomolecules has made it possible for us to disentangle the complex processes that shaped the ancient faunal diversity across millennia, with the potential to aid in implicating probable causes of species extinction and how humans impacted the genetics and ecology of wild and domestic species. However, even now, few studies explore interdisciplinary biomolecular approaches to reveal ancient faunal diversity dynamics in relation to environmental and anthropogenic impact. This review will approach how biomolecules have been implemented in a broad variety of topics and species, from the extinct Pleistocene megafauna to ancient wild and domestic stocks, as well as how their future use has the potential to offer an enhanced understanding of drivers of past faunal diversity on Earth.

Characterization of whole mitogenome sequence of the Tongde yak (Bos grunniens)

Tongde County is located in the southeast of Qinghai Province, China, harboring rich yak genetic resources. In the present study, the complete mitochondrial genome (mitogenome) of the Tongde yak (Bos grunniens) was firstly sequenced using Illumina sequencing technique and the corresponding sequence characterization was identified. Our results showed that the mitogenome of Tongde yak is a circular molecule with 16,323 bp length consisting of 37 genes (13 protein-coding genes, 2 rRNA genes, 22 tRNA genes) and a non-coding control region (D-loop), which is consistent with most bovine species. The overall nucleotide composition was found as: A (33.72%), T (27.27%), C (25.80%), and G (13.21%), respectively, yielding a higher AT content (60.99%). The complete mitogenome sequence of Tongde yak would provide useful information for further studies on its genetic resource conservation and molecular breeding programmes in the future.

An Annotated Draft Genome for the Andean Bear, Tremarctos ornatus

The Andean bear is the only extant member of the Tremarctine subfamily and the only extant ursid species to inhabit South America. Here, we present an annotated de novo assembly of a nuclear genome from a captive-born female Andean bear, Mischief, generated using a combination of short and long DNA and RNA reads. Our final assembly has a length of 2.23 Gb, and a scaffold N50 of 21.12 Mb, contig N50 of 23.5 kb, and BUSCO score of 88%. The Andean bear genome will be a useful resource for exploring the complex phylogenetic history of extinct and extant bear species and for future population genetics studies of Andean bears.

Evaluating the role of reference-genome phylogenetic distance on evolutionary inference

When a high-quality genome assembly of a target species is unavailable, an option to avoid the costly de novo assembly process is a mapping-based assembly. However, mapping shotgun data to a distant relative may lead to biased or erroneous evolutionary inference. Here, we used short-read data from a mammal (beluga whale) and a bird species (rowi kiwi) to evaluate whether reference genome phylogenetic distance can impact downstream demographic (Pairwise Sequentially Markovian Coalescent) and genetic diversity (heterozygosity, runs of homozygosity) analyses. We mapped to assemblies of species of varying phylogenetic distance (from conspecific to genome-wide divergence of >7%), and de novo assemblies created using cross-species scaffolding. We show that while reference genome phylogenetic distance has an impact on demographic analyses, it is not pronounced until using a reference genome with >3% divergence from the target species. When mapping to cross-species scaffolded assemblies, we are unable to replicate the original beluga demographic results, but are able with the rowi kiwi, presumably reflecting the more fragmented nature of the beluga assemblies. We find that increased phylogenetic distance has a pronounced impact on genetic diversity estimates; heterozygosity estimates deviate incrementally with increasing phylogenetic distance. Moreover, runs of homozygosity are largely undetectable when mapping to any nonconspecific assembly. However, these biases can be reduced when mapping to a cross-species scaffolded assembly. Taken together, our results show that caution should be exercised when selecting reference genomes. Cross-species scaffolding may offer a way to avoid a costly, traditional de novo assembly, while still producing robust, evolutionary inference.

Environmental genomics of Late Pleistocene black bears and giant short-faced bears

Analysis of ancient environmental DNA (eDNA) has revolutionized our ability to describe biological communities in space and time,1-3 by allowing for parallel sequencing of DNA from all trophic levels.4-8 However, because environmental samples contain sparse and fragmented data from multiple individuals, and often contain closely related species,9 the field of ancient eDNA has so far been limited to organellar genomes in its contribution to population and phylogenetic studies.5,6,10,11 This is in contrast to data from fossils12,13 where full-genome studies are routine, despite these being rare and their destruction for sequencing undesirable.14-16 Here, we report the retrieval of three low-coverage (0.03×) environmental genomes from American black bear (Ursus americanus) and a 0.04× environmental genome of the extinct giant short-faced bear (Arctodus simus) from cave sediment samples from northern Mexico dated to 16-14 thousand calibrated years before present (cal kyr BP), which we contextualize with a new high-coverage (26×) and two lower-coverage giant short-faced bear genomes obtained from fossils recovered from Yukon Territory, Canada, which date to ∼22-50 cal kyr BP. We show that the Late Pleistocene black bear population in Mexico is ancestrally related to the present-day Eastern American black bear population, and that the extinct giant short-faced bears present in Mexico were deeply divergent from the earlier Beringian population. Our findings demonstrate the ability to separately analyze genomic-scale DNA sequences of closely related species co-preserved in environmental samples, which brings the use of ancient eDNA into the era of population genomics and phylogenetics.

Recovery and analysis of ancient beetle DNA from subfossil packrat middens using high-throughput sequencing

The study of ancient DNA is revolutionizing our understanding of paleo-ecology and the evolutionary history of species. Insects are essential components in many ecosystems and constitute the most diverse group of animals. Yet they are largely neglected in ancient DNA studies. We report the results of the first targeted investigation of insect ancient DNA to positively identify subfossil insects to species, which includes the recovery of endogenous content from samples as old as ~ 34,355 ybp. Potential inhibitors currently limiting widespread research on insect ancient DNA are discussed, including the lack of closely related genomic reference sequences (decreased mapping efficiency) and the need for more extensive collaborations with insect taxonomists. The advantages of insect-based studies are also highlighted, especially in the context of understanding past climate change. In this regard, insect remains from ancient packrat middens are a rich and largely uninvestigated resource for exploring paleo-ecology and species dynamics over time.

A Fast and Efficient Single-stranded Genomic Library Preparation Method Optimized for Ancient DNA

We present a protocol to prepare extracted DNA for sequencing on the Illumina sequencing platform that has been optimized for ancient and degraded DNA. Our approach, the Santa Cruz Reaction or SCR, uses directional splinted ligation of Illumina’s P5 and P7 adapters to convert natively single-stranded DNA and heat denatured double-stranded DNA into sequencing libraries in a single enzymatic reaction. To demonstrate its efficacy in converting degraded DNA molecules, we prepare 5 ancient DNA extracts into sequencing libraries using the SCR and 2 of the most commonly used approaches for preparing degraded DNA for sequencing: BEST, which targets and converts double-stranded DNA, and ssDNA2.0, which targets and converts single-stranded DNA. We then compare the efficiency with which each approach recovers unique molecules, or library complexity, given a standard amount of DNA input. We find that the SCR consistently outperforms the BEST protocol in recovering unique molecules and, despite its relative simplicity to perform and low cost per library, has similar performance to ssDNA2.0 across a wide range of DNA inputs. The SCR is a cost- and time-efficient approach that minimizes the loss of unique molecules and makes accessible a taxonomically, geographically, and a temporally broader sample of preserved remains for genomic analysis.

Environmental palaeogenomic reconstruction of an Ice Age algal population

Palaeogenomics has greatly increased our knowledge of past evolutionary and ecological change, but has been restricted to the study of species that preserve either as or within fossils. Here we show the potential of shotgun metagenomics to reveal population genomic information for a taxon that does not preserve in the body fossil record, the algae Nannochloropsis. We shotgun sequenced two lake sediment samples dated to the Last Glacial Maximum and reconstructed full chloroplast and mitochondrial genomes to explore within-lake population genomic variation. This revealed two major haplogroups for each organellar genome, which could be assigned to known varieties of N. limnetica, although we show that at least three haplotypes were present using our minimum haplotype diversity estimation method. These approaches demonstrate the utility of lake sedimentary ancient DNA (sedaDNA) for population genomic analysis, thereby opening the door to environmental palaeogenomics, which will unlock the full potential of sedaDNA.

Lammers et al. use sedimentary ancient DNA to reconstruct palaeogenomes of Nannochloropsis. This study demonstrates the value of sedaDNA for palaeogenomic reconstructions and population genomic analysis.

Genome-wide genetic variation coupled with demographic and ecological niche modeling of the dusky-footed woodrat (Neotoma fuscipes) reveal patterns of deep divergence and widespread Holocene expansion across northern California

Understanding how species have responded to past climate change may help refine projections of how species and biotic communities will respond to future change. Here, we integrate estimates of genome-wide genetic variation with demographic and niche modeling to investigate the historical biogeography of an important ecological engineer: the dusky-footed woodrat, Neotoma fuscipes. We use RADseq to generate a genome-wide dataset for 71 individuals from across the geographic distribution of the species in California. We estimate population structure using several model-based methods and infer the demographic history of regional populations using a site frequency spectrum-based approach. Additionally, we use ecological niche modeling to infer current and past (Last Glacial Maximum) environmental suitability across the species' distribution. Finally, we estimate the directionality and possible spatial origins of regional population expansions. Our analyses indicate this species is subdivided into three regionally distinct populations, with the deepest divergence occurring ~1.7 million years ago across the modern-day San Francisco-Bay Delta region; a common biogeographic barrier for the flora and fauna of California. Our models of environmental suitability through time coincide with our estimates of population expansion, with relative long-term stability in the southern portion of the range, and more recent expansion into the northern end of the range. Our study illustrates how the integration of genome-wide data with spatial and demographic modeling can reveal the timing and spatial extent of historic events that determine patterns of biotic diversity and may help predict biotic response to future change.

Using in silico predicted ancestral genomes to improve the efficiency of paleogenome reconstruction

Paleogenomics is the nascent discipline concerned with sequencing and analysis of genome-scale information from historic, ancient, and even extinct samples. While once inconceivable due to the challenges of DNA damage, contamination, and the technical limitations of PCR-based Sanger sequencing, following the dawn of the second-generation sequencing revolution, it has rapidly become a reality. However, a significant challenge facing ancient DNA studies on extinct species is the lack of closely related reference genomes against which to map the sequencing reads from ancient samples. Although bioinformatic efforts to improve the assemblies have focused mainly in mapping algorithms, in this article we explore the potential of an alternative approach, namely using reconstructed ancestral genome as reference for mapping DNA sequences of ancient samples. Specifically, we present a preliminary proof of concept for a general framework and demonstrate how under certain evolutionary divergence thresholds, considerable mapping improvements can be easily obtained.

Isolation, Library Preparation, and Bioinformatic Analysis of Historical and Ancient Plant DNA

The ability to sequence DNA retrieved from ancient and historical material plays a crucial role in reinforcing evolutionary and anthropological inference. While the focus of the field is largely on analyzing DNA from ancient hominids and other animals, we have also learned from plant ancient DNA (aDNA), in particular, about human farming practices, crop domestication, environment management, species invasion, and adaptation to various environmental conditions. In the following protocols, we outline best practices for plant aDNA isolation, preparation for sequencing, bioinformatic processing, and authentication. We describe the process all the way from processing of archaeological or historical plant material to characterizing and authenticating sequencing reads. In alternative protocols, we include modifications to this process that are tailored to strongly degraded DNA. Throughout, we stress the importance of precautionary measures to successfully analyze aDNA. Finally, we discuss the evolution of the archaeogenomics field and the development of new methods, which both shaped this protocol. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Isolation of aDNA Alternate Protocol 1: Isolation of ultra-short DNA (Dabney modification) Support Protocol 1: Preparation of PTB-based mix Support Protocol 2: Preparation of binding buffer Basic Protocol 2: Preparation of genomic libraries Alternate Protocol 2: Preparation of genomic libraries with uracil removal Basic Protocol 3: Bioinformatic processing and authentication of aDNA.

Using paleo-archives to safeguard biodiversity under climate change

Strategies for 21st-century environmental management and conservation under global change require a strong understanding of the biological mechanisms that mediate responses to climate- and human-driven change to successfully mitigate range contractions, extinctions, and the degradation of ecosystem services. Biodiversity responses to past rapid warming events can be followed in situ and over extended periods, using cross-disciplinary approaches that provide cost-effective and scalable information for species' conservation and the maintenance of resilient ecosystems in many bioregions. Beyond the intrinsic knowledge gain such integrative research will increasingly provide the context, tools, and relevant case studies to assist in mitigating climate-driven biodiversity losses in the 21st century and beyond.

An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice

Gene duplication is an important evolutionary mechanism allowing to provide new genetic material and thus opportunities to acquire new gene functions for an organism, with major implications such as speciation events. Various processes are known to allow a gene to be duplicated and different models explain how duplicated genes can be maintained in genomes. Due to their particular importance, the identification of duplicated genes is essential when studying genome evolution but it can still be a challenge due to the various fates duplicated genes can encounter. In this review, we first describe the evolutionary processes allowing the formation of duplicated genes but also describe the various bioinformatic approaches that can be used to identify them in genome sequences. Indeed, these bioinformatic approaches differ according to the underlying duplication mechanism. Hence, understanding the specificity of the duplicated genes of interest is a great asset for tool selection and should be taken into account when exploring a biological question.

Fostering Responsible Research on Ancient DNA

Anticipating and addressing the social implications of scientific work is a fundamental responsibility of all scientists. However, expectations for ethically sound practices can evolve over time as the implications of science come to be better understood. Contemporary researchers who work with ancient human remains, including those who conduct ancient DNA research, face precisely this challenge as it becomes clear that practices such as community engagement are needed to address the important social implications of this work. To foster and promote ethical engagement between researchers and communities, we offer five practical recommendations for ancient DNA researchers: (1) formally consult with communities; (2) address cultural and ethical considerations; (3) engage communities and support capacity building; (4) develop plans to report results and manage data; and (5) develop plans for long-term responsibility and stewardship. Ultimately, every member of a research team has an important role in fostering ethical research on ancient DNA.

Jointly Inferring the Dynamics of Population Size and Sampling Intensity from Molecular Sequences

Estimating past population dynamics from molecular sequences that have been sampled longitudinally through time is an important problem in infectious disease epidemiology, molecular ecology, and macroevolution. Popular solutions, such as the skyline and skygrid methods, infer past effective population sizes from the coalescent event times of phylogenies reconstructed from sampled sequences but assume that sequence sampling times are uninformative about population size changes. Recent work has started to question this assumption by exploring how sampling time information can aid coalescent inference. Here, we develop, investigate, and implement a new skyline method, termed the epoch sampling skyline plot (ESP), to jointly estimate the dynamics of population size and sampling rate through time. The ESP is inspired by real-world data collection practices and comprises a flexible model in which the sequence sampling rate is proportional to the population size within an epoch but can change discontinuously between epochs. We show that the ESP is accurate under several realistic sampling protocols and we prove analytically that it can at least double the best precision achievable by standard approaches. We generalize the ESP to incorporate phylogenetic uncertainty in a new Bayesian package (BESP) in BEAST2. We re-examine two well-studied empirical data sets from virus epidemiology and molecular evolution and find that the BESP improves upon previous coalescent estimators and generates new, biologically useful insights into the sampling protocols underpinning these data sets. Sequence sampling times provide a rich source of information for coalescent inference that will become increasingly important as sequence collection intensifies and becomes more formalized.

The past, present and future of ancient bacterial DNA

Groundbreaking studies conducted in the mid-1980s demonstrated the possibility of sequencing ancient DNA (aDNA), which has allowed us to answer fundamental questions about the human past. Microbiologists were thus given a powerful tool to glimpse directly into inscrutable bacterial history, hitherto inaccessible due to a poor fossil record. Initially plagued by concerns regarding contamination, the field has grown alongside technical progress, with the advent of high-throughput sequencing being a breakthrough in sequence output and authentication. Albeit burdened with challenges unique to the analysis of bacteria, a growing number of viable sources for aDNA has opened multiple avenues of microbial research. Ancient pathogens have been extracted from bones, dental pulp, mummies and historical medical specimens and have answered focal historical questions such as identifying the aetiological agent of the black death as Yersinia pestis. Furthermore, ancient human microbiomes from fossilized faeces, mummies and dental plaque have shown shifts in human commensals through the Neolithic demographic transition and industrial revolution, whereas environmental isolates stemming from permafrost samples have revealed signs of ancient antimicrobial resistance. Culminating in an ever-growing repertoire of ancient genomes, the quickly expanding body of bacterial aDNA studies has also enabled comparisons of ancient genomes to their extant counterparts, illuminating the evolutionary history of bacteria. In this review we summarize the present avenues of research and contextualize them in the past of the field whilst also pointing towards questions still to be answered.

Craniodental and Postcranial Characters of Non-Avian Dinosauria Often Imply Different Trees

Despite the increasing importance of molecular sequence data, morphology still makes an important contribution to resolving the phylogeny of many groups, and is the only source of data for most fossils. Most systematists sample morphological characters as broadly as possible on the principle of total evidence. However, it is not uncommon for sampling to be focused on particular aspects of anatomy, either because characters therein are believed to be more informative, or because preservation biases restrict what is available. Empirically, the optimal trees from partitions of morphological data sets often represent significantly different hypotheses of relationships. Previous work on hard-part versus soft-part characters across animal phyla revealed significant differences in about a half of sampled studies. Similarly, studies of the craniodental versus postcranial characters of vertebrates revealed significantly different trees in about one-third of cases, with the highest rates observed in non-avian dinosaurs. We test whether this is a generality here with a much larger sample of 81 published data matrices across all major dinosaur groups. Using the incongruence length difference test and two variants of the incongruence relationship difference test, we found significant incongruence in about 50% of cases. Incongruence is not uniformly distributed across major dinosaur clades, being highest (63%) in Theropoda and lowest (25%) in Thyreophora. As in previous studies, our partition tests show some sensitivity to matrix dimensions and the amount and distribution of missing entries. Levels of homoplasy and retained synapomorphy are similar between partitions, such that incongruence must partly reflect differences in patterns of homoplasy between partitions, which may itself be a function of modularity and mosaic evolution. Finally, we implement new tests to determine which partition yields trees most similar to those from the entire matrix. Despite no bias across dinosaurs overall, there are striking differences between major groups. The craniodental characters of Ornithischia and the postcranial characters of Saurischia yield trees most similar to the "total evidence" trees derived from the entire matrix. Trees from these same character partitions also tend to be most stratigraphically congruent: a mutual consilience suggesting that those partitions yield more accurate trees. [Dinosauria; homoplasy; partition homogeneity.].

Hybridization ddRAD-sequencing for population genomics of nonmodel plants using highly degraded historical specimen DNA

Species' responses at the genetic level are key to understanding the long-term consequences of anthropogenic global change. Herbaria document such responses, and, with contemporary sampling, provide high-resolution time-series of plant evolutionary change. Characterizing genetic diversity is straightforward for model species with small genomes and a reference sequence. For nonmodel species-with small or large genomes-diversity is traditionally assessed using restriction-enzyme-based sequencing. However, age-related DNA damage and fragmentation preclude the use of this approach for ancient herbarium DNA. Here, we combine reduced-representation sequencing and hybridization-capture to overcome this challenge and efficiently compare contemporary and historical specimens. Specifically, we describe how homemade DNA baits can be produced from reduced-representation libraries of fresh samples, and used to efficiently enrich historical libraries for the same fraction of the genome to produce compatible sets of sequence data from both types of material. Applying this approach to both Arabidopsis thaliana and the nonmodel plant Cardamine bulbifera, we discovered polymorphisms de novo in an unbiased, reference-free manner. We show that the recovered genetic variation recapitulates known genetic diversity in A. thaliana, and recovers geographical origin in both species and over time, independent of bait diversity. Hence, our method enables fast, cost-efficient, large-scale integration of contemporary and historical specimens for assessment of genome-wide genetic trends over time, independent of genome size and presence of a reference genome.

Horseshoe-based Bayesian nonparametric estimation of effective population size trajectories

Phylodynamics is an area of population genetics that uses genetic sequence data to estimate past population dynamics. Modern state-of-the-art Bayesian nonparametric methods for recovering population size trajectories of unknown form use either change-point models or Gaussian process priors. Change-point models suffer from computational issues when the number of change-points is unknown and needs to be estimated. Gaussian process-based methods lack local adaptivity and cannot accurately recover trajectories that exhibit features such as abrupt changes in trend or varying levels of smoothness. We propose a novel, locally adaptive approach to Bayesian nonparametric phylodynamic inference that has the flexibility to accommodate a large class of functional behaviors. Local adaptivity results from modeling the log-transformed effective population size a priori as a horseshoe Markov random field, a recently proposed statistical model that blends together the best properties of the change-point and Gaussian process modeling paradigms. We use simulated data to assess model performance, and find that our proposed method results in reduced bias and increased precision when compared to contemporary methods. We also use our models to reconstruct past changes in genetic diversity of human hepatitis C virus in Egypt and to estimate population size changes of ancient and modern steppe bison. These analyses show that our new method captures features of the population size trajectories that were missed by the state-of-the-art methods.

Adaptive introgression as a driver of local adaptation to climate in European white oaks

Latitudinal and elevational gradients provide valuable experimental settings for studies of the potential impact of global warming on forest tree species. The availability of long-term phenological surveys in common garden experiments for traits associated with climate, such as bud flushing for sessile oaks (Quercus petraea), provide an ideal opportunity to investigate this impact. We sequenced 18 sessile oak populations and used available sequencing data for three other closely related European white oak species (Quercus pyrenaica, Quercus pubescens, and Quercus robur) to explore the evolutionary processes responsible for shaping the genetic variation across latitudinal and elevational gradients in extant sessile oaks. We used phenotypic surveys in common garden experiments and climatic data for the population of origin to perform genome-wide scans for population differentiation and genotype-environment and genotype-phenotype associations. The inferred historical relationships between Q. petraea populations suggest that interspecific gene flow occurred between Q. robur and Q. petraea populations from cooler or wetter areas. A genome-wide scan of differentiation between Q. petraea populations identified single nucleotide polymorphisms (SNPs) displaying strong interspecific relative divergence between these two species. These SNPs followed genetic clines along climatic or phenotypic gradients, providing further support for the likely contribution of introgression to the adaptive divergence of Q. petraea populations. Overall, the results indicate that outliers and associated SNPs are Q. robur ancestry-informative. We discuss the results of this study in the framework of the postglacial colonization scenario, in which introgression and diversifying selection have been proposed as essential drivers of Q. petraea microevolution.

Inference and visualization of DNA damage patterns using a grade of membership model

MOTIVATION

Quality control plays a major role in the analysis of ancient DNA (aDNA). One key step in this quality control is assessment of DNA damage: aDNA contains unique signatures of DNA damage that distinguish it from modern DNA, and so analyses of damage patterns can help confirm that DNA sequences obtained are from endogenous aDNA rather than from modern contamination. Predominant signatures of DNA damage include a high frequency of cytosine to thymine substitutions (C-to-T) at the ends of fragments, and elevated rates of purines (A & G) before the 5' strand-breaks. Existing QC procedures help assess damage by simply plotting for each sample, the C-to-T mismatch rate along the read and the composition of bases before the 5' strand-breaks. Here we present a more flexible and comprehensive model-based approach to infer and visualize damage patterns in aDNA, implemented in an R package aRchaic. This approach is based on a 'grade of membership' model (also known as 'admixture' or 'topic' model) in which each sample has an estimated grade of membership in each of K damage profiles that are estimated from the data.

RESULTS

We illustrate aRchaic on data from several aDNA studies and modern individuals from 1000 Genomes Project Consortium (2012). Here, aRchaic clearly distinguishes modern from ancient samples irrespective of DNA extraction, lab and sequencing protocols. Additionally, through an in-silico contamination experiment, we show that the aRchaic grades of membership reflect relative levels of exogenous modern contamination. Together, the outputs of aRchaic provide a concise visual summary of DNA damage patterns, as well as other processes generating mismatches in the data.

AVAILABILITY AND IMPLEMENTATION

aRchaic is available for download from https://www.github.com/kkdey/aRchaic.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

More Arrows in the Ancient DNA Quiver: Use of Paleoepigenomes and Paleomicrobiomes to Investigate Animal Adaptation to Environment

Whether and how epigenetic mechanisms and the microbiome play a role in mammalian adaptation raised considerable attention and controversy, mainly because they have the potential to add new insights into the Modern Synthesis. Recent attempts to reconcile neo-Darwinism and neo-Lamarckism in a unified theory of molecular evolution give epigenetic mechanisms and microbiome a prominent role. However, supporting empirical data are still largely missing. Because experimental studies using extant animals can hardly be done over evolutionary timescales, we propose that advances in ancient DNA techniques provide a valid alternative. In this piece, we evaluate 1) the possible roles of epigenomes and microbiomes in animal adaptation, 2) advances in the retrieval of paleoepigenome and paleomicrobiome data using ancient DNA techniques, and 3) the plasticity of either and interactions between the epigenome and the microbiome, while emphasizing that it is essential to take both into account, as well as the underlying genetic factors that may confound the findings. We propose that advanced ancient DNA techniques should be applied to a wide range of past animals, so novel dynamics in animal evolution and adaption can be revealed.

Evolutionary History, Genomic Adaptation to Toxic Diet, and Extinction of the Carolina Parakeet

As the only endemic neotropical parrot to have recently lived in the northern hemisphere, the Carolina parakeet (Conuropsis carolinensis) was an iconic North American bird. The last surviving specimen died in the Cincinnati Zoo in 1918 [1]. The cause of its extinction remains contentious: besides excessive mortality associated to habitat destruction and active hunting, their survival could have been negatively affected by its range having become increasingly patchy [2] or by the exposure to poultry pathogens [3, 4]. In addition, the Carolina parakeet showed a predilection for cockleburs, an herbaceous plant that contains a powerful toxin, carboxyatractyloside, or CAT [5], which did not seem to affect them but made the birds notoriously toxic to most predators [3]. To explore the demographic history of this bird, we generated the complete genomic sequence of a preserved specimen held in a private collection in Espinelves (Girona, Spain), as well as of a close extant relative, Aratinga solstitialis. We identified two non-synonymous genetic changes in two highly conserved proteins known to interact with CAT that could underlie a specific dietary adaptation to this toxin. Our genomic analyses did not reveal evidence of a dramatic past demographic decline in the Carolina parakeet; also, its genome did not exhibit the long runs of homozygosity that are signals of recent inbreeding and are typically found in endangered species. As such, our results suggest its extinction was an abrupt process and thus likely solely attributable to human causes.

Genetically informed captive breeding of hybrids of an extinct species of Galapagos tortoise

Hybridization poses a major challenge for species conservation because it threatens both genetic integrity and adaptive potential. Yet, hybridization can occasionally offer unprecedented opportunity for species recovery if the genome of an extinct taxon is present among living hybrids such that selective breeding could recapture it. We explored the design elements for establishing a captive-breeding program for Galapagos tortoises (Chelonoidis spp.) built around individuals with admixed ancestry involving an extinct species. The target individuals were hybrids between the extinct species from Floreana Island, C. niger, and an extant species, C. becki, which were recently found in the endemic range of C. becki, from Wolf Volcano on Isabela Island. We combined genotypic data from 35 tortoises with high ancestry from C. niger with forward-in-time simulations to explore captive breeding strategies that maximized overall genetic diversity and ancestry from C. niger while accommodating resource constraints, species biology, and the urgency to return tortoises to Floreana Island for facilitating ecosystem restoration. Overall genetic diversity was maximized when in the simulation tortoises were organized in relatively small breeding groups. Substantial amounts of the C. niger genome were captured despite limited resources available for selectively breeding tortoises in captivity. Genetic diversity was maximized when captive-bred offspring were released to the wild rather than being used as additional breeders. Our results provide genetic-based and practical guidance on the inclusion of hybrids with genomic representation from extinct taxa into species restoration programs and informs the ongoing debate on the value of hybrids in biodiversity conservation.

Sediment Cores from White Pond, South Carolina, contain a Platinum Anomaly, Pyrogenic Carbon Peak, and Coprophilous Spore Decline at 12.8 ka

A widespread platinum (Pt) anomaly was recently documented in Greenland ice and 11 North American sedimentary sequences at the onset of the Younger Dryas (YD) event (~12,800 cal yr BP), consistent with the YD Impact Hypothesis. We report high-resolution analyses of a 1-meter section of a lake core from White Pond, South Carolina, USA. After developing a Bayesian age-depth model that brackets the late Pleistocene through early Holocene, we analyzed and quantified the following: (1) Pt and palladium (Pd) abundance, (2) geochemistry of 58 elements, (3) coprophilous spores, (4) sedimentary organic matter (OC and sedaDNA), (5) stable isotopes of C (δ13C) and N (δ15N), (6) soot, (7) aciniform carbon, (8) cryptotephra, (9) mercury (Hg), and (10) magnetic susceptibility. We identified large Pt and Pt/Pd anomalies within a 2-cm section dated to the YD onset (12,785 ± 58 cal yr BP). These anomalies precede a decline in coprophilous spores and correlate with an abrupt peak in soot and C/OC ratios, indicative of large-scale regional biomass burning. We also observed a relatively large excursion in δ15N values, indicating rapid climatic and environmental/hydrological changes at the YD onset. Our results are consistent with the YD Impact Hypothesis and impact-related environmental and ecological changes.

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.

The presence and impact of reference bias on population genomic studies of prehistoric human populations

Haploid high quality reference genomes are an important resource in genomic research projects. A consequence is that DNA fragments carrying the reference allele will be more likely to map successfully, or receive higher quality scores. This reference bias can have effects on downstream population genomic analysis when heterozygous sites are falsely considered homozygous for the reference allele. In palaeogenomic studies of human populations, mapping against the human reference genome is used to identify endogenous human sequences. Ancient DNA studies usually operate with low sequencing coverages and fragmentation of DNA molecules causes a large proportion of the sequenced fragments to be shorter than 50 bp-reducing the amount of accepted mismatches, and increasing the probability of multiple matching sites in the genome. These ancient DNA specific properties are potentially exacerbating the impact of reference bias on downstream analyses, especially since most studies of ancient human populations use pseudo-haploid data, i.e. they randomly sample only one sequencing read per site. We show that reference bias is pervasive in published ancient DNA sequence data of prehistoric humans with some differences between individual genomic regions. We illustrate that the strength of reference bias is negatively correlated with fragment length. Most genomic regions we investigated show little to no mapping bias but even a small proportion of sites with bias can impact analyses of those particular loci or slightly skew genome-wide estimates. Therefore, reference bias has the potential to cause minor but significant differences in the results of downstream analyses such as population allele sharing, heterozygosity estimates and estimates of archaic ancestry. These spurious results highlight how important it is to be aware of these technical artifacts and that we need strategies to mitigate the effect. Therefore, we suggest some post-mapping filtering strategies to resolve reference bias which help to reduce its impact substantially.

Phylogenetic incongruence and homoplasy in the appendages and bodies of arthropods: why broad character sampling is best

Notwithstanding the rapidly increasing sampling density of molecular sequence data, morphological characters still make an important contribution to our understanding of the evolutionary relationships of arthropod groups. In many clades, characters relating to the number and morphological specialization of appendages are ascribed particular phylogenetic significance and may be preferentially sampled. However, previous studies have shown that partitions of morphological character matrices often imply significantly different phylogenies. Here, we ask whether a similar incongruence is observed in the appendage and non-appendage characters of arthropods. We apply tree length (incongruence length difference, ILD) and tree distance (incongruence relationship difference, IRD) tests to these partitions in an empirical sample of 53 published neontological datasets for arthropods. We find significant incongruence about one time in five: more often than expected, but markedly less often than in previous partition studies. We also find similar levels of homoplasy in limb and non-limb characters, both in terms of internal consistency and consistency relative to molecular trees. Taken together, these findings imply that sampled limb and non-limb characters are of similar phylogenetic utility and quality, and that a total evidence approach to their analysis is preferable.

Ancient Mammalian and Plant DNA from Late Quaternary Stalagmite Layers at Solkota Cave, Georgia

Metagenomic analysis is a highly promising technique in paleogenetic research that allows analysis of the complete genomic make-up of a sample. This technique has successfully been employed to archaeological sediments, but possible leaching of DNA through the sequence limits interpretation. We applied this technique to the analysis of ancient DNA (aDNA) from Late Quaternary stalagmites from two caves in Western Georgia, Melouri Cave and Solkota. Stalagmites form closed systems, limiting the effect of leaching, and can be securely dated with U-series. The analyses of the sequence data from the Melouri Cave stalagmite revealed potential contamination and low preservation of DNA. However, the two Solkota stalagmites preserved ancient DNA molecules of mammals (bear, roe deer, bats) and plants (chestnut, hazelnut, flax). The aDNA bearing layers from one of the two Solkota stalagmites were dated to between ~84 ka and ~56 ka BP by U-series. The second Solkota stalagmite contained excessive detrital clay obstructing U-series dating, but it also contained bear bones with a minimum age of ~50 BP uncalibrated years and ancient DNA molecules. The preservation of authentic ancient DNA molecules in Late Quaternary speleothems opens up a new paleogenetic archive for archaeological, paleontological and paleoenvironmental research.

The Promise of Paleogenomics Beyond Our Own Species

Paleogenomics, also known as genome-wide ancient DNA analysis, is transforming our understanding of the human past, but has been much less intensively used to understand the history of other species. However, paleogenomic studies of non-human animals and plants have the potential to address an equally rich range of evolutionary, paleoecological, paleoenvironmental, and archaeological research questions. Three recent case studies of cave bears, horses, and maize provide examples of the ways that paleogenomics can be used to examine potential causes of extinctions and dynamic processes of domestication. Much more research in these areas is needed, and we conclude by highlighting key future directions.