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The 1918 H1N1 influenza pandemic, known as the Spanish flu, was the most devastating pandemic in recent history, causing an estimated 50 to 100 million deaths worldwide. The virus responsible for the pandemic was an entirely avian-like, highly virulent strain of influenza A virus that likely spilled over to humans from North American waterfowl shortly before its global spread. To better understand the origin of the virus, this Registered Report proposes to use phylogenomics and phylodynamics to reconstruct the evolutionary history of influenza A viruses in North American shorebird and duck populations during the late 19th and early 20th century, sampling wet specimens collected by the Smithsonian’s National Museum of Natural History (NMNH). Investigations of such museum specimens were previously attempted in two papers, “1917 avian influenza virus sequences suggest that the 1918 pandemic virus did not acquire its hemagglutinin directly from birds” by Fanning et al. [1] and “Relationship of pre-1918 avian influenza HA and NP sequences to subsequent avian influenza strains” by Reid et al. [2]. However, the positive results reported were later shown to result from contamination [3], highlighting fundamental limits to ancient biomolecular research at the time of the studies. Based on the latest developments in the field, we will reexamine these and other specimens to address the following hypotheses: 1) Historic North American avian influenza A virus sequences belong to Western hemispheric avian influenza A virus clades, within which they appear as early offshoots; 2) If detected, H1 segments from historic North American avian influenza viruses are most closely related to the 1918 human pandemic influenza virus H1 segments; and 3) Internal gene segments from North American avian influenza viruses originate in the middle to late 19th century.

The ancient DNA revolution of the past 35 years has driven an explosion in the breadth, nuance, and diversity of questions that are approachable using ancient biomolecules, and plant research has been a constant, indispensable facet of these developments. Using archaeological, paleontological, and herbarium plant tissues, researchers have probed plant domestication and dispersal, plant evolution and ecology, paleoenvironmental composition and dynamics, and other topics across related disciplines. Here, we review the development of the ancient DNA discipline and the role of plant research in its progress and refinement. We summarize our understanding of long-term plant DNA preservation and the characteristics of degraded DNA. In addition, we discuss challenges in ancient DNA recovery and analysis and the laboratory and bioinformatic strategies used to mitigate them. Finally, we review recent applications of ancient plant genomic research.

The genus Cucurbita (squashes, pumpkins, gourds) contains numerous domesticated lineages with ancient New World origins. It was broadly distributed in the past but has declined to the point that several of the crops' progenitor species are scarce or unknown in the wild. We hypothesize that Holocene ecological shifts and megafaunal extinctions severely impacted wild Cucurbita, whereas their domestic counterparts adapted to changing conditions via symbiosis with human cultivators. First, we used high-throughput sequencing to analyze complete plastid genomes of 91 total Cucurbita samples, comprising ancient (n = 19), modern wild (n = 30), and modern domestic (n = 42) taxa. This analysis demonstrates independent domestication in eastern North America, evidence of a previously unknown pathway to domestication in northeastern Mexico, and broad archaeological distributions of taxa currently unknown in the wild. Further, sequence similarity between distant wild populations suggests recent fragmentation. Collectively, these results point to wild-type declines coinciding with widespread domestication. Second, we hypothesize that the disappearance of large herbivores struck a critical ecological blow against wild Cucurbita, and we take initial steps to consider this hypothesis through cross-mammal analyses of bitter taste receptor gene repertoires. Directly, megafauna consumed Cucurbita fruits and dispersed their seeds; wild Cucurbita were likely left without mutualistic dispersal partners in the Holocene because they are unpalatable to smaller surviving mammals with more bitter taste receptor genes. Indirectly, megafauna maintained mosaic-like landscapes ideal for Cucurbita, and vegetative changes following the megafaunal extinctions likely crowded out their disturbed-ground niche. Thus, anthropogenic landscapes provided favorable growth habitats and willing dispersal partners in the wake of ecological upheaval.

© 2014 The Authors. The colonization of the human environment by plants, and the consequent evolution of domesticated forms is increasingly being viewed as a co-evolutionary plant-human process that occurred over a long time period, with evidence for the co-evolutionary relationship between plants and humans reaching ever deeper into the hominin past. This developing view is characterized by a change in emphasis on the drivers of evolution in the case of plants. Rather than individual species being passive recipients of artificial selection pressures and ultimately becoming domesticates, entire plant communities adapted to the human environment. This evolutionary scenario leads to systems level genetic expectations from models that can be explored through ancient DNA and Next Generation Sequencing approaches. Emerging evidence suggests that domesticated genomes fit well with these expectations, with periods of stable complex evolution characterized by large amounts of change associated with relatively small selective value, punctuated by periods in which changes in one-half of the plant-hominin relationship cause rapid, low-complexity adaptation in the other. A corollary of a single plant-hominin co-evolutionary process is that clues about the initiation of the domestication process may well lie deep within the hominin lineage.