Middens provide rich sources of fossil material from both plants and animals, which can be used to investigate ecological responses to environmental change over the last 50,000 years (Balk, Betancourt, & Smith, 2019 Becklin, Medeiros, Sale, & Ward, 2014 Butterfield, Anderson, Holmgren, & Betancourt, 2019 Butterfield, Holmgren, Anderson, & Batancourt, 2019 Dézerald, Latorre, Betancourt, Brito Vera, & González, 2019 Holmgren, Hunter, & Betancourt, 2019). Since 1994, another 1,000 middens produced by other rodents ( Abrocoma, Phyllotis) have been studied from western South America (Latorre, Betancourt, Rylander, & Quade, 2002). Since 1960, >2000 fossil packrat ( Neotoma) middens have been analyzed and archived from western North America (Strickland, Thompson, & Anderson, 2001). Middens are radiocarbon‐dated from either fecal pellets, multiple plant fragments, or even an individual plant fragment using accelerator mass spectrometry (AMS) dating (Van Devender et al., 1985). Because the foraging range of these small rodents is limited, plant macrofossils are assumed to originate from plants growing within 100 m of the midden (Dial & Czaplewsk, 1990). One exception are fossil rodent middens, ubiquitous cave deposits that have been well studied across arid parts of North and South Americas and that contain abundant, diverse, and well‐preserved plant macrofossils and other remains (Betancourt & Saavedra, 2002 Betancourt, Devender, & Martin, 1990).įossil rodent middens are amalgamations of plant and animal remains embedded in cemented blocks of crystallized urine and preserved for millennia in arid land caves and rock shelters. This is a tall order for most kinds of geologic deposits. Paleogenomic studies of plants that aim to reconstruct past genetic variation require well‐preserved aDNA from many samples spanning millennia and broad geographic distributions. Various metagenomic and metabarcoding methods have been proposed. In recent years, much progress has been made on the recovery of aDNA from a variety of substrates including lake, bog, and cave sediments for a range of organisms including bacteria, archaea, plants, and hominins (e.g., Ahmed et al., 2018 Clarke et al., 2019 Parducci et al., 2019 Pedersen et al., 2016 Slon et al., 2017).
Much of the progress of ancient DNA (aDNA) has focused on hominins and large mammals, specifically from colder environments at high latitudes and elevations that enhance aDNA preservation (Birks & Birks, 2016 Hagelberg, Hofreiter, & Keyser, 2015). Steady progress in paleogenetics and paleogenomics over the past few decades is revolutionizing how we study biogeography, evolution, and population dynamics. The prospects for gaining more paleoecological insights from aDNA for rodent middens will continue to improve with optimization of laboratory methods, decreasing sequencing costs, and increasing computational power. With repeated sampling and deep sequencing, analysis of packrat midden aDNA from well‐preserved midden material can provide highly detailed characterizations of past communities of plants, animals, bacteria, and fungi present as trace DNA fossils. Amplicon sequencing of ITS2 and rbcL provided minimal data for some middens, but failed at amplifying the highly fragmented DNA present in others. Plant taxonomic diversity in the middens is shown to change through time and tracks changes in assemblages determined by morphological examination of the plant remains. Eukaryotic taxa identified belonged primarily to vascular plants with smaller proportions mapping to ascomycete fungi, arthropods, chordates, and nematodes. Eleven Illumina HiSeq 2500 libraries were successfully sequenced, and between 0.11% and 6.7% of reads were classified using Centrifuge against the NCBI “nt” database. Here, we explore the use of shotgun metagenomics to study the aDNA obtained from packrat middens up to 32,000 C 14 years old. Midden contents are so well preserved that fragments of endogenous ancient DNA (aDNA) can be extracted and analyzed across millennia. In arid parts of western North America, packrat ( Neotoma spp.) middens preserve plant and animal remains for tens of thousands of years.
Fossil rodent middens are powerful tools in paleoecology.
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