Hybridization capture with in-solution oligonucleotide probes has quickly become the preferred method for enriching specific DNA loci from degraded or ancient samples prior to high-throughput sequencing (HTS). Several companies synthesize sets of probes for in-solution hybridization capture, but these commercial reagents are usually expensive. Methods for economical in-house probe synthesis have been described, but they do not directly address one of the major advantages of commercially synthesised probes: that probe sequences matching many species can be synthesised in parallel and pooled. The ability to make "phylogenetically diverse" probes increases the cost-effectiveness of commercial probe sets, as they can be used across multiple projects (or for projects involving multiple species). However, it is labour-intensive to replicate this with in-house methods, as template molecules must first be generated for each species of interest. While it has been observed that probes can be used to enrich for phylogenetically distant targets, the ability of this effect to compensate for the lack of phylogenetically diverse probes in in-house synthesised probe sets has not been tested. In this study, we present a refined protocol for in-house RNA probe synthesis and evaluated the ability of probes generated using this method from a single species to successfully enrich for the target locus in phylogenetically distant species. We demonstrated that probes synthesized using long-range PCR products from a placental mammal mitochondrion (Bison spp.) could be used to enrich for mitochondrial DNA in birds and marsupials (but not plants). Importantly, our results were obtained for approximately a third of the cost of similar commercially available reagents.
Significance The extent to which the fossil record provides an accurate picture of past life is an important issue that is often difficult to assess. We genetically sexed 277 mammalian subfossils using high-throughput sequencing of ancient DNA, and found a strong male bias (∼75%) in Pleistocene bison ( n = 186) and brown bears ( n = 91), matching signals previously reported for mammoth. Similarly, a male bias was also found in species of nearly all mammal orders in 4 large museum collections. For mammals, we suggest both male behavior and appearance can lead to increased chances of representation in fossil and museum collections, and this previously unrecognized sex bias could have substantial implications for views of past population and ecological processes.
The Bering Land Bridge connecting North America and Eurasia was periodically exposed and inundated by oscillating sea levels during the Pleistocene glacial cycles. This land connection allowed the intermittent dispersal of animals, including humans, between Western Beringia (far northeast Asia) and Eastern Beringia (northwest North America), changing the faunal community composition of both continents. The Pleistocene glacial cycles also had profound impacts on temperature, precipitation and vegetation, impacting faunal community structure and demography. While these palaeoenvironmental impacts have been studied in many large herbivores from Beringia (e.g., bison, mammoths, horses), the Pleistocene population dynamics of the diverse guild of carnivorans present in the region are less well understood, due to their lower abundances. In this study, we analyse mitochondrial genome data from ancient brown bears (Ursus arctos; n = 103) and lions (Panthera spp.; n = 39), two megafaunal carnivorans that dispersed into North America during the Pleistocene. Our results reveal striking synchronicity in the population dynamics of Beringian lions and brown bears, with multiple waves of dispersal across the Bering Land Bridge coinciding with glacial periods of low sea levels, as well as synchronous local extinctions in Eastern Beringia during Marine Isotope Stage 3. The evolutionary histories of these two taxa underline the crucial biogeographical role of the Bering Land Bridge in the distribution, turnover and maintenance of megafaunal populations in North America.
ABSTRACT European bison ( Bison bonasus ) are the largest endemic vertebrates in Europe, and one of the few megafaunal species to have survived the mass megafaunal extinction during the Pleistocene/Holocene transition (12-9 thousand years ago). Untangling their evolutionary history would provide valuable information about the response of European megafauna to periods of rapid environmental change. However, a severe and recent population bottleneck obscures much of the population history that could be inferred from the genomes of modern individuals. While several studies have attempted to analyse ancient European bison populations directly using ancient DNA, their datasets were limited in temporal and geographic range. In this study we present the most comprehensive dataset of ancient European bison mitochondrial genomes to date, with 131 ancient bison samples from across the Eurasian continent covering over 50 thousand years. We reveal patterns of bison distribution and concurrent environmental changes across a broad geographical and temporal range. In particular, population expansions following periods of extensive forest reduction combined with a decrease in anthropogenic pressures suggest that European bison remain preferentially adapted to an open steppe environment through to the present day.
Two genera and multiple species of short-faced bear from the Americas went extinct during or toward the end of the Pleistocene, and all belonged to the endemic New World subfamily Tremarctinae. Two of these species were giants, growing in excess of 1,000 kg, but it remains uncertain how these extinct bears were related to the sole surviving short-faced bear: the spectacled bear (Tremarctos ornatus). Ancient mitochondrial DNA has recently suggested phylogenetic relationships among these lineages that conflict with interpretations based on morphology. However, widespread hybridisation and incomplete lineage sorting among extant bears mean that the mitochondrial phylogeny frequently does not reflect the true species tree. Here we present ancient nuclear genome sequences from representatives of the two extinct short-faced bear genera, Arctotherium and Arctodus. Our new data support a third hypothesis for the relationships among short-faced bears, which conflicts with existing mitochondrial and morphological data. Based on genome-wide D-statistics, we suggest that the extant spectacled bear derives substantial ancestry from Pleistocene hybridisation with an extinct short-faced bear lineage, resulting in a discordant phylogenetic signal between the mitochondrion and portions of the nuclear genome.
Abstract Subtropical and temperate rainforests of Central Eastern Australia are some of the largest remaining fragments of their kind globally. The biota of these rainforests appears to comprise two broad biogeographical elements: a more ancient (Miocene or older) and typically upland temperate (‘Gondwanan’) element and a younger (Plio-Pleistocene) lowland tropical element. We present the first phylogenetic synthesis of the spatiotemporal origins for the eight bird taxa endemic to Central Eastern Australian Rainforests. At least five of these eight focal taxa show Plio-Pleistocene divergences from their respective northern sister taxa, consistent with origins driven by recent expansion and contraction of lowland rainforest. In contrast, two more strictly upland species, the rufous scrub-bird (Atrichornis rufescens) and the logrunner (Orthonyx temminckii), diverged from their nearest living relatives during the Miocene, suggesting potentially longer histories of persistence and more temperate origins. Finally, we did not recover reciprocal monophyly in mitogenomes from the two extant lyrebirds, Albert’s lyrebird (Menura alberti) and the superb lyrebird (Menura novaehollandiae). The disparate divergence ages recovered among all eight taxa are consistent with the biota of the Central Eastern Australian Rainforests comprising isolates either of younger age and tropical lowland origins or of older age and temperate upland origins.
Summary Two genera and multiple species of short-faced bear from the Americas went extinct during or toward the end of the Pleistocene, and all belonged to the endemic New World subfamily Tremarctinae [1-7]. Two of these species were giants, growing in excess of 1,000 kg [6, 8, 9], but it remains uncertain how these extinct bears were related to the sole surviving short-faced bear: the spectacled bear ( Tremarctos ornatus ). Ancient mitochondrial DNA has recently suggested phylogenetic relationships among these lineages that conflict with interpretations based on morphology [1, 10-12]. However, widespread hybridisation and incomplete lineage sorting among extant bears mean that the mitochondrial phylogeny frequently does not reflect the true species tree [13, 14]. Here we present ancient nuclear genome sequences from representatives of the two extinct short-faced bear genera, Arctotherium and Arctodus . Our new data support a third hypothesis for the relationships among short-faced bears, which conflicts with existing mitochondrial and morphological data. Based on genome-wide D-statistics, we suggest that the extant spectacled bear derives substantial ancestry from Pleistocene hybridisation with an extinct short-faced bear lineage, resulting in a discordant phylogenetic signal between the mitochondrion and portions of the nuclear genome.
Abstract The Bering Land Bridge connecting North America and Eurasia was periodically exposed and inundated by oscillating sea levels during the Pleistocene glacial cycles. This land connection allowed the intermittent dispersal of animals, including humans, between Western Beringia (far north-east Asia) and Eastern Beringia (north-west North America), changing the faunal community composition of both continents. The Pleistocene glacial cycles also had profound impacts on temperature, precipitation, and vegetation, impacting faunal community structure and demography. While these paleoenvironmental impacts have been studied in many large herbivores from Beringia ( e.g ., bison, mammoths, horses), the Pleistocene population dynamics of the diverse guild of carnivorans present in the region are less well understood, due to their lower abundances. In this study, we analyze mitochondrial genome data from ancient brown bears ( Ursus arctos ; n = 103) and lions ( Panthera spp.; n = 39), two megafaunal carnivorans that dispersed into North America during the Pleistocene. Our results reveal striking synchronicity in the population dynamics of Beringian lions and brown bears, with multiple waves of dispersal across the Bering Land Bridge coinciding with glacial periods of low sea levels, as well as synchronous local extinctions in Eastern Beringia during Marine Isotope Stage 3. The evolutionary histories of these two taxa underscore the crucial biogeographic role of the Bering Land Bridge in the distribution, turnover, and maintenance of megafaunal populations in North America.
SUMMARY Five novel species, Auerbachia scomberoidi n. sp., Auerbachia chaetodoni n. sp., Auerbachia caranxi n. sp., Coccomyxa colurodontidis n. sp. and Coccomyxa gobiodoni n. sp. are described from the gall bladders of marine teleosts. These species descriptions provide the first record of Auerbachia from Australian waters. Each species is characterized morphologically, including additional measurements for Auerbachia spp. and small subunit ribosomal DNA (SSU rDNA) sequences were determined for molecular phylogenetic analyses. All 5 species were each recovered from a single (and different) species of host. Phylogenetic analyses revealed a close genetic relatedness between members of Auerbachia and Coccomyxa . Based on these phylogenetic data, on obvious paraphyly displayed by the Myxidiidae and on priority, we propose the re-establishment of the family Coccomyxidae to house all species of the genera, Coccomyxa , Auerbachia and Globospora .
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