Hybridization capture approaches allow targeted high-throughput sequencing analysis at reduced costs compared to shotgun sequencing. Hybridization capture is particularly useful in analyses of genomic data from ancient, environmental, and forensic samples, where target content is low, DNA is fragmented and multiplex PCR or other targeted approaches often fail. Here, we describe a DNA bait synthesis approach for hybridization capture that we call Circular Nucleic acid Enrichment Reagent, or CNER (pronounced 'snare'). The CNER method uses rolling-circle amplification followed by restriction digestion to discretize microgram quantities of hybridization probes. We demonstrate the utility of the CNER method by generating probes for a panel of 23 771 known sites of single nucleotide polymorphism in the horse genome. Using these probes, we capture and sequence from a panel of ten ancient horse DNA libraries, comparing CNER capture efficiency to a commercially available approach. With about one million read pairs per sample, CNERs captured more targets (90.5% versus 66.5%) at greater mean depth than an alternative commercial approach.

Ancient hair and remnant plant DNA are important environmental proxies that preserve for millennia in specific archaeological contexts. However, recovery has been rare from late Pleistocene sites and more may be found if deliberately sought. Once discovered, singular hair fragments are not easily identified to taxa through comparative analyses and environmental DNA (eDNA) extraction can be difficult depending on preservation or contamination. In this paper, we present our methods for the combined recovery of ancient hair specimens and eDNA from sediments to improve our understanding of late Pleistocene environments from the Holzman site along Shaw Creek in interior Alaska. The approach serves as a useful case study for learning more about local environmental changes.

Polar bears (Ursus maritimus) and brown bears (Ursus arctos) are sister species possessing distinct physiological and behavioural adaptations that evolved over the last 500,000 years. However, comparative and population genomics analyses have revealed that several extant and extinct brown bear populations have relatively recent polar bear ancestry, probably as the result of geographically localized instances of gene flow from polar bears into brown bears. Here, we generate and analyse an approximate 20X paleogenome from an approximately 100,000-year-old polar bear that reveals a massive prehistoric admixture event, which is evident in the genomes of all living brown bears. This ancient admixture event was not visible from genomic data derived from living polar bears. Like more recent events, this massive admixture event mainly involved unidirectional gene flow from polar bears into brown bears and occurred as climate changes caused overlap in the ranges of the two species. These findings highlight the complex reticulate paths that evolution can take within a regime of radically shifting climate.

The Bering Land Bridge (BLB) last connected Eurasia and North America during the Late Pleistocene. Although the BLB would have enabled transfers of terrestrial biota in both directions, it also acted as an ecological filter whose permeability varied considerably over time. Here we explore the possible impacts of this ecological corridor on genetic diversity within, and connectivity among, populations of a once wide-ranging group, the caballine horses (Equus spp.). Using a panel of 187 mitochondrial and eight nuclear genomes recovered from present-day and extinct caballine horses sampled across the Holarctic, we found that Eurasian horse populations initially diverged from those in North America, their ancestral continent, around 1.0-0.8 million years ago. Subsequent to this split our mitochondrial DNA analysis identified two bidirectional long-range dispersals across the BLB ~875-625 and ~200-50 thousand years ago, during the Middle and Late Pleistocene. Whole genome analysis indicated low levels of gene flow between North American and Eurasian horse populations, which probably occurred as a result of these inferred dispersals. Nonetheless, mitochondrial and nuclear diversity of caballine horse populations retained strong phylogeographical structuring. Our results suggest that barriers to gene flow, currently unidentified but possibly related to habitat distribution across Beringia or ongoing evolutionary divergence, played an important role in shaping the early genetic history of caballine horses, including the ancestors of living horses within Equus ferus.

The remains of the extinct Merck’s rhinoceros ( Stephanorhinus kirchbergensis (Jäger 1839)), well studied in Western Europe, are rare in Russia. However, thanks to the work of a number of researchers, the geography of the finds and the reconstructed range of the species have been significantly expanded. The time of the optimal existence of Merck’s rhinoceros in Yakutia is now recognized as the Middle Pleistocene; the latest finds, dating from the beginning of the late Pleistocene, are known from the southeast of Western Siberia. We provide new radiocarbon dates for the root of a tooth and bone tissue from a previously unstudied lower jaw of the Merck’s rhinoceros from Altai (AltR), whose taxonomic identity we confirm using genomic analysis. Both dates provide an age estimate of around 40 thousand years, which corresponds to the Karginsky time (MIS 3), and are the youngest for the species on the territory of Russia. The pollen spectrum from the soil filling the bone canal characterizes plant communities of open landscapes with forest areas on the upland or in the floodplain, and reflects either local features of the environment or communities of the cold stage within the Karginsky interstadial. A second Merck’s rhinoceros from the Chondon River (ChR), in extreme northeast Yakutia, was determined by previous researchers to have lived either 45–70 thousand years ago or during the beginning of the Middle Pleistocene. Considering what habitats were available in the region, we propose that the ChR could have lived during the last—Kazantsevo—interglacial (MIS 5e) or later. Both finds, AltR and ChR, extend the temporal range of the species existence.

The remains of a Holocene extinct steppe bison, Bison priscus Bojanus 1827, that died 9.5 thousand years ago, were discovered on the Rauchua River (Chukotka, Russia) in 2012. Sample F-3246 yielded ancient DNA and, when compared to other extant and extinct Bison lineages, clustered outside the known bison genetic diversity, suggesting that this bison represented a divergent and heretofore unknown lineage of extinct bison. While this conclusion is supported by a morphological analysis of sample F-3246, additional examples of this divergent bison phenotype and genotype are required in order to understand its position in bison evolutionary history. Here, we assemble complete mitochondrial genomes from 26 additional ancient Bison samples from northern Siberia, aiming to improve the knowledge of the evolutionary history and geographic range of the Rauchua bison lineage. Surprisingly, we did not identify the Rauchua haplotype in any of the newly tested bison, including those discovered from the Rauchua River locality. Nonetheless, additional mitochondrial genomic data from Siberian bison, and a new high-coverage mitogenome recovered from the original Rauchua bison (F-3246), confirm the existence of the deeply divergent Glade and shed new light on the evolutionary history of bison during the Pleistocene to Holocene transition in Siberia.

Museum collections are essential for reconstructing and understanding past biodiversity. Many museum specimens are, however, challenging to identify. Museum samples may be incomplete, have an unusual morphology, or represent juvenile individuals, all of which complicate accurate identification. In some cases, inaccurate identification can lead to false biogeographic reconstructions with cascading impacts on paleontological and paleoecological research. Here, we analyzed an unusual Equid mandible found in the Far North of the Taymyr peninsula that was identified morphologically as Equus hemionus, an ancestor of present-day Asiatic wild asses. If correct, this identification represents the only finding of a putative Late Pleistocene hemione in the Arctic region, and is therefore critical to understanding wild ass evolution and paleoecology. To confirm the accuracy of this specimen's taxonomic assignment, we used ancient DNA and mitochondrial hybridization capture to identify and place this specimen in the larger equid phylogeny. We find that the specimen is actually a member of E. caballus, the ancestor of domestic horses. Our study demonstrates the utility of ancient DNA to validate morphological identification, in particular of incomplete, otherwise problematic, or taxonomically unusual museum specimens.

EquCab2, a high-quality reference genome for the domestic horse, was released in 2007. Since then, it has served as the foundation for nearly all genomic work done in equids. Recent advances in genomic sequencing technology and computational assembly methods have allowed scientists to improve reference assemblies of large animal and plant genomes in terms of contiguity and composition. In 2014, the equine genomics research community began a project to improve the reference sequence for the horse, building upon the solid foundation of EquCab2 and incorporating new short-read data, long-read data, and proximity ligation data. The result, EquCab3, is presented here. The count of non-N bases in the incorporated chromosomes is improved from 2.33Gb in EquCab2 to 2.41Gb from EquCab3. Contiguity has also been improved nearly 40-fold with a contig N50 of 4.5Mb and scaffold contiguity enhanced to where all but one of the 32 chromosomes is comprised of a single scaffold.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

This paper reports the results of an in-depth analysis of the frozen remains of a woolly mammoth (Mammuthus primigenius) named Zhenya, which has been dated to 48,000 cal BP. The carcass, found near the mouth of the Yenisey River in eastern Siberia, was a juvenile male whose ontogenetic age at death was 8-10 AEY. Its reconstructed live height at the shoulders (pSH 227.4 cm) was the equal of some adult female woolly mammoths and extant elephants. The large stature and a flaked off tusk tip that matches breaks on tusks of male African elephants are indirect indications that this mammoth most likely had reached sexual maturity, had been expelled from its maternal herd, and had been in at least one fight with another male. The mammoth's bones were relatively healthy, although some had minor lesions. Rudimentary upper second molars (M2/m2) were present, but no lower second molars were found in the alveoli, and the left tusk had never developed. Despite the abnormal development of the upper and lower second molars, the cheek teeth which were in wear (Dp4/dp4 and M1/m1) showed normal function without any indications of developmental delay. The completed growth of the light-colored dentin bands on the tusk strongly suggests the Fall of the year was the season of death. This season is also supported by accumulated fat in the upper parts of the torso, indicative of physiological preparation for the winter ahead. The few minor traces of carnivore scavenging, the little disturbed condition of the carcass, and the absence of bone modifications made by human actions, along with the social status of this young male animal, are interpreted here as highly probable evidence that the Zhenya Mammoth died from unrecoverable injuries inflicted during a bull-to-bull fight. The mineralogical analysis of site sediments revealed that the mammoth's burial in situ took place in the Yenisey River valley seasonally inundated by the river, which together with Fall's freezing temperatures protected the carcass from scavengers. An analysis of ancient DNA provides strong support for Zhenya's mitochondrial lineage within the deeply diverging clade III haplogroup B. (C) 2017 Elsevier Ltd and INQUA. All rights reserved.

Despite predictions of the classic, hybrid-sterility model of chromosomal speciation, some organisms demonstrate high rate of karyotype evolution. This rate is especially impressive in Agrodiaetus butterflies that rapidly evolved the greatest chromosome number diversity known in animal kingdom within a single subgenus. Here we analyzed karyotype evolution in Agrodiaetus using phylogenetic comparative methods. We found that chromosome numbers possess a strong phylogenetic signal. This disproves the chromosome megaevolution model that proposes multiple chromosome rearrangements to accumulate independently in each of closely related species. We found that Brownian motion gives a more adequate description of observed trait changes than Ornstein-Uhlenbeck model. This indicates that chromosome numbers evolve via random walk along branches of the phylogeny. We discovered a correlation between karyotype changes and phylogeny branch lengths. This gradual pattern is inconsistent with the hybrid-sterility model which, due to association of major chromosome changes with cladogenetic events, predicts a high degree of punctualism in karyotype evolution. Thus, low underdominace of chromosomal rearrangements and/or prevalence of the recombination-suppression model over the hybrid-sterility model of chromosome speciation are the most common engines of the runaway chromosome number change observed.

Previous articleNext article No AccessGeneticsInvasion Genetics: The Baker and Stebbins Legacy. Edited by Spencer C. H. Barrett, Robert I. Colautti, Katrina M. Dlugosch, and Loren H. Rieseberg. Hoboken (New Jersey): Wiley. $85.00. xiv + 380 p. + 10 pl.; ill.; index. ISBN: 978-1-118-92216-3. 2017.Devon Pearse, Helen Holmlund, Julie Herman, Sara Grove, Jacob Winnikoff, Karen Tanner, Shelley Sianta, Nicholas Macias, and Alisa VershininaDevon PearseEcology & Evolutionary Biology, University of California, Santa Cruz, California Search for more articles by this author , Helen HolmlundEcology & Evolutionary Biology, University of California, Santa Cruz, California Search for more articles by this author , Julie HermanEcology & Evolutionary Biology, University of California, Santa Cruz, California Search for more articles by this author , Sara GroveEcology & Evolutionary Biology, University of California, Santa Cruz, California Search for more articles by this author , Jacob WinnikoffEcology & Evolutionary Biology, University of California, Santa Cruz, California Search for more articles by this author , Karen TannerEcology & Evolutionary Biology, University of California, Santa Cruz, California Search for more articles by this author , Shelley SiantaEcology & Evolutionary Biology, University of California, Santa Cruz, California Search for more articles by this author , Nicholas MaciasEcology & Evolutionary Biology, University of California, Santa Cruz, California Search for more articles by this author , and Alisa VershininaEcology & Evolutionary Biology, University of California, Santa Cruz, California Search for more articles by this author Ecology & Evolutionary Biology, University of California, Santa Cruz, CaliforniaEcology & Evolutionary Biology, University of California, Santa Cruz, CaliforniaEcology & Evolutionary Biology, University of California, Santa Cruz, CaliforniaEcology & Evolutionary Biology, University of California, Santa Cruz, CaliforniaEcology & Evolutionary Biology, University of California, Santa Cruz, CaliforniaEcology & Evolutionary Biology, University of California, Santa Cruz, CaliforniaEcology & Evolutionary Biology, University of California, Santa Cruz, CaliforniaEcology & Evolutionary Biology, University of California, Santa Cruz, CaliforniaEcology & Evolutionary Biology, University of California, Santa Cruz, CaliforniaPDFPDF PLUSFull Text Add to favoritesDownload CitationTrack CitationsPermissionsReprints Share onFacebookTwitterLinkedInRedditEmail SectionsMoreDetailsFiguresReferencesCited by The Quarterly Review of Biology Volume 92, Number 3September 2017 Published in association with Stony Brook University Article DOIhttps://doi.org/10.1086/693625 Views: 28Total views on this site For permission to reuse, please contact [email protected]PDF download Crossref reports no articles citing this article.

In hexapods, unlike the majority of animals, development without fertilization is a common phenomenon. They evolved a striking diversity of unisexual reproductive types that include a variety of modes starting from spontaneous parthenogenesis in females to the production of impaternate males with different variants in between. Many reports about parthenogenetic species have accumulated over time. Here, we present a review of various parthenogenetic hexapod groups with a particular focus on their chromosome systems and ploidy level. We show that conclusions about the reproductive mode often lack solid evidence and sometimes inefficiently demonstrate how parthenogenesis is maintained in corresponding groups. In this review, basal hexapods (Protura, Collembola, Diplura), primarily wingless insect groups ('Apterygota') and non-holometabolous insects are listed with references to a variety of their unisexual reproductive modes.

Ribosomal DNA clusters and telomeric repeats are important parts of eukaryotic genome. However, little is known about their organization and localization in karyotypes of organisms with holocentric chromosomes. Here we present first cytogenetic study of these molecular structures in seven blue butterflies of the genus Polyommatus Latreille, 1804 with low and high chromosome numbers (from n=10 to n=ca.108) using fluorescence in situ hybridization (FISH) with 18S rDNA and (TTAGG) n telomeric probes. FISH with the 18S rDNA probe showed the presence of two different variants of the location of major rDNA clusters in Polyommatus species: with one or two rDNA-carrying chromosomes in haploid karyotype. We discuss evolutionary trends and possible mechanisms of changes in the number of ribosomal clusters. We also demonstrate that Polyommatus species have the classical insect (TTAGG) n telomere organization. This chromosome end protection mechanism probably originated de novo in small chromosomes that evolved via fragmentations.

A phylogenetic comparative method was employed to study karyotype evolution in the Agrodiaetus phyllis species complex characterized by high variation in haploid chromosome number (from 10 to 134). We found that different phylogenetic lineages of this group have different rates of chromosome-number changes. Chromosome numbers in the complex possess a phylogenetic signal, and their evolutionary transformation is difficult to explain in terms of punctual and gradual evolution.

Agrodiaetus alcestis (Zerny, 1932) and A. demavendi (Pfeiffer, 1938) belong to the "brown" complex of the genus Agrodiaetus Hübner, 1822. This complex includes several cryptic species which are extremely uniform in wing colouration and genitalia structure, but have distinct chromosome numbers. In this paper we analyse karyotypes of A. alcestis karacetinae Lukhtanov et Dantchenko, 2002 and A. demavendi in populations from Iran. We demonstrate that A. alcestis karacetinae and A. demavendi are sympatric in the provinces Esfahan, Lorestan, Hamadan, Kurdestan, Kermanshah, and Markazi. The haploid chromosome number of A. alcestis karacetinae is found to be n=19 in all the populations studied. The karyotype of A. demavendi is not stable. The lowest chromosome numbers n=63-67 is observed in the south of the revealed distribution range (provinces Esfahan and Lorestan). The highest chromosome numbers (n=73-74) is found in Northwestern Iran in provinces Kurdestan and Zanjan. We also confirm that A. alcestis sensu lato appears as a polyphyletic taxon on the Bayesian phylogenetic tree inferred from the mitochondrial COI barcodes and should be most likely divided in two different species: A. alcestis sensu stricto and A. karacetinae. The new data on occurrence of A. admetus and A. ripartii in Iran are discussed.