The first complete mitochondrial genome data of the Afghan pika Ochotona rufescens (Lagomorpha, Ochotonidae), near the type locality.

The Afghan pika Ochotona rufescens (Gray, 1842) is widely distributed across the mountains of Afghanistan, Iran, Pakistan, and southwestern Turkmenistan, most often at elevations between 2,000 and 3,000 m. Here we present, for the first time, the complete mitochondrial genomes of two specimens of the nominotypical subspecies Ochotona rufescens rufescens, de novo assembled from Illumina short reads of fragmented probe-enriched DNA. The lengths of the circular mitogenomes are 16,408 bp and 16,407 bp, respectively. Both mitogenomes contain 13 protein-coding genes (PCGs), two ribosomal RNAs (16S rRNA and 12S rRNA), 22 transfer RNA genes, and a control region. The gene NAD6 and the tRNA (Gln), tRNA (Ala), tRNA (Asn), tRNA (Cys), tRNA (Tyr), tRNA (Ser), tRNA (Glu), and tRNA (Pro) are encoded on the light strand while the rest are encoded on the heavy strand. The overall nucleotide composition was ∼30% for A, 25% for T, 15% for G, and 29% for C. The mitogenome data are available in the GenBank under the accession numbers ON859136 and ON859137.

The center cannot hold: A Bayesian chronology for the collapse of Tiwanaku.

The timing of Tiwanaku's collapse remains contested. Here we present a generational-scale chronology of Tiwanaku using Bayesian models of 102 radiocarbon dates, including 45 unpublished dates. This chronology tracks four community practices: residing short- vs. long-term, constructing monuments, discarding decorated ceramics, and leaving human burials. Tiwanaku was founded around AD 100 and around AD 600, it became the region's principal destination for migrants. It grew into one of the Andes' first cities and became famous for its decorated ceramics, carved monoliths, and large monuments. Our Bayesian models show that monument building ended ~AD 720 (the median of the ending boundary). Around ~AD 910, burials in tombs ceased as violent deaths began, which we document for the first time in this paper. Ritualized murders are limited to the century leading up to ~AD 1020. Our clearest proxy for social networks breaking down is a precise estimate for the end of permanent residence, ~AD 1010 (970-1050, 95%). This major inflection point was followed by visitors who used the same ceramics until ~AD 1040. Temporary camps lasted until roughly ~AD 1050. These four events suggest a rapid, city-wide collapse at ~AD 1010-1050, lasting just ~20 years (0-70 years, 95%). These results suggest a cascading breakdown of community practices and social networks that were physically anchored at Tiwanaku, though visitors continued to leave informal burials for centuries. This generation-scale chronology suggests that collapse 1) took place well before reduced precipitation, hence this was not a drought-induced societal change and 2) a few resilient communities sustained some traditions at other sites, hence the chronology for the site of Tiwanaku cannot be transposed to all sites with similar material culture.

Ancient DNA of narrow-headed vole reveal common features of the Late Pleistocene population dynamics in cold-adapted small mammals.

The narrow-headed vole, collared lemming and common vole were the most abundant small mammal species across the Eurasian Late Pleistocene steppe-tundra environment. Previous ancient DNA studies of the collared lemming and common vole have revealed dynamic population histories shaped by climatic fluctuations. To investigate the extent to which species with similar adaptations share common evolutionary histories, we generated a dataset comprised the mitochondrial genomes of 139 ancient and 6 modern narrow-headed voles from several sites across Europe and northwestern Asia covering approximately the last 100 thousand years (kyr). We inferred Bayesian time-aware phylogenies using 11 radiocarbon-dated samples to calibrate the molecular clock. Divergence of the main mtDNA lineages across the three species occurred during marine isotope stages (MIS) 7 and MIS 5, suggesting a common response of species adapted to open habitat during interglacials. We identified several time-structured mtDNA lineages in European narrow-headed vole, suggesting lineage turnover. The timing of some of these turnovers was synchronous across the three species, allowing us to identify the main drivers of the Late Pleistocene dynamics of steppe- and cold-adapted species.

Population dynamics and demographic history of Eurasian collared lemmings.

BACKGROUND: Ancient DNA studies suggest that Late Pleistocene climatic changes had a significant effect on population dynamics in Arctic species. The Eurasian collared lemming (Dicrostonyx torquatus) is a keystone species in the Arctic ecosystem. Earlier studies have indicated that past climatic fluctuations were important drivers of past population dynamics in this species. RESULTS: Here, we analysed 59 ancient and 54 modern mitogenomes from across Eurasia, along with one modern nuclear genome. Our results suggest population growth and genetic diversification during the early Late Pleistocene, implying that collared lemmings may have experienced a genetic bottleneck during the warm Eemian interglacial. Furthermore, we find multiple temporally structured mitogenome clades during the Late Pleistocene, consistent with earlier results suggesting a dynamic late glacial population history. Finally, we identify a population in northeastern Siberia that maintained genetic diversity and a constant population size at the end of the Pleistocene, suggesting suitable conditions for collared lemmings in this region during the increasing temperatures associated with the onset of the Holocene. CONCLUSIONS: This study highlights an influence of past warming, in particular the Eemian interglacial, on the evolutionary history of the collared lemming, along with spatiotemporal population structuring throughout the Late Pleistocene.

The first complete mitochondrial genome data of the pygmy rabbit Brachylagus idahoensis, the world's smallest leporid.

The pygmy rabbit Brachylagus idahoensis (Merriam, 1891) is the smallest extant leporid, which naturally occurs in the Great Basin and adjacent areas in western parts of the United States of America. Its distribution is strongly associated with the sagebrush (Artemisia ssp.) vegetation. Here we present, for the first time, the complete mitochondrial genome of Brachylagus idahoensis, de novo assembled from Illumina short reads of fragmented probe-enriched DNA. The circular mitogenome is 17,021 bp in length and contains 13 protein-coding genes (PCGs), two ribosomal RNAs (16S rRNA and 12S rRNA), 22 transfer RNA genes, and a control region. The gene NAD6 and the tRNA(Gln), tRNA(Ala), tRNA(Asn), tRNA(Cys), tRNA(Tyr), tRNA(Ser), tRNA(Glu) and tRNA(Pro) are encoded on the light strand while the rest are encoded on the heavy strand. The overall nucleotide composition was 30.78% for A, 28.5% for T, 13.62% for G and 27.08% for C. The mitogenome data are available in the GenBank under the accession number OL436257.

Stable isotopes unveil one millennium of domestic cat paleoecology in Europe.

The domestic cat is the world's most popular pet and one of the most detrimental predators in terrestrial ecosystems. Effective protection of wildlife biodiversity demands detailed tracking of cat trophic ecology, and stable isotopes serve as a powerful proxy in dietary studies. However, a variable diet can make an isotopic pattern unreadable in opportunistic predators. To evaluate the usefulness of the isotopic method in cat ecology, we measured C and N isotope ratios in hundreds of archaeological cat bones. We determined trends in cat trophic paleoecology in northern Europe by exploiting population-scale patterns in animals from diverse locations. Our dataset shows a high variability of isotopic signals related to the socio-economic and/or geomorphological context. This points toward regularities in isotopic patterns across past cat populations. We provide a generalized guide to interpret the isotopic ecology of cats, emphasizing that regional isotopic baselines have a major impact on the isotopic signal.

The Tien Shan vole (Microtus ilaeus; Rodentia: Cricetidae) as a new species in the Late Pleistocene of Europe.

Grey voles (subgenus Microtus) represent a complex of at least seven closely related and partly cryptic species. The range of these species extends from the Atlantic to the Altai Mountains, but most of them occur east of the Black Sea. Using ancient DNA analyses of the Late Pleistocene specimens, we identified a new mtDNA lineage of grey voles in Europe. Phylogenetic analysis of mitochondrial DNA cytochrome b sequences from 23 voles from three caves, namely, Emine-Bair-Khosar (Crimea, Ukraine), Cave 16 (Bulgaria), and Bacho Kiro (Bulgaria), showed that 14 specimens form a previously unrecognized lineage, sister to the Tien Shan vole. The average sequence divergence of this lineage and the extant Tien Shan vole was 4.8%, which is similar to the divergence of grey vole forms, which are considered distinct species or being on the verge of speciation; M. arvalis and M. obscurus or M. mystacinus and M. rossiaemeridionalis. We estimated the time to the most recent common ancestor of the grey voles to be 0.66 Ma, which is over twice the recent estimates, while the divergence of the extant Tien Shan vole and the new lineage to be 0.29 Ma. Our discovery suggests that grey voles may have been more diversified in the past and that their ranges may have differed substantially from current ones. It also underlines the utility of ancient DNA to decipher the evolutionary history of voles.

Ancient genomes reveal long-range influence of the pre-Columbian culture and site of Tiwanaku.

Tiwanaku civilization flourished in the Lake Titicaca basin between 500 and 1000 CE and at its apogee influenced wide areas across the southern Andes. Despite a considerable amount of archaeological data, little is known about the Tiwanaku population. We analyzed 17 low-coverage genomes from individuals dated between 300 and 1500 CE and demonstrated genetic continuity in the Lake Titicaca basin throughout this period, which indicates that the substantial cultural and political changes in the region were not accompanied by large-scale population movements. Conversely, the ritual center of Tiwanaku revealed high diversity, including individuals with primarily local genetic ancestry and those with foreign admixture or provenance from as far as the Amazon. Nonetheless, most human offerings associated with the Akapana platform exhibited pure Titicaca basin ancestry and dated to ca. 950 CE­the onset of Tiwanaku's decline as a sociopolitical center. Our results strengthen the view of Tiwanaku as a complex and far-reaching polity.

Ancestors of domestic cats in Neolithic Central Europe: Isotopic evidence of a synanthropic diet.

Cat remains from Poland dated to 4,200 to 2,300 y BCE are currently the earliest evidence for the migration of the Near Eastern cat (NE cat), the ancestor of domestic cats, into Central Europe. This early immigration preceded the known establishment of housecat populations in the region by around 3,000 y. One hypothesis assumed that NE cats followed the migration of early farmers as synanthropes. In this study, we analyze the stable isotopes in six samples of Late Neolithic NE cat bones and further 34 of the associated fauna, including the European wildcat. We approximate the diet and trophic ecology of Late Neolithic felids in a broad context of contemporary wild and domestic animals and humans. In addition, we compared the ecology of Late Neolithic NE cats with the earliest domestic cats known from the territory of Poland, dating to the Roman Period. Our results reveal that human agricultural activity during the Late Neolithic had already impacted the isotopic signature of rodents in the ecosystem. These synanthropic pests constituted a significant proportion of the NE cat's diet. Our interpretation is that Late Neolithic NE cats were opportunistic synanthropes, most probably free-living individuals (i.e., not directly relying on a human food supply). We explore niche partitioning between studied NE cats and the contemporary native European wildcats. We find only minor differences between the isotopic ecology of both these taxa. We conclude that, after the appearance of the NE cat, both felid taxa shared the ecological niches.

Unusual Clinical Presentation of Giant Extragenital Condyloma.

Dear editor, Condylomata accuminatum (CA) is a human papillomavirus (HPV) related sexually transmitted infection (STI), clinically characterized by solitary or even clustered dark red or pink lesions solely affecting the anogenital area (1). CA involving the extragenital, non-mucosal skin has been sporadically reported (2-4). Diagnosis of CA is usually straightforward when the lesions are located on the anogenital area. However, involvement of extragenital skin may pose a diagnostic challenge. Herein, we report a rare case of giant linear extragenital CA without coexisting genital lesions, diagnosed with a synergic intervention of dermatoscopy and clinics. A 70-year-old Caucasian man was referred to our department for an atypical asymptomatic seborrheic keratosis presenting as a linear verrucous plaque (20 × 2 cm) with few solitary reddish satellite papules on the abdomen (Figure 1, a). No similar lesions were present in both cutaneous and mucosal districts. Medical history was unremarkable, and the patient denied having recent sexual intercourse or any history of condylomas. Remarkably, the patient underwent a diet in the last 8 months that resulted in a loss of 30 kg. We employed dermatoscopy to further assess the lesions, highlighting a finger-like pattern on the main lesion (Figure 1, c), while satellite lesions presented a mosaic pattern (Figure 1, b). The clinical appearance and these dermatoscopic findings were suggestive of condyloma acuminatum (CA), but due to its extraordinary presentation we also performed an incisional biopsy. Histopathological examination reviled features compatible with the diagnosis of CA (Figure 1, d, e). To better characterized the HPV genotype (high-risk and low-risk HPV) a polymerase chain reaction (PCR) from lesional tissue sample was performed and found HPV type 6 positivity. The lesions were successfully removed by electrosurgery. Regular follow-up was scheduled. Sexually transmitted infections (STIs) were also screened, namely syphilis, gonorrhea, chlamydia trachomatis, and HIV status. In addition, laboratory tests and imaging examinations (radiography of the chest and ultrasound examination of the abdomen) revealed no pathological findings. CA involving the extragenital skin has been reported within intertriginous areas, including the inframammary fold, the groin, and the axillary vault, as well as mucosal surface such as intraoral and conjunctival mucosa (1-5). In most cases, extragenital CA coexisted with genital lesions. Staples et al. reported three obese patients with extragenital CA on the skin of the abdominal pannus (3). However, all of the patients had involvement of the inguinal folds, from where the CA had extended. Generally, CA is acquired by genital, oral, or anal sexual contact. Among the wide spectrum of HPV genotypes, types 6 and 11 are responsible of 90% of CA (1). Our paradigmatic case allows us reflect on the concept of transitory immune dysregulation due to a significant amount of weight loss, and the position of the lesions in particular seems to suggest that frictional triggers may disrupt the barrier integrity, leading to higher probability of infection. Dermoscopy is a noninvasive diagnostic tool with a significant role in the assessment of melanocytic and non-melanocytic skin tumors. Furthermore, the utility of dermatoscopy has expanded to the field of inflammatory and infectious skin disease, where dermoscopy enhances the differential diagnosis between them. Seborrheic keratosis, as the most common benign epithelial tumor, can occur anywhere in the skin excluding the palms, soles, and mucosa (6). In the anogenital area, seborrheic keratosis usually resembles CA. However, dermatoscopically, seborrheic keratosis can be immediately identified by the presence of milia-like cysts, comedo-like openings, fissures, finger-print structures, and sharply demarcated borders (6). In contrast, reports of CA dermoscopy suggested four different dermoscopic patterns: fingerlike, mosaic, knoblike, and the most commonly, an unspecific pattern (7). Our case showed that dermoscopy of extragenital CA presented a mosaic pattern in an early stage of CA, while fully developed lesions revealed a fingerlike pattern, as has previously been reported by Dong et al. (7), where two different stages of clinical development of CA exhibit distinctive dermoscopic patterns, which correlates with our case. We did not observe the typical dermoscopic features of seborrheic keratosis. CA arising in an extragenital area is very rare and perhaps also underestimated. Thus, dermatologists should be aware of this unusual presentation even in the absence of genital HPV involvement. Moreover, dermoscopy may facilitate CA recognition in a such uncommon location. To our knowledge, this is the first report of extragenital condyloma acuminatum documented dermoscopically.

Highly divergent lineage of narrow-headed vole from the Late Pleistocene Europe.

During the Late Pleistocene, narrow-headed voles (Lasiopodomys gregalis) inhabited Eurasia's vast territories, frequently becoming the dominant small mammal species among steppe-tundra communities. We investigated the relationship between this species' European and Asiatic populations by sequencing the mtDNA genomes of two extant specimens from Russia and 10 individuals from five Central European sites, dated to the post-LGM period. Phylogenetic analyses based on a large portion of mtDNA genomes highly supported the positioning of L. gregalis within Arvicolinae. The phylogeny based on mtDNA cytochrome b sequences revealed a deep divergence of European narrow-headed voles from Asiatic ones and their sister position against the extant L. gregalis and L. raddei. The divergence of the European lineage was estimated to a minimum 230 thousand years ago. This suggest, contrary to the current biogeographic hypotheses, that during the interglacial periods narrow-headed vole did not retreat from Europe but survived the unfavourable conditions within the refugial areas. Based on this result, we propose to establish a cryptic species status for the Late Pleistocene European narrow-headed vole and to name this taxon Lasiopodomys anglicus.

Human-mediated dispersal of cats in the Neolithic Central Europe.

Archeological and genetic evidence suggest that all domestic cats derived from the Near Eastern wildcat (Felis silvestris lybica) and were first domesticated in the Near East around 10,000 years ago. The spread of the domesticated form in Europe occurred much later, primarily mediated by Greek and Phoenician traders and afterward by Romans who introduced cats to Western and Central Europe around 2000 years ago. We investigated mtDNA of Holocene Felis remains and provide evidence of an unexpectedly early presence of cats bearing the Near Eastern wildcat mtDNA haplotypes in Central Europe, being ahead of Roman period by over 2000 years. The appearance of the Near Eastern wildcats in Central Europe coincides with the peak of Neolithic settlement density, moreover most of those cats belonged to the same mtDNA lineages as those domesticated in the Near East. Thus, although we cannot fully exclude that the Near Eastern wildcats appeared in Central Europe as a result of introgression with European wildcat, our findings support the hypothesis that the Near Eastern wildcats spread across Europe together with the first farmers, perhaps as commensal animals. We also found that cats dated to the Neolithic period belonged to different mtDNA lineages than those brought to Central Europe in Roman times, this supports the hypothesis that the gene pool of contemporary European domestic cats might have been established from two different source populations that contributed in different periods.

Microsatellite Mutation Rate in Atlantic Sturgeon (Acipenser oxyrinchus).

Understanding mutation rates can greatly extend the utility of population and conservation genetic analyses. Herein, we present an estimate of genome-wide microsatellite mutation rate in Atlantic sturgeon (Acipenser oxyrinchus) based on parent-offspring transmission patterns. We screened 307 individuals for parentage and mutation-rate analysis applying 43 variable markers. Out of 13228 allele transfers, 11 mutations were detected, producing a mutation rate of 8.3 × 10-4 per locus per generation (95% confidence interval: 1.48 × 10-3, 4.15 × 10-4). Single-step mutations predominated and there were trends toward mutations in loci with greater polymorphism and allele length. Two of the detected mutations were most probably cluster mutations, being identified in 12 and 28 sibs, respectively. Finally, we observed evidences of polyploidy based on the sporadic presence of 3 or 4 alleles per locus in the genotyped individuals, supporting previous reports of incomplete diploidization in Atlantic sturgeon.

Retreat and extinction of the Late Pleistocene cave bear (Ursus spelaeus sensu lato).

The cave bear (Ursus spelaeus sensu lato) is a typical representative of Pleistocene megafauna which became extinct at the end of the Last Glacial. Detailed knowledge of cave bear extinction could explain this spectacular ecological transformation. The paper provides a report on the youngest remains of the cave bear dated to 20,930 ± 140 14C years before present (BP). Ancient DNA analyses proved its affiliation to the Ursus ingressus haplotype. Using this record and 205 other dates, we determined, following eight approaches, the extinction time of this mammal at 26,100-24,300 cal. years BP. The time is only slightly earlier, i.e. 27,000-26,100 cal. years BP, when young dates without associated collagen data are excluded. The demise of cave bear falls within the coldest phase of the last glacial period, Greenland Stadial 3. This finding and the significant decrease in the cave bear records with cooling indicate that the drastic climatic changes were responsible for its extinction. Climate deterioration lowered vegetation productivity, on which the cave bear strongly depended as a strict herbivore. The distribution of the last cave bear records in Europe suggests that this animal was vanishing by fragmentation into subpopulations occupying small habitats. One of them was the Kraków-Czestochowa Upland in Poland, where we discovered the latest record of the cave bear and also two other, younger than 25,000 14C years BP. The relatively long survival of this bear in karst regions may result from suitable microclimate and continuous access to water provided by deep aquifers, indicating a refugial role of such regions in the Pleistocene for many species.

Complete mitochondrial genome sequences of Atlantic sturgeon, Acipenser oxyrinchus oxyrinchus, Gulf sturgeon, A. o. desotoi and European sturgeon A. sturio (Acipenseriformes: Acipenseridae) obtained through next generation sequencing.

Complete mitochondrial genome sequences of European sturgeon and two subspecies of the North American, Atlantic and Gulf sturgeons were determined using MiSeq Illumina technology. All three genomes show typical vertebrate organization. They possess 22 tRNA genes, 13 protein-coding genes, 2 rRNA (ribosomal RNA) genes and a non-coding control region. Excluding ND6, all protein-coding genes are on the heavy strand. The whole mitogenome sequences have been deposited in GenBank under accession numbers KP997216-KP997218.

Genomics and the challenging translation into conservation practice.

The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice as scaling up to genome-wide data can improve traditional conservation genetic inferences and provide qualitatively novel insights. However, the generation of genomic data and subsequent analyses and interpretations remain challenging and largely confined to academic research in ecology and evolution. This generates a gap between basic research and applicable solutions for conservation managers faced with multifaceted problems. Before the real-world conservation potential of genomic research can be realized, we suggest that current infrastructures need to be modified, methods must mature, analytical pipelines need to be developed, and successful case studies must be disseminated to practitioners.

Immunophenotyping of amelanotic melanoma. A case report.

Amelanotic malignant melanoma (AMM) is a subtype of cutaneous melanoma with little or no pigment upon visual inspection. The lack of pigmentation is the reason for late diagnosis of lesions and a poor prognosis. We report a case of a 55-year-old female with an AMM diagnosed by immunophenotyping. Monoclonal antibodies S-100, HMB-45, and antibodies to cytokeratin were used. Our patient underwent a wide local excision (a 2 cm wide margin) 2 years ago. So far there are no signs of a recurrence. In doubtful cases, immunophenotyping with monoclonal antibodies HMB-45 and S-100 is important for confirming the correct diagnosis of AMM.