Was Coccidioides a Pre-Columbian Hitchhiker to Southcentral Washington?

Coccidioides immitis, a pathogenic environmental fungus that causes Valley fever (coccidioidomycosis) primarily in the American Southwest and parts of Central and South America, has emerged over the past 12 years in the Columbia River Basin region, near the confluence with the Yakima River, in southcentral Washington state, USA. An initial autochthonous Washington human case was found in 2010, stemming from a wound derived from soil contamination during an all-terrain vehicle crash. Subsequent analysis identified multiple positive soil samples from the park where the crash occurred (near the Columbia River in Kennewick, WA), and from another riverside location several kilometers upstream from the park location. Intensified disease surveillance identified several more cases of coccidioidomycosis in the region that lacked any relevant travel history to known endemic locales. Genomic analysis of both patient and soil isolates from the Washington cases determined that all samples from the region are phylogenetically closely related. Given the genomic and the epidemiological link between case and environment, C. immitis was declared to be a newly endemic fungus in the region, spawning many questions as to the scope of its presence, the causes of its recent emergence, and what it predicts about the changing landscape of this disease. Here, we review this discovery through a paleo-epidemiological lens in the context of what is known about C. immitis biology and pathogenesis and propose a novel hypothesis for the cause of the emergence in southcentral Washington. We also try to place it in the context of our evolving understanding of this regionally specific pathogenic fungus.

Unexpected malocclusion in a 13,000-Year-old Late Pleistocene young woman from Mexico.

To analyze the etiological factors behind the malocclusion of a Late Pleistocene woman (named Naia), who is the best-preserved of the earliest individuals of the American continent. The examination of Naia's malocclusion was performed through cephalometric and occlusal analyses, and by measuring her mandible. Her data were then compared to published data for modern, medieval, and postmedieval samples and seven Late Pleistocene individuals. Naia presented her permanent dentition fully erupted, except for the impacted mandibular third molars. She presented a class II molar malocclusion with crowding. The dental widths and mandible measurements were similar to or smaller than modern standards. The degree of dental wear was light. The cephalometric analysis confirmed a skeletal class II relationship, with a retrusive mandible and protruded upper incisors. Naia's mild level of dental wear is consistent with a low masticatory force, in a time when the norm was a high amount of grinding. The low masticatory forces help explain Naia's small jaws and crowding. However, it does not clarify Angle's class II relationship. Naia is an example that environmental factors are insufficient to explain the onset of malocclusions and emphasizes the importance of understanding hereditary factors' role.

Dire wolves were the last of an ancient New World canid lineage.

Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America1, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7 million years ago. In contrast to numerous examples of hybridization across Canidae2,3, there is no evidence for gene flow between dire wolves and either North American grey wolves or coyotes. This suggests that dire wolves evolved in isolation from the Pleistocene ancestors of these species. Our results also support an early New World origin of dire wolves, while the ancestors of grey wolves, coyotes and dholes evolved in Eurasia and colonized North America only relatively recently.

Paleoindian ochre mines in the submerged caves of the Yucatán Peninsula, Quintana Roo, Mexico.

Investigations in the now-submerged cave systems on the Yucatán Peninsula continue to yield evidence for human presence during the Pleistocene-Holocene transition. Skeletal remains are scattered throughout the caves of Quintana Roo, most representing individuals who died in situ. The reasons why they explored these underground environments have remained unclear. Here, we announce the discovery of the first subterranean ochre mine of Paleoindian age found in the Americas, offering compelling evidence for mining in three cave systems on the eastern Yucatán over a ~2000-year period between ~12 and 10 ka. The cave passages exhibit preserved evidence for ochre extraction pits, speleothem digging tools, shattered and piled flowstone debris, cairn navigational markers, and hearths yielding charcoal from highly resinous wood species. The sophistication and extent of the activities demonstrate a readiness to venture into the dark zones of the caves to prospect and collect what was evidently a highly valued mineral resource.

Oral health and diet of a young Late Pleistocene woman from Quintana Roo, Mexico.

OBJECTIVES: To increase understanding of the subsistence practices of the first Americans through analysis of the near-complete dentition of a young woman dating to the terminal Pleistocene of the Yucatan Peninsula, Mexico. MATERIALS AND METHODS: The skeleton is that of "Naia" a 15 to 17-year-old female from the submerged natural trap of Hoyo Negro found in association with remains of numerous extinct species of megafauna. Superbly preserved remains included the skull with 28 teeth, which are analyzed for evidence of caries, periodontal disease, wear patterns, and malocclusion. RESULTS: Naia exhibits a high frequency of dental caries, along with aggressive periodontal disease that threatened all her teeth, particularly her incisors. Dental attrition was extremely light for a hunter-gatherer, reaching to four on the Molnar scale on only one tooth. Lack of wear is associated with severe mandibular retrognathia, and low masticatory forces. DISCUSSION: Naia's dental condition is compared with that of other northern Paleoamericans, mostly females, dating before 11,000 cal BP. These exhibit a high degree of variability in both caries and tooth wear. All, however, exhibit rapid anterior wear owing to technological use of the front teeth. Naia exhibits the highest rate of caries, similar to that of the earliest South Americans, and one of the lowest rates of attrition. This demonstrates that she had a nonabrasive diet that was at least seasonally rich in carbohydrates. This does not mean her diet was low in meat, however, because similarly light dental attrition is seen in the Arch Lake female, a Paleoamerican from a big-game hunting society.

Yucatán carnivorans shed light on the Great American Biotic Interchange.

The Great American Biotic Interchange is considered to be a punctuated process, primarily occurring during four major pulses that began approximately 2.5 Ma. Central America and southeastern Mexico have a poor fossil record of this dynamic faunal history due to tropical climates. Exploration of submerged caves in the Yucatán, particularly the natural trap Hoyo Negro, is exposing a rich and remarkably well-preserved late Pleistocene fauna. Radiometric dates on megafauna range from approximately 38 400-12 850 cal BP, and extinct species include the ursid Arctotherium wingei and canid Protocyon troglodytes. Both genera were previously thought to be indigenous to and confined to South America and appear to represent an instance of large placental mammals, descended from North American progenitors, migrating back north across the Panama Isthmus. This discovery expands the distribution of these carnivorans greater than 2000 km outside South America. Their presence along with a diverse sloth assemblage suggests a more complex history of these organisms in Middle America. We suggest that landscape and ecological changes caused by latest Pleistocene glaciation supported an interchange pulse that included A. wingei, P. troglodytes and Homo sapiens.

Anthropology. Response to Comment on "Late Pleistocene human skeleton and mtDNA link Paleoamericans and modern Native Americans".

Prüfer and Meyer raise concerns over the mitochondrial DNA (mtDNA) results we reported for the Hoyo Negro individual, citing failure of a portion of these data to conform to their expectations of ancient DNA (aDNA). Because damage patterns in aDNA vary, outright rejection of our findings on this basis is unwarranted, especially in light of our other observations.

Late Pleistocene human skeleton and mtDNA link Paleoamericans and modern Native Americans.

Because of differences in craniofacial morphology and dentition between the earliest American skeletons and modern Native Americans, separate origins have been postulated for them, despite genetic evidence to the contrary. We describe a near-complete human skeleton with an intact cranium and preserved DNA found with extinct fauna in a submerged cave on Mexico's Yucatan Peninsula. This skeleton dates to between 13,000 and 12,000 calendar years ago and has Paleoamerican craniofacial characteristics and a Beringian-derived mitochondrial DNA (mtDNA) haplogroup (D1). Thus, the differences between Paleoamericans and Native Americans probably resulted from in situ evolution rather than separate ancestry.

Patterns of mtDNA diversity in northwestern North America.

The mitochondrial DNA (mtDNA) haplogroups of 54 full-blooded modern and 64 ancient Native Americans from northwestern North America were determined. The control regions of 10 modern and 30 ancient individuals were sequenced and compared. Within the Northwest, the frequency distribution for haplogroup A is geographically structured, with haplogroup A decreasing with distance from the Pacific Coast. The haplogroup A distribution suggests that a prehistoric population intrusion from the subarctic and coastal region occurred on the Columbia Plateau in prehistoric times. Overall, the mtDNA pattern in the Northwest suggests significant amounts of gene flow among Northwest Coast, Columbia Plateau, and Great Basin populations.