Domestication is a good model for the study of evolutionary processes because of the recent evolution of crop species (<12,000 years ago), the key role of selection in their origins, and good archaeological and historical data on their spread and diversification. Recent studies, such as quantitative trait locus mapping, genome-wide association studies and whole-genome resequencing studies, have identified genes that are associated with the initial domestication and subsequent diversification of crops. Together, these studies reveal the functions of genes that are involved in the evolution of crops that are under domestication, the types of mutations that occur during this process and the parallelism of mutations that occur in the same pathways and proteins, as well as the selective forces that are acting on these mutations and that are associated with geographical adaptation of crop species.

/pdf/evolution-of-crop-species-genetics-of-domestication-and-33m82b0rxv.pdf

Evolution of crop species: genetics of domestication and diversification

Modern strains of Mycobacterium tuberculosis from the Americas are closely related to those from Europe, supporting the assumption that human tuberculosis was introduced post-contact1. This notion, however, is incompatible with archaeological evidence of pre-contact tuberculosis in the New World2. Comparative genomics of modern isolates suggests that M. tuberculosis attained its worldwide distribution following human dispersals out of Africa during the Pleistocene epoch3, although this has yet to be confirmed with ancient calibration points. Here we present three 1,000-year-old mycobacterial genomes from Peruvian human skeletons, revealing that a member of the M. tuberculosis complex caused human disease before contact. The ancient strains are distinct from known human-adapted forms and are most closely related to those adapted to seals and sea lions. Two independent dating approaches suggest a most recent common ancestor for the M. tuberculosis complex less than 6,000 years ago, which supports a Holocene dispersal of the disease. Our results implicate sea mammals as having played a role in transmitting the disease to humans across the ocean.

/pdf/pre-columbian-mycobacterial-genomes-reveal-seals-as-a-source-3mn5u63f97.pdf

Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis

Humans are hosts to nearly 300 species of parasitic worms and over 70 species of protozoa, some derived from our primate ancestors and some acquired from the animals we have domesticated or come in contact with during our relatively short history on Earth. Our knowledge of parasitic infections extends into antiquity, and descriptions of parasites and parasitic infections are found in the earliest writings and have been confirmed by the finding of parasites in archaeological material. The systematic study of parasites began with the rejection of the theory of spontaneous generation and the promulgation of the germ theory. Thereafter, the history of human parasitology proceeded along two lines, the discovery of a parasite and its subsequent association with disease and the recognition of a disease and the subsequent discovery that it was caused by a parasite. This review is concerned with the major helminth and protozoan infections of humans: ascariasis, trichinosis, strongyloidiasis, dracunculiasis, lymphatic filariasis, loasis, onchocerciasis, schistosomiasis, cestodiasis, paragonimiasis, clonorchiasis, opisthorchiasis, amoebiasis, giardiasis, African trypanosomiasis, South American trypanosomiasis, leishmaniasis, malaria, toxoplasmosis, cryptosporidiosis, cyclosporiasis, and microsporidiosis.

https://cmr.asm.org/content/cmr/16/1/174.full.pdf

History of Human Parasitology

Domestication of Plants in the Americas: Insights from Mendelian and Molecular Genetics

Almost all known human specific parasites have been found in ancient feces. A review of the paleoparasitological helminth and intestinal protozoa findings available in the literature is presented. We also report the new paleoparasitologic findings from the examination performed in samples collected in New and Old World archaeological sites. New finds of ancylostomid, Ascaris lumbricoides, Trichuris trichiura, Enterobius vermicularis, Trichostrongylus spp., Diphyllobothrium latum, Hymenolepis nana and Acantocephalan eggs are reported. According to the findings, it is probable that A. lumbricoides was originally a human parasite. Human ancylostomids, A. lumbricoides and T. trichiura, found in the New World in pre-Columbian times, have not been introduced into the Americas by land via Beringia. These parasites could not supported the cold climate of the region. Nomadic prehistoric humans that have crossed the Bering Land Bridge from Asia to the Americas in the last glaciation, probably during generations, would have lost these parasites, which life cycles need warm temperatures in the soil to be transmitted from host to host. Alternative routes are discussed for human parasite introduction into the Americas.

https://www.arca.fiocruz.br/bitstream/icict/24719/2/HumanIntestinal.pdf

Human intestinal parasites in the past: new findings and a review

Maize (Zea mays ssp. mays) is among the world's most important and ancient domesticated crops. Although the chronology of its domestication and initial dispersals out of Mexico into Central and South America has become more clear due to molecular and multiproxy archaeobotanical research, important problems remain. Among them is the paucity of information on maize's early morphological evolution and racial diversification brought about in part by the poor preservation of macrofossils dating to the pre-5000 calibrated years before the present period from obligate dispersal routes located in the tropical forest. We report newly discovered macrobotanical and microbotanical remains of maize that shed significant light on the chronology, land race evolution, and cultural contexts associated with the crop's early movements into South America and adaptation to new environments. The evidence comes from the coastal Peruvian sites of Paredones and Huaca Prieta, Peru; dates from the middle and late preceramic and early ceramic periods (between ca. 6700 and 3000 calibrated years before the present); and constitutes some of the earliest known cobs, husks, stalks, and tassels. The macrobotanical record indicates that a diversity of racial complexes characteristic of the Andean region emerged during the preceramic era. In addition, accelerator mass spectrometry radiocarbon determinations carried out directly on different structures of preserved maize plants strongly suggest that assays on burned cobs are more reliable than those on unburned cobs. Our findings contribute to knowledge of the early diffusion of maize and agriculture and have broader implications for understanding the development of early preindustrial human societies.

https://www.pnas.org/content/pnas/109/5/1755.full.pdf

Preceramic maize from Paredones and Huaca Prieta, Peru

by RAU'L PATRUCCO, RAUL TELLO, and Duccio BONAVIA Laboratorio de Inmunologia nd Instituto de Medicina Tropical \"Alexander von Humboldt\" (Patrucco), Instituto de Medicina Tropical \"Alexander von Humboldt\" (Tello), and Laboratorio de Prehistoria, Departamento de Biologia (Bonavia), Universidad Peruana Cayetano Heredia, Apartado 5045, Lima, Peru. 2 ix 82 In 1896 Harshberger suggested that examination of human fecal material could provide information about the diet of prehistoric man. It was only in 1910, however, that Young definitively introduced paleoscatology as a tool for such research (see Bryant 1974). Van Cleave and Ross (1947) and Callen and Cameron (1955, 1960) modified and adapted Young's methods for the study of intestinal parasites in the ancient inhabitants of North America and Mexico. In Peru, despite the fact that ancient organic material is well preserved under the exceptionally dry climatic conditions of the coastal desert, this methodology has seldom been used. Since 1974, the Laboratorio de Prehistoria de la Universidad Peruana Cayetano Heredia in Lima has been engaged in archaeological studies of the Preceramic site Los Gavilanes. This site is located near the beach line in the Huarmey Valley, in a desert area of the north-central coast of Peru 292 km north of Lima (lat. 10?02'45\" S, long. 78?10'21\" W) (Grobman and Bonavia 1978). A preliminary report on the Los Gavilanes material, with special reference to its paleobotanical aspects, has been published (Grobman and Bonavia 1978). The present article is a report of a paleoscatological analysis of human material recovered from various levels excavated during 1976 and 1977. Los Gavilanes was first inhabited at least 5,000 years ago; three periods of occupation have been established by stratigraphic studies (Bonavia and Grobman 1979). Insufficient remains were left during the first period for dating in absolute terms. The second period left abundant cultural material, organic debris, and remains of stone buildings. Radiocarbon dating of the debris yielded a date of 4 140 + 160 B.P. (GX5070)-4,730 + 190 B.P. after Damons et al.'s (1974) correction. Thermoluminescence dating produced a date of 4,800 + 500 B.P. (BOR-20). The third period left structures in the form of silos built with materials from the previous period and used for storing maize. Radiocarbon analysis of materials from this period yielded dates of 3,750 + 110 B.P. (GIF-3664) and 3,755 + 155 B.P. (GX-5078)-4,227 + 145 and 4,227 + 181 after Damons et al.'s (1974) correction (Bonavia and Grobman 1979). Excavations at Los Gavilanes uncovered 52 coprolites; 22 from the second period, 22 from the third period, and 8 of uncertain stratigraphic context. Each specimen was rehydrated in an aqueous solution of 0.5%7 trisodium phosphate (Na3PO4) according to the method of Callen (1967). (All the characteristics of the hydrated coprolites fit Callen's [p. 281] criteria for human origin, especially the dark-brown color reported also by Bryant [1974:5]. Samples of our material have been studied by Glendon H. Weir of the Palynology Laboratory of Texas A & M University, who has confirmed its human origin.) One sample from the second occupation (2700-2850 B.C.) contained parasite eggs that we have identified as belonging to the genus Diphyllobothrium; they are ovoid, with an inconspicuous operculum and a smooth shell of moderate thickness enclosing FIG. 1. Diphyllobothrium pacificum egg (X 400) from Los Gavilanes (all photos reproduced at65%o f original size).

Parasitological studies of coprolites of pre-Hispanic Peruvian populations

A late Pleistocene human presence at Huaca Prieta, Peru, and early Pacific Coastal adaptations

Los camélidos sudamericanos : Una introducción a su estudio

Renewed in-depth multi-disciplinary investigation of a large coastal mound settlement in Peru has extended the occupation back more than 7000 years to a first human exploitation ~13720 BP. Research by the authors has chronicled the prehistoric sequence from the activities of the first maritime foragers to the construction of the black mound and the introduction of horticulture and monumentality. The community of Huaca Prieta emerges as innovative, complex and ritualised, as yet with no antecedents

Duccio Bonavia

Papers

Preceramic maize from Paredones and Huaca Prieta, Peru

Parasitological studies of coprolites of pre-Hispanic Peruvian populations

A late Pleistocene human presence at Huaca Prieta, Peru, and early Pacific Coastal adaptations

Los camélidos sudamericanos : Una introducción a su estudio

Chronology, mound-building and environment at Huaca Prieta, coastal Peru, from 13 700 to 4000 years ago