Interrogation of modern and ancient genomes reveals the complex domestic history of cattle

Magee, David A.; MacHugh, David E.; Edwards, Ceiridwen J.

doi:10.2527/af.2014-0017

Cited by 37 publications

(26 citation statements)

References 97 publications

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“…The most prominent phenotypic difference between these two species is the presence of a cervico‐thoracic hump in indicine cattle (Magee et al . ). Indicine cattle also demonstrate enhanced physiological characteristics such as greater heat, tick and gastrointestinal parasite resistance and lower nutritional requirements (Canavez et al .…”

Section: Tropical African Cattle Breedsmentioning

confidence: 97%

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Tropically adapted cattle of Africa: perspectives on potential role of copy number variations

et al. 2015

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Africa is host to diverse and locally adapted cattle breeds that are expected to survive the harsh and extreme tropical environments associated with diseases and parasite infections, heat stress and episodes of feed and water scarcity. Genomic copy number variations (CNVs) are considered to be primary role players in cattle breed formation and adaptation where isolation and genetic drift together with subsequent mutations have created an enormous diversity of local populations. CNVs are modifications in DNA structure comprising deletions, duplications and insertions that are >1 kb in size. Despite attracting much attention, the frequency and pattern of bovine CNV events, especially in African cattle breeds, are for the most part largely unknown. Characterization of genetic variation in the indigenous cattle of Africa will be a vital step toward dissecting the molecular mechanisms underlying phenotypic variation and local adaptation. This review therefore aims to describe the current knowledge regarding bovine CNVs and the implications and potentials they encompass for dissecting genetic adaptation and the genotypic skeleton of tropical African cattle populations.

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Section: Tropical African Cattle Breedsmentioning

confidence: 97%

“…The various cattle breeds worldwide comprise subgroups of one or the other of these lines or some mixture of the two (Magee et al . ).…”

Section: Tropical African Cattle Breedsmentioning

confidence: 97%

Tropically adapted cattle of Africa: perspectives on potential role of copy number variations

et al. 2015

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“…; Piperno, McMichael, and Bush ). aDNA has been a crucial tool in understanding this phenomenon, as illustrated by work done on the domestication of the aurochs, Bos primigenitus , and the spread of domesticated cattle, Bos taurus , out of the Levant and into the rest of the world (Magee, MacHugh, and Edwards ; Orlando ; Scheu ; Scheu et al. ; Zeder ).…”

Section: Tracking and Recovering Lost Genetic Diversitymentioning

confidence: 99%

“…This, in turn, has led to deeper and expanded concepts of humanity's ability to impact the environment, especially in pre-Industrial contexts, and thus to greater understanding of the dynamics of contemporary anthropogenic climate change (Beach et al 2015;Cordeiro et al 2014;Dull et al 2010;McGovern et al 2007;Piperno, McMichael, and Bush 2015). aDNA has been a crucial tool in understanding this phenomenon, as illustrated by work done on the domestication of the aurochs, Bos primigenitus, and the spread of domesticated cattle, Bos taurus, out of the Levant and into the rest of the world (Magee, MacHugh, and Edwards 2014;Orlando 2015;Scheu 2017;Scheu et al 2015;Zeder 2015).…”

Section: Origins Of the Anthropocenementioning

confidence: 99%

Ancient DNA as a Tool for Navigating the Anthropocene

Hambrecht¹

2017

Culture Agric Food & Envi

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Ancient DNA (aDNA) analysis has led to significant breakthroughs in our understanding of the origin of our own species as well as that of many commensal and wild species. New approaches in aDNA research promise to make it a major tool for adaptation to and mitigation of the impacts of the rapidly changing climates of the Anthropocene. This article reviews a number of these new lines of research and their current and potential future contributions to responding to climate change, particularly in two areas: the generation of deeper baseline data on ecological and environmental change, and the tracking and recovery of lost genetic diversity to strengthen the resilience of living species. The article argues that aDNA analysis is creating a powerful new pathway for archeology to engage with the challenges of the Anthropocene.

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“…However, it is hard to define if the host jump affected taurine- or indicine-like cattle first, since no consensus can easily be reached to define who among Bos taurus and B. indicus migrated into ECF endemic regions first [6–8]. Indeed, African taurine cattle might have reached eastern Africa sometime between ~8,000 and 1,500 YBP [7,8], and the most ancient zebuine colonization wave is estimated to have occurred between ~4,000-2,000 YBP from the Asian continent, as suggested by the first certain archaeological record dated 1,750 YBP [6]. Once T. parva spread to domestic populations, coevolution between the parasite and the new hosts likely led to the divergence between buffalo- ( T. parva lawracei ) and cattle-specific ( T. parva parva ) parasite strains [9,10], and to the appearance of infection-tolerant indigenous herds [11,12].…”

Section: Introductionmentioning

confidence: 99%

Combining landscape genomics and ecological modelling to investigate local adaptation of indigenous Ugandan cattle to East Coast fever

Vajana

Barbato

Colli

et al. 2018

Preprint

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63East Coast fever (ECF) is a fatal sickness affecting cattle populations of eastern, central, 64and southern Africa. The disease is transmitted by the tick Rhipicephalus appendiculatus, and 65 caused by the protozoan Theileria parva parva, which invades host lymphocytes and promotes 66 their clonal expansion. Importantly, indigenous cattle show tolerance to infection in ECF-67 endemically stable areas. Here, the putative genetic bases underlying ECF-tolerance were 68 investigated using molecular data and epidemiological information from 823 indigenous cattle 69 from Uganda. Vector distribution and host infection risk were estimated over the study area and 70 subsequently tested as triggers of local adaptation by means of landscape genomics analysis. We 71 identified 41 and seven candidate adaptive loci for tick resistance and infection tolerance, 72 respectively. Among the genes associated with the candidate adaptive loci are PRKG1 and SLA2. 73 PRKG1 was already described as associated with tick resistance in indigenous South African 74 cattle, due to its role into inflammatory response. SLA2 is part of the regulatory pathways 75 involved into lymphocytes' proliferation. Additionally, local ancestry analysis suggested the 76 zebuine origin of the genomic region candidate for tick resistance. 77 Author summary 78The tick-borne parasite Theileria parva parva infects cattle populations of eastern, central 79 and southern Africa, by causing a highly fatal pathology called "East Coast fever". The disease is 80 especially severe for the exotic breeds imported to Africa, as well as outside the endemic areas of 81 East Africa. In these regions, indigenous cattle populations can survive to infection, and this 82 5 tolerance might result from unique adaptations evolved to fight the disease. We investigated this 83 hypothesis by using a method named "landscape genomics", with which we compared the genetic 84 characteristics of indigenous Ugandan cattle coming from areas at different infection risk, and 85 located genomic sites potentially attributable to tolerance. In particular, the method pinpointed 86 two genes, one (PRKG1) involved into inflammatory response and potentially affecting East 87Coast fever vector attachment, the other (SLA2) involved into lymphocytes proliferation, a 88 process activated by T. parva parva infection. Our findings can orientate future research on the 89 genetic basis of East Coast fever-tolerance, and derive from a general method that can be applied 90 to investigate adaptation in analogous host-vector-parasite systems. Characterization of the 91 genetic factors underlying East Coast-fever-tolerance represents an essential step towards 92 enhancing sustainability and productivity of local agroecosystems. 93

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Interrogation of modern and ancient genomes reveals the complex domestic history of cattle

Cited by 37 publications

References 97 publications

Tropically adapted cattle of Africa: perspectives on potential role of copy number variations

Tropically adapted cattle of Africa: perspectives on potential role of copy number variations

Ancient DNA as a Tool for Navigating the Anthropocene

Combining landscape genomics and ecological modelling to investigate local adaptation of indigenous Ugandan cattle to East Coast fever

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