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Buglione M, Rivieccio E, Aceto S, Paturzo V, Biondi C, Fulgione D. The Domestication of Wild Boar Could Result in a Relaxed Selection for Maintaining Olfactory Capacity. Life (Basel) 2024; 14:1045. [PMID: 39202786 PMCID: PMC11355481 DOI: 10.3390/life14081045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 08/15/2024] [Accepted: 08/20/2024] [Indexed: 09/03/2024] Open
Abstract
Domesticated animals are artificially selected to exhibit desirable traits, however not all traits of domesticated animals are the result of deliberate selection. Loss of olfactory capacity in the domesticated pig (Sus scrofa domesticus) is one example. We used whole transcriptome analysis (RNA-Seq) to compare patterns of gene expression in the olfactory mucosa of the pig and two subspecies of wild boar (Sus scrofa), and investigate candidate genes that could be responsible for the loss of olfactory capacity. We identified hundreds of genes with reductions in transcript abundance in pig relative to wild boar as well as differences between the two subspecies of wild boar. These differences were detected mainly in genes involved in the formation and motility of villi, cilia and microtubules, functions associated with olfaction. In addition, differences were found in the abundances of transcripts of genes related to immune defenses, with the highest levels in continental wild boar subspecies. Overall, the loss of olfactory capacity in pigs appears to have been accompanied by reductions in the expression of candidate genes for olfaction. These changes could have resulted from unintentional selection for reduced olfactory capacity, relaxed selection for maintaining olfactory capacity, pleiotropic effects of genes under selection, or other non-selective processes. Our findings could be a cornerstone for future researches on wild boars, pigs, feral populations, and their evolutionary trajectories, aimed to provide tools to better calibrate species management as well as guidelines for breeders.
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Affiliation(s)
- Maria Buglione
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (M.B.); (S.A.); (V.P.); (C.B.)
| | - Eleonora Rivieccio
- Department of Humanities Studies, University of Naples Federico II, 80133 Naples, Italy;
| | - Serena Aceto
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (M.B.); (S.A.); (V.P.); (C.B.)
| | - Vincenzo Paturzo
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (M.B.); (S.A.); (V.P.); (C.B.)
| | - Carla Biondi
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (M.B.); (S.A.); (V.P.); (C.B.)
| | - Domenico Fulgione
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (M.B.); (S.A.); (V.P.); (C.B.)
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Zhang F, Liu Q, Gong P, Wang Y, Shi C, Zhu L, Zhao J, Yao W, Luo J. Genome-wide association study provided insights into the polled phenotype and polled intersex syndrome (PIS) in goats. BMC Genomics 2024; 25:661. [PMID: 38956513 PMCID: PMC11218382 DOI: 10.1186/s12864-024-10568-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 06/26/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Breeding polled goats is a welfare-friendly approach for horn removal in comparison to invasive methods. To gain a comprehensive understanding of the genetic basis underlying polledness in goats, we conducted whole-genome sequencing of 106 Xinong Saanen dairy goats, including 33 horned individuals, 70 polled individuals, and 3 polled intersexuality syndrome (PIS) individuals. METHODS The present study employed a genome-wide association study (GWAS) and linkage disequilibrium (LD) analysis to precisely map the genetic locus underlying the polled phenotype in goats. RESULTS The analysis conducted in our study revealed a total of 320 genome-wide significant single nucleotide polymorphisms (SNPs) associated with the horned/polled phenotype in goats. These SNPs exhibited two distinct peaks on chromosome 1, spanning from 128,817,052 to 133,005,441 bp and from 150,336,143 to 150,808,639 bp. The present study identified three genome-wide significant SNPs, namely Chr1:129789816, Chr1:129791507, and Chr1:129791577, as potential markers of PIS-affected goats. The results of our LD analysis suggested a potential association between MRPS22 and infertile intersex individuals, as well as a potential association between ERG and the polled trait in goats. CONCLUSION We have successfully identified three marker SNPs closely linked to PIS, as well as several candidate genes associated with the polled trait in goats. These results may contribute to the development of SNP chips for early prediction of PIS in goats, thereby facilitating breeding programs aimed at producing fertile herds with polled traits.
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Affiliation(s)
- Fuhong Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, P. R. China
| | - Qingqing Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, P. R. China
| | - Ping Gong
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, Urumchi, 830000, P. R. China
| | - Yaling Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, P. R. China
| | - Chenbo Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, P. R. China
| | - Lu Zhu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, P. R. China
| | - Jianqing Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, P. R. China
| | - Weiwei Yao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, P. R. China
| | - Jun Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, P. R. China.
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Fonseca PAS, Suárez-Vega A, Arranz JJ, Gutiérrez-Gil B. Integration of selective sweeps across the sheep genome: understanding the relationship between production and adaptation traits. Genet Sel Evol 2024; 56:40. [PMID: 38773423 PMCID: PMC11106937 DOI: 10.1186/s12711-024-00910-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/07/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Livestock populations are under constant selective pressure for higher productivity levels for different selective purposes. This pressure results in the selection of animals with unique adaptive and production traits. The study of genomic regions associated with these unique characteristics has the potential to improve biological knowledge regarding the adaptive process and how it is connected to production levels and resilience, which is the ability of an animal to adapt to stress or an imbalance in homeostasis. Sheep is a species that has been subjected to several natural and artificial selective pressures during its history, resulting in a highly specialized species for production and adaptation to challenging environments. Here, the data from multiple studies that aim at mapping selective sweeps across the sheep genome associated with production and adaptation traits were integrated to identify confirmed selective sweeps (CSS). RESULTS In total, 37 studies were used to identify 518 CSS across the sheep genome, which were classified as production (147 prodCSS) and adaptation (219 adapCSS) CSS based on the frequency of each type of associated study. The genes within the CSS were associated with relevant biological processes for adaptation and production. For example, for adapCSS, the associated genes were related to the control of seasonality, circadian rhythm, and thermoregulation. On the other hand, genes associated with prodCSS were related to the control of feeding behaviour, reproduction, and cellular differentiation. In addition, genes harbouring both prodCSS and adapCSS showed an interesting association with lipid metabolism, suggesting a potential role of this process in the regulation of pleiotropic effects between these classes of traits. CONCLUSIONS The findings of this study contribute to a deeper understanding of the genetic link between productivity and adaptability in sheep breeds. This information may provide insights into the genetic mechanisms that underlie undesirable genetic correlations between these two groups of traits and pave the way for a better understanding of resilience as a positive ability to respond to environmental stressors, where the negative effects on production level are minimized.
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Affiliation(s)
- Pablo A S Fonseca
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071, León, Spain
| | - Aroa Suárez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071, León, Spain
| | - Juan J Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071, León, Spain
| | - Beatriz Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071, León, Spain.
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Alam O, Purugganan MD. Domestication and the evolution of crops: variable syndromes, complex genetic architectures, and ecological entanglements. THE PLANT CELL 2024; 36:1227-1241. [PMID: 38243576 PMCID: PMC11062453 DOI: 10.1093/plcell/koae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/01/2023] [Accepted: 12/14/2023] [Indexed: 01/21/2024]
Abstract
Domestication can be considered a specialized mutualism in which a domesticator exerts control over the reproduction or propagation (fitness) of a domesticated species to gain resources or services. The evolution of crops by human-associated selection provides a powerful set of models to study recent evolutionary adaptations and their genetic bases. Moreover, the domestication and dispersal of crops such as rice, maize, and wheat during the Holocene transformed human social and political organization by serving as the key mechanism by which human societies fed themselves. Here we review major themes and identify emerging questions in three fundamental areas of crop domestication research: domestication phenotypes and syndromes, genetic architecture underlying crop evolution, and the ecology of domestication. Current insights on the domestication syndrome in crops largely come from research on cereal crops such as rice and maize, and recent work indicates distinct domestication phenotypes can arise from different domestication histories. While early studies on the genetics of domestication often identified single large-effect loci underlying major domestication traits, emerging evidence supports polygenic bases for many canonical traits such as shattering and plant architecture. Adaptation in human-constructed environments also influenced ecological traits in domesticates such as resource acquisition rates and interactions with other organisms such as root mycorrhizal fungi and pollinators. Understanding the ecological context of domestication will be key to developing resource-efficient crops and implementing more sustainable land management and cultivation practices.
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Affiliation(s)
- Ornob Alam
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Institute for the Study of the Ancient World, New York University, New York, NY, 10028, USA
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5
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Liu X, Jones M. Needs for a conceptual bridge between biological domestication and early food globalization. Proc Natl Acad Sci U S A 2024; 121:e2219055121. [PMID: 38536744 PMCID: PMC11032431 DOI: 10.1073/pnas.2219055121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024] Open
Abstract
The past 15 y has seen much development in documentation of domestication of plants and animals as gradual traditions spanning millennia. There has also been considerable momentum in understanding the dispersals of major domesticated taxa across continents spanning thousands of miles. The two processes are often considered within different theoretical strains. What is missing from our repertoire of explanations is a conceptual bridge between the protracted process over millennia and the multiregional, globally dispersed nature of domestication. The evidence reviewed in this paper bears upon how we conceptualize domestication as an episode or a process. By bringing together the topics of crop domestication and crop movement, those complex, protracted, and continuous outcomes come more clearly into view.
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Affiliation(s)
- Xinyi Liu
- Department of Anthropology, Washington University in St. Louis, St. Louis, MO63130
| | - Martin Jones
- McDonald Institute for Archaeological Research, University of Cambridge, CambridgeCB2 3DZ, United Kingdom
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Pezo-Lanfranco L, Colonese AC. The role of farming and fishing in the rise of social complexity in the Central Andes: a stable isotope perspective. Sci Rep 2024; 14:4582. [PMID: 38403727 PMCID: PMC10894859 DOI: 10.1038/s41598-024-55436-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 02/23/2024] [Indexed: 02/27/2024] Open
Abstract
For many years, the rise of stratified societies along the Central Andean coast, known as the birthplace of Andean civilization, has been closely linked to a marine-oriented economy. This hypothesis has recently been challenged by increasing evidence of plant management and cultivation among Andean populations long before the emergence of complex societies and monumental architecture. The extent to which marine and plant-based economies were integrated and their contributions to early sedentism, population growth, and intra-community stratification, however, remain subjects of ongoing and contentious debate. Using Bayesian Mixing Models we reanalyze the previously published stable isotopes (δ15Ncollagen, δ13Ccollagen, δ13Capatite) values of 572 human individuals from 39 archaeological sites in the Central Andes dated between ca. 7000 BCE and 200 CE to reconstruct dietary regimes in probabilistic terms. Our results reveal that fish, terrestrial fauna, and cultivated plants variably contributed to the diet of prehistoric Andean populations; in coastal and middle valley settlements plant cultivation, not fishing, fueled the development of the earliest complex societies during the Formative Period (from 3000 BCE). Similarly, in the highlands the societies that built ceremonial centers show a plant-based economy. Our findings also show that maize only became a staple food (> 25% dietary contribution) in more recent phases of Andean prehistory, around 500 BCE.
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Affiliation(s)
- Luis Pezo-Lanfranco
- Institute of Environmental Science and Technology (ICTA), Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain.
- Department of Prehistory, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain.
| | - André Carlo Colonese
- Institute of Environmental Science and Technology (ICTA), Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
- Department of Prehistory, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
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Janák V, Novák K, Kyselý R. Late History of Cattle Breeds in Central Europe in Light of Genetic and Archaeogenetic Sources-Overview, Thoughts, and Perspectives. Animals (Basel) 2024; 14:645. [PMID: 38396613 PMCID: PMC10886113 DOI: 10.3390/ani14040645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
Although Europe was not a primary centre of cattle domestication, its expansion from the Middle East and subsequent development created a complex pattern of cattle breed diversity. Many isolated populations of local historical breeds still carry the message about the physical and genetic traits of ancient populations. Since the way of life of human communities starting from the eleventh millennium BP was strongly determined by livestock husbandry, the knowledge of cattle diversity through the ages is helpful in the interpretation of many archaeological findings. Historical cattle diversity is currently at the intersection of two leading directions of genetic research. Firstly, it is archaeogenetics attempting to recover and interpret the preserved genetic information directly from archaeological finds. The advanced archaeogenetic approaches meet with the population genomics of extant cattle populations. The immense amount of genetic information collected from living cattle, due to its key economic role, allows for reconstructing the genetic profiles of the ancient populations backwards. The present paper aims to place selected archaeogenetic, genetic, and genomic findings in the picture of cattle history in Central Europe, as suggested by archaeozoological and historical records. Perspectives of the methodical connection between the genetic approaches and the approaches of traditional archaeozoology, such as osteomorphology and osteometry, are discussed. The importance, actuality, and effectiveness of combining different approaches to each archaeological find, such as morphological characterization, interpretation of the historical context, and molecular data, are stressed.
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Affiliation(s)
- Vojtěch Janák
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Letenská 4, 118 00 Praha, Czech Republic
- Department of Genetics and Breeding, Institute of Animal Science, Přátelství 815, 104 00 Praha, Czech Republic;
- Department of Archaeology, Faculty of Arts, Charles University, Nám. Jana Palacha 2, 116 38 Praha, Czech Republic
| | - Karel Novák
- Department of Genetics and Breeding, Institute of Animal Science, Přátelství 815, 104 00 Praha, Czech Republic;
| | - René Kyselý
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Letenská 4, 118 00 Praha, Czech Republic
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Li Y, Zhou X, Zhao K, Liu J, Chen G, Zhang Y, Ma J, Sun N, Li X. Cultivation and morphology of jujube (Ziziphus Jujuba Mill.) in the Qi River Basin of Northern China during the Neolithic Period. Sci Rep 2024; 14:2305. [PMID: 38280899 PMCID: PMC10821880 DOI: 10.1038/s41598-024-52260-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/16/2024] [Indexed: 01/29/2024] Open
Abstract
This transition from gathering to cultivation is a significant aspect of studying early agricultural practices. Fruit trees are an essential component of food resources and have played a vital role in both ancient and modern agricultural production systems. The jujube (Ziziphus jujuba Mill.), with its long history of cultivation in northern China, holds great importance in uncovering the diet of prehistoric humans and understanding the origins of Chinese agricultural civilization. This paper focuses on the domestication of jujube by analyzing the morphology of jujube stones found in three Neolithic sites in northern China's Qi River basin, Zhujia, Wangzhuang, and Dalaidian. The measurements of these jujube kernels are compared with those found in other areas of northern China, as well as modern jujube kernels that were collected. The measurements revealed that the length-to-diameter (L/D) ratio of sour jujube kernels ranged from 1.36 to 1.78, whereas the L/D ratio of cultivated jujube stones varied between 1.96 and 4.23. Furthermore, jujube stones obtained from Zhujia and Wangzhuang sites exhibit pointed ends and possess an elongated oval or narrow oval shape overall, which is indicative of clearly artificial domestication traits. Therefore, this study suggests that jujube was selected and cultivated as an important food supplement in the Qi River basin no later than around 6200 BP.
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Affiliation(s)
- Yanpeng Li
- School of Earth Science and Resources, Chang'an University, Xi'an, 710054, China
- Key Laboratory of Vertebrate Evolution and Human Origin of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Xinying Zhou
- Key Laboratory of Vertebrate Evolution and Human Origin of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China.
- CAS Center for Excellence in Life and Paleoenvironment, Beijing, 100044, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
| | - Keliang Zhao
- Key Laboratory of Vertebrate Evolution and Human Origin of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing, 100044, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Junchi Liu
- Key Laboratory of Vertebrate Evolution and Human Origin of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing, 100044, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Guanhan Chen
- Key Laboratory of Vertebrate Evolution and Human Origin of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing, 100044, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yaping Zhang
- Key Laboratory of Vertebrate Evolution and Human Origin of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing, 100044, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiacheng Ma
- Key Laboratory of Vertebrate Evolution and Human Origin of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing, 100044, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Nan Sun
- School of Earth Science and Resources, Chang'an University, Xi'an, 710054, China.
| | - Xiaoqiang Li
- Key Laboratory of Vertebrate Evolution and Human Origin of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing, 100044, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
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Bull K, Davies G, Jenkins TP, Peachey L. The faecal microbiome of Exmoor ponies shows step-wise compositional changes with increasing levels of management by humans. Equine Vet J 2024; 56:159-170. [PMID: 37264698 DOI: 10.1111/evj.13961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 05/05/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND Horses can suffer from gastrointestinal (GI) disease in domestic environments, often precipitated by human-led changes in management. Understanding the consequences of these changes on equine gut microbiota is key to the prevention of such disease episodes. OBJECTIVE Profile the faecal microbiota of adult female Exmoor ponies under three management conditions, representing increasing levels of management by humans, encompassing different diets; whilst controlling for age, breed and sex. STUDY DESIGN Cross-sectional descriptive. METHODS Faecal samples were collected from three populations of Exmoor ponies kept under contrasting management conditions: 29 adult female ponies in groups with low management (LM) (n = 10), medium management (MM) (n = 10) and high management (HM) (n = 9) levels, based on diet, drug use, handling and exercise. Faecal microbial composition was profiled via high-throughput sequencing of the bacterial 16S rRNA gene, and functional metagenome predictions. RESULTS We observed profound step-wise changes in microbiome structure in the transition from LM to MM to HM. A relatively high abundance of Proteobacteria and Tenericutes was associated with the HM group; higher abundance of Methanobacteria was observed in the LM group. The MM group had intermediate levels of these taxa and exhibited high 'within group' variation in alpha diversity. Functional predictions revealed increased amino acid and lipid metabolism in HM; energy metabolism in LM and carbohydrate metabolism and immune/metabolic disease pathways in MM. MAIN LIMITATIONS Low group sizes, incomplete knowledge of bacterial genomes in equine gut microbiota and it was not possible to assess the relative impact of diet, drug use, handling and exercise on the microbiome as variables were confounded. CONCLUSIONS Human-led management factors had profound step-wise effects on faecal microbial composition. Based on functional metagenome predictions, we hypothesise that dietary differences between groups were the major driver of observed differences.
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Affiliation(s)
- Katie Bull
- School of Veterinary Sciences, University of Bristol, Bristol, UK
| | - Gareth Davies
- School of Veterinary Sciences, University of Bristol, Bristol, UK
| | - Timothy P Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Laura Peachey
- School of Veterinary Sciences, University of Bristol, Bristol, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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10
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Leonetti S, Cimarelli G, Hersh TA, Ravignani A. Why do dogs wag their tails? Biol Lett 2024; 20:20230407. [PMID: 38229554 PMCID: PMC10792393 DOI: 10.1098/rsbl.2023.0407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/11/2023] [Indexed: 01/18/2024] Open
Abstract
Tail wagging is a conspicuous behaviour in domestic dogs (Canis familiaris). Despite how much meaning humans attribute to this display, its quantitative description and evolutionary history are rarely studied. We summarize what is known about the mechanism, ontogeny, function and evolution of this behaviour. We suggest two hypotheses to explain its increased occurrence and frequency in dogs compared to other canids. During the domestication process, enhanced rhythmic tail wagging behaviour could have (i) arisen as a by-product of selection for other traits, such as docility and tameness, or (ii) been directly selected by humans, due to our proclivity for rhythmic stimuli. We invite testing of these hypotheses through neurobiological and ethological experiments, which will shed light on one of the most readily observed yet understudied animal behaviours. Targeted tail wagging research can be a window into both canine ethology and the evolutionary history of characteristic human traits, such as our ability to perceive and produce rhythmic behaviours.
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Affiliation(s)
- Silvia Leonetti
- Comparative Bioacoustics Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
- Department of Human Neurosciences, Sapienza University of Rome, Rome, Italy
| | - Giulia Cimarelli
- Domestication Lab, Konrad Lorenz Institute of Ethology, Department of Interdisciplinary Life Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Taylor A. Hersh
- Comparative Bioacoustics Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Marine Mammal Institute, Oregon State University, Newport, OR, USA
| | - Andrea Ravignani
- Comparative Bioacoustics Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Department of Human Neurosciences, Sapienza University of Rome, Rome, Italy
- Center for Music in the Brain, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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11
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Siali C, Niinimäki S, Harvati K, Karakostis FA. Reconstructing patterns of domestication in reindeer using 3D muscle attachment areas. ARCHAEOLOGICAL AND ANTHROPOLOGICAL SCIENCES 2023; 16:19. [PMID: 38162318 PMCID: PMC10756864 DOI: 10.1007/s12520-023-01910-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/23/2023] [Indexed: 01/03/2024]
Abstract
The use of reindeer has been a crucial element in the subsistence strategies of past Arctic and Subarctic populations. However, the spatiotemporal occurrence of systematic herding practices has been difficult to identify in the bioarchaeological record. To address this research gap, this study proposes a new virtual anthropological approach for reconstructing habitual physical activity in reindeer, relying on the protocols of the "Validated Entheses based Reconstruction of Activity" (VERA) method. Following blind analytical procedures, we focused on eight muscle attachment sites ("entheses") in 36 reindeer free ranging in the wild, 21 specimens in captivity (zoo), and eight racing reindeer (habitual runners). Importantly, our analyses accounted for the effects of variation by subspecies, sex, age, and estimated body size. Our results showed clear differences across activity groups, leading to the development of discriminant function equations with cross-validated accuracies ranging from approximately 88 to 100%. The reliability of our functions was additionally confirmed using a blind test involving six zoo individuals not included in the initial dataset. Our findings support the use of the proposed approach for identifying domestication-related activities in zooarchaeological contexts, introducing a valuable tool for locating suspected domestication hotspots and elucidating the nature of past human-reindeer interactions. Supplementary Information The online version contains supplementary material available at 10.1007/s12520-023-01910-5.
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Affiliation(s)
- Christina Siali
- Palaeoanthropology, Senckenberg Centre for Human Evolution and Palaeoenvironment, Institute for Archaeological Sciences, Eberhard Karls University of Tübingen, Tubingen, Germany
| | - Sirpa Niinimäki
- Archaeology, History, Culture and Communication Studies, Faculty of Humanities, University of Oulu, Oulu, Finland
| | - Katerina Harvati
- Palaeoanthropology, Senckenberg Centre for Human Evolution and Palaeoenvironment, Institute for Archaeological Sciences, Eberhard Karls University of Tübingen, Tubingen, Germany
- DFG Centre of Advanced Studies ‘Words, Bones, Genes, Tools’, Eberhard Karls University of Tübingen, Tubingen, Germany
| | - Fotios Alexandros Karakostis
- Palaeoanthropology, Senckenberg Centre for Human Evolution and Palaeoenvironment, Institute for Archaeological Sciences, Eberhard Karls University of Tübingen, Tubingen, Germany
- DFG Centre of Advanced Studies ‘Words, Bones, Genes, Tools’, Eberhard Karls University of Tübingen, Tubingen, Germany
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12
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Li H, Jin L, Wang Y, Hu S, Long K, Li M. Identification and analysis of circRNAs in the prefrontal cortices of wild boar and domestic pig. Anim Biotechnol 2023; 34:2596-2607. [PMID: 35960868 DOI: 10.1080/10495398.2022.2109040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Domestication caused significant differences in morphology and behavior between wild and domestic pigs. However, the regulatory role of circRNA in this event is unclear. Here, we analyzed circRNA expression patterns in the prefrontal cortices of wild boar and domestic pigs to determine the potential role of circRNAs in domestication. We identified a total of 11,375 circRNAs and found that 349 and 354 circRNAs were up-regulated in wild boar and Rongchang pig, respectively. Functional enrichment analysis showed that host genes of significantly highly-expressed circRNAs in wild boar were significantly enriched in neural synapse-related categories and the categories of 'regulation of defense response (p = 0.028)' and 'neural retina development (p = 4.32 × 10-3)'. Host genes of significantly highly-expressed circRNAs in Rongchang pig were specifically involved in 'chordate embryonic development (p = 2.38 × 10-4)'. Additionally, we constructed circRNA-miRNA-mRNA regulatory axes in wild boar and Rongchang pig and found more regulatory axes in wild boar that potentially regulate synaptic activities. We identified multiple circRNAs that may be related to domesticated characteristics, such as ssc_circ_6179 (ssc_circ_6179-ssc-miR-9847-HRH3, related to aggression) and ssc_circ_3027 (ssc_circ_3027-ssc-miR-4334-5p-HCRTR1, related to attention). This study provides a resource for further investigation of the molecular basis of pig domestication.
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Affiliation(s)
- Hengkuan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yuhao Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Silu Hu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Keren Long
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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13
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Ferreira VHB, Lansade L, Calandreau L, Cunha F, Jensen P. Are domesticated animals dumber than their wild relatives? A comprehensive review on the domestication effects on animal cognitive performance. Neurosci Biobehav Rev 2023; 154:105407. [PMID: 37769929 DOI: 10.1016/j.neubiorev.2023.105407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/03/2023]
Abstract
Animal domestication leads to diverse behavioral, physiological, and neurocognitive changes in domesticated species compared to their wild relatives. However, the widely held belief that domesticated species are inherently less "intelligent" (i.e., have lower cognitive performance) than their wild counterparts requires further investigation. To investigate potential cognitive disparities, we undertook a thorough review of 88 studies comparing the cognitive performance of domesticated and wild animals. Approximately 30% of these studies showed superior cognitive abilities in wild animals, while another 30% highlighted superior cognitive abilities in domesticated animals. The remaining 40% of studies found similar cognitive performance between the two groups. Therefore, the question regarding the presumed intelligence of wild animals and the diminished cognitive ability of domesticated animals remains unresolved. We discuss important factors/limitations for interpreting past and future research, including environmental influences, diverse objectives of domestication (such as breed development), developmental windows, and methodological issues impacting cognitive comparisons. Rather than perceiving these limitations as constraints, future researchers should embrace them as opportunities to expand our understanding of the complex relationship between domestication and animal cognition.
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Affiliation(s)
- Vitor Hugo Bessa Ferreira
- IFM Biology, AVIAN Behavioural Genomics and Physiology group, Linköping University, 581 83 Linköping, Sweden; INRAE, CNRS, IFCE, Université de Tours, Centre Val de Loire UMR Physiologie de la Reproduction et des Comportements, 37380 Nouzilly, France.
| | - Léa Lansade
- INRAE, CNRS, IFCE, Université de Tours, Centre Val de Loire UMR Physiologie de la Reproduction et des Comportements, 37380 Nouzilly, France
| | - Ludovic Calandreau
- INRAE, CNRS, IFCE, Université de Tours, Centre Val de Loire UMR Physiologie de la Reproduction et des Comportements, 37380 Nouzilly, France
| | - Felipe Cunha
- IFM Biology, AVIAN Behavioural Genomics and Physiology group, Linköping University, 581 83 Linköping, Sweden
| | - Per Jensen
- IFM Biology, AVIAN Behavioural Genomics and Physiology group, Linköping University, 581 83 Linköping, Sweden.
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14
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Pohle AK, Zalewski A, Muturi M, Dullin C, Farková L, Keicher L, Dechmann DKN. Domestication effect of reduced brain size is reverted when mink become feral. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230463. [PMID: 37416828 PMCID: PMC10320332 DOI: 10.1098/rsos.230463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/12/2023] [Indexed: 07/08/2023]
Abstract
A typical consequence of breeding animal species for domestication is a reduction in relative brain size. When domesticated animals escape from captivity and establish feral populations, the larger brain of the wild phenotype is usually not regained. In the American mink (Neovison vison), we found an exception to this rule. We confirmed the previously described reduction in relative braincase size and volume compared to their wild North American ancestors in mink bred for their fur in Poland, in a dataset of 292 skulls. We then also found a significant regrowth of these measures in well-established feral populations in Poland. Closely related, small mustelids are known for seasonal reversible changes in skull and brain size. It seems that these small mustelids are able to regain the brain size, which is adaptive for living in the wild, and flexibly respond to selection accordingly.
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Affiliation(s)
- Ann-Kathrin Pohle
- Department of Migration, Max Planck Institute of Animal Behavior, Am Obstberg 1, 78315 Radolfzell, Germany
- Department for the Ecology of Animal Societies, Max Planck Institute of Animal Behavior, Bücklestraße 5a, 78467 Konstanz, Germany
- University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Andrzej Zalewski
- Mammal Research Institute, Polish Academy of Sciences, 17-230 Białowieża, Poland
| | - Marion Muturi
- Department of Migration, Max Planck Institute of Animal Behavior, Am Obstberg 1, 78315 Radolfzell, Germany
| | - Christian Dullin
- Department for Diagnostic and Interventional Radiology, University Medical Center Goettingen, Robert-Koch-Straße 40, 37075 Goettingen, Germany
- Department Translational Molecular Imaging, Max Planck Institute for Multidisciplinary Sciences, Herman-Rein-Straße 3, 37075 Goettingen, Germany
- Department for Diagnostic and Interventional Radiology, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany
| | - Lucie Farková
- Department of Migration, Max Planck Institute of Animal Behavior, Am Obstberg 1, 78315 Radolfzell, Germany
- Department of Zoology, Charles University, Viničná 7, 128 00 Prague, Czech Republic
| | - Lara Keicher
- Department of Migration, Max Planck Institute of Animal Behavior, Am Obstberg 1, 78315 Radolfzell, Germany
- University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Dina K. N. Dechmann
- Department of Migration, Max Planck Institute of Animal Behavior, Am Obstberg 1, 78315 Radolfzell, Germany
- University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
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15
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Flint-Garcia S, Feldmann MJ, Dempewolf H, Morrell PL, Ross-Ibarra J. Diamonds in the not-so-rough: Wild relative diversity hidden in crop genomes. PLoS Biol 2023; 21:e3002235. [PMID: 37440605 PMCID: PMC10368281 DOI: 10.1371/journal.pbio.3002235] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/25/2023] [Indexed: 07/15/2023] Open
Abstract
Crop production is becoming an increasing challenge as the global population grows and the climate changes. Modern cultivated crop species are selected for productivity under optimal growth environments and have often lost genetic variants that could allow them to adapt to diverse, and now rapidly changing, environments. These genetic variants are often present in their closest wild relatives, but so are less desirable traits. How to preserve and effectively utilize the rich genetic resources that crop wild relatives offer while avoiding detrimental variants and maladaptive genetic contributions is a central challenge for ongoing crop improvement. This Essay explores this challenge and potential paths that could lead to a solution.
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Affiliation(s)
- Sherry Flint-Garcia
- Plant Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Columbia, Missouri, United States of America
| | - Mitchell J. Feldmann
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | | | - Peter L. Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, Center for Population Biology, and Genome Center, University of California, Davis, California, United States of America
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16
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Smits M, Joosten H, Faye B, Burger P. Domestication of the Dromedary Revisited and Its Consequences for Legislation as to Keeping Livestock or Pet Animals. Animals (Basel) 2023; 13:2050. [PMID: 37443848 DOI: 10.3390/ani13132050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/13/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023] Open
Abstract
Being in an advanced stage of domestication is a newly proposed requirement to decide which animals can be safely kept by humans. Dutch legislators were the first to apply it and other European countries may be tempted to adopt a similar approach. Unexpectedly, the Dutch assessors considered the dromedary (Camelus dromedarius) as being insufficiently domesticated and this species will therefore no longer be able to be kept as a production animal from 2024 onwards. In a recent publication on this topic, we showed that the domestication of the dromedary is actually very advanced. In this paper, we apply the same criteria that were used by the Dutch assessors to determine the degree of domestication, taking into account the most recent scientific developments in this area, even though it should be noted that these criteria have neither been peer-reviewed, nor published in an international scientific journal. For the sake of comparison, and in order to validate the procedure, we also applied these criteria to the house cat. The results confirm that the dromedary is highly domesticated, but also that the house cat (Felis silvestris catus) is at most semi-domesticated. Obviously, we agree with the decision of the Dutch legislators to place the house cat on the positive list, but our analysis demonstrates that this was decided on false grounds. Our analysis makes it clear that the requirement of being in an advanced stage of domestication is not suitable. Instead of maintaining this requirement, we recommend implementing evidence-based, peer-reviewed methods to decide which animals can be kept by humans, and to include species specific-guidelines in the legislation on how this can be achieved safely.
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Affiliation(s)
- Marcel Smits
- European Camel Research Society, Johanniterlaan 7, 6721 XX Bennekom, The Netherlands
| | - Han Joosten
- Microbiologist, Chemin de Crocus 1, 1073 Mollie Margot, Switzerland
| | - Bernard Faye
- UMR SELMET, CIRAD-ES, Campus International de Baillarguet, 34398 Montpellier, France
| | - Pamela Burger
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Savoyenstrasse 1, 1160 Vienna, Austria
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17
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Dwivedi SL, Chapman MA, Abberton MT, Akpojotor UL, Ortiz R. Exploiting genetic and genomic resources to enhance productivity and abiotic stress adaptation of underutilized pulses. Front Genet 2023; 14:1193780. [PMID: 37396035 PMCID: PMC10311922 DOI: 10.3389/fgene.2023.1193780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/07/2023] [Indexed: 07/04/2023] Open
Abstract
Underutilized pulses and their wild relatives are typically stress tolerant and their seeds are packed with protein, fibers, minerals, vitamins, and phytochemicals. The consumption of such nutritionally dense legumes together with cereal-based food may promote global food and nutritional security. However, such species are deficient in a few or several desirable domestication traits thereby reducing their agronomic value, requiring further genetic enhancement for developing productive, nutritionally dense, and climate resilient cultivars. This review article considers 13 underutilized pulses and focuses on their germplasm holdings, diversity, crop-wild-crop gene flow, genome sequencing, syntenic relationships, the potential for breeding and transgenic manipulation, and the genetics of agronomic and stress tolerance traits. Recent progress has shown the potential for crop improvement and food security, for example, the genetic basis of stem determinacy and fragrance in moth bean and rice bean, multiple abiotic stress tolerant traits in horse gram and tepary bean, bruchid resistance in lima bean, low neurotoxin in grass pea, and photoperiod induced flowering and anthocyanin accumulation in adzuki bean have been investigated. Advances in introgression breeding to develop elite genetic stocks of grass pea with low β-ODAP (neurotoxin compound), resistance to Mungbean yellow mosaic India virus in black gram using rice bean, and abiotic stress adaptation in common bean, using genes from tepary bean have been carried out. This highlights their potential in wider breeding programs to introduce such traits in locally adapted cultivars. The potential of de-domestication or feralization in the evolution of new variants in these crops are also highlighted.
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Affiliation(s)
| | - Mark A. Chapman
- Biological Sciences, University of Southampton, Southampton, United Kingdom
| | | | | | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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18
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Tancredi D, Cardinali I. Being a Dog: A Review of the Domestication Process. Genes (Basel) 2023; 14:genes14050992. [PMID: 37239352 DOI: 10.3390/genes14050992] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/19/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
The process of canine domestication represents certainly one of the most interesting questions that evolutionary biology aims to address. A "multiphase" view of this process is now accepted, with a first phase during which different groups of wolves were attracted by the anthropogenic niche and a second phase characterized by the gradual establishment of mutual relationships between wolves and humans. Here, we provide a review of dog (Canis familiaris) domestication, highlighting the ecological differences between dogs and wolves, analyzing the molecular mechanisms which seem to have influenced the affiliative behaviors first observed in Belyaev's foxes, and describing the genetics of ancient European dogs. Then, we focus on three Mediterranean peninsulas (Balkan, Iberian and Italian), which together represent the main geographic area for studying canine domestication dynamics, as it has shaped the current genetic variability of dog populations, and where a well-defined European genetic structure was pinpointed through the analysis of uniparental genetic markers and their phylogeny.
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Affiliation(s)
- Domenico Tancredi
- Department of Chemistry, Biology and Biotechnology, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, Università degli Studi di Perugia, 06123 Perugia, Italy
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19
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Pelletier M, Discamps E, Bignon-Lau O, Salmi AK. Investigating the domestication and early management of reindeer (Rangifer tarandus) in the Sámi archaeological context from teeth geometric morphometrics. Sci Rep 2023; 13:6174. [PMID: 37061658 PMCID: PMC10105696 DOI: 10.1038/s41598-023-33422-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/12/2023] [Indexed: 04/17/2023] Open
Abstract
For centuries, reindeer herding has been an integral part of the subsistence, lifeways, economy and cosmology of the Sámi of northern Fennoscandia. Despite its importance, the timing and details of early reindeer domestication are still highly debated. Identifying domesticated individuals in the archaeological record remains complicated due to the presence of two interbreeding subspecies in Fennoscandia and a mixed socio-economic organisation by Sámi populations, which was mainly a combination of wild reindeer hunting and small-scale reindeer herding. This study proposes methodological improvement for identifying domestic individuals using 2D landmark and sliding semi-landmark based geometric morphometrics on the isolated lower molars of 389 modern specimens, and 90 teeth from four archaeological sites in Finnish Lapland. Our results indicate that despite the significant impact of wear on overall tooth morphology, our protocol is very useful for identifying subspecies (classification accuracy of the two species is between 78 and 91% depending on the wear class) and understanding the morphological changes induced by the domestication process. We suggest that the morphological variation observable among modern populations has been impacted by recent changes in herding strategies in northern Fennoscandia, and that the archaeological domesticated reindeer populations were relatively different, probably due to selection by the Sámi. This study also highlights the importance of using other direct evidence or contextual archaeological data to better trace the early evidence of a domesticated reindeer economy in northern Fennoscandia, and aid in reconstructing the socio-economic changes in Sámi populations over time.
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Affiliation(s)
- Maxime Pelletier
- Archaeology, History, Culture and Communication Studies, Faculty of Humanities, University of Oulu, Oulu, Finland.
| | - Emmanuel Discamps
- CNRS UMR5608 TRACES, University of Toulouse Jean Jaurès, Toulouse, France
| | | | - Anna-Kaisa Salmi
- Archaeology, History, Culture and Communication Studies, Faculty of Humanities, University of Oulu, Oulu, Finland
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20
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Townsend C, Ferraro JV, Habecker H, Flinn MV. Human cooperation and evolutionary transitions in individuality. Philos Trans R Soc Lond B Biol Sci 2023; 378:20210414. [PMID: 36688393 PMCID: PMC9869453 DOI: 10.1098/rstb.2021.0414] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 10/31/2022] [Indexed: 01/24/2023] Open
Abstract
A major evolutionary transition in individuality involves the formation of a cooperative group and the transformation of that group into an evolutionary entity. Human cooperation shares principles with those of multicellular organisms that have undergone transitions in individuality: division of labour, communication, and fitness interdependence. After the split from the last common ancestor of hominoids, early hominins adapted to an increasingly terrestrial niche for several million years. We posit that new challenges in this niche set in motion a positive feedback loop in selection pressure for cooperation that ratcheted coevolutionary changes in sociality, communication, brains, cognition, kin relations and technology, eventually resulting in egalitarian societies with suppressed competition and rapid cumulative culture. The increasing pace of information innovation and transmission became a key aspect of the evolutionary niche that enabled humans to become formidable cooperators with explosive population growth, the ability to cooperate and compete in groups of millions, and emergent social norms, e.g. private property. Despite considerable fitness interdependence, the rise of private property, in concert with population explosion and socioeconomic inequality, subverts potential transition of human groups into evolutionary entities due to resurgence of latent competition and conflict. This article is part of the theme issue 'Human socio-cultural evolution in light of evolutionary transitions'.
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Affiliation(s)
- Cathryn Townsend
- Department of Anthropology, Baylor University, Waco, TX 76798-7334, USA
| | - Joseph V. Ferraro
- Department of Anthropology, Baylor University, Waco, TX 76798-7334, USA
| | - Heather Habecker
- Department of Psychology and Neuroscience, Baylor University, Waco, TX 76798-7334, USA
| | - Mark V. Flinn
- Department of Anthropology, Baylor University, Waco, TX 76798-7334, USA
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21
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Shavit A, Sharon G. Can models of evolutionary transition clarify the debates over the Neolithic Revolution? Philos Trans R Soc Lond B Biol Sci 2023; 378:20210413. [PMID: 36688395 PMCID: PMC9869441 DOI: 10.1098/rstb.2021.0413] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The 'Neolithic Revolution,' sometimes referred to as the emergence of agriculture at its earliest in the southern Levant, is the most significant shift in human history, shaping the world we live in today. Yet, after 100 years of study, its major cause, tempo (gradual or revolutionary), and impact of human intentionality remain disputed. Here, we examine the research potential of an evolutionary transition in individuality (ETI) to clarify this dramatic shift. Applying an ETI research perspective reveals how different causes and conditions lead to the same result, enabling a holistic view rather than a reduction of 'Neolithic' to 'agriculture,' or to one major climatic condition, inheritance system or standard evolutionary model, thus allowing us to clarify and bypass some of these heated, unresolved disputes. Additionally, unlike current archaeological emphasis on 'where,' 'when,' 'why' and 'how' questions, the ETI perspective offers a productive path for resolving a fundamental preliminary anomaly: why and how could the Neolithic lifeway evolve at all, given the selfish interest of individuals in a hunter-gatherer group? We do not intend to solve the shift to Neolithic lifeways, only to offer a fresh lens for examining it, emphasizing the relevance of tracking within and between group differences. This article is part of the theme issue 'Human socio-cultural evolution in light of evolutionary transitions'.
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Affiliation(s)
- Ayelet Shavit
- Department of Interdisciplinary Studies, Tel Hai College, 1220800, Israel,Department of Humanities and Arts, Technion, 3200003 Israel
| | - Gonen Sharon
- Department of Humanities and Arts, Technion, 3200003 Israel
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22
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Transcriptomics and Selection Pressure Analysis Reveals the Influence Mechanism of PLIN1 Protein on the Development of Small Size in Min Pigs. Int J Mol Sci 2023; 24:ijms24043947. [PMID: 36835359 PMCID: PMC9960057 DOI: 10.3390/ijms24043947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023] Open
Abstract
Body size is an important biological phenotypic trait that has attracted substantial attention. Small domestic pigs can serve as excellent animal models for biomedicine and also help meet sacrificial culture needs in human societies. Although the mechanisms underlying vertebral development regulating body size variation in domestic pigs during the embryonic period have been well described, few studies have examined the genetic basis of body size variation in post embryonic developmental stages. In this study, seven candidate genes-PLIN1, LIPE, PNPLA1, SCD, FABP5, KRT10 and IVL-significantly associated with body size were identified in Min pigs, on the basis of weighted gene co-expression network analysis (WGCNA), and most of their functions were found to be associated with lipid deposition. Six candidate genes except for IVL were found to have been subjected to purifying selection. PLIN1 had the lowest ω value (0.139) and showed heterogeneous selective pressure among domestic pig lineages with different body sizes (p < 0.05). These results suggested that PLIN1 is an important genetic factor regulating lipid deposition and consequently affecting body size variation in pigs. The culture of whole pig sacrifice in Manchu during the Qing Dynasty in China might have contributed to the strong artificial domestication and selection of Hebao pigs.
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23
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Gressier C. Mutualism on Australian heritage breed farms. ANTHROPOLOGY TODAY 2023. [DOI: 10.1111/1467-8322.12782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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24
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Kavesh MA. Donkey trade: Challenges to sustaining mutualism in rural Pakistan. ANTHROPOLOGY TODAY 2023. [DOI: 10.1111/1467-8322.12786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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25
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The past 12,000 years of behavior, adaptation, population, and evolution shaped who we are today. Proc Natl Acad Sci U S A 2023; 120:e2209613120. [PMID: 36649411 PMCID: PMC9942852 DOI: 10.1073/pnas.2209613120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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26
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Sun CF, Zhang XH, Dong JJ, You XX, Tian YY, Gao FY, Zhang HT, Shi Q, Ye X, Shi Q, Ye X. Whole-genome resequencing reveals recent signatures of selection in five populations of largemouth bass ( Micropterus salmoides). Zool Res 2023; 44:78-89. [PMID: 36349358 PMCID: PMC9841193 DOI: 10.24272/j.issn.2095-8137.2022.274] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Largemouth bass ( Micropterus salmoides) is an economically important fish species in North America, Europe, and China. Various genetic improvement programs and domestication processes have modified its genome sequence through selective pressure, leaving nucleotide signals that can be detected at the genomic level. In this study, we sequenced 149 largemouth bass fish, including protospecies (imported from the US) and improved breeds (four domestic breeding populations from China). We detected genomic regions harboring certain genes associated with improved traits, which may be useful molecular markers for practical domestication, breeding, and selection. Subsequent analyses of genetic diversity and population structure revealed that the improved breeds have undergone more rigorous genetic changes. Through selective signal analysis, we identified hundreds of putative selective sweep regions in each largemouth bass line. Interestingly, we predicted 103 putative candidate genes potentially subjected to selection, including several associated with growth (p sst1 and grb10), early development ( klf9, sp4, and sp8), and immune traits ( pkn2, sept2, bcl6, and ripk2). These candidate genes represent potential genomic landmarks that could be used to improve important traits of biological and commercial interest. In summary, this study provides a genome-wide map of genetic variations and selection footprints in largemouth bass, which may benefit genetic studies and accelerate genetic improvement of this economically important fish.
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Affiliation(s)
- Cheng-Fei Sun
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Xin-Hui Zhang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun-Jian Dong
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Xin-Xin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan-Yuan Tian
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Feng-Ying Gao
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - He-Tong Zhang
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China,E-mail:
| | - Xing Ye
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China,
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Piva HC. Semiotically Mediated Human-Bee Communication in the Practice of Brazilian Meliponiculture. BIOSEMIOTICS 2022; 16:105-124. [PMID: 36620503 PMCID: PMC9803400 DOI: 10.1007/s12304-022-09519-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
UNLABELLED Stingless bees are among the most dominant pollinators in the south tropics. As such, the rational beekeeping of stingless bee species, called meliponiculture, is an ancient and relevant activity, related to sustainable agricultural development, and which connects traditional knowledge to innovation and novelty. Given the relevance of this topic, this paper discusses the possibilities of a semiotically mediated communication between humans and Meliponini (stingless bees). Zoosemiotics, as the studies of animal views of the world, is the ideal modelling system for the investigation of the possibilities of mutual understanding between these two species. Starting from the premise that, for there to be inter-specific communication, there must be a shared code, and that this depends on the biological makeup and sensory apparatus of both organisms involved in the communication process, this research suggests that a possible way to communicate with stingless bees is with the use of olfactory (chemical) signals, since this channel seems to be common to both humans and bees. Considering that for human-animal relations one party must be able to recognize the other (iconic learning), it is revealed that chemical signals do allow bees to recognize individual humans, even going so far as profiling this person as 'not a threat'. Finally, bees are seen to act cooperatively while the beekeeper is taking action to protect and maintain the nest, something that can be interpreted as an opening of semiotic relations, where the bees are deeming the beekeeper as part of their social group. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12304-022-09519-2.
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Pigs as Pets: Early Human Relations with the Sulawesi Warty Pig ( Sus celebensis). Animals (Basel) 2022; 13:ani13010048. [PMID: 36611658 PMCID: PMC9817959 DOI: 10.3390/ani13010048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/15/2022] [Accepted: 12/15/2022] [Indexed: 12/25/2022] Open
Abstract
The Sulawesi warty pig (S. celebensis) is a wild and still-extant suid that is endemic to the Indonesian island of Sulawesi. It has long been theorised that S. celebensis was domesticated and/or deliberately introduced to other islands in Indonesia prior to the advent of the Neolithic farming transition in the region. Thus far, however, there has been no empirical support for this idea, nor have scientists critiqued the argument that S. celebensis was a pre-Neolithic domesticate in detail. Here, it is proposed that early foragers could have formed a relationship with S. celebensis that was similar in essence to the close association between Late Pleistocene foragers in Eurasia and the wild wolf ancestors of domestic dogs. That is, a longstanding practice of hunter-gatherers intensively socialising wild-caught S. celebensis piglets for adoption into human society as companion animals ('pets') may have altered the predator-prey dynamic, brought aspects of wild pig behaviour and reproduction under indirect human selection and control, and caused changes that differentiated human-associated pigs from their solely wild-living counterparts.
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The Flourishing Camel Milk Market and Concerns about Animal Welfare and Legislation. Animals (Basel) 2022; 13:ani13010047. [PMID: 36611656 PMCID: PMC9817819 DOI: 10.3390/ani13010047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/17/2022] [Accepted: 12/19/2022] [Indexed: 12/25/2022] Open
Abstract
The worldwide dromedary milk production has increased sharply since the beginning of this century due to prolonged shelf life, improved food-safety and perceived health benefits. Scientific confirmation of health claims will expand the market of dromedary milk further. As a result, more and more dromedaries will be bred for one purpose only: the highest possible milk production. However, intensive dromedary farming systems have consequences for animal welfare and may lead to genetic changes. Tighter regulations will be implemented to restrict commercialization of raw milk. Protocols controlling welfare of dromedaries and gene databases of milk-dromedaries will prevent negative consequences of intensive farming. In countries where dromedaries have only recently been introduced as production animal, legislators have limited expertise on this species. This is exemplified by an assessment on behalf of the Dutch government, recommending prohibiting keeping this species from 2024 onwards because the dromedary was deemed to be insufficiently domesticated. Implementation of this recommendation in Dutch law would have devastating effects on existing dromedary farms and could also pave the way for adopting similar measures in other European countries. In this paper it is shown that the Dutch assessment lacks scientific rigor. Awareness of breeders and legislators for the increasing knowledge about dromedaries and their products would strengthen the position of dromedaries as one of the most adapted and sustainable animals.
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Wang Y, Zhao Z, Miao X, Wang Y, Qian X, Chen L, Wang C, Li S. eSMC: a statistical model to infer admixture events from individual genomics data. BMC Genomics 2022; 23:827. [PMCID: PMC9748406 DOI: 10.1186/s12864-022-09033-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022] Open
Abstract
Abstract
Background
Inferring historical population admixture events yield essential insights in understanding a species demographic history. Methods are available to infer admixture events in demographic history with extant genetic data from multiple sources. Due to the deficiency in ancient population genetic data, there lacks a method for admixture inference from a single source. Pairwise Sequentially Markovian Coalescent (PSMC) estimates the historical effective population size from lineage genomes of a single individual, based on the distribution of the most recent common ancestor between the diploid’s alleles. However, PSMC does not infer the admixture event.
Results
Here, we proposed eSMC, an extended PSMC model for admixture inference from a single source. We evaluated our model’s performance on both in silico data and real data. We simulated population admixture events at an admixture time range from 5 kya to 100 kya (5 years/generation) with population admix ratio at 1:1, 2:1, 3:1, and 4:1, respectively. The root means the square error is $$\pm 7.61$$
±
7.61
kya for all experiments. Then we implemented our method to infer the historical admixture events in human, donkey and goat populations. The estimated admixture time for both Han and Tibetan individuals range from 60 kya to 80 kya (25 years/generation), while the estimated admixture time for the domesticated donkeys and the goats ranged from 40 kya to 60 kya (8 years/generation) and 40 kya to 100 kya (6 years/generation), respectively. The estimated admixture times were concordance to the time that domestication occurred in human history.
Conclusion
Our eSMC effectively infers the time of the most recent admixture event in history from a single individual’s genomics data. The source code of eSMC is hosted at https://github.com/zachary-zzc/eSMC.
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ICRP PUBLICATION 153 Approved by the Commission in September 2022. Ann ICRP 2022; 51:9-95. [PMID: 36942865 DOI: 10.1177/01466453221142702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Veterinary use of radiation in the diagnosis, management, and treatment of disease has expanded and diversified, as have the corresponding radiological protection concerns. Radiological exposure of personnel involved in veterinary procedures and, where applicable, members of the public providing assistance (e.g. owners or handlers) has always been included within the system of radiological protection. Veterinary practice is now addressed explicitly as the modern complexities associated with this practice warrant dedicated consideration, and there is a need to clarify and strengthen the application of radiological protection principles in this area. The Commission recommends that the system of radiological protection should be applied in veterinary practice principally for the protection of humans, but with explicit attention to the protection of exposed animals. Additionally, consideration should be given to the risk of potential contamination of the environment associated with applications of nuclear medicine in veterinary practice. This publication focuses primarily on justification and optimisation in veterinary practice, and sets the scene for more detailed guidance to follow in future Recommendations. It is intended for a wide-ranging audience, including radiological protection professionals, veterinary staff, students, education and training providers, and members of the public, as an introduction to radiological protection in veterinary practice.© 2022 ICRP. Published by SAGE.
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Wilson LAB. Developmental instability in domesticated mammals. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:484-494. [PMID: 34813170 DOI: 10.1002/jez.b.23108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Measures of fluctuating asymmetry (FA) have been adopted widely as an estimate of developmental instability. Arising from various sources of stress, developmental instability is associated with an organism's capacity to maintain fitness. The process of domestication has been framed as an environmental stress with human-specified parameters, suggesting that FA may manifest to a larger degree among domesticates compared to their wild relatives. This study used three-dimensional geometric morphometric landmark data to (a) quantify the amount of FA in the cranium of six domestic mammal species and their wild relatives and, (b) provide novel assessment of the commonalities and differences across domestic/wild pairs concerning the extent to which random variation arising from the developmental system assimilates into within-population variation. The majority of domestic mammals showed greater disparity for asymmetric shape, however, only two forms (Pig, Dog) showed significantly higher disparity as well as a higher degree of asymmetry compared to their wild counterparts (Wild Boar, Wolf). Contra to predictions, most domestic and wild forms did not show a statistically significant correspondence between symmetric shape variation and FA, however, a moderate correlation value was recorded for most pairs (r-partial least squares >0.5). Within pairs, domestic and wild forms showed similar correlation magnitudes for the relationship between the asymmetric and symmetric components. In domesticates, new variation may therefore retain a general, conserved pattern in the gross structuring of the cranium, whilst also being a source for response to selection on specific features.
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Affiliation(s)
- Laura A B Wilson
- School of Archaeology and Anthropology, The Australian National University, Canberra, ACT, Australia
- School of Biological, Earth, and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
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Huanel OR, Quesada-Calderón S, Ríos Molina C, Morales-González S, Saenz-Agudelo P, Nelson WA, Arakaki N, Mauger S, Faugeron S, Guillemin ML. Pre-domestication bottlenecks of the cultivated seaweed Gracilaria chilensis. Mol Ecol 2022; 31:5506-5523. [PMID: 36029170 DOI: 10.1111/mec.16672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 08/02/2022] [Accepted: 08/09/2022] [Indexed: 12/24/2022]
Abstract
Gracilaria chilensis is the main cultivated seaweed in Chile. The low genetic diversity observed in the Chilean populations has been associated with the over-exploitation of natural beds and/or the founder effect that occurred during post-glacial colonization from New Zealand. How these processes have affected its evolutionary trajectory before farming and incipient domestication is poorly understood. In this study, we used 2232 single nucleotide polymorphisms (SNPs) to assess how the species' evolutionary history in New Zealand (its region of origin), the founder effect linked to transoceanic dispersion and colonization of South America, and the recent over-exploitation of natural populations have influenced the genetic architecture of G. chilensis in Chile. The contrasting patterns of genetic diversity and structure observed between the two main islands in New Zealand attest to the important effects of Quaternary glacial cycles on G. chilensis. Approximate Bayesian Computation (ABC) analyses indicated that Chatham Island and South America were colonized independently near the end of the Last Glacial Maximum and emphasized the importance of coastal and oceanic currents during that period. Furthermore, ABC analyses inferred the existence of a recent and strong genetic bottleneck in Chile, matching the period of over-exploitation of the natural beds during the 1970s, followed by rapid demographic expansion linked to active clonal propagation used in farming. Recurrent genetic bottlenecks strongly eroded the genetic diversity of G. chilensis prior to its cultivation, raising important challenges for the management of genetic resources in this incipiently domesticated species.
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Affiliation(s)
- Oscar R Huanel
- Núcleo Milenio MASH, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.,IRL 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Roscoff, France
| | - Suany Quesada-Calderón
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,AUSTRAL-omics, Vicerrectoría de Investigación, Desarrollo y Creación Artística, Universidad Austral de Chile, Valdivia, Chile
| | - Cristian Ríos Molina
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Sarai Morales-González
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Pablo Saenz-Agudelo
- IRL 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Roscoff, France.,Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,ANID- Millennium Science Initiative Nucleus (NUTME), Las Cruces, Chile
| | - Wendy A Nelson
- National Institute of Water and Atmospheric Research, Wellington, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Natalia Arakaki
- Instituto del Mar del Perú, Banco de Germoplasma de Organismos Acuáticos, Chucuito, Callao, Peru
| | - Stéphane Mauger
- IRL 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Roscoff, France
| | - Sylvain Faugeron
- Núcleo Milenio MASH, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.,IRL 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Roscoff, France
| | - Marie-Laure Guillemin
- IRL 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Roscoff, France.,Núcleo Milenio MASH, Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
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Xu B, Yang G, Jiao B, Zhu H. Analysis of ancient and modern horse genomes reveals the critical impact of lncRNA-mediated epigenetic regulation on horse domestication. Front Genet 2022; 13:944933. [PMID: 36276948 PMCID: PMC9579347 DOI: 10.3389/fgene.2022.944933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/08/2022] [Indexed: 11/22/2022] Open
Abstract
Background: The domestication of horses has played critical roles in human civilizations. The excavation of ancient horse DNA provides crucial data for studying horse domestication. Studies of horse domestication can shed light on the general mechanisms of animal domestication. Objective: We wish to explore the gene transcription regulation by long noncoding RNAs (lncRNAs) that influence horse domestication. Methods: First, we assembled the ancient DNA sequences of multiple horses at different times and the genomes of horses, donkeys, and Przewalski horses. Second, we extracted sequences of lncRNA genes shared in ancient horses and sequences of lncRNA genes and the promoter regions of domestication-critical genes shared in modern horses, modern donkeys, and Przewalski horses to form two sample groups. Third, we used the LongTarget program to predict potential regulatory interactions between these lncRNAs and these domestication-critical genes and analyzed the differences between the regulation in ancient/modern horses and between horses/donkeys/Przewalski horses. Fourth, we performed functional enrichment analyses of genes that exhibit differences in epigenetic regulation. Results: First, genes associated with neural crest development and domestication syndrome are important targets of lncRNAs. Second, compared with undomesticated Przewalski horses, more lncRNAs participate in the epigenetic regulation in modern horses and donkeys, suggesting that domestication is linked to more epigenetic regulatory changes. Third, lncRNAs’ potential target genes in modern horses are mainly involved in two functional areas: 1) the nervous system, behavior, and cognition, and 2) muscle, body size, cardiac function, and metabolism. Conclusion: Domestication is linked to substantial epigenetic regulatory changes. Genes associated with neural crest development and domestication syndrome underwent noticeable lncRNA-mediated epigenetic regulation changes during horse domestication.
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Affiliation(s)
- Baoyan Xu
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Medical Engineering Department, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Guixian Yang
- Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Baowei Jiao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Science, Kunming, China
| | - Hao Zhu
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- *Correspondence: Hao Zhu,
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Does the Domestication Syndrome Apply to the Domestic Pig? Not Completely. Animals (Basel) 2022; 12:ani12182458. [PMID: 36139318 PMCID: PMC9495052 DOI: 10.3390/ani12182458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 09/13/2022] [Accepted: 09/13/2022] [Indexed: 01/21/2023] Open
Abstract
The ‘domestication syndrome’ defines a suite of features that domesticated animals possess as the result of the artificial selection operated by Homo sapiens since the Neolithic. An interesting anthropological question is whether such features, including increased tameness and reduced aggression, apply to all domesticated forms. We investigated this issue in the domestic pig (Sus scrofa). We video-recorded and analysed aggression and social play (mostly play-fighting) sessions from piglets (three litters; n = 24) and wild boar hybrids (domestic pig mother x wild boar father; three litters; n = 27) from 6–50 days of age, raised in the same woodland/grassland habitat and extensive farming management (ethical farm ‘Parva Domus’, Cavagnolo, Torino). Play and aggression session structure was assessed via Asymmetry (AI; offensive/defensive pattern balance), Shannon (H′; pattern variability), and Pielou (J; pattern evenness) indices. We found that piglets played more (especially after the 20th day of life) and engaged in less variable and uniform sessions than wild boar hybrids. Compared to hybrids, piglets showed less variable but more frequent (especially when approaching weaning) and asymmetrical aggressive events. Thus, the domestication syndrome does not seem to fully apply to either social play or aggression, possibly because artificial selection has produced greater tameness of pigs towards humans than towards conspecifics.
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Wild Meets Domestic in the Near Eastern Neolithic. Animals (Basel) 2022; 12:ani12182335. [PMID: 36139195 PMCID: PMC9494956 DOI: 10.3390/ani12182335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/03/2022] [Accepted: 09/05/2022] [Indexed: 12/03/2022] Open
Abstract
Simple Summary Many recent theorists argue that reliance on binary oppositions to structure thought is a feature of the modern West, and therefore an inappropriate model for prehistory. While the world is usually more complicated than dualistic models, I suggest their use is not limited to modern Western cultures. Rather, we should determine whether they apply in each instance, and if the terms are defined in the same way. Here, I examine whether inhabitants of the earlier Neolithic in the Near East, the time of the first livestock herding, distinguished between wild and domestic animals. Lacking written records, I analyze imagery and animal remains. Zooarchaeologists use demographic profiles, size change, and other data to assess whether ancient people hunted or herded animals. I add contextual analysis to identify special treatment of animal remains that indicates they have ritual power, and choices in animal depictions. Three case studies each present windows into how animals were valued, showing that wild and domestic animals were treated differently, and thus a wild/domestic conceptual distinction existed. Moreover, differences between wild and domestic animals, and regional differences in the roles of specific species, shaped how both wild and domestic animals spread in the early days of agriculture. Abstract The categories of wild and domestic are one of the classic ways the nature/culture dichotomy manifests itself in human interactions with the environment. Some argue that this distinction is not helpful and a projection of modern thought, and certainly the boundaries are complicated. However, we should try to determine in each case whether it was meaningful to particular people in the past. Here I explore whether wild and domestic were relevant concepts to the inhabitants of the Neolithic Near East in their relations with animals around the time when livestock herding began. Drawing on depictions of animals and the treatment of living animals and their remains, I examine three case studies (Cyprus, Upper Mesopotamia, and Çatalhöyük in central Anatolia) to evaluate whether emic distinctions between wild and domestic existed. I conclude that this was in fact a crucial distinction that shaped economic choices as well as ritual activities. Differential treatment of wild and domestic animals indicates that they were accorded different forms of personhood. The particular nature of human relations with wild animals helped shape the spread of both wild and domestic animals.
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Human-Plant Coevolution: A modelling framework for theory-building on the origins of agriculture. PLoS One 2022; 17:e0260904. [PMID: 36070287 PMCID: PMC9451104 DOI: 10.1371/journal.pone.0260904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 07/21/2022] [Indexed: 11/23/2022] Open
Abstract
The domestication of plants and the origin of agricultural societies has been the focus of much theoretical discussion on why, how, when, and where these happened. The ‘when’ and ‘where’ have been substantially addressed by different branches of archaeology, thanks to advances in methodology and the broadening of the geographical and chronological scope of evidence. However, the ‘why’ and ‘how’ have lagged behind, holding on to relatively old models with limited explanatory power. Armed with the evidence now available, we can return to theory by revisiting the mechanisms allegedly involved, disentangling their connection to the diversity of trajectories, and identifying the weight and role of the parameters involved. We present the Human-Plant Coevolution (HPC) model, which represents the dynamics of coevolution between a human and a plant population. The model consists of an ecological positive feedback system (mutualism), which can be reinforced by positive evolutionary feedback (coevolution). The model formulation is the result of wiring together relatively simple simulation models of population ecology and evolution, through a computational implementation in R. The HPC model captures a variety of potential scenarios, though which conditions are linked to the degree and timing of population change and the intensity of selective pressures. Our results confirm that the possible trajectories leading to neolithisation are diverse and involve multiple factors. However, simulations also show how some of those factors are entangled, what are their effects on human and plant populations under different conditions, and what might be the main causes fostering agriculture and domestication.
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Shev GT, Laffoon JE. Paleodietary reconstruction of endemic rodents from the precolumbian Dominican Republic: Discriminating wild feeding behavior from diets linked to human niche construction activities. INTERNATIONAL JOURNAL OF OSTEOARCHAEOLOGY 2022; 32:976-995. [PMID: 36618439 PMCID: PMC9804766 DOI: 10.1002/oa.3149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/14/2022] [Accepted: 07/27/2022] [Indexed: 06/17/2023]
Abstract
In the Greater Antilles, certain animal taxa that have long been theorized to have been managed by indigenous peoples prior to AD1492, the main candidates being a group of endemic caviomorph rodents known as hutias (Capromyinae). This isotopic study investigates the paleodiets of several species of endemic rodents from three late precolonial sites in the northern Dominican Republic: El Flaco (cal. ad 990-1452), El Carril (cal. ad 1030-1262), and La Entrada (cal. ad 840-900) to assess whether human influence over animal diets can be determined. We examined bone collagen carbon (δ13Cco) and nitrogen (δ15N) and tooth enamel carbon (δ13Cen) isotope values of three species of hutias, Isolobodon portoricensis, Isolobodon montanus, and Plagiodontia aedium, alongside edible rat (Brotomys sp.), and domestic guinea pig (Cavia porcellus). To estimate dietary source contributions, we employed a Bayesian dietary mixing model (FRUITS v.3.0) and ran three different permutations to assess the relative contributions of C3 or C4/CAM plants. The addition of an extra 79 wild C3 and 40 wild C4/CAM plant species' isotope values from published sources to an established isotopic foodweb for the Caribbean region enabled us to discriminate between wild and domestic C3 and C4/CAM plant food sources in two of these models. Our results provide evidence of the significant consumption of domestic C4/CAM plants by some animals. This likely represents maize (Zea mays) consumption, which is known to have been ubiquitously cultivated by indigenous peoples in the region. This is particularly the case for I. portoricensis, as FRUITS modeling suggests that a few individuals consumed C4/CAM plants well beyond their expected natural diets as determined from feeding studies of extant hutia species. This may indicate human influence over endemic rodent diets due to niche construction activities such as horticultural practices and may reflect either opportunistic feeding on human produce or the purposeful supplementation of hutia diets by humans.
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Affiliation(s)
- Gene T. Shev
- Faculty of ArchaeologyLeiden UniversityLeidenThe Netherlands
| | - Jason E. Laffoon
- Faculty of ArchaeologyLeiden UniversityLeidenThe Netherlands
- Geology & Geochemistry ClusterVrije Universiteit AmsterdamAmsterdamThe Netherlands
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Huang G, Peng S, Li Y. Variation of photosynthesis during plant evolution and domestication: implications for improving crop photosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4886-4896. [PMID: 35436322 DOI: 10.1093/jxb/erac169] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/16/2022] [Indexed: 06/14/2023]
Abstract
Studies investigating the mechanisms underlying the variation of photosynthesis along plant phylogeny and especially during domestication are of great importance, and may provide new insights to further improve crop photosynthesis. In the present study, we compiled a database including 542 sets of data of leaf gas exchange parameters and leaf structural and chemical traits in ferns and fern allies, gymnosperms, non-crop angiosperms, and crops. We found that photosynthesis was dramatically improved from ferns and fern allies to non-crop angiosperms, and further increased in crops. The improvement of photosynthesis during phylogeny and domestication was related to increases in carbon dioxide diffusional capacities and, to a lesser extent, biochemical capacity. Cell wall thickness rather than chloroplast surface area facing intercellular airspaces drives the variation of mesophyll conductance. The variation of the maximum carboxylation rate was not related to leaf nitrogen content. The slope of the relationship between mass-based photosynthesis and nitrogen was lower in crops than in non-crop angiosperms. These findings suggest that the manipulation of cell wall thickness is the most promising approach to further improve crop photosynthesis, and that an increase of leaf nitrogen will be less efficient in improving photosynthesis in crops than in non-crop angiosperms.
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Affiliation(s)
- Guanjun Huang
- National Key Laboratory of Crop Genetic Improvement, Ministry of Agriculture Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shaobing Peng
- National Key Laboratory of Crop Genetic Improvement, Ministry of Agriculture Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yong Li
- National Key Laboratory of Crop Genetic Improvement, Ministry of Agriculture Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
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Clement CR. Control is not necessary in domestication. Trends Ecol Evol 2022; 37:823-824. [PMID: 35868882 DOI: 10.1016/j.tree.2022.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 01/08/2023]
Affiliation(s)
- Charles R Clement
- Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2936 - Petrópolis, 69067-375 Manaus, Amazonas, Brazil.
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Bates J. The Fits and Starts of Indian Rice Domestication: How the Movement of Rice Across Northwest India Impacted Domestication Pathways and Agricultural Stories. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.924977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Rice is currently the staple food for over 3.5 billion people and is arguably the most important crop exploited by humans. Understanding how we came to the point where a single crop dominates the lives of almost half of the Earth’s population has major significance for our future, even more so given the climatic instability we face today, as rice is a cereal that is dependent on water to an extreme degree. In this study, the nature of early rice agriculture in South Asia is explored, looking at how this critical crop may have begun to be exploited, cultivated, and then brought under agricultural regimes during the long span between c.6500 and 1500 BC. There is now clear evidence for early Holocene cultivation of rice in the Middle Gangetic plains of northern India, but there is still considerable debate about the timing of when this cultivation began and whether it involved domestication of rice. By 3200 BC, however, rice agriculture was present outside the Ganges in the Indus Civilization. The data show accelerated domestication in the Indus environment and agricultural systems that played a part in later hybridization with the arrival of Chinese rice. Understanding how this move from its place of origin to a new environment may have become entangled in the domestication pathways of South Asia rice prior to the arrival of Chinese rice c.1500 BC are important to the overall rice story, as they play into modern concerns relating to biodiversity and different ways of growing and watering rice.
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Archaeobotanical and chemical investigations on wine amphorae from San Felice Circeo (Italy) shed light on grape beverages at the Roman time. PLoS One 2022; 17:e0267129. [PMID: 35767534 PMCID: PMC9242518 DOI: 10.1371/journal.pone.0267129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 04/02/2022] [Indexed: 11/19/2022] Open
Abstract
We hereby investigate the pitch used for coating three Roman amphorae from San Felice Circeo (Italy) through a multidisciplinary study. The identification of molecular biomarkers by gas chromatography—mass spectrometry is combined with archaeobotanical evidence of pollen and plant tissues of Vitis flowers. Diterpenic chemical markers together with Pinus pollen and wood revealed Pinaceae tar coating. Aporate 3-zonocolpate pollen, identified as Vitis, together with tartaric, malic and pyruvic acids elucidate the grape-fermented nature of the content. Our conclusions open new consideration on the use of grape derivatives that cannot be supported by traditional analytical methods. Based on the finds of aporate Vitis pollen, found also in local modern and Middle Pleistocene samples, we hypothesize the use of autochthonous vines. The presence of a medicinal wine (historically reported as oenanthium) is also considered. We interrogate Vitis pollen capacity to target grapevine domestication, thereby providing innovative tools to understand such an important process. We anticipate our study to encourage a more systematic multidisciplinary approach regarding the analyses of wine amphorae.
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Kanne K. Riding, Ruling, and Resistance: Equestrianism and Political Authority in the Hungarian Bronze Age. CURRENT ANTHROPOLOGY 2022. [DOI: 10.1086/720271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Purugganan MD. What is domestication? Trends Ecol Evol 2022; 37:663-671. [PMID: 35534288 DOI: 10.1016/j.tree.2022.04.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/12/2022] [Accepted: 04/11/2022] [Indexed: 01/06/2023]
Abstract
The nature of domestication is often misunderstood. Most definitions of the process are anthropocentric and center on human intentionality, which minimizes the role of unconscious selection and also excludes non-human domesticators. An overarching, biologically grounded definition of domestication is discussed, which emphasizes its core nature as a coevolutionary process that arises from a specialized mutualism, in which one species controls the fitness of another in order to gain resources and/or services. This inclusive definition encompasses both human-associated domestication of crop plants and livestock as well as other non-human domesticators, such as insects. It also calls into question the idea that humans are themselves domesticated, given that evolution of human traits did not arise through the control of fitness by another species.
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Affiliation(s)
- Michael D Purugganan
- Center for Genomics and Systems Biology, New York University, New York, NY 10011, USA; Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates; Institute for the Study of the Ancient World, New York University, New York, NY 10028, USA.
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The Feeding Landscape: Bird and Human Use of Food Resources across a Biocultural Landscape of the Colombian Andes. SUSTAINABILITY 2022. [DOI: 10.3390/su14084789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Agriculture impacts both human welfare and biodiversity at the same time. Still, social and ecological assessments have commonly analyzed the relevance of agroecosystems separately. We evaluated the human and avian feeding use of the biocultural landscape in Jardín, Colombia, using a socioecological approach. Together with farmers, we identified the main socioecological units of the landscape (i.e., fincas, grazing lands, town, forests) and determined the use of each unit in terms of food foraging from forests, crop cultivation, cattle grazing, food commercialization, and food industrialization. We compared the richness of the food resources produced among finca sections (i.e., gardens, coffee–banana plantations, grazing lands). Then, we surveyed avian behavior to contrast the richness of bird species, feeding use and intensity, and food types consumed by birds among the units. Fincas were shown to play a pivotal role in feeding both humans and birds. Gardens provide food for people as well as nectarivore and frugivore birds. Coffee–banana plantations are economically relevant, but their food provision is limited and could be enhanced by increasing the diversity of the food crops within them. The town supports commerce and granivorous birds, whereas grazing lands have limited feeding importance. Forests are used by birds to capture invertebrates but do not supply much food for the people. Our approach fosters the identification of key socioecological units, demonstrating that studying both humans and wildlife enhances the comprehension of biocultural landscapes.
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Zarazúa-Carbajal M, Chávez-Gutiérrez M, Peña-Mondragón JL, Casas A. Ecological Knowledge and Management of Fauna Among the Mexicatl of the Sierra Negra, México: An Interpretive Approach. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.760805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Generally motivated by the relevance of animals in human subsistence, the management of fauna has taken different shapes throughout the world. This study aims to analyse a typology of management forms, exploring their relationship with the motivation to maintain coexistence and use of fauna and mitigate negative human-fauna interactions by the Mexicatl (Nahua) people in Central Mexico. We generally expected to find a broad spectrum of management types in a gradient of interactions intensity. This is because we hypothesised that the more meaningful these interactions due to the magnitude of benefit or damage, philias, or phobias among other positive or negative perceptions, and ecological aspects and management viability, the more actions and practices might be motivated to maintain or mitigate them. We conducted a qualitative research based on interpretivist approaches, mixing qualitative and quantitative analyses, to register the Mexicatl names of fauna present in the area and recognised by locals and to analyse the influence of local ecological knowledge (LEK) and natural history as perceived by people on the use, conflicts, and management practices regarding local fauna. In order to gather such information, in 2018 and 2019 we generated 356 free lists of fauna and 20 sessions of group interviews about the presence of animals in the area, the Mexicatl name, information on distribution, diet, use, management, and other facts. We used visual stimuli with children and young people from schools of basic and intermediate levels in five rural communities and the municipal head of Coyomeapan, Puebla. We also generated free lists and in-depth interviews with 18 persons older than 16 years. People recognised 114 animal items, the most salient being 11 domestic and 14 wild animals including deer, medium and small mammals, snakes, and birds. For both domestic and wild fauna, people reported 18 use categories and three types of damage (crop losses, predation of domestic animals, and damages to health). LEK interacted with traditional celebrations, religious beliefs, land tenure, and migration to define preferences and management types of fauna. Bushmeat demand, especially for Mazama temama and Cuniculus paca, was related to a perception of healthy nutrition properties. Management actions included husbandry of domestic animals, extraction of wild animals for supply, or to avoid damages, captivity, tolerance to damage, protection of seeds and domestic animals threatened by wild fauna, regulations for extraction of wild fauna, and agreements to prevent conflicts. Mixed quantitative and qualitative approaches allowed the interpretation of the human-fauna interactions related to subsistence, coexistence, and the high relevance of LEK, perceptions, religious beliefs, ecosystem, socio-demographic factors, and animal behaviour and habits, which are crucial factors that influence the shaping of management practices. Local management strategies of fauna were diverse and contribute to biocultural conservation and theoretical construction on domestication.
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Gutaker RM, Chater CCC, Brinton J, Castillo-Lorenzo E, Breman E, Pironon S. Scaling up neodomestication for climate-ready crops. CURRENT OPINION IN PLANT BIOLOGY 2022; 66:102169. [PMID: 35065528 DOI: 10.1016/j.pbi.2021.102169] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/15/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
We can increase the stability of our food systems against environmental variability and climate change by following the footsteps of our ancestors and domesticating edible wild plants. Reinforced by recent advances in comparative genomics and gene editing technologies, neodomestication opens possibilities for a rapid generation of new crops. By starting the candidate selection pipeline with climatic parameters, we orient neodomestication efforts to increase food security against climate change. We highlight the fact that the edible species conservation and characterization will be key in this process. Utilization of genetic resources, entrusted to conservationists and researchers by local communities, has to be conducted with highest ethical standards and benefit-sharing in mind.
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Affiliation(s)
- Rafal M Gutaker
- Royal Botanic Gardens, Kew, Kew Green, Richmond, Surrey, TW9 3AE, UK.
| | - Caspar C C Chater
- Royal Botanic Gardens, Kew, Kew Green, Richmond, Surrey, TW9 3AE, UK
| | - Jemima Brinton
- Royal Botanic Gardens, Kew, Kew Green, Richmond, Surrey, TW9 3AE, UK
| | - Elena Castillo-Lorenzo
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath, West Sussex, RH17 6TN, UK
| | - Elinor Breman
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath, West Sussex, RH17 6TN, UK
| | - Samuel Pironon
- Royal Botanic Gardens, Kew, Kew Green, Richmond, Surrey, TW9 3AE, UK.
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Eda M, Itahashi Y, Kikuchi H, Sun G, Hsu KH, Gakuhari T, Yoneda M, Jiang L, Yang G, Nakamura S. Multiple lines of evidence of early goose domestication in a 7,000-y-old rice cultivation village in the lower Yangtze River, China. Proc Natl Acad Sci U S A 2022; 119:e2117064119. [PMID: 35254874 PMCID: PMC8944903 DOI: 10.1073/pnas.2117064119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/10/2022] [Indexed: 11/25/2022] Open
Abstract
Poultry are farmed globally, with chicken (Gallus gallus domesticus) being the leading domesticated species. Although domestic chicken bones have been reported from some Early Holocene sites, their origin is controversial and there is no reliable domestic chicken bone older than the Middle Holocene. Here, we studied goose bones from Tianluoshan—a 7,000-y-old rice cultivation village in the lower Yangtze River valley, China—using histological, geochemical, biochemical, and morphological approaches. Histological analysis revealed that one of the bones was derived from a locally bred chick, although no wild goose species breed in southern China. The analysis of oxygen-stable isotope composition supported this observation and further revealed that some of the mature bones were also derived from locally bred individuals. The nitrogen-stable isotope composition showed that locally bred mature birds fed on foods different from those eaten by migrant individuals. Morphological analysis revealed that the locally bred mature birds were homogenous in size, whereas radiocarbon dating clearly demonstrated that the samples from locally bred individuals were ∼7,000 y old. The histological, geochemical, biochemical, morphological, and contextual evidence suggest that geese at Tianluoshan village were at an early stage of domestication. The goose population appears to have been maintained for several generations without the introduction of individuals from other populations and may have been fed cultivated paddy rice. These findings indicate that goose domestication dates back 7,000 y, making geese the oldest domesticated poultry species in history.
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Affiliation(s)
- Masaki Eda
- Hokkaido University Museum, Hokkaido University, Hokkaido 060-0810, Japan
| | - Yu Itahashi
- Faculty of Humanities and Social Sciences, University of Tsukuba, Ibaraki 305-8571, Japan
- The University Museum, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hiroki Kikuchi
- Department of Archaeology and Museology, Lanzhou University, Gansu 730020, China
| | - Guoping Sun
- Zhejiang Provincial Institute of Cultural Relics and Archaeology, Zhejiang 310012, China
| | - Kai-hsuan Hsu
- Graduate School of Humanities and Human Sciences, Hokkaido University, Hokkaido 060-0810, Japan
| | - Takashi Gakuhari
- Center for the Study of Ancient Civilizations and Cultural Resources, Kanazawa University, Ishikawa 920-1192, Japan
| | - Minoru Yoneda
- The University Museum, The University of Tokyo, Tokyo 113-0033, Japan
| | - Leping Jiang
- Zhejiang Provincial Institute of Cultural Relics and Archaeology, Zhejiang 310012, China
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Kuo WH, Liu SH, Chang CC, Hsieh CL, Li YH, Ito T, Won H, Kokubugata G, Chung KF. Plastome phylogenomics of Allaeanthus, Broussonetia and Malaisia (Dorstenieae, Moraceae) and the origin of B. × kazinoki. JOURNAL OF PLANT RESEARCH 2022; 135:203-220. [PMID: 35080694 DOI: 10.1007/s10265-022-01369-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Species of Broussonetia have been essential in the development of papermaking technology. In Japan and Korea, a hybrid between B. monoica and B. papyrifera (= B. × kazinoki) known as kōzo and daknamu is still the major source of raw materials for making traditional paper washi and hanji, respectively. Despite their cultural and practical significance, however, the origin and taxonomy of kōzo and daknamu remain controversial. Additionally, the long-held generic concept of Broussonetia s.l., which included Sect. Allaeanthus and Sect. Broussonetia, was challenged as phylogenetic analyses showed Malaisia is sister to the latter section. To re-examine the taxonomic proposition that recognizes Allaeanthus, Broussonetia, and Malaisia (i.e., Broussonetia alliance), plastome and nuclear ribosomal DNA (nrDNA) sequences of six species of the alliance were assembled. Characterized by the canonical quadripartite structure, genome alignments and contents of the six plastomes (160,121-162,594 bp) are highly conserved, except for the pseudogenization and/or loss of the rpl22 gene. Relationships of the Broussonetia alliance are identical between plastome and nrDNA trees, supporting the maintenance of Malaisia and the resurrection of Allaeanthus. The phylogenomic relationships also indicate that the monoecy in B. monoica is a derived state, possibly resulting from hybridization between the dioecious B. kaempferi (♀) and B. papyrifera (♂). Based on the hypervariable ndhF-rpl32 intergenic spacer selected by sliding window analysis, phylogeographic analysis indicates that B. monoica is the sole maternal parent of B. × kazinoki and that daknamu carries multiple haplotypes, while only one haplotype was detected in kōzo. Because hybridizations between B. monoica and B. papyrifera are unidirectional and have occurred rarely in nature, our data suggest that daknamu might have originated via deliberate hybrid breeding selected for making hanji in Korea. On the contrary, kōzo appears to have a single origin and the possibility of a Korean origin cannot be ruled out.
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Affiliation(s)
- Wen-Hsi Kuo
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan
- Department of Biology, Washington University, St. Louis, MO, USA
| | - Shih-Hui Liu
- Department of Biological Sciences, National Sun Yat- sen University, Kaohsiung, Taiwan
| | - Chiung-Chih Chang
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan
| | - Chia-Lun Hsieh
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan
| | - Yi-Hsuan Li
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan
| | - Takuro Ito
- The Center for Academic Resources and Archives/Botanical Gardens, Tohoku University, Sendai, Miyagi, Japan
| | - Hyosig Won
- Department of Biological Science and Institute of Natural Sciences, Daegu University, Gyungsan, Gyungbuk, South Korea
| | - Goro Kokubugata
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan
| | - Kuo-Fang Chung
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan.
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Marco S, Loredana M, Riccardo V, Raffaella B, Walter C, Luca N. Microbe-assisted crop improvement: a sustainable weapon to restore holobiont functionality and resilience. HORTICULTURE RESEARCH 2022; 9:uhac160. [PMID: 36204199 PMCID: PMC9531342 DOI: 10.1093/hr/uhac160] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/22/2022] [Accepted: 07/08/2022] [Indexed: 06/16/2023]
Abstract
In the past years, breeding programs have been mainly addressed on pushing the commercial features, forgetting important traits, such as those related to environmental stress resilience, that are instead present in wild relatives. Among the traits neglected by breeding processes, the ability to recruit beneficial microorganisms that recently is receiving a growing attention due to its potentiality. In this context, this review will provide a spotlight on critical issues of the anthropocentric point of view that, until now, has characterized the selection of elite plant genotypes. Its effects on the plant-microbiome interactions, and the possibility to develop novel strategies mediated by the exploitation of beneficial root-microbe interactions, will be discussed. More sustainable microbial-assisted strategies might in fact foster the green revolution and the achievement of a more sustainable agriculture in a climatic change scenario.
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Affiliation(s)
| | | | - Velasco Riccardo
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano (TV), Italy
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