The relations between evolution and domestication reconsidered - Implications for systematics, ecology, and nature conservation

The Study of Geographical Distribution in the Analysis of Domestication as an Evolutionary Process: Tensions in Alphonse de Candolle's Approach

Interest in the study of domesticated plants increased near the end of the 18th century, mainly because of their economic potential. In the 19th century, there was a new focus on the historical understanding of species, their origin, changes in their distribution, and their evolutionary history. Charles Darwin developed an extended interpretation of species domestication, considering variations, reproduction, inheritance, and modification as standard processes between wild and domesticated organisms. In this context, one relatively neglected aspect was the geographical distribution of domesticated species. Alphonse de Candolle addressed and developed in detail the question of the geographical origin of cultivated plants. Since 1836 Alphonse de Candolle had been studying the topic and obtained evidence that contributed to understanding aspects such as the center of origin, dispersion, competition, selection, and time of domestication. Although Darwin himself admitted that Géographie botanique raisonnée (de Candolle, Alphonse,de. Géographie botanique raisonnée; ou, exposition des faits principaux et des lois concernant la distribution géographique des plantes de l'epoque actuelle, 2ème tome. Paris: Masson.) was of great help to him in the development of his evolutionary theory, the importance of de Candolle's contribution is seldom recognized. Our purpose is to detail the dialogue between Alphonse de Candolle and Darwin on the geography of domesticated plants, to understand some of the most critical discussions that contributed to the reinterpretation of domestication under the Darwinian proposal of modified descent.

Genomic analysis unveils reduced genetic variability but increased proportion of heterozygotic genotypes of the intensively managed mezcal agave, Agave angustifolia

PREMISE

The central Oaxaca Basin has a century-long history of agave cultivation and is hypothesized to be the region of origin of other cultivated crops. Widely cultivated for mezcal production, the perennial crop known as "espadín" is putatively derived from wild Agave angustifolia. Nevertheless, little is known about its genetic relationship to the wild A. angustifolia or how the decades-long clonal propagation has affected its genetics.

METHODS

Using restriction-site-associated DNA sequencing and over 8000 single-nucleotide polymorphisms, we studied aspects of the population genomics of wild and cultivated A. angustifolia in Puebla and Oaxaca, Mexico. We assessed patterns of genetic diversity, inbreeding, distribution of genetic variation, and differentiation among and within wild populations and plantations.

RESULTS

Genetic differentiation between wild and cultivated plants was strong, and both gene pools harbored multiple unique alleles. Nevertheless, we found several cultivated individuals with high genetic affinity with wild samples. Higher heterozygosity was observed in the cultivated individuals, while in total, they harbored considerably fewer alleles and presented higher linkage disequilibrium compared to the wild plants. Independently of geographic distance among sampled plantations, the genetic relatedness of the cultivated plants was high, suggesting a common origin and prevalent role of clonal propagation.

CONCLUSIONS

The considerable heterozygosity found in espadín is contained within a network of highly related individuals, displaying high linkage disequilibrium generated by decades of clonal propagation and possibly by the accumulation of somatic mutations. Wild A. angustifolia, on the other hand, represents a significant genetic diversity reservoir that should be carefully studied and conserved.

Going Wild in the City-Animal Feralization and Its Impacts on Biodiversity in Urban Environments

Domestication describes a range of changes to wild species as they are increasingly brought under human selection and husbandry. Feralization is the process whereby a species leaves the human sphere and undergoes increasing natural selection in a wild context, which may or may not be geographically adjacent to where the originator wild species evolved prior to domestication. Distinguishing between domestic, feral, and wild species can be difficult, since some populations of so-called "wild species" are at least partly descended from domesticated "populations" (e.g., junglefowl, European wild sheep) and because transitions in both directions are gradual rather than abrupt. In urban settings, prior selection for coexistence with humans provides particular benefit for a domestic organism that undergoes feralization. One risk is that such taxa can become invasive not just at the site of release/escape but far away. As humanity becomes increasingly urban and pristine environments rapidly diminish, we believe that feralized populations also hold conservation value.

Renewing Lost Genetic Variability with a Classical Yeast Genetics Approach

Due to their long domestication time course, many industrial Saccharomyces cerevisiae strains are adopted in numerous processes mostly for historical reasons instead of scientific and technological needs. As such, there is still significant room for improvement for industrial yeast strains relying on yeast biodiversity. This paper strives to regenerate biodiversity with the innovative application of classic genetic methods to already available yeast strains. Extensive sporulation was indeed applied to three different yeast strains, specifically selected for their different origins as well as backgrounds, with the aim of clarifying how new variability was generated. A novel and easy method to obtain mono-spore colonies was specifically developed, and, to reveal the extent of the generated variability, no selection after sporulation was introduced. The obtained progenies were then tested for their growth in defined mediums with high stressor levels. A considerable and strain-specific increase in both phenotypic and metabolomic variability was assessed, and a few mono-spore colonies were found to be of great interest for their future exploitation in selected industrial processes.

Changes in Neuropeptide Prohormone Genes among Cetartiodactyla Livestock and Wild Species Associated with Evolution and Domestication

The impact of evolution and domestication processes on the sequences of neuropeptide prohormone genes that participate in cell–cell signaling influences multiple biological process that involve neuropeptide signaling. This information is important to understand the physiological differences between Cetartiodactyla domesticated species such as cow, pig, and llama and wild species such as hippopotamus, giraffes, and whales. Systematic analysis of changes associated with evolutionary and domestication forces in neuropeptide prohormone protein sequences that are processed into neuropeptides was undertaken. The genomes from 118 Cetartiodactyla genomes representing 22 families were mined for 98 neuropeptide prohormone genes. Compared to other Cetartiodactyla suborders, Ruminantia preserved PYY2 and lost RLN1. Changes in GNRH2, IAPP, INSL6, POMC, PRLH, and TAC4 protein sequences could result in the loss of some bioactive neuropeptides in some families. An evolutionary model suggested that most neuropeptide prohormone genes disfavor sequence changes that incorporate large and hydrophobic amino acids. A compelling finding was that differences between domestic and wild species are associated with the molecular system underlying ‘fight or flight’ responses. Overall, the results demonstrate the importance of simultaneously comparing the neuropeptide prohormone gene complement from close and distant-related species. These findings broaden the foundation for empirical studies about the function of the neuropeptidome associated with health, behavior, and food production.

Humans, megafauna and landscape structure – Rock engravings from Namibia encourage a comparative approach to central Europe and southern Africa

This paper deals with reflections that arose after observing prehistoric rock engravings at different locations in Namibia. These observations stimulated comparative considerations with focus on southern Africa and central Europe. Similar to the Aurignacian rock art of European origin, the most common motifs in the Namibian rock engravings are large animals. While in Europe, the species that served as a blueprint for the illustration of Aurignacian rock art have mostly disappeared, the megafauna illustrated on the rock engravings in Namibia can still be found in the immediate vicinity of the rock art. Against this background, we discuss and further develop a comparative regional approach. We reconstruct and evaluate the suitability of African savannas and still-existing megafauna communities as an appropriate reference-frame for natural European grassland systems and extinct associated warm-adapted megafauna (Eemian Interglacial megafauna). Special attention is laid on the unique situation in Africa in the light of a global extinction wave of megafauna following increasing human activity in the Late Quaternary. This leads us to discuss the use of domesticated ungulates as surrogate taxa to fulfill ecosystem functions in Europe as part of concepts termed “rewilding” or “naturalistic grazing”. After critically examining these concepts, we conclude that using domesticated forms as representatives of extinct or locally disappeared species in Europe has its justification to some extent. If, however, the naturally occurring megaherbivore community still exists (Africa), these naturally occurring species should be given priority due to their organismic abilities and limitations adapted to the harsh conditions in their specific environment. Finally, we discuss the application of (transboundary) protected areas as effective instruments to mitigate human-wildlife conflicts. A holistic approach, including nature conservation and preservation of cultural achievements (domesticated forms, grazing systems), appears promising for the effective protection of the natural African savanna ecosystems with their unique fauna elements, as illustrated in rock engravings that inspired us to write this paper.

Disentangling the Multidimensional Relationship between Livestock Breeds and Ecosystem Services

Simple Summary

Livestock breeds represent the diversity of livestock animals. They participate in the delivery of ecosystem services (ES), i.e., the benefits to humans provided by nature. In recent years, the contribution of livestock breeds to ES has received attention in livestock research. Additionally, there is increasing interest in integrating this knowledge into policies to make agriculture more sustainable. In this work, we elaborate on livestock breed characteristics that are key to the study of livestock breed contributions to ES. Thus, we explore the natural and human factors that have produced livestock breeds as ecologically and culturally mediated entities. In addition, we review the different roles of livestock breeds as biodiversity components. Finally, we examine how livestock breeds participate in livestock system heterogeneity. By integrating these aspects, we might better understand how livestock breeds provide and modulate ES provision and, therefore, how to improve breed conservation and livestock policies toward more sustainable farming.

Abstract

There is an increasing interest in assessing livestock breed contributions to ecosystem services (ES) and including this knowledge in decision making. However, this task has been limited due to the complexity of the multidimensional relationship between livestock diversity and ecosystem services. In this work, we elaborate on the livestock breed characteristics central to developing a comprehensive approach to livestock breed inclusion in the ecosystem services framework. Thus, we explore the multidimensional nature of livestock breeds, i.e., as eco-cultural entities, biodiversity components, and drivers of livestock system heterogeneity and functioning. First, anthropogenic and natural factors have acted jointly to develop breeds as eco-cultural entities. This fact represents an opportunity to move toward farming system sustainability by Nature-Based Solutions and Nature’s Contribution to People paradigms. Second, livestock breeds are components of biodiversity, and as such, can be framed as goods, as final ecosystem services, and as regulators of ecosystem processes. Third, livestock breeds contribute to livestock system heterogeneity and resilience. By integrating these aspects, we might better understand how livestock breeds provide and modulate ecosystem service provision and, therefore, how to improve breed conservation and livestock policies toward farming system sustainability.

Fruit Colour and Novel Mechanisms of Genetic Regulation of Pigment Production in Tomato Fruits

Fruit colour represents a genetic trait with ecological and nutritional value. Plants mainly use colour to attract animals and favour seed dispersion. Thus, in many species, fruit colour coevolved with frugivories and their preferences. Environmental factors, however, represented other adaptive forces and further diversification was driven by domestication. All these factors cooperated in the evolution of tomato fruit, one of the most important in human nutrition. Tomato phylogenetic history showed two main steps in colour evolution: the change from green-chlorophyll to red-carotenoid pericarp, and the loss of the anthocyanic pigmentation. These events likely occurred with the onset of domestication. Then spontaneous mutations repeatedly occurred in carotenoid and phenylpropanoid pathways, leading to colour variants which often were propagated. Introgression breeding further enriched the panel of pigmentation patterns. In recent decades, the genetic determinants underneath tomato colours were identified. Novel evidence indicates that key regulatory and biosynthetic genes undergo mechanisms of gene expression regulation that are much more complex than what was imagined before: post-transcriptional mechanisms, with RNA splicing among the most common, indeed play crucial roles to fine-tune the expression of this trait in fruits and offer new substrate for the rise of genetic variables, thus providing further evolutionary flexibility to the character.

Epigenetic mechanisms in sex determination and in the evolutionary transitions between sexual systems

The hypothesis that epigenetic mechanisms of gene expression regulation have two main roles in vertebrate sex is presented. First, and within a given generation, by contributing to the acquisition and maintenance of (i) the male or female function once during the lifetime in individuals of gonochoristic species; and (ii) the male and female function in the same individual, either at the same time in simultaneous hermaphrodites, or first as one sex and then as the other in sequential hermaphrodites. Second, if environmental conditions change, epigenetic mechanisms may have also a role across generations, by providing the necessary phenotypic plasticity to facilitate the transition: (i) from one sexual system to another, or (ii) from one sex-determining mechanism to another. Furthermore, if the environmental change lasts enough time, epimutations could facilitate assimilation into genetic changes that stabilize the new sexual system or sex-determining mechanism. Examples supporting these assertions are presented, caveats or difficulties and knowledge gaps identified, and possible ways to test this hypothesis suggested.

This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)’.

Back to the Origins: Background and Perspectives of Grapevine Domestication

Domestication is a process of selection driven by humans, transforming wild progenitors into domesticated crops. The grapevine (Vitis vinifera L.), besides being one of the most extensively cultivated fruit trees in the world, is also a fascinating subject for evolutionary studies. The domestication process started in the Near East and the varieties obtained were successively spread and cultivated in different areas. Whether the domestication occurred only once, or whether successive domestication events occurred independently, is a highly debated mystery. Moreover, introgression events, breeding and intense trade in the Mediterranean basin have followed, in the last thousands of years, obfuscating the genetic relationships. Although a succession of studies has been carried out to explore grapevine origin and different evolution models are proposed, an overview of the topic remains pending. We review here the findings obtained in the main phylogenetic and genomic studies proposed in the last two decades, to clarify the fundamental questions regarding where, when and how many times grapevine domestication took place. Finally, we argue that the realization of the pan-genome of grapes could be a useful resource to discover and track the changes which have occurred in the genomes and to improve our understanding about the domestication.

Singular patterns of skull shape and brain size change in the domestication of South American camelids

Patterns of selection in South American camelids (Lamini) and their unique demographic history establish the llama and alpaca as remarkable cases of domestication among large herd animals. Skull shape is implicated in many changes reported between wild and domestic taxa. We apply 3D geometric morphometric methods to describe skull shape, form, and size, differences among the four species of Lamini. In so doing, we test if domesticated Lamini exhibit changes similar to those in other domesticated groups: not only in the skull, but also in brain and body size. In contrast to other domesticated artiodactyls, very little change has occurred in domestic alpacas and llamas compared to their wild counterparts. Nevertheless, their differences are statistically significant and include a flatter cranium, inclined palate and increased airorhynchy in the domestics. Selection pressures that contrast with those on other herd animals, as well as recent population bottlenecks, likely have influenced the morphological patterns we note in Lamini. High-resolution 3D morphospace allows skull size, shape, and form (shape + size), to discriminate all four species, with form providing the greatest separation. These results help differentiate morphologically the Lamini, which in nature are distinguished mainly by body size, and provide an additional tool to archaeologists for distinction of wild and domestic remains. Most of our shape analyses suggest a marginally closer relationship between the alpaca and vicuña, to the exclusion of the guanaco, supporting the genetic relationships for this group. The expected brain size change between wild and domestic populations is lower than previously thought, with a 15.4% reduction in llama, and 6.8% reduction in alpaca. This is the lowest reduction in brain size thus far reported among domesticated Artiodactyla.

Revisiting Cattle Temperament in Beef Cow-Calf Systems: Insights from Farmers' Perceptions about an Autochthonous Breed

Understanding temperament is an important part of cattle production since undesirable temperament may cause serious problems associated with aggression, maternal care, and human safety. However, little is known about how farmers define or assess temperament, especially in autochthonous cattle breeds. The aim of this study was to explore perceptions of farmers about the temperament of the Pyrenean cattle breed with special attention to beef cow-calf systems in Spain. The methodology used to obtain the information was focus group discussions (FGD). Farmers defined temperament as a behavioural response to challenging situations imposed by human handling. Specific terms used were related to active or passive reactions to fear (e.g., "strong", "aggressive", "nervous", "fearful"). The speed of response to stimuli was also important. Female temperament was thought to become more docile with age while bull temperament was more variable. Maternal aggressiveness was highlighted as a potential human safety problem, but also desirable in an extensively bred animal who may need to defend calves against predators. Anatomical characteristics were seen as unreliable predictors of temperament, while behavioural indicators were more widely used, such as "alertness", which was a general trait of the breed, and "gaze", which, when associated with an alert expression, suggests a potential threat. Sensory acuity, such as sight and smell, were thought to be related with temperament in some FGDs but there was no overall agreement as to whether different behavioural responses were due to differences in sensory acuity. The results from the study could be useful during training programs or in the development of new genetic selection schemes and evaluation protocols involving cattle temperament.

Molecules, Mechanisms, and Disorders of Self-Domestication: Keys for Understanding Emotional and Social Communication from an Evolutionary Perspective

The neural crest hypothesis states that the phenotypic features of the domestication syndrome are due to a reduced number or disruption of neural crest cells (NCCs) migration, as these cells differentiate at their final destinations and proliferate into different tissues whose activity is reduced by domestication. Comparing the phenotypic characteristics of modern and prehistoric man, it is clear that during their recent evolutionary past, humans also went through a process of self-domestication with a simultaneous prolongation of the period of socialization. This has led to the development of social abilities and skills, especially language, as well as neoteny. Disorders of neural crest cell development and migration lead to many different conditions such as Waardenburg syndrome, Hirschsprung disease, fetal alcohol syndrome, DiGeorge and Treacher-Collins syndrome, for which the mechanisms are already relatively well-known. However, for others, such as Williams-Beuren syndrome and schizophrenia that have the characteristics of hyperdomestication, and autism spectrum disorders, and 7dupASD syndrome that have the characteristics of hypodomestication, much less is known. Thus, deciphering the biological determinants of disordered self-domestication has great potential for elucidating the normal and disturbed ontogenesis of humans, as well as for the understanding of evolution of mammals in general.

Landscape Transformation Influences Responses of Terrestrial Small Mammals to Land Use Intensity in North-Central Namibia

In this study, we investigate and compare the response patterns of small mammal communities to increasing land use intensity in two study areas: private farmland at the southern boundary of Etosha National Park and smallholder farmland in Tsumeb agricultural area. Species richness, community composition and a standardized capture index (RCI) are compared between sites of (a) increasing grazing pressure of ungulates (Etosha) and (b) increasing conversion of bushland to arable land (Tsumeb). Within each study area, we found clear response patterns towards increasing land use intensity. However, patterns differ significantly between the two areas. Within the less-transformed area (Etosha), high land use intensity results in a decrease in the RCI but not species richness. Small mammal communities remain relatively stable, but ecosystem functions (e.g., bioturbation, seed dispersal) are weakened. Within the more-transformed area (Tsumeb), high land use intensity leads to a decrease in species richness and increasing RCIs of two common pest species. The disappearance of a balanced community and the dramatic increase in a few pest species has the potential to threaten human livelihoods (e.g., crop damage, disease vectors). Our comparative approach clearly indicates that Gerbilliscus leucogaster is a possible candidate for an ecological indicator of ecosystem integrity. Mastomys natalensis has the potential to become an important pest species when bushland is transformed into irrigated arable land. Our results support the importance of area-specific conservation and management measures in savanna ecosystems.

Comparing the tractability of young hand-raised wolves (Canis lupus) and dogs (Canis familiaris)

Dogs live in 45% of households, integrated into various human groups in various societies. This is certainly not true for wolves. We suggest that dogs' increased tractability (meant as individual dogs being easier to control, handle and direct by humans, in contrast to trainability defined as performance increase due to training) makes a crucial contribution to this fundamental difference. In this study, we assessed the development of tractability in hand-raised wolves and similarly raised dogs. We combined a variety of behavioural tests: fetching, calling, obeying a sit signal, hair brushing and walking in a muzzle. Wolf (N = 16) and dog (N = 11) pups were tested repeatedly, between the ages of 3-24 weeks. In addition to hand-raised wolves and dogs, we also tested mother-raised family dogs (N = 12) for fetching and calling. Our results show that despite intensive socialization, wolves remained less tractable than dogs, especially in contexts involving access to a resource. Dogs' tractability appeared to be less context dependent, as they followed human initiation of action in more contexts than wolves. We found no evidence that different rearing conditions (i.e. intensive socialization vs. mother rearing) would affect tractability in dogs. This suggests that during domestication dogs might have been selected for increased tractability, although based on the current data we cannot exclude that the differential speed of development of dogs and wolves or the earlier relocation of wolves to live as a group explains some of the differences we found.

Mapping Shade Availability and Use in Zoo Environments: A Tool for Evaluating Thermal Comfort

For many species in zoos, particularly megafauna vulnerable to heat stress, shade is a key environmental resource. However, shade availability has received comparatively less attention than other aspects of the zoo environment. In this study, we share a simple low-cost approach that we applied to document shade availability across 33 zoo enclosures. We then combined these assessments with behavioral observations of enclosure use and shade-seeking behavior during summer months in a case study focused on Sichuan takin (Budorcas taxicolor tibetana) (n = 3), a large cold-adapted bovid. Behavioral observations were conducted before and after installation of a shade sail for the takin. Results indicated that shade availability varied widely across zoo enclosures, with the percent of shaded space ranging from 85 % to 22 % across enclosures during summer months. Shade was a dynamic resource and increased throughout the year and fluctuated across the day, with the least shade available midday. Takin showed general preferences for shaded areas near the walls of their enclosure but were observed using newly available shade from the shade sail after its installation. These accessible methods can be easily applied to assess shade within existing enclosures, evaluate enclosure modifications, and provide guidance for the design of new enclosures.

Long-Term Socialization with Humans Affects Human-Directed Behavior in Goats

Throughout their evolutionary history, humans have tried to domesticate a variety of wild terrestrial mammals, resulting in a limited number that has been successfully domesticated. Among these domesticated species, domestic goats (Capra aegagrus hircus) are a useful model species to study the effects of ontogenesis on the socio-cognitive abilities of domestic non-companion animals in their interactions with humans. To this end, the behavioral responses of two groups of goats with a different background of human socialization (high and low socialization) were compared in the impossible task test, an experimental paradigm aimed to study socio-cognitive skills and the tendency to interact with humans. Our results show that, when the task became impossible to solve, goats with a higher level of socialization interacted with the experimenter for a greater amount of time than subjects in the low socialization group, whereas the latter group exhibited increased door directed behavior. Overall, highly socialized goats made more social contact with humans compared to the other group in the impossible task paradigm.