An Ecological and Evolutionary Framework for Commensalism in Anthropogenic Environments

Sentinels in the shadows: Exploring Toxoplasma gondii and other Sarcocystidae parasites in synanthropic rodents and their public health implications

Synanthropic rodents play a crucial role in maintaining the life cycle of Toxoplasma gondii in anthropized regions and can serve as indicators of environmental oocyst contamination. This investigation aimed to explore the occurrence of T. gondii infection within synanthropic rodent populations using a molecular diagnostic technique targeting the 18S rDNA gene, which is generic for Coccidia, with subsequent specific PCR confirmation. We examined 97 brown rats (Rattus norvegicus), 67 black rats (R. rattus), 47 house mice (Mus musculus), and 1 common shrew (Sorex araneus). PCR tests were conducted on the brain, heart, and tongue tissues. PCR tested positive in at least one of the examined tissues in 26 R. norvegicus (26.8%), 13 R. rattus (19.4%), and 13 M. musculus (27.6%). Sequencing comparisons by BLAST allowed us to identify four different species of cyst-forming Apicomplexa. In particular, T. gondii DNA was detected in 13 (6.1%) rodents, Hammondia hammondi (including H. hammondi-like organisms) in 36 (17%) subjects, Besnoitia sp. (in two cases identified as B. besnoiti) in 8 (3.7%), and Sarcocystis gigantea in two (0.94%). Rodents from peri-urban and urban environments can act as indicators of environmental contamination by oocysts of apicomplexan parasites with cats as definitive hosts, such as T. gondii, H. hammondi, and S. gigantea, the latter of which has never been previously recorded in rodents. Moreover, the presence of B. besnoiti, a parasite with an unidentified definitive host in Europe, sheds light on the potential role of these hosts as infection sentinels.

The ratting of North America: A 350-year retrospective on Rattus species compositions and competition

While the impacts of black (Rattus rattus) and brown (Rattus norvegicus) rats on human society are well documented-including the spread of disease, broad-scale environmental destruction, and billions spent annually on animal control-little is known about their ecology and behavior in urban areas due to the challenges of studying animals in city environments. We use isotopic and ZooMS analysis of archaeological (1550s-1900 CE) rat remains from eastern North America to provide a large-scale framework for species arrival, interspecific competition, and dietary ecology. Brown rats arrived earlier than expected and rapidly outcompeted black rats in coastal urban areas. This replacement happened despite evidence that the two species occupy different trophic positions. Findings include the earliest molecularly confirmed brown rat in the Americas and show a deep ecological structure to how rats exploit human-structured areas, with implications for understanding urban zoonosis, rat management, and ecosystem planning as well as broader themes of rat dispersal, phylogeny, evolutionary ecology, and climate impacts.

Demographic history and the efficacy of selection in the globally invasive mosquito Aedes aegypti

Aedes aegypti is the main vector species of yellow fever, dengue, zika and chikungunya. The species is originally from Africa but has experienced a spectacular expansion in its geographic range to a large swath of the world, the demographic effects of which have remained largely understudied. In this report, we examine whole-genome sequences from 6 countries in Africa, North America, and South America to investigate the demographic history of the spread of Ae. aegypti into the Americas its impact on genomic diversity. In the Americas, we observe patterns of strong population structure consistent with relatively low (but probably non-zero) levels of gene flow but occasional long-range dispersal and/or recolonization events. We also find evidence that the colonization of the Americas has resulted in introduction bottlenecks. However, while each sampling location shows evidence of a past population contraction and subsequent recovery, our results suggest that the bottlenecks in America have led to a reduction in genetic diversity of only ~35% relative to African populations, and the American samples have retained high levels of genetic diversity (expected heterozygosity of ~0.02 at synonymous sites) and have experienced only a minor reduction in the efficacy of selection. These results evoke the image of an invasive species that has expanded its range with remarkable genetic resilience in the face of strong eradication pressure.

A Survey of Public Opinion on Community Cats' General Health and Relationship Quality with Residents in Urban China

The management and coexistence of community cats in urban areas is a growing concern amid global urbanization. Through a survey-based investigation, we examine the residents' perceptions of the general health of community cats and human-cat relationships in urban China. The data from 5382 participants revealed that approximately 70% of participants perceived community cats as being in good health, and 60% reported harmonious or non-conflict coexistence between residents and these cats. Around 45% of the participants rescued or helped community cats, 38% expressed their intention to adopt, and 18% complained about the issues of community cats to management staff. Linear, logistic, and multilevel-logistic regressions were employed to examine the associations between the types of cities and communities or the participants' socio-demographics and the perceived well-being of community cats or human-cat relationships. The results show that the cats in fourth-tier cities (e.g., county-level cities) had poorer living conditions than in first-tier cities (e.g., Beijing), while the cats in urban village communities (e.g., villages in the city) were less likely to exhibit good health than in ordinary commercial housing communities. The results also show that socio-demographic variables, such as educational attainment, marital status, and income level, predicted participants' relationships with community cats. This study is the first of its kind. It provides valuable insights for stakeholders to develop effective policies and interventions on cat management, emphasizing the need for tailored strategies in diverse urban settings and populations.

Population genomic structure of a widespread, urban-dwelling mammal: The eastern grey squirrel (Sciurus carolinensis)

Urbanization is a persistent and widespread driver of global environmental change, potentially shaping evolutionary processes due to genetic drift and reduced gene flow in cities induced by habitat fragmentation and small population sizes. We tested this prediction for the eastern grey squirrel (Sciurus carolinensis), a common and conspicuous forest-dwelling rodent, by obtaining 44K SNPs using reduced representation sequencing (ddRAD) for 403 individuals sampled across the species' native range in eastern North America. We observed moderate levels of genetic diversity, low levels of inbreeding, and only a modest signal of isolation-by-distance. Clustering and migration analyses show that estimated levels of migration and genetic connectivity were higher than expected across cities and forested areas, specifically within the eastern portion of the species' range dominated by urbanization, and genetic connectivity was less than expected within the western range where the landscape is fragmented by agriculture. Landscape genetic methods revealed greater gene flow among individual squirrels in forested regions, which likely provide abundant food and shelter for squirrels. Although gene flow appears to be higher in areas with more tree cover, only slight discontinuities in gene flow suggest eastern grey squirrels have maintained connected populations across urban areas in all but the most heavily fragmented agricultural landscapes. Our results suggest urbanization shapes biological evolution in wildlife species depending strongly on the composition and habitability of the landscape matrix surrounding urban areas.

Dingoes, companions in life and death: The significance of archaeological canid burial practices in Australia

The dingo, also known as the Australian native dog, was introduced in the late Holocene. Dingoes were primarily wild animals but a number resided in Aboriginal people's camps. Traditionally, these individuals were taken from wild litters before weaning and raised by Aboriginal people. It is generally believed that these dingoes were not directly provided for, and upon sexual maturity, returned to reproduce in the wild. However, some died while in the company of people and, were buried in occupation sites. This Australian practice parallels the burial of domestic dogs in many regions of the Asia-Pacific and beyond but has attracted very little research. We explore the historical and archaeological evidence for dingo burial, examining its different forms, chronological and geographic distribution, and cultural significance. Dingoes were usually buried in the same manner as Aboriginal community members and often in areas used for human burial, sometimes alongside people. This practice probably occurred from the time of their introduction until soon after European colonisation. We present a case study of dingo burials from Curracurrang Rockshelter (NSW) which provides insights into the lives of ancient tame dingoes, and suggests that domestication and genetic continuity between successive camp-dwelling generations may have occurred prior to European contact.

Sharing space between native and invasive small mammals: Study of commensal communities in Senegal

Urbanization processes are taking place at a very high rate, especially in Africa. At the same time, a number of small mammal species, be they native or invasive, take advantage of human-induced habitat modifications. They represent commensal communities of organisms that cause a number of inconveniences to humans, including potential reservoirs of zoonotic diseases. We studied via live trapping and habitat characterization such commensal small mammal communities in small villages to large cities of Senegal, to try to understand how the species share this particular space. Seven major species were recorded, with exotic invasive house mice (Mus musculus) and black rats (Rattus rattus) dominating in numbers. The shrew Crocidura olivieri appeared as the main and more widespread native species, while native rodent species (Mastomys natalensis, M. erythroleucus, Arvicanthis niloticus and Praomys daltoni) were less abundant and/or more localized. Habitat preferences, compared between species in terms of room types and characteristics, showed differences among house mice, black rats and M. natalensis especially. Niche (habitat component) breadth and overlap were measured. Among invasive species, the house mouse showed a larger niche breadth than the black rat, and overall, all species displayed high overlap values. Co-occurrence patterns were studied at the global and local scales. The latter show cases of aggregation (between the black rat and native species, for instance) and of segregation (as between the house mouse and the black rat in Tambacounda, or between the black rat and M. natalensis in Kédougou). While updating information on commensal small mammal distribution in Senegal, a country submitted to a dynamic process of invasion by the black rat and the house mouse, we bring original information on how species occupy and share the commensal space, and make predictions on the evolution of these communities in a period of ever-accelerating global changes.

The Role of Veterinarians in Managing Community Cats: A Contextualized, Comprehensive Approach for Biodiversity, Public Health, and Animal Welfare

Homeless cats are a major problem in Europe, with hundreds of thousands abandoned every year. While many die, others can adapt to a lifestyle of roaming freely and establish community cat populations that tend to cluster together in groups. These groups of cats are typically found in urban areas that offer food and shelter to the cats. Animal welfare organizations often care for these cats, providing them with food, shelter, and medical attention. Despite this, conflicts can arise due to the presence of free-roaming cats, with some individuals advocating for drastic measures such as trapping and killing the cats to reduce their populations. However, it is essential to note that such methods are frequently illegal, inhumane, and ultimately ineffective in most situations. A thorough assessment of the impact of cats on a particular natural area requires a comprehensive cat census, a detailed study of the species being preyed upon, and an investigation into the prevalence of zoonotic or epizootic diseases. Moreover, veterinary experts assert that the public health risks associated with cats are often overstated. This article aims to provide a nuanced perspective on the impact of cats on biodiversity in natural areas, while also discussing their role in transmitting the main zoonotic diseases identified in European countries in recent years, with a particular focus on Spain. Effective cat control programs should focus on non-lethal methods such as trap-neuter-return (TNR) and adoption. TNR has proven to be the most effective and humane method of controlling the free-roaming cat population, but its effectiveness is influenced by several factors, including adoption programs and public education on responsible pet ownership. According to Spanish veterinarians, sustainable and science-based solutions such as TNR programs are the best way to achieve population control of free-roaming cats. The veterinary profession should raise awareness regarding sterilization, vaccination, and identification of cats and the consequences of abandonment. They oppose lethal control and removal of cats from the environment, which are ineffective and unethical methods. To promote animal welfare, veterinary professionals must collaborate with public administrations to implement long-term, sustainable solutions to the problem of cat overpopulation. Greater social awareness regarding the importance of sterilization and identification to prevent abandonment and reduce the number of free-roaming cats is also needed. Despite the challenges presented by homeless cat populations in Spain and the rest of Europe, there are many reasons for optimism. Animal welfare organizations and veterinary professionals are actively collaborating to develop humane and effective solutions to manage community cats, including programs such as TNR and adoption. Furthermore, these initiatives are gaining momentum and support from emerging laws and regulations, such as the recent Spanish animal welfare law. Through these efforts, we can reduce the number of free-roaming cats and improve their quality of life.

Pests or prey? Micromammal species within an ancient anthropic environment at the Norse settlement site of Tuquoy (Westray, Orkney)

Micromammals, like rodents and shrews, adapt rapidly to take advantage of new food sources, habitats and ecological niches, frequently thriving in anthropogenic environments. Their remains, often retrieved during archaeological investigations, can be a valuable source of information about the past environmental conditions as well as interspecies interactions and human activity. However, the research on such finds rarely covers multiple approaches, often relying on single species or data type (e.g. identification/information for proxy studies). Here we investigate micromammal remains from the Norse and medieval (AD tenth-fourteenth centuries) archaeological site at Tuquoy, Orkney, to elucidate the relationships between micromammals, humans and other species present using a variety of data. Four micromammal species were identified, and their species dynamics as well as relationships with humans could be inferred by tracking changes in spatial and temporal location of remains, from their taphonomic history and by age estimation for individual animals. A larger, predatory assemblage was also identified, with species composition differing from that in the rest of the archaeological assemblage, and possibly therefore representing small mammal species composition in the wild. The assemblage was probably deposited by a diurnal raptor, though identification to species is not certain due to post-depositional processes.

Dispersal abilities favor commensalism in animal-plant interactions under climate change

Scientists still poorly understand how biotic interactions and dispersal limitation jointly interact and affect the ability of species to track suitable habitats under climate change. Here, we examine how animal-plant interactions and dispersal limitations might affect the responses of Brazil nut-dependent frogs facing projected climate change. Using ecological niche modelling and dispersal simulations, we forecast the future distributions of the Brazil nut tree and three commensalist frog species over time (2030, 2050, 2070, and 2090) in the regional rivalry (SSP370) scenario that includes great challenges to mitigation and adaptation. With the exception of one species, projections point to a decrease in suitable habitats of up to 40.6%. For frog species with potential reductions of co-occurrence areas, this is expected to reduce up to 23.8% of suitable areas for binomial animal-plant relationships. Even so, biotic interactions should not be lost over time. Species will depend on their own dispersal abilities to reach analogous climates in the future for maintaining ecological and evolutionary processes associated with commensal taxa. However, ecological and evolutionary processes associated with commensal taxa should be maintained in accordance with their own dispersal ability. When dispersal limitation is included in the models, the suitable range of all three frog species is reduced considerably by the end of the century. This highlights the importance of dispersal limitation inclusion for forecasting future distribution ranges when biotic interactions matter.

Carbon and nitrogen isotopic similarity between the endangered Darwin's fox (Lycalopex fulvipes) and sympatric free-ranging dogs in Chiloé Island, Chile

Darwin's fox is an opportunistic omnivorous predator native to Chile classified as endangered by the IUCN Red List. Habitat use by Darwin's foxes can be negatively affected by the presence of free-ranging dogs that range freely across native and non-native habitats and can be a source of fox mortality. The objective of this study was to analyze the isotopic similarity of Darwin's fox and sympatric free-ranging dogs in Chiloé Island to determine the impact of anthropogenic environmental alterations on wild predators. We use hair samples to characterise and compare their δ¹³C and δ¹⁵N values and to evaluate isotopic similarity and isotope niches overlap. A generalised linear model was used to associate the isotope value with landscape variables (forest cover and vegetation type) and distance to the nearest house. We found no significant differences in δ¹³C or δ¹⁵N values between foxes and dogs, and a marginally significant isotope niche overlap (59.4 %). None of the selected variables at landscape and site scale were related to isotope values. Although our study is not a probe of direct contact between foxes and free-ranging dogs, the high isotopic similarity highlights the risk of pathogen spillover from free-ranging dogs to Darwin's foxes.

Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history

The distribution of the black rat (Rattus rattus) has been heavily influenced by its association with humans. The dispersal history of this non-native commensal rodent across Europe, however, remains poorly understood, and different introductions may have occurred during the Roman and medieval periods. Here, in order to reconstruct the population history of European black rats, we first generate a de novo genome assembly of the black rat. We then sequence 67 ancient and three modern black rat mitogenomes, and 36 ancient and three modern nuclear genomes from archaeological sites spanning the 1st-17th centuries CE in Europe and North Africa. Analyses of our newly reported sequences, together with published mitochondrial DNA sequences, confirm that black rats were introduced into the Mediterranean and Europe from Southwest Asia. Genomic analyses of the ancient rats reveal a population turnover in temperate Europe between the 6th and 10th centuries CE, coincident with an archaeologically attested decline in the black rat population. The near disappearance and re-emergence of black rats in Europe may have been the result of the breakdown of the Roman Empire, the First Plague Pandemic, and/or post-Roman climatic cooling.

‘Archaeogenetic analysis of black rat remains reveals that this species was introduced into temperate Europe twice, in the Roman and medieval periods. This population turnover was likely associated with multiple historical and environmental factors.’

In Its Southern Edge of Distribution, the Tawny Owl (Strix aluco) Is More Sensitive to Extreme Temperatures Than to Rural Development

Simple Summary

Tawny Owls occur in a wide range, with Israel being the southernmost country where they occur. This country’s climate is warming rapidly and it also undergoes an extensive urban and agricultural development. However, it is unknown to what extent these processes would endanger the Tawny Owls living there. To gain insight about this question, we surveyed Tawny Owls in the field, tracked the number of hatchlings in their nests, and also analyzed how their diet varied between different environments. We trained models of Tawny Owl distribution, number of hatchlings and diet using climate and land use variables to figure out to what extent climate change and development impact this species’ Israeli population. We found that Tawny Owls prefer relatively cool, rainy and wooded areas within Israel, and occur more often in villages compared to open fields. Tawny Owls raised more hatchlings in pine forests, especially when spring temperatures were moderate and following rainy winters. Tawny Owls preyed predominantly on Günther’s Voles everywhere, but took more birds in rural environments compared to forests. Our results suggest that climate change, which would increase spring temperatures and decrease rainfall, is a larger threat to Tawny Owls in Israel than rural development.

Abstract

Populations at the warm edge of distribution are more genetically diverse, and at the same time are more susceptible to climate change. Between 1987–1996, we studied Tawny Owls in Israel, the species’ global southern edge of distribution and a country undergoing a rapid land cover transformation for over a century. To assess the potential impacts of land cover transformation, we modelled the species’ most suitable habitat and climate and analyzed how climate and habitat affected the nesting success and prey selection. Moreover, we monitored Tawny Owl juveniles’ survival and ontogeny from eggs to dietary independent young, to find out whether the Israeli population is a sink. While the species distribution model correctly predicted the Tawny Owl’s densest areas of occurrence, it failed to predict its occurrence in adjacent regions. The model also predicted that areas included in the species’ historical range remained suitable habitats. The number of fledglings increased with precipitation and in rural settings but was adversely affected by extreme temperatures. While voles dominated the diet in all habitats, the Tawny Owl’s diet is considerably more variable than other Israeli owls. Our results suggest that the Tawny Owl can adapt to rural-agricultural environments, but is susceptible to climate change.

Symbiotic Relationships in Business Ecosystem: A Systematic Literature Review

The business ecosystem shares many unique features with the biological ecosystem due to its origins. Similar to the biological ecosystem, the business ecosystem also emphasizes symbiotic relationships among symbionts (i.e., participants of a business ecosystem). In this study, we have broadened and deepened our knowledge of symbiosis in a business ecosystem, focusing on how each relationship develops and evolves through the interaction between keystone species and symbionts. We have introduced the typology of symbiotic relationships and highlighted the significant role of keystone species in business ecosystems. We defined three symbiosis types based on the analysis results: mutualism, commensalism, and parasitism. The findings indicated that each relationship continuously transitions into different symbiotic relationships as the relationship between the participants changes. The results also showed that a keystone species, a leader of a business ecosystem, can contribute to the success of a business ecosystem by strategically managing their relationship with symbionts.

Wildlife Affordances of Urban Infrastructure: A Framework to Understand Human-Wildlife Space Use

Landscape affordances, what the environment offers an animal, are inherently species-specific to the extent that each taxon has unique needs and responses to landscape characteristics. Wildlife responses to landscape features range on a continuum from avoidance to attraction and quantifying these habits are the backbone of wildlife movement ecology. In anthropogenically modified landscapes, many taxa do not occupy areas heavily influenced by humans, while some species seem to flourish, such as coyotes (Canis latrans) and pigeons (Columba livia). Sufficient overlap in landscapes designed for human purposes (e.g., freeway underpasses, channelized waterways, and cemeteries) but which are also suitable for wildlife (e.g., by providing sources of food, shelter, and refuge) underlies wildlife persistence in urban areas and is increasingly important in the world's largest metropoles. Studying these overlapping worlds of humans and wildlife in cities provides a rich foundation for broadening human perceptions of cities as ecosystems that exhibit emergent hybridity, whereby certain anthropogenic features of urban landscapes can be used by wildlife even as they maintain their utility for humans. By examining scaling dynamics of the infrastructural signature, the phenomena of urban wildlife movement patterns conforming to the shapes of human infrastructural forms, we hope to expand on prior research in wildlife landscape ecology by stressing the importance of understanding the overlapping worlds of humans and wildlife. Further knowledge of the urban ecological commons is necessary to better design cities where emergent hybridity is leveraged toward the management goals of reducing human wildlife conflict and promoting biodiversity.

Genomic analysis unveils mechanisms of northward invasion and signatures of plateau adaptation in the Asian house rat

The Asian house rat (AHR), Rattus tanezumi, has recently invaded the northern half of China. The AHR is a highly adaptive rat species that has also successfully conquered the Qinghai-Tibet Plateau (QTP) and replaced the brown rat (BR), R. norvegicus, at the edge of the QTP. Here, we assembled a draft genome of the AHR and explored the mechanisms of its northward invasion and the genetic basis underlying plateau adaptation in this species. Population genomic analyses revealed that the northwardly invasive AHRs consisted of two independent and genetically distinct populations which might result from multiple independent primary invasion events. One invasive population exhibited reduced genetic diversity and distinct population structure compared with its source population, while the other displayed preserved genetic polymorphisms and little genetic differentiation from its source population. Genes involved in G-protein coupled receptors and carbohydrate metabolism may contribute to the local adaptation of northern AHRs. In particular, RTN4 was identified as a key gene for AHRs in the QTP that favours adaptation to high-altitude hypoxia. Coincidently, the physiological performance and transcriptome profiles of hypoxia-exposed rats both showed better hypoxia adaptation in AHRs than in BRs that failed to colonize the heart of the QTP, which may have facilitated the replacement of the BR population by the invading AHRs at the edge of the QTP. This study provides profound insights into the multiple origins of the northwardly invasive AHR and the great tolerance to hypoxia in this species.

Pattern and pace of morphological change due to variable human impact: the case of Japanese macaques

Human impact influences morphological variation in animals, as documented in many captive and domestic animal populations. However, there are different levels of human impact, and their influence on the pattern and rate of morphological variation remains unclear. This study contributes to the ongoing debate via the examination of cranial and mandibular shape and size variation and pace of change in Japanese macaques (Macaca fuscata). This species is ideal for tackling such questions because different wild, wild-provisioned, and captive populations have been monitored and collected over seven decades. Linear measurements were taken on 70 skulls from five populations, grouped into three 'human impact groups' (wild, wild-provisioned, and captive). This made it possible to investigate the pattern and pace of skull form changes among the human impact groups as well as over time within the populations. It was found that the overall skull shape tends to differ among the human impact groups, with captive macaques having relatively longer rostra than wild ones. Whether these differences are a result of geographic variation or variable human impact, related to nutritional supply and mechanical properties of the diet, is unclear. However, this pattern of directed changes did not seem to hold when the single captive populations were examined in detail. Although environmental conditions have probably been similar for the two examined captive populations (same captive locality), skull shape changes over the first generations in captivity were mostly different. This varying pattern, together with a consistent decrease in body size in the captive populations over generations, points to genetic drift playing a role in shaping skull shape and body size in captivity. In the captive groups investigated here, the rates of change were found to be high compared to literature records from settings featuring different degrees of human impact in different species, although they still lie in the range of field studies in a natural context. This adds to the view that human impact might not necessarily lead to particularly fast rates of change.

Current and Forthcoming Approaches for Benchmarking Genetic and Genomic Diversity

The current attrition of biodiversity extends beyond loss of species and unique populations to steady loss of a vast genomic diversity that remains largely undescribed. Yet the accelerating development of new techniques allows us to survey entire genomes ever faster and cheaper, to obtain robust samples from a diversity of sources including degraded DNA and residual DNA in the environment, and to address conservation efforts in new and innovative ways. Here we review recent studies that highlight the importance of carefully considering where to prioritize collection of genetic samples (e.g., organisms in rapidly changing landscapes or along edges of geographic ranges) and what samples to collect and archive (e.g., from individuals of little-known subspecies or populations, even of species not currently considered endangered). Those decisions will provide the sample infrastructure to detect the disappearance of certain genotypes or gene complexes, increases in inbreeding levels, and loss of genomic diversity as environmental conditions change. Obtaining samples from currently endangered, protected, and rare species can be particularly difficult, thus we also focus on studies that use new, non-invasive ways of obtaining genomic samples and analyzing them in these cases where other sampling options are highly constrained. Finally, biological collections archiving such samples face an inherent contradiction: their main goal is to preserve biological material in good shape so it can be used for scientific research for centuries to come, yet the technologies that can make use of such materials are advancing faster than collections can change their standardized practices. Thus, we also discuss current and potential new practices in biological collections that might bolster their usefulness for future biodiversity conservation research.

A refined proposal for the origin of dogs: the case study of Gnirshöhle, a Magdalenian cave site

Dogs are known to be the oldest animals domesticated by humans. Although many studies have examined wolf domestication, the geographic and temporal origin of this process is still being debated. To address this issue, our study sheds new light on the early stages of wolf domestication during the Magdalenian period (16–14 ka cal BP) in the Hegau Jura region (Southwestern Germany and Switzerland). By combining morphology, genetics, and isotopes, our multidisciplinary approach helps to evaluate alternate processes driving the early phases of domestication. The isotope analysis uncovered a restricted, low δ¹⁵N protein diet for all analyzed Gnirshöhle specimens, while morphological examinations and phylogenetic relationships did not unequivocally assign them to one or the other canid lineage. Intriguingly, the newly generated mitochondrial canid genomes span the entire genetic diversity of modern dogs and wolves. Such high mitochondrial diversity could imply that Magdalenian people tamed and reared animals originating from different wolf lineages. We discuss our results in light of three ecological hypotheses and conclude that both domestication and the existence of a specialized wolf ecomorph are highly probable. However, due to their proximity to humans and a restricted diet, we propose domestication as the most likely scenario explaining the patterns observed herein.

Enhanced problem-solving ability as an adaptation to urban environments in house mice

Humans have a large impact on the distribution and abundance of animal species worldwide. The ecological effects of human-altered environments are being increasingly recognized and understood, but their effects on evolution are largely unknown. Enhanced cognitive abilities and the ability to innovate have been suggested as crucial traits for thriving in human-altered habitats. We tested if house mice (Mus musculus) subspecies have evolved enhanced innovative problem-solving abilities throughout their commensal lives with humans. The time that subspecies lived commensally with humans ranges between approximately 3000 years to more than 11 000 years, thus providing an excellent example of human-animal coexistence. In addition, we tested whether differences in problem-solving were mediated by differences in object and place exploration, motivation, persistence or inhibitory control. We found that populations of subspecies living commensally the longest excelled in problem-solving across seven food-extraction tasks over subspecies living commensally short or intermediate times. These differences were not mediated by exploration, motivation, persistence or inhibitory control suggesting that subspecies have evolved better cognitive abilities when living commensally in urban environments. This suggests that the ability to problem-solve may be an important trait promoting prosperity in human-altered environments.

Widespread genetic connectivity of feral pigeons across the Northeastern megacity

Urbanization may restrict, facilitate, or have no effect on gene flow, depending on the organism and extent of urbanization. In human commensals, with high dispersal ability, urbanization can facilitate gene flow by providing continuous suitable habitat across a wide range. Additionally, suburban or rural areas with lower human population density may act as a barrier to gene flow for these human commensals. Spatial population genetic approaches provide a means to understand genetic connectivity across geographically expansive areas that encompass multiple metropolitan areas. Here, we examined the spatial genetic patterns of feral pigeons (Columba livia) living in cities in the eastern United States. We focused our sampling on the Northeastern megacity, which is a region covering six large cities (Boston, Providence, New York City, Philadelphia, Baltimore, and Washington, DC). We performed ddRAD-Seqon 473 samples, recovered 35,200 SNPs, and then used multiple evolutionary clustering analyses to investigate population structuring. These analyses revealed that pigeons formed two genetic clusters-a northern cluster containing samples from Boston and Providence and a southern cluster containing all other samples. This substructuring is possibly due to reduced urbanization across coastal Connecticut that separates Boston and Providence from New York and mid-Atlantic cities. We found that pairs of pigeons within 25 km are highly related (Mantel r = 0.217, p = .001) and that beyond 50 km, pigeons are no more related than they would be at random. Our analysis detected higher-than-expected gene flow under an isolation by distance model within each city. We conclude that the extreme urbanization characteristic of the Northeastern megacity is likely facilitating gene flow in feral pigeons.

The evolutionary consequences of human-wildlife conflict in cities

Human-wildlife interactions, including human-wildlife conflict, are increasingly common as expanding urbanization worldwide creates more opportunities for people to encounter wildlife. Wildlife-vehicle collisions, zoonotic disease transmission, property damage, and physical attacks to people or their pets have negative consequences for both people and wildlife, underscoring the need for comprehensive strategies that mitigate and prevent conflict altogether. Management techniques often aim to deter, relocate, or remove individual organisms, all of which may present a significant selective force in both urban and nonurban systems. Management-induced selection may significantly affect the adaptive or nonadaptive evolutionary processes of urban populations, yet few studies explicate the links among conflict, wildlife management, and urban evolution. Moreover, the intensity of conflict management can vary considerably by taxon, public perception, policy, religious and cultural beliefs, and geographic region, which underscores the complexity of developing flexible tools to reduce conflict. Here, we present a cross-disciplinary perspective that integrates human-wildlife conflict, wildlife management, and urban evolution to address how social-ecological processes drive wildlife adaptation in cities. We emphasize that variance in implemented management actions shapes the strength and rate of phenotypic and evolutionary change. We also consider how specific management strategies either promote genetic or plastic changes, and how leveraging those biological inferences could help optimize management actions while minimizing conflict. Investigating human-wildlife conflict as an evolutionary phenomenon may provide insights into how conflict arises and how management plays a critical role in shaping urban wildlife phenotypes.

Dispersal ability predicts spatial genetic structure in native mammals persisting across an urbanization gradient

As the rate of urbanization continues to increase globally, a growing body of research is emerging that investigates how urbanization shapes the movement-and consequent gene flow-of species in cities. Of particular interest are native species that persist in cities, either as small relict populations or as larger populations of synanthropic species that thrive alongside humans in new urban environments. In this study, we used genomic sequence data (SNPs) and spatially explicit individual-based analyses to directly compare the genetic structure and patterns of gene flow in two small mammals with different dispersal abilities that occupy the same urbanized landscape to evaluate how mobility impacts genetic connectivity. We collected 215 white-footed mice (Peromyscus leucopus) and 380 big brown bats (Eptesicus fuscus) across an urban-to-rural gradient within the Providence, Rhode Island (U.S.A.) metropolitan area (population =1,600,000 people). We found that mice and bats exhibit clear differences in their spatial genetic structure that are consistent with their dispersal abilities, with urbanization having a stronger effect on Peromyscus mice. There were sharp breaks in the genetic structure of mice within the Providence urban core, as well as reduced rates of migration and an increase in inbreeding with more urbanization. In contrast, bats showed very weak genetic structuring across the entire study area, suggesting a near-panmictic gene pool likely due to the ability to disperse by flight. Genetic diversity remained stable for both species across the study region. Mice also exhibited a stronger reduction in gene flow between island and mainland populations than bats. This study represents one of the first to directly compare multiple species within the same urban-to-rural landscape gradient, an important gap to fill for urban ecology and evolution. Moreover, here we document the impacts of dispersal capacity on connectivity for native species that have persisted as the urban landscape matrix expands.

Fast-lived Hosts and Zoonotic Risk

Because most emerging human pathogens originate in mammals, many studies aim to identify host traits that determine the risk of sourcing zoonotic outbreaks. Studies regularly assert that 'fast-lived' mammal species exhibiting greater fecundity and shorter lifespans tend to host more zoonoses; however, the causes of this association remain poorly understood and they cover a range of immune and nonimmune mechanisms. We discuss these drivers in the context of evolutionary ecology and wildlife-human interactions. Ultimately, differentiating these mechanisms will require linking interspecific variation in life history with immunity, pathogen diversity, transmissibility, and zoonotic risk, and critical data gaps currently limit our ability to do so. We highlight sampling and analytical frameworks to address this gap and to better inform zoonotic reservoir prediction.

Our Current Understanding of Commensalism

Commensalisms, interactions between two species in which one species benefits and the other experiences no net effect, are frequently mentioned in the ecological literature but are surprisingly little studied. Here we review and synthesize our limited understanding of commensalism. We then argue that commensalism is not a single type of interaction; rather, it is a suite of phenomena associated with distinct ecological processes and evolutionary consequences. For each form of commensalism we define, we present evidence for how, where, and why it occurs, including when it is evolutionarily persistent and when it is an occasional outcome of interactions that are usually mutualistic or antagonistic. We argue that commensalism should be of great interest in the study of species interactions due to its location at the center of the continuum between positive and negative outcomes. Finally, we offer a roadmap for future research.

On the ground and in the heights: Does exploratory activity differ in commensal and non-commensal spiny mice?

Human settlements represent a specific environment where commensal animals are exposed to different selective pressures than their wild-living conspecifics. Despite the importance of commensal rodents for human health and economy, little is known about how a transition to a commensal way of life changes the behaviour of the animals. We tested twelve populations of spiny mice (Acomys spp.) in two open field-type tests - a vertical test and a hole board test. In the vertical test, a wire mesh for climbing was offered to spiny mice. We used a multipopulation approach using two commensal and ten non-commensal spiny mouse populations to account for inter-population variability. We aimed to investigate whether there are differences in behaviour of commensal and non-commensal populations with special regard to their exploratory activity both on the ground and on the wire mesh. We found that all non-commensal populations behaved similarly despite their long separate evolutionary histories. Contrary, the commensal populations were less exploratory on the ground in both tests. We concluded that this change was associated with their transition to commensalism. This shows that selective pressures of the commensal environment are able to induce noticeable changes in behaviour after a very short evolutionary time.

Fox dietary ecology as a tracer of human impact on Pleistocene ecosystems

Nowadays, opportunistic small predators, such as foxes (Vulpes vulpes and Vulpes lagopus), are well known to be very adaptable to human modified ecosystems. However, the timing of the start of this phenomenon in terms of human impact on ecosystems and of the implications for foxes has hardly been studied. We hypothesize that foxes can be used as an indicator of past human impact on ecosystems, as a reflection of population densities and consequently to track back the influence of humans on the Pleistocene environment. To test this hypothesis, we used stable isotope analysis (δ¹³C, δ¹⁵N) of bone collagen extracted from faunal remains from several archaeological sites located in the Swabian Jura (southwest Germany) and covering a time range over three important cultural periods, namely the Middle Palaeolithic (older than 42,000 years ago) attributed to Neanderthals, and the early Upper Palaeolithic periods Aurignacian and Gravettian (42,000 to 30,000 years ago) attributed to modern humans. We then ran Bayesian statistic systems (SIBER, mixSIAR) to reconstruct the trophic niches and diets of Pleistocene foxes. We observed that during the Middle Palaeolithic period, when Neanderthals sparsely populated the Swabian Jura, the niches occupied by foxes suggest a natural trophic behavior. In contrast, during the early Upper Palaeolithic periods, a new trophic fox niche appeared, characterized by a restricted diet on reindeer. This trophic niche could be due to the consumption of human subsidies related to a higher human population density and the resulting higher impact on the Pleistocene environment by modern humans compared to Neanderthals. Furthermore, our study suggests that, a synanthropic commensal behavior of foxes started already in the Aurignacian, around 42,000 years ago.

Tracking the Near Eastern origins and European dispersal of the western house mouse

The house mouse (Mus musculus) represents the extreme of globalization of invasive mammals. However, the timing and basis of its origin and early phases of dispersal remain poorly documented. To track its synanthropisation and subsequent invasive spread during the develoment of complex human societies, we analyzed 829 Mus specimens from 43 archaeological contexts in Southwestern Asia and Southeastern Europe, between 40,000 and 3,000 cal. BP, combining geometric morphometrics numerical taxonomy, ancient mitochondrial DNA and direct radiocarbon dating. We found that large late hunter-gatherer sedentary settlements in the Levant, c. 14,500 cal. BP, promoted the commensal behaviour of the house mouse, which probably led the commensal pathway to cat domestication. House mouse invasive spread was then fostered through the emergence of agriculture throughout the Near East 12,000 years ago. Stowaway transport of house mice to Cyprus can be inferred as early as 10,800 years ago. However, the house mouse invasion of Europe did not happen until the development of proto urbanism and exchange networks - 6,500 years ago in Eastern Europe and 4000 years ago in Southern Europe - which in turn may have driven the first human mediated dispersal of cats in Europe.

On the Doorstep, Rodents in Homesteads and Kitchen Gardens

Scarcely investigated in terms of small mammals, kitchen gardens and homesteads form a subset of environments. Using results of snap trapping, we present the first data on small mammal species diversity, gender and age structure, relative abundance, body fitness, and reproduction parameters in these commensal habitats (kitchen gardens, homestead gardens, houses, and outbuildings). We expected that (i) house mice should be the dominant species in buildings, while striped field mice should be dominant in gardens, (ii) body condition should be the highest in buildings, (iii) body condition should increase in the autumn, irrespective of the habitat, and (iv) breeding failures in the form of disrupted pregnancies should be observed. Not all of the predictions were confirmed. From the seven recorded species, gardens and outbuildings were dominated by yellow-necked mice, while bank voles dominated in buildings where food was available. The number of recorded species and diversity index increased during the autumn months. The body condition was highest in rodents that were trapped in gardens. It decreased towards winter, with the exception of the striped field mouse. Breeding disturbances were recorded in all of the most numerous species, comprising 16.7-100% of all observed pregnancies.

Gridlock and beltways: the genetic context of urban invasions

The rapid expansion of urban land across the globe presents new and numerous opportunities for invasive species to spread and flourish. Ecologists historically rejected urban ecosystems as important environments for ecology and evolution research but are beginning to recognize the importance of these systems in shaping the biology of invasion. Urbanization can aid the introduction, establishment, and spread of invaders, and these processes have substantial consequences on native species and ecosystems. Therefore, it is valuable to understand how urban areas influence populations at all stages in the invasion process. Population genetic tools are essential to explore the driving forces of invasive species dispersal, connectivity, and adaptation within cities. In this review, we synthesize current research about the influence of urban landscapes on invasion genetics dynamics. We conclude that urban areas are not only points of entry for many invasive species, they also facilitate population establishment, are pools for genetic diversity, and provide corridors for further spread both within and out of cities. We recommend the continued use of genetic studies to inform invasive species management and to understand the underlying ecological and evolutionary processes governing successful invasion.

Commensalism outweighs phylogeographical structure in its effect on phenotype of a Sudanian savanna rodent

The murid rodent Praomys daltoni is widespread in Sudanian savanna and woodlands of West Africa, and previous study of mitochondrial DNA variability suggested that it encompasses the phenotypically (small, grey-bellied) and ecologically (commensal) distinct form, Praomys derooi. Here, we comprehensively examined the genetic and morphological diversity within the complex. Six mitochondrial lineages showed a fine-scale phylogeographical pattern, whereas delimitation based on nuclear loci pooled four of them into a single widespread unit. A newly discovered lineage from southern Mauritania stands apart from the rest of the complex and might represent an unrecognized species. At the same time, the internal position of P. derooi (C2 mitochondrial lineage) was confirmed by the multilocus analysis. The magnitude of genetic distances between major phylogeographical lineages was typical for interspecific divergence in other clades of Praomys, despite the little differences among them in morphology (skull and upper molar row shapes). The most pronounced morphological shift was associated with a transition to commensalism, especially in P. derooi, but also in other lineages. This makes the whole complex a suitable model for the study of phenotypic novelty, the evolution of commensalism and conditions for ecological speciation.

Anthropogenic effects on the physiology and behaviour of chacma baboons in the Cape Peninsula of South Africa

As animals increasingly occupy habitats in proximity to humans, with home ranges a mosaic of natural and anthropogenic landscapes, it becomes imperative from a conservation perspective to understand the impacts of human activities on wildlife. Many non-human primates share habitats with humans, an ability stemming largely from shared ecological needs due to our close evolutionary relationship. Such proximity, however, is often accompanied by direct conflict between humans and wildlife, leading to higher stress levels, injuries, mortality and behavioural changes, with detrimental effects on long-term health and fitness. Glucocorticoid (GC) hormones, which are released in response to ecological and social challenges, are increasingly employed to understand responses to anthropogenic disturbance. Here we investigate physiological and behavioural responses of female chacma baboons (Papio ursinus) to variation in spatial overlap and conflict with humans in their natural home range. The baboons resided in the Tokai Section of Table Mountain National Park in the Cape Peninsula of South Africa, where their home range included four types of habitats: protected, suburban, agricultural and mosaic areas. We studied the largest group of baboons in Tokai (70 individuals) and examined the effects of ranging in these different habitats on the faecal GCs and behaviour of all adult females in the troop (N = 16). We found time spent ranging in more anthropogenic habitats to be associated with higher levels of GCs, more aggression, less time socializing and shorter grooming bouts. Self-directed behaviour, however, varied and did not necessarily reflect physiological measures of stress. Taken together, the results of this study highlight the risks associated with ranging in anthropogenic environments and point to the need for a multifaceted approach to studying the negative impacts of human activities on animals so as to better inform conservation practices.

Falcon genomics in the context of conservation, speciation, and human culture

Here, we review the diversity, evolutionary history, and genomics of falcons in the context of their conservation and interactions with humans, and provide a perspective on how new genomic approaches may be applied to expand our knowledge of these topics. For millennia, humans and falcons (genus Falco) have developed unique relationships through falconry, religious rituals, conservation efforts, and human lifestyle transitions. From an evolutionary perspective, falcons remain an enigma. Having experienced several recent radiations, they have reached an unparalleled and almost global distribution, with an intrageneric species richness that is roughly an order of magnitude higher than typical within their family (Falconidae) and across other birds (Phylum: Aves). This diversity has evolved in the context of unusual genomic architecture that includes unique chromosomal rearrangements, relatively low chromosome counts, extremely low microdeletion rates, and high levels of nuclear mitochondrial DNA segments (NUMTs). These genomic peculiarities combine with high levels of ecological and organismal diversity and a legacy of human interactions to make falcons obvious candidates for evolutionary studies, providing unique research opportunities in common topics, including chromosomal evolution, the mechanics of speciation, local adaptation, domestication, and urban adaptation.

Male and female bats differ in their use of a large urban park

Understanding how wildlife respond to ever-encroaching urbanization is of great concern. Bats are the second-most speciose mammalian order and while many appear to be urban adapted, we currently have a limited understanding of their demography and habitat use within urban environments. Using a combination of captures to obtain demographic data, radio-telemetry to examine foraging and roosting behaviour, and data on diet and prey availability, we examined how big brown bats (Eptesicus fuscus), a synurbic species, use an urban green space (High Park) in Canada’s largest city centre, Toronto. We found that adult males outnumbered adult females more than two to one and that males were found throughout the park, while females were concentrated in an area with greater access to water, but lower prey availability. We also found that bats of both sexes were in poorer body condition than reported for other non-urban areas, including a site within southern Ontario. Our data suggest that High Park may not provide adequate resources for reproductive females as they were never found roosting in the park and beetles, their preferred prey, were limited. Although previous studies suggest urban green spaces may offer refuge to bats, most have not considered sex-specific responses to urbanization as they have largely been based on acoustic surveys. Our study therefore highlights the importance of considering demographic differences in response to urbanization to better inform urban management plans and green space development.

Invisible barriers: anthropogenic impacts on inter- and intra-specific interactions as drivers of landscape-independent fragmentation

Anthropogenically induced fragmentation constitutes a major threat to biodiversity. Presently, conservation research and actions focus predominantly on fragmentation caused directly by physical transformation of the landscape (e.g. deforestation, agriculture, urbanization, roads, etc.). While there is no doubt that landscape features play a key role in fragmenting populations or enhancing connectivity, fragmentation may also come about by processes other than the transformation of the landscape and which may not be readily visible. Such landscape-independent fragmentation (LIF) usually comes about when anthropogenic disturbance alters the inter- and intra-specific interactions among and within species. LIF and its drivers have received little attention in the scientific literature and in the management of wildlife populations. We discuss three major classes of LIF processes and their relevance for the conservation and management of species and habitats: (i) interspecific dispersal dependency, in which populations of species that rely on other species for transport and propagation become fragmented as the transporting species declines; (ii) interspecific avoidance induction, where species are excluded from habitats and corridors owing to interspecific interactions resulting from anthropogenically induced changes in community structure (e.g. exclusions by increased predation pressure); and (iii) intraspecific behavioural divergence, where populations become segregated owing to anthropogenically induced behavioural differentiation among them.

This article is part of the theme issue ‘Linking behaviour to dynamics of populations and communities: application of novel approaches in behavioural ecology to conservation'.

Independent amylase gene copy number bursts correlate with dietary preferences in mammals

The amylase gene (AMY), which codes for a starch-digesting enzyme in animals, underwent several gene copy number gains in humans (Perry et al., 2007), dogs (Axelsson et al., 2013), and mice (Schibler et al., 1982), possibly along with increased starch consumption during the evolution of these species. Here, we present comprehensive evidence for AMY copy number expansions that independently occurred in several mammalian species which consume diets rich in starch. We also provide correlative evidence that AMY gene duplications may be an essential first step for amylase to be expressed in saliva. Our findings underscore the overall importance of gene copy number amplification as a flexible and fast evolutionary mechanism that can independently occur in different branches of the phylogeny.

The role of life experience in affecting persistence: A comparative study between free-ranging dogs, pet dogs and captive pack dogs

Persistence in object manipulation has been consistently associated with problem-solving success and it is known to be affected, at the individual level, by life experience. Differences in life experiences are particularly poorly studied in the problem-solving context and mainly refer to the comparison between wild and captive animals. Dogs represent interesting study subjects, since dog populations differ widely in their life experiences. In this comparative study we investigated subjects' persistence when presenting a novel object containing food that could not be accessed (impossible task) to three dog populations with very diverse life experiences: free-ranging village dogs (in Morocco), pet dogs (in Vienna) and captive pack living dogs (Wolf Science Center-WSC). We found that pet dogs and captive dogs (WSC) were more manipulative and persistent than free-ranging dogs. The low persistence of free ranging-dogs is unlikely the effect of a lack of exposure to objects, since they are confronted with many human’ artefacts in their environment daily. Instead, we suggest that the higher persistence of captive dogs and pet dogs in comparison to free-ranging dogs might be due to their increased experience of human-mediated object interaction. This provides subjects with a socially guided experience in manipulating and interacting with objects increasing their motivation to engage in such tasks.

Peri-urban black rats host a rich assembly of ticks and healthier rats have more ticks

The black rat Rattus rattus has a distribution that includes much of Earth's terrestrial surface, and has adapted to exploit both habitats extensively modified by humans and rural habitats. Despite the fact that R. rattus are nearly ubiquitous, few studies have investigated urban or peri-urban R. rattus as potential hosts for ticks. In this study, we identified the species of ticks that parasitize R. rattus in a remnant bush area within Sydney, Australia. We then examined the relationship between ticks and R. rattus by testing several rat body characteristics as predictors of tick abundance. We show that larva and nymphs of five species of native Australian tick parasitize R. rattus in urban Australia. The most abundance species was Ixodes holocyclus, a tick of veterinary and human health concern. We found that ticks were more abundant on R. rattus in better condition, for larva and nymphs of I. holocyclus and I. tasmani. Rattus rattus supports a rich assembly of ticks in a remnant forest in urban Australia, and as the R. rattus in best condition have the most ticks, tick parasitism at the levels observed does not appear to negatively impact R. rattus. Our findings illustrate that R. rattus, and other human commensal species, may be important hosts for ticks in human modified environments.

A roadmap for urban evolutionary ecology

Urban ecosystems are rapidly expanding throughout the world, but how urban growth affects the evolutionary ecology of species living in urban areas remains largely unknown. Urban ecology has advanced our understanding of how the development of cities and towns change environmental conditions and alter ecological processes and patterns. However, despite decades of research in urban ecology, the extent to which urbanization influences evolutionary and eco-evolutionary change has received little attention. The nascent field of urban evolutionary ecology seeks to understand how urbanization affects the evolution of populations, and how those evolutionary changes in turn influence the ecological dynamics of populations, communities, and ecosystems. Following a brief history of this emerging field, this Perspective article provides a research agenda and roadmap for future research aimed at advancing our understanding of the interplay between ecology and evolution of urban-dwelling organisms. We identify six key questions that, if addressed, would significantly increase our understanding of how urbanization influences evolutionary processes. These questions consider how urbanization affects nonadaptive evolution, natural selection, and convergent evolution, in addition to the role of urban environmental heterogeneity on species evolution, and the roles of phenotypic plasticity versus adaptation on species' abundance in cities. Our final question examines the impact of urbanization on evolutionary diversification. For each of these six questions, we suggest avenues for future research that will help advance the field of urban evolutionary ecology. Lastly, we highlight the importance of integrating urban evolutionary ecology into urban planning, conservation practice, pest management, and public engagement.