Influence of hybridization on niche shifts in expanding coyote populations

Diet selection in the Coyote Canis latrans

The Coyote (Canis latrans) is one of the most studied species in North America with at least 445 papers on its diet alone. While this research has yielded excellent reviews of what coyotes eat, it has been inadequate to draw deeper conclusions because no synthesis to date has considered prey availability. We accounted for prey availability by investigating the prey selection of coyotes across its distribution using the traditional Jacobs' index method, as well as the new iterative preference averaging (IPA) method on scats and biomass. We found that coyotes selected for Dall's Sheep (Ovis dalli), White-tailed Deer (Odocoileus virginianus), Eastern Cottontail Rabbit (Sylvilagus floridanus), and California Vole (Microtus californicus), which yielded a predator-to-preferred prey mass ratio of 1:2. We also found that coyotes avoided preying on other small mammals, including carnivorans and arboreal species. There was strong concordance between the traditional and IPA method on scats, but this pattern was weakened when biomass was considered. General linear models revealed that coyotes preferred to prey upon larger species that were riskier to hunt, reflecting their ability to hunt in groups, and were least likely to hunt solitary species. Coyotes increasingly selected Mule Deer (O. hemionus) and Snowshoe Hare (Lepus americanus) at higher latitudes, whereas Black-tailed Jackrabbit (L. californicus) were increasingly selected toward the tropics. Mule Deer were increasingly selected at higher coyote densities, while Black-tailed Jackrabbit were increasingly avoided at higher coyote densities. Coyote predation could constrain the realized niche of prey species at the distributional limits of the predator through their increased efficiency of predation reflected in increased prey selection values. These results are integral to improved understandings of Coyote ecology and can inform predictive analyses allowing for spatial variation, which ultimately will lead to better understandings about the ecological role of the coyote across different ecosystems.

Coyotes in New York City Carry Variable Genomic Dog Ancestry and Influence Their Interactions with Humans

Coyotes are ubiquitous on the North American landscape as a result of their recent expansion across the continent. They have been documented in the heart of some of the most urbanized cities, such as Chicago, Los Angeles, and New York City. Here, we explored the genomic composition of 16 coyotes in the New York metropolitan area to investigate genomic demography and admixture for urban-dwelling canids in Queens County, New York. We identified moderate-to-high estimates of relatedness among coyotes living in Queens (r = 0.0-0.5) and adjacent neighborhoods, suggestive of a relatively small population. Although we found low background levels of domestic-dog ancestry across most coyotes in our sample (5%), we identified a male suspected to be a first-generation coyote-dog hybrid with 46% dog ancestry, as well as his two putative backcrossed offspring that carried approximately 25% dog ancestry. The male coyote-dog hybrid and one backcrossed offspring each carried two transposable element insertions that are associated with human-directed hypersociability in dogs and gray wolves. An additional, unrelated coyote with little dog ancestry also carried two of these insertions. These genetic patterns suggest that gene flow from domestic dogs may become an increasingly important consideration as coyotes continue to inhabit metropolitan regions.

The natural history and ecology of melanism in red wolf and coyote populations of the southeastern United States – evidence for Gloger’s rule

Background

Gloger’s rule postulates that animals should be darker colored in warm and humid regions where dense vegetation and dark environments are common. Although rare in Canis populations, melanism in wolves is more common in North America than other regions globally and is believed to follow Gloger’s rule. In the temperate forests of the southeastern United States, historical records of red wolf (Canis rufus) and coyote (Canis latrans) populations document a consistent presence of melanism. Today, the melanistic phenotype is extinct in red wolves while occurring in coyotes and red wolf-coyote hybrids who occupy the red wolf's historical range. To assess if Gloger’s rule could explain the occurrence and maintenance of melanistic phenotypes in Canis taxa, we investigated differences in morphology, habitat selection, and survival associated with pelage color using body measurements, GPS tracking data, and long-term capture-mark-recapture and radio-telemetry data collected on coyotes and hybrids across the southeastern United States.

Results

We found no correlation between morphometrics and pelage color for Canis taxa. However, we observed that melanistic coyotes and hybrids experienced greater annual survival than did their gray conspecifics. Furthermore, we observed that melanistic coyotes maintained larger home ranges and exhibited greater selection for areas with dense canopy cover and wetlands than did gray coyotes.

Conclusions

In the southeastern United States, pelage color influenced habitat selection by coyotes and annual survival of coyotes and hybrids providing evidence that Gloger’s rule is applicable to canids inhabiting regions with dense canopy cover and wetlands. Greater annual survival rates observed in melanistic Canis may be attributed to better concealment in areas with dense canopy cover such as coastal bottomland forests. We suggest that the larger home range sizes of melanistic coyotes may reflect the trade-off of reduced foraging efficiency in lower quality wetland habitat for improved survival. Larger home ranges and differential use of land cover by melanistic coyotes may facilitate weak assortative mating in eastern coyote populations, in which melanistic animals may have lower success of finding compatible mates in comparison to gray conspecifics. We offer that our observations provide a partial explanation for why melanism is relatively low (< 10%) but consistent within coyote populations throughout southeastern parts of their range.

Climate change and niche unfilling tend to favor range expansion of Moina macrocopa Straus 1820, a potentially invasive cladoceran in temporary waters

Non-native species' introductions have increased in the last decades primarily due to anthropogenic causes such as climate change and globalization of trade. Moina macrocopa, a stress-tolerant cladoceran widely used in bioassays and aquaculture, is spreading in temporary and semi-temporary natural ponds outside its natural range. Here, we characterize the variations in the climatic niche of M. macrocopa during its invasions outside the native Palearctic range following introduction into the American continent. Specifically, we examined to what extent the climatic responses of this species have diverged from those characteristics for its native range. We also made predictions for its potential distribution under current and future scenarios. We found that the environmental space occupied by this species in its native and introduced distribution areas shares more characteristics than randomly expected. However, the introduced niche has a high degree of unfilling when displacing its original space towards the extension to drier and hotter conditions. Accordingly, M. macrocopa can invade new areas where it has not yet been recorded in response to warming temperatures and decreasing winter precipitation. In particular, temporary ponds are more vulnerable environments where climatic and environmental stresses may also lower biotic resistance.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10750-022-04835-7.

Spatial variation in diet-microbe associations across populations of a generalist North American carnivore

Generalist species, by definition, exhibit variation in niche attributes that promote survival in changing environments. Increasingly, phenotypes previously associated with a species, particularly those with wide or expanding ranges, are dissolving and compelling greater emphasis on population-level characteristics. In the present study, we assessed spatial variation in diet characteristics, gut microbiome and associations between these two ecological traits across populations of coyotes Canis latrans. We highlight the influence of the carnivore community in shaping these relationships, as the coyote varied from being an apex predator to a subordinate, mesopredator across sampled populations. We implemented a scat survey across three distinct coyote populations in Michigan, USA. We used carbon (δ¹³ C) and nitrogen (δ¹⁵ N) isotopic values to reflect consumption patterns and trophic level, respectively. Corresponding samples were also paired with 16S rRNA sequencing to describe the microbial community and correlate with isotopic values. Although consumption patterns were comparable, we found spatial variation in trophic level among coyote populations. Specifically, δ¹⁵ N was highest where coyotes were the apex predator and lowest where coyotes co-occurred with grey wolves Canis lupus. The gut microbial community exhibited marked spatial variation across populations with the lowest operational taxonomic units diversity found where coyotes occurred at their lowest trophic level. Bacteriodes and Fusobacterium dominated the microbiome and were positively correlated across all populations. We found no correlation between δ¹³ C and microbial community attributes. However, positive associations between δ¹⁵ N and specific microbial genera increased as coyotes ascended trophic levels. Coyotes provide a model for exploring implications of niche plasticity because they are a highly adaptable, wide-ranging omnivore. As coyotes continue to vary in trophic position and expand their geographic range, we might expect increased divergence within their microbial community, changes in physiology and alterations in behaviour.

Evidence of ecological niche shift in Rhododendron ponticum (L.) in Britain: Hybridization as a possible cause of rapid niche expansion

Biological invasions threaten global biodiversity and natural resources. Anticipating future invasions is central to strategies for combating the spread of invasive species. Ecological niche models are thus increasingly used to predict potential distribution of invasive species. In this study, we compare ecological niches of Rhododendron ponticum in its native (Iberian Peninsula) and invasive (Britain) ranges. Here, we test the conservation of ecological niche between invasive and native populations of R. ponticum using principal component analysis, niche dynamics analysis, and MaxEnt-based reciprocal niche modeling. We show that niche overlap between native and invasive populations is very low, leading us to the conclusion that the two niches are not equivalent and are dissimilar. We conclude that R. ponticum occupies novel environmental conditions in Britain. However, the evidence of niche shift presented in this study should be treated with caution because of nonanalogue climatic conditions between native and invasive ranges and a small population size in the native range. We then frame our results in the context of contradicting genetic evidence on possible hybridization of this invasive species in Britain. We argue that the existing contradictory studies on whether hybridization caused niche shift in R. ponticum are not sufficient to prove or disprove this hypothesis. However, we present a series of theoretical arguments which indicate that hybridization is a likely cause of the observed niche expansion of R. ponticum in Britain.

Canid collision—expanding populations of coyotes (Canis latrans) and crab-eating foxes (Cerdocyon thous) meet up in Panama

The rise of the Panamanian Isthmus 3–4 million years ago enabled the first dispersal of mammals between North and South America in what is known as the Great American Biotic Interchange. Modern deforestation threatens the historic forest connectivity and creates new habitat for open-country species, as documented by recent expansions of North American coyotes (Canis latrans) and South American crab-eating foxes (Cerdocyon thous) into Central America. We used camera traps to map the expansions of these species into eastern Panama and found that, by 2015, coyote populations had colonized most agricultural area west of Lago Bayano. Most of our camera arrays east of this point documented crab-eating foxes, and evidence from roadkills showed some foxes had advanced farther west, but we never documented both species at the same camera-trap array, suggesting the possibility of fine-scale spatial avoidance. We used a data fusion approach to build species distribution models combining our camera surveys with records from the literature and roadkill. While the auxiliary data improved the predictive accuracy for both species, few clear habitat patterns emerged, which might reflect the generalist tendencies of these canids, or the fact that both are in the early stages of colonizing the region. Camera-trap photos showed that both species were nocturnal and revealed some dog-like morphology in coyotes, which could indicate their recent hybridization with dogs (Canis familiaris). Our continued monitoring of the Darién documented single coyotes moving through the western edge of the area in 2016 and 2018. This leaves only the great Darién forests between coyotes and South America. If deforestation continues in the region, these two invasive canids could represent the first of a new, Not-So-Great American Biotic Interchange, where generalist species adapted to human disturbance cross continents and threaten native biota.

High genomic diversity and candidate genes under selection associated with range expansion in eastern coyote (Canis latrans) populations

Range expansion is a widespread biological process, with well-described theoretical expectations associated with the colonization of novel ranges. However, comparatively few empirical studies address the genomic outcomes accompanying the genome-wide consequences associated with the range expansion process, particularly in recent or ongoing expansions. Here, we assess two recent and distinct eastward expansion fronts of a highly mobile carnivore, the coyote (Canis latrans), to investigate patterns of genomic diversity and identify variants that may have been under selection during range expansion. Using a restriction-associated DNA sequencing (RADseq), we genotyped 394 coyotes at 22,935 SNPs and found that overall population structure corresponded to their 19th century historical range and two distinct populations that expanded during the 20th century. Counter to theoretical expectations for populations to bottleneck during range expansions, we observed minimal evidence for decreased genomic diversity across coyotes sampled along either expansion front, which is likely due to hybridization with other Canis species. Furthermore, we identified 12 SNPs, located either within genes or putative regulatory regions, that were consistently associated with range expansion. Of these 12 genes, three (CACNA1C, ALK, and EPHA6) have putative functions related to dispersal, including habituation to novel environments and spatial learning, consistent with the expectations for traits under selection during range expansion. Although coyote colonization of eastern North America is well-publicized, this study provides novel insights by identifying genes associated with dispersal capabilities in coyotes on the two eastern expansion fronts.

Mapping the expansion of coyotes (Canis latrans) across North and Central America

The geographic distribution of coyotes (Canislatrans) has dramatically expanded since 1900, spreading across much of North America in a period when most other mammal species have been declining. Although this considerable expansion has been well documented at the state/provincial scale, continent-wide descriptions of coyote spread have portrayed conflicting distributions for coyotes prior to the 1900s, with popularly referenced anecdotal accounts showing them restricted to the great plains, and more obscure, but data-rich accounts suggesting they ranged across the arid west. To provide a scientifically credible map of the coyote’s historical range (10,000–300 BP) and describe their range expansion from 1900 to 2016, we synthesized archaeological and fossil records, museum specimens, peer-reviewed reports, and records from wildlife management agencies. Museum specimens confirm that coyotes have been present in the arid west and California throughout the Holocene, well before European colonization. Their range in the late 1800s was undistinguishable from earlier periods, and matched the distribution of non-forest habitat in the region. Coyote expansion began around 1900 as they moved north into taiga forests, east into deciduous forests, west into costal temperate rain forests, and south into tropical rainforests. Forest fragmentation and the extirpation of larger predators probably enabled these expansions. In addition, hybridization with wolves (C.lupus, C.lycaon, and/or C.rufus) and/or domestic dogs has been documented in the east, and suspected in the south. Our detailed account of the original range of coyotes and their subsequent expansion provides the core description of a large scale ecological experiment that can help us better understand the predator-prey interactions, as well as evolution through hybridization.

Demographic history influences spatial patterns of genetic diversityin recently expanded coyote (Canis latrans) populations

Human-mediated range expansions have increased in recent decades and represent unique opportunities to evaluate genetic outcomes of establishing peripheral populations across broad expansion fronts. Over the past century, coyotes (Canis latrans) have undergone a pervasive range expansion and now inhabit every state in the continental United States. Coyote expansion into eastern North America was facilitated by anthropogenic landscape changes and followed two broad expansion fronts. The northern expansion extended through the Great Lakes region and southern Canada, where hybridization with remnant wolf populations was common. The southern and more recent expansion front occurred approximately 40 years later and across territory where gray wolves have been historically absent and remnant red wolves were extirpated in the 1970s. We conducted a genetic survey at 10 microsatellite loci of 482 coyotes originating from 11 eastern U.S. states to address how divergent demographic histories influence geographic patterns of genetic diversity. We found that population structure corresponded to a north-south divide, which is consistent with the two known expansion routes. Additionally, we observed extremely high genetic diversity, which is atypical of recently expanded populations and is likely the result of multiple complex demographic processes, in addition to hybridization with other Canis species. Finally, we considered the transition of allele frequencies across geographic space and suggest the mid-Atlantic states of North Carolina and Virginia as an emerging contact zone between these two distinct coyote expansion fronts.

Wide prevalence of hybridization in two sympatric grasshopper species may be shaped by their relative abundances

BACKGROUND

Hybridization between species is of conservation concern as it might threaten the genetic integrity of species. Anthropogenic factors can alter hybridization dynamics by introducing new potentially hybridizing species or by diminishing barriers to hybridization. This may even affect sympatric species pairs through environmental change, which so far has received little attention. We studied hybridization prevalence and the underlying behavioral mechanisms in two sympatric grasshopper species, a rare specialist (Chorthippus montanus) and a common generalist (Chorthippus parallelus). We conducted a mate choice experiment with constant intraspecific density and varying heterospecific density, i.e. varying relative frequency of both species.

RESULTS

Mate choice was frequency-dependent in both species with a higher risk of cross-mating with increasing heterospecific frequency, while conspecific mating increased linearly with increasing conspecific density. This illustrates that reproductive barriers could be altered by environmental change, if the relative frequency of species pairs is affected. Moreover, we performed a microsatellite analysis to detect hybridization in twelve syntopic populations (and four allotopic populations). Hybrids were detected in nearly all syntopic populations with hybridization rates reaching up to 8.9 %. Genetic diversity increased for both species when hybrids were included in the data set, but only in the common species a positive correlation between hybridization rate and genetic diversity was detected.

CONCLUSION

Our study illustrates that the relative frequency of the two species strongly determines the effectiveness of reproductive barriers and that even the more choosy species (Ch. montanus) may face a higher risk of hybridization if population size decreases and its relative frequency becomes low compared to its sister species. The asymmetric mate preferences of both species may lead to quasi-unidirectional gene flow caused by unidirectional backcrossing. This might explain why genetic diversity increased only in the common species, but not in the rare one. Altogether, the hybridization rate was much higher than expected for a widely sympatric species pair.

Influence of niche similarity on hybridization between Myriophyllum sibiricum and M. spicatum

The impact of ecological factors on natural hybridization is of widespread interest. Here, we asked whether climate niche influences hybridization between the two closely related plant species Myriophyllum sibiricum and M. spicatum. Eight microsatellite loci and two chloroplast fragments were used to investigate the occurrence of hybridization between these two species in two co-occurring regions: north-east China (NEC) and the Qinghai-Tibetan Plateau (QTP). The climate niches of the species were quantified by principal component analysis with bioclimatic data, and niche comparisons were performed between the two species in each region. Reciprocal hybridization was observed, and M. sibiricum was favoured as the maternal species. Furthermore, hybrids were rare in NEC but common in the QTP. Accordingly, in NEC, the two species were climatically distinct, and hybrids only occurred in the narrow geographical or ecological transition zone, whereas in the QTP, obvious niche overlaps were found for the two species, and hybrids occurred in multiple contact zones. This association between hybridization pattern and climate niche similarity suggests that the level of hybridization was promoted by niche overlap. Compared with the parental species, similar climate niches were found for the hybrid populations in the QTP, indicating that other environmental factors rather than climate were important for hybrid persistence. Our findings highlight the significance of climate niche with respect to hybridization patterns in plants.