Acknowledging uncertainty in evolutionary reconstructions of ecological niches

Reconstructing ecological niche evolution can provide insight into the biogeography and diversification of evolving lineages. However, comparative phylogenetic methods may infer the history of ecological niche evolution inaccurately because (a) species' niches are often poorly characterized; and (b) phylogenetic comparative methods rely on niche summary statistics rather than full estimates of species' environmental tolerances. Here, we propose a new framework for coding ecological niches and reconstructing their evolution that explicitly acknowledges and incorporates the uncertainty introduced by incomplete niche characterization. Then, we modify existing ancestral state inference methods to leverage full estimates of environmental tolerances. We provide a worked empirical example of our method, investigating ecological niche evolution in the New World orioles (Aves: Passeriformes: Icterus spp.). Temperature and precipitation tolerances were generally broad and conserved among orioles, with niche reduction and specialization limited to a few terminal branches. Tools for performing these reconstructions are available in a new R package called nichevol.     

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.     

Competition and Facilitation in the Capuchin–Squirrel Monkey Relationship

In Guyana, the range of the brown capuchin, Cebus apella, meets the range of its congener, the wedge‐capped capuchin, C. olivaceus, with the two species exhibiting a mutually exclusive patchy distribution. Squirrel monkeys, Saimiri sciureus, and C. apella form ubiquitous interspecific associations, but the reason remains debatable. With a large biogeographic field study, we tested the degree to which the distribution and abundance of Cebus and S. sciureus is determined by habitat type, fruit availability, and geography (i.e., determinants of the fundamental niche) relative to interspecific interactions, such as competition and facilitation (i.e., the realized niche). We used the competition between the two capuchin monkeys as a natural experiment that subjected S. sciureus to C. apella and C. olivaceus ‘treatments’. Using spatial regression models and principal components analysis, we found that S. sciureus was associated with seasonally flooded forests, and was correlated with fruit abundance and diversity (fundamental niche), but was also correlated with C. apella density even when accounting for habitat and fruit availability (realized niche). Saimiri sciureus density was unrelated to C. olivaceus density. Cebus apella was associated with a variety of forest types, but particularly included disturbed and edge habitats such as logged forests, seasonally flooded forests, and upland savanna, in addition to mature forest. Cebus apella was also positively correlated with S. sciureus density and negatively correlated with the density of C. olivaceus. In contrast, C. olivaceus avoided riparian areas and was associated with mixed‐height forests on sloped mountainous terrain. In sum, interspecific interactions such as competition between species of Cebus and facilitation between C. apella and S. sciureus were as important as habitat and fruit availability in determining the distribution and abundance of these primates.     

Sex and occupation time influence niche space of a recovering keystone predator

Predators exert strong effects on ecological communities, particularly when they re‐occupy areas after decades of extirpation. Within species, such effects can vary over time and by sex and cascade across trophic levels. We used a space‐for‐time substitution to make foraging observations of sea otters (Enhydra lutris) across a gradient of reoccupation time (1–30 years), and nonmetric multidimensional scaling (nMDS) analysis to ask whether (a) sea otter niche space varies as a function of occupation time and (b) whether niche space varies by sex. We found that niche space varied among areas of different occupation times. Dietary niches at short occupation times were dominated by urchins (Mesocentrotus and Strongylocentrotus spp; >60% of diets) in open habitats at 10–40 m depths. At longer occupation times, niches were dominated by small clams (Veneroida; >30% diet), mussels (Mytilus spp; >20% diet), and crab (Decapoda; >10% diet) in shallow (<10 m) kelp habitats. Diet diversity was lowest (H′ = 1.46) but energy rich (~37 kcal/min) at the earliest occupied area and highest, but energy poor (H′ = 2.63, ~9 kcal/min) at the longest occupied area. A similar transition occurred through time at a recently occupied area. We found that niche space also differed between sexes, with bachelor males consuming large clams (>60%), and urchins (~25%) from deep waters (>40 m), and females and territorial males consuming smaller, varied prey from shallow waters (<10 m). Bachelor male diets were less diverse (H′ = 2.21) but more energy rich (~27 kcal/min) than territorial males (H′ = 2.54, ~13 kcal/min) and females (H′ = 2.74, ~11 kcal/min). Given recovering predators require adequate food and space, and the ecological interactions they elicit, we emphasize the importance of investigating niche space over the duration of recovery and considering sex‐based differences in these interactions.     

Age‐related variation in the trophic characteristics of a marsupial carnivore,the Tasmanian devil Sarcophilus harrisii

Age‐related changes in diet have implications for competitive interactions and for predator–prey dynamics, affecting individuals and groups at different life stages. To quantify patterns of variation and ontogenetic change in the diets of Tasmanian devils Sarcophilus harrisii, a threatened marsupial carnivore, we analyzed variation in the stable isotope composition of whisker tissue samples taken from 91 individual devils from Wilmot, Tasmania from December 2014 to February 2017. Both δ¹³C and δ¹⁵N decreased with increasing age in weaned Tasmanian devils, indicating that as they age devils rely less on small mammals and birds, and more on large herbivores. Devils <12 months old had broader group isotopic niches, as estimated by Bayesian standard ellipses (SEA_B mode = 1.042) than devils from 12 to 23 months old (mode = 0.541) and devils ≥24 months old (mode = 0.532). Devils <24 months old had broader individual isotopic niches (SEA_B mode range 0.492–1.083) than devils ≥24 months old (mode range 0.092–0.240). A decrease in δ¹⁵N from the older whisker sections to the more recently grown sections in devils <24 months old likely reflects the period of weaning in this species, as this pattern was not observed in devils ≥24 months old. Our data reveal changes in the isotopic composition of devil whiskers with increasing age, accompanied by a reduction in isotopic variation both among population age classes and within individuals, reflecting the effect of weaning in early life, and a likely shift from an initially diverse diet of small mammals, birds, and invertebrates towards increasing consumption of larger herbivores in adulthood.     

High invasion potential of Hydrilla verticillata in the Americas predicted using ecological niche modeling combined with genetic data

Ecological niche modeling is an effective tool to characterize the spatial distribution of suitable areas for species, and it is especially useful for predicting the potential distribution of invasive species. The widespread submerged plant Hydrilla verticillata (hydrilla) has an obvious phylogeographical pattern: Four genetic lineages occupy distinct regions in native range, and only one lineage invades the Americas. Here, we aimed to evaluate climatic niche conservatism of hydrilla in North America at the intraspecific level and explore its invasion potential in the Americas by comparing climatic niches in a phylogenetic context. Niche shift was found in the invasion process of hydrilla in North America, which is probably mainly attributed to high levels of somatic mutation. Dramatic changes in range expansion in the Americas were predicted in the situation of all four genetic lineages invading the Americas or future climatic changes, especially in South America; this suggests that there is a high invasion potential of hydrilla in the Americas. Our findings provide useful information for the management of hydrilla in the Americas and give an example of exploring intraspecific climatic niche to better understand species invasion.     

Kit ligand has a critical role in mouse yolk sac and aorta–gonad–mesonephros hematopoiesis

Few studies report on the in vivo requirement for hematopoietic niche factors in the mammalian embryo. Here, we comprehensively analyze the requirement for Kit ligand (Kitl) in the yolk sac and aorta–gonad–mesonephros (AGM) niche. In‐depth analysis of loss‐of‐function and transgenic reporter mouse models show that Kitl‐deficient embryos harbor decreased numbers of yolk sac erythro‐myeloid progenitor (EMP) cells, resulting from a proliferation defect following their initial emergence. This EMP defect causes a dramatic decrease in fetal liver erythroid cells prior to the onset of hematopoietic stem cell (HSC)‐derived erythropoiesis, and a reduction in tissue‐resident macrophages. Pre‐HSCs in the AGM require Kitl for survival and maturation, but not proliferation. Although Kitl is expressed widely in all embryonic hematopoietic niches, conditional deletion in endothelial cells recapitulates germline loss‐of‐function phenotypes in AGM and yolk sac, with phenotypic HSCs but not EMPs remaining dependent on endothelial Kitl upon migration to the fetal liver. In conclusion, our data establish Kitl as a critical regulator in the in vivoAGM and yolk sac endothelial niche.     

Capture efficiency and trophic adaptations of a specialist and generalist predator: A comparison

Specialist true predators are expected to exhibit higher capture efficiencies for the capture of larger and dangerous prey than generalist predators due to their possession of specialized morphological and behavioral adaptations. We used an araneophagous spider (Lampona murina) and a generalist spider (Drassodes lapidosus) as phylogenetically related model species and investigated their realized and fundamental trophic niches and their efficacy with respect to prey capture and prey handling. The trophic niche of both species confirmed that Lampona had a narrow trophic niche with a predominance of spider prey (including conspecifics), while the niche of Drassodes was wide, without any preference. DNA analysis of the gut contents of Lampona spiders collected in the field revealed that spiders form a significant part of its natural diet. Lampona captured significantly larger prey than itself and the prey captured by Drassodes. As concerns hunting strategy, Lampona grasped the prey with two pairs of legs possessing scopulae, whereas Drassodes immobilized prey with silk. Lampona possess forelegs equipped with scopulae and a thicker cuticle similar to other nonrelated araneophagous spiders. Lampona fed for a longer time and extracted more nutrients than Drassodes. We show that specialized behavioral and morphological adaptations altogether increase the hunting efficiency of specialists when compared to generalists.     

Characterizing the trophic niches of stocked and resident cyprinid fishes: consistency in partitioning over time,space and body sizes

Hatchery‐reared fish are commonly stocked into freshwaters to enhance recreational angling. As these fishes are often of high trophic position and attain relatively large sizes, they potentially interact with functionally similar resident fishes and modify food‐web structure. Hatchery‐reared barbel Barbus barbus are frequently stocked to enhance riverine cyprinid fish communities in Europe; these fish can survive for over 20 years and exceed 8 kg. Here, their trophic consequences for resident fish communities were tested using cohabitation studies, mainly involving chub Squalius cephalus, a similarly large‐bodied, omnivorous and long‐lived species. These studies were completed over three spatial scales: pond mesocosms, two streams and three lowland rivers, and used stable isotope analysis. Experiments in mesocosms over 100 days revealed rapid formation of dietary specializations and discrete trophic niches in juvenile B. barbus and S. cephalus. This niche partitioning between the species was also apparent in the streams over 2 years. In the lowland rivers, where fish were mature individuals within established populations, this pattern was also generally apparent in fishes of much larger body sizes. Thus, the stocking of these hatchery‐reared fish only incurred minor consequences for the trophic ecology of resident fish, with strong patterns of trophic niche partitioning and diet specialization. Application of these results to decision‐making frameworks should enable managers to make objective decisions on whether cyprinid fish should be stocked into lowland rivers according to ecological risk.     

Climate‐driven geographic distribution of the desert locust during recession periods: Subspecies’ niche differentiation and relative risks under scenarios of climate change

The desert locust is an agricultural pest that is able to switch from a harmless solitarious stage, during recession periods, to swarms of gregarious individuals that disperse long distances and affect areas from western Africa to India during outbreak periods. Large outbreaks have been recorded through centuries, and the Food and Agriculture Organization keeps a long‐term, large‐scale monitoring survey database in the area. However, there is also a much less known subspecies that occupies a limited area in Southern Africa. We used large‐scale climatic and occurrence data of the solitarious phase of each subspecies during recession periods to understand whether both subspecies climatic niches differ from each other, what is the current potential geographical distribution of each subspecies, and how climate change is likely to shift their potential distribution with respect to current conditions. We evaluated whether subspecies are significantly specialized along available climate gradients by using null models of background climatic differences within and between southern and northern ranges and applying niche similarity and niche equivalency tests. The results point to climatic niche conservatism between the two clades. We complemented this analysis with species distribution modeling to characterize current solitarious distributions and forecast potential recession range shifts under two extreme climate change scenarios at the 2050 and 2090 time horizon. Projections suggest that, at a global scale, the northern clade could contract its solitarious recession range, while the southern clade is likely to expand its recession range. However, local expansions were also predicted in the northern clade, in particular in southern and northern margins of the current geographical distribution. In conclusion, monitoring and management practices should remain in place in northern Africa, while in Southern Africa the potential for the subspecies to pose a threat in the future should be investigated more closely.