Nitrogen and carbon stable isotope analysis sheds light on trophic competition between two syntopic land iguana species from Galápagos.

Coexistence between closely related species can lead to intense competition for resources. Stable isotope analysis (SIA) is a reliable tool to estimate the extent of species competition. We employed SIA to evaluate niche partitioning among two syntopic species of Galápagos land iguanas: Conolophus subcristatus and C. marthae. Samples were collected on Wolf Volcano, Isabela Island, where C. marthae is endemic and syntopic with C. subcristatus. We determined δ13C and δ15N ratios and described the isotopic niche of each species using corrected standard ellipse area (SEAc). We tested for differentiation between the isotopic niches, while controlling for sex, body size, spatial location of samples and mean annual primary productivity at capture points, using bivariate linear models. Despite the extensive overlap of the isotopic niches, we found species and sex to be a significant, interacting predictor of a sample's location in the δ13C, δ15N space, indicating the existence of niche partitioning mechanisms acting between species and sexes. We also found that body size and productivity at the capture points, compounded with yet undetermined spatial effects, explain ca. 75% of the differences observed between species and sexes, providing evidence for differential microhabitat and food-items usage. Our study provides essential baselines for evaluating conservation actions for C. marthae, such as the potential translocation to a sanctuary area free of competition from C. subcristatus.

Population dynamics and genetic connectivity in recent chimpanzee history.

Knowledge on the population history of endangered species is critical for conservation, but whole-genome data on chimpanzees (Pan troglodytes) is geographically sparse. Here, we produced the first non-invasive geolocalized catalog of genomic diversity by capturing chromosome 21 from 828 non-invasive samples collected at 48 sampling sites across Africa. The four recognized subspecies show clear genetic differentiation correlating with known barriers, while previously undescribed genetic exchange suggests that these have been permeable on a local scale. We obtained a detailed reconstruction of population stratification and fine-scale patterns of isolation, migration, and connectivity, including a comprehensive picture of admixture with bonobos (Pan paniscus). Unlike humans, chimpanzees did not experience extended episodes of long-distance migrations, which might have limited cultural transmission. Finally, based on local rare variation, we implement a fine-grained geolocalization approach demonstrating improved precision in determining the origin of confiscated chimpanzees.

Quantitative estimates of glacial refugia for chimpanzees (Pan troglodytes) since the Last Interglacial (120,000 BP).

Paleoclimate reconstructions have enhanced our understanding of how past climates have shaped present-day biodiversity. We hypothesize that the geographic extent of Pleistocene forest refugia and suitable habitat fluctuated significantly in time during the late Quaternary for chimpanzees (Pan troglodytes). Using bioclimatic variables representing monthly temperature and precipitation estimates, past human population density data, and an extensive database of georeferenced presence points, we built a model of changing habitat suitability for chimpanzees at fine spatio-temporal scales dating back to the Last Interglacial (120,000 BP). Our models cover a spatial resolution of 0.0467° (approximately 5.19 km2 grid cells) and a temporal resolution of between 1000 and 4000 years. Using our model, we mapped habitat stability over time using three approaches, comparing our modeled stability estimates to existing knowledge of Afrotropical refugia, as well as contemporary patterns of major keystone tropical food resources used by chimpanzees, figs (Moraceae), and palms (Arecacae). Results show habitat stability congruent with known glacial refugia across Africa, suggesting their extents may have been underestimated for chimpanzees, with potentially up to approximately 60,000 km2 of previously unrecognized glacial refugia. The refugia we highlight coincide with higher species richness for figs and palms. Our results provide spatio-temporally explicit insights into the role of refugia across the chimpanzee range, forming the empirical foundation for developing and testing hypotheses about behavioral, ecological, and genetic diversity with additional data. This methodology can be applied to other species and geographic areas when sufficient data are available.

Recent genetic connectivity and clinal variation in chimpanzees.

Much like humans, chimpanzees occupy diverse habitats and exhibit extensive behavioural variability. However, chimpanzees are recognized as a discontinuous species, with four subspecies separated by historical geographic barriers. Nevertheless, their range-wide degree of genetic connectivity remains poorly resolved, mainly due to sampling limitations. By analyzing a geographically comprehensive sample set amplified at microsatellite markers that inform recent population history, we found that isolation by distance explains most of the range-wide genetic structure of chimpanzees. Furthermore, we did not identify spatial discontinuities corresponding with the recognized subspecies, suggesting that some of the subspecies-delineating geographic barriers were recently permeable to gene flow. Substantial range-wide genetic connectivity is consistent with the hypothesis that behavioural flexibility is a salient driver of chimpanzee responses to changing environmental conditions. Finally, our observation of strong local differentiation associated with recent anthropogenic pressures portends future loss of critical genetic diversity if habitat fragmentation and population isolation continue unabated.

Population Dynamics and Structural Effects at Short and Long Range Support the Hypothesis of the Selective Advantage of the G614 SARS-CoV-2 Spike Variant.

SARS-CoV-2 epidemics quickly propagated worldwide, sorting virus genomic variants in newly established propagules of infections. Stochasticity in transmission within and between countries or an actual selective advantage could explain the global high frequency reached by some genomic variants. Using statistical analyses, demographic reconstructions, and molecular dynamics simulations, we show that the globally invasive G614 spike variant 1) underwent a significant demographic expansion in most countries explained neither by stochastic effects nor by overrepresentation in clinical samples, 2) increases the spike S1/S2 furin-like site conformational plasticity (short-range effect), and 3) modifies the internal motion of the receptor-binding domain affecting its cross-connection with other functional domains (long-range effect). Our results support the hypothesis of a selective advantage at the basis of the spread of the G614 variant, which we suggest may be due to structural modification of the spike protein at the S1/S2 proteolytic site, and provide structural information to guide the design of variant-specific drugs.

Sooty mangabeys scavenge on nuts cracked by chimpanzees and red river hogs-An investigation of inter-specific interactions around tropical nut trees.

Carrion scavenging is a well-studied phenomenon, but virtually nothing is known about scavenging on plant material, especially on remnants of cracked nuts. Just like meat, the insides of hard-shelled nuts are high in energetic value, and both foods are difficult to acquire. In the Taï forest, chimpanzees (Pan troglodytes) and red river hogs (Potamochoerus porcus) crack nuts by using tools or strong jaws, respectively. In this study, previously collected non-invasive camera trap data were used to investigate scavenging by sooty mangabeys (Cercocebus atys), two species of Guinea fowl (Agelestres meleagrides; Guttera verreauxi), and squirrels (Scrunidae spp.) on the nut remnants cracked by chimpanzees and red river hogs. We investigated how scavengers located nut remnants, by analyzing their visiting behavior in relation to known nut-cracking events. Furthermore, since mangabeys are infrequently preyed upon by chimpanzees, we investigated whether they perceive an increase in predation risk when approaching nut remnants. In total, 190 nut-cracking events were observed in four different areas of Taï National Park, Ivory Coast. We could confirm that mangabeys scavenged on the nuts cracked by chimpanzees and hogs and that this enabled them to access food source that would not be accessible otherwise. We furthermore found that mangabeys, but not the other species, were more likely to visit nut-cracking sites after nut-cracking activities than before, and discuss the potential strategies that the monkeys could have used to locate nut remnants. In addition, mangabeys showed elevated levels of vigilance at the chimpanzee nut-cracking sites compared with other foraging sites, suggesting that they perceived elevated danger at these sites. Scavenging on remnants of cracked nuts is a hitherto understudied type of foraging behavior that could be widespread in nature and increases the complexity of community ecology in tropical rainforests.

Do chimpanzees anticipate an object's weight? A field experiment on the kinematics of hammer-lifting movements in the nut-cracking Taï chimpanzees.

When humans are about to manipulate an object, our brains use visual cues to recall an internal representation to predict its weight and scale the lifting force accordingly. Such a long-term force profile, formed through repeated experiences with similar objects, has been proposed to improve manipulative performance. Skillful object manipulation is crucial for many animals, particularly those that rely on tools for foraging. However, despite enduring interest in tool use in non-human animals, there has been very little investigation of their ability to form an expectation about an object's weight. In this study, we tested whether wild chimpanzees use long-term force profiles to anticipate the weight of a nut-cracking hammer from its size. To this end, we conducted a field experiment presenting chimpanzees with natural wooden hammers and artificially hollowed, lighter hammers of the same size and external appearance. We used calibrated videos from camera traps to extract kinematic parameters of lifting movements. We found that, when lacking previous experience, chimpanzees lifted hollowed hammers with a higher acceleration than natural hammers (overshoot effect). After using a hammer to crack open one nut, chimpanzees tuned down the lifting acceleration for the hollowed hammers, but continued lifting natural hammers with the same acceleration. Our results show that chimpanzees anticipate the weight of an object using long-term force profiles and suggest that, similarly to humans, they use internal representations of weight to plan their lifting movements.

Which Latitudinal Gradients for Genetic Diversity?

A recent global analysis of GenBank DNA sequences from amphibians and mammals indicated consistent poleward decrease of intraspecific genetic diversity in both classes. We highlight that this result was biased by not accounting for distance decay of similarity and reanalyse the datasets, revealing distinct latitudinal gradients in mammals and amphibians.

Long live the alien: is high genetic diversity a pivotal aspect of crested porcupine (Hystrix cristata) long-lasting and successful invasion?

Studying the evolutionary dynamics of an alien species surviving and continuing to expand after several generations can provide fundamental information on the relevant features of clearly successful invasions. Here, we tackle this task by investigating the dynamics of the genetic diversity in invasive crested porcupine (Hystrix cristata) populations, introduced to Italy about 1500 years ago, which are still growing in size, distribution range and ecological niche. Using genome-wide RAD markers, we describe the structure of the genetic diversity and the demographic dynamics of the H. cristata invasive populations and compare their genetic diversity with that of native African populations of both H. cristata and its sister species, H. africaeaustralis. First, we demonstrate that genetic diversity is lower in both the invasive Italian and the North Africa source range relative to other native populations from sub-Saharan and South Africa. Second, we find evidence of multiple introduction events in the invasive range followed by very limited gene flow. Through coalescence-based demographic reconstructions, we also show that the bottleneck at introduction was mild and did not affect the introduced genetic diversity. Finally, we reveal that the current spatial expansion at the northern boundary of the range is following a leading-edge model characterized by a general reduction of genetic diversity towards the edge of the expanding range. We conclude that the level of genome-wide diversity of H. cristata invasive populations is less important in explaining its successful invasion than species-specific life-history traits or the phylogeographic history in the native source range.

Testing Classical Species Properties with Contemporary Data: How "Bad Species" in the Brassy Ringlets (Erebia tyndarus complex, Lepidoptera) Turned Good.

All species concepts are rooted in reproductive, and ultimately genealogical, relations. Genetic data are thus the most important source of information for species delimitation. Current ease of access to genomic data and recent computational advances are blooming a plethora of coalescent-based species delimitation methods. Despite their utility as objective approaches to identify species boundaries, coalescent-based methods (1) rely on simplified demographic models that may fail to capture some attributes of biological species, (2) do not make explicit use of the geographic information contained in the data, and (3) are often computationally intensive. In this article, we present a case of species delimitation in the Erebia tyndarus species complex, a taxon regarded as a classic example of problematic taxonomic resolution. Our approach to species delimitation used genomic data to test predictions rooted in the biological species concept and in the criterion of coexistence in sympatry. We (1) obtained restriction-site associated DNA (RAD) sequencing data from a carefully designed sample, (2) applied two genotype clustering algorithms to identify genetic clusters, and (3) performed within-clusters and between-clusters analyses of isolation by distance as a test for intrinsic reproductive barriers. Comparison of our results with those from a Bayes factor delimitation coalescent-based analysis, showed that coalescent-based approaches may lead to overconfident splitting of allopatric populations, and indicated that incorrect species delimitation is likely to be inferred when an incomplete geographic sample is analyzed. While we acknowledge the theoretical justification and practical usefulness of coalescent-based species delimitation methods, our results stress that, even in the phylogenomic era, the toolkit for species delimitation should not dismiss more traditional, biologically grounded, approaches coupling genomic data with geographic information.

The evolutionary jigsaw puzzle of the surviving trout (Salmo trutta L. complex) diversity in the Italian region. A multilocus Bayesian approach.

Mediterranean trout populations display a diversity of phenotypes, representing a valuable model for the study of adaptation and a puzzling dilemma for taxonomists and biogeographers, which is further entangled by the widespread introgression of allochthonous genes. In this paper we analysed DNA polymorphism at multiple loci (sequence variation of the mitochondrial control region and eight nuclear fragments and length variation at eleven nuclear microsatellite loci) in representative samples of the autochthonous taxonomic diversity described in Italian trout populations (Salmo marmoratus, S. carpio, S. cenerinus, S. cettii and S. fibreni) and in samples from hatchery-originated strains of Atlantic S. trutta. We employed model-based clustering and Approximate Bayesian Computation in order to: (i) describe the phylogeographic structure of Italian autochthonous trout populations; (ii) evaluate a set of evolutionary/biogeographic models. The inclusion of hatchery-originated strains allowed to account for man-mediated allochthonous introgression in Italian populations. Our results (i) showed that the analysed sample consists of two main autochthonous evolutionary lineages, including the marble trout populations on one side ('marble' lineage) and the three peninsular populations of S. cettii, S. cenerinus and S. fibreni on the other side ('peninsular' lineage); (ii) indicated that S. carpio originated from a 'peninsular' population, with a possible, limited contribution from the 'marble' lineage; (iii) pointed out that the 'marble' lineage started diverging before the separation of the 'peninsular' lineage from Atlantic S. trutta; (iv) suggested that a model of divergence involving gene flow from the 'peninsular' population into the ancestral gene pool of 'marble' trout is most consistent with the genetic data; (v) provided evidence that the autochthonous trout gene pools in the Tyrrhenian and Adriatic basins of the Italian peninsula started diverging very recently (most likely after the last glacial maximum).

King penguin demography since the last glaciation inferred from genome-wide data.

How natural climate cycles, such as past glacial/interglacial patterns, have shaped species distributions at the high-latitude regions of the Southern Hemisphere is still largely unclear. Here, we show how the post-glacial warming following the Last Glacial Maximum (ca 18 000 years ago), allowed the (re)colonization of the fragmented sub-Antarctic habitat by an upper-level marine predator, the king penguin Aptenodytes patagonicus. Using restriction site-associated DNA sequencing and standard mitochondrial data, we tested the behaviour of subsets of anonymous nuclear loci in inferring past demography through coalescent-based and allele frequency spectrum analyses. Our results show that the king penguin population breeding on Crozet archipelago steeply increased in size, closely following the Holocene warming recorded in the Epica Dome C ice core. The following population growth can be explained by a threshold model in which the ecological requirements of this species (year-round ice-free habitat for breeding and access to a major source of food such as the Antarctic Polar Front) were met on Crozet soon after the Pleistocene/Holocene climatic transition.