Noninvasive paternity assignment in Gombe chimpanzees

The relative success of chimpanzee male mating strategies, the role of male dominance rank and the success of inbreeding avoidance behaviour can only be assessed when paternities are known. We report the probable paternities of 14 chimpanzees included in a long‐term behavioural study of chimpanzees (Pan troglodytes schweinfurthii) at Gombe National Park, Tanzania. DNA samples were collected noninvasively from shed hair and faeces and genotyped using 13–16 microsatellite loci characterized in humans. All 14 offspring could be assigned to fathers within the community. While there is a positive relationship between male rank and reproductive success, we demonstrate that a range of male mating strategies (possessiveness, opportunistic mating and consortships) can lead to paternity across all male ranks. Several adult females were at risk of breeding with close male relatives. Most successfully avoided close inbreeding but in one case a high‐ranking male in the community mated with his mother and produced an offspring. In contrast to recent data on chimpanzees (P. t. verus) from the Taï forest, Côte d’Ivoire, no evidence of extra‐group paternity was observed in our study. Reanalysis of Taï data using a likelihood approach casts doubt on the occurrence of extra‐group paternity in that community as well.     

The Long‐term Impact of Timber Harvesting on the Resource Base of Chimpanzees in Kibale National Park,Uganda

Commercial timber harvesting results in the loss of critical habitat for tropical forest fauna, and large‐bodied frugivores (including chimpanzees and most other apes) may experience particularly detrimental effects. Few quantitative data, however, are available to evaluate the long‐term impact of harvesting on chimpanzees and other apes. In particular, few data are available to compare population demographics and/or forest composition before and after timber harvesting at the same site. Utilizing detailed forestry department records of logging operations conducted in the late 1960s, present‐day botanical surveys, and long‐term data on the feeding ecology of chimpanzees in Kibale National Park (KNP), Uganda, I examined the impact that logging has had on KNP chimpanzee communities of known size and demography. Although some important chimpanzee food resources were harvested in high abundance during commercial logging operations, the overall impact on the most predominant dietary items (those making up roughly 75% of the chimpanzees' diet) and on presumably critical subsistence resources was limited. Furthermore, the low density of chimpanzees inhabiting the logged region of KNP is apparently not attributable to the impact of logging at the site: comparisons of resource densities at this ‘low‐chimpanzee‐density’ site with that of an unlogged and ‘high‐chimpanzee‐density’ KNP site did not differ when logging concessions at the low‐chimpanzee‐density site were excluded from the analysis. This study suggests that low‐intensity logging can be compatible with the conservation of large‐bodied frugivores, provided that dietary data are taken into account in forest management planning.     

Comparison of diaphyseal growth between the Libben population and the Hamann-Todd chimpanzee sample

The differences in limb lengths and proportions between humans and chimpanzees are widely known. Humans have relatively shorter forelimbs and longer hind limbs than chimpanzees. Humans have a longer period of long bone formation than chimpanzees. Recent advances in estimating age-at-death in chimpanzees from their dentition have allowed us to reexamine long bone growth in chimpanzees using their skeletal remains and compare it with similar data for humans. A chronological normalization procedure allowing direct interspecific comparison of long bone growth is presented. The preadult chimpanzee sample (n = 43) is from the Hamann-Todd Osteological Collection from the Cleveland Museum of Natural History. All human specimens (n = 202) are from the late Woodland Libben Population currently housed at Kent State University. Relying on these cross-sectional data, we conclude that both species elongate their femora at similar absolute (length per unit time) but different relative (length relative to normalized dental age) rates. The species differ in the absolute growth rate of the humerus but share a common normalized rate of growth. Forelimb segment proportion differences between species are due to differential elongation rates of the segments. Hind limb diaphyseal proportions are the same in both species, which suggests that changes in segment length are proportional. Therefore, alternative developmental mechanisms exist in these closely related species which can produce changes in limb length. © 1996 Wiley-Liss, Inc.     

The FORMNET‐B database: monitoring the biomass and dynamics of disturbed and degraded tropical forests

The biomass and dynamics of disturbed and degraded tropical forests have mostly been ignored in the recent scientific literature, partly because of a spotlight on old‐growth forests but also due to a lack of long‐term data from degraded forests. There is a pressing need to understand the rates and patterns of growth, mortality and recruitment in degraded forests, not only because they are increasing in area relative to old‐growth forests, but also due to their potential capacity to sequester large amounts of carbon dioxide from the atmosphere. This paper introduces a permanent forest plot network and database, FORMNET‐B (GIVD ID# NA‐BZ‐001), designed to study the long‐term dynamics of disturbed and degraded tropical forests in Belize, Central America.     

Energetic costs of territorial boundary patrols by wild chimpanzees

Chimpanzees are well known for their territorial behavior. Males who belong to the same community routinely patrol their territories, occasionally making deep incursions into those of their neighbors. Male chimpanzees may obtain several fitness benefits by participating in territorial boundary patrols, but patrolling is also likely to involve fitness costs. Patrollers risk injury or even death, and patrols may be energetically costly and may involve opportunity costs. Although territorial patrols have been reported at all long‐term chimpanzee study sites, quantitative data on their energetic costs have not previously been available. I evaluated the energy costs of patrolling for male chimpanzees at Ngogo, Kibale National Park, Uganda during 14 months of observation. In 29 patrols and matched control periods, I recorded the distances covered and time spent traveling and feeding by chimpanzees. I found that male chimpanzees covered longer distances, spent more time traveling, and spent less time feeding during patrols than during control periods. These results support the hypothesis that chimpanzees incur energetic costs while patrolling and suggest that ecological factors may constrain the ability of chimpanzees to patrol. Am. J. Primatol. 72:93–103, 2010. © 2009 Wiley‐Liss, Inc.     

Sixteen years of winter stress: an assessment of cold hardiness,growth performance and survival of hybrid poplar clones at a boreal planting site

In recent years, thousands of hectares of hybrid poplar plantations have been established in Canada for the purpose of carbon sequestration and wood production. However, boreal planting environments pose special challenges that may compromise the long‐term survival and productivity of such plantations. In this study, we evaluated the effect of winter stress, that is, frequent freeze‐thaw and extreme cold events, on growth and survival of 47 hybrid poplar clones in a long‐term field experiment. We further assessed physiological and structural traits that are potentially important for cold tolerance for a selected set of seven clones. We found that trees with narrow xylem vessels showed reduced freezing‐induced embolism and showed superior productivity after 16 growing seasons. With respect to cold hardiness of living tissues, we only observed small differences among clones in early autumn, which were nonetheless significantly correlated to growth. Maximum winter cold hardiness and the timing of leaf senescence and budbreak were not related to growth or survival. In conclusion, our data suggest that reduction of freezing‐induced embolism due to small vessel diameters is an essential adaptive trait to ensure long‐term productivity of hybrid poplar plantations in boreal planting environments.     

Reactions of Bili‐Uele Chimpanzees to Humans in Relation to Their Distance From Roads and Villages

In order to assess the impact of human activities on chimpanzee behavior, we compared reactions to humans of Eastern chimpanzees (Pan troglodytes schweinfurthii) living in proximity to and at a distance from roads and settlements in the Bili‐Uele landscape in Northern Democratic Republic of the Congo (DRC). We found that chimpanzees in the remote Gangu Forest were more likely to show curious or neutral reactions to us and were less likely to flee than those living closer to roads. In addition, arboreal contact durations with Gangu chimpanzees lasted significantly longer than elsewhere. The most likely explanation for this phenomenon is that with increasing distance from roads, chimpanzees have in the recent past had fewer negative encounters with humans, and thus never learned to fear them. The discovery of this population of “naïve chimpanzees” presents us with an important research and conservation opportunity that may result in the installation of a long‐term research site and increased protection of the population. Am. J. Primatol. 74:721‐733, 2012. © 2012 Wiley Periodicals, Inc.     

New Genetic Evidence on the Evolution of Chimpanzee Populations and Implications for Taxonomy

Primatologists widely recognize chimpanzees as belonging to a single species, Pan troglodytes, which they traditionally have further divided into 3 subspecies: west African P. t. verus, central African P. t. troglodytes, and east African P. t. schweinfurthii. Previously, we suggested that the phylogeographic history of chimpanzees may be different from that implied by the widely used taxonomy of the species. We based the suggestion on only a limited sample of haplotypes from the first hypervariable region (HVRI) of mitochondrial (mt)DNA from chimpanzees in Nigeria. We have now compiled a more geographically comprehensive genetic database for chimpanzees, including samples obtained near the Niger and Sanaga Rivers. Our database is composed of 254 HVRI haplotypes from chimpanzees of known geographic origin, including 79 unique HVRI haplotypes from chimpanzees living in Nigeria and Cameroon. The genetic data provide clear evidence that a major phylogeographic break between chimpanzee lineages occurs near the Sanaga River in central Cameroon and suggest the need for a reclassification of chimpanzees.     

Incidence of Extrafloral Nectaries and Their Relationship with Growth and Survival of Lowland Tropical Rain Forest Trees

Mutualistic relationships between organisms have long captivated biologists, and extrafloral nectaries, or nectar‐producing glands, found on many plants are a good example. The nectar produced from these glands provides food for ants, which may defend the plant from potential herbivores in turn. However, relatively little is known about their impact on the long‐term growth and survival of plants that produce them. To better understand the ecological significance of extrafloral nectaries, we examined their incidence on lowland tropical rain forest trees in Yasuní National Park in Amazonian Ecuador, and collated data from two other tropical lowland forest sites (Barro Colorado Island, Panamá and Pasoh Forest Reserve, Malaysia). At Yasuní, extrafloral nectaries were found on 137 of 1123 species censused (12.2%), widely distributed among different angiosperm families. This rate of incidence is high but consistent with other tropical locations. Furthermore, this study adds 18 new genera and two new families (Urticaceae and Caricaceae) to the list of taxa exhibiting extrafloral nectaries. Using demographic data from long‐term forest dynamics plots at each site, we compared the growth and mortality rates of species with extrafloral nectaries to those without. After controlling for phylogeny, no general relationship between extrafloral nectary presence and demographic rates could be detected, suggesting little demographic signal from any community‐wide ecological effects.     

Gastrointestinal parasites of the chimpanzee population introduced onto Rubondo Island National Park,Tanzania

The release of any species into a novel environment can evoke transmission of parasites that do not normally parasitize the host as well as potentially introducing new parasites into the environment. Species introductions potentially incur such risks, yet little is currently known about the parasite fauna of introduced primate species over the long term. We describe the results of long‐term monitoring of the intestinal parasite fauna of an unprovisioned, reproducing population of chimpanzees introduced 40 years earlier (1966–1969) onto Rubondo Island in Lake Victoria, Tanzania, a non‐native habitat for chimpanzees. Two parasitological surveys (March 1997–October 1998 and October 2002–December 2005) identified Entamoeba spp. including E. coli, Iodamoeba buetschlii, Troglodytella abrassarti, Chilomastix mesnili, Trichuris sp., Anatrichosoma sp., Strongyloides spp., Strongylida fam. gen. sp., Enterobius anthropopitheci, Subulura sp., Ascarididae gen. sp., and Protospirura muricola. The parasite fauna of the Rubondo chimpanzees is similar to wild chimpanzees living in their natural habitats, but Rubondo chimpanzees have a lower prevalence of strongylids (9%, 3.8%) and a higher prevalence of E. anthropopitheci (8.6%, 17.9%) than reported elsewhere. Species prevalence was similar between our two surveys, with the exception of Strongyloides spp. being higher in the first survey. None of these species are considered to pose a serious health risk to chimpanzees, but continued monitoring of the population and surveys of the parasitic fauna of the two coinhabitant primate species and other animals, natural reservoir hosts of some of the same parasites, is important to better understand the dynamics of host–parasite ecology and potential long‐term implications for chimpanzees introduced into a new habitat. Am. J. Primatol. 72:307–316, 2010. © 2009 Wiley‐Liss, Inc.     

A quadratic correlation between long‐term mean group size and group density in a cooperatively breeding passerine

Both mean group size (MGS) and mean group density (MGD) are critical indices to characterize a population of cooperatively breeding birds. When a population reaches its carrying capacity, both long‐term MGS and long‐term MGD will remain relatively stable. However, there has been little study of how these two variables relate. The Masked laughingthrush Garrulax perspicillatus is a cooperatively breeding bird living in fragmented habitats. During 2010 and 2012‐2016, we used song playback to observe and confirm the group sizes and territory ranges of the birds and the data of bird presence to determine habitat suitability. By grouping the nearest territories according to their geographical coordinates, we divided the whole study area into 12 subareas and the whole population into 12 subpopulations. Then, we calculated both MGS and MGD for different time durations for each subpopulation. Finally, using MGD as independent variable and MGS as the dependent variable, we explored the correlations between MGS and MGD by fitting quadratic functions and modeling quadratic regression. Both MGS and MGD were averaged for different time durations and were cross‐related. Our results show that the MGS for more than 2 years significantly correlated with MGD for more than 3 years in a reverse parabolic shape, differing from that of short‐term effects. Our findings suggest that long‐term MGD is a better predictor of long‐term habitat quality and that long‐term MGS is determined by long‐term habitat quality in Masked Laughingthrushes. Based on above findings, we can infer that: (1) Long‐term habitat quality determines the long‐term MGS, but it sets no prerequisite for the status and source of group members; (2) Long‐term MGS in certain populations is adapted to the corresponding level of long‐term habitat quality, it facilitates us to predict the helper effects on current or future survival or reproduction in different situations. These findings and inferences are both helpful for us to understand the evolution of cooperative breeding.     

Long‐term metapopulation study of the Glanville fritillary butterfly (Melitaea cinxia): survey methods,data management,and long‐term population trends

Long‐term observational studies conducted at large (regional) spatial scales contribute to better understanding of landscape effects on population and evolutionary dynamics, including the conditions that affect long‐term viability of species, but large‐scale studies are expensive and logistically challenging to keep running for a long time. Here, we describe the long‐term metapopulation study of the Glanville fritillary butterfly (Melitaea cinxia) that has been conducted since 1991 in a large network of 4000 habitat patches (dry meadows) within a study area of 50 by 70 km in the Åland Islands in Finland. We explain how the landscape structure has been described, including definition, delimitation, and mapping of the habitat patches; methods of field survey, including the logistics, cost, and reliability of the survey; and data management using the EarthCape biodiversity platform. We describe the long‐term metapopulation dynamics of the Glanville fritillary based on the survey. There has been no long‐term change in the overall size of the metapopulation, but the level of spatial synchrony and hence the amplitude of fluctuations in year‐to‐year metapopulation dynamics have increased over the years, possibly due to increasing frequency of exceptional weather conditions. We discuss the added value of large‐scale and long‐term population studies, but also emphasize the need to integrate more targeted experimental studies in the context of long‐term observational studies. For instance, in the case of the Glanville fritillary project, the long‐term study has produced an opportunity to sample individuals for experiments from local populations with a known demographic history. These studies have demonstrated striking differences in dispersal rate and other life‐history traits of individuals from newly established local populations (the offspring of colonizers) versus individuals from old, established local populations. The long‐term observational study has stimulated the development of metapopulation models and provided an opportunity to test model predictions. This combination of empirical studies and modeling has facilitated the study of key phenomena in spatial dynamics, such as extinction threshold and extinction debt.     

Resocialization of a group of ex-laboratory chimpanzees, Pan troglodytes.

In order to determine if socially deprived chimpanzees could establish an integrated social unit and reproduce, a group of wild-born individuals from a single-cage laboratory environment were released onto a small island in a South Florida tourist park in 1975. The present study was undertaken during June and July of 1988 to evaluate the long term results of the experiment and to document the reproductive history of the chimpanzees since their release on the island. The evidence presented in this paper suggests that it is possible for laboratory chimpanzees to be resocialized and to reproduce successfully.     

The RAINFOR database: monitoring forest biomass and dynamics

Problem: Data from over 100 permanent sample plots which have been studied for 10–20 years need a suitable system for storage which allows simple data manipulation and retrieval for analysis. Methods: A relational database linking tree records, taxonomic nomenclature and corresponding environmental data has been built in MS Access as part of the RAINFOR project. Conclusion: The database allows flexible and long‐term use of a large amount of data: more than 100 tree plots across Amazonia, incorporating over 80 000 records of individual trees and over 300 000 total records of tree diameter measurements from successive censuses. The database is designed to enable linkages to existing soil, floristic or plant‐trait databases. This database will be a useful tool for exploring the impact of environmental factors on forest structure and dynamics at local to continental scales, and long term changes in forest ecology. As an early example of its potential, we explore the impact of different methodological assumptions on estimates of tropical forest biomass and carbon storage.     

Changing growth response to wildfire in old‐growth ponderosa pine trees in montane forests of north central Idaho

North American fire‐adapted forests are experiencing changes in fire frequency and climate. These novel conditions may alter postwildfire responses of fire‐adapted trees that survive fires, a topic that has received little attention. Historical, frequent, low‐intensity wildfire in many fire‐adapted forests is generally thought to have a positive effect on the growth and vigor of trees that survive fires. Whether such positive effects can persist under current and future climate conditions is not known. Here, we evaluate long‐term responses to recurrent 20th‐century fires in ponderosa pine, a fire‐adapted tree species, in unlogged forests in north central Idaho. We also examine short‐term responses to individual 20th‐century fires and evaluate whether these responses have changed over time and whether potential variability relates to climate variables and time since last fire. Growth responses were assessed by comparing tree‐ring measurements from trees in stands burned repeatedly during the 20th century at roughly the historical fire frequency with trees in paired control stands that had not burned for at least 70 years. Contrary to expectations, only one site showed significant increases in long‐term growth responses in burned stands compared with control stands. Short‐term responses showed a trend of increasing negative effects of wildfire (reduced diameter growth in the burned stand compared with the control stand) in recent years that had drier winters and springs. There was no effect of time since the previous fire on growth responses to fire. The possible relationships of novel climate conditions with negative tree growth responses in trees that survive fire are discussed. A trend of negative growth responses to wildfire in old‐growth forests could have important ramifications for forest productivity and carbon balance under future climate scenarios.     

A note on the responses of chimpanzees (Pan troglodytes) to live self-images on television monitors

The majority of studies on self-recognition in animals have been conducted using a mirror as the test device; little is known, however, about the responses of non-human primates toward their own images in media other than mirrors. This study provides preliminary data on the reactions of 10 chimpanzees to live self-images projected on two television monitors, each connected to a different video camera. Chimpanzees could see live images of their own faces, which were approximately life-sized, on one monitor. On the other monitor, they could see live images of their whole body, which were approximately one-fifth life-size, viewed diagonally from behind. In addition, several objects were introduced into the test situation. Out of 10 chimpanzees tested, 2 individuals performed self-exploratory behaviors while watching their own images on the monitors. One of these two chimpanzees successively picked up two of the provided objects in front of a monitor, and watched the images of these objects on the monitor. The results indicate that these chimpanzees were able to immediately recognize live images of themselves or objects on the monitors, even though several features of these images differed from those of their previous experience with mirrors.     

Incubation temperature influences survival in a small passerine bird

In birds parental incubation behaviour is an important factor shaping the environmental conditions under which the embryos develop, and sub‐optimal incubation temperatures are known to negatively affect early growth and development. It is less well known if variation in incubation temperature can impose life‐long differences in individual performance and survival. In the present study we investigated the effects of incubation temperature on long‐term survival in a small passerine bird. Using our captive population of the zebra finch Taeniopygia guttata we artificially incubated eggs at three biologically relevant temperatures (35.9, 37.0 and 37.9°C) for two‐thirds of the incubation period and then monitored individual lifespan of the hatched chicks for two and a half years. We found that individuals from eggs incubated under the lowest temperature exhibited significantly lower long‐term survival compared to those which had been incubated at the highest temperature. Our results show that incubation temperature in birds, and thus parental incubation behaviour, play an important role in shaping the life‐history trajectories of offspring.     

Ant-dipping among the chimpanzees of Bossou,Guinea, and some comparisons with other sites

We present a detailed study of ant‐dipping among the wild chimpanzees (Pan troglodytes verus) of Bossou, in southeastern Guinea, West Africa. Observations suggest a strong influence of prey (Dorylusspp.) characteristics, including aggressiveness and/or gregariousness, on tool length and technique employed by the chimpanzees. Bossou chimpanzees exhibit two ant‐dipping techniques: 1) direct mouthing, and 2) pull‐through. In addition, they were observed dipping for several species of Dorylus ants, classed into two categories: Red and Black. Tool length was longer when dipping in higher‐risk contexts, i.e., at the ants' nest site or on Black ants. The pull‐through technique was almost exclusively associated with dipping at the nest site. This latter technique was associated with tools over 50cm long, whereas direct mouthing was the only technique observed with tools <50cm long. Our experimental findings, together with our observations on the behavior of the chimpanzees, suggest that at the nest, the pull‐through technique was a more efficient technique than direct mouthing. We review our results in the context of ant‐dipping observed at two other long‐term chimpanzee study sites, i.e., Gombe (Tanzania) and Taï (Côte d'Ivoire), where differences in tool length, technique used, and focal Dorylus ant species have been reported. Finally, we urge similar detailed studies of this tool‐use behavior in both Gombe and Taï to shed further light upon our results and their implications. Am. J. Primatol. 58:133–148, 2002. © 2002 Wiley‐Liss, Inc.     

Latitude and protection affect decadal trends in reef trophic structure over a continental scale

The relative roles of top‐down (consumer‐driven) and bottom‐up (resource‐driven) forcing in exploited marine ecosystems have been much debated. Examples from a variety of marine systems of exploitation‐induced, top‐down trophic forcing have led to a general view that human‐induced predator perturbations can disrupt entire marine food webs, yet other studies that have found no such evidence provide a counterpoint. Though evidence continues to emerge, an unresolved debate exists regarding both the relative roles of top‐down versus bottom‐up forcing and the capacity of human exploitation to instigate top‐down, community‐level effects. Using time‐series data for 104 reef communities spanning tropical to temperate Australia from 1992 to 2013, we aimed to quantify relationships among long‐term trophic group population density trends, latitude, and exploitation status over a continental‐scale biogeographic range. Specifically, we amalgamated two long‐term monitoring databases of marine community dynamics to test for significant positive or negative trends in density of each of three key trophic levels (predators, herbivores, and algae) across the entire time series at each of the 104 locations. We found that trophic control tended toward bottom‐up driven in tropical systems and top‐down driven in temperate systems. Further, alternating long‐term population trends across multiple trophic levels (a method of identifying trophic cascades), presumably due to top‐down trophic forcing, occurred in roughly fifteen percent of locations where the prerequisite significant predator trends occurred. Such alternating trophic trends were significantly more likely to occur at locations with increasing predator densities over time. Within these locations, we found a marked latitudinal gradient in the prevalence of long‐term, alternating trophic group trends, from rare in the tropics (<5% of cases) to relatively common in temperate areas (~45%). Lastly, the strongest trends in predator and algal density occurred in older no‐take marine reserves; however, exploitation status did not affect the likelihood of alternating long‐term trophic group trends occurring. Our data suggest that the type and degree of trophic forcing in this system are likely related to one or more covariates of latitude, and that ecosystem resiliency to top‐down control does not universally vary in this system based on exploitation level.     

snpqc – an R pipeline for quality control of Illumina SNP genotyping array data

In genome‐wide association studies, quality control (QC) of genotypes is important to avoid spurious results. It is also important to maintain long‐term data integrity, particularly in settings with ongoing genotyping (e.g. estimation of genomic breeding values). Here we discuss snpqc , a fully automated pipeline to perform QC analyses of Illumina SNP array data. It applies a wide range of common quality metrics with user‐defined filtering thresholds to generate a comprehensive QC report and a filtered dataset, including a genomic relationship matrix, ready for further downstream analyses which make it amenable for integration in high‐throughput environments. snpqc also builds a database to store genotypic, phenotypic and quality metrics to ensure data integrity and the option of integrating more samples from subsequent runs. The program is generic across species and array designs, providing a convenient interface between the genotyping laboratory and downstream genome‐wide association study or genomic prediction.