Newly Discovered Bale Monkey Populations in Forest Fragments in Southern Ethiopia: Evidence of Crop Raiding, Hybridization With Grivets, and Other Conservation Threats

Terrestrial medium and large-sized mammalian species diversity in Michole Community Protected Forest, southern Ethiopia

The study on medium and large-sized mammalian species' diversity and distribution is important for conservation efforts in the different protected areas of Ethiopia. The present study was intended to investigate the species diversity of medium and large-sized mammalian fauna between October 2019 and July 2020 in Michole Community Protected Forest, southern Ethiopia. The study was conducted by stratification of the study area into three habitat types: riverine forest (3.37 km2), woodland (4.14 km2), and grassland with scattered trees (2.33 km2) based on the vegetation cover. A diurnal transect survey method was implemented to record the mammalian species diversity. A total of 18 representative sample transect lines (six in riverine forest, four in grassland with scattered trees, and eight in woodland habitats) that varied in length and width were used. A total of 17 species of medium and large-sized mammalian species were identified and recorded in the study area. As a result, the orders Carnivora and Primates have the greatest abundance, while the order Lagomorpha has the least. Anubis baboon (Papio anubis) was the most abundant species (15.14%), followed by Spotted hyena (Crocuta crocuta) (12.98%), Crested porcupine (Hystrix cristata) (12.51%), Vervet monkey (Chlorocebus aethiops) (10.35%), Common duiker (Sylvicapra grimmia) (8.80%), and Giant root-rat (Tachyoryctes macrocephalus) (8.65%). The distributions of mammals among the three habitat types were comparable. The riverine forest harbored the highest mammalian diversity index (H′ = 2.35) followed by the woodland (H′ = 2.32), and the grassland with scattered trees (H′ = 2.30), respectively. The greatest species similarity was recorded in woodland (0.902). The study area harbors considerable mammalian species that are threatened by interacting anthropogenic factors. So, urgent conservation measures by concerned sectors are needed to safeguard these animals and their habitat.

Sleeping Site and Tree Selection by Bale Monkeys (Chlorocebus djamdjamensis) at Kokosa Forest Fragment in Southern Ethiopia

Although selecting advantageous sleeping sites is crucial for nonhuman primates, the extent to which different factors contribute to their selection remains largely unknown for many species. We investigated hypotheses relating to predator avoidance, food access, and thermoregulation to explain the sleeping behavior of Bale monkeys (Chlorocebus djamdjamensis) occupying a degraded fragmented forest, Kokosa, in the southern Ethiopian Highlands. We found that the study group reused 11 out of 20 sleeping sites used during the 42 study days over a 6-month period. Sleeping sites were usually close to the last feeding trees of the day (mean distance =15.2 m) and/or the first feeding trees of the next morning (mean distance = 13.5 m). This may reflect an attempt to maximize feeding efficiency and reduce travel costs. Compared to the mean trees in the study area, sleeping trees were significantly shorter. Bale monkeys selected sleeping places in trees with high foliage density above and below them, lending support to the hypothesis that they select sleeping places that can conceal them from predators and at the same time offer shelter from cold weather. The monkeys also frequently huddled at night. Our results suggest that predator avoidance, access to food resources, and thermoregulation all likely influence the selection of sleeping sites by Bale monkeys.

Distribution and conservation status of Boutourlini's blue monkey (Cercopithecus mitis boutourlinii), a Vulnerable subspecies endemic to western Ethiopia

Reliable data on the distribution and threats facing primate species are crucial to identifying priority sites for conservation and designing effective management plans. Boutourlini's blue monkey (Cercopithecus mitis boutourlinii) is a little-known arboreal primate endemic to the forests of western Ethiopia. This subspecies is categorized as Vulnerable on the International Union for Conservation of Nature (IUCN) Red List and the distribution of extant populations is largely unknown. To increase our knowledge of the spatial distribution and conservation status of Boutourlini's blue monkey, we carried out intensive reconnaissance surveys from January 2010 to May 2011 across approximately 40% of its potential range and conducted interviews with local people at each of the survey locations. We carried out geospatial analyses and mapped the distribution of Boutourlini's blue monkey localities with respect to elevation, protected area status, and changes in forest cover over time using ArcGIS 10.4.0. Through our surveys, we discovered 30 previously unknown Boutourlini's blue monkey populations in three administrative regions of western Ethiopia (Amhara, Oromia, and Southern Nations, Nationalities and People's Regions). A total of 34 different groups were sighted and counted at the survey sites, averaging 14.7 members (range 8-23) per group. There are now 32 Boutourlini's blue monkey populations of recently confirmed occurrence at altitudes ranging from 1039 to 2780 m asl, seven in forests of greater than 50 km². Crop feeding by Boutourlini's blue monkeys was reported by people at seven sites and confirmed through direct observation at three of these sites. None of the known extant populations of Boutourlini's blue monkeys occur within a strictly protected area (e.g., national park) where exploitative human activities are outlawed. A complete reassessment of the distribution and conservation status of Boutourlini's blue monkey will require further surveys across the remaining approximately 60% of its potential range.

Large Mammal Diversity and Endemism at Geremba Mountain Fragment, Southern Ethiopia

Outside protected areas in Ethiopia, there is a lack of information concerning mammalian diversity and ecology. Consequently, the findings of the research on large mammals at Geremba Mountain constitute one of the steps towards a continuing effort to document the diversity and distribution of Ethiopian mammals. The survey was conducted to investigate the species composition, relative abundance, and population structure of large mammals at Geremba Mountain fragment from August 2017 to February 2018, covering both dry and wet seasons. Direct (sighting) and indirect (scat) survey techniques were employed using systematically established transect lines and sampling plots, respectively. Transects and plots were established across three dominant habitat types (modified dry ever green Afromontane forest, alpine bamboo forest, and Erica scrubland). A total of 10 large mammal species were recorded including two endemic mammals, namely, Chlorocebus djamdjamensis and Tragelaphus scriptus meneliki. There was a statistically significant difference in the abundance of species among habitat types at Geremba Mountain. The highest diversity index was recorded in the alpine bamboo forest habitat (D = 7.142, H′ = 2.052), and the Erica scrubland had the lowest. Papio anubis was the most abundant species while Felis serval was the least abundant species. The populations of most of the species were characterized by more adult and more female individuals. However, promising young individuals of the endemic mammals (C. djamdjamensis and T. s. meneliki) and Papio anubis were recorded. The mountain fragment is an isolated island that is totally disconnected with other fragments in the region, so attempts should be made to connect the fragment with other fragments using wildlife corridors.

Forest fragments become farmland: Dietary Response of wild chimpanzees (Pan troglodytes) to fast-changing anthropogenic landscapes

Behavioral flexibility, including an ability to modify feeding behavior, is a key trait enabling primates to survive in forest fragments. In human-dominated landscapes, unprotected forest fragments can become progressively degraded, and may be cleared entirely, challenging the capacity of primates to adjust to the changes. We examined responses of wild chimpanzees (Pan troglodytes schweinfurthii) to major habitat change: that is, clearance of forest fragments for agriculture. Over 7 years, fragments in Bulindi, Uganda, were reduced in size by 80%. We compared the chimpanzees' diet at the start and end of this period of rapid deforestation, using data derived mainly from fecal analysis. Similar to other long-term study populations, chimpanzees in Bulindi have a diverse diet comprising over 169 plant foods. However, extensive deforestation seemed to impact their feeding ecology. Dietary changes after fragment clearance included reduced overall frugivory, reduced intake of figs (Ficus spp.; formerly a dietary "staple" for these chimpanzees), and reduced variety of fruits in fecal samples. Nevertheless, the magnitude of most changes was remarkably minor given the extent of forest loss. Agricultural fruits increased in dietary importance, with crops accounting for a greater proportion of fruits in fecal samples after deforestation. In particular, cultivated jackfruit (Artocarpus heterophyllus) became a "staple" food for the chimpanzees but was scarcely eaten before fragment clearance. Crops offer some nutritional benefits for primates, being high in carbohydrate energy and low in hard-to-digest fiber. Thus, crop feeding may have offset foraging costs associated with loss of wild foods and reduced overall frugivory for the chimpanzees. The adaptability of many primates offers hope for their conservation in fragmented, rural landscapes. However, long-term data are needed to establish whether potential benefits (i.e. energetic, reproductive) of foraging in agricultural matrix habitats outweigh fitness costs from anthropogenic mortality risk for chimpanzees and other adaptable primates.

Crop Foraging, Crop Losses, and Crop Raiding

Crop foraging or crop raiding concerns wildlife foraging and farmers’ reactions and responses to it. To understand crop foraging and its value to wildlife or its implications for humans requires a cross-disciplinary approach that considers the behavior and ecology of wild animals engaging in this behavior; the types and levels of competition for resources between people and wildlife; people's perceptions of and attitudes toward wildlife, including animals that forage on crops; and discourse about animals and their behaviors and how these discourses can be used for expressing dissent and distress about other social conflicts. So, to understand and respond to conflicts about crop damage, we need to look beyond what people lose, i.e., crop loss and economic equivalence, and focus more on what people say about wildlife and why they say it.

Population genetic structure and evolutionary history of Bale monkeys (Chlorocebus djamdjamensis) in the southern Ethiopian Highlands

Background

Species with a restricted geographic distribution, and highly specialized habitat and dietary requirements, are particularly vulnerable to extinction. The Bale monkey (Chlorocebus djamdjamensis) is a little-known arboreal, bamboo-specialist primate endemic to the southern Ethiopian Highlands. While most Bale monkeys inhabit montane forests dominated by bamboo, some occupy forest fragments where bamboo is much less abundant. We used mitochondrial DNA (mtDNA) sequences to analyse the genetic structure and evolutionary history of Bale monkeys covering the majority of their remaining distribution range. We analysed 119 faecal samples from their two main habitats, continuous forest (CF) and fragmented forests (FF), and sequenced 735 bp of the hypervariable region I (HVI) of the control region. We added 12 orthologous sequences from congeneric vervets (C. pygerythrus) and grivets (C. aethiops) as well as animals identified as hybrids, previously collected in southern Ethiopia.

Results

We found strong genetic differentiation (with no shared mtDNA haplotypes) between Bale monkey populations from CF and FF. Phylogenetic analyses revealed two distinct and highly diverged clades: a Bale monkey clade containing only Bale monkeys from CF and a green monkey clade where Bale monkeys from FF cluster with grivets and vervets. Analyses of demographic history revealed that Bale monkey populations (CF and FF) have had stable population sizes over an extended period, but have all recently experienced population declines.

Conclusions

The pronounced genetic structure and deep mtDNA divergence between Bale monkey populations inhabiting CF and FF are likely to be the results of hybridization and introgression of the FF population with parapatric Chlorocebus species, in contrast to the CF population, which was most likely not impacted by hybridization. Hybridization in the FF population was probably enhanced by an alteration of the bamboo forest habitat towards a more open woodland habitat, which enabled the parapatric Chlorocebus species to invade the Bale monkey's range and introgress the FF population. We therefore propose that the CF and FF Bale monkey populations should be managed as separate units when developing conservation strategies for this threatened species.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1217-y) contains supplementary material, which is available to authorized users.

Dietary flexibility of Bale monkeys (Chlorocebus djamdjamensis) in southern Ethiopia: effects of habitat degradation and life in fragments

BACKGROUND

Understanding the effects of habitat modification on the feeding strategies of threatened species is essential to designing effective conservation management plans. Bale monkeys (Chlorocebus djamdjamensis) are endemic to the rapidly shrinking montane forests of the southern Ethiopian Highlands. Most populations inhabit continuous bamboo forest subsisting largely on the young leaves and shoots of a single species of bamboo. Because of habitat disturbance in recent decades, however, there are now also several dozen small populations inhabiting isolated forest fragments where bamboo has been degraded. During 12-months, we assessed Bale monkey responses to habitat degradation by comparing habitat composition, phenological patterns, and feeding ecology in a largely undisturbed continuous forest (Continuous groups A and B) and in two fragments (Patchy and Hilltop groups).

RESULTS

We found that habitat quality and food availability were much lower in fragments than in continuous forest. In response to the relative scarcity of bamboo in fragments, Bale monkeys spent significantly less time feeding on the young leaves and shoots of bamboo and significantly more time feeding on non-bamboo young leaves, fruits, seeds, stems, petioles, and insects in fragments than in continuous forest. Groups in fragments also broadened their diets to incorporate many more plant species (Patchy: ≥ 47 and Hilltop: ≥ 35 species)-including several forbs, graminoids and cultivated crops-than groups in continuous forest (Continuous A: 12 and Continuous B: 8 species). Nevertheless, bamboo was still the top food species for Patchy group (30% of diet) as well as for both continuous forest groups (mean = 81%). However, in Hilltop group, for which bamboo was especially scarce, Bothriochloa radicans (Poaceae), a grass, was the top dietary species (15% of diet) and bamboo ranked 10th (2%).

CONCLUSIONS

We demonstrate that Bale monkeys are more dietarily flexible than previously thought and able to cope with some degradation of their primary bamboo forest habitat. However, crop raiding and other terrestrial foraging habits more common among fragment groups may place them at greater risk of hunting by humans. Thus, longitudinal monitoring is necessary to evaluate the long-term viability of Bale monkey populations in fragmented habitats.

Ecological plasticity in the gastrointestinal microbiomes of Ethiopian Chlorocebus monkeys

Human activities can cause habitat degradation that may alter the types and quality of available food resources and thus influence the microbiomes of wild animal populations. Furthermore, seasonal shifts in food availability may cause adaptive responses in the gut microbiome to meet the need for different metabolic capabilities. Here, we demonstrate local-scale population structure in the gastrointestinal microbiotas of Chlorocebus monkeys, in southern Ethiopia, in response to varying degrees of human encroachment. We further provide evidence of adaptation to ecological conditions associated with the dry and wet seasons, and show seasonal effects to be more pronounced in areas with limited human activity. Finally, we report species-level microbiota differences between the endemic Ethiopian Bale monkey, an ecological specialist, and generalist Chlorocebus species from the same geographical region.

Diet and activity patterns of Arsi geladas in low-elevation disturbed habitat south of the Rift Valley at Indetu, Ethiopia

Understanding the basic natural history of threatened primate taxa is crucial to developing and implementing successful conservation strategies for them. Data on feeding ecology and activity patterns are particularly important for identifying the strategies through which primates invest time and foraging effort towards survival and reproduction at a given locale. Here, we report the results of the first study of the diet and activity budget of Arsi geladas, a population of < 1000 individuals endemic to a heavily disturbed region of the southern Ethiopian Highlands and believed to represent a new taxon of geladas. We conducted our research on a band of 34 individuals belonging to five, one-male units at Indetu, eastern Arsi, Ethiopia, from August 2010 to May 2011 (excluding March 2011). Feeding accounted for 41.7% of total scans, followed by moving (20.3%), resting (19.0%), and social behavior (19.0%). Feeding and moving increased and resting and socializing decreased during the dry season when food availability was probably lower than during the wet season. Geladas ate mostly graminoid leaves (51.7% of feeding scans) though they also consumed graminoid rhizomes (24.4%), forb tubers (7.1%), forb leaves (7.1%), cactus, shrub, and tree fruits (3.6%), graminoid corms (1.7%), forb roots (1.6%), and unidentified items (3.0%). Underground foods (corms, rhizomes, roots, and tubers) accounted for 22-47% (mean = 35%) of the monthly (n = 9) diet and were eaten slightly more during the wet season than during the dry season. Contributions of human crops to the gelada diet could not be quantified without creating conflict between farmers and researchers, though we did note that geladas visited farms on 5-10% of study days. Threats from farmers, children, and dogs limited the geladas' access to crops once they entered the farms. Further research involving questionnaire surveys of farmers, direct observation of crop damage by geladas, and DNA metabarcoding of gelada feces are crucial to the development of strategies to mitigate human-gelada conflict in the densely populated Arsi Zone of Ethiopia.

The Demographic and Adaptive History of the African Green Monkey

Relatively little is known about the evolutionary history of the African green monkey (genus Chlorocebus) due to the lack of sampled polymorphism data from wild populations. Yet, this characterization of genetic diversity is not only critical for a better understanding of their own history, but also for human biomedical research given that they are one of the most widely used primate models. Here, I analyze the demographic and selective history of the African green monkey, utilizing one of the most comprehensive catalogs of wild genetic diversity to date, consisting of 1,795,643 autosomal single nucleotide polymorphisms in 25 individuals, representing all five major populations: C. a. aethiops, C. a. cynosurus, C. a. pygerythrus, C. a. sabaeus, and C. a tantalus. Assuming a mutation rate of 5.9 × 10-9 per base pair per generation and a generation time of 8.5 years, divergence time estimates range from 523 to 621 kya for the basal split of C. a. aethiops from the other four populations. Importantly, the resulting tree characterizing the relationship and split-times between these populations differs significantly from that presented in the original genome paper, owing to their neglect of within-population variation when calculating between population-divergence. In addition, I find that the demographic history of all five populations is well explained by a model of population fragmentation and isolation, rather than novel colonization events. Finally, utilizing these demographic models as a null, I investigate the selective history of the populations, identifying candidate regions potentially related to adaptation in response to pathogen exposure.

Effective spatial scales for evaluating environmental determinants of population density in Yakushima macaques

Population densities of wildlife species tend to be correlated with resource productivity of habitats. However, wildlife density has been greatly modified by increasing human influences. For effective conservation, we must first identify the significant factors that affect wildlife density, and then determine the extent of the areas in which the factors should be managed. Here, we propose a protocol that accomplishes these two tasks. The main threats to wildlife are thought to be habitat alteration and hunting, with increases in alien carnivores being a concern that has arisen recently. Here, we examined the effect of these anthropogenic disturbances, as well as natural factors, on the local density of Yakushima macaques (Macaca fuscata yakui). We surveyed macaque densities at 30 sites across their habitat using data from 403 automatic cameras. We quantified the effect of natural vegetation (broad-leaved forest, mixed coniferous/broad-leaved forest, etc.), altered vegetation (forestry area and agricultural land), hunting pressure, and density of feral domestic dogs (Canis familiaris). The effect of each vegetation type was analyzed at numerous spatial scales (between 150 and 3,600-m radii from the camera locations) to determine the best scale for explaining macaque density (effective spatial scale). A model-selection procedure (generalized linear mixed model) was used to detect significant factors affecting macaque density. We detected that the most effective spatial scale was 400 m in radius, a scale that corresponded to group range size of the macaques. At this scale, the amount of broad-leaved forest was selected as a positive factor, whereas mixed forest and forestry area were selected as negative factors for macaque density. This study demonstrated the importance of the simultaneous evaluation of all possible factors of wildlife population density at the appropriate spatial scale.

Systems biology of the vervet monkey

Nonhuman primates (NHP) provide crucial biomedical model systems intermediate between rodents and humans. The vervet monkey (also called the African green monkey) is a widely used NHP model that has unique value for genetic and genomic investigations of traits relevant to human diseases. This article describes the phylogeny and population history of the vervet monkey and summarizes the use of both captive and wild vervet monkeys in biomedical research. It also discusses the effort of an international collaboration to develop the vervet monkey as the most comprehensively phenotypically and genomically characterized NHP, a process that will enable the scientific community to employ this model for systems biology investigations.

Discordance Between Spatial Distributions of Y-Chromosomal and Mitochondrial Haplotypes in African Green Monkeys ( spp.): A Result of Introgressive Hybridization or Cryptic Diversity?

Introgressive hybridization may cause substantial discordances among phylogenies based on different genetic markers. Such discordances have been found in diverse mammal species including primates. A recent study of mitochondrial DNA (mtDNA) revealed several poly- and paraphyletic relationships in African green monkeys (Chlorocebus), suggesting contemporary and/or ancient introgressive hybridization among almost all parapatric species of the genus. However, mtDNA analyses alone do not allow us to draw conclusions concerning introgression events. In this study we analyzed two Y chromosomal (Y-chr) markers for 30 African green monkey samples and compared the resulting genetic relationships to those based on published mtDNA data. In line with the results for mtDNA, we found no Y-chr evidence of hypothesized hybridization among Chlorocebus sabaeus and C. tantalus in the northern part of the contact zone in West Africa, and we found two distinct and distantly related Y-chr haplotypes within the range of C. tantalus, suggesting possible cryptic genetic diversity rather than ancient introgressive hybridization in this species. In contrast, Y-chr data revealed monophyletic relationships within Chlorocebus pygerythrus from East Africa, suggesting that mtDNA paraphylies found in this species are most likely to be the result of ancient introgressive hybridization and subsequent cytonuclear extinction of an earlier taxon. Our results accentuate the importance of analyzing sex chromosomal data in addition to mtDNA to obtain more information on the potential outcomes of hybridization with respect to genetic and species diversity. Analysis of more diverse nuclear marker sets is needed to obtain a more complete picture of the African green monkey evolution.

Mitochondrial diversity and distribution of African green monkeys (chlorocebus gray, 1870)

African green monkeys (Chlorocebus) represent a widely distributed and morphologically diverse primate genus in sub-Saharan Africa. Little attention has been paid to their genetic diversity and phylogeny. Based on morphological data, six species are currently recognized, but their taxonomy remains disputed. Here, we aim to characterize the mitochondrial (mt) DNA diversity, biogeography and phylogeny of African green monkeys. We analyzed the complete mitochondrial cytochrome b gene of 126 samples using feces from wild individuals and material from zoo and museum specimens with clear geographical provenance, including several type specimens. We found evidence for nine major mtDNA clades that reflect geographic distributions rather than taxa, implying that the mtDNA diversity of African green monkeys does not conform to existing taxonomic classifications. Phylogenetic relationships among clades could not be resolved suggesting a rapid early divergence of lineages. Several discordances between mtDNA and phenotype indicate that hybridization may have occurred in contact zones among species, including the threatened Bale monkey (Chlorocebus djamdjamensis). Our results provide both valuable data on African green monkeys' genetic diversity and evolution and a basis for further molecular studies on this genus.