Matrix heterogeneity affects population size of the harvest mice: Bayesian estimation of matrix resistance and model validation

It has been increasingly recognized that landscape matrices are an important factor determining patch connectivity and hence the population size of organisms living in highly fragmented landscapes. However, most previous studies estimated the effect of matrix heterogeneity using prior information regarding dispersal or habitat preferences of a focal organism. Here we estimated matrix resistance of harvest mice in agricultural landscapes using a novel pattern‐oriented modeling with Bayesian estimation and no prior information, and then conducted model validation using data sets independent from those used for model construction. First, we investigated the distribution patterns of harvest mice for approximately 400 habitat patches, and estimated matrix resistance for different matrix types using statistical models incorporating patch size, patch environment, and patch connectivity. We used Bayesian estimation with a Markov chain Monte Carlo algorithm, and searched for appropriate matrix resistance that best explained the distribution pattern. Patch connectivity as well as patch quality was an important determinant of local population size for the harvest mice. Moreover, matrix resistance was far from uniform, with rice and crop fields exhibiting low resistance and forests, creeks, roads and residential areas showing much higher resistance. The deviance explained by this model (heterogeneous matrix model) was much larger than that obtained by the model with no consideration of matrix heterogeneity (homogeneous matrix model). Second, we obtained distribution data from five additional landscapes that were more fragmented than that used for model construction, and used them for model validation. The heterogeneous matrix model well predicted the population size for four out of five landscapes. In contrast, the homogeneous model considerably overestimated population sizes in all cases. Our approach is widely applicable to species living in fragmented landscapes, especially those for which prior information regarding movement or dispersal is difficult to obtain.     

Kinda baboons (Papio kindae) and grayfoot chacma baboons (P. ursinus griseipes) hybridize in the Kafue river valley, Zambia

The ranges of small kinda (Papio kindae) and much larger grayfooted chacma (P. ursinus griseipes) baboons adjoin in the Kafue National Park, Zambia. In a visual survey of baboons at 48 sites in the Kafue River drainage we found that, contrary to previous reports, groups at the species interface near the town of Ngoma are phenotypically diverse and presumably formed by multigenerational hybridization. Mitochondrial and/or Y-chromosome genetic markers from fecal samples (N=164) collected at 29 sites support this conclusion. Groups with phenotypic signs of a history of hybridization also had taxon-specific mitochondria and Y-haplotypes from both parental species. Although the distribution of mitochondrial haplotypes largely mirrored that of external phenotypes, a significant proportion of male specimens from grayfoot as well as hybrid groups carried kinda Y-chromosomes, and kinda Y-chromosomes were involved in all observed cases of mitochondrial/Y-chromosome discordance. These observations are consistent with, though they do not prove, a population history in which the range of chacmas and the hybrid zone have advanced at the expense of the kinda range. They also suggest that, unexpectedly, kinda male×chacma female matings are much more common than the reciprocal cross in the ancestry of hybrids. We suggest that distinctive male kinda behavior and the "juvenile" appearance of kinda baboons of both sexes, perhaps combined with obstetric difficulties of a small kinda female carrying the large offspring of a chacma male, may account for this bias.     

Troop size and human-modified habitat affect the ranging patterns of a chacma baboon population in the cape peninsula, South Africa

Differences in group size and habitat use are frequently used to explain the extensive variability in ranging patterns found across the primate order. However, with few exceptions, our understanding of primate ranging patterns stems from studies of single groups and both intra- and inter-specific meta-analyses. Studies with many groups and those that incorporate whole populations are rare but important for testing socioecological theory in primates. We quantify the ranging patterns of nine chacma baboon troops in a single population and use Spearman rank correlations and generalized linear mixed models to analyze the effects of troop size and human-modified habitat (a proxy for good quality habitat) on home range size, density (individuals/km(2) ), and daily path length. Intrapopulation variation in home range sizes (1.5-37.7 km(2) ), densities (1.3-12.1 baboons/km(2) ), and daily path lengths (1.80-6.61 km) was so vast that values were comparable to those of baboons inhabiting the climatic extremes of their current distribution. Both troop size and human-modified habitat had an effect on ranging patterns. Larger troops had larger home ranges and longer daily path lengths, while troops that spent more time in human-modified habitat had shorter daily path lengths. We found no effect of human-modified habitat on home range size or density. These results held when we controlled for the effects of both a single large outlier troop living exclusively in human-modified habitat and baboon monitors on our spatial variables. Our findings confirm the ability of baboons, as behaviorally adaptable dietary generalists, to not only survive but also to thrive in human-modified habitats with adjustments to their ranging patterns in accordance with current theory. Our findings also caution that studies focused on only a small sample of groups within a population of adaptable and generalist primate species may underestimate the variability in their respective localities.     

Inter- and intrahabitat dietary variability of chacma baboons (Papio ursinus) in South African savannas based on fecal delta13C, delta15N, and %N

Baboons are dietary generalists, consuming a wide range of food items in varying proportions. It is thus difficult to quantify and explain the dietary behavior of these primates. We present stable carbon (delta(13)C) and nitrogen (delta(15)N) isotopic data, and percentage nitrogen (%N), of feces from chacma baboons (Papio ursinus) living in two savanna environments of South Africa: the mountainous Waterberg region and the low-lying Kruger National Park. Baboons living in the more homogeneous landscapes of the Waterberg consume a more isotopically heterogeneous diet than their counterparts living in Kruger Park. Grasses and other C(4)-based foods comprise between approximately 10-20% (on average) of the bulk diet of Kruger Park baboons. Carbon isotopic data from the Waterberg suggest diets of approximately 30-50% grass, which is higher than generally reported for baboons across the African savanna. Based on observations of succulent-feeding, we propose that baboons in the Waterberg consume a mix of C(4) grasses and CAM-photosynthesizing succulents in combined proportions varying between approximately 5-75% (average, approximately 35%). Fecal delta(15)N of baboons is lower than that of sympatric ungulates, which may be due to a combination of low levels of faunivory, foraging on subterranean plant parts, or the use of human foods in the case of Kruger Park populations. Fecal N levels in baboons are consistently higher than those of sympatric ungulate herbivores, indicating that baboons consume a greater proportion of protein-rich foods than do other savanna mammals. These data suggest that chacma baboons adapt their dietary behavior so as to maximize protein intake, regardless of their environment.     

Mitochondrial phylogeny and systematics of baboons (Papio)

Baboons (Papio, s.s.) comprise a series of parapatric allotaxa (subspecies or closely related species) widely distributed in sub-Saharan Africa. Despite extensive studies of their ecology, morphology, and behavior, disagreement about their phylogenetic relationships continues, as expressed in the current coexistence of at least three major, competing taxonomic treatments. To help resolve this situation, we sequenced approximately 900 bases of mitochondrial DNA of 40 individuals from five of the widely recognized "major" allotaxa. Total sequence diversity (>5%) is high compared to most primate species. Major mitochondrial clades correspond to recognized allotaxa, with the important exception that haplotypes from yellow and olive baboons form a single, monophyletic clade within which the two allotaxa do not comprise mutually exclusive clusters. The major clades fall unambiguously into the pattern: (chacma (Guinea (hamadryas (yellow + olive)))). This phylogeny does not support taxonomies that oppose hamadryas to all other baboons ("desert" vs. "savanna"), but is compatible with the view that all definable allotaxa should be recognized as coordinates, either as "phylogenetic" species or "biological" subspecies. The close relationship and unsegregated distribution of haplotypes from Kenyan and Tanzanian yellow and olive baboons are unexplained, but may reflect introgression across the documented hybrid zone. The overall phylogeny, when combined with paleontological data, suggests a southern African origin for extant Papio baboons, with all extant lineages sharing a common mitochondrial ancestor at approximately 1.8 Ma.     

The Effects of Permanent Injury on the Behavior and Diet of Commensal Chacma Baboons (Papio ursinus) in the Cape Peninsula,South Africa

Primates may suffer injury from both natural (fights with conspecifics, predators) and human-induced (snares, power-lines and guns) causes. Though behavioral flexibility may allow primates to compensate for injuries, permanent disabilities, such as the loss of a limb, may adversely affect both foraging and locomotory efficiency and ultimately the survival and fitness of individuals. In the Cape Peninsula, South Africa, members of the chacma baboon population (Papio ursinus) experience chronic levels of conflict with humans that manifests in high levels (15%) of disabled baboons in groups that overlap with residential areas. In this study we investigate the potential impact of such disabilities by comparing the behavior and diet of disabled baboons with uninjured baboons matched closely for age, sex, and social status from groups of a similar size and composition for 8 mo, from May to December 2005. Disabled baboons spent more time resting and traveling and less time feeding than uninjured baboons. Disabled and uninjured baboons had similar diets but the former consumed fewer food items with high handling costs and fed more on high return foods than the latter. There was no difference in the frequency of grooming or social vigilance behaviors, as might be expected if disability had compromised either competitive ability or predation risk. Further, there was no difference in the survival of disabled or uninjured individuals in each group. Together these results suggest that while permanent injury may affect the behavior and diet of Peninsula baboons, that these constraints may be offset by access to anthropogenic food sources and the lack of natural predators. Disability in baboons may lead to obligate raiding of high-return anthropogenic foods, which is an important challenge for the ongoing management of this population.     

Demographic history of a common pioneer tree,Zanthoxylum ailanthoides,reconstructed using isolation-with-migration model

The Japanese prickly ash, Zanthoxylum ailanthoides Siebold & Zucc. (Rutaceae), is one of the most common pioneer tree species that grow in disturbed areas, such as canopy gaps, in Japanese warm-temperate evergreen oak forests. The strong genetic structure of its current population might suggest long-term isolation of subpopulations by demographic events, in addition to ecological features of this species. Analyses of genome-wide nucleotide variation using model-based approaches are necessary to achieve a good understanding of the demographic history of a species. In this study, we analyzed the nucleotide variation in natural populations of Z. ailanthoides using a computer program that applied the isolation-with-migration model to quantitatively infer the demographic history. Nucleotide variations at 10 or 26 nuclear loci in six populations from a wide range of the species distribution were analyzed. The maximum likelihood estimate of the divergence time between the current populations in the two hypothetical refugia of Z. ailanthoides was approximately 24,000 years. Unexpectedly, the estimated size of the ancestral population was larger than the sizes of the two current populations. The results suggested a relatively recent divergence of these two populations and rapid formation of strong genetic structure among subpopulations. The large ancestral population may indicate a more complex demographic history during or after the last glacial period than the simple isolation-with-migration model implies.     

Past bottlenecks and current population fragmentation of endangered huemul deer (<Emphasis Type="Italic">Hippocamelus bisulcus</Emphasis>): implications for preservation of genetic diversity

Small populations in fragmented habitats can lose genetic variation through drift and inbreeding. The huemul (Hippocamelus bisulcus) is an endangered deer endemic to the southern Andes of Chile and Argentina. Huemul numbers have declined by 99% and its distribution by 50% since European settlement. The total population is estimated at less than 2,000 individuals and is highly fragmented. At one isolated population in Chilean Patagonia we sampled 56 individuals between 2005 and 2007 and genotyped them at 14 microsatellite loci. Despite low genetic variability (average 2.071 alleles/locus and average H _O of 0.341), a low inbreeding coefficient (F _IS) of 0.009 suggests nearly random mating. Population genetic bottleneck tests suggest both historical and contemporary reductions in population size. Simulations indicated that the population must be maintained at 75% of the current size of 120 individuals to maintain 90% of its current genetic diversity over the next 100 years. Potential management strategies to maintain genetic variability and limit future inbreeding include the conservation and establishment of habitat corridors to facilitate gene flow and the enlargement of protected areas to increase effective population size.     

Progressions of adult male chacma baboons (Papio ursinus) in the moremi wildlife reserve

It has been suggested that the sociospatial organization of baboon progressions has a protective function in which the most physically powerful troop members, the adult males, play a key role. This theory implies regularities in adult male progression order for different species of savannah baboons with similar social systems. Quantitative progression data are available from two such similar baboon species, olive and yellow, but not from the third, chacma. The order of movement of 15 adult male chacma baboons was determined from 40 progressions observed at the Moremi Wildlife Reserve, Botswana. The chacma males were most often found in the front sixth of progressions, next most often in the second sixth, and about equally often from there to the rear. As expected from the protection theory, this frontal positioning is consistent with available quantitative data from other species of savannah baboons.     

High genetic diversity and no inbreeding in the endangered copper redhorse, Moxostoma hubbsi (Catostomidae, Pisces): the positive sides of a long generation time

The evolutionary potential of a species is determined by its genetic diversity. Thus, management plans should integrate genetic concerns into active conservation efforts. The copper redhorse (Moxostoma hubbsi) is an endangered species, with an endemic distribution limited to the Richelieu River and a short section of the St Lawrence River in Quebec, Canada. The population, gradually fragmented since 1849, is characterized by a decline in population size and a lack of recruitment. A total of 269 samples were collected between 1984 and 2004 and genotyped using 22 microsatellite loci, which indicated that these fish comprise a single population, with a global F(ST) value of only 0.0038. Despite a small census size ( approximately 500), a high degree of genetic diversity was observed compared to common values for freshwater fishes (average number of 12.5 alleles/locus and average HO of 0.77 +/- 0.08). No difference was observed between expected and observed pairwise values of relatedness (r(xy): -0.00013 +/- 0.11737), suggesting an outbred population. Long-term Ne was estimated at 4476 whereas contemporary Ne values ranged from 107 to 568, suggesting a pronounced yet gradual demographic decline of the population, as no bottleneck could be detected for the recent past. By means of simulations, we estimated Ne would need to remain at more than approximately 400 to retain 90% of the genetic diversity over 100 years. Overall, these observations corroborate other recent empirical studies confirming that long generation times may act as a buffering effect contributing to a reduction in the pace of genetic diversity erosion in threatened species.     

A Non-Lévy Random Walk in Chacma Baboons: What Does It Mean?

The Lévy walk is found from amoebas to humans and has been described as the optimal strategy for food research. Recent results, however, have generated controversy about this conclusion since animals also display alternatives to the Lévy walk such as the Brownian walk or mental maps and because movement patterns found in some species only seem to depend on food patches distribution. Here I show that movement patterns of chacma baboons do not follow a Lévy walk but a Brownian process. Moreover this Brownian walk is not the main process responsible for movement patterns of baboons. Findings about their speed and trajectories show that baboons use metal maps and memory to find resources. Thus the Brownian process found in this species appears to be more dependent on the environment or might be an alternative when known food patches are depleted and when animals have to find new resources.     

Inbreeding and reproductive success in a natural chacma baboon,Papio cynocephalus ursinus,population

Six of 19 male chacma baboons living in a natural environment in Botswana were born in troops where they attained alpha status. At least three of these six males sired young in their natal troops. Nine other paternal males were immigrants, hence they were more distantly related to their mates, who were all natal. Offspring of natal and immigrant parents survived equally well to 90 days. These observations suggest that for this and other mammalian species the evolutionary history of a population may determine inbreeding costs.     

Variation at a chloroplast minisatellite locus reveals the signature of habitat fragmentation and genetic bottlenecks in the rare orchid Anacamptis palustris (Orchidaceae)

Geoclimatic changes during the Oligocene and more recent anthropogenic influences have shaped the current distribution and population structure of Mediterranean plant species. Anacamptis palustris (Orchidaceae) is a typical member of coastal wetlands, which have become increasingly fragmented and isolated. As a consequence, this orchid has become rare in the recent past. Length variation at a chloroplast minisatellite locus was used to estimate genetic variation within and between the largest extant populations of A. palustris. Genetic diversity was positively correlated with population size. Estimation of observed and expected gene diversity and analyses of haplotype number and haplotype frequency distributions provided evidence for population bottlenecks in the history of small populations. Comparison with an earlier study suggests that nuclear allozyme diversity was most likely lost during the Oligocene and could not recover subsequently due to low mutation rates, whereas genetic variation was restored at the highly variable chloroplast minisatellite locus. Population bottlenecks indicated by cpDNA variation occurred most likely as a consequence of more recent anthropogenic changes. The comparison of molecular markers with different levels of polymorphism provided valuable insights into the processes shaping genetic diversity and population structure in this rare orchid.     

A NEW ABUNDANCE ESTIMATE FOR VAQUITAS: FIRST STEP FOR RECOVERY1

A line-transect survey specifically designed to estimate vaquita (Phocoena sinus) abundance over its entire range was carried out by three boats in the summer of 1997. There was a total of 125 sightings of vaquita groups, mainly due to the use of large 25 ± 150 binoculars, which were seven times more effective in detecting vaquitas than hand-held 7 ± binoculars. Results confirmed that the range of the vaquita is restricted to the northwestern corner of the Gulf of California, Mexico, but that the boundaries of the Upper Gulf of California and Colorado River Delta Biosphere Reserve do not correspond well with the distribution of vaquitas. The shallow water north of the town of San Felipe was found to have a higher density of animals than had been indicated by previous surveys. The total population size was estimated to be 567 animals, with a 95% confidence interval from 177 to 1,073. This estimate is an improvement over previous estimates, which had low numbers of sightings, relied on parameters taken from other species, and/or did not cover all areas where vaquitas could potentially be found. The 1997 estimate was more than twice the 1993 estimate, but there are several reasons why the numbers cannot be directly compared, and it should not be concluded the population is increasing. This first complete estimate of vaquita abundance can be a beginning for the recovery of this highly endangered species.     

Trade-offs in skillacquisition and time allocation among juvenile chacma baboons

We hypothesize that juvenile baboons are less efficient foragers than adult baboons owing to their small size, lower level of knowledge and skill, and/or lesser ability to maintain access to resources. We predict that as resources are more difficult to extract, juvenile baboons will demonstrate lower efficiency than adults will because of their lower levels of experience. In addition, we hypothesize that juvenile baboons will be more likely to allocate foraging time to easier-to-extract resources owing to their greater efficiency in acquiring those resources. We use feeding efficiency and time allocation data collected on a wild, free-ranging, non-provisioned population of chacma baboons (Papio hamadryas ursinus) in the Moremi Wildlife Reserve, Okavango Delta, Botswana to test these hypotheses. The major findings of this study are: 1. Juvenile baboons are significantly less efficient foragers than adult baboons primarily for difficult-to-extract resources. We propose that this age-dependent variation in efficiency is due to differences in memory and other cognitive functions related to locating food resources, as is indicated by the greater amount of time juvenile baboons spend searching for food. There is no evidence that smaller body size or competitive disruption influences the differences in return rates found between adult and juvenile baboons in this study. 2. An individual baboon’s feeding efficiency for a given resource can be used to predict the duration of its foraging bouts for that resource. These results contribute both to our understanding of the ontogeny of behavioral development in nonhuman primates, especially regarding foraging ability, and to current debate within the field of human behavioral ecology regarding the evolution of the juvenile period in primates and humans. Sara E. Johnson is Assistant Professor of Anthropology at California State University, Fullerton. She received her Ph.D. in Anthropology (Human Evolutionary Ecology) from the University of New Mexico in 2001. She uses behavioral ecology and life history theory to address her research interests in the evolution of primate and human growth; ecological variation and phenotypic plasticity in growth and development; ecological variation in life course trajectories, including fertility, health, morbidity, and mortality differentials; food acquisition and production related to nutrition; societal transofmration and roles of the elderly among indigenous peoples; and women’s reproductive and productive roles in both traditional and nontraditional societies. For the past decade she has conducted research on these issues in several different populations, including chacma baboons in the Okavango Delta of Botswana, two multiethnic communities of forager/agropastoralists in the Okavango Delta of Botswana, and among New Mexican men. John Bock is Associate Professor of Anthropology at California State University at Fullerton and is Associate Editor of Human Nature. He received a Ph.D. in Anthropology (Human Evolutionary EcologY) from the University of New Mexico in 1995, and from 1995 to 1998 was an Andrew W. Mellon Foundation postdoctoral fellow in demography and epidemiology at the National Centre for Epidemiology and Population Health at Australian National University. His recent research has focused on applying life history theory to understanding the evolution of the primate and human juvenile period. Bock has been conducting research among the Okavango Delta peoples of Botswana since 1992, and his current research there is an examination of child development and family demography in relation to socioecology and the HIV/AIDS epidemic. Other research is focused on health disparties among minorities and indigenous peoples in Botswana and the United States related to differential access to health care.     

Pleistocene Aridification Cycles Shaped the Contemporary Genetic Architecture of Southern African Baboons

Plio-Pleistocene environmental change influenced the evolutionary history of many animal lineages in Africa, highlighting key roles for both climate and tectonics in the evolution of Africa’s faunal diversity. Here, we explore diversification in the southern African chacma baboon Papio ursinus sensu lato and reveal a dominant role for increasingly arid landscapes during past glacial cycles in shaping contemporary genetic structure. Recent work on baboons (Papio spp.) supports complex lineage structuring with a dominant pulse of diversification occurring 1-2Ma, and yet the link to palaeoenvironmental change remains largely untested. Phylogeographic reconstruction based on mitochondrial DNA sequence data supports a scenario where chacma baboon populations were likely restricted to refugia during periods of regional cooling and drying through the Late Pleistocene. The two lineages of chacma baboon, ursinus and griseipes, are strongly geographically structured, and demographic reconstruction together with spatial analysis of genetic variation point to possible climate-driven isolating events where baboons may have retreated to more optimum conditions during cooler, drier periods. Our analysis highlights a period of continuous population growth beginning in the Middle to Late Pleistocene in both the ursinus and the PG2 griseipes lineages. All three clades identified in the study then enter a state of declining population size (Nef) through to the Holocene; this is particularly marked in the last 20,000 years, most likely coincident with the Last Glacial Maximum. The pattern recovered here conforms to expectations based on the dynamic regional climate trends in southern Africa through the Pleistocene and provides further support for complex patterns of diversification in the region’s biodiversity.