Despite increasing conflict at human–wildlife interfaces, there exists little research on how the attributes and behavior of individual wild animals may influence human–wildlife interactions. Adopting a comparative approach, we examined the impact of animals’ life-history and social attributes on interactions between humans and (peri)urban macaques in Asia. For 10 groups of rhesus, long-tailed, and bonnet macaques, we collected social behavior, spatial data, and human–interaction data for 11–20 months on pre-identified individuals. Mixed-model analysis revealed that, across all species, males and spatially peripheral individuals interacted with humans the most, and that high-ranking individuals initiated more interactions with humans than low-rankers. Among bonnet macaques, but not rhesus or long-tailed macaques, individuals who were more well-connected in their grooming network interacted more frequently with humans than less well-connected individuals. From an evolutionary perspective, our results suggest that individuals incurring lower costs related to their life-history (males) and resource-access (high rank; strong social connections within a socially tolerant macaque species), but also higher costs on account of compromising the advantages of being in the core of their group (spatial periphery), are the most likely to take risks by interacting with humans in anthropogenic environments. From a conservation perspective, evaluating individual behavior will better inform efforts to minimize conflict-related costs and zoonotic-risk.
Long‐tailed macaques (
We performed population genetic analyses and phylogenetic reconstruction on nuclear single nucleotide polymorphisms (SNPs) from shotgun sequencing of 75 long‐tailed macaque museum specimens from localities throughout Southeast Asia.
We show that shotgun sequencing of museum specimens yields sufficient genome coverage (average ~1.7%) for reconstructing population relationships using SNP data. Contrary to expectations of divergent results between nuclear and mitochondrial genomes for a female philopatric species, phylogeographical patterns based on nuclear SNPs proved to be closely similar to those found using mitogenomes. In particular, population genetic analyses and phylogenetic reconstruction from the nDNA identify two major clades within
Overall, we demonstrate that low‐coverage sequencing of nDNA from museum specimens provides enough data for examining broad phylogeographic patterns, although greater genome coverage and sequencing depth would be needed to distinguish between very closely related populations, such as those throughout the Philippines.
- NSF-PAR ID:
- 10456343
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- American Journal of Physical Anthropology
- Volume:
- 173
- Issue:
- 1
- ISSN:
- 0002-9483
- Page Range / eLocation ID:
- p. 21-33
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
more » « less
Abstract -
more » « less
Abstract Objectives Cyclical submergence and re‐emergence of the Sunda Shelf throughout the Pleistocene served as a dynamic biogeographic landscape, across which long‐tailed macaques (
Macaca fascicularis ) have migrated and evolved. Here, we tested the integrity of the previously reported continental‐insular haplotype divide reported among Y and mitochondrial DNA lineages across multiple studies.Materials and Methods The continental‐insular haplotype divide was tested by heavily sampling wild macaques from two important biogeographic regions within Sundaland: (1) Singapore, the southernmost tip of continental Asia and (2) Bali, Indonesia, the southeastern edge of the Indonesian archipelago, immediately west of Wallace's line. Y DNA was haplotyped for samples from Bali, deep within the Indonesian archipelago. Mitochondrial D‐loop from both islands was analyzed against existing data using Maximum Likelihood and Bayesian approaches.
Results We uncovered both “continental” and “insular” Y DNA haplotypes in Bali. Between Singapore and Bali we found 52 unique mitochondrial haplotypes, none of which had been previously described. Phylogenetic analyses confirmed a major haplogroup division within Singapore and identified five new Singapore subclades and two primary subclades in Bali.
Discussion While we confirmed the continental‐insular divide among mtDNA haplotypes, maintenance of both Y DNA haplotypes on Bali, deep within the Indonesian archipelago calls into question the mechanism by which Y DNA diversity has been maintained. It also suggests the continental‐insular designation is less appropriate for Y DNA, leading us to propose geographically neutral Y haplotype designations.
-
more » « less
Abstract Species in the genus
Macaca typically live in multimale‐multifemale social groups with male macaques exhibiting some of the largest testis: body weight ratios among primates. Males are believed to experience intense levels of sperm competition. Several spermatogenesis genes are located on the Y‐chromosome and, interestingly, occasional hybridization between two species has led to the introgression of the rhesus macaque (Macaca mulatta ) Y‐chromosome deep into the range of the long‐tailed macaque (M .fascicularis ). These observations have led to the prediction that the successful introgression of the rhesus Y‐haplotype is due to functional differences in spermatogenesis genes compared to those of the native long‐tailed Y‐haplotype. We examine here four Y‐chromosomal loci—RBMY ,XKRY , and two nearly identical copies ofCDY —and their corresponding protein sequences. The genes were surveyed in representative animals from north of, south of, and within the rhesus x long‐tailed introgression zone. Our results show a series of non‐synonymous amino acid substitutions present between the two Y‐haplotypes. Protein structure modeling via I‐TASSER revealed different folding patterns between the two species' Y‐proteins, and functional predictions via TreeSAAP further reveal physicochemical differences as a result of non‐synonymous substitutions. These differences inform our understanding of the evolution of primate Y‐proteins involved in spermatogenesis and, in turn, have biomedical implications for human male fertility. -
more » « less
Premise Long‐distance dispersal has been important in explaining the present distributions of many plant species. Despite being infrequent, such dispersal events have considerable evolutionary consequences, because bottlenecks during colonization can result in reduced genetic diversity. We examined the phylogeographic history of
Lycium carolinianum , a widespread taxon that ranges from southeastern North America to several Pacific islands, with intraspecific diversity in sexual and mating systems.Methods We used Bayesian, likelihood, and coalescent approaches with nuclear and plastid sequence data and genome‐wide single nucleotide polymorphisms to reconstruct the dispersal history of this species. We also compared patterns of genetic variation in mainland and island populations using single nucleotide polymorphisms and allelic diversity at the
S‐RNase mating system gene.Results Lycium carolinianum is monophyletic and dispersed once from the North American mainland, colonizing the Pacific islands ca. 40,100 years ago. This dispersal was accompanied by a loss of genetic diversity in SNPs and theS‐RNase locus due to a colonization bottleneck and the loss of self‐incompatibility. Additionally, we documented at least two independent transitions to gynodioecy: once following the colonization of the Hawaiian Islands and loss of self‐incompatibility, and a second time associated with polyploidy in the Yucatán region of Mexico.Conclusions Long‐distance dispersal via fleshy, bird dispersed fruits best explains the unusually widespread distribution of
L. carolinianum . The collapse of diversity at theS‐RNase locus in island populations suggests that self‐fertilization may have facilitated the subsequent colonization of Pacific islands following a single dispersal from mainland North America. -
Kalendar, Ruslan (Ed.)more » « less
The use of museum specimens for research in microbial evolutionary ecology remains an under-utilized investigative dimension with important potential. Despite this potential, there remain barriers in methodology and analysis to the wide-spread adoption of museum specimens for such studies. Here, we hypothesized that there would be significant differences in taxonomic prediction and related diversity among sample type (museum or fresh) and sequencing strategy (medium-depth shotgun metagenomic or 16S rRNA gene). We found dramatically higher predicted diversity from shotgun metagenomics when compared to 16S rRNA gene sequencing in museum and fresh samples, with this differential being larger in museum specimens. Broadly confirming these hypotheses, the highest diversity found in fresh samples was with shotgun sequencing using the Rep200 reference inclusive of viruses and microeukaryotes, followed by the WoL reference database. In museum-specimens, community diversity metrics also differed significantly between sequencing strategies, with the alpha-diversity ACE differential being significantly greater than the same comparisons made for fresh specimens. Beta diversity results were more variable, with significance dependent on reference databases used. Taken together, these findings demonstrate important differences in diversity results and prompt important considerations for future experiments and downstream analyses aiming to incorporate microbiome datasets from museum specimens.
