Contrasting effects of forest fragmentation on the genetics and microbiomes of an endangered arboreal primate
- 1The Hebrew University of Jerusalem
Abstract
Landscape fragmentation, one of the leading drivers of biodiversity loss, can reshape both the genetics and microbiomes of wild populations. Although fragmentation is generally expected to limit gene flow and erode genetic diversity, and to disrupt host-associated microbial communities, these responses arise via different pathways and may therefore diverge within the same population. To understand how fragmentation simultaneously shapes population genetics and gut microbiomes, we analyzed fecal-derived host genomic and microbiome data from endangered, arboreal black howler monkeys (Alouatta pigra) across a fragmentation gradient. We then integrated these data with measures of ecological connectivity, habitat quality, and demography to identify the drivers of genetic and microbiome variation and structure. Multivariate analyses indicated that genetic patterns were shaped by both connectivity and habitat quality, whereas microbiome variation was driven mainly by habitat quality. Contrary to expectations under reduced realized connectivity with increasing isolation, monkeys showed the strongest gene flow signal in the most fragmented region, and higher genetic diversity and lower inbreeding than monkeys in continuous forest. Relatedness and isolation-by-distance patterns suggested that fragmentation has sex-specific effects on movement, disrupting the usual pattern of short-range male dispersal in the most fragmented region. Gut microbiomes, however, showed predicted negative responses to fragmentation: individuals in highly fragmented habitat had lower microbial diversity and compositional shifts consistent with lower-quality diets and increased exposure to disturbed environments. These results show contrasting biological responses to fragmentation within a single population, with genetic patterns likely resulting from compensatory behavioral flexibility and microbiome patterns reflecting local habitat degradation. Our findings underscore the need for conservation assessments that integrate multiple dimensions of population health rather than relying on any single indicator of fragmentation impact.
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BibTeX
@misc{klass2026contrasting,
title = {{Contrasting effects of forest fragmentation on the genetics and microbiomes of an endangered arboreal primate}},
author = {K. Klass and S. Van Belle and E. Wikberg and G. Duytschaever and M. L. Savo Sardaro and A. Morales-Guerrero and O. Peled and K. D. Harris and R. M. Petersen and M. L. Morrison and M. Soffer and A. Di Fiore and K. R. Amato and A. D. Melin and J. A. Teichroeb and G. Greenbaum},
howpublished = {bioRxiv},
year = {2026},
month = jun,
doi = {10.64898/2026.06.14.732134},
url = {https://www.biorxiv.org/content/10.64898/2026.06.14.732134v2},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Contrasting effects of forest fragmentation on the genetics and microbiomes of an endangered arboreal primate
AU - K. Klass
AU - S. Van Belle
AU - E. Wikberg
AU - G. Duytschaever
AU - M. L. Savo Sardaro
AU - A. Morales-Guerrero
AU - O. Peled
AU - K. D. Harris
AU - R. M. Petersen
AU - M. L. Morrison
AU - M. Soffer
AU - A. Di Fiore
AU - K. R. Amato
AU - A. D. Melin
AU - J. A. Teichroeb
AU - G. Greenbaum
PY - 2026
DA - 2026/06/14
PB - bioRxiv
DO - 10.64898/2026.06.14.732134
UR - https://www.biorxiv.org/content/10.64898/2026.06.14.732134v2
AB - Landscape fragmentation, one of the leading drivers of biodiversity loss, can reshape both the genetics and microbiomes of wild populations. Although fragmentation is generally expected to limit gene flow and erode genetic diversity, and to disrupt host-associated microbial communities, these responses arise via different pathways and may therefore diverge within the same population. To understand how fragmentation simultaneously shapes population genetics and gut microbiomes, we analyzed fecal-derived host genomic and microbiome data from endangered, arboreal black howler monkeys (Alouatta pigra) across a fragmentation gradient. We then integrated these data with measures of ecological connectivity, habitat quality, and demography to identify the drivers of genetic and microbiome variation and structure. Multivariate analyses indicated that genetic patterns were shaped by both connectivity and habitat quality, whereas microbiome variation was driven mainly by habitat quality. Contrary to expectations under reduced realized connectivity with increasing isolation, monkeys showed the strongest gene flow signal in the most fragmented region, and higher genetic diversity and lower inbreeding than monkeys in continuous forest. Relatedness and isolation-by-distance patterns suggested that fragmentation has sex-specific effects on movement, disrupting the usual pattern of short-range male dispersal in the most fragmented region. Gut microbiomes, however, showed predicted negative responses to fragmentation: individuals in highly fragmented habitat had lower microbial diversity and compositional shifts consistent with lower-quality diets and increased exposure to disturbed environments. These results show contrasting biological responses to fragmentation within a single population, with genetic patterns likely resulting from compensatory behavioral flexibility and microbiome patterns reflecting local habitat degradation. Our findings underscore the need for conservation assessments that integrate multiple dimensions of population health rather than relying on any single indicator of fragmentation impact.
ER -