High Relatedness in Mouse lemur species
Abstract
Within-species genetic studies of primates have typically focused on parentage within groups or phylogeographic relationships among sparsely sampled populations. Most of these studies use a small number of microsatellites, which can only identify close relatives and may give a poor approximation of the overall relatedness in the population. This project compares relatedness within two sympatric species of mouse lemur (Microcebus berthae and M. murinus) in the Central Menabe region of western Madagascar. While M. murinus has a broad range, M. berthae is confined to a single dwindling forest. Samples were collected throughout the entire forest, with 52 samples from M. berthae and 195 samples from M. murinus. Using single polymorphism (SNP) data collected by ddRADseq, relatedness levels could be calculated to degrees unobtainable with microsatellite data. Applying a naïve relatedness estimator, both populations are found to be highly inbred for both species. Most standard estimators assume a largely unrelated population sample and are likely to be inappropriate for most fine-scale primate population studies. Utilizing a triadic likelihood estimator for relatedness (which does not assume inbreeding is absent), the estimates were reduced, albeit still showing substantial relatedness for both species. Relatedness visualizations demonstrate that pockets of high relatedness are present against a background of already elevated relatedness. This pattern causes the bias in standard relatedness estimates and could be present in many other primate populations, suggesting that caution should be used when estimating relatedness using microsatellites and standard relatedness estimators.
Collaborators: Dr. Peter Kappeler, Dr. Livia Schäffler
Skills
Within-species genetic studies of primates have typically focused on parentage within groups or phylogeographic relationships among sparsely sampled populations. Most of these studies use a small number of microsatellites, which can only identify close relatives and may give a poor approximation of the overall relatedness in the population. This project compares relatedness within two sympatric species of mouse lemur (Microcebus berthae and M. murinus) in the Central Menabe region of western Madagascar. While M. murinus has a broad range, M. berthae is confined to a single dwindling forest. Samples were collected throughout the entire forest, with 52 samples from M. berthae and 195 samples from M. murinus. Using single polymorphism (SNP) data collected by ddRADseq, relatedness levels could be calculated to degrees unobtainable with microsatellite data. Applying a naïve relatedness estimator, both populations are found to be highly inbred for both species. Most standard estimators assume a largely unrelated population sample and are likely to be inappropriate for most fine-scale primate population studies. Utilizing a triadic likelihood estimator for relatedness (which does not assume inbreeding is absent), the estimates were reduced, albeit still showing substantial relatedness for both species. Relatedness visualizations demonstrate that pockets of high relatedness are present against a background of already elevated relatedness. This pattern causes the bias in standard relatedness estimates and could be present in many other primate populations, suggesting that caution should be used when estimating relatedness using microsatellites and standard relatedness estimators.
Collaborators: Dr. Peter Kappeler, Dr. Livia Schäffler
Skills
- Next Generation Sequencing Library Preparation (ddRADseq method)
- Bioinformatics:
- Python scripts
- Stacks
- R
Deforestation in Madagascar's Dry and Humid Forests
Abstract
Anthropogenic forest loss is severe, recent, and accelerating. In Madagascar alone, almost 40% of original forested areas have been lost since the 1950s. Deforestation negatively affects many already threatened, endemic species by destroying their habitats and lowering their populations. Deforestation of humid and dry forests results in different climatic outcomes. For example, removal of humid forests leads to drier conditions at local scales. We used satellite imagery to quantify and compare deforestation trends across humid and dry forests in Madagascar and compared these results to census data for human populations. Between 2000 and 2014, approximately 8,485 square km of dry forest and 25,827 square km of humid forest have been lost. Deforestation rates are stable in dry forests and decreasing in humid forests. Deforestation was less prevalent in the more densely populated humid regions of the forest than in its less populated arid counterpart. One possible reason for this in that dry forests are situated on a more even slope and therefore are easier to log.
Collaborators: Catherine Zhou, Pablo De Castro Gomez
Skills
Anthropogenic forest loss is severe, recent, and accelerating. In Madagascar alone, almost 40% of original forested areas have been lost since the 1950s. Deforestation negatively affects many already threatened, endemic species by destroying their habitats and lowering their populations. Deforestation of humid and dry forests results in different climatic outcomes. For example, removal of humid forests leads to drier conditions at local scales. We used satellite imagery to quantify and compare deforestation trends across humid and dry forests in Madagascar and compared these results to census data for human populations. Between 2000 and 2014, approximately 8,485 square km of dry forest and 25,827 square km of humid forest have been lost. Deforestation rates are stable in dry forests and decreasing in humid forests. Deforestation was less prevalent in the more densely populated humid regions of the forest than in its less populated arid counterpart. One possible reason for this in that dry forests are situated on a more even slope and therefore are easier to log.
Collaborators: Catherine Zhou, Pablo De Castro Gomez
Skills
- GIS and raster manipulation
- Bioinformatics: R
- Mentoring high school students as part of the Student Research Mentoring Program with the American Museum of Natural History
Genetic Structure and Gene Flow in Mouse Lemurs
Kirindy Forest, study area of dissertation research
Abstract
There is a critical need to ensure that the effects of current (and accelerating) habitat fragmentation are identified and differentiated from the genetic signatures of long-past events and environmental circumstances. The long term goals in this research area are to differentiate between the effects of recent habitat fragmentation and long-term evolutionary demographic history and population structure on primate species. Research results in this area will inform our understanding of ecological and evolutionary diversification in fragmented landscapes and offer guidance to conservation programs. The specific objective of this research proposal is to use genome-wide genetic data to compare and contrast genetic diversity, population structure, demographic history, and recent and historical gene flow in two sympatric mouse lemur species in western Madagascar: the endangered Mme. Berthe’s mouse lemur (Microcebus berthae) and the non-threatened gray mouse lemur (M. murinus).
Collaborators: Dr. Peter Kappeler, Dr. Livia Schäffler
Skills
There is a critical need to ensure that the effects of current (and accelerating) habitat fragmentation are identified and differentiated from the genetic signatures of long-past events and environmental circumstances. The long term goals in this research area are to differentiate between the effects of recent habitat fragmentation and long-term evolutionary demographic history and population structure on primate species. Research results in this area will inform our understanding of ecological and evolutionary diversification in fragmented landscapes and offer guidance to conservation programs. The specific objective of this research proposal is to use genome-wide genetic data to compare and contrast genetic diversity, population structure, demographic history, and recent and historical gene flow in two sympatric mouse lemur species in western Madagascar: the endangered Mme. Berthe’s mouse lemur (Microcebus berthae) and the non-threatened gray mouse lemur (M. murinus).
Collaborators: Dr. Peter Kappeler, Dr. Livia Schäffler
Skills
- Next Generation Sequencing Library Preparation (ddRADseq method)
- GIS and raster manipulation
- Species distribution modeling
- Landscape genetic analyses
- Bioinformatics:
- Python scripts
- Stacks
- R
Morphological Variation in Mouse Lemurs
Abstract
A major focus of evolutionary primatology is understanding how morphological variation is partitioned relative to ecological gradients and landscape barriers. Many studies of primates examine the distribution of morphological variation relative to neighboring and other closely related species in order to understand the relationship between morphology and environment. There is growing awareness of the diversity found within and between mouse lemurs at a genetic level. This newly described variation in mouse lemurs can also be studied using a morphological approach. I studied morphological variation in two species of mouse lemur (Microcebus murinus and Microcebus griseorufus) that are found in neighboring locations in Madagascar as well as being closely related sister species. Using skins collections from the American Museum of Natural History, I collected measurements on fur coloration differences. Pelage coloration differences between M. murinus and M. griseorufus are limited to facial and ventral locations, with dorsal coloration playing a minor role. Coloration is known to have several purposes, such as concealment, species/kin recognition, and sexual signals. Differences between species can be caused by several factors, such as genetic drift as well as selection by factors listed above. The causes for the differences in these mouse lemurs is unknown, but overall, M. griseorufus is lighter in coloration compared to M. murinus.
Collaborators: Joralyssa Conley, Aryanna Myles
Skills
A major focus of evolutionary primatology is understanding how morphological variation is partitioned relative to ecological gradients and landscape barriers. Many studies of primates examine the distribution of morphological variation relative to neighboring and other closely related species in order to understand the relationship between morphology and environment. There is growing awareness of the diversity found within and between mouse lemurs at a genetic level. This newly described variation in mouse lemurs can also be studied using a morphological approach. I studied morphological variation in two species of mouse lemur (Microcebus murinus and Microcebus griseorufus) that are found in neighboring locations in Madagascar as well as being closely related sister species. Using skins collections from the American Museum of Natural History, I collected measurements on fur coloration differences. Pelage coloration differences between M. murinus and M. griseorufus are limited to facial and ventral locations, with dorsal coloration playing a minor role. Coloration is known to have several purposes, such as concealment, species/kin recognition, and sexual signals. Differences between species can be caused by several factors, such as genetic drift as well as selection by factors listed above. The causes for the differences in these mouse lemurs is unknown, but overall, M. griseorufus is lighter in coloration compared to M. murinus.
Collaborators: Joralyssa Conley, Aryanna Myles
Skills
- Mentoring high school students as part of the Student Research Mentoring Program with the American Museum of Natural History
- Utilization of the Primate Collections at the American Museum of Natural History
Behavior and Dominance Effects in Blue Monkeys
Abstract
Many studies of cercopithecine monkeys implicate dominance rank as an important variable influencing fitness, but there is growing awareness of the paucity of data for many species, and variation in rank’s effects. We studied how dominance rank affected the exposure of wild adult female Cercopithecus mitis to predators. Dominance hierarchies in blue monkeys have been characterized as stable but shallow. Focusing on adult females in two study groups inhabiting the Kakamega Forest, Kenya, we monitored their location in the canopy and in individual tree crowns over a two month period. Although blue monkeys are generally arboreal, we found that high-ranking females were somewhat more likely than low-rankers to use the ground, which is likely risky. Otherwise, rank did not predict the location of individuals in the trees, and concomitant exposure to aerial predators. Our results confirm a previous report from a third group in our study population. They are also consistent with other findings suggesting that dominance rank has limited effects on behavior in this species, despite being readily detectable. Effects of dominance rank are clearly variable in cercopithecines.
Collaborators: Dr. Marina Cords, Colins Mutai
Skills
Many studies of cercopithecine monkeys implicate dominance rank as an important variable influencing fitness, but there is growing awareness of the paucity of data for many species, and variation in rank’s effects. We studied how dominance rank affected the exposure of wild adult female Cercopithecus mitis to predators. Dominance hierarchies in blue monkeys have been characterized as stable but shallow. Focusing on adult females in two study groups inhabiting the Kakamega Forest, Kenya, we monitored their location in the canopy and in individual tree crowns over a two month period. Although blue monkeys are generally arboreal, we found that high-ranking females were somewhat more likely than low-rankers to use the ground, which is likely risky. Otherwise, rank did not predict the location of individuals in the trees, and concomitant exposure to aerial predators. Our results confirm a previous report from a third group in our study population. They are also consistent with other findings suggesting that dominance rank has limited effects on behavior in this species, despite being readily detectable. Effects of dominance rank are clearly variable in cercopithecines.
Collaborators: Dr. Marina Cords, Colins Mutai
Skills
- 3 months field experience in Kakamega Forest, Kenya
- Collection of behavioral data (focal follows)
- Conservation activities with local communities
