High variation of mitochondrial <scp>DNA</scp> diversity as compared to nuclear microsatellites in mammalian populations

Saitoh, Takashi

doi:10.1111/1440-1703.12190

Cited by 6 publications

(4 citation statements)

References 54 publications

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“…Wimmer et al (2002) found 13 mtDNA haplotypes in 85 individuals of M. murinus, revealed 4 haplotypes among 46 individuals (sampled in 1 year) of the sympatric Mirza coquereli, and Gerloff et al (1999) detected 5 haplotypes in a population of 36 bonobos. The mtDNA haplotype diversity of M. griseorufus (0.921), calculated according to Saitoh (2021), is higher than that of M. murinus (0.508) and M. coquereli (0.660). While it is difficult to compare different higher taxa, social units, and sampling areas, M. grisoeurufus is very diverse and ranks among the top 15% of the 66 terrestrial mammal species compiled by Saitoh (2021).…”

Section: Discussionmentioning

confidence: 75%

“…The mtDNA haplotype diversity of M. griseorufus (0.921), calculated according to Saitoh (2021), is higher than that of M. murinus (0.508) and M. coquereli (0.660). While it is difficult to compare different higher taxa, social units, and sampling areas, M. grisoeurufus is very diverse and ranks among the top 15% of the 66 terrestrial mammal species compiled by Saitoh (2021).…”

Section: Discussionmentioning

confidence: 75%

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Habitat quality affects the social organization in mouse lemurs (Microcebus griseorufus)

Abel

Giertz

Ratovonamana

et al. 2023

Behav Ecol Sociobiol

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Species can either maintain a certain social organization in different habitats or show different social organizations in similar habitats. The reasons underlying this variability are not always clear but might have consequences for population dynamics, especially under changing environmental conditions. Among mammals, the primate genus Microcebus lives in small groups of closely related females, derived from female philopatry and dispersed males, as illustrated by the well-studied Microcebus murinus. Here, we studied the genetic structure of a population of the congeneric Microcebus griseorufus, inhabiting three adjacent habitats with different resource availabilities. In order to learn more about the plasticity of the species’ social organization under these different conditions, we analyzed the spatial arrangement of mitochondrial haplotypes of 122 individuals. The study revealed high haplotype diversity and a pronounced difference in spatial distribution between the sexes. Females exhibited spatial aggregation of haplotypes, suggesting a system of female philopatry and matrilines, similar to M. murinus. Male haplotypes were dispersed, and males were more likely to carry rare haplotypes, indicating higher dispersal activity. These findings hint towards the unity of the social organization across the genus Microcebus, suggesting a phylogenetic origin of the social organization. Yet, with decreasing resources, the clustering of female haplotypes declined and approached a random distribution in the marginal habitat, with cluster sizes correlating with resource availability as predicted by the socioecological model. Our study supports the notion that social organization is shaped by both phylogenetic origin and ecological conditions, at least in these small primates. Significance statement Impacts of habitat degradation are mostly described in terms of changes in population densities in relation to the reduction of resources. This neglects the possible effects of altered social organizations due to declining resources or population densities. Using a genetic sampling of three subpopulations of mouse lemurs in Madagascar along a gradient of food availability up to the limit of the species’ ecological tolerance, we show that their social organization consisting of spatial clusters of closely related females and overdispersed males converges towards random spatial distributions of both sexes with declining food availability.

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Section: Discussionmentioning

confidence: 75%

Section: Discussionmentioning

confidence: 75%

Habitat quality affects the social organization in mouse lemurs (Microcebus griseorufus)

Abel

Giertz

Ratovonamana

et al. 2023

Behav Ecol Sociobiol

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“…Genetic differentiation statistics were also calculated by SNP data (Text S1). Generally, genetic diversity and genetic drift pressure differ between nuclear DNA and mtDNA (Toews and Brelsford 2012;Morin et al 2018;Saitoh 2021). However, at the spatial scale at which gene flow is dominant, because the theoretical pattern of being inversely proportional to migration is common (Allendorf et al 2022), genetic differentiation should be synchronized regardless of markers in the absence of sex differences.…”

Section: Population Structure Genetic Diversity and Genetic Different...mentioning

confidence: 99%

Testing the applicability of environmental DNA metabarcoding to landscape genetics

Nakajima,

Tsuri

2024

Preprint

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Landscape genetics is a field dealing with local genetic differences and contributes to strategic conservation planning. Recently, environmental DNA (eDNA) metabarcoding has proven useful not only for detecting species but also for assessing genetic diversity and genetic structure on a large scale such as in phylogeography. However, it remains unclear whether eDNA analysis also has sufficient power to perform the landscape genetics, which focuses on a local scale. To reveal the applicability of eDNA to landscape genetics, we conducted an eDNA metabarcoding analysis of the mitochondrial DNA D-loop region of the fluvial sculpin Cottus nozawae in the upper Sorachi River in Japan and compared the results with inferences based on traditional tissue-based approaches. As a result, the spatial distribution of haplotypes was generally consistent between the eDNA- and tissue-based approaches. In addition, the genetic differentiation statistics calculated using eDNA and tissue samples were highly correlated when compared in the same genetic region. Furthermore, if an inference based on genome-wide SNP data from tissue samples was taken as known truth, the inference by eDNA was not necessarily inferior to the inference by the same region from tissue samples. Finally, we confirmed that analyses using eDNA data can reveal patterns such as isolation-by-distance shown in previous studies on this species, indicating the applicability of eDNA to basic landscape genetics. Even though some limitations remain, eDNA may have great potential for conducting basic landscape genetics.

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“…Tigers are known to exhibit female philopatry and male-biased dispersal therefore we may expect to see stronger structure in matrilineally inherited markers. This pattern of male-biased dispersal is common among mammals and results in patterns of nested mitochondrial DNA structure even when there is continued gene flow [74,75]. While this pattern of NE divergence reflects the inferences in Kolipakam et al [40], PCA and structure analysis in Armstrong et al [36] do not show this separation, and our genome-wide analysis indicates that the NE does not differentiate until higher K. This outcome and the shared ancestry between the NE and some CI populations in Kolipakam et al [40] suggests that there has been continued gene flow between tigers in the NE and CI.…”

Section: (B) Nuclear Markersmentioning

confidence: 99%

How methodological changes have influenced our understanding of population structure in threatened species: insights from tiger populations across India

Aylward

Sagar

Natesh

et al. 2022

Phil. Trans. R. Soc. B

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Unprecedented advances in sequencing technology in the past decade allow a better understanding of genetic variation and its partitioning in natural populations. Such inference is critical to conservation: to understand species biology and identify isolated populations. We review empirical population genetics studies of Endangered Bengal tigers within India, where 60–70% of wild tigers live. We assess how changes in marker type and sampling strategy have impacted inferences by reviewing past studies, and presenting three novel analyses including a single-nucleotide polymorphism (SNP) panel, genome-wide SNP markers, and a whole-mitochondrial genome network. At a broad spatial scale, less than 100 SNPs revealed the same patterns of population clustering as whole genomes (with the exception of one additional population sampled only in the SNP panel). Mitochondrial DNA indicates a strong structure between the northeast and other regions. Two studies with more populations sampled revealed further substructure within Central India. Overall, the comparison of studies with varied marker types and sample sets allows more rigorous inference of population structure. Yet sampling of some populations is limited across all studies, and these should be the focus of future sampling efforts. We discuss challenges in our understanding of population structure, and how to further address relevant questions in conservation genetics. This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.

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High variation of mitochondrial DNA diversity as compared to nuclear microsatellites in mammalian populations

Cited by 6 publications

References 54 publications

Habitat quality affects the social organization in mouse lemurs (Microcebus griseorufus)

Habitat quality affects the social organization in mouse lemurs (Microcebus griseorufus)

Testing the applicability of environmental DNA metabarcoding to landscape genetics

How methodological changes have influenced our understanding of population structure in threatened species: insights from tiger populations across India

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