Testing theoretical metapopulation conditions with genotypic data from Boreal Chorus Frogs (Pseudacris maculata)

2019 ◽  
Vol 97 (11) ◽  
pp. 1042-1053
Author(s):  
Shawn M. Billerman ◽  
Brett R. Jesmer ◽  
Alexander G. Watts ◽  
Peter E. Schlichting ◽  
Marie-Josée Fortin ◽  
...  
Keyword(s):  
Demographic Data ◽  
Methodological Framework ◽  
Effective Population ◽  
Pseudacris Maculata ◽  
Breeding Populations ◽  
Chorus Frogs ◽  
Population Sizes ◽  
Feasible Alternative ◽  
Landscape Genetic

The metapopulation concept has far-reaching implications in ecology and conservation biology. Hanski’s criteria operationally define metapopulations, yet testing them is hindered by logistical and financial constraints inherent to the collection of long-term demographic data. Hence, ecologists and conservationists often assume metapopulation existence for dispersal-limited species that occupy patchy habitats. To advance understanding of metapopulation theory and improve conservation of metapopulations, we used population and landscape genetic tools to develop a methodological framework for evaluating Hanski’s criteria. We used genotypic data (11 microsatellite loci) from a purported metapopulation of Boreal Chorus Frogs (Pseudacris maculata (Agassiz, 1850)) in Colorado, U.S.A., to test Hanski’s four criteria. We found support for each criterion: (1) significant genetic differentiation between wetlands, suggesting distinct breeding populations; (2) wetlands had small effective population sizes and recent bottlenecks, suggesting populations do not experience long-term persistence; (3) population graphs provided evidence of gene flow between patches, indicating potential for recolonization; and (4) multiscale bottleneck analyses suggest asynchrony, indicating that simultaneous extinction of all populations was unlikely. Our methodological framework provides a logistically and financially feasible alternative to long-term demographic data for identifying amphibian metapopulations.

Demography and reproductive ecology of the Columbia spotted frog (Rana luteiventris) across the Palouse

2005 ◽  
Vol 83 (5) ◽  
pp. 702-711 ◽  
Author(s):  
Abbey B Davis ◽  
Paul A Verrell
Keyword(s):  
Population Size ◽  
Reproductive Ecology ◽  
Small Population ◽  
Effective Population ◽  
Small Population Size ◽  
Rana Luteiventris ◽  
Breeding Populations ◽  
The Status ◽  
Population Sizes

Here we report on the demography and reproductive ecology of the Columbia spotted frog (Rana luteiventris Thompson, 1913) breeding in ponds across the Palouse Bioregion of Washington and Idaho. Spotted frogs are unusual, if not unique, among temperate ranids in that males establish the oviposition site before females become active. Females laid at one or two communal sites in shallow water. Our breeding populations were small, never exceeding 50 adults counted, and most displayed male-biased sex ratios. We estimated effective population sizes (Ne) as ranges determined by extremes in male breeding success; these varied between 3.2 and 37.8. Even the latter falls below the minimum required for long-term population viability. Small population size may make spotted frogs vulnerable to genetic problems and environmental insults. Communal oviposition certainly renders a population's reproductive effort vulnerable to variation in hydroperiod, which we observed during the dry spring of 2004. In the absence of information on the degree of "connectedness" among our ponds as subunits of more resilient metapopulations, we suggest that small population size and communal oviposition likely render R. luteiventris vulnerable to anthropogenic disturbance. Furthermore, the status of R. luteiventris on the Palouse may be less secure than assumed currently.

scholarly journals Reducing bias in population and landscape genetic inferences: the effects of sampling related individuals and multiple life stages

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1813 ◽  
Author(s):  
William Peterman ◽  
Emily R. Brocato ◽  
Raymond D. Semlitsch ◽  
Lori S. Eggert
Keyword(s):  
Best Practice ◽  
Isolation By Distance ◽  
Life Stage ◽  
Population Sample ◽  
Life Stages ◽  
Effective Population ◽  
Data Set ◽  
Sibling Pairs ◽  
Population Sizes ◽  
Landscape Genetic

In population or landscape genetics studies, an unbiased sampling scheme is essential for generating accurate results, but logistics may lead to deviations from the sample design. Such deviations may come in the form of sampling multiple life stages. Presently, it is largely unknown what effect sampling different life stages can have on population or landscape genetic inference, or how mixing life stages can affect the parameters being measured. Additionally, the removal of siblings from a data set is considered best-practice, but direct comparisons of inferences made with and without siblings are limited. In this study, we sampled embryos, larvae, and adultAmbystoma maculatumfrom five ponds in Missouri, and analyzed them at 15 microsatellite loci. We calculated allelic richness, heterozygosity and effective population sizes for each life stage at each pond and tested for genetic differentiation (FSTandDC) and isolation-by-distance (IBD) among ponds. We tested for differences in each of these measures between life stages, and in a pooled population of all life stages. All calculations were done with and without sibling pairs to assess the effect of sibling removal. We also assessed the effect of reducing the number of microsatellites used to make inference. No statistically significant differences were found among ponds or life stages for any of the population genetic measures, but patterns of IBD differed among life stages. There was significant IBD when using adult samples, but tests using embryos, larvae, or a combination of the three life stages were not significant. We found that increasing the ratio of larval or embryo samples in the analysis of genetic distance weakened the IBD relationship, and when usingDC, the IBD was no longer significant when larvae and embryos exceeded 60% of the population sample. Further, power to detect an IBD relationship was reduced when fewer microsatellites were used in the analysis.

scholarly journals Reducing bias in population and landscape genetic inferences: The effects of sampling related individuals and multiple life stages

2015 ◽  
Author(s):  
William Peterman ◽  
Emily R Brocato ◽  
Raymond D Semlitsch ◽  
Lori S Eggert
Keyword(s):  
Isolation By Distance ◽  
Life Stage ◽  
Population Sample ◽  
Life Stages ◽  
Effective Population ◽  
Sibling Pairs ◽  
Target Sample Size ◽  
Population Sizes ◽  
Landscape Genetic ◽  
Genetic Inference

In population or landscape genetics studies, an unbiased sampling scheme is essential for generating accurate results, but logistics may lead to deviations from the sample design. Such deviations may come in the form of sampling multiple life stages. Presently, it is largely unknown what effect sampling different life stages can have on population or landscape genetic inference, or how mixing life stages can affect the parameters being measured. In this study, we sampled embryos, larvae, and adult Ambystoma maculatum from five ponds in Missouri, and analyzed them at 15 microsatellite loci. We calculated allelic richness, heterozygosity and effective population sizes for each life stage at each pond and tested for genetic differentiation (FST and DC) and isolation-by-distance (IBD) among ponds. We tested for differences in each of these measures between life stages, and in a pooled population of all life stages. All calculations were done with and without sibling pairs to assess the effect of sibling removal. No statistically significant differences were found among ponds or life stages for any of the population genetic measures, but patterns of IBD differed among life stages. There was significant IBD when using adult samples, but tests using embryos, larvae, or a combination of the three life stages were not significant. Further, we found that increasing the ratio of larval or embryo samples in the analysis of genetic distance weakened the IBD relationship, and when using DC, the IBD was no longer significant when larvae and embryos exceeded 60% of the population sample. Our findings suggest that it may be possible to mix life stages to reach target sample size quotas, but researchers should nonetheless proceed with caution depending upon the goals and objectives of the study.

scholarly journals Reducing bias in population and landscape genetic inferences: The effects of sampling related individuals and multiple life stages

2015 ◽  
Author(s):  
William Peterman ◽  
Emily R Brocato ◽  
Raymond D Semlitsch ◽  
Lori S Eggert
Keyword(s):  
Isolation By Distance ◽  
Life Stage ◽  
Population Sample ◽  
Life Stages ◽  
Effective Population ◽  
Sibling Pairs ◽  
Target Sample Size ◽  
Population Sizes ◽  
Landscape Genetic ◽  
Genetic Inference

In population or landscape genetics studies, an unbiased sampling scheme is essential for generating accurate results, but logistics may lead to deviations from the sample design. Such deviations may come in the form of sampling multiple life stages. Presently, it is largely unknown what effect sampling different life stages can have on population or landscape genetic inference, or how mixing life stages can affect the parameters being measured. In this study, we sampled embryos, larvae, and adult Ambystoma maculatum from five ponds in Missouri, and analyzed them at 15 microsatellite loci. We calculated allelic richness, heterozygosity and effective population sizes for each life stage at each pond and tested for genetic differentiation (FST and DC) and isolation-by-distance (IBD) among ponds. We tested for differences in each of these measures between life stages, and in a pooled population of all life stages. All calculations were done with and without sibling pairs to assess the effect of sibling removal. No statistically significant differences were found among ponds or life stages for any of the population genetic measures, but patterns of IBD differed among life stages. There was significant IBD when using adult samples, but tests using embryos, larvae, or a combination of the three life stages were not significant. Further, we found that increasing the ratio of larval or embryo samples in the analysis of genetic distance weakened the IBD relationship, and when using DC, the IBD was no longer significant when larvae and embryos exceeded 60% of the population sample. Our findings suggest that it may be possible to mix life stages to reach target sample size quotas, but researchers should nonetheless proceed with caution depending upon the goals and objectives of the study.

scholarly journals Pygoscelid penguins breeding distribution and population trends at Lions Rump rookery, King George Island

2013 ◽  
Vol 34 (1) ◽  
pp. 87-99 ◽  
Author(s):  
Małgorzata Korczak−Abshire ◽  
Michał Węgrzyn ◽  
Piotr J. Angiel ◽  
Maja Lisowska
Keyword(s):  
Environmental Changes ◽  
King George Island ◽  
Time Intervals ◽  
Breeding Populations ◽  
Population Sizes ◽  
Natural Response ◽  
Gis System ◽  
The Antarctic ◽  
Pygoscelid Penguins

AbstractLong term changes (46 years) in the abundance of pygoscelid penguins breeding populations and nests distribution in the Lions Rump (King George Island) colony were in− vestigated in three time intervals, according to previously published two censuses and one original study conducted in 2010. At that time a detailed colony map based on the GIS system was made. Results of this study showed different trends for each investigated species. In the last three decades Adélie penguin breeding populations showed strong declining tendencies (69.61%). In contrast, the population of gentoo penguins represents the reverse trend, increasing 171.85% over the same period. Observed changes in both penguin population sizes are reflected in the different spatial and geographic distribution of their nests. The population changes observed at the Lions Rump colony are consistent with the relevant pygoscelid penguin tendencies in the western Antarctic Peninsula region. Breeding penguin population dynamics at Lions Rump area with a minimal disturbance by human activity may well illustrate a natural response of those birds to environmental changes in the Antarctic.

scholarly journals Estimation of Long-Term Effective Population Sizes Through the History of Durum Wheat Using Microsatellite Data

Genetics ◽  
2004 ◽  
Vol 169 (3) ◽  
pp. 1589-1599 ◽  
Author(s):  
A.-C. Thuillet ◽  
T. Bataillon ◽  
S. Poirier ◽  
S. Santoni ◽  
J. L. David
Keyword(s):  
Durum Wheat ◽  
Microsatellite Data ◽  
Effective Population ◽  
Population Sizes ◽  
History Of

scholarly journals Whole-genome sequences suggest long term declines of spotted owl (Strix occidentalis) (Aves: Strigiformes: Strigidae) populations in California

2018 ◽  
Author(s):  
Zachary R. Hanna ◽  
John P. Dumbacher ◽  
Rauri C.K. Bowie ◽  
Jeffrey D. Wall
Keyword(s):  
Isolation By Distance ◽  
Whole Genome ◽  
Population Declines ◽  
Effective Population ◽  
Spotted Owl ◽  
Strix Occidentalis ◽  
Genome Data ◽  
Population Sizes ◽  
California Spotted Owl

AbstractWe analyzed whole-genome data of four spotted owls (Strix occidentalis) to provide a broad-scale assessment of the genome-wide nucleotide diversity across S. occidentalis populations in California. We assumed that each of the four samples was representative of its population and we estimated effective population sizes through time for each corresponding population. Our estimates provided evidence of long-term population declines in all California S. occidentalis populations. We found no evidence of genetic differentiation between northern spotted owl (S. o. caurina) populations in the counties of Marin and Humboldt in California. We estimated greater differentiation between populations at the northern and southern extremes of the range of the California spotted owl (S. o. occidentalis) than between populations of S. o. occidentalis and S. o. caurina in northern California. The San Diego County S. o. occidentalis population was substantially diverged from the other three S. occidentalis populations. These whole-genome data support a pattern of isolation-by-distance across spotted owl populations in California, rather than elevated differentiation between currently recognized subspecies.

scholarly journals Genetic purging in captive endangered ungulates with extremely low effective population sizes

Heredity ◽  
2021 ◽  
Author(s):  
Eugenio López-Cortegano ◽  
Eulalia Moreno ◽  
Aurora García-Dorado
Keyword(s):  
Natural Selection ◽  
Population Size ◽  
Inbreeding Depression ◽  
Captive Breeding ◽  
Random Mating ◽  
Management Strategies ◽  
Effective Population ◽  
Population Sizes ◽  
Genetic Purging

AbstractInbreeding threatens the survival of small populations by producing inbreeding depression, but also exposes recessive deleterious effects in homozygosis allowing for genetic purging. Using inbreeding-purging theory, we analyze early survival in four pedigreed captive breeding programs of endangered ungulates where population growth was prioritized so that most adult females were allowed to contribute offspring according to their fitness. We find evidence that purging can substantially reduce inbreeding depression in Gazella cuvieri (with effective population size Ne = 14) and Nanger dama (Ne = 11). No purging is detected in Ammotragus lervia (Ne = 4), in agreement with the notion that drift overcomes purging under fast inbreeding, nor in G. dorcas (Ne = 39) where, due to the larger population size, purging is slower and detection is expected to require more generations. Thus, although smaller populations are always expected to show smaller fitness (as well as less adaptive potential) than larger ones due to higher homozygosis and deleterious fixation, our results show that a substantial fraction of their inbreeding load and inbreeding depression can be purged when breeding contributions are governed by natural selection. Since management strategies intended to maximize the ratio from the effective to the actual population size tend to reduce purging, the search for a compromise between these strategies and purging could be beneficial in the long term. This could be achieved either by allowing some level of random mating and some role of natural selection in determining breeding contributions, or by undertaking reintroductions into the wild at the earliest opportunity.

Karyotypic Evolution and Long-Term Effective Population Sizes of Birds

The Auk ◽  
1984 ◽  
Vol 101 (1) ◽  
pp. 99-102 ◽  
Author(s):  
George F. Barrowclough ◽  
Gerald F. Shields
Keyword(s):  
Geographic Variation ◽  
Karyotypic Evolution ◽  
Effective Population ◽  
Allelic Frequencies ◽  
Demographic Modeling ◽  
Population Sizes ◽  
History Of ◽  
Karyotypic Change ◽  
Wide Assortment

Abstract Rates of karyotypic change in birds are used to estimate that, over the longterm history of a wide assortment of genera, avian effective population sizes have averaged on the order of 100. This result is consistent with the results of electrophoretic studies of geographic variation of allelic frequencies within species but is somewhat less consistent with the results obtained from demographic modeling. Three methodologically independent analyses have now corroborated the hypothesis that avian effective population sizes are typically of the order of 102 or larger.

Sign in / Sign up

Export Citation Format

Share Document