scholarly journals Testing the Effect of the Toba Volcanic Eruption on Population Sizes in Worldwide Mammal Species

2020 ◽  
Author(s):  
Nicole S. Torosin ◽  
Jennifer A. Raff ◽  
M. Geoffrey Hayes
Keyword(s):  
Volcanic Eruption ◽  
Population Expansion ◽  
Population Bottleneck ◽  
Sudden Expansion ◽  
Mammal Species ◽  
Show Evidence ◽  
Sudden Expansion Model ◽  
Population Sizes ◽  
Sufficient Magnitude ◽  
Expansion Model

AbstractThe volcanic eruption of Toba in northern Sumatra at 71 kyBP (±5 kyBP) emitted sulfur gas and deposited thick layers of dust throughout the surrounding region. It is thought to have had a significant and dramatic cooling impact on the paleoclimate worldwide. Ambrose [1] conjectured this to be the cause of the contemporaneous (50-100 kyBP) population bottleneck observed in humans. We hypothesize that a volcanic winter of sufficient magnitude to cause a population bottleneck in humans would similarly affect other mammals. To test this hypothesis, we estimated pairwise mismatch distributions using mtDNA control region sequences of 28 mammal species archived on NCBI to assess whether each species underwent a population bottleneck. For any species fitting the sudden expansion model, we estimated the timing of the bottleneck and compared it to the date range of the Toba eruption. Only 3 of the 28 species show evidence of rapid population expansion overlapping in time with the Toba eruption. Therefore, the hypothesis that the volcanic winter triggered by the Toba eruption caused a significant bottleneck impacting mammal species worldwide is not supported by mitochondrial evidence. Our results question the hypothesis that the Toba eruption contributed to the bottleneck observed in humans at this time.

The genetic structure of the spectacled bear (Tremarctos ornatus; Ursidae, Carnivora) in Colombia by means of mitochondrial and microsatellite markers

2020 ◽  
Vol 101 (4) ◽  
pp. 1072-1090
Author(s):  
Manuel Ruiz-García ◽  
Jessica Yanina Arias Vásquez ◽  
Héctor Restrepo ◽  
Carlos Herney Cáceres-Martínez ◽  
Joseph Mark Shostell
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Isolation By Distance ◽  
Phylogenetic Analyses ◽  
Population Expansion ◽  
Sudden Expansion ◽  
Population Decrease ◽  
Geographical Regions ◽  
Show Evidence

Abstract The spectacled bear (Ursidae: Tremarctos ornatus) is an emblematic umbrella species and one of the top carnivores in the Andean mountains. It is also listed as vulnerable by IUCN and as endangered by CITES. We analyzed the genetic structure of this species in nine geographical regions representing the three Andean Cordilleras in Colombia. We sequenced six mitochondrial genes in 115 spectacled bears; a subset of these specimens (n = 61) were genotyped at seven nuclear microsatellites. We addressed three objectives: 1) determine the genetic diversity and historical demographic changes of the spectacled bear in Colombia; 2) determine phylogeographic patterns of genetic divergence among spectacled bear populations in Colombia; and 3) estimate the levels of gene flow among different regions of Colombia. Our analyses show evidence of high mitochondrial genetic diversity in spectacled bears, both in Colombia as well as in each of the nine regions, most particularly Norte de Santander, Nariño, and Antioquia-Córdoba. In addition, we detected population expansion in Colombia that occurred around 24,000 years ago, followed by a population decrease during the last 7,000 years, and a sudden expansion in the last 300 years. Phylogenetic analyses showed few well-supported clades, with some haplotypes detected in all the departments and Colombian Andean Cordilleras, and other haplotypes restricted to certain geographical areas (Antioquia, Norte de Santander, Cundinamarca, and Nariño). We detected significant genetic heterogeneity among some departments and among the three Colombian Andean Cordilleras for both mitochondrial and nuclear genes. Nevertheless, the moderate levels of gene flow estimated from FST statistics suggest that geographical barriers have not been definitive obstacles to the dispersion of the spectacled bear throughout Colombia. Despite these gene flow estimates, significant spatial autocorrelation was detected for spectacled bear in Colombia, where two kinds of spatial patterns were discovered: genetic patches of 144 km of diameter, and isolation by distance among bears separated from 578 to 800 km. The two most northern spectacled bear populations of Colombia (Norte de Santander and Antioquia) also were the two most differentiated. Their distinctiveness may qualify them as distinct Management Units (MUs) in the context of conservation policies for the spectacled bear in Colombia.

scholarly journals Genetic diversity in migratory bats: Results from RADseq data for three tree bat species at an Ohio windfarm

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1647 ◽  
Author(s):  
Michael G. Sovic ◽  
Bryan C. Carstens ◽  
H. Lisle Gibbs
Keyword(s):  
Genetic Structure ◽  
Wind Farm ◽  
Nuclear Dna ◽  
Effective Population ◽  
Genetic Analyses ◽  
Lasiurus Cinereus ◽  
Time Migration ◽  
Show Evidence ◽  
Population Sizes ◽  
Wind Facility

Genetic analyses can identify the scale at which wildlife species are impacted by human activities, and provide demographic information useful for management. Here, we use thousands of nuclear DNA genetic loci to assess whether genetic structure occurs withinLasiurus cinereus(Hoary Bat),L. borealis(Red Bat), andLasionycteris noctivagans(Silver-Haired Bat) bats found at a wind turbine site in Ohio, and to also estimate demographic parameters in each of these three groups. Our specific goals are to: 1) demonstrate the feasibility of isolating RADseq loci from these tree bat species, 2) test for genetic structure within each species, including any structure that may be associated with time (migration period), and 3) use coalescent-based modeling approaches to estimate genetically-effective population sizes and patterns of population size changes over evolutionary timescales. Thousands of loci were successfully genotyped for each species, demonstrating the value of RADseq for generating polymorphic loci for population genetic analyses in these bats. There was no evidence for genetic differentiation between groups of samples collected at different times throughout spring and fall migration, suggesting that individuals from each species found at the wind facility are from single panmictic populations. Estimates of present-day effective population sizes varied across species, but were consistently large, on the order of 105–106. All populations show evidence of expansions that date to the Pleistocene. These results, along with recent work also suggesting limited genetic structure in bats across North America, argue that additional biomarker systems such as stable-isotopes or trace elements should be investigated as alternative and/or complementary approaches to genetics for sourcing individuals collected at single wind farm sites.

scholarly journals Patterns of Nucleotide Diversity of theldpACircadian Gene in Closely Related Species of Cyanobacteria from Extreme Cold Deserts

2012 ◽  
Vol 79 (5) ◽  
pp. 1516-1522 ◽  
Author(s):  
Ka Wai Ng ◽  
Stephen B. Pointing ◽  
Volodymyr Dvornyk
Keyword(s):  
Related Species ◽  
Nucleotide Diversity ◽  
Population Expansion ◽  
Nucleotide Polymorphism ◽  
Effective Population ◽  
Closely Related Species ◽  
Content Type ◽  
Population Sizes ◽  
Extreme Cold ◽  
Small Effective Population Size

ABSTRACTIn the circadian system of cyanobacteria, theldpAgene is a component of the input to the clock. We comparatively analyzed nucleotide polymorphism of this gene in populations of two closely related species of cyanobacteria (denoted asSynechococcusspecies S1 and S2, respectively) from extreme cold deserts in Antarctica, the Canadian Arctic, and Tibet. Although both species manifested similarly high haplotype diversities (0.990 and 0.809, respectively), the nucleotide diversity differed significantly (0.0091 in S1 and 0.0037 in S2). The populations of species S2 were more differentiated (FST= 0.2242) compared to those of species S1 (FSTbetween 0.0296 and 0.1188). An analysis of positive selection with several tests yielded highly significant values (P< 0.01) for both species. On the other hand, these results may be somewhat compromised by fluctuating population sizes of the species. The apparent selection pressure coupled with the pronounced demographic factors, such as population expansion, small effective population size, and genetic drift, may thus result in the observed significant interpopulation differentiation and subsequent speciation of cyanobacteria.

scholarly journals Assessing genetic diversity and connectivity in a tule elk (Cervus canadensis nannodes) metapopulation in Northern California

2021 ◽  
Author(s):  
Thomas J. Batter ◽  
Joshua P. Bush ◽  
Benjamin N. Sacks
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Population Expansion ◽  
Active Management ◽  
Genetic Connectivity ◽  
Effective Population ◽  
Sex Marker ◽  
Cervus Canadensis ◽  
Population Sizes ◽  
Tule Elk

AbstractThe tule elk (Cervus canadensis nannodes) is a California endemic subspecies that experienced an extreme bottleneck (potentially two individuals) in the mid-1800s. Through active management, including reintroductions, the subspecies has grown to approximately 6000 individuals spread across 22 recognized populations. The populations tend to be localized and separated by unoccupied intervening habitat, prompting targeted translocations to ensure gene flow. However, little is known about the genetic status or connectivity among adjacent populations in the absence of active translocations. We used 19 microsatellites and a sex marker to obtain baseline data on the genetic effective population sizes and functional genetic connectivity of four of these populations, three of which were established since the 1980s and one of which was established ~ 100 years ago. A Bayesian assignment approach suggested the presence of 5 discrete genetic clusters, which corresponded to the four primary populations and two subpopulations within the oldest of them. Effective population sizes ranged from 15 (95% CI 10–22) to 51 (95% CI 32–88). We detected little or no evidence of gene flow among most populations. Exceptions were a signature of unidirectional gene flow to one population founded by emigrants of the other 30 years earlier, and bidirectional gene flow between subpopulations within the oldest population. We propose that social cohesion more than landscape characteristics explained population structure, which developed over many generations corresponding to population expansion. Whether or which populations can grow and reach sufficient effective population sizes on their own or require translocations to maintain genetic diversity and population growth is unclear. In the future, we recommend pairing genetic with demographic monitoring of these and other reintroduced elk populations, including targeted monitoring following translocations to evaluate their effects and necessity.

scholarly journals Global demographic history of human populations inferred from whole mitochondrial genomes

2018 ◽  
Vol 5 (8) ◽  
pp. 180543 ◽  
Author(s):  
Eleanor F. Miller ◽  
Andrea Manica ◽  
William Amos
Keyword(s):  
Demographic History ◽  
Population Expansion ◽  
Human Populations ◽  
Population Mixing ◽  
Neolithic Transition ◽  
Current Location ◽  
Geographical Regions ◽  
Population Sizes ◽  
History Of ◽  
Complete Mtdna

The Neolithic transition has led to marked increases in census population sizes across the world, as recorded by a rich archaeological record. However, previous attempts to detect such changes using genetic markers, especially mitochondrial DNA (mtDNA), have mostly been unsuccessful. We use complete mtDNA genomes from over 1700 individuals, from the 1000 Genomes Project Phase 3, to explore changes in populations sizes in five populations for each of four major geographical regions, using a sophisticated coalescent-based Bayesian method (extended Bayesian skyline plots) and mutation rates calibrated with ancient DNA. Despite the power and sophistication of our analysis, we fail to find size changes that correspond to the Neolithic transitions of the study populations. However, we do detect a number of size changes, which tend to be replicated in most populations within each region. These changes are mostly much older than the Neolithic transition and could reflect either population expansion or changes in population structure. Given the amount of migration and population mixing that occurred after these ancient signals were generated, we caution that modern populations will often carry ghost signals of demographic events that occurred far away from their current location.

scholarly journals Molecular evolutionary consequences of island colonisation

2015 ◽  
Author(s):  
Jennifer James ◽  
Robert Lanfear ◽  
Adam Eyre-Walker
Keyword(s):  
Genetic Diversity ◽  
Population Bottleneck ◽  
Surprising Result ◽  
Population Bottlenecks ◽  
Adaptive Potential ◽  
Effective Population ◽  
Island Species ◽  
Population Sizes ◽  
Evolutionary Consequences ◽  
The Relationship

Island endemics are likely to experience population bottlenecks; they also have restricted ranges. Therefore we expect island species to have small effective population sizes (Ne) and reduced genetic diversity compared to their mainland counterparts. As a consequence, island species may have inefficient selection and reduced adaptive potential. We used both polymorphisms and substitutions to address these predictions, improving on the approach of recent studies that only used substitution data. This allowed us to directly test the assumption that island species have small values of Ne. We found that island species had significantly less genetic diversity than mainland species; however, this pattern could be attributed to a subset of island species that had undergone a recent population bottleneck. When these species were excluded from the analysis, island and mainland species had similar levels of genetic diversity, despite island species occupying considerably smaller areas than their mainland counterparts. We also found no overall difference between island and mainland species in terms of effectiveness of selection or mutation rate. Our evidence suggests that island colonisation has no lasting impact on molecular evolution. This surprising result highlights gaps in our knowledge of the relationship between census and effective population size.

scholarly journals The potential distributions, and estimated spatial requirements and population sizes, of the medium to large-sized mammals in the planning domain of the Greater Addo Elephant National Park project

Koedoe ◽  
2002 ◽  
Vol 45 (2) ◽  
Author(s):  
A.F. Boshoff ◽  
G.I.H. Kerley ◽  
R.M. Cowling ◽  
S.L. Wilson
Keyword(s):  
National Park ◽  
Suitable Habitat ◽  
Eastern Cape ◽  
Mammal Species ◽  
Park Planning ◽  
Ecological Requirements ◽  
Spreadsheet Models ◽  
Population Sizes ◽  
Identification Of Species ◽  
Potential Population

The Greater Addo Elephant National Park project (GAENP) involves the establishment of a mega biodiversity reserve in the Eastern Cape, South Africa. Conservation planning in the GAENP planning domain requires systematic information on the potential distributions and estimated spatial requirements, and population sizes of the medium to largesized mammals. The potential distribution of each species is based on a combination of literature survey, a review of their ecological requirements, and consultation with conservation scientists and managers. Spatial requirements were estimated within 21 Mammal Habitat Classes derived from 43 Land Classes delineated by expert-based vegetation and river mapping procedures. These estimates were derived from spreadsheet models based on forage availability estimates and the metabolic requirements of the respective mammal species, and that incorporate modifications of the agriculture-based Large Stock Unit approach. The potential population size of each species was calculated by multiplying its density estimate with the area of suitable habitat. Population sizes were calculated for pristine, or near pristine, habitats alone, and then for these habitats together with potentially restorable habitats for two park planning domain scenarios. These data will enable (a) the measurement of the effectiveness of the GAENP in achieving predetermined demographic, genetic and evolutionary targets for mammals that can potentially occur in selected park sizes and configurations, (b) decisions regarding acquisition of additional land to achieve these targets to be informed, (c) the identification of species for which targets can only be met through metapopulation management,(d) park managers to be guided regarding the re-introduction of appropriate species, and (e) the application of realistic stocking rates. Where possible, the model predictions were tested by comparison with empirical data, which in general corroborated the predictions. All estimates should be considered as testable hypotheses.

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