scholarly journals Demographic inference provides insights into the extirpation and ecological dominance of eusocial snapping shrimps

2020 ◽  
Author(s):  
Solomon T. C. Chak ◽  
Stephen E. Harris ◽  
Kristin M. Hultgren ◽  
J. Emmett Duffy ◽  
Dustin R. Rubenstein
Keyword(s):  
Life Histories ◽  
Environmental Changes ◽  
Population Declines ◽  
Effective Population ◽  
Social Traits ◽  
Population Sizes ◽  
Demographic Inference ◽  
Ecological Dominance ◽  
Snapping Shrimps ◽  
Eusocial Species

AbstractEusocial animals often achieve ecological dominance in the ecosystems where they occur, a process that may be linked to their demography. That is, reproductive division of labor and high reproductive skew in eusocial species is predicted to result in more stable effective population sizes that may make groups more competitive, but also lower effective population sizes that may make groups more susceptible to inbreeding and extinction. We examined the relationship between demography and social organization in one of the few animal lineages where eusociality has evolved recently and repeatedly among close relatives, the Synalpheus snapping shrimps. Although eusocial species often dominate the reefs where they occur by outcompeting their non-eusocial relatives for access to sponge hosts, many eusocial species have recently become extirpated across the Caribbean. Coalescent-based historical demographic inference in 12 species found that across nearly 100,000 generations, eusocial species tended to have lower but more stable effective population sizes through time. Our results are consistent with the idea that stable population sizes may enable eusocial shrimps to be more competitively dominant, but they also suggest that recent population declines are likely caused by eusocial shrimps’ heightened sensitivity to anthropogenically-driven environmental changes as a result of their low effective population sizes and localized dispersal, rather than to natural cycles of inbreeding and extinction. Thus, although the unique life histories and demography of eusocial shrimps has likely contributed to their persistence and ecological dominance over evolutionary timescales, these social traits may also make them vulnerable to contemporary environmental change.

scholarly journals Continent-wide effects of urbanization on bird and mammal genetic diversity

2019 ◽  
Author(s):  
C. Schmidt ◽  
M. Domaratzki ◽  
R.P. Kinnunen ◽  
J. Bowman ◽  
C.J. Garroway
Keyword(s):  
Genetic Diversity ◽  
Environmental Changes ◽  
Bird Species ◽  
Population Level ◽  
Natural Environments ◽  
Population Declines ◽  
Effective Population ◽  
Human Footprint ◽  
Rate Of Increase ◽  
Population Sizes

AbstractUrbanization and associated environmental changes are causing global declines in vertebrate populations. In general, population declines of the magnitudes now detected should lead to reduced effective population sizes for animals living in proximity to humans and disturbed lands. This is cause for concern because effective population sizes set the rate of genetic diversity loss due to genetic drift, the rate of increase in inbreeding, and the efficiency with which selection can act on beneficial alleles. We predicted that the effects of urbanization should decrease effective population size and genetic diversity, and increase population-level genetic differentiation. To test for such patterns, we repurposed and reanalyzed publicly archived genetic data sets for North American birds and mammals. After filtering, we had usable raw genotype data from 85 studies and 41,023 individuals, sampled from 1,008 locations spanning 41 mammal and 25 bird species. We used census-based urban-rural designations, human population density, and the Human Footprint Index as measures of urbanization and habitat disturbance. As predicted, mammals sampled in more disturbed environments had lower effective population sizes and genetic diversity, and were more genetically differentiated from those in more natural environments. There were no consistent relationships detectable for birds. This suggests that, in general, mammal populations living near humans may have less capacity to respond adaptively to further environmental changes, and be more likely to suffer from effects of inbreeding.

scholarly journals Continent-wide effects of urbanization on bird and mammal genetic diversity

2020 ◽  
Vol 287 (1920) ◽  
pp. 20192497 ◽  
Author(s):  
C. Schmidt ◽  
M. Domaratzki ◽  
R. P. Kinnunen ◽  
J. Bowman ◽  
C. J. Garroway
Keyword(s):  
Genetic Diversity ◽  
Environmental Changes ◽  
Bird Species ◽  
Population Level ◽  
Natural Environments ◽  
Population Declines ◽  
Effective Population ◽  
Human Footprint ◽  
Rate Of Increase ◽  
Population Sizes

Urbanization and associated environmental changes are causing global declines in vertebrate populations. In general, population declines of the magnitudes now detected should lead to reduced effective population sizes for animals living in proximity to humans and disturbed lands. This is a cause for concern because effective population sizes set the rate of genetic diversity loss due to genetic drift, the rate of increase in inbreeding and the efficiency with which selection can act on beneficial alleles. We predicted that the effects of urbanization should decrease effective population size and genetic diversity, and increase population-level genetic differentiation. To test for such patterns, we repurposed and reanalysed publicly archived genetic datasets for North American birds and mammals. After filtering, we had usable raw genotype data from 85 studies and 41 023 individuals, sampled from 1008 locations spanning 41 mammal and 25 bird species. We used census-based urban–rural designations, human population density and the Human Footprint Index as measures of urbanization and habitat disturbance. As predicted, mammals sampled in more disturbed environments had lower effective population sizes and genetic diversity, and were more genetically differentiated from those in more natural environments. There were no consistent relationships detectable for birds. This suggests that, in general, mammal populations living near humans may have less capacity to respond adaptively to further environmental changes, and be more likely to suffer from effects of inbreeding.

scholarly journals Deep-Time Demographic Inference Suggests Ecological Release as Driver of Neoavian Adaptive Radiation

Diversity ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 164 ◽  
Author(s):  
Peter Houde ◽  
Edward L. Braun ◽  
Lawrence Zhou
Keyword(s):  
Evolutionary Biology ◽  
Gene Tree ◽  
Difficult Problem ◽  
Gene Trees ◽  
Effective Population ◽  
Deep Time ◽  
Ecological Release ◽  
Population Sizes ◽  
Demographic Inference ◽  
Gene Tree Discordance

Assessing the applicability of theory to major adaptive radiations in deep time represents an extremely difficult problem in evolutionary biology. Neoaves, which includes 95% of living birds, is believed to have undergone a period of rapid diversification roughly coincident with the Cretaceous–Paleogene (K-Pg) boundary. We investigate whether basal neoavian lineages experienced an ecological release in response to ecological opportunity, as evidenced by density compensation. We estimated effective population sizes (Ne) of basal neoavian lineages by combining coalescent branch lengths (CBLs) and the numbers of generations between successive divergences. We used a modified version of Accurate Species TRee Algorithm (ASTRAL) to estimate CBLs directly from insertion–deletion (indel) data, as well as from gene trees using DNA sequence and/or indel data. We found that some divergences near the K-Pg boundary involved unexpectedly high gene tree discordance relative to the estimated number of generations between speciation events. The simplest explanation for this result is an increase in Ne, despite the caveats discussed herein. It appears that at least some early neoavian lineages, similar to the ancestor of the clade comprising doves, mesites, and sandgrouse, experienced ecological release near the time of the K-Pg mass extinction.

New DNA coalescent models and old population genetics software†

2016 ◽  
Vol 73 (9) ◽  
pp. 2178-2180 ◽  
Author(s):  
W. Stewart Grant ◽  
Einar Árnason ◽  
Bjarki Eldon
Keyword(s):  
Dna Sequences ◽  
Life Histories ◽  
Laboratory Data ◽  
Model Parameters ◽  
Effective Population ◽  
Coalescent Model ◽  
Null Distributions ◽  
Life History Pattern ◽  
Population Sizes ◽  
Software Programs

Abstract The analyses of often large amounts of field and laboratory data depend on computer programs to generate descriptive statistics and to test hypotheses. The algorithms in these programs are often complex and can be understood only with advanced training in mathematics and programming, topics that are beyond the capabilities of most fisheries biologists and empirical population geneticists. The backward looking Kingman coalescent model, based on the classic forward-looking Wright–Fisher model of genetic change, is used in many genetics software programs to generate null distributions against which to test hypotheses. An article in this issue by Niwa et al. shows that the assumption of bifurcations at nodes in the Kingman coalescent model is inappropriate for highly fecund Japanese sardines, which have type III life histories. Species with this life history pattern are better modelled with multiple mergers at the nodes of a coalescent gene genealogy. However, only a few software programs allow analysis with multiple-merger coalescent models. This parameter misspecification produces demographic reconstructions that reach too far into the past and greatly overestimates genetically effective population sizes (the number of individuals actually contributing to the next generation). The results of Niwa et al. underline the need to understand the assumptions and model parameters in the software programs used to analyse DNA sequences.

scholarly journals Coalescent models at small effective population sizes and population declines are positively misleading

2019 ◽  
Author(s):  
M. Elise Lauterbur
Keyword(s):  
Genetic Diversity ◽  
Sample Size ◽  
Population Size ◽  
Effective Population Size ◽  
Genetic Relationships ◽  
Population Decline ◽  
Population Declines ◽  
Effective Population ◽  
Analytical Approximations ◽  
Population Sizes

AbstractPopulation genetics employs two major models for conceptualizing genetic relationships among individuals – outcome-driven (coalescent) and process-driven (forward). These models are complementary, but the basic Kingman coalescent and its extensions make fundamental assumptions to allow analytical approximations: a constant effective population size much larger than the sample size. These make the probability of multiple coalescent events per generation negligible. Although these assumptions are often violated in species of conservation concern, conservation genetics often uses coalescent models of effective population sizes and trajectories in endangered species. Despite this, the effect of very small effective population sizes, and their interaction with bottlenecks and sample sizes, on such analyses of genetic diversity remains unexplored. Here, I use simulations to analyze the influence of small effective population size, population decline, and their relationship with sample size, on coalescent-based estimates of genetic diversity. Compared to forward process-based estimates, coalescent models significantly overestimate genetic diversity in oversampled populations with very small effective sizes. When sampled soon after a decline, coalescent models overestimate genetic diversity in small populations regardless of sample size. Such overestimates artificially inflate estimates of both bottleneck and population split times. For conservation applications with small effective population sizes, forward simulations that do not make population size assumptions are computationally tractable and should be considered instead of coalescent-based models. These findings underscore the importance of the theoretical basis of analytical techniques as applied to conservation questions.

scholarly journals Eusociality in snapping shrimps is associated with larger genomes and an accumulation of transposable elements

2021 ◽  
Vol 118 (24) ◽  
pp. e2025051118
Author(s):  
Solomon T. C. Chak ◽  
Stephen E. Harris ◽  
Kristin M. Hultgren ◽  
Nicholas W. Jeffery ◽  
Dustin R. Rubenstein
Keyword(s):  
Transposable Elements ◽  
Genome Size ◽  
Social Evolution ◽  
Repetitive Elements ◽  
Genome Architecture ◽  
Ancestral State ◽  
Effective Population ◽  
Snapping Shrimps ◽  
The Relationship ◽  
Eusocial Species

Despite progress uncovering the genomic underpinnings of sociality, much less is known about how social living affects the genome. In different insect lineages, for example, eusocial species show both positive and negative associations between genome size and structure, highlighting the dynamic nature of the genome. Here, we explore the relationship between sociality and genome architecture in Synalpheus snapping shrimps that exhibit multiple origins of eusociality and extreme interspecific variation in genome size. Our goal is to determine whether eusociality leads to an accumulation of repetitive elements and an increase in genome size, presumably due to reduced effective population sizes resulting from a reproductive division of labor, or whether an initial accumulation of repetitive elements leads to larger genomes and independently promotes the evolution of eusociality through adaptive evolution. Using phylogenetically informed analyses, we find that eusocial species have larger genomes with more transposable elements (TEs) and microsatellite repeats than noneusocial species. Interestingly, different TE subclasses contribute to the accumulation in different species. Phylogenetic path analysis testing alternative causal relationships between sociality and genome architecture is most consistent with the hypothesis that TEs modulate the relationship between sociality and genome architecture. Although eusociality appears to influence TE accumulation, ancestral state reconstruction suggests moderate TE abundances in ancestral species could have fueled the initial transitions to eusociality. Ultimately, we highlight a complex and dynamic relationship between genome and social evolution, demonstrating that sociality can influence the evolution of the genome, likely through changes in demography related to patterns of reproductive skew.

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 Demographic inference through approximate-Bayesian-computation skyline plots

2017 ◽  
Author(s):  
Miguel Navascués ◽  
Raphaël Leblois ◽  
Concetta Burgarella
Keyword(s):  
Approximate Bayesian Computation ◽  
Graphical Representation ◽  
Natural Populations ◽  
Composite Likelihood ◽  
Bayesian Computation ◽  
Mathematical Function ◽  
Effective Population ◽  
Population Sizes ◽  
Demographic Inference ◽  
Approximate Bayesian

AbstractThe skyline plot is a graphical representation of historical effective population sizes as a function of time. Past population sizes for these plots are estimated from genetic data, without a priori assumptions on the mathematical function defining the shape of the demographic trajectory. Because of this flexibility in shape, skyline plots can, in principle, provide realistic descriptions of the complex demographic scenarios that occur in natural populations. Currently, demographic estimates needed for skyline plots are estimated using coalescent samplers or a composite likelihood approach. Here, we provide a way to estimate historical effective population sizes using an Approximate Bayesian Computation (ABC) framework. We assess its performance using simulated and actual microsatellite datasets. Our method correctly retrieves the signal of contracting, constant and expanding populations, although the graphical shape of the plot is not always an accurate representation of the true demographic trajectory, particularly for recent changes in size and contracting populations. Because of the flexibility of ABC, similar approaches can be extended to other types of data, to multiple populations, or to other parameters that can change through time, such as the migration rate.

scholarly journals A tradeoff between robustness to environmental fluctuations and speed of evolution

2019 ◽  
Author(s):  
Max Schmid ◽  
Maria Paniw ◽  
Maarten Postuma ◽  
Arpat Ozgul ◽  
Frédéric Guillaume
Keyword(s):  
Environmental Change ◽  
Life Histories ◽  
Evolutionary Dynamics ◽  
Environmental Changes ◽  
Environmental Variability ◽  
Large Population ◽  
Survival Rates ◽  
Adult Survival ◽  
Population Declines ◽  
Environmental Fluctuations

AbstractOrganisms must cope with both short- and long-term environmental changes to persist. In this study we investigated whether life histories trade-off between their robustness to short-term environmental perturbations and their ability to evolve directional trait changes. We could confirm the tradeoff by modeling the eco-evolutionary dynamics of life-histories along the fast-slow pace-of-life continuum. Offspring dormancy and high adult survival rates allowed for large population sizes to be maintained in face of interannual environmental fluctuations but limited the speed of trait evolution with ongoing environmental change. In contrast, precocious offspring maturation and short-living adults promoted evolvability while lowering demographic robustness. This tradeoff had immediate consequences on extinction dynamics in variable environments. High evolvability allowed short-lived species to cope with long-lasting gradual environmental change, but came at the expense of more pronounced population declines and extinction rates from environmental variability. Higher robustness of slow life-histories helped them persist better on short timescales.

scholarly journals Genetic structure of a patchily distributed philopatric migrant: implications for management and conservation

2017 ◽  
Author(s):  
Anastasios Bounas ◽  
Dimitris Tsaparis ◽  
Ron Efrat ◽  
Gradimir Gradev ◽  
Marco Gustin ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Spatial Genetic Structure ◽  
Peripheral Populations ◽  
Population Declines ◽  
Effective Population ◽  
Genetic Structuring ◽  
Mediterranean Populations ◽  
Continental Scale ◽  
Population Sizes ◽  
Lesser Kestrel

Significant demographic fluctuations can have major genetic consequences in wild populations. The Lesser Kestrel (Falco naumanni) has suffered from both population declines and range fragmentation during the second half of the 20th century. In this study we analysed multilocus microsatellite data to assess the genetic structure of the species. Our analysis revealed significant genetic structuring of Lesser Kestrel populations, not only at cross-continental scale, but also regionally within Central and Eastern (CE) Mediterranean. We detected signs of genetic bottlenecks in some of the peripheral populations coupled with small effective population sizes. Values of genetic differentiation among the largest populations were low, albeit significant, whereas the small peripheral CE Mediterranean populations showed higher levels of differentiation from all other populations. Gene flow levels were relatively low among the discontinuously distributed populations of the CE Mediterranean region. We argue that the observed spatial genetic structure can be attributed at some level to the past demographic decline experienced by the species. Finally, we identify management units in the region, and inform the design of conservation actions aiming at the increase of population sizes and dispersal rates among peripheral populations.

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