Phylogeography and demographic inference of the endangered sei whale, with implications for conservation

2021 ◽  
Author(s):  
María José Pérez‐Álvarez ◽  
Francisca Rodríguez ◽  
Sebastián Kraft ◽  
Nicolás Segovia ◽  
Carlos Olavarría ◽  
...  
Keyword(s):  
Demographic Inference

scholarly journals Correction to: The IICR and the non-stationary structured coalescent: towards demographic inference with arbitrary changes in population structure

Heredity ◽  
2021 ◽  
Vol 126 (4) ◽  
pp. 706-706
Author(s):  
Willy Rodríguez ◽  
Olivier Mazet ◽  
Simona Grusea ◽  
Armando Arredondo ◽  
Josué M. Corujo ◽  
...  
Keyword(s):  
Population Structure ◽  
Structured Coalescent ◽  
Demographic Inference

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.

scholarly journals Inferring the Demographic History of Inbred Species from Genome-Wide SNP Frequency Data

2020 ◽  
Vol 37 (7) ◽  
pp. 2124-2136
Author(s):  
Paul D Blischak ◽  
Michael S Barker ◽  
Ryan N Gutenkunst
Keyword(s):  
Puma Concolor ◽  
Demographic History ◽  
Random Mating ◽  
Simulated Data ◽  
Conservation Agriculture ◽  
Model Fit ◽  
Parameter Estimates ◽  
History Of ◽  
Demographic Inference ◽  
Inbred Populations

Abstract Demographic inference using the site frequency spectrum (SFS) is a common way to understand historical events affecting genetic variation. However, most methods for estimating demography from the SFS assume random mating within populations, precluding these types of analyses in inbred populations. To address this issue, we developed a model for the expected SFS that includes inbreeding by parameterizing individual genotypes using beta-binomial distributions. We then take the convolution of these genotype probabilities to calculate the expected frequency of biallelic variants in the population. Using simulations, we evaluated the model’s ability to coestimate demography and inbreeding using one- and two-population models across a range of inbreeding levels. We also applied our method to two empirical examples, American pumas (Puma concolor) and domesticated cabbage (Brassica oleracea var. capitata), inferring models both with and without inbreeding to compare parameter estimates and model fit. Our simulations showed that we are able to accurately coestimate demographic parameters and inbreeding even for highly inbred populations (F = 0.9). In contrast, failing to include inbreeding generally resulted in inaccurate parameter estimates in simulated data and led to poor model fit in our empirical analyses. These results show that inbreeding can have a strong effect on demographic inference, a pattern that was especially noticeable for parameters involving changes in population size. Given the importance of these estimates for informing practices in conservation, agriculture, and elsewhere, our method provides an important advancement for accurately estimating the demographic histories of these species.

scholarly journals Genetic structure and demographic inference of the regular sea urchin Sterechinus neumayeri (Meissner, 1900) in the Southern Ocean: The role of the last glaciation

PLoS ONE ◽  
2018 ◽  
Vol 13 (6) ◽  
pp. e0197611 ◽  
Author(s):  
Angie Díaz ◽  
Karin Gérard ◽  
Claudio González-Wevar ◽  
Claudia Maturana ◽  
Jean-Pierre Féral ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Southern Ocean ◽  
Sea Urchin ◽  
Sterechinus Neumayeri ◽  
Last Glaciation ◽  
Demographic Inference

scholarly journals Demographic inference under the coalescent in a spatial continuum

2016 ◽  
Vol 111 ◽  
pp. 43-50 ◽  
Author(s):  
Stéphane Guindon ◽  
Hongbin Guo ◽  
David Welch
Keyword(s):  
Demographic Inference ◽  
Spatial Continuum

scholarly journals Geometry of the Sample Frequency Spectrum and the Perils of Demographic Inference

Genetics ◽  
2018 ◽  
Vol 210 (2) ◽  
pp. 665-682 ◽  
Author(s):  
Zvi Rosen ◽  
Anand Bhaskar ◽  
Sebastien Roch ◽  
Yun S. Song
Keyword(s):  
Frequency Spectrum ◽  
Sample Frequency ◽  
Demographic Inference

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 Sometimes hidden but always there: the assumptions underlying genetic inference of demographic histories

2020 ◽  
Vol 376 (1816) ◽  
pp. 20190719 ◽  
Author(s):  
Liisa Loog
Keyword(s):  
Genetic Variation ◽  
Size Structure ◽  
Genetic Data ◽  
Archaeological Material ◽  
Genome Wide ◽  
Demographic Processes ◽  
Theoretical Population ◽  
Laboratory Procedures ◽  
Demographic Inference ◽  
Genetic Inference

Demographic processes directly affect patterns of genetic variation within contemporary populations as well as future generations, allowing for demographic inference from patterns of both present-day and past genetic variation. Advances in laboratory procedures, sequencing and genotyping technologies in the past decades have resulted in massive increases in high-quality genome-wide genetic data from present-day populations and allowed retrieval of genetic data from archaeological material, also known as ancient DNA. This has resulted in an explosion of work exploring past changes in population size, structure, continuity and movement. However, as genetic processes are highly stochastic, patterns of genetic variation only indirectly reflect demographic histories. As a result, past demographic processes need to be reconstructed using an inferential approach. This usually involves comparing observed patterns of variation with model expectations from theoretical population genetics. A large number of approaches have been developed based on different population genetic models that each come with assumptions about the data and underlying demography. In this article I review some of the key models and assumptions underlying the most commonly used approaches for past demographic inference and their consequences for our ability to link the inferred demographic processes to the archaeological and climate records. This article is part of the theme issue ‘Cross-disciplinary approaches to prehistoric demography’.

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