Article
Evolutionary Biology
John K. Kelly
Summary: This study characterizes the evolution of SNPs in a population of yellow monkeyflower. It finds that most SNPs exhibit minimal change over time, consistent with neutral evolution. However, a subset of SNPs display strong fluctuations in frequency, which are driven by selection and have a ripple effect on genome-wide variation.
Article
Biology
Yuseob Kim
Summary: When a population has partial protection from fluctuating selection, such as the presence of a seed bank, the variance in fitness decreases and reproductive success is enhanced. This study explores the impact of this "refuge" from fluctuating selection using a mathematical model that combines demographic and evolutionary dynamics. Contrary to classical predictions, alleles that increase population size fluctuation are positively selected if population density is weakly regulated. This study also reveals the emergence of oscillatory polymorphism under strong density regulation with a constant carrying capacity, highlighting the importance of considering joint demographic and population genetic changes in models to discover novel eco-evolutionary dynamics.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Thibault Latrille, Vincent Lanore, Nicolas Lartillot
Summary: Mutation-selection phylogenetic codon models are a principled approach for studying the interplay between mutation, selection, and drift, but their assumption of constant genetic drift is unrealistic. By introducing variation in effective population size and mutation rate between lineages, the model can better account for the joint evolutionary process of these lineage-specific variables. The model, tested on simulated and empirical data, suggests reasonable reconstructions of evolutionary trends, although potential issues with assumptions about epistatic interactions between sites remain.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Agriculture, Dairy & Animal Science
Katri Sarviaho, Pekka Uimari, Katja Martikainen
Summary: Genomic selection has been utilized in dairy cattle breeding to predict breeding values accurately and increase genetic gain. However, there is a concern that genetic diversity may decrease due to increased inbreeding rate and decreased effective population size. This research aimed to estimate the impact of genomic selection on inbreeding rate and effective population size using both pedigree and genomic data.
JOURNAL OF ANIMAL BREEDING AND GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Aparna Lajmi, Felix Glinka, Eyal Privman
Summary: Double-digest Restriction-site Associated DNA sequencing (ddRADseq) is commonly used for generating genomic data in evolutionary and ecological studies. However, designing a ddRADseq experiment can be challenging due to various factors. This study investigates the effects of enzyme choice and size selection on sequencing efficiency and develops a user-friendly webtool, ddgRADer, to aid in experimental design and improve sequencing efficiency.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Multidisciplinary Sciences
Anubhab Khan, Kaushalkumar Patel, Harsh Shukla, Ashwin Viswanathan, Tom van der Valk, Udayan Borthakur, Parag Nigam, Arun Zachariah, Yadavendradev Jhala, Marty Kardos, Uma Ramakrishnan
Summary: Habitat fragmentation leads to small populations, increasing the risk of inbreeding depression. Small populations can reduce inbreeding depression by purging deleterious recessive alleles. The study on Indian tiger populations found differences in inbreeding levels and mutation load between small and large populations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Evolutionary Biology
Langqing Liu, Mirte Bosse, Hendrik-Jan Megens, Manon de Visser, Martien A. M. Groenen, Ole Madsen
Summary: Human disturbance and climate change have a negative impact on habitat integrity and size, leading to population decline and habitat fragmentation for wild fauna and flora. Analysis of the genomic data of the pygmy hog reveals a very small historical population size with no recent inbreeding, but evidence of harmful mutation accumulation exceeding purifying selection. Care must be taken in conservation efforts to prevent further inbreeding depression and mitigate potential environmental changes.
EVOLUTIONARY APPLICATIONS
(2021)
Article
Genetics & Heredity
Siliang Song, Jianzhi Zhang
Summary: The natural environment fluctuates, affecting the fitness of organisms. The commonly used measure of geometric mean fitness may be misleading due to genetic drift. In this study, a new measure called effective fitness is proposed, which captures the overall effect of fluctuating selection more accurately by considering average expected allele frequency change caused by selection.
G3-GENES GENOMES GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Nathan W. Byer, Matthew L. Holding, Miranda M. Crowell, Todd W. Pierson, Thomas E. Dilts, Eveline S. Larrucea, Kevin T. Shoemaker, Marjorie D. Matocq
Summary: The study revealed that spatially separated populations of pygmy rabbits exhibit local adaptation, potentially driven by genetic loci with functional annotations related to plant secondary compound metabolism. Additionally, populations in the Mono Basin of California likely diverged from other Great Basin populations during late Pleistocene climate oscillations, demonstrating adaptive differentiation despite limited gene flow and small effective population size.
Article
Biodiversity Conservation
Lucia Sainz-Escudero, Marta Vila, Silvia Perea, Mario Garcia-Paris
Summary: The fairy shrimp Branchinectella media, a low dispersal organism, exhibits strong genetic structure among geographically isolated Iberian populations, indicating limited dispersal success. However, high effective population sizes ensure persistence of B. media populations against genetic stochasticity. These results suggest that rescue-effect may not be essential for population persistence if high effective population sizes and adequate levels of genetic diversity are maintained in low dispersing Anostraca.
CONSERVATION GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Yann X. C. Bourgeois, Ben H. Warren
Summary: The continuous improvement of high-throughput sequencing techniques has enabled the production of whole genome data in various species, which in turn provides better tools for integrating selection into historical frameworks. However, the plethora of analytical tools may confuse users and hinder the dissemination of the latest methods.
Article
Agriculture, Dairy & Animal Science
Njabulo M. Dlamini, Edgar F. Dzomba, Mpumelelo Magawana, Sphamandla Ngcamu, Farai C. Muchadeyi
Summary: This study investigated the genetic diversity and similarities and differences within and between two conservation herds of the South African Nguni Cattle. The results showed reduced genetic diversity in the two herds, calling for measures to protect the diversity of the South African Nguni cattle.
Article
Genetics & Heredity
Guoyu Hu, Duy Ngoc Do, Ghader Manafiazar, Alyson A. Kelvin, Mehdi Sargolzaei, Graham Plastow, Zhiquan Wang, Younes Miar
Summary: Understanding the genetic structure is crucial for genomic selection in domestic animals. This study genotyped 2,973 American minks of six different color types and analyzed their linkage disequilibrium, genetic diversity, and population structure. The results showed that there is a close genetic relationship among different color types, with most genetic variation occurring within rather than between color types. The study also identified the minimum number of single nucleotide polymorphisms required for accurate genomic selection programs in two farms.
FRONTIERS IN GENETICS
(2023)
Review
Ecology
Krystyna Nadachowska-Brzyska, Mateusz Konczal, Wieslaw Babik
Summary: Effective population size (Ne) is a key evolutionary parameter that determines genetic variation levels and selection efficacy. Ne estimation and interpretation are essential in evolutionary and conservation biology, with diverse applications and methods available. Recent advancements in estimating temporal Ne trends provide a comprehensive understanding of the evolutionary continuum.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
William Walton, Graham N. Stone, Konrad Lohse
Summary: While significant changes in effective population size were observed in Iberian refuge populations during the Quaternary, there is little evidence to suggest that these changes were shared across the seven species of chalcid parasitoid wasps associated with oak cynipid galls, indicating largely idiosyncratic demographic histories within this ecological guild.