More Like this

1. Genetic diversity in S vaneti and its implications for the human settlement of the H ighland C aucasus

   https://doi.org/10.1002/ajpa.23324  

   Yardumian, Aram ; Shengelia, Ramaz ; Chitanava, David ; Laliashvili, Shorena ; Bitadze, Lia ; Laliashvili, Irma ; Villanea, Fernando ; Sanders, Akiva ; Azzam, Andrew ; Groner, Victoria ; et al ( October 2017 , American Journal of Physical Anthropology)
2. Genetic and physical interactions between the organellar mechanosensitive ion channel homologs MSL 1, MSL 2, and MSL 3 reveal a role for inter‐organellar communication in plant development

   https://doi.org/10.1002/pld3.124  

   Lee, Josephine S. ; Wilson, Margaret E. ; Richardson, Ryan A. ; Haswell, Elizabeth S. ( March 2019 , Plant Direct)

   Plant development requires communication on many levels, including between cells and between organelles within a cell. For example, mitochondria and plastids have been proposed to be sensors of environmental stress and to coordinate their responses. Here we present evidence for communication between mitochondria and chloroplasts during leaf and root development, based on genetic and physical interactions between threeMechanosensitive channel ofSmall conductance‐Like (MSL) proteins fromArabidopsis thaliana.MSLproteins areArabidopsishomologs of the bacterialMechanosensitivechannel ofSmall conductance (MscS), which relieves cellular osmotic pressure to protect against lysis during hypoosmotic shock.MSL1 localizes to the inner mitochondrial membrane, whileMSL2 andMSL3 localize to the inner plastid membrane and are required to maintain plastid osmotic homeostasis during normal growth and development. In this study, we characterized the phenotypic effect of a genetic lesion inMSL1, both in wild type and inmsl2 msl3mutant backgrounds.msl1single mutants appear wild type for all phenotypes examined. The characteristic leaf rumpling inmsl2 msl3double mutants was exacerbated in themsl1 msl2 msl3triple mutant. However, the introduction of themsl1lesion into themsl2 msl3mutant background suppressed othermsl2 msl3mutant phenotypes, including ectopic callus formation, accumulation of superoxide and hydrogen peroxide in the shoot apical meristem, decreased root length, and reduced number of lateral roots. All these phenotypes could be recovered by molecular complementation with a transgene containing a wild type version ofMSL1. In yeast‐based interaction studies,MSL1 interacted with itself, but not withMSL2 orMSL3. These results establish that the abnormalities observed inmsl2 msl3double mutants is partially dependent on the presence of functionalMSL1 and suggest a possible role for communication between plastid and mitochondria in seedling development.

    

   more » « less
3. P ool P arty 2: An integrated pipeline for analysing pooled or indexed low‐coverage whole‐genome sequencing data to discover the genetic basis of diversity

   https://doi.org/10.1111/1755-0998.13888  

   Willis, Stuart ; Micheletti, Steven ; Andrews, Kimberly R. ; Narum, Shawn ( November 2023 , Molecular Ecology Resources)

   Whole‐genome sequencing data allow survey of variation from across the genome, reducing the constraint of balancing genome sub‐sampling with estimating recombination rates and linkage between sampled markers and target loci. As sequencing costs decrease, low‐coverage whole‐genome sequencing of pooled or indexed‐individual samples is commonly utilized to identify loci associated with phenotypes or environmental axes in non‐model organisms. There are, however, relatively few publicly available bioinformatic pipelines designed explicitly to analyse these types of data, and fewer still that process the raw sequencing data, provide useful metrics of quality control and then execute analyses. Here, we present an updated version of a bioinformatics pipeline calledPoolParty2that can effectively handle either pooled or indexed DNA samples and includes new features to improve computational efficiency. Using simulated data, we demonstrate the ability of our pipeline to recover segregating variants, estimate their allele frequencies accurately, and identify genomic regions harbouring loci under selection. Based on the simulated data set, we benchmark the efficacy of our pipeline with another bioinformatic suite,angsd, and illustrate the compatibility and complementarity of these suites usingangsdto generate genotype likelihoods as input for identifying linkage outlier regions using alignment files and variants provided byPoolParty2. Finally, we apply our updated pipeline to an empirical dataset of low‐coverage whole genomic data from population samples of Columbia River steelhead trout (Oncorhynchus mykiss), results from which demonstrate the genomic impacts of decades of artificial selection in a prominent hatchery stock. Thus, we not only demonstrate the utility ofPoolParty2for genomic studies that combine sequencing data from multiple individuals, but also illustrate how it compliments other bioinformatics resources such asangsd.

    

   more » « less
4. Genetic contributions to dental dimensions in brown‐mantled tamarins ( Saguinus fuscicollis ) and rhesus macaques ( Macaca mulatta )

   https://doi.org/10.1002/ajpa.23744  

   Hardin, Anna M. ( December 2018 , American Journal of Physical Anthropology)

   The use of dental metrics in phylogenetic reconstructions of fossil primates assumes variation in tooth size is highly heritable. Quantitative genetic studies in humans and baboons have estimated high heritabilities for dental traits, providing a preliminary view of the variability of dental trait heritability in nonhuman primate species. To expand upon this view, the heritabilities and evolvabilities of linear dental dimensions are estimated in brown‐mantled tamarins (Saguinus fuscicollis) and rhesus macaques (Macaca mulatta).

   Quantitative genetic analyses were performed on linear dental dimensions collected from 302 brown‐mantled tamarins and 364 rhesus macaques. Heritabilities were estimated in SOLAR using pedigrees from each population, and evolvabilities were calculated manually.

   Tamarin heritability estimates range from 0.19 to 0.99, and 25 of 26 tamarin estimates are significantly different from zero. Macaque heritability estimates range from 0.08 to 1.00, and 25 out of 28 estimates are significantly different from zero.

   Dental dimensions are highly heritable in captive brown‐mantled tamarins and free‐ranging rhesus macaques. The range of heritability estimates in these populations is broadly similar to those of baboons and humans. Evolvability tends to increase with heritability, although evolvability is high relative to heritability in some dimensions. Estimating evolvability helps to contextualize differences in heritability, and the observed relationship between evolvability and heritability in dental dimensions requires further investigation.

    

   more » « less
5. Phylogeography of Pogonomyrmex barbatus and P. rugosus harvester ants with genetic and environmental caste determination

   https://doi.org/10.1002/ece3.1507  

   Mott, Brendon M. ; Gadau, Jürgen ; Anderson, Kirk E. ( June 2015 , Ecology and Evolution)

   We present a phylogeographic study of at least six reproductively isolated lineages of new world harvester ants within thePogonomyrmex barbatusandP. rugosusspecies group. The genetic and geographic relationships within this clade are complex: Four of the identified lineages show genetic caste determination (GCD) and are divided into two pairs. Each pair has evolved under a mutualistic system that necessitates sympatry. These paired lineages are dependent upon one another because theirGCDrequires interlineage matings for the production of F1 hybrid workers, and intralineage matings are required to produce queens. ThisGCDsystem maintains genetic isolation among these interdependent lineages, while simultaneously requiring co‐expansion and emigration as their distributions have changed over time. It has also been demonstrated that three of these fourGCDlineages have undergone historical hybridization, but the narrower sampling range of previous studies has left questions on the hybrid parentage, breadth, and age of these groups. Thus, reconstructing the phylogenetic and geographic history of this group allows us to evaluate past insights and hypotheses and to plan future inquiries in a more complete historical biogeographic context. Using mitochondrialDNAsequences sampled across most of the morphospecies’ ranges in the U.S.A. and Mexico, we conducted a detailed phylogeographic study. Remarkably, our results indicate that one of theGCDlineage pairs has experienced a dramatic range expansion, despite the genetic load and fitness costs of theGCDsystem. Our analyses also reveal a complex pattern of vicariance and dispersal inPogonomyrmexharvester ants that is largely concordant with models of late Miocene, Pliocene, and Pleistocene range shifts among various arid‐adapted taxa in North America.

    

   more » « less