Genetic Variation and Random Drift in Autotetraploid Populations

The rate of decay of genetic variation is determined for randomly mating autotetraploid populations of finite size, and the equilibrium homozygosity under mutation and random drift is calculated. It is shown that heterozygosity is lost at a slower rate than in diploid populations, and that the equilibrium heterozygosity with mutation and random drift is higher than for diploids. Outcrossing populations as well as populations that randomly self are analyzed. A method of comparing genetic variation between autotetraploid and diploid populations is proposed. Our treatment suggests that the ``gametic homozygosity' provides a unified approach for comparing genotypes within a population as well as comparing genetic variation between populations with different levels of ploidy.     

Genome analysis of intergeneric hybrids of apomictic and sexual Australian Elymus species with wheat,barley and rye: implication for the transfer of apomixis to cereals

Summary Four hybrids were obtained between three Australian Elymus taxa and three cereal grains: wheat, rye, and barley. Mean meiotic metaphase-I configurations were 41.14 I, 0.42 rod II, 0.003 ring II, and 0.01 III for E. scabrus var plurinervis x Triticum aestivum (1 hybrid plant), 22.27 I, 2.63 rod II, 0.06 ring II, and 0.12 III for E. scabrus var scabrus x Secale cereale (4 hybrid plants), and 26.65 I, 0.66 rod II, 0.00 ring II, and 0.01 III for E. scabrus var plurinervis x Hordeum vulgare (13 hybrid plants). The I genome of barley also paired very little in a B_III hybrid of apomictic E. rectisetus x H. vulgare (2 hybrid plants). Megasporogenesis in this B_III hybrid was at least facultatively apomeiotic, with the same sort of nuclear elongation, apomeiotic division, and dyad formation seen previously in E. rectisetus itself. All four hybrid combinations were sterile. While spike morphology in the E. scabrus x T. aestivum and E. scabrus x H. vulgare hybrids were intermediate to their parents, E. scabrus x S. cereale and E. rectisetus x H. vulgare looked like their maternal parents.     

Exploring the legacy of African and Indigenous Caribbean admixture in Puerto Rico

Objectives

From an anthropological genetic perspective, little is known about the ethnogenesis of African descendants in Puerto Rico. Furthermore, historical interactions between Indigenous Caribbean and African descendant peoples that may be reflected in the ancestry of contemporary populations are understudied. Given this dearth of genetic research and the precedence for Afro-Indigenous interactions documented by historical, archeological, and other lines of evidence, we sought to assess the biogeographic origins of African descendant Puerto Ricans and to query the potential for Indigenous ancestry within this community.

Materials and Methods

Saliva samples were collected from 58 self-identified African descendant Puerto Ricans residing in Puerto Rico. We sequenced whole mitochondrial genomes and genotyped Y chromosome haplogroups for each male individual (n = 25). Summary statistics, comparative analyses, and network analysis were used to assess diversity and variation in haplogroup distribution between the sample and comparative populations.

Results

As indicated by mitochondrial haplogroups, 66% had African, 5% had European, and 29% had Indigenous American matrilines. Along the Y chromosome, 52% had African, 28% had Western European, 16% had Eurasian, and, notably, 4% had Indigenous American patrilines. Both mitochondrial and Y chromosome haplogroup frequencies were significantly different from several comparative populations.

Discussion

Biogeographic origins are consistent with historical accounts of African, Indigenous American, and European ancestry. However, this first report of Indigenous American paternal ancestry in Puerto Rico suggests distinctive features within African descendant communities on the island. Future studies expanding sampling and incorporating higher resolution genetic markers are necessary to more fully understand African descendant history in Puerto Rico.     

HomeRange: A global database of mammalian home ranges

Motivation

Home range is a common measure of use of space by animals because it provides ecological information that is useful for conservation applications. In macroecological studies, values are typically aggregated to species means to examine general patterns of use of space by animals. However, this ignores the environmental context in which the home range was estimated and does not account for intraspecific variation in home range size. In addition, the focus of macroecological studies on home ranges has historically been biased towards terrestrial mammals. The use of aggregated numbers and the terrestrial focus limit our ability to examine home-range patterns across different environments, their variation in time and variation between different levels of organization. Here, we introduce HomeRange, a global database with 75,611 home-range values across 960 different species of mammals, including terrestrial, aquatic and aerial species.

Main types of variables contained

The dataset contains estimates of home ranges of mammals, species names, methodological information on data collection, method of home-range estimation, period of data collection, study coordinates and name of location, in addition to species traits derived from the studies, such as body mass, life stage, reproductive status and locomotor habit.

Spatial location and grain

The collected data are distributed globally. Across studies, the spatial accuracy varies, with the coarsest resolution being 1°.

Time period and grain

The data represent information published between 1939 and 2022. Across studies, the temporal accuracy varies; some studies report start and end dates specific to the day, whereas for other studies only the month or year is reported.

Major taxa and level of measurement

Mammalian species from 24 of the 27 different taxonomic orders. Home-range estimates range from individual-level values to population-level averages.

Software format

Data are supplied as a comma-delimited text file (.csv) and can be loaded directly into R using the “HomeRange” R package ( https://github.com/SHoeks/HomeRange ).     

The early life of Octopus vulgaris (Cephalopoda: Octopodidae) in the plankton and at settlement: a change in lifestyle

Newly hatched young of the benthic, coastal-living octopod, Octopus vulgaris , enter the plankton and remain there for perhaps eight weeks. At hatching the arms are short and bear a few, large, primary suckers. The buccal mass is relatively large in proportion to the size of the animal. The eyes are large. The central nervous system has fairly well-defined lobes, some of which develop earlier than others. We shall follow the development of several features of O. vulgaris from hatching, through its life in the plankton until settlement and correlate them with changes in the brain and behaviour.     

Respiratory muscle reserve in rats during heavy exercise

Gosselin, Luc E., David Megirian, Joshua Rodman, DonnaMueller, and Gaspar A. Farkas. Respiratory muscle reserve in ratsduring heavy exercise. J. Appl.Physiol. 83(4): 1405-1409, 1997.The extent towhich the respiratory pump muscles limit maximal aerobic capacity inquadrupeds is not entirely clear. To examine the effect of reducedrespiratory muscle reserve on aerobic capacity, whole bodypeak oxygen consumption(O_{2 peak}) wasmeasured in healthy Sprague-Dawley rats before and after Sham,unilateral, or bilateral hemidiaphragm denervation (Dnv) surgery.O_{2 peak} wasdetermined by using a graded treadmill running test.Hemidiaphragm paralysis was verified after testing byrecording the absence of electromyographic activity duringinspiration. Before surgery, O_{2 peak} averaged 86, 87, and 92 ml · kg¹ · min¹for the Sham, unilateral, and bilateral Dnv groups, respectively. Twoweeks after surgery, there was no significant change inO_{2 peak} foreither the Sham or unilateral Dnv group. However,O_{2 peak} decreased~19% in the bilateral Dnv group 2 wk after surgery. These findingsstrongly suggest that the pulmonary system in rats is designed suchthat during heavy exercise, the remaining respiratory pump muscles areable to compensate for the loss of one hemidiaphragm, but not of both.

     

High-resolution solution structure of siamycin II: Novel amphipathic character of a 21-residue peptide that inhibits HIV fusion

Summary The 21-amino acid peptides siamycin II (BMY-29303) and siamycin I (BMY-29304), derived from Streptomyces strains AA3891 and AA6532, respectively, have been found to inhibit HIV-1 fusion and viral replication in cell culture. The primary sequence of siamycin II is CLGIGSCNDFAGCGYAIVCFW. Siamycin I differs by only one amino acid; it has a valine residue at position 4. In both peptides, disulfide bonds link Cys¹ with Cys¹³ and Cys⁷ with Cys¹⁹, and the side chain of Asp⁹ forms an amide bond with the N-terminus. Siamycin II, when dissolved in a 50:50 mixture of DMSO and H₂O, yields NOESY spectra with exceptional numbers of cross peaks for a peptide of this size. We have used 335 NOE distance constraints and 13 dihedral angle constraints to generate an ensemble of 30 siamycin II structures; these have average backbone atom and all heavy atom rmsd values to the mean coordinates of 0.24 and 0.52 Å, respectively. The peptide displays an unusual wedge-shaped structure, with one face being predominantly hydrophobic and the other being predominantly hydrophilic. Chemical shift and NOE data show that the siamycin I structure is essentially identical to siamycin II. These peptides may act by preventing oligomerization of the HIV transmembrane glycoprotein gp41, or by interfering with interactions between gp41 and the envelope glycoprotein gp120, the cell membrane or membrane-bound proteins [Frèchet, D. et al. (1994) Biochemistry, 33, 42–50]. The amphipathic nature of siamycin II and siamycin I suggests that a polar (or apolar) site on the target protein may be masked by the apolar (or polar) face of the peptide upon peptide/protein complexation.Abbreviations ABNR adopted basis Newton Raphson - AIDS acquired immunodeficiency syndrome - CW continuous wave - DMSO dimethylsulfoxide - DQF-COSY two-dimensional double-quantum-filtered correlation spectroscopy - HIV human immunodeficiency virus - HSQC heteronuclear single-quantum coherence - NOE nuclear Overhauser enhancement - NOESY two-dimensional nuclear Overhauser enhancement spectroscopy - ppm parts per million - P.E.-COSY two-dimensional primitive exclusive correlation spectroscopy - REDAC redundant dihedral angle constraint - rf radio frequency - rmsd root-mean-square difference - SIV simian immunodeficiency virus - sw spectral width - _m mixing time - TOCSY two-dimensional total correlation spectroscopy - TSP trimethylsilyl-2,2,3,3-²H₄-propionate - 2D two-dimensional     

Refined solution structure of human profilin I.

Profilin is a ubiquitous eukaryotic protein that binds to both cytosolic actin and the phospholipid phosphatidylinositol-4,5-bisphosphate. These dual competitive binding capabilities of profilin suggest that profilin serves as a link between the phosphatidyl inositol cycle and actin polymerization, and thus profilin may be an essential component in the signaling pathway leading to cytoskeletal rearrangement. The refined three-dimensional solution structure of human profilin I has been determined using multidimensional heteronuclear NMR spectroscopy. Twenty structures were selected to represent the solution conformational ensemble. This ensemble of structures has root-mean-square distance deviations from the mean structure of 0.58 A for the backbone atoms and 0.98 A for all non-hydrogen atoms. Comparison of the solution structure of human profilin to the crystal structure of bovine profilin reveals that, although profilin adopts essentially identical conformations in both states, the solution structure is more compact than the crystal structure. Interestingly, the regions that show the most structural diversity are located at or near the actin-binding site of profilin. We suggest that structural differences are reflective of dynamical properties of profilin that facilitate favorable interactions with actin. The global folding pattern of human profilin also closely resembles that of Acanthamoeba profilin I, reflective of the 22% sequence identity and approximately 45% sequence similarity between these two proteins.