Explanatory pluralism in evolutionary biology

The ontological dependence of one domain on another is compatible with the explanatory autonomy of the less basic domain. That autonomy results from the fact that the relationship between two domains can be very complex. In this paper I distinguish two different types of complexity, two ways the relationship between domains can fail to be transparent, both of which are relevant to evolutionary biology. Sometimes high level explanations preserve a certain type of causal or counterfactual information which would be lost at the lower level; I argue that this is central to the proper understanding of the adaptationist program. Sometimes high level kinds are multiply realised by lower level kinds: I argue that this is central to the understanding of macroevolution.     

PET1402, a nuclear gene required for proteolytic processing of cytochrome oxidase subunit 2 in yeast

The nuclear mutation pet ts1402 prevents proteolytic processing of the precursor of cytochrome oxidase subunit 2 (cox2) in Saccharomyces cerevisiae. The structural gene PET1402 was isolated by genetic complementation of the temperature-sensitive mutation. DNA sequence analysis identified a 1206-bp open reading frame, which is located 215 by upstream of the PET122 gene. The DNA sequence of PET1402 predicts a hydrophobic, integral membrane protein with four transmembrane segments and a typical mitochondrial targeting sequence. Weak sequence similarity was found to two bacterial proteins of unknown function. Haploid cells containing a null allelle of PET1402 are respiratory deficient.     

Fractionation of bovine spermatozoa for sex selection: A rapid immunomagnetic technique to remove spermatozoa that contain the H-Y antigen

A study was conducted to rapidly fractionate bovine spermatozoa on the basis of cell-surface H-Y antigen (i.e., Y chromosome-bearing spermatozoa). A novel, rapid immunomagnetic method was developed for removal of spermatozoa that bound to anti-H-Y IgG. Fluorescent labeling and flow cytometry were used to measure the efficiency with which spermatozoa binding to anti-H-Y were removed by the immunomagnetic technique. Washed bovine spermatozoa (n=7 bulls) were treated with a mouse monoclonal IgG antibody to H-Y antigen (MoAb 12/49). Fluorescent labeled goat antibody against mouse IgG was added to label those spermatozoa with cell-surface H-Y antigens. Supermagnetized polymer beads coated with an anti-antibody to the MoAb 12/49 were then added to the spermatozoa. After 20 min of incubation, spermatozoa were exposed for 2 min to a magnet, causing the magnetized particles to adhere to the sides of the tube. Nonmagnetized spermatozoa in the supernatent were aspirated and analyzed for fluorescent label by flow cytometry. Approximately 50% of spermatozoa not subjected to immunomagnetic separation were fluorescent labeled, and about one-half of the spermatozoa were observed microscopically to be bound to the magnetized polymer beads prior to magnetic separation (P<0.05). Following magnetic separation, only 1.2% (P<0.05) of the spermatozoa in the magnetic supernatent were fluorescent labeled. Assuming that only Y chromosome-bearing spermatozoa have cell-surface H-Y antigens, the present immunomagnetic fractionation removed almost all of the Y chromosome-bearing spermatozoa, leaving a population that was greater than 98% X chromosome-bearing spermatozoa.     

Molecular chaperones and the biogenesis of mitochondria and peroxisomes

Summary— A review of the proteinaceous machinery involved in protein sorting pathways and protein folding and assembly in mitochondria and peroxisomes is presented. After considering the various sorting pathways and targeting signals of mitochondrial and peroxisomal proteins, we make a comparative dissection of the protein factors involved in: i) the stabilization of cytosolic precursor proteins in a translocation competent conformation; ii) the membrane import apparatus of mitochondria and peroxisomes; iii) the processing of mitochondrial precursor proteins, and the eventual processing of certain peroxisomal precursor, in the interior of the organelles; and iv) the requirement of molecular chaperones for appropriate folding and assembly of imported proteins in the matrix of both organelles. Those aspects of mitochondrial biogenesis that have developed rapidly during the last few years, such as the requirement of molecular chaperones, are stressed in order to stimulate further parallel investigations aimed to understand the origin, biochemistry, molecular biology and pathology of peroxisomes. In this regard, a brief review of findings from our group and others is presented in which the role of the F₁-ATPase α-subunit is pointed out as a molecular chaperone of mitochondria and chloroplasts. In addition, data are presented that could question our previous indication that the immunoreactive protein found in the rat liver peroxisomes is due to the presence of the F₁-ATPase α-subunit.     

Disentangling the historical routes to community assembly in the global epicentre of biodiversity

Aim

The exceptional turnover in biota with elevation and number of species coexisting at any elevation makes tropical mountains hotspots of biodiversity. However, understanding the historical processes through which species arising in geographical isolation (i.e. allopatry) assemble along the same mountain slope (i.e. sympatry) remains a major challenge. Multiple models have been proposed including (1) the sorting of already elevationally divergent species, (2) the displacement of elevation upon secondary contact, potentially followed by convergence, or (3) elevational conservatism, in which ancestral elevational ranges are retained. However, the relative contribution of these processes to generating patterns of elevational overlap and turnover is unknown.

Location

Tropical mountains of Central- and South-America.

Time Period

The last 12 myr.

Major Taxa Studied

Birds.

Methods

We collate a dataset of 165 avian sister pairs containing estimates of phylogenetic age, geographical and regional elevational range overlap. We develop a framework based on continuous-time Markov models to infer the relative frequency of different historical pathways in explaining present-day overlap and turnover of sympatric species along elevational gradients.

Results

We show that turnover of closely related bird species across elevation can predominantly be explained by displacement of elevation ranges upon contact (81%) rather than elevational divergence in allopatry (19%). In contrast, overlap along elevation gradients is primarily (88%) explained by conservatism of elevational ranges rather than displacement followed by elevational expansion (12%).

Main Conclusions

Bird communities across elevation gradients are assembled through a mix of processes, including the sorting, displacement and conservatism of species elevation ranges. The dominant role of conservatism in explaining co-occurrence of species on mountain slopes rejects more complex scenarios requiring displacement followed by expansion. The ability of closely related species to coexist without elevational divergence provides a direct and faster pathway to sympatry and helps explain the exceptional species richness of tropical mountains.     

On the integrated interpretation of indirect site ordinations: a case study using semi-arid vegetation in southeastern Spain

The need for rigorous methods of interpreting indirect site ordinations is discussed and the problem of oblique habitat and phytosociological trends is emphasized. A sequential approach, termed integrated interpretation, is introduced to overcome this problem. It first involves a technique termed rotational correlation a linear form of trend surface analysis, which locates the best fit between a habitat variable and the coordinates of a pluridimensional ordination. The coordinates at positions of best fit are then used to produce two-way site-species tables (seriation arrays) which summarize floristic variation in relation to each major habitat trend. The seriation arrays can also be used to identify groups of differential species. Integrated interpretation is demonstrated using semi-arid vegetation from Murcia Province, SE Spain. A two-axis site ordination of vegetation data by non-metric multidimensional scaling is shown to have two oblique trends related to aspect-induced topoclimates and types of past anthropogenic disturbance. Rotation of the configuration to maximum linear correlation achieves very high levels of explanation for each factor. Rotated ordination coordinates from the correlation analysis are used to obtain two seriation arrays and floristic noda which relate directly to the two underlying habitat trends. A floristic discontinuity is revealed on the topoclimate continuum and it is hypothesized that temperature conditions are a major determinant of floristic composition, but that moisture partly determines vegetational cover and phytomass. Several patterns of past cultivation are detected and associated with five main kinds of geomorphological unit, together with some evidence that the rate of succession is partly determined by topoclimate. The integrated approach to interpretation is compared with visual methods and other multivariate techniques. A case is made for increased interpretational rigour in site coordinate studies, especially the discontinuation of trend-seeking using individual unrotated ordination axes.Nomenclature of vascular plants follows Tutin et al. (1964–1980) Flora Europaea 5 Vols. Cambridge University Press, Cambridge. Nomenclature of syntaxa follows Rivas-Goday & Rivas-Martinez (1967).I am indebted to J. A. Michel, Dr M. A. Abdelrahman and Monica M. Dargie for field assistance. Field discussion with Dr R. L. Wright, Dr M. P. Austin and Professor F. Esteve Chueca was most helpful; the latter assisted with confirmation of vascular plant voucher specimens. Non-vascular taxonomy was determined by Dr C. Humphries (mosses and one alga) and Dr O. L. Gilbert (lichens). An anonymous referee suggested an approximation of the analytical solution to rotational correlation, and Dr N. R. J. Fieller assisted with its confirmation. The project was assisted by a grant from the University of Sheffield Research Fund.     

Fractionation of plant protoplast types by iso-osmotic density gradient centrifugation

Summary A simple effective technique for the fractionation of protoplast populations is described. Protoplasts are separated by low-speed centrifugation in an iso-osmotic, discontinuous density gradient system on the basis of differences in their buoyant densities. At a constant osmolality of 660±20 mOs/kg H₂O, the gradients provide a density range from 1.017 to 1.069 g/cm³ at 20 °C which corresponds to the buoyant densities of most protoplast types studied. Characteristics of the KMC/S-density gradient system and factors affecting the fractionation were investigated. Protoplasts were isolated from various tissues and cultivars of tobacco, barley, wheat, rye, oat and maize. Their density-dependent distribution profiles in KMC/S-gradients and their average buoyant densities were determined under standardized conditions. Great differences in the buoyant densities were found between protoplasts of different tissues. Mixed populations of two types of protoplasts, differing in buoyant density by about 15–20 mg/cm³, were separated to give highly purified fractions. Factors affecting the buoyant densities of protoplasts have been investigated. Ploidy level and species differences did not significantly affect the fractionation profiles. However, an age-dependent variation in the average buoyant density of tobacco mesophyll protoplasts was observed. Fractionation of tobacco mesophyll protoplasts and their subsequent regeneration to plants demonstrates the practicability and physiological compatibility of the KMC/S-density gradient system under sterile conditions. The morphogenetic potential of protoplasts was not affected by the separation procedure or the gradient components.     

Methods for the isolation of viable gonadotropin-releasing hormone (LRF) neurons

Studies were conducted in order to determine if selected neurons could be isolated from the brain using Sepharose-linked recognition complexes directed against or related to the biosynthetic/neurosecretory product of the desired neuronal population. Immunoreactive LRF neurons were precipitated when dispersed cells of adult male rats were incubated successively in media containing free LRF antiserum followed by the exposure of LRF bound to Sepharose-4B. The radioimmunoassayable LRF content of the isolated cells was 88% of that contained in fresh frozen tissue of a contemporary group of rats and trypan blue exclusion indicated that at least 85% of the neurons were viable. Furthermore, based on immunocytochemistry and cresyl violet staining in combination with immunocytochemistry, the isolated cell fraction appeared to be free from other types of cells and also exhibited assayable LRF release when challenged with potassium. These results suggest that the neuroendocrine properties of hypothalamic neurons may be exploited in order to isolate viable cells for acute in vitro experiments.     

The toad’s warts: Discordance creates bumpy expectations of mitochondrial‐nuclear evolution between species

Discordance between the mitochondrial and nuclear genomes is a prevalent phenomenon in nature, in which the underlying processes responsible are considered to be important in shaping genetic variation in natural populations. Among the evolutionary processes that best explain such genomic mismatches incomplete lineage sorting and introgression are commonly identified, however, many studies are unable to distinguish between these hypotheses, which has become a major challenge in the field. In this issue of Molecular Ecology, Firneno et al. (2020) present an elegant exploration of mitochondrial‐nuclear discordance in Mesoamerican toads. Integrating genome‐scale and spatial data to test between these hypotheses within an empirical model testing framework, they find strong support that incomplete lineage sorting explains the observed discordance. Their work, along with many previous articles in Molecular Ecology, highlights the commonality of mito‐nuclear discordance among species despite the expectations of tightly concerted mitochondrial and nuclear genome evolution. It is increasingly clear that the nuclear genomes of many species are (at least for short periods of evolutionary time) functionally compatible with multiple, divergent mitochondrial haplotypes. As such, we suggest future research not only seeks to understand the processes causing spatial mito‐nuclear discordance (e.g. incomplete lineage sorting, introgression), but also explores those that maintain discordance through time and space (e.g. relaxed selection on mito‐nuclear interactions, heterozygosity, population demographics). We also discuss the vital role that taxonomy plays in interpreting patterns of mito‐nuclear discordance when data‐consistent yet differing taxonomies are used, such as treating allopatrically distributed taxa as multiple isolated populations versus multiple micro‐endemic species.