Perspective: Reproductive isolation caused by natural selection against immigrants from divergent habitats

The classification of reproductive isolating barriers laid out by Dobzhansky and Mayr has motivated and structured decades of research on speciation. We argue, however, that this classification is incomplete and that the unique contributions of a major source of reproductive isolation have often been overlooked. Here, we describe reproductive barriers that derive from the reduced survival of immigrants upon reaching foreign habitats that are ecologically divergent from their native habitat. This selection against immigrants reduces encounters and thus mating opportunities between individuals from divergently adapted populations. It also reduces the likelihood that successfully mated immigrant females will survive long enough to produce their hybrid offspring. Thus, natural selection against immigrants results in distinctive elements of premating and postmating reproductive isolation that we hereby dub "immigrant inviability." We quantify the contributions of immigrant inviability to total reproductive isolation by examining study systems where multiple components of reproductive isolation have been measured and demonstrate that these contributions are frequently greater than those of traditionally recognized reproductive barriers. The relevance of immigrant inviability is further illustrated by a consideration of population-genetic theory, a review of selection against immigrant alleles in hybrid zone studies, and an examination of its participation in feedback loops that influence the evolution of additional reproductive barriers. Because some degree of immigrant inviability will commonly exist between populations that exhibit adaptive ecological divergence, we emphasize that these barriers play critical roles in ecological modes of speciation. We hope that the formal recognition of immigrant inviability and our demonstration of its evolutionary importance will stimulate more explicit empirical studies of its contributions to speciation.     

Water as a conformational editor in protein folding

As molecules approach one another in aqueous solution, desolvation free energy barriers to association are encountered. Experiments suggest these (de)solvation effects contribute to the free energy barriers separating the folded and unfolded states of protein molecules. To explore their influence on the energy landscapes of protein folding reactions, we have incorporated desolvation barriers into a semi-realistic, off-lattice protein model that uses a simplified physico-chemical force-field determined solely by the sequence of amino acids. Monte Carlo sampling techniques were used to study the effects on the thermodynamics and kinetics of folding of a number of systems, diverse in structure and sequence. In each case, desolvation barriers increase the stability of the native conformation and the cooperativity of the major folding/unfolding transition. The folding times of these systems are reduced significantly upon inclusion of desolvation barriers, demonstrating that the particulate nature of the solvent engenders a more defined route to the native fold.     

Evaluation of Adult White Sturgeon Swimming Capabilities and Applications to Fishway Design

Concern over passage of sturgeon barriers, has focused attention on fishway design that accommodates its swimming performance. In order to evaluate swimming performance, regarding fish ladder type partial barriers, wild adult sturgeons, Acipenser transmontanus; 121–76m fork length, were captured in the San Francisco Bay Estuary and Yolo Bypass toe drain. Hydrodynamic forces and kinematic parameters for swimming performance data were collected in a laboratory flume under three flow conditions through barriers and ramp. The experiments were conducted in a 24.4 m long, 2.1 m wide, and 1.62 m deep aluminum channel. Two geometric configurations of the laboratory model were designed based on channel characteristics that have been identified in natural river systems. At a given swimming speed and fish size, the highest guidance efficiencies of successful white sturgeon passage as a function of flow depth, flow velocity, turbulence intensity, Reynolds number, Froude number and shear velocity observed in the steady flow condition, tested with the horizontal ramp structure, occurred at an approach velocity of 0.33 ms^-1. The guidance efficiency of successful sturgeon passage increased both with increasing flow velocity and Froude number, and decreased both with the flow depth and the turbulence intensity. This study also provides evidence that tail beat frequency increases significantly with swimming speed, but tail beat frequency decreases with fish total length. Stride length increases both with swimming speed and fish total length. The importance of unsteady forces is expressed by the reduced frequency both with swimming speed and fish total length. Regression analysis indicates that swimming kinematic variables are explained by the swimming speed, the reduced frequency and the fish total length. The results emphasize the importance of fish ladder type patchiness when a fishway is designed for the passage of sturgeon.     

The impact of multiple biogeographic barriers and hybridization on species-level differentiation

• Premise of the study: The glacial cycles of the Quaternary did not impact Australia in the same way as Europe and North America. Here we investigate the history of population isolation, species differentiation, and hybridization in the southeastern Australian landscape, using five species of Lomatia (Proteaceae). We use a chloroplast DNA phylogeography to assess chloroplast haplotype (chlorotype) sharing among these species and whether species with shared distributions have been affected by shared biogeographic barriers. • Methods: We used six chloroplast DNA simple sequence repeats (cpSSR) across five species of Lomatia, sampled across their entire distributional range in southeastern Australia. Resulting size data were combined, presented as a network, and visualized on a map. Biogeographical barriers were tested using AMOVA. To explore hypotheses of chlorotype origin, we converted the network into a cladogram and reconciled with all possible species trees using parsimony-based tree mapping. • Key results: Some chlorotypes were shared across multiple species of Lomatia in the study, including between morphologically differentiated species. Chlorotypes were either widespread in distribution or geographically restricted to specific regions. Biogeographical structure was identified across the range of Lomatia. The most parsimonious reconciled tree incorporated horizontal transfer of chlorotypes. • Conclusions: Lomatia shows evidence of both incomplete lineage sorting and extensive hybridization between co-occurring species. Although the species in the study appear to have responded to a number of biogeographic barriers to varying degrees, our findings identified the Hunter River Valley as the most important long-term biogeographic barrier for the genus in southeastern Australia.     

The novel peptide PACAP-TAT with enhanced traversing ability attenuates the severe lung injury induced by repeated smoke inhalation

Pituitary adenylate cyclase-activating polypeptide (PACAP) is a potential therapeutic peptide with anti-inflammatory and anti-oxidative effects. In order to increase the efficiency of traversing biological barriers, a novel fusion peptide PACAP-TAT was produced by tagging PACAP at its C-terminus with 11-amino acid TAT protein transduction domain. The results of characteristic assays showed that PACAP-TAT activated PACAP specific receptor PAC1 with the same potency as PACAP and PACAP-TAT crossed blood–brain barrier (BBB), blood–air barrier (BAB) and blood–testis barrier (BTB) with the efficiency about 2.5-fold higher than that of PACAP. Both PACAP-TAT and PACAP were used treat the mice with lung injury induced by repeated smoke inhalation. It was shown that both PACAP-TAT and PACAP decreased the mortality, increased the body weight and inhibited the edema and vascular permeability in the lungs of the mice received repeated smoke inhalation, while PACAP-TAT displayed more marked effects than PACAP. PACAP-TAT decreased myeloperoxidase (MPO) activity, increased catalase (CAT) activity and down-regulated interleukin 6 (IL-6) and malondialdehyde (MDA) levels in the lungs with a significantly higher efficiency than PACAP. The histopathological analysis also showed that PACAP-TAT attenuated the cell filtration and bronchi epithelial hyperplasia more significantly than PACAP. Moreover the leukocyte count in blood and the serum superoxide dismutase (SOD) activity in the mice treated with PACAP-TAT were significantly different from that in mice treated with PACAP (p < 0.05). All these data indicated that PACAP-TAT with increased traversing ability was more effective than PACAP in protecting the mice from the lung injury induced by repeated smoke inhalation.     

Spatially explicit models of divergence and genome hitchhiking

Strong barriers to genetic exchange can exist at divergently selected loci, whereas alleles at neutral loci flow more readily between populations, thus impeding divergence and speciation in the face of gene flow. However, ‘divergence hitchhiking’ theory posits that divergent selection can generate large regions of differentiation around selected loci. ‘Genome hitchhiking’ theory suggests that selection can also cause reductions in average genome‐wide rates of gene flow, resulting in widespread genomic divergence (rather than divergence only around specific selected loci). Spatial heterogeneity is ubiquitous in nature, yet previous models of genetic barriers to gene flow have explored limited combinations of spatial and selective scenarios. Using simulations of secondary contact of populations, we explore barriers to gene flow in various selective and spatial contexts in continuous, two‐dimensional, spatially explicit environments. In general, the effects of hitchhiking are strongest in environments with regular spatial patterning of starkly divergent habitat types. When divergent selection is very strong, the absence of intermediate habitat types increases the effects of hitchhiking. However, when selection is moderate or weak, regular (vs. random) spatial arrangement of habitat types becomes more important than the presence of intermediate habitats per se. We also document counterintuitive processes arising from the stochastic interplay between selection, gene flow and drift. Our results indicate that generalization of results from two‐deme models requires caution and increase understanding of the genomic and geographic basis of population divergence.     

POPULATION STRUCTURE AND SPECIATION IN TROPICAL SEAS: GLOBAL PHYLOGEOGRAPHY OF THE SEA URCHIN DIADEMA

Abstract.— The causes of speciation in the sea are rarely obvious, because geographical barriers are not conspicuous and dispersal abilities or marine organisms, particularly those of species with planktonic larvae, are hard to determine. The phylogenetic relations of species in cosmopolitan genera can provide information on the likely mode of their formation. We reconstructed the phylogeny of the pantropical and subtropical sea urchin genus Diadema, using sequences of mitochondrial DNA from 482 individuals collected around the world, to determine the efficacy of barriers to gene flow and to ascertain the history of possible dispersal and vicariance events that led to speciation. We also compared 22 isozyme loci between all described species except D. palmeri. The mitochondrial DNA data show that the two deepest lineages are found in the Indian and West Pacific Oceans. (Indo‐Pacific) Diadema setosum diverged first from all other extant Diadema, probably during the initiation of wide fluctuations in global sea levels in the Miocene. The D. setosum clade then split 3‐5 million years ago into two clades, one found around the Arabian Peninsula and the other in the Indo‐West Pacific. On the lineage leading to the other species of Diadema, the deepest branch is composed of D. palmeri, apparently separated when the climate of New Zealand became colder and other tropical echinoids at these islands went extinct. The next lineage to separate is composed of a currently unrecognized species of Diadema that is found at Japan and the Marshall Islands. Diadema mexicanum in the eastern Pacific separated next, whereas D. paucispinum, D. savignyi, and D. antillarum from the western and central Atlantic, and (as a separate clade) D. antillarum from the eastern Atlantic form a shallow polytomy. Apparently, Indo‐Pacific populations of Diadema maintained genetic contact with Atlantic ones around the southern tip of Africa for some time after the Isthmus of Panama was complete. Diadema paucispinum contains two lineages: D. paucispinum sensu stricto is not limited to Hawaii as previously thought, but extends to Easter Island, Pitcairn, and Okinawa; A second mitochondrial clade of D. paucispinum extends from East Africa and Arabia to the Philippines and New Guinea. A more recent separation between West Indian Ocean and West Pacific populations was detected in D. setosum. Presumably, these genetic discontinuities are the result of water flow restrictions in the straits between northern Australia and Southeast Asia during Pleistocene episodes of low sea level. Diadema savignyi is characterized by high rates of gene flow from Kiribati in the central Pacific all the way to the East African Coast. In the Atlantic, there is a biogeographic barrier between the Caribbean and Brazil, possibly caused by fresh water outflow from the Amazon and the Orinoco Rivers. Diadema antillarum populations of the central Atlantic islands of Ascension and St. Helena are genetically isolated and phylogenetically derived from Brazil. Except for its genetic separation by the mid‐Atlantic barrier, Diadema seems to have maintained connections through potential barriers to dispersal (including the Isthmus of Panama) more recently than did Eucidaris or Echinometra, two other genera of sea urchins in which phylogeography has been studied. Nevertheless, the mtDNA phylogeography of Diadema includes all stages expected from models of allopatric differentiation. There are anciently separated clades that now overlap in their geographic distribution, clades isolated in the periphery of the genus range that have remained in the periphery, clades that may have been isolated in the periphery but have since spread towards the center, closely related clades on either side of an existing barrier, and closely related monophyletic entities on either side of an historical barrier that have crossed the former barrier line, but have not attained genetic equilibrium. Except for D. paucispinum and D. savignyi, in which known hybridization may have lodged mtDNA from one species into the genome of the other, closely related clades are always allopatric, and only distantly related ones overlap geographically. Thus, the phylogenetic history and distribution of extant species of Diadema is by and large consistent with allopatric speciation.     

Morphology and coexistence of congeneric ectoparasite species: reinforcement of reproductive isolation?

Assuming that differences or similarities in morphology among congeneric parasite species living in the same habitat are not a random pattern, several hypotheses explaining morphological differences were tested: (i) reproductive isolation, (ii) niche restriction resulting from competition, and (iii) niche specialization. Congeneric monogenean (platyhelminth) ectoparasites parasitizing the gills of one host species were used as an ecological model. Morphometric distances of the attachment organ and morphometric distances of the copulatory organ between species pairs were calculated, Levin's niche size and Renkonen niche overlap indices were applied. Our results support the prediction that the function of niche segregation is to achieve reproductive isolation of related species in order to prevent hybridization (reinforcement of reproductive barriers). Parasite species living in the same niche differ greatly in the size of copulatory organ. Moreover, species coexistence is facilitated by an increase in morphometric distances of copulatory organ and niche centre distances. Our results also show that species living in overlapping niches have similar attachment organs, which supports the prediction that morphologically similar species have the same ecological requirements within one host and suggests small effects of interspecific competition for the evolution of morphological diversity of attachment organs. Specialist adaptations also seem to facilitate species coexistence and affect the niche distribution within host species. Parasite species that can colonize more than one host species, i.e. generalists, occupy more distant niches within host species than strictly host-specific parasites. © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 76, 125–135.     

Evaluation of Slurry Wall Construction Using Paper Clay for Containment of Contaminated Groundwater

Slurry walls have been used widely as passive vertical barriers to control the horizontal flow of groundwater and contaminants and therefore limit the migration of contaminants through the subsurface. The material used as slurry to reduce contaminant transport is expected to form a filter cake with low permeability along the sides of the trench wall/excavation face. In this article, paper mill sludge (hereafter referred to as paper clay) is investigated as a possible slurry. Previous research by Moo Young et al. (2000) has shown that paper clay has several properties that make its use in vertical barriers very promising. It can be compacted to low permeability values (10^?7?cm/s to 10^?9?cm/s) and has a high organic content that may act as a potential carbon source for microbial growth and sorption sites for heavy metal attenuation. To determine the feasibility of paper clay in a slurry, column testing to determine the dispersion coefficient for transport modeling, slump testing, and filter cake formation tests were performed. It is shown that the coefficient of hydrodynamic dispersion within paper clay is in the order of 10^?7?cm²/ s. It is also shown that paper clay can achieve the required slump of between 5.08 and 15.24?cm (2 and 6 in) similar to that of a workable soil-bentonite backfill. Furthermore, it is shown that the filter cakes that are formed have permeability values similar to those of soil-bentonite filter cakes.