Dispersal Reduction: Causes, Genomic Mechanisms, and Evolutionary Consequences.

Recent biological analyses suggest that reductions in dispersal ability have been key drivers of diversification across numerous lineages. We synthesise emerging data to highlight similarities regarding the causes and consequences of dispersal reduction across taxa and ecosystems, as well as the diverse genomic mechanisms underpinning these shifts. Natural selection has acted on standing genetic variation within taxa to drive often rapid - and in some cases parallel - losses of dispersal, and ultimately speciation. Such shifts can thus represent an important nexus between adaptive and neutral diversification processes, with substantial evolutionary consequences. Recognition of the links between these concepts that are emerging from different fields, taxa and ecosystems is transforming our understanding of the fascinating role of dispersal reduction in the formation of biodiversity.

Swimming against the current: genetic structure, host mobility and the drift paradox in trematode parasites.

Life-cycle characteristics and habitat processes can potentially interact to determine gene flow and genetic structuring of parasitic species. In this comparative study, we analysed the genetic structure of two freshwater trematode species with different life histories using cytochrome c oxidase I gene (COI) sequences and examined the effect of a unidirectional river current on their genetic diversity at 10 sites along the river. We found moderate genetic structure consistent with an isolation-by-distance pattern among subpopulations of Coitocaecum parvum but not in Stegodexamene anguillae. These contrasting parasite population structures were consistent with the relative dispersal abilities of their most mobile hosts (i.e. their definitive hosts). Genetic diversity decreased, as a likely consequence of unidirectional river flow, with increasing distance upstream in C. parvum, which utilizes a definitive host with only restricted mobility. The absence of such a pattern in S. anguillae suggests that unidirectional river flow affects parasite species differently depending on the dispersal abilities of their most mobile host. In conclusion, genetic structure, genetic diversity loss and drift are stronger in parasites whose most mobile hosts have low dispersal abilities and small home ranges. An additional prediction can be made for parasites under unidirectional drift: those parasites that stay longer in their benthic intermediate host or have more than one benthic intermediate hosts would have relatively high local recruitment and hence increased retention of upstream genetic diversity.

Evolutionary consequences of microhabitat: population-genetic structuring in kelp- vs. rock-associated chitons.

Rafting has long been invoked as a key marine dispersal mechanism, but biologists have thus far produced little genetic evidence to support this hypothesis. We hypothesize that coastal species associated with buoyant seaweeds should experience enhanced population connectivity owing to rafting. In particular, invertebrates strongly associated with the buoyant bull-kelp Durvillaea antarctica might be expected to have lower levels of population-genetic differentiation than taxa mainly exploiting nonbuoyant substrates. We undertook a comparative genetic study of two codistributed, congeneric chiton species, assessing population connectivity at scales of 61-516 km, using ≥ 186 polymorphic AFLP loci per species. Consistent with predictions, population-genetic differentiation was weaker in the kelp-associated Sypharochiton sinclairi than in the rock-associated S. pelliserpentis. Additionally, while we found a significant positive correlation between genetic and oceanographic distances in both chiton species, the correlation was stronger in S. pelliserpentis (R(2) = 0.28) than in S. sinclairi (R(2) = 0.18). These data support the hypothesis that epifaunal taxa can experience enhanced population-genetic connectivity as a result of their rafting ability.

Isolation and characterization of microsatellite loci from the yellow-eyed penguin (Megadyptes antipodes).

Twelve microsatellite loci were isolated and characterized in the endangered yellow-eyed penguin (Megadyptes antipodes) using enriched genomic libraries. Polymorphic loci revealed two to eight alleles per locus and observed heterozygosity ranged from 0.21 to 0.77. These loci will be suitable for assessing current and historical patterns of genetic variability in yellow-eyed penguins.

In vitro human immunodeficiency virus type 1 resistance selections with combinations of tenofovir and emtricitabine or abacavir and lamivudine.

Human immunodeficiency virus type 1 (HIV-1) resistance development was evaluated in vitro by using combinations of the drugs tenofovir and emtricitabine or abacavir and lamivudine, as well as by using the compounds individually. Emtricitabine- and lamivudine-resistant HIV-1 isolates with the M184I or M184V mutation in reverse transcriptase were readily selected in the cultures with emtricitabine alone, lamivudine alone, and the two drug combinations and conferred high-level resistance to emtricitabine and lamivudine. Tenofovir-resistant HIV-1 isolates with the K65R mutation occurred in both the culture with tenofovir alone and the culture with the combination of emtricitabine and tenofovir. The S68N and S68K mutations were also observed in the tenofovir cultures, with no detectable impact on resistance, suggesting a possible compensatory role in viral fitness. At low concentrations of emtricitabine and tenofovir, the M184I mutation appeared first, followed by the K65R mutation, in a subset of viruses. At intermediate concentrations of emtricitabine and tenofovir, viruses harboring the K65R mutation or a novel K65N and K70R double mutation grew before they gave rise to mutants with K65R and M184V/I double mutations at higher emtricitabine concentrations. Abacavir resistance was characterized by the accumulation of the M184V, Y115F, and K65R mutations in the abacavir culture, while the M184V and L74V mutations were selected in combination with lamivudine. In the presence of the abacavir resistance mutations, viral growth was strong even in the presence of high concentrations of abacavir. In contrast, viral growth was markedly impaired in the cultures with high tenofovir concentrations, even in the presence of K65R. In conclusion, these studies show that HIV-1 mutants with a K65R and M184V genotype are generated under maximum selection pressure from the combination of tenofovir and emtricitabine.

River capture, range expansion, and cladogenesis: the genetic signature of freshwater vicariance.

River capture is potentially a key geomorphological driver of range expansion and cladogenesis in freshwater-limited taxa. While previous studies of freshwater fish, in particular, have indicated strong relationships between historical river connections and phylogeographic pattern, their analyses have been restricted to single taxa and geological hypotheses were typically constructed a posteriori. Here we assess the broader significance of river capture among taxa by testing multiple species for the genetic signature of a recent river capture event in New Zealand. During the Quaternary an upper tributary of the Clarence River system was diverted into the headwaters of the Wairau River catchment. Mitochondrial DNA (control region and cytochrome b) sequencing of two native galaxiid fishes (Galaxias vulgaris and Galaxias divergens) supports headwater exchange: populations from the Clarence and Wairau Rivers are closely related sister-groups, whereas samples from the geographically intermediate Awatere River are genetically divergent. The upland bully Gobiomorphus breviceps (Eleotridae), in contrast, lacks a genetic signature of the capture event. We hypothesize that there is an increased likelihood of observing genetic signatures from river capture events when they facilitate range expansion, as is inferred for the two galaxiid taxa studied here. When river capture merely translocates genetic lineages among established populations, by contrast, we suggest that the genetic signature of capture is less likely to be retained, as might be inferred for G. breviceps. Rates of molecular evolution calibrated against this recent event were elevated relative to traditional estimates, consistent with the contribution of polymorphisms to branch lengths at shallow phylogenetic levels prior to fixation by purifying selection and drift.

Phylogeographical disjunction in abundant high-dispersal littoral gastropods.

Abstract Phylogeographical disjunctions in high-dispersal marine taxa are variously ascribed to palaeogeographical conditions or contemporary ecological factors. Associated biogeographical studies, however, seldom incorporate the sampling design required to confidently discriminate among such competing hypotheses. In the current study, over 7800 gastropod specimens were examined for operculum colour, and 129 specimens genetically, to test ecological and historical biogeographical hypotheses relating to biogeographical disjunction in the Southern Hemisphere, and to southern Australia in particular. Mitochondrial DNA sequence analysis of the high-dispersal intertidal gastropod Nerita atramentosa in southern Australia (88 specimens; 18 localities) revealed an east-west phylogeographical split involving two highly divergent clades (26.0 +/- 1.9%) exhibiting minimal geographical overlap in the southeast. The eastern clade of Nerita atramentosa is also widespread in northern New Zealand (43 specimens, 10 localities), but no significant genetic differentiation is explained by the Tasman Sea, a 2000-km-wide oceanic barrier. Spatial genetic structure was not detected within either clade, consistent with the species' dispersive planktotrophic phase lasting for 5-6 months. Digital analysis of operculum colouration revealed substantial differences between eastern (tan) and western (black) specimens. Genetic analysis and visual inspection of 88 Australian specimens revealed a completely nonrandom association between mtDNA data and operculum colouration. Independent examination of a further 7822 specimens from 14 sites in southern Australia revealed both colour morphs at all localities, but reinforced the phylogeographical data by indicating a marked turnover in colour morph abundance associated with a palaeogeographical barrier: Wilsons Promontory. This sharp biogeographical disjunction is in marked contrast to the species' high dispersal abilities. The genetic similarity of Nerita morio (Easter Island) and the eastern Australian + New Zealand lineage (1.1 +/- 0.3%) provides further evidence of long-distance dispersal in southern Nerita. Phylogenetic relationships of nine species (four genera) of Neritidae, an almost exclusively tropical gastropod family, are consistent with the hypothesis that southern temperate black nerites comprise a monophyletic radiation.

Phylogeography of a high-dispersal New Zealand sea-star: does upwelling block gene-flow?

New Zealand's (NZ) geographical isolation, extensive coastline and well-characterized oceanography offer a valuable system for marine biogeographical research. Here we use mtDNA control region sequences in the abundant endemic sea-star Patiriella regularis to test the following literature-based predictions: that coastal upwelling disrupts north-south gene flow and promotes population differentiation (hypothesis 1); and that an invasive Tasmanian population of the species was introduced anthropogenically from southern New Zealand (hypothesis 2). We sequenced 114 samples from 22 geographical locations, including nine sites from North Island, nine from South Island, one from Stewart Island and three from Tasmania. Our analysis of these sequences revealed an abundance of shallow phylogenetic lineages within P. regularis (68 haplotypes, mean divergence 0.9%). We detected significant genetic heterogeneity between pooled samples from northern vs. southern New Zealand (FST = 0.072; P = 0.0002), consistent with the hypothesis that upwelling disrupts gene flow between these regions (hypothesis 1). However, we are currently unable to rule out the alternative hypothesis that Cook Strait represents a barrier to dispersal (North Island vs. South Island; FST = 0.031; P = 0.0467). The detection of significant spatial structure in NZ samples is consistent with restricted gene flow, and the strong structure evident in northern NZ may be facilitated by distinct ocean current systems. Four shared haplotypes and nonsignificant differentiation (FST = 0.025; P = 0.2525) between southern New Zealand and Tasmanian samples is consistent with an anthropogenic origin for the latter population (hypothesis 2).

Genes meet geology: fish phylogeographic pattern reflects ancient, rather than modern, drainage connections.

We used DNA analysis of the freshwater Galaxias vulgaris complex (Pisces: Galaxiidae) to test a geological hypothesis of drainage evolution in South Island, New Zealand. Geological evidence suggests that the presently north-flowing Nevis River branch of the Clutha/Kawarau River system (Otago) once flowed south into the Nokomai branch of the Mataura system (Southland). The flow reversal is thought to have resulted from fault and fold activity associated with post-Miocene uplift. Mitochondrial DNA sequence data (control region and cytochrome b genes; 76 individuals; maximum divergence 7.1%) corroborate this geomorphological hypothesis: The Nevis River retains a freshwater fish species (Galaxias gollumoides; five sites; 10 haplotypes) that is otherwise restricted to Southland (nine sites; 15 haplotypes). There is no indication that the Nevis River lineage of G. gollumoides lives elsewhere in the Clutha/ Kawarau system (> 30 sites). Likewise, two widespread Clutha lineages (G. 'sp D'; G. anomalus-G. pullus) are apparently absent from the Nevis (> 30 sites). In particular, G. 'sp D' lives throughout much of the Clutha (12 sites, 23 haplotypes), including a tributary of the Kawarau, but is absent from the Nevis itself. Conventional molecular clock calibrations (based on a minimum Nevis-Mataura haplotype divergence of 3.0%) indicate that the Nevis flow reversal may have occurred in the early-mid Pleistocene, which is roughly consistent with geological data. The broad phylogeographic structure evident in the Clutha system is consistent with the sedentary nature of nonmigratory galaxiids. Our study reinforces the value of combining biological and geological data for the formulation and testing of historical hypotheses.

Reexposure breeds recall: effects of experience on 9-month-olds' ordered recall.

On the basis of three experiences, 9-month-olds recall specific events after one month. We tested whether multiple experiences are necessary, or merely facilitative, of 9-month-olds' long-term recall. In two experiments, using deferred imitation, infants were exposed to multi-step sequences either one time, two times, or three times prior to a one-month delay. In Experiment 1, regardless of the number of experiences, infants did not demonstrate recall. In Experiment 2, infants were tested on and reexposed to the events after one week; recall was tested again one month later. Performance after 1 week in Experiment 2 was greater than performance after one month in Experiment 1. Moreover, presumably as a function of reexposure after one week, infants recalled the individual actions of the events one month later. Infants in the three-experience condition also evidenced ordered recall after one month. Implications for the developmental status of the neural substrate supporting long-term recall are discussed.

Cladogenesis and loss of the marine life-history phase in freshwater galaxiid fishes (Osmeriformes: Galaxiidae).

Switches from migratory (diadromous) to nonmigratory (freshwater) life histories are known to have occurred repeatedly in some aquatic taxa. However, the significance of the loss of diadromy as an initiator for speciation remains poorly understood. The rivers of New Zealand's South Island house a species flock of recently derived nonmigratory galaxiid fishes known as the Galaxias vulgaris complex. Members of this complex are morphologically and genetically similar to the diadromous G. brevipinnis found in New Zealand and southeastern Australia. We hypothesised that South Island's G. vulgaris complex (at least 10 nonmigratory lineages) represents a number of independent radiations from a migratory G. brevipinnis stock, with repeated loss of diadromy. Sequence data were obtained for 31 ingroup samples (G. vulgaris complex and G. brevipinnis) plus four outgroup taxa. A well-resolved phylogeny based on 5039 base pairs of the mitochondrial genome suggests that diadromy has been lost on three separate occasions. Thus, speciation in these galaxiid fishes is partly an incidental phenomenon caused by switches from diadromous to nonmigratory strategies. However, much of the subsequent nonmigratory diversity is monophyletic, suggesting that drainage evolution (vicariance) has also played a major role in cladogenesis. Levels of sequence divergence among major ingroup lineages (1.6-12.7%) suggest that the radiation is considerably older relative to Northern Hemisphere (postglacial) complexes of salmonid, osmerid, and gasterosteid fishes. Sympatric taxa are not monophyletic, suggesting that their coexistence reflects secondary contact rather than sympatric speciation. The monophyly of New Zealand G. brevipinnis is well supported, but both mitochondrial DNA and nuclear sequences indicate that G. brevipinnis is paraphyletic on an intercontinental scale. The divergence (maximum 11.5%) between Tasmanian and New Zealand G. brevipinnis, although large, supports marine dispersal rather than vicariance as the principle biogeographic mechanism on an intercontinental scale.

Biogeography of a southern hemisphere freshwater fish: how important is marine dispersal?

Galaxias maculatus is one of the world's most widely distributed freshwater fish. This species has a marine-tolerant juvenile phase, and a geographical range extending through much of the southern hemisphere. We conducted phylogeographic analyses of 163 control region haplotypes of G. maculatus, including samples from New Zealand (five locations), Tasmania (one location) and Chile (one location). A lack of genetic structure among New Zealand samples suggests that marine dispersal facilitates considerable gene flow on an intra-continental scale. The discovery of a Tasmanian-like haplotype in one of 144 New Zealand samples indicates that inter-continental marine dispersal occurs but is insufficient to prevent mitochondrial DNA differentiation among continents. The sister relationship of Tasmanian and New Zealand clades implies that marine dispersal is an important biogeographical mechanism for this species. However, a vicariant role in the divergence of eastern and western Pacific G. maculatus cannot be rejected.

Across the Southern Alps by river capture? Freshwater fish phylogeography in South Island, New Zealand.

We used DNA analysis of galaxiid fish to test a hypothesis of localized headwater capture in South Island, New Zealand. The restricted western, but widespread eastern, distributions of three nonmigratory freshwater fish species suggest that part of the east-flowing Waiau River has been captured by the west-flowing Buller River. However, mitochondrial control region (Kimura 2-parameter distance = 4.1-5.4%) and microsatellite flanking sequences do not support a relationship between Waiau (N = 4 fish sequences) and western populations (N = 8) of Galaxias vulgaris. Instead, the point of capture is probably to the north-east, perhaps the Nelson lakes region. Phylogenetic analysis indicates that western populations, along with populations in the north-east (N = 18), represent a previously unidentified monophyletic Evolutionarily Significant Unit, possibly a cryptic species. We suggest a general caveat for zoogeographic conclusions based on distributional data alone.

Molecular phylogenetics and biogeography of galaxiid fishes (Osteichthyes: Galaxiidae): dispersal, vicariance, and the position of Lepidogalaxias salamandroides.

The galaxiid fishes exhibit a gondwanan distribution. We use mitochondrial DNA sequences to test conflicting vicariant and dispersal biogeographic hypotheses regarding the Southern Hemisphere range of this freshwater group. Although phylogenetic resolution of cytochrome b and 16S rRNA sequences is largely limited to more recent divergences, our data indicate that the radiation can be interpreted as several relatively recent dispersal events superimposed on an ancient gondwanan radiation. Genetic relationships contradict the findings of recent morphological analyses of galaxioid fishes. In particular, we examine several hypotheses regarding phylogenetic placement of the enigmatic Lepidogalaxias. Although most workers consider Lepidogalaxias to be an unusual scaled member of the Southern Hemisphere galaxioids, it has also been suggested that this species is related to the Northern Hemisphere esocoids. Our data strongly suggest that this species is not a galaxiid, and the alternative hypothesized esocoid relationship cannot be rejected. The species-rich genus Galaxias is shown to be polyphyletic and the generic taxonomy of the Galaxiinae is reassessed in the light of phylogenetic relationships. Juvenile saltwater-tolerance is phylogenetically distributed throughout the Galaxiinae, and the loss of this migratory phase may be a major cause of speciation.

Extreme intraspecific mitochondrial DNA sequence divergence in Galaxias maculatus (Osteichthys: Galaxiidae), one of the world's most widespread freshwater fish.

Biogeographic controversies surrounding the widespread freshwater fish, Galaxias maculatus, were addressed with DNA sequence data. Mitochondrial cytochrome b and 16S rRNA sequences were obtained from representatives of six populations of this species. Substantial levels of cytochrome b (maximum 14.6%) and 16S rRNA sequence divergence (maximum 6.0%) were detected between western Pacific (Tasmania-New Zealand) and South American (Chile-Falkland Islands) haplotypes. A considerable level of divergence was also detected between Tasmanian and New Zealand haplotypes (maximum 5.1%) and within and among Chilean and Falkland Island G. maculatus (maximum 3. 8%). The phylogenetic structure of haplotypes conflicts with the accepted pattern of continental fragmentation. Molecular clock calibrations suggest that haplotype divergences postdate the fragmentation of Gondwana. These findings point to marine dispersal rather than ancient vicariance as an explanation for the wide distribution. The phylogenetic structure of South American haplotypes was not consistent with their geographic distribution. We consider factors such as population divergence, population size, dispersal, secondary contact, and philopatry as potential causes of the high level of mtDNA nucleotide diversity in this species.

Structure of human lactoferrin at 3.2-A resolution.

The three-dimensional structure of human milk lactoferrin, a member of the transferrin family, has been determined crystallographically at 3.2-A resolution. The molecule has two-fold internal homology. The N- and C-terminal halves form two separate globular lobes, connected by a short alpha-helix, and carry one iron-binding site each. Each lobe has the same folding, based on two domains of similar supersecondary structure, with the iron site at the domain interface. Each iron atom is coordinated by four protein ligands: two tyrosines, one histidine, and one aspartate. A probable CO3(2-) (or HCO3-) ion is suggested by the electron density, bound to iron and adjacent to an arginine side chain and a helix N terminus. The protein folding and location of the binding sites show marked similarities with those of other binding proteins, notably the sulfate-binding protein from Salmonella typhimurium.

Vision and kinesthesis in spatial short-term memory.

This investigation examined the effects of different localizing cues on the precision with which subjects can recall the position of a target in space. The availability of the cues--vision, kinesthesis, or both--was varied during both learning and recall. Subjects (age range 26 to 58 yr.) placed the stimulus or watched it being placed. The stimulus was removed, and subjects replaced or indicated its replacement location. Results show a striking similarity of performance for all subjects and significant performance differences relative to the different cues. The results provide information about intramodal and intermodal visual and kinesthetic transfer effects and about the effects of unimodal and multimodal input in such transfer. Results confirm a dominance of vision over kinesthesis, i.e., "kinesthetic memory" does not provide as accurate localizing information as does "visual memory."

The crystal and molecular structure of the polymeric copper (II) complex of inosine 5'-monophosphate. A comparison with the previously reported zinc analogue.

X-ray analysis of [Cu . (5'-IMP) . H2O] has shown a structure containing polymeric chains of composition [Cu.5'-IMP]n in which the copper atom is directly bound to N(7) of the base and to three oxygen atoms of different phosphate groups. Whereas the coordination geometry in the analogous zinc complex resembles a distorted tetrahedrom, that in the copper complex is a distorted square plane with weak axial interactions.