Deleterious epistatic interactions between electron transport system protein-coding loci in the copepod Tigriopus californicus

Southern introgression increases adaptive immune gene variability in northern range margin populations of Fire-bellied toad

Northern range margin populations of the European fire-bellied toad (Bombina bombina) have rapidly declined during recent decades. Extensive agricultural land use has fragmented the landscape, leading to habitat disruption and loss, as well as eutrophication of ponds. In Northern Germany (Schleswig-Holstein) and Southern Sweden (Skåne), this population decline resulted in decreased gene flow from surrounding populations, low genetic diversity, and a putative reduction in adaptive potential, leaving populations vulnerable to future environmental and climatic changes. Previous studies using mitochondrial control region and nuclear transcriptome-wide SNP data detected introgressive hybridization in multiple northern B. bombina populations after unreported release of toads from Austria. Here, we determine the impact of this introgression by comparing the body conditions (proxy for fitness) of introgressed and nonintrogressed populations and the genetic consequences in two candidate genes for putative local adaptation (the MHC II gene as part of the adaptive immune system and the stress response gene HSP70 kDa). We detected regional differences in body condition and observed significantly elevated levels of within individual MHC allele counts in introgressed Swedish populations, associated with a tendency toward higher body weight, relative to regional nonintrogressed populations. These differences were not observed among introgressed and nonintrogressed German populations. Genetic diversity in both MHC and HSP was generally lower in northern than Austrian populations. Our study sheds light on the potential benefits of translocations of more distantly related conspecifics as a means to increase adaptive genetic variability and fitness of genetically depauperate range margin populations without distortion of local adaptation.

Chromosome-Wide Impacts on the Expression of Incompatibilities in Hybrids of Tigriopus californicus

Chromosome rearrangements such as inversions have been recognized previously as contributing to reproductive isolation by maintaining alleles together that jointly contribute to deleterious genetic interactions and postzygotic reproductive isolation. In this study, an impact of potential incompatibilities merely residing on the same chromosome was found in crosses of populations of the copepod Tigriopus californicus When genetically divergent populations of this copepod are crossed, hybrids show reduced fitness, and deviations from expected genotypic ratios can be used to determine regions of the genome involved in deleterious interactions. In this study, a set of markers was genotyped for a cross of two populations of T. californicus, and these markers show widespread deviations from Mendelian expectations, with entire chromosomes showing marked skew. Despite the importance of mtDNA/nuclear interactions in incompatibilities in this system in previous studies, in these crosses the expected patterns stemming from these interactions are not widely apparent. Females lack recombination in this species, and a striking difference is observed between male and female backcrosses. This suggests that the maintenance of multiple loci on individual chromosomes can enable some incompatibilities, perhaps playing a similar role in the initial rounds of hybridization to chromosomal rearrangements in preserving sets of alleles together that contribute to incompatibilities. Finally, it was observed that candidate pairs of incompatibility regions are not consistently interacting across replicates or subsets of these crosses, despite the repeatability of the deviations at many of the single loci themselves, suggesting that more complicated models of Dobzhansky-Muller incompatibilities may need to be considered.

Paraphyly and budding speciation in the hairy snail (Pulmonata, Hygromiidae)

Delimitation of species is often complicated by discordance of morphological and genetic data. This may be caused by the existence of cryptic or polymorphic species. The latter case is particularly true for certain snail species showing an exceptionally high intraspecific genetic diversity. The present investigation deals with the Trochulus hispidus complex, which has a complicated taxonomy. Our analyses of the COI sequence revealed that individuals showing a T. hispidus phenotype are distributed in nine highly differentiated mitochondrial clades (showing p-distances up to 19%). The results of a parallel morphometric investigation did not reveal any differentiation between these clades, although the overall variability is quite high. The phylogenetic analyses based on 12S, 16S and COI sequences show that the T. hispidus complex is paraphyletic with respect to several other morphologically well-defined Trochulus species (T. clandestinus, T. villosus, T. villosulus and T. striolatus) which form well-supported monophyletic groups. The nc marker sequence (5.8S-ITS2-28S) shows only a clear separation of T. o. oreinos and T. o. scheerpeltzi, and a weakly supported separation of T. clandestinus, whereas all other species and the clades of the T. hispidus complex appear within one homogeneous group. The paraphyly of the T. hispidus complex reflects its complicated history, which was probably driven by geographic isolation in different glacial refugia and budding speciation. At our present state of knowledge, it cannot be excluded that several cryptic species are embedded within the T. hispidus complex. However, the lack of morphological differentiation of the T. hispidus mitochondrial clades does not provide any hints in this direction. Thus, we currently do not recommend any taxonomic changes. The results of the current investigation exemplify the limitations of barcoding attempts in highly diverse species such as T. hispidus.

Pacific and Atlantic Lepeophtheirus salmonis (Krøyer, 1838) are allopatric subspecies: Lepeophtheirus salmonis salmonis and L. salmonis oncorhynchi subspecies novo

Background

The salmon louse Lepeophtheirus salmonis is a parasitic copepod that infects salmonids in the Pacific and Atlantic oceans. Although considered as a single species, morphological and biological differences have been reported between lice from the two oceans. Likewise, studies based on nucleotide sequencing have demonstrated that sequence differences between Atlantic and Pacific L. salmonis are highly significant, albeit smaller than the divergence observed between congeneric copepod species.

Results

We demonstrated reproductive compatibility between L. salmonis from the two oceans and successfully established F2 hybrid strains using separate maternal lines from both the Pacific and Atlantic. The infection success for the F2 hybrid strains were similar to results typically observed for non hybrid lice strains in the rearing facility used. Lepeophtheirus salmonis COI and 16S sequences divergence between individuals from the Pacific and the Atlantic oceans was high compared to what may be expected within a copepod species and phylogenetic analysis showed that they consistently formed monophyletic clades representing their origin from the Pacific or Atlantic oceans.

Conclusions

Lepeophtheirus salmonis from the Pacific and Atlantic oceans are reproductively compatible at least until adults at the F2 hybrid stage, and should not be regarded as separate species based on reproductive segregation or sequence divergence levels. Reported biological and genetic differences in L. salmonis seen in conjunction with the reported genetic diversity commonly observed between and within species demonstrate that Atlantic and Pacific L. salmonis should be regarded as two subspecies: Lepeophtheirus salmonis salmonis and L. salmonis oncorhynchi subsp. nov.

Hybrid breakdown weakens under thermal stress in population crosses of the copepod Tigriopus californicus

The outcome of hybridization can be impacted by environmental conditions, which themselves can contribute to reproductive isolation between taxa. In crosses of genetically divergent populations, hybridization can have both negative and positive impacts on fitness, the balance between which might be tipped by changes in the environment. Genetically divergent populations of the intertidal copepod Tigriopus californicus have been shown to differ in thermal tolerance at high temperatures along a latitudinal gradient. In this study, a series of crosses were made between pairs of genetically divergent populations of T. californicus, and the thermal tolerance of these hybrids was tested. In most cases, the first-generation hybrids had relatively high thermal tolerance and the second-generation hybrids were not generally reduced below the less-tolerant parental population for high temperature tolerance. This pattern contrasts with previous studies from crosses of genetically divergent populations of this copepod, which often shows hybrid breakdown in these second-generation hybrids for other measures of fitness. These results suggest that high temperature stress could either increase the positive impacts of hybridization or decrease the negative impacts of hybridization resulting in lowered hybrid breakdown in these population crosses.

The genetics of hybrid incompatibilities

Incompatibilities in interspecific hybrids, such as sterility and lethality, are widely observed causes of reproductive isolation and thus contribute to speciation. Because hybrid incompatibilities are caused by divergence in each of the hybridizing species, they also reveal genomic changes occurring on short evolutionary time scales that have functional consequences. These changes include divergence in protein-coding gene sequence, structure, and location, as well as divergence in noncoding DNAs. The most important unresolved issue is understanding the evolutionary causes of the divergence within species that in turn leads to incompatibility between species. Surprisingly, much of this divergence does not appear to be driven by ecological adaptation but may instead result from responses to purely mutational mechanisms or to internal genetic conflicts.

Complex deleterious interactions associated with malic enzyme may contribute to reproductive isolation in the copepod Tigriopus californicus

Dobzhansky-Muller incompatibilities can result from the interactions of more than a single pair of interacting genes and there are several different models of how such complex interactions can be structured. Previous empirical work has identified complex conspecific epistasis as a form of complex interaction that has contributed to postzygotic reproductive isolation between taxa, but other forms of complexity are also possible. Here, I probe the genetic basis of reproductive isolation in crosses of the intertidal copepod Tigriopus californicus by looking at the impact of markers in genes encoding metabolic enzymes in F₂ hybrids. The region of the genome associated with the locus ME2 is shown to have strong, repeatable impacts on the fitness of hybrids in crosses and epistatic interactions with another chromosomal region marked by the GOT2 locus in one set of crosses. In a cross between one of these populations and a third population, these two regions do not appear to interact despite the continuation of a large effect of the ME2 region itself in both crosses. The combined results suggest that the ME2 chromosomal region is involved in incompatibilities with several unique partners. If these deleterious interactions all stem from the same factor in this region, that would suggest a different form of complexity from complex conspecific epistasis, namely, multiple independent deleterious interactions stemming from the same factor. Confirmation of this idea will require more fine-scale mapping of the interactions of the ME2 region of the genome.

Interpopulation hybridization results in widespread viability selection across the genome in Tigriopus californicus

Background

Genetic interactions within hybrids influence their overall fitness. Understanding the details of these interactions can improve our understanding of speciation. One experimental approach is to investigate deviations from Mendelian expectations (segregation distortion) in the inheritance of mapped genetic markers. In this study, we used the copepod Tigriopus californicus, a species which exhibits high genetic divergence between populations and a general pattern of reduced fitness in F2 interpopulation hybrids. Previous studies have implicated both nuclear-cytoplasmic and nuclear-nuclear interactions in causing this fitness reduction. We identified and mapped population-diagnostic single nucleotide polymorphisms (SNPs) and used these to examine segregation distortion across the genome within F2 hybrids.

Results

We generated a linkage map which included 45 newly elucidated SNPs and 8 population-diagnostic microsatellites used in previous studies. The map, the first available for the Copepoda, was estimated to cover 75% of the genome and included markers on all 12 T. californicus chromosomes. We observed little segregation distortion in newly hatched F2 hybrid larvae (fewer than 10% of markers at p < 0.05), but strikingly higher distortion in F2 hybrid adult males (45% of markers at p < 0.05). Hence, segregation distortion was primarily caused by selection against particular genetic combinations which acted between hatching and maturity. Distorted markers were not distributed randomly across the genome but clustered on particular chromosomes. In contrast to other studies in this species we found little evidence for cytonuclear coadaptation. Instead, different linkage groups exhibited markedly different patterns of distortion, which appear to have been influenced by nuclear-nuclear epistatic interactions and may also reflect genetic load carried within the parental lines.

Conclusion

Adult male F2 hybrids between two populations of T. californius exhibit dramatic segregation distortion across the genome. Distorted loci are clustered within specific linkage groups, and the direction of distortion differs between chromosomes. This segregation distortion is due to selection acting between hatching and adulthood.

The nature of interactions that contribute to postzygotic reproductive isolation in hybrid copepods

Deleterious interactions within the genome of hybrids can lower fitness and result in postzygotic reproductive isolation. Understanding the genetic basis of these deleterious interactions, known as Dobzhansky-Muller incompatibilities, is the subject of intense current study that seeks to elucidate the nature of these deleterious interactions. Hybrids from crosses of individuals from genetically divergent populations of the intertidal copepod Tigriopus californicus provide a useful model in which to study Dobzhansky-Muller incompatibilities. Studies of the basis of postzygotic reproductive isolation in this species have revealed a number of patterns. First, there is evidence for a breakdown in genomic coadaptation between mtDNA-encoded and nuclear-encoded proteins that can result in a reduction in hybrid fitness in some crosses. It appears from studies of the individual genes involved in these interactions that although this coadaptation could lead to asymmetries between crosses, patterns of genotypic viabilities are not often consistent with simple models of genomic coadaptation. Second, there is a large impact of environmental factors on these deleterious interactions suggesting that they are not strictly intrinsic in nature. Temperature in particular appears to play an important role in determining the nature of these interactions. Finally, deleterious interactions in these hybrid copepods appear to be complex in terms of the number of genetic factors that interact to lead to reductions in hybrid fitness. This complexity may stem from three or more factors that all interact to cause a single incompatibility or the same factor interacting with multiple other factors independently leading to multiple incompatibilities.

Hybrid dysfunction: population genetic and quantitative genetic perspectives

In the wake of seminal work by Dobzhansky and Muller, hybrid dysfunction is usually attributed to incompatible mutations in different genes arising in different populations. This Dobzhansky-Muller (D-M) model is among the most important contributions of theoretical population genetics. Here I make formal connections between the D-M model and the quantitative genetic interpretation of hybrid dysfunction as a combination of additive, dominance, and epistatic effects. Concerns over conceptual differences between the two approaches are unwarranted; the D-M model can be expressed as a special case of the statistical model developed for line-cross analysis in quantitative genetics. This unified theoretical framework encourages application of quantitative genetic methods to the study of speciation.

Cytonuclear conflict in interpopulation hybrids: the role of RNA polymerase in mtDNA transcription and replication

Organismal fitness requires functional integration of nuclear and mitochondrial genomes. Structural and regulatory elements coevolve within lineages and several studies have found that interpopulation hybridization disrupts mitonuclear interactions. Because mitochondrial RNA polymerase (mtRPOL) plays key roles in both mitochondrial DNA (mtDNA) replication and transcription, the interaction between mtRPOL and coevolved regulatory sites in the mtDNA may be central to mitonuclear integration. Here, we generate interpopulation hybrids between divergent populations of the copepod Tigriopus californicus to obtain lines having different combinations of mtRPOL and mtDNA. Lines were scored for mtDNA copy number and ATP6 (mtDNA) gene expression. We find that there is a genotype-dependent negative association between mitochondrial transcriptional response and mtDNA copy number. We argue that an observed increase in mtDNA copy number and reduced mtDNA transcription in hybrids reflects the regulatory role of mtRPOL; depending on the mitonuclear genotype, hybridization may disrupt the normal balance between transcription and replication of the mitochondrial genome.

Rapid fixation of non-native alleles revealed by genome-wide SNP analysis of hybrid tiger salamanders

Background

Hybrid zones represent valuable opportunities to observe evolution in systems that are unusually dynamic and where the potential for the origin of novelty and rapid adaptation co-occur with the potential for dysfunction. Recently initiated hybrid zones are particularly exciting evolutionary experiments because ongoing natural selection on novel genetic combinations can be studied in ecological time. Moreover, when hybrid zones involve native and introduced species, complex genetic patterns present important challenges for conservation policy. To assess variation of admixture dynamics, we scored a large panel of markers in five wild hybrid populations formed when Barred Tiger Salamanders were introduced into the range of California Tiger Salamanders.

Results

At three of 64 markers, introduced alleles have largely displaced native alleles within the hybrid populations. Another marker (GNAT1) showed consistent heterozygote deficits in the wild, and this marker was associated with embryonic mortality in laboratory F2's. Other deviations from equilibrium expectations were idiosyncratic among breeding ponds, consistent with highly stochastic demographic effects.

Conclusion

While most markers retain native and introduced alleles in expected proportions, strong selection appears to be eliminating native alleles at a smaller set of loci. Such rapid fixation of alleles is detectable only in recently formed hybrid zones, though it might be representative of dynamics that frequently occur in nature. These results underscore the variable and mosaic nature of hybrid genomes and illustrate the potency of recombination and selection in promoting variable, and often unpredictable genetic outcomes. Introgression of a few, strongly selected introduced alleles should not necessarily affect the conservation status of California Tiger Salamanders, but suggests that genetically pure populations of this endangered species will be difficult to maintain.

Investigations of fine-scale phylogeography in Tigriopus californicus reveal historical patterns of population divergence

Background

The intertidal copepod Tigriopus californicus is a model for studying the process of genetic divergence in allopatry and for probing the nature of genetic changes that lead to reproductive isolation. Although previous studies have revealed a pattern of remarkably high levels of genetic divergence between the populations of this species at several spatial scales, it is not clear what types of historical processes are responsible. Particularly lacking are data that can yield insights into population history from the finest scales of geographic resolution.

Results

Sequence variation in both cytochrome b (CYTB, mtDNA) and the rieske iron-sulfur protein (RISP, nuclear) are examined at a fine scale within four different regions for populations of T. californicus. High levels of genetic divergence are seen for both genes at the broader scale, and genetic subdivision is apparent at nearly all scales in these populations for these two genes. Patterns of polymorphism and divergence in both CYTB and RISP suggest that selection may be leading to non-neutral evolution of these genes in several cases but a pervasive pattern of neither selection nor coadaptation is seen for these markers.

Conclusion

The use of sequence data at a fine-scale of resolution in this species has provided novel insights into the processes that have resulted in the accumulation of genetic divergence among populations. This divergence is likely to result from an interplay between a limited dispersal ability for this copepod and the temporal instability of copepod habitat. Both shorter-term processes such as the extinction/recolonization dynamics of copepod pools and longer-term processes such as geological uplift of coastline and sea level changes appear to have impacted the patterns of differentiation. Some patterns of sequence variation are consistent with selection acting upon the loci used in this study; however, it appears that most phylogeographic patterns are the result of history and not selection on these genes in this species.

Influence of environment and mitochondrial heritage on the ecological characteristics of fish in a hybrid zone

BACKGROUND

Ecological characteristics (growth, morphology, reproduction) arise from the interaction between environmental factors and genetics. Genetic analysis of individuals' life history traits might be used to improve our understanding of mechanisms that form and maintain a hybrid zone.

METHODOLOGY/PRINCIPAL FINDINGS

A fish hybrid zone was used to characterize the process of natural selection. Data were collected during two reproductive periods (2001 and 2002) and 1117 individuals (nase, Chondrostama nasus nasus, sofie C. toxostoma toxostoma and hybrids) were sampled. Reproductive dates of the two parental species overlapped at sympatric sites. The nase had an earlier reproductive period than the sofie; males had longer reproductive periods for both species. Hybridisation between female nase and male sofie was the most likely. Hybrids had a reproductive period similar to the inherited parental mitochondrial type. Growth and reproductive information from different environments has been synthesised following a bayesian approach of the von Bertalanffy model. Hybrid life history traits appear to link with maternal heritage. Hybrid size from the age of two and size at first maturity appeared to be closer to the size of the maternal origin species (nase or sofie). Median growth rates for hybrids were similar and intermediate between those of the parental species. We observed variable life history traits for hybrids and pure forms in the different parts of the hybrid zone. Geometrical analysis of the hybrid fish shape gave evidence of two main morphologies with a link to maternal heritage.

CONCLUSIONS/SIGNIFICANCE

Selective mating seemed to be the underlying process which, with mitochondrial heritage, could explain the evolution of the studied hybrid zone. More generally, we showed the importance of studies on hybrid zones and specifically the study of individuals' ecological characteristics, to improve our understanding of speciation.

Genotype-dependent variation of mitochondrial transcriptional profiles in interpopulation hybrids

Hybridization between populations can disrupt gene expression, frequently resulting in deleterious hybrid phenotypes. Reduced fitness in interpopulation hybrids of the marine copepod Tigriopus californicus has been traced to interactions between the nuclear and mitochondrial genomes. Here, we determine transcript levels of four to six genes involved in the mitochondrial oxidative phosphorylation pathway for a series of parental and inbred hybrid lines using RT-qPCR. Both nuclear and mitochondrial-encoded genes are included in the analysis. Although all genes studied are up-regulated under salinity stress, only expression of genes located on the mtDNA differed among lines. Because mitochondrial genes are transcribed by a dedicated RNA polymerase encoded in the nuclear genome, we compare transcript levels among hybrid lines with different combinations of mitochondrial RNA polymerase and mtDNA genotypes. Lines bearing certain mtDNA-mitochondrial RNA polymerase genotypic combinations show a diminished capacity to up-regulate mitochondrial genes in response to hypoosmotic stress. Effects on the transcriptional profile depend on the specific interpopulation cross and are correlated with viability effects. We hypothesize that disruption of the mitochondrial transcriptional system in F(2) hybrids may play a central role in hybrid breakdown.

Cytonuclear genic incompatibilities cause increased mortality in male F2 hybrids of Nasonia giraulti and N. vitripennis

The haplodiploid wasp genus Nasonia is a promising model for studying the evolution of genic incompatibilities due to the existence of interfertile species and haploid males. The latter allows for significantly reducing the sample size required to detect and map recessive dysfunctional genic interactions. We exploited these features to study the genetics of intrinsic hybrid inviability in male F2 hybrids of Nasonia giraulti and N. vitripennis. Analyzing marker segregation in 225 hybrid embryos, we inferred a linkage map with 38 framework markers. The markers were tested for marker transmission ratio distortion (MTRD) and interchromosomal linkage disequilibrium in populations of embryonic and adult hybrids. We found evidence for four transmission ratio distorting loci (TRDL). Three TRDL showed a deficit of the N. giraulti allele in hybrids with N. vitripennis cytoplasm. A separate TRDL exhibited a deficiency of the N. vitripennis allele in hybrids with N. giraulti cytoplasm. We ascribe the observed MTRD in adult hybrids to cytonuclear genic incompatibilities causing differential mortality during development since hybrid embryos did not show MTRD. The identified cytonuclear genic incompatibilities in F2 hybrids with N. vitripennis cytoplasm account for most of the intrinsic hybrid inviability in this cross. The high mortality rate in F2 hybrids with N. giraulti cytoplasm cannot be explained by the single identified TRDL alone, however.

Synergistic fitness interactions and a high frequency of beneficial changes among mutations accumulated under relaxed selection in Saccharomyces cerevisiae

Spontaneous mutations were accumulated for approximately 4800 generations in 48 lines of yeast protected from effective selection by frequent passage through single-cell bottlenecks. Changes in fitness were evaluated by direct competition with matched parental stocks differing only at a selectively neutral marker locus. Average fitness declined by approximately 5% over the course of the experiment. The rate of change increased sharply in later generations, strongly suggesting synergistic epistasis. Divergence among lines increased rapidly relative to the change in average fitness and also at an accelerating pace. Both results are well matched by a model assuming that fitness cost increases exponentially (approximately second order) with the number of accumulated mutations. This result is consistent with fitness loss due primarily to interactions between specific pairs of gene products. I also estimate that approximately 25% of the mutations with detectable fitness effects were beneficial. This result can be explained by the fact that the effects of most mutations are small relative to the distance from a local fitness optimum.

Interpopulation hybrid breakdown maps to the mitochondrial genome

Hybrid breakdown, or outbreeding depression, is the loss of fitness observed in crosses between genetically divergent populations. The role of maternally inherited mitochondrial genomes in hybrid breakdown has not been widely examined. Using laboratory crosses of the marine copepod Tigriopus californicus, we report that the low fitness of F(3) hybrids is completely restored in the offspring of maternal backcrosses, where parental mitochondrial and nuclear genomic combinations are reassembled. Paternal backcrosses, which result in mismatched mitochondrial and nuclear genomes, fail to restore hybrid fitness. These results suggest that fitness loss in T. californicus hybrids is completely attributable to nuclear-mitochondrial genomic interactions. Analyses of ATP synthetic capacity in isolated mitochondria from hybrid and backcross animals found that reduced ATP synthesis in hybrids was also largely restored in backcrosses, again with maternal backcrosses outperforming paternal backcrosses. The strong fitness consequences of nuclear-mitochondrial interactions have important, and often overlooked, implications for evolutionary and conservation biology.

Three divergent mitochondrial genomes from California populations of the copepod Tigriopus californicus

Previous work on the harpacticoid copepod Tigriopus californicus has focused on the extensive population differentiation in three mtDNA protein coding genes (COXI, COXII, Cytb). In order to get a more complete understanding of mtDNA evolution in this species, we sequenced three complete mitochondrial genomes (one from each of three California populations) and compared them to two published mtDNA genomes from an Asian congener, Tigriopus japonicus. Several features of the mtDNA genome appear to be conserved within the genus: 1) the unique order of the protein coding genes, rRNA genes and most of the tRNA genes, 2) the genome is compact, varying between 14.3 and 14.6 kb, and 3) all genes are encoded on the same strand of the mtDNA. Within T. californicus, extremely high levels of nucleotide divergence (>20%) are observed across much of the mitochondrial genome. Inferred amino acid sequences of the proteins encoded in the mtDNAs also show high levels of divergence; at the extreme, the three ND3 variants in T. californicus showed >25% amino acid substitutions, compared with <3% amino acid divergence at the previously studied COXI locus. Unusual secondary structures make functional assignments of some tRNAs difficult. The only apparent tRNA(trp) in these genomes completely overlaps the 5' end of the 16S rRNA in all three T. californicus mtDNAs. Although not previously noted, this feature is also conserved in T. japonicus mtDNAs; whether this sequence is processed into a functional tRNA has not been determined. The putative control region contains a duplicated segment of different length (from 88 to 155 bp) in each of the T. californicus sequences. In each case, the duplicated segments are not tandem repeats; despite their different lengths, the distance between the start of the first and the start of the second repeat is conserved (520 bp). The functional significance, if any, of this repeat structure remains unknown.

A linkage map reveals a complex basis for segregation distortion in an interpopulation cross in the moss Ceratodon purpureus

We report the construction of a linkage map for the moss Ceratodon purpureus (n = 13), based on a cross between geographically distant populations, and provide the first experimental confirmation of maternal chloroplast inheritance in bryophytes. From a mapping population of 288 recombinant haploid gametophytes, genotyped at 121 polymorphic AFLP loci, three gene-based nuclear loci, one chloroplast marker, and sex, we resolved 15 linkage groups resulting in a map length of approximately 730 cM. We estimate that the map covers more than three-quarters of the C. purpureus genome. Approximately 35% of the loci were sex linked, not including those in recombining pseudoautosomal regions. Nearly 45% of the loci exhibited significant segregation distortion (alpha = 0.05). Several pairs of unlinked distorted loci showed significant deviations from multiplicative genotypic frequencies, suggesting that distortion arises from genetic interactions among loci. The distorted autosomal loci all exhibited an excess of the maternal allele, suggesting that these interactions may involve nuclear-cytoplasmic factors. The sex ratio of the progeny was significantly male biased, and the pattern of nonrandom associations among loci indicates that this results from interactions between the sex chromosomes. These results suggest that even in interpopulation crosses, multiple mechanisms act to influence segregation ratios.

The copepod Tigriopus: a promising marine model organism for ecotoxicology and environmental genomics

There is an increasing body of evidence to support the significant role of invertebrates in assessing impacts of environmental contaminants on marine ecosystems. Therefore, in recent years massive efforts have been directed to identify viable and ecologically relevant invertebrate toxicity testing models. Tigriopus, a harpacticoid copepod has a number of promising characteristics which make it a candidate worth consideration in such efforts. Tigriopus and other copepods are widely distributed and ecologically important organisms. Their position in marine food chains is very prominent, especially with regard to the transfer of energy. Copepods also play an important role in the transportation of aquatic pollutants across the food chains. In recent years there has been a phenomenal increase in the knowledge base of Tigriopus spp., particularly in the areas of their ecology, geophylogeny, genomics and their behavioural, biochemical and molecular responses following exposure to environmental stressors and chemicals. Sequences of a number of important marker genes have been studied in various Tigriopus spp., notably T. californicus and T. japonicus. These genes belong to normal biophysiological functions (e.g. electron transport system enzymes) as well as stress and toxic chemical exposure responses (heat shock protein 20, glutathione reductase, glutathione S-transferase). Recently, 40,740 expressed sequenced tags (ESTs) from T. japonicus, have been sequenced and of them, 5,673 ESTs showed significant hits (E-value, >1.0E-05) to the red flour beetle Tribolium genome database. Metals and organic pollutants such as antifouling agents, pesticides, polycyclic aromatic hydrocarbons (PAH) and polychrlorinated biphenyls (PCB) have shown reproducible biological responses when tested in Tigriopus spp. Promising results have been obtained when Tigriopus was used for assessment of risk associated with exposure to endocrine-disrupting chemicals (EDCs). Application of environmental gene expression techniques has allowed evaluation of transcriptional changes in T. japonicus with the ultimate aim of understanding the mechanisms of action of environmental stressors. Through a better understanding of toxicological mechanisms, ecotoxicologists may use this ecologically relevant species in risk assessment studies in marine systems. The combination of uses as a whole-animal bioassay and gene expression studies indicate that Tigriopus may serve as an excellent tool to evaluate the impacts of marine pollution throughout the coastal region. The purpose of this review is to illustrate the potential of using Tigriopus to fulfill the niche as an important invertebrate marine model organism for ecotoxicology and environmental genomics. In addition, the knowledge gaps and areas for further studies have also been discussed.

Novelties in hybrid zones: crossroads between population genomic and ecological approaches

BACKGROUND

Interspecific hybridization is widespread, occurring in a taxonomically diverse array of species. The Cyprinidae family, which displays more than 30% hybridization, is a good candidate for studies of processes underlying isolation and speciation, such as genetic exchange between previously isolated lineages. This is particularly relevant in the case of recent hybridization between an invasive species, Chondrostoma nasus nasus (from Eastern Europe), and C. toxostoma toxostoma (a threatened species endemic to southern France), in which bidirectional introgressive hybridization has been demonstrated.

METHODOLOGY/PRINCIPAL FINDINGS

We studied 128 specimens from reference populations and 1495 hybrid zone specimens (two years of sampling and four stations), using five molecular markers (one mitochondrial gene, four nuclear introns), morphology (meristic and plastic characters) and life history traits (weight, size, coefficient of condition, sex, age, shoaling). We identified 65 hybrid combinations and visualized spatial and temporal changes in composition. The direction of mitochondrial introgression was density-dependent in favor of the rarer species and we demonstrate that the sexual selection hypothesis is a preponderant explanation in the asymmetry of introgression. Despite genomic evolution in the hybrid zone, convergence was observed for body shape and coefficient of condition, indicating changes in foraging behavior with respect to reference populations, reflecting strong environmental pressure.

CONCLUSIONS/SIGNIFICANCE

The complex rules of hybrid zone dynamics are established very early in the contact zone. We propose "inheritance from the rare species" as a new evolutionary hypothesis for animal models. The endemic species was not assimilated by the invasive species. Survival rates for this species were highest in the middle of the river (the warmest part) due to a trade-off between food availability and fecundity. The environment-independent hybrid combination may result from nuclear-mitochondrial interactions involving the Tpi1b gene or a gene linked to this gene (Chromosome 16). This genomic region is also responsible for shoaling behavior in Danio rerio and is a promising zone for studies of changes in population dynamics and advances in integrated studies of hybrid zones.

Speciation genetics: evolving approaches

Much progress has been made in the past two decades in understanding Darwin's mystery of the origins of species. Applying genomic techniques to the analysis of laboratory crosses and natural populations has helped to determine the genetic basis of barriers to gene flow which create new species. Although new methodologies have not changed the prevailing hypotheses about how species form, they have accelerated the pace of data collection. By facilitating the compilation of case studies, advances in genetic techniques will help to provide answers to the next generation of questions concerning the relative frequency and importance of different processes that cause speciation.