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

Disproportionate role of nuclear-encoded proteins in organismal and mitochondrial thermal performance in a copepod

Determining the mechanisms by which organisms evolve thermal tolerance is crucial to predicting how populations may respond to changes in local temperature regimes. Although evidence of relationships between mitochondrial background and thermal adaptation have been found, the presence of both nuclear-encoded and mitochondrial DNA (mtDNA)-encoded proteins warrants experiments aimed at parsing out the relative role of each genome in thermal adaptation. We investigated the relative role of mtDNA-encoded products in thermal tolerance between two divergent populations of Tigriopus californicus using first-generation (F1) hybrids that vary in maternally inherited mtDNA but are heterozygous for population-specific alleles across nuclear loci. We tested two measures of thermal tolerance, (1) survivorship to acute thermal stress and (2) thermal stability of mitochondrial performance in Complex I-fueled ATP synthesis, both across a range of increasing temperatures. We found that the southern population (San Diego, CA, USA) outperformed the northern population (Strawberry Hill, OR, USA) in survivorship, and that both reciprocal F1 hybrid crosses had intermediate survival. Mitochondria from the San Diego population displayed greater stability in ATP synthesis with increasing temperatures compared with those from Strawberry Hill. Interestingly, hybrids from both cross directions had synthesis profiles that were very similar to that of Strawberry Hill. Taken together, these results suggest that the relative role of the mtDNA in these phenotypes is negligible compared with that of elements encoded by nuclear DNA in this system.

Genetic incompatibilities in reciprocal hybrids between populations of Tigriopus californicus with low to moderate mitochondrial sequence divergence

All mitochondrial-encoded proteins and RNAs function through interactions with nuclear-encoded proteins, which are critical for mitochondrial performance and eukaryotic fitness. Coevolution maintains inter-genomic (i.e., mitonuclear) compatibility within a taxon, but hybridization can disrupt coevolved interactions, resulting in hybrid breakdown. Thus, mitonuclear incompatibilities may be important mechanisms underlying reproductive isolation and, potentially, speciation. Here we utilize Pool-seq to assess the effects of mitochondrial genotype on nuclear allele frequencies in fast- and slow-developing reciprocal inter-population F2 hybrids between relatively low-divergence populations of the intertidal copepod Tigriopus californicus. We show that mitonuclear interactions lead to elevated frequencies of coevolved (i.e., maternal) nuclear alleles on two chromosomes in crosses between populations with 1.5% or 9.6% fixed differences in mitochondrial DNA nucleotide sequence. However, we also find evidence of excess mismatched (i.e., noncoevolved) alleles on three or four chromosomes per cross, respectively, and of allele frequency differences consistent with effects involving only nuclear loci (i.e., unaffected by mitochondrial genotype). Thus, our results for low-divergence crosses suggest an underlying role for mitonuclear interactions in variation in hybrid developmental rate, but despite substantial effects of mitonuclear coevolution on individual chromosomes, no clear bias favoring coevolved interactions overall.

Frequent Paternal Mitochondrial Inheritance and Rapid Haplotype Frequency Shifts in Copepod Hybrids

Mitochondria are assumed to be maternally inherited in most animal species, and this foundational concept has fostered advances in phylogenetics, conservation, and population genetics. Like other animals, mitochondria were thought to be solely maternally inherited in the marine copepod Tigriopus californicus, which has served as a useful model for studying mitonuclear interactions, hybrid breakdown, and environmental tolerance. However, we present PCR, Sanger sequencing, and Illumina Nextera sequencing evidence that extensive paternal mitochondrial DNA (mtDNA) transmission is occurring in inter-population hybrids of T. californicus. PCR on four types of crosses between three populations (total sample size of 376 F1 individuals) with 20% genome-wide mitochondrial divergence showed 2% to 59% of F1 hybrids with both paternal and maternal mtDNA, where low and high paternal leakage values were found in different cross directions of the same population pairs. Sequencing methods further verified nucleotide similarities between F1 mtDNA and paternal mtDNA sequences. Interestingly, the paternal mtDNA in F1s from some crosses inherited haplotypes that were uncommon in the paternal population. Compared to some previous research on paternal leakage, we employed more rigorous methods to rule out contamination and false detection of paternal mtDNA due to non-functional nuclear mitochondrial DNA fragments. Our results raise the potential that other animal systems thought to only inherit maternal mitochondria may also have paternal leakage, which would then affect the interpretation of past and future population genetics or phylogenetic studies that rely on mitochondria as uniparental markers.

Multigenerational Life-History Responses to pH in Distinct Populations of the Copepod Tigriopus californicus

Intertidal zones are highly dynamic and harsh habitats: organisms that persist there must face many stressors, including drastic changes in seawater pH, which can be strongly influenced by biological processes. Coastal ecosystems are heterogeneous in space and time, and populations can be exposed to distinct selective pressures and evolve different capacities for acclimation to changes in pH. Tigriopus californicus is a harpacticoid copepod found in high-shore rock pools on the west coast of North America. It is a model system for studying population dynamics in diverse environments, but little is known about its responses to changes in seawater pH. I quantified the effects of pH on the survivorship, fecundity, and development of four T. californicus populations from San Juan Island, Washington, across three generations. For all populations and generations, copepod cultures had lower survivorship and delayed development under extended exposure to higher pH treatments (pH 7.5 and pH 8.0), whereas cultures maintained in lower pH (7.0) displayed stable population growth over time. Reciprocal transplants between treatments demonstrated that these pH effects were reversible. Life histories were distinct between populations, and there were differences in the magnitudes of pH effects on development and culture growth that persisted through multiple generations. These results suggest that T. californicus might not have the generalist physiology that might be expected of an intertidal species, and it could be adapted to lower average pH conditions than those that occur in adjacent open waters.

The role of mitonuclear incompatibilities in allopatric speciation

Aerobic metabolism in eukaryotic cells requires extensive interactions between products of the nuclear and mitochondrial genomes. Rapid evolution of the mitochondrial genome, including fixation of both adaptive and deleterious mutations, creates intrinsic selection pressures favoring nuclear gene mutations that maintain mitochondrial function. As this process occurs independently in allopatry, the resulting divergence between conspecific populations can subsequently be manifest in mitonuclear incompatibilities in inter-population hybrids. Such incompatibilities, mitonuclear versions of Bateson-Dobzhansky-Muller incompatibilities that form the standard model for allopatric speciation, can potentially restrict gene flow between populations, ultimately resulting in varying degrees of reproductive isolation. The potential role of mitonuclear incompatibilities in speciation is further enhanced where mtDNA substitution rates are elevated compared to the nuclear genome and where population structure maintains allopatry for adequate time to evolve multiple mitonuclear incompatibilities. However, the fact that mitochondrial introgression occurs across species boundaries has raised questions regarding the efficacy of mitonuclear incompatibilities in reducing gene flow. Several scenarios now appear to satisfactorily explain this phenomenon, including cases where differences in mtDNA genetic load may drive introgression or where co-introgression of coadapted nuclear genes may support the function of introgressed mtDNA. Although asymmetries in reproductive isolation between taxa are consistent with mitonuclear incompatibilities, interactions between autosomes and sex chromosomes yield similar predictions that are difficult to disentangle. With regard to establishing reproductive isolation while in allopatry, existing studies clearly suggest that mitonuclear incompatibilities can contribute to the evolution of barriers to gene flow. However, there is to date relatively little definitive evidence supporting a primary role for mitonuclear incompatibilities in the speciation process.

Pervasive Mitonuclear Coadaptation Underlies Fast Development in Interpopulation Hybrids of a Marine Crustacean

Cellular energy production requires coordinated interactions between genetic components from the nuclear and mitochondrial genomes. This coordination results in coadaptation of interacting elements within populations. Interbreeding between divergent gene pools can disrupt coadapted loci and result in hybrid fitness breakdown. While specific incompatible loci have been detected in multiple eukaryotic taxa, the extent of the nuclear genome that is influenced by mitonuclear coadaptation is not clear in any species. Here, we used F₂ hybrids between two divergent populations of the copepod Tigriopus californicus to examine mitonuclear coadaptation across the nuclear genome. Using developmental rate as a measure of fitness, we found that fast-developing copepods had higher ATP synthesis capacity than slow developers, suggesting variation in developmental rates is at least partly associated with mitochondrial dysfunction. Using Pool-seq, we detected strong biases for maternal alleles across 7 (of 12) chromosomes in both reciprocal crosses in high-fitness hybrids, whereas low-fitness hybrids showed shifts toward the paternal population. Comparison with previous results on a different hybrid cross revealed largely different patterns of strong mitonuclear coadaptation associated with developmental rate. Our findings suggest that functional coadaptation between interacting nuclear and mitochondrial components is reflected in strong polygenic effects on this life-history phenotype, and reveal that molecular coadaptation follows independent evolutionary trajectories among isolated populations.

Tolerance Patterns and Transcriptomic Response to Extreme and Fluctuating Salinities across Populations of the Intertidal Copepod Tigriopus californicus

AbstractPopulations that tolerate extreme environmental conditions with frequent fluctuations can give valuable insights into physiological limits and adaptation. In some estuarine and marine ecosystems, organisms must adapt to extreme and fluctuating salinities, but not much is known about how varying salinities impact local adaptation across a wide geographic range. We used eight geographically and genetically divergent populations of the intertidal copepod Tigriopus californicus to test whether northern populations have greater tolerance to low salinity stresses, as they experience greater precipitation and less evaporation. We used a common-garden experiment approach and exposed all populations to acute low (1 and 3 ppt) and high (110 and 130 ppt) salinities for 24 h and to a fluctuation between baseline salinity and moderate low (7 ppt) and high (80 ppt) salinities for over 49 h. We also performed RNA sequencing at several time points during the fluctuation between baseline and salinity of 7 ppt to understand the molecular basis of divergence between two populations with differing physiological responses. We present these novel findings: (1) acute low salinity conditions caused more deaths than high salinity; (2) molecular processes that elevate proline levels increased in salinity of 7 ppt, which contrasts with other physiological studies in T. californicus that mainly associated accumulation of proline with hyperosmotic stress; and (3) tolerance to a salinity fluctuation did not follow a latitudinal trend but was instead governed by a complex interplay of factors, including population and duration of salinity stress. This highlights the importance of including a wider variety of environmental conditions in empirical studies to understand local adaptation.

Allele-Specific Expression and Evolution of Gene Regulation Underlying Acute Heat Stress Response and Local Adaptation in the Copepod Tigriopus californicus

Geographic variation in environmental temperature can select for local adaptation among conspecific populations. Divergence in gene expression across the transcriptome is a key mechanism for evolution of local thermal adaptation in many systems, yet the genetic mechanisms underlying this regulatory evolution remain poorly understood. Here we examine gene expression in 2 locally adapted Tigriopus californicus populations (heat tolerant San Diego, SD, and less tolerant Santa Cruz, SC) and their F1 hybrids during acute heat stress response. Allele-specific expression (ASE) in F1 hybrids was used to determine cis-regulatory divergence. We found that the number of genes showing significant allelic imbalance increased under heat stress compared to unstressed controls. This suggests that there is significant population divergence in cis-regulatory elements underlying heat stress response. Specifically, the number of genes showing an excess of transcripts from the more thermal tolerant (SD) population increased with heat stress while that number of genes with an SC excess was similar in both treatments. Inheritance patterns of gene expression also revealed that genes displaying SD-dominant expression phenotypes increase in number in response to heat stress; that is, across loci, gene expression in F1's following heat stress showed more similarity to SD than SC, a pattern that was absent in the control treatment. The observed patterns of ASE and inheritance of gene expression provide insight into the complex processes underlying local adaptation and thermal stress response.

Phylogeography and genetic diversity of the copepod family Cyclopidae (Crustacea: Cyclopoida) from freshwater ecosystems of Southeast Nigeria

Background

Copepods are key components of aquatic ecosystems and can help regulate the global carbon cycle. Much attention has been paid to the species diversity of copepods worldwide, but the phylogeography and genetic diversity of copepods in Nigeria is unexplored.

Results

Using a mitochondrial cytochrome c oxidase subunit I marker, we preformed phylogenetic and phylogeographic analyses for Cyclopidae copepods in Southeast Nigeria. A high species diversity of Cyclopidae in Nigeria: 5 species of Tropocyclops, 5 species of Mesocyclops and 2 species of Thermocyclops from Cyclopidae were identified in 15 populations. Moreover, we detected 18 unique haplotypes, which fell into two distinct clades. Pairwise genetic distances (uncorrected p-distances) among the species of Cyclopidae ranged from 0.05 to 0.257. Several species co-existed in the same lake, and some haplotypes were shared among different geographic populations, suggesting a dispersal of Cyclopidae in our sampling region. Finally, we found that the population genetic diversity for each species of Cyclopidae was low in Nigeria.

Conclusions

Our findings explored the species diversity and distribution of copepods within the family Cyclopidae for 15 Nigerian freshwater ecosystems: a high species diversity of Cyclopidae copepods was detected over a small geographic sampling range. Results from this study contribute to a better understanding of copepod diversity of Nigerian freshwater ecosystems.

Variation in Thermal Tolerance and Its Relationship to Mitochondrial Function Across Populations of Tigriopus californicus

Variation in thermal tolerance plays a key role in determining the biogeographic distribution of organisms. Consequently, identifying the mechanistic basis for thermal tolerance is necessary for understanding not only current species range limits but also the capacity for range limits to shift in response to climate change. Although variation in mitochondrial function likely contributes to variation in thermal tolerance, the extent to which mitochondrial function underlies local thermal adaptation is not fully understood. In the current study, we examine variation in thermal tolerance and mitochondrial function among three populations of the intertidal copepod Tigriopus californicus found across a latitudinal thermal gradient along the coast of California, USA. We tested (1) acute thermal tolerance using survivorship and knockdown assays, (2) chronic thermal tolerance using survivorship of nauplii and developmental rate, and (3) mitochondrial performance at a range of temperatures using ATP synthesis fueled by complexes I, II, and I&II, as well as respiration of permeabilized fibers. We find evidence for latitudinal thermal adaptation: the southernmost San Diego population outperforms the northernmost Santa Cruz in measures of survivorship, knockdown temperature, and ATP synthesis rates during acute thermal exposures. However, under a chronic thermal regime, survivorship and developmental rate are more similar in the southernmost and northernmost population than in the mid-range population (Abalone Cove). Though this pattern is unexpected, it aligns well with population-specific rates of ATP synthesis at these chronic temperatures. Combined with the tight correlation of ATP synthesis decline and knockdown temperature, these data suggest a role for mitochondria in setting thermal range limits and indicate that divergence in mitochondrial function is likely a component of adaptation across latitudinal thermal gradients.

Phenotypic and transcriptomic responses to salinity stress across genetically and geographically divergent Tigriopus californicus populations

Species inhabiting the North American west coast intertidal must tolerate an extremely variable environment, with large fluctuations in both temperature and salinity. Uncovering the mechanisms for this tolerance is key to understanding species' persistence. We tested for differences in salinity tolerance between populations of Tigriopus californicus copepods from locations in northern (Bodega Reserve) and southern (San Diego) California known to differ in temperature, precipitation and humidity. We also tested for differences between populations in their transcriptomic responses to salinity. Although these two populations have ~20% mtDNA sequence divergence and differ strongly in other phenotypic traits, we observed similarities in their phenotypic and transcriptomic responses to low and high salinity stress. Salinity significantly affected respiration rate (increased under low salinity and reduced under high salinity), but we found no significant effect of population on respiration or a population by salinity interaction. Under high salinity, there was no population difference in knock-down response, but northern copepods had a smaller knock-down under low salinity stress, corroborating previous results for T. californicus. Northern and southern populations had a similar transcriptomic response to salinity based on a principle components analysis, although differential gene expression under high salinity stress was three times lower in the northern population compared to the southern population. Transcripts differentially regulated under salinity stress were enriched for "amino acid transport" and "ion transport" annotation categories, supporting previous work demonstrating that the accumulation of free amino acids is important for osmotic regulation in T. californicus.

Short-range phenotypic divergence among genetically distinct parapatric populations of an Australian funnel-web spider

Speciation involves divergence at genetic and phenotypic levels. Where substantial genetic differentiation exists among populations, examining variation in multiple phenotypic characters may elucidate the mechanisms by which divergence and speciation unfold. Previous work on the Australian funnel-web spider Atrax sutherlandi Gray (2010; Records of the Australian Museum62, 285-392; Mygalomorphae: Hexathelidae: Atracinae) has revealed a marked genetic structure along a 110-kilometer transect, with six genetically distinct, parapatric populations attributable to past glacial cycles. In the present study, we explore variation in three classes of phenotypic characters (metabolic rate, water loss, and morphological traits) within the context of this phylogeographic structuring. Variation in metabolic and water loss rates shows no detectable association with genetic structure; the little variation observed in these rates may be due to the spiders' behavioral adaptations (i.e., burrowing), which buffer the effects of climatic gradients across the landscape. However, of 17 morphological traits measured, 10 show significant variation among genetic populations, in a disjunct manner that is clearly not latitudinal. Moreover, patterns of variation observed for morphological traits serving different organismic functions (e.g., prey capture, burrowing, and locomotion) are dissimilar. In contrast, a previous study of an ecologically similar sympatric spider with little genetic structure indicated a strong latitudinal response in 10 traits over the same range. The congruence of morphological variation with deep phylogeographic structure in Tallaganda's A. sutherlandi populations, as well as the inconsistent patterns of variation across separate functional traits, suggest that the spiders are likely in early stages of speciation, with parapatric populations independently responding to local selective forces.

Locally adapted populations of a copepod can evolve different gene expression patterns under the same environmental pressures

As populations diverge in allopatry, but under similar thermal conditions, do similar thermal performance phenotypes evolve by maintaining similar gene expression patterns, or does genetic divergence lead to divergent patterns of gene expression between these populations? We used genetically divergent populations of the copepod Tigriopus californicus, whose performance at different thermal conditions is well characterized, to investigate transcriptome-wide expression responses under two different thermal regimes: (1) a nonvariable temperature regime and (2) a regime with variable temperature. Our results show the expression profiles of the response to these regimes differed substantially among populations, even for populations that are geographically close. This pattern was accentuated when populations were raised in the variable temperature environment. Less heat-tolerant populations mounted strong but divergent responses to the different thermal regimes, with a large heat-shock response observed in one population, and an apparent reduction in the expression of genes involved in basic cellular processes in the other. Our results suggest that as populations diverge in allopatry, they may evolve starkly different responses to changes in temperature, at the gene expression level, while maintaining similar thermal performance phenotypes.

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.

Seasonal and Cyclical Changes in Genetic Composition of the Marine Intertidal Rock Pool Copepod Tigriopus brevicornis

Tigriopus brevicornis is a marine rock pool copepod widely distributed along Atlantic coasts. Due to the absence of a known dispersal mechanism by free swimming stages, exchanges between populations over long distances are questionable. In order to analyse the evolution of an isolated supralittoral rock pool population, sampling of the copepod was performed monthly during 1 year and compared to samplings over 5 years in the same rock pool, as well as from other rock pools. Using ITS1 analysis, cyclical changes in genetic composition were detected. Our results give clear indications concerning the segregation of the rock pool population and a lack of gene flow among outside populations. A network analysis shows the presence of several shared dominant haplotypes and also singletons differing by one mutation point. F(st) analyses indicate that the main changes occur in autumn and winter. The few analogies of ITS1 sequences with nearby populations may indicate that new migrants must re-colonise the pools from surrounding rock crevices in the intertidal habitat where they may have found a refuge after bad weather conditions.

Phylogenetic information content of Copepoda ribosomal DNA repeat units: ITS1 and ITS2 impact

The utility of various regions of the ribosomal repeat unit for phylogenetic analysis was examined in 16 species representing four families, nine genera, and two orders of the subclass Copepoda (Crustacea). Fragments approximately 2000 bp in length containing the ribosomal DNA (rDNA) 18S and 28S gene fragments, the 5.8S gene, and the internal transcribed spacer regions I and II (ITS1 and ITS2) were amplified and analyzed. The DAMBE (Data Analysis in Molecular Biology and Evolution) software was used to analyze the saturation of nucleotide substitutions; this test revealed the suitability of both the 28S gene fragment and the ITS1/ITS2 rDNA regions for the reconstruction of phylogenetic trees. Distance (minimum evolution) and probabilistic (maximum likelihood, Bayesian) analyses of the data revealed that the 28S rDNA and the ITS1 and ITS2 regions are informative markers for inferring phylogenetic relationships among families of copepods and within the Cyclopidae family and associated genera. Split-graph analysis of concatenated ITS1/ITS2 rDNA regions of cyclopoid copepods suggested that the Mesocyclops, Thermocyclops, and Macrocyclops genera share complex evolutionary relationships. This study revealed that the ITS1 and ITS2 regions potentially represent different phylogenetic signals.

The necessity of DNA taxonomy to reveal cryptic diversity and spatial distribution of meiofauna, with a focus on Nemertea

Meiofauna represent one of the most abundant and diverse communities in marine benthic ecosystems. However, an accurate assessment of diversity at the level of species has been and remains challenging for these microscopic organisms. Therefore, for many taxa, especially the soft body forms such as nemerteans, which often lack clear diagnostic morphological traits, DNA taxonomy is an effective means to assess species diversity. Morphological taxonomy of Nemertea is well documented as complicated by scarcity of unambiguous character states and compromised by diagnoses of a majority of species (and higher clades) being inadequate or based on ambiguous characters and character states. Therefore, recent studies have advocated for the primacy of molecular tools to solve the taxonomy of this group. DNA taxonomy uncovers possible hidden cryptic species, provides a coherent means to systematize taxa in definite clades, and also reveals possible biogeographic patterns. Here, we analyze diversity of nemertean species by considering the barcode region of the mitochondrial gene Cytochrome Oxidase subunit I (COI) and different species delineation approaches in order to infer evolutionarily significant units. In the aim to uncover actual diversity of meiofaunal nemerteans across different sites in Central America, COI sequences were obtained for specimens assigned here to the genera Cephalothrix, Ototyphlonemertes, and Tetrastemma-like worms, each commonly encountered in our sampling. Additional genetic, taxonomic, and geographic data of other specimens belonging to these genera were added from GenBank. Results are consistent across different DNA taxonomy approaches, and revealed (i) the presence of several hidden cryptic species and (ii) numerous potential misidentifications due to traditional taxonomy. (iii) We additionally test a possible biogeographic pattern of taxonomic units revealed by this study, and, except for a few cases, the putative species seem not to be widely distributed, in contrast to what traditional taxonomy would suggest for the recognized morphotypes.

Gene conversion yields novel gene combinations in paralogs of GOT1 in the copepod Tigriopus californicus

Background

Gene conversion of duplicated genes can slow the divergence of paralogous copies over time but can also result in other interesting evolutionary patterns. Islands of genetic divergence that persist in the face of gene conversion can point to gene regions undergoing selection for new functions. Novel combinations of genetic variation that differ greatly from the original sequence can result from the transfer of genetic variation between paralogous genes by rare gene conversion events. Genetically divergent populations of the copepod Tigriopus californicus provide an excellent model to look at the patterns of divergence among paralogs across multiple independent evolutionary lineages.

Results

In this study the evolution of a set of paralogous genes encoding putative aspartate transaminase proteins (called GOT1 here) are examined in populations of the copepod T. californicus. One pair of duplicated genes, GOT1p1 and GOT1p2, has regions of high divergence between the copies in the face of apparent on-going gene conversion. The GOT1p2 gene also has unique haplotypes in two populations that appear to have resulted from a transfer of genetic variation via inter-paralog gene conversion. A second pair of duplicated genes GOT1Sr and GOT1Sd also shows evidence of gene conversion, but this gene conversion does not appear to have maintained each as a functional copy in all populations.

Conclusions

The patterns of conservation and sequence divergence across this set of paralogous genes among populations of T. californicus suggest that some interesting evolutionary patterns are occurring at these loci. The results for the GOT1p1/GOT1p2 paralogs illustrate how gene conversion can factor in the creation of a mosaic pattern of regions of high divergence and low divergence. When coupled with rare gene conversion events of divergent regions, this pattern can result in the formation of novel proteins differing substantially from either original protein. The evolutionary patterns across these paralogs show how gene conversion can both constrain and facilitate diversification of genetic sequences.

Diversifying selection underlies the origin of allozyme polymorphism at the phosphoglucose isomerase locus in Tigriopus californicus

The marine copepod Tigriopus californicus lives in intertidal rock pools along the Pacific coast, where it exhibits strong, temporally stable population genetic structure. Previous allozyme surveys have found high frequency private alleles among neighboring subpopulations, indicating that there is limited genetic exchange between populations. Here we evaluate the factors responsible for the diversification and maintenance of alleles at the phosphoglucose isomerase (Pgi) locus by evaluating patterns of nucleotide variation underlying previously identified allozyme polymorphism. Copepods were sampled from eleven sites throughout California and Baja California, revealing deep genetic structure among populations as well as genetic variability within populations. Evidence of recombination is limited to the sample from Pescadero and there is no support for linkage disequilibrium across the Pgi locus. Neutrality tests and codon-based models of substitution suggest the action of natural selection due to elevated non-synonymous substitutions at a small number of sites in Pgi. Two sites are identified as the charge-changing residues underlying allozyme polymorphisms in T. californicus. A reanalysis of allozyme variation at several focal populations, spanning a period of 26 years and over 200 generations, shows that Pgi alleles are maintained without notable frequency changes. Our data suggest that diversifying selection accounted for the origin of Pgi allozymes, while McDonald-Kreitman tests and the temporal stability of private allozyme alleles suggests that balancing selection may be involved in the maintenance of amino acid polymorphisms within populations.

Fine-scale genetic breaks driven by historical range dynamics and ongoing density-barrier effects in the estuarine seaweed Fucus ceranoides L

BACKGROUND

Factors promoting the emergence of sharp phylogeographic breaks include restricted dispersal, habitat discontinuity, physical barriers, disruptive selection, mating incompatibility, genetic surfing and secondary contact. Disentangling the role of each in any particular system can be difficult, especially when species are evenly distributed across transition zones and dispersal barriers are not evident. The estuarine seaweed Fucus ceranoides provides a good example of highly differentiated populations along its most persistent distributional range at the present rear edge of the species distribution, in NW Iberia. Intrinsic dispersal restrictions are obvious in this species, but have not prevented F. ceranoides from vastly expanding its range northwards following the last glaciation, implying that additional factors are responsible for the lack of connectivity between neighbouring southern populations. In this study we analyze 22 consecutive populations of F. ceranoides along NW Iberia to investigate the processes generating and maintaining the observed high levels of regional genetic divergence.

RESULTS

Variation at seven microsatellite loci and at mtDNA spacer sequences was concordant in revealing that Iberian F. ceranoides is composed of three divergent genetic clusters displaying nearly disjunct geographical distributions. Structure and AFC analyses detected two populations with an admixed nuclear background. Haplotypic diversity was high in the W sector and very low in the N sector. Within each genetic cluster, population structure was also pervasive, although shallower.

CONCLUSIONS

The deep divergence between sectors coupled with the lack of support for a role of oceanographic barriers in defining the location of breaks suggested 1) that the parapatric genetic sectors result from the regional reassembly of formerly vicariant sub-populations, and 2) that the genetic discontinuities at secondary contact zones (and elsewhere) are maintained despite normal migration rates. We conclude that colonization and immigration, as sources of gene-flow, have very different genetic effects. Migration between established populations is effectively too low to prevent their differentiation by drift or to smooth historical differences inherited from the colonization process. F. ceranoides, but possibly low-dispersal species in general, appear to be unified to a large extent by historical, non-equilibrium processes of extinction and colonization, rather than by contemporary patterns of gene flow.

Spatially structured populations with a low level of cryptic diversity in European marine Gastrotricha

Species of the marine meiofauna such as Gastrotricha are known to lack dispersal stages and are thus assumed to have low dispersal ability and low levels of gene flow between populations. Yet, most species are widely distributed, and this creates a paradox. To shed light on this apparent paradox, we test (i) whether such wide distribution may be due to misidentification and lumping of cryptic species with restricted distributions and (ii) whether spatial structures exist for the phylogeography of gastrotrichs. As a model, we used the genus Turbanella in NW Europe. DNA taxonomy using a mitochondrial and a nuclear marker supports distinctness of four traditional species (Turbanella ambronensis, T. bocqueti, T. mustela and T. cornuta) and provides evidence for two cryptic species within T. hyalina. An effect of geography on the within-species genetic structure is indeed present, with the potential for understanding colonization processes and for performing phylogeographic inference from microscopic animals. On the other hand, the occurrence of widely distributed haplotypes indicates long-distance dispersal as well, despite the assumed low dispersal ability of gastrotrichs.

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.

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.

Early life benefits and later life costs of a two amino acid deletion in Drosophila simulans

Linking naturally occurring genotypic variation to the organismal phenotype is critical to our understanding of, and ability to, model biological processes such as adaptation to novel environments, disease, and aging. Rarely, however, does a simple mutation cause a single simple observable trait. Rather it is more common for a mutation to elicit an entangled web of responses. Here, we employ biochemistry as the thread to link a naturally occurring two amino acid deletion in a nuclear encoded mitochondrial protein with physiological benefits and costs in the fly Drosophila simulans. This nuclear encoded gene produces a protein that is imported into the mitochondrion and forms a subunit of complex IV (cytochrome c oxidase, or cox) of the electron transport chain. We observe that flies homozygous for the deletion have an advantage when young but pay a cost later in life. These data show that the organism responds to the deletion in a complex manner that gives insight into the mechanisms that influence mitochondrial bioenergetics and aspects of organismal physiology.

Interpopulation patterns of divergence and selection across the transcriptome of the copepod Tigriopus californicus

The accumulation of genetic incompatibilities between isolated populations is thought to lead to the evolution of intrinsic postzygotic isolation. The molecular basis for these mechanisms, however, remains poorly understood. The intertidal copepod Tigriopus californicus provides unique opportunities for addressing mechanistic questions regarding the early stages of speciation; hybrids between highly divergent populations are fertile and viable, but exhibit reduced fitness at the F(2) or later generations. Given the current scarcity of genomic information in taxa at incipient stages of reproductive isolation, we utilize high-throughout 454 pyrosequencing to characterize a substantial fraction of protein-coding regions (the transcriptome) of T. californicus. Our sequencing effort was divided equally between two divergent populations in order to estimate levels of divergence and to reveal patterns of selection across the transcriptome. Assembly of sequences generated over 40,000 putatively unique transcripts (unigenes) for each population, 19,622 of which were orthologous between populations. BLAST searches of public databases determined protein identity and functional features for 15,402 and 12,670 unigenes, respectively. Based on rates of nonsynonymous and synonymous substitutions in 5897 interpopulation orthologs (those >150 bp and with at least 2X coverage), we identified 229 potential targets of positive selection. Many of these genes are predicted to be involved in several metabolic processes, and to function in hydrolase, peptidase and binding activities. The library of T. californicus coding regions, annotated with their predicted functions and level of divergence, will serve as an invaluable resource for elucidating molecular mechanisms underlying the early stages of speciation.

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.

Phylogeography of supralittoral rocky intertidal Ligia isopods in the pacific region from central California to central Mexico

Background

Ligia isopods are widely distributed in the Pacific rocky intertidal shores from central California to central Mexico, including the Gulf of California. Yet, their biological characteristics restrict them to complete their life cycles in a very narrow range of the rocky intertidal supralittoral. Herein, we examine phylogeographic patterns of Ligia isopods from 122 localities between central California and central Mexico. We expect to find high levels of allopatric diversity. In addition, we expect the phylogeographic patterns to show signatures of past vicariant events that occurred in this geologically dynamic region.

Methodology/Principal Findings

We sequenced two mitochondrial genes (Cytochrome Oxidase I and 16S ribosomal DNA). We conducted Maximum Likelihood and Bayesian phylogenetic analyses. We found many divergent clades that, in general, group according to geography. Some of the most striking features of the Ligia phylogeographic pattern include: (1) deep mid-peninsular phylogeographic breaks on the Pacific and Gulf sides of Baja peninsula; (2) within the Gulf lineages, the northern peninsula is most closely related to the northern mainland, while the southern peninsula is most closely related to the central-southern mainland; and, (3) the southernmost portion of the peninsula (Cape Region) is most closely related to the southernmost portion of mainland.

Conclusions/Significance

Our results shed light on the phylogenetic relationships of Ligia populations in the study area. This study probably represents the finest-scale phylogeographic examination for any organism to date in this region. Presence of highly divergent lineages suggests multiple Ligia species exist in this region. The phylogeographic patterns of Ligia in the Gulf of California and Baja peninsula are incongruent with a widely accepted vicariant scenario among phylogeographers, but consistent with aspects of alternative geological hypotheses and phylo- and biogeographic patterns of several other taxa. Our findings contribute to the ongoing debate regarding the geological origin of this important biogeographic region.

Sharp phylogeographic breaks and patterns of genealogical concordance in the brine shrimp Artemia franciscana

Genealogical concordance is a critical overlay of all phylogenetic analyses, irrespective of taxonomic level. To assess such patterns of congruence we have compiled and derived sequence data for two mitochondrial (16S rRNA, COI) and two nuclear (ITS1, p26) markers in 14 American populations of the hypersaline branchiopod Artemia franciscana. Cladistic analysis revealed three reciprocally monophyletic mitochondrial clades. For nuclear DNA, incomplete lineage sorting was evident presumably as a result of slower coalescence or male-mediated dispersal. Our findings capture the genealogical interval between gene splitting and population divergence. In this sense, strong indications are provided in favour of a superspecies status and ongoing speciation in A. franciscana.