Thermal performance curves (TPCs), which quantify how an ectotherm's body temperature (T b ) affects its performance or fitness, are often used in an attempt to predict organismal responses to climate change. Here, we examine the key -but often biologically unreasonable -assumptions underlying this approach; for example, that physiology and thermal regimes are invariant over ontogeny, space and time, and also that TPCs are independent of previously experienced T b. We show how a critical consideration of these assumptions can lead to biologically useful hypotheses and experimental designs. For example, rather than assuming that TPCs are fixed during ontogeny, one can measure TPCs for each major life stage and incorporate these into stage-specific ecological models to reveal the life stage most likely to be vulnerable to climate change. Our overall goal is to explicitly examine the assumptions underlying the integration of TPCs with T b , to develop a framework within which empiricists can place their work within these limitations, and to facilitate the application of thermal physiology to understanding the biological implications of climate change.

The copepod Tigriopus californicus shows extensive population divergence and is becoming a model for understanding allopatric differentiation and the early stages of speciation. Here, we report a high-quality reference genome for one population (~190 megabases across 12 scaffolds, and ~15,500 protein-coding genes). Comparison with other arthropods reveals 2,526 genes presumed to be specific to T. californicus, with an apparent proliferation of genes involved in ion transport and receptor activity. Beyond the reference population, we report re-sequenced genomes of seven additional populations, spanning the continuum of reproductive isolation. Populations show extreme mitochondrial DNA divergence, with higher levels of amino acid differentiation than observed in other taxa. Across the nuclear genome, we find elevated protein evolutionary rates and positive selection in genes predicted to interact with mitochondrial DNA and the proteins and RNA it encodes in multiple pathways. Together, these results support the hypothesis that rapid mitochondrial evolution drives compensatory nuclear evolution within isolated populations, thereby providing a potentially important mechanism for causing intrinsic reproductive isolation.

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The extensive interaction between mitochondrial-encoded and nuclear-encoded subunits of electron transport system (ETS) enzymes in mitochondria is expected to lead to intergenomic coadaptation. Whether this coadaptation results from adaptation to the environment or from fixation of deleterious mtDNA mutations followed by compensatory nuclear gene evolution is unknown. The intertidal copepod Tigriopus californicus shows extreme divergence in mtDNA sequence and provides an excellent model system for study of intergenomic coadaptation. Here, we examine genes encoding subunits of complex III of the ETS, including the mtDNA-encoded cytochrome b (CYTB), the nuclear-encoded rieske iron-sulfur protein (RISP), and cytochrome c(1) (CYC1). We compare levels of polymorphism within populations and divergence between populations in these genes to begin to untangle the selective forces that have shaped evolution in these genes. CYTB displays dramatic divergence between populations, but sequence analysis shows no evidence for positive selection driving this divergence. CYC1 and RISP have lower levels of sequence divergence between populations than CYTB, but, again, sequence analysis gives no evidence for positive selection acting on them. However, an examination of variation at cytochrome c (CYC), a nuclear-encoded protein that transfers electrons between complex III and complex IV provides evidence for selective divergence. Hence, it appears that rapid evolution in mitochondrial-encoded subunits is not always associated with rapid divergence in interacting subunits (CYC1 and RISP), but can be in some cases (CYC). Finally, a comparison of nuclear-encoded and mitochondrial-encoded genes from T. californicus suggests that substitution rates in the mitochondrial-encoded genes are dramatically increased relative to nuclear genes.

Because of their extensive functional interaction, mitochondrial DNA (mtDNA) and nuclear genes may evolve to form coadapted complexes within reproductively isolated populations. As a consequence of coadaptation, the fitness of particular nuclear alleles may depend on mtDNA genotype. Among populations of the copepod Tigriopus californicus, there are high levels of amino acid substitutions in both the mtDNA genes encoding subunits of cytochrome c oxidase (COX) and the nuclear gene encoding cytochrome c (CYC), the substrate for COX. Because of the functional interaction between enzyme and substrate proteins, we hypothesized that the fitness of CYC genotypes would depend on mtDNA genotype. To test this hypothesis, segregation ratios for CYC and a second nuclear marker (histone H1) unrelated to mitochondrial function were scored in F2 progeny of several reciprocal interpopulation crosses. Genotypic ratios at the CYC locus (but not the H1 locus) differed between reciprocal crosses and differed from expected Mendelian ratios, suggesting that CYC genotypic fitnesses were strongly influenced by cytoplasmic (including mtDNA) background. However, in most cases the nature of the deviations from Mendelian ratios and differences between reciprocal crosses are not consistent with simple coevolution between CYC and mtDNA background. In a cross in which both newly hatched larvae and adults were sampled, only the adult sample showed deviations from Mendelian ratios, indicating that genotypic viabilities differed. In two of six crosses, large genotypic ratio differences for CYC were observed between the sexes. These results suggest that significant variation in nuclear-mtDNA coadaptation may exist between T. californicus populations and that the relative viability of specific cytonuclear allelic combinations is somehow affected by sex.

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.

The evolution of intrinsic postzygotic isolation can be explained by the accumulation of Dobzhansky‐Muller incompatibilities (DMI). Asymmetries in the levels of hybrid inviability and hybrid sterility are commonly observed between reciprocal crosses, a pattern that can result from the involvement of uniparentally inherited factors. The mitochondrial genome is one such factor that appears to participate in DMI in some crosses but the frequency of its involvement versus biparentally inherited factors is unclear. Here we assess the relative importance of incompatibilities between nuclear factors (nuclear‐nuclear) versus those between mitochondrial and nuclear factors (mito‐nuclear) in a species that lacks sex chromosomes. We used a Pool‐seq approach to survey three crosses among genetically divergent populations of the copepod, Tigriopus californicus, for regions of the genome that are affected by hybrid inviability. Results from reciprocal crosses suggest that mito‐nuclear incompatibilities are more common than nuclear‐nuclear incompatibilities overall. These results suggest that in the presence of very high levels of nucleotide divergence between mtDNA haplotypes, mito‐nuclear incompatibilities can be important for the evolution of intrinsic postzygotic isolation. This is particularly interesting considering this species lacks sex chromosomes, which have been shown to harbor a particularly high number of nuclear‐nuclear DMI in several other species.

The genetic incompatibilities that underlie F2 hybrid breakdown and reproductive isolation between allopatric populations may be susceptible to environmental interactions. Here we show that epistatic interactions between cytochrome c (CYC) alleles and mitochondrial DNA (mtDNA) variation are dramatically influenced by environmental temperature in interpopulation hybrids of the copepod Tigriopus californicus. CYC is a nuclear-encoded gene that functionally interacts with electron transport system (ETS) complexes composed in part of mtDNA-encoded proteins. Previous studies have provided evidence for functional coadaptation between CYC and ETS complex IV (cytochrome c oxidase) and for cytoplasmic effects on the fitness of CYC genotype in copepod hybrids. In this study, selection on CYC genotype is shown to continue into advanced generation hybrids (F2-F8) increasing the likelihood that CYC itself is involved in the interaction (and not a linked factor). Relative viabilities varied markedly between copepods raised in two different temperature/light regimes. These results suggest that both intrinsic coadaptation and extrinsic selection will influence the outcome of natural hybridizations between populations. Furthermore, the results indicate that the fitness of particular hybrid genotypes depends on additional non-mtDNA encoded genes that interact with CYC.