Evolutionary mechanisms of habitat invasions, using the copepod Eurytemora affinis as a model system

Ionic regulatory strategies of crabs: the transition from water to land

Terrestrial crabs (brachyurans and anomurans) have invaded land following a variety of pathways from marine and/or via freshwater environments. This transition from water to land requires physiological, ecological, and behavioral adaptations to allow the exploitation of these new environmental conditions. Arguably, the management of salt and water balance (e.g., osmoregulation) is integral for their survival and success in an environment where predominantly low-salinity aquatic (e.g., freshwater) water sources are found, sometimes in only minimal amounts. This requires a suite of morphological and biochemical modifications, especially at the branchial chamber of semi-terrestrial and terrestrial crabs to allow reprocessing of urine to maximize ion uptake. Using knowledge gained from electrophysiology, biochemistry, and more recent molecular biology techniques, we present summarized updated models for ion transport for all major taxonomic groups of terrestrial crabs. This is an exciting and fast-moving field of research, and we hope that this review will stimulate further study. Terrestrial crabs retain their crown as the ideal model group for studying the evolutionary pathways that facilitated terrestrial invasion.

Evolution of ion transporter Na+/K+-ATPase expression in the osmoregulatory maxillary glands of an invasive copepod

While many freshwater invaders originate from saline habitats, the physiological mechanisms involved are poorly understood. We investigated the evolution of ion transporter Na+/K+-ATPase (NKA) protein expression between ancestral saline and freshwater invading populations of the copepod Eurytemora carolleae (Atlantic clade of the E. affinis complex). We compared in situ NKA expression between populations under common-garden conditions at three salinities in the maxillary glands. We found the evolution of reduced NKA expression in the freshwater population under freshwater conditions and reduced plasticity (canalization) across salinities, relative to the saline population. Our results support the hypothesis that maxillary glands are involved in ion reabsorption from excretory fluids at low-salinity conditions in the saline population. However, mechanisms of freshwater adaptation, such as increased ion uptake from the environment, might reduce the need for ion reabsorption in the freshwater population. These patterns of ion transporter expression contribute insights into the evolution of ionic regulation during habitat change.

A rare non-canonical splice site in Trema orientalis SYMRK does not affect its dual symbiotic functioning in endomycorrhiza and rhizobium nodulation

BACKGROUND

Nitrogen-fixing nodules occur in ten related taxonomic lineages interspersed with lineages of non-nodulating plant species. Nodules result from an endosymbiosis between plants and diazotrophic bacteria; rhizobia in the case of legumes and Parasponia and Frankia in the case of actinorhizal species. Nodulating plants share a conserved set of symbiosis genes, whereas related non-nodulating sister species show pseudogenization of several key nodulation-specific genes. Signalling and cellular mechanisms critical for nodulation have been co-opted from the more ancient plant-fungal arbuscular endomycorrhizal symbiosis. Studies in legumes and actinorhizal plants uncovered a key component in symbiotic signalling, the LRR-type SYMBIOSIS RECEPTOR KINASE (SYMRK). SYMRK is essential for nodulation and arbuscular endomycorrhizal symbiosis. To our surprise, however, despite its arbuscular endomycorrhizal symbiosis capacities, we observed a seemingly critical mutation in a donor splice site in the SYMRK gene of Trema orientalis, the non-nodulating sister species of Parasponia. This led us to investigate the symbiotic functioning of SYMRK in the Trema-Parasponia lineage and to address the question of to what extent a single nucleotide polymorphism in a donor splice site affects the symbiotic functioning of SYMRK.

RESULTS

We show that SYMRK is essential for nodulation and endomycorrhization in Parasponia andersonii. Subsequently, it is revealed that the 5'-intron donor splice site of SYMRK intron 12 is variable and, in most dicotyledon species, doesn't contain the canonical dinucleotide 'GT' signature but the much less common motif 'GC'. Strikingly, in T. orientalis, this motif is converted into a rare non-canonical 5'-intron donor splice site 'GA'. This SYMRK allele, however, is fully functional and spreads in the T. orientalis population of Malaysian Borneo. A further investigation into the occurrence of the non-canonical GA-AG splice sites confirmed that these are extremely rare.

CONCLUSION

SYMRK functioning is highly conserved in legumes, actinorhizal plants, and Parasponia. The gene possesses a non-common 5'-intron GC donor splice site in intron 12, which is converted into a GA in T. orientalis accessions of Malaysian Borneo. The discovery of this functional GA-AG splice site in SYMRK highlights a gap in our understanding of splice donor sites.

Genome architecture underlying salinity adaptation in the invasive copepod Eurytemora affinis species complex: A review

With climate change, habitat salinity is shifting rapidly throughout the globe. In addition, many destructive freshwater invaders are recent immigrants from saline habitats. Recently, populations of the copepod Eurytemora affinis species complex have invaded freshwater habitats multiple times independently from saline estuaries on three continents. This review discusses features of this species complex that could enhance their evolutionary potential during rapid environmental change. Remarkably, across independent freshwater invasions, natural selection has repeatedly favored the same alleles far more than expected. This high degree of parallelism is surprising, given the expectation of nonparallel evolution for polygenic adaptation. Factors such as population structure and the genome architecture underlying critical traits under selection might help drive rapid adaptation and parallel evolution. Given the preponderance of saline-to-freshwater invasions and climate-induced salinity change, the principles found here could provide invaluable insights into mechanisms operating in other systems and the potential for adaptation in a changing planet.

Non-MHC immunity genes do not affect parasite load in European invasive populations of common raccoon

Understanding the evolutionary mechanisms behind invasion success enables predicting which alien species and populations are the most predisposed to become invasive. Parasites may mediate the success of biological invasions through their effect on host fitness. The evolution of increased competitive ability (EICA) hypothesis assumes that escape from parasites during the invasion process allows introduced species to decrease investment in immunity and allocate resources to dispersal and reproduction. Consequently, the selective pressure of parasites on host species in the invasive range should be relaxed. We used the case of the raccoon Procyon lotor invasion in Europe to investigate the effect of gastrointestinal pathogen pressure on non-MHC immune genetic diversity of newly established invasive populations. Despite distinct differences in parasite prevalence between analysed populations, we detected only marginal associations between two analysed SNPs and infection intensity. We argue that the differences in parasite prevalence are better explained by detected earlier associations with specific MHC-DRB alleles. While the escape from native parasites seems to allow decreased investment in overall immunity, which relaxes selective pressure imposed on immune genes, a wide range of MHC variants maintained in the invasive range may protect from newly encountered parasites.

Swimming behavior and energy metabolism of the calanoid copepod invader Sinodiaptomus sarsi

The appearance of invasive species threatens the integrity of aquatic ecosystems. Much is known about dispersal and introduction mechanisms while little is known on the biological properties of invasive species, such as behavior and energy efficiency, allowing them to successfully colonize new environments and compete with native species. This study examines the functional features of the Asian invasive copepod Sinodiaptomus sarsi (Rylov, 1923) that has invaded Europe since 2016. We focused on the energy metabolism and kinematic parameters of the main swimming types (i.e., gliding, hovering, small relocation jumps, and the escape reaction) of females and males of S. sarsi. Based on the above parameters, the mechanical energy for swimming and the respiration energy needed for movement were calculated. Females and males spend up to 95% of time hovering and slowly gliding at a speed of up to 0.5 cm s-1. During the remaining time, the average swimming speed was 8 cm s-1 by small jumps. In contrast, the average speed was 42 cm s-1 during escape swimming. Non-ovigerous females moved faster than ovigerous females during all relocation swimming types except for upward gliding. While performing small jumps with a frequency of 0.79 Hz, the respiration rate of active non-ovigerous females (0.32 ± 0.03 µg O2 ind-1 h-1) was 2.1 times higher than that of anesthetized individuals. The respiration energy associated with movement was 2.6 * 10-3 J h-1, while the total mechanical energy was only 4.2% of this value. The low energy cost of feeding along with the high speed of locomotion may explain the success of this Asian invader in European waters.

Introduction to "HaloDaSH: The deep and shallow history of aquatic life's passages between marine and freshwater habitats"

This series of papers highlights research into how biological exchanges between salty and freshwater habitats have transformed the biosphere. Life in the ocean and in freshwaters have long been intertwined; multiple major branches of the tree of life originated in the oceans and then adapted to and diversified in freshwaters. Similar exchanges continue to this day, including some species that continually migrate between marine and fresh waters. The series addresses key themes of transitions, transformations, and current threats with a series of questions: When did major colonizations of fresh waters happen? What physiographic changes facilitated transitions? What organismal characteristics facilitate colonization? Once a lineage has colonized freshwater, how frequently is there a return to the sea? Have transitions impelled diversification? How do organisms adapt physiologically to changes in halohabitat, and are such adaptive changes predictable? How do marine and freshwater taxa differ in morphology? How are present-day global changes in the environment influencing halohabitat and how are organisms contending with them? The purpose of the symposium and the papers in this volume is to integrate findings at multiple levels of biological organization and from disparate fields, across biological and geoscience disciplines.

Recognizing salinity threats in the climate crisis

Climate change is causing habitat salinity to transform at unprecedented rates across the globe. While much of the research on climate change has focused on rapid shifts in temperature, far less attention has focused on the effects of changes in environmental salinity. Consequently, predictive studies on the physiological, evolutionary, and migratory responses of organisms and populations to the threats of salinity change are relatively lacking. This omission represents a major oversight, given that salinity is among the most important factors that define biogeographic boundaries in aquatic habitats. In this perspective, we briefly touch on responses of organisms and populations to rapid changes in salinity occurring on contemporary time scales. We then discuss factors that might confer resilience to certain taxa, enabling them to survive rapid salinity shifts. Next, we consider approaches for predicting how geographic distributions will shift in response to salinity change. Finally, we identify additional data that are needed to make better predictions in the future. Future studies on climate change should account for the multiple environmental factors that are rapidly changing, especially habitat salinity.

Ion Transporter Gene Families as Physiological Targets of Natural Selection During Salinity Transitions in a Copepod

Salinity is a key factor that structures biodiversity on the planet. With anthropogenic change, such as climate change and species invasions, many populations are facing rapid and dramatic changes in salinity throughout the globe. Studies on the copepod Eurytemora affinis species complex have implicated ion transporter gene families as major loci contributing to salinity adaptation during freshwater invasions. Laboratory experiments and population genomic surveys of wild populations have revealed evolutionary shifts in genome-wide gene expression and parallel genomic signatures of natural selection during independent salinity transitions. Our results suggest that balancing selection in the native range and epistatic interactions among specific ion transporter paralogs could contribute to parallel freshwater adaptation. Overall, these studies provide unprecedented insights into evolutionary mechanisms underlying physiological adaptation during rapid salinity change.

Ecological Filtering and Exaptation in the Evolution of Marine Snakes

AbstractConvergent evolution is often attributed to adaptation of form to function, but it can also result from ecological filtering, exaptation, or nonaptation. Testing among these possibilities is critical to understanding how and why morphological similarities emerge independently in multiple lineages. To address this challenge, we combined multiple preexisting phylogenetic methods to jointly estimate the habitats and morphologies of lineages within a phylogeny. We applied this approach to the invasions of snakes into the marine realm. We utilized a data set for 1,243 extant snake species consisting of newly compiled biome occupancy information and preexisting data on reproductive strategy, body mass, and environmental temperature and elevation. We find evidence for marine clades arising from a variety of aquatic and terrestrial habitats. Furthermore, there is strong evidence of ecological filtering for nonmarine ancestors that were already viviparous, had slightly larger-than-average body sizes, and lived in environments with higher-than-average temperatures and lower-than-average elevations. In aggregate, similarities among independent lineages of marine snakes result from a combination of exaptation and strong ecological filtering. Strong barriers to entry of new habitats appear to be more important than common adaptations following invasions for producing similarities among independent lineages invading a shared, novel habitat.

The evolution of marine dwelling in Diptera

Marine dwelling in Diptera has been relatively unexplored and the frequency of transitions to the marine environment and the evolutionary history remain poorly understood. By reviewing records from the World Register of Marine Species and using ancestral state reconstruction methods, we build on the fly tree of life phylogeny and ecological descriptions of marine life history. Our ancestral state reconstruction analyses suggest marine dwelling is lacking as an ancestral trait for the most recent common ancestor to Diptera. While many transitions in Empidoidea, Sciomyzoidea, Tipulomorpha, and Culicomorpha seem to have been gradual, other transitions in Tephritoidea and Tabanomorpha were found likely to have been stochastic occurrences. From the collection of 532 marine species, we reveal several independent transitions to the marine environment throughout the fly tree of life. Considering the results from our analysis, we outline potential adaptations for marine flies and discuss the barriers of colonizing the marine environment and the implications to the mechanisms for salt tolerance.

Were all trilobites fully marine? Trilobite expansion into brackish water during the early Palaeozoic

Trilobites, key components of early Palaeozoic communities, are considered to have been invariably fully marine. Through the integration of ichnological, palaeobiological, and sedimentological datasets within a sequence-stratigraphical framework, we challenge this assumption. Here, we report uncontroversial trace and body fossil evidence of their presence in brackish-water settings. Our approach allows tracking of some trilobite groups foraying into tide-dominated estuaries. These trilobites were tolerant to salinity stress and able to make use of the ecological advantages offered by marginal-marine environments migrating up-estuary, following salt wedges either reflecting amphidromy or as euryhaline marine wanderers. Our data indicate two attempts of landward exploration via brackish water: phase 1 in which the outer portion of estuaries were colonized by olenids (Furongian-early late Tremadocian) and phase 2 involving exploration of the inner to middle estuarine zones by asaphids (Dapingian-Darriwilian). This study indicates that tolerance to salinity stress arose independently among different trilobite groups.

Pre-introduction introgression contributes to parallel differentiation and contrasting hybridization outcomes between invasive and native marine mussels

Non-native species experience novel selection pressures in introduced environments and may interbreed with native lineages. Species introductions therefore provide opportunities to investigate repeated patterns of adaptation and introgression across replicated contact zones. Here, we investigate genetic parallelism between multiple introduced populations of the invasive marine mussel, Mytilus galloprovincialis, in the absence (South Africa and California) and presence of hybridization with a native congener (Mytilus planulatus in Batemans Bay and Sydney Harbour, Australia). Repeatability in post-introduction differentiation from native-range populations varied between genetically distinct Atlantic and Mediterranean lineages, with Atlantic-derived introductions displaying high differentiation (maxF_ST  > 0.4) and parallelism at outlier loci. Identification of long noncoding RNA transcripts (lncRNA) additionally allowed us to clarify that parallel responses are largely limited to protein-coding loci, with lncRNAs likely evolving under evolutionary constraints. Comparisons of independent hybrid zones revealed differential introgression most strongly in Batemans Bay, with an excess of M. galloprovincialis ancestry and resistance to introgression at loci differentiating parental lineages (M. planulatus and Atlantic M. galloprovincialis). Additionally, contigs putatively introgressed with divergent alleles from a closely related species, Mytilus edulis, showed stronger introgression asymmetries compared with genome-wide trends and also diverged in parallel in both Atlantic-derived introductions. These results suggest that divergent demographic histories experienced by introduced lineages, including pre-introduction introgression, influence contemporary admixture dynamics. Our findings build on previous investigations reporting contributions of historical introgression to intrinsic reproductive architectures shared between marine lineages and illustrate that interspecific introgression history can shape differentiation between colonizing populations and their hybridization with native congeners.

Multi-omic approach provides insights into osmoregulation and osmoconformation of the crab Scylla paramamosain

Osmoregulation and osmoconformation are two mechanisms through which aquatic animals adapt to salinity fluctuations. The euryhaline crab Scylla paramamosain, being both an osmoconformer and osmoregulator, is an excellent model organism to investigate salinity adaptation mechanisms in brachyurans. In the present study, we used transcriptomic and proteomic approaches to investigate the response of S. paramamosain to salinity stress. Crabs were transferred from a salinity of 25 ppt to salinities of 5 ppt or 33 ppt for 6 h and 10 days. Data from both approaches revealed that exposure to 5 ppt resulted in upregulation of ion transport and energy metabolism associated genes. Notably, acclimation to low salinity was associated with early changes in gene expression for signal transduction and stress response. In contrast, exposure to 33 ppt resulted in upregulation of genes related to amino acid metabolism, and amino acid transport genes were upregulated only at the early stage of acclimation to this salinity. Our study reveals contrasting mechanisms underlying osmoregulation and osmoconformation within the salinity range of 5–33 ppt in the mud crab, and provides novel candidate genes for osmotic signal transduction, thereby providing insights on understanding the salinity adaptation mechanisms of brachyuran crabs.

Rapid evolution of genome-wide gene expression and plasticity during saline to freshwater invasions by the copepod Eurytemora affinis species complex

Saline migrants into freshwater habitats constitute among the most destructive invaders in aquatic ecosystems throughout the globe. However, the evolutionary and physiological mechanisms underlying such habitat transitions remain poorly understood. To explore the mechanisms of freshwater adaptation and distinguish between adaptive (evolutionary) and acclimatory (plastic) responses to salinity change, we examined genome-wide patterns of gene expression between ancestral saline and derived freshwater populations of the Eurytemora affinis species complex, reared under two different common-garden conditions (0 versus 15 PSU). We found that evolutionary shifts in gene expression (between saline and freshwater inbred lines) showed far greater changes and were more widespread than acclimatory responses to salinity (0 versus 15 PSU). Most notably, 30-40 genes showing evolutionary shifts in gene expression across the salinity boundary were associated with ion transport function, with inorganic cation transmembrane transport forming the largest Gene Ontology category. Of particular interest was the sodium transporter, the Na⁺ /H⁺ antiporter (NHA) gene family, which was discovered in animals relatively recently. Thirty key ion regulatory genes, such as NHA paralogue #7, demonstrated concordant evolutionary and plastic shifts in gene expression, suggesting the evolution of ion transporter function and plasticity during rapid invasions into novel salinities. Moreover, freshwater invasions were associated with the evolution of reduced plasticity in the freshwater population, again for the same key ion transporters, consistent with the predicted evolution of canalization following adaptation to stressful conditions. Our results have important implications for understanding evolutionary and physiological mechanisms of range expansions by some of the most widespread invaders in aquatic habitats.

Adaptation potential of the copepod Eurytemora affinis to a future warmer Baltic Sea

To predict effects of global change on zooplankton populations, it is important to understand how present species adapt to temperature and how they respond to stressors interacting with temperature. Here, we ask if the calanoid copepod Eurytemora affinis from the Baltic Sea can adapt to future climate warming. Populations were sampled at sites with different temperatures. Full sibling families were reared in the laboratory and used in two common garden experiments (a) populations crossed over three temperature treatments 12, 17, and 22.5°C and (b) populations crossed over temperature in interaction with salinity and algae of different food quality. Genetic correlations of the full siblings' development time were not different from zero between 12°C and the two higher temperatures 17 and 22.5°C, but positively correlated between 17 and 22.5°C. Hence, a population at 12°C is unlikely to adapt to warmer temperature, while a population at ≥17°C can adapt to an even higher temperature, that is, 22.5°C. In agreement with the genetic correlations, the population from the warmest site of origin had comparably shorter development time at high temperature than the populations from colder sites, that is, a cogradient variation. The population with the shortest development time at 22.5°C had in comparison lower survival on low quality food, illustrating a cost of short development time. Our results suggest that populations from warmer environments can at present indirectly adapt to a future warmer Baltic Sea, whereas populations from colder areas show reduced adaptation potential to high temperatures, simply because they experience an environment that is too cold.

Comparing raccoon major histocompatibility complex diversity in native and introduced ranges: Evidence for the importance of functional immune diversity for adaptation and survival in novel environments

The adaptive potential of invasive species is related to the genetic diversity of the invader, which is influenced by genetic drift and natural selection. Typically, the genetic diversity of invaders is studied with neutral genetic markers; however, the expectation of reduced diversity has not been consistently supported by empirical studies. Here, we describe and interpret genetic diversity at both neutral microsatellite loci and the immune-related MHC-DRB locus of native and invasive populations of raccoon to better understand of how drift and selection impact patterns of genetic diversity during the invasion process. We found that despite the loss of many MHC (major histocompatibility complex) alleles in comparison with native populations, functional MHC supertypes are preserved in the invasive region. In the native raccoon population, the number of supertypes within individuals was higher than expected under a neutral model. The high level of individual functional divergence may facilitate the adaptation to local conditions in the invasive range. In the invasive populations, we also detected increased population structure at microsatellites compared to the MHC locus, further suggesting that balancing selection is acting on adaptively important regions of the raccoon genome. Finally, we found that alleles known to exhibit resistance to rabies in the native range, Prlo-DRB*4, Prlo-DRB*16 and Prlo-DRB*102, were the most common alleles in the European populations, suggesting directional selection is acting on this locus. Our research shows empirical support for the importance of functional immune diversity for adaptation and survival in novel environments.

Animal, Fungi, and Plant Genome Sequences Harbor Different Non-Canonical Splice Sites

Most protein-encoding genes in eukaryotes contain introns, which are interwoven with exons. Introns need to be removed from initial transcripts in order to generate the final messenger RNA (mRNA), which can be translated into an amino acid sequence. Precise excision of introns by the spliceosome requires conserved dinucleotides, which mark the splice sites. However, there are variations of the highly conserved combination of GT at the 5' end and AG at the 3' end of an intron in the genome. GC-AG and AT-AC are two major non-canonical splice site combinations, which have been known for years. Recently, various minor non-canonical splice site combinations were detected with numerous dinucleotide permutations. Here, we expand systematic investigations of non-canonical splice site combinations in plants across eukaryotes by analyzing fungal and animal genome sequences. Comparisons of splice site combinations between these three kingdoms revealed several differences, such as an apparently increased CT-AC frequency in fungal genome sequences. Canonical GT-AG splice site combinations in antisense transcripts are a likely explanation for this observation, thus indicating annotation errors. In addition, high numbers of GA-AG splice site combinations were observed in Eurytemoraaffinis and Oikopleuradioica. A variant in one U1 small nuclear RNA (snRNA) isoform might allow the recognition of GA as a 5' splice site. In depth investigation of splice site usage based on RNA-Seq read mappings indicates a generally higher flexibility of the 3' splice site compared to the 5' splice site across animals, fungi, and plants.

Copepod Embryonic Dormancy: "An Egg Is Not Just an Egg"

Long-lasting embryonic dormancy in invertebrates defies our understanding of what constitutes life because, for example, eggs of some copepods can delay hatching for decades or even centuries. Copepods, often millimeter-sized crustaceans, are some of the most numerous multicellular organisms on earth and are key organisms in most aquatic food webs. Some important free-living marine and estuarine species overwinter or oversummer by arrested embryogenesis in dormancy. The present contribution discusses the complex mechanisms behind embryonic dormancy by compiling knowledge from the 42 calanoid copepods from the superfamily Centropagoidea with well-described embryonic dormancy, which has been of scientific interest for decades. However, the determination of categories of copepod resting eggs-that is, diapause and quiescence, transitions between categories, the mechanisms controlling arrested development by the embryos, and how they interact with their surroundings-is not fully understood. Moreover, a clear link between the presence of the free-swimming population and their resting eggs in sediments is still not convincingly demonstrated. Here I evaluate the relative significance of potential cues driving the production of and the phase shift between egg categories. Understanding the initiation and termination of embryonic dormancy is of great importance for fundamental science-that is, population and food web ecology as well as climate science, aquaculture live feed, and ballast water research. Molecular techniques are developing rapidly, especially within health sciences, thus providing relevant tools applicable for plankton research. Here I suggest that applying molecular methods in addition to traditional physiological approaches in future research will lead to greater understanding of copepod embryonic dormancy, one of nature's wonders.

Complete mitochondrial genome of the calanoid copepod Eurytemora affinis (Calanoida, Temoridae)

The complete mitochondrial genome was sequenced from the calanoid copepod Eurytemora affinis. The sequenced total genome size was 18,553 bp. The mitochondrial genome of E. affinis has 13 protein-coding genes (PCGs), two rRNAs, and 22 tRNAs. Of 13 PCGs, ND1, ND5, and ATP6 genes had incomplete stop codons TA–, T—, and TA–, respectively. Furthermore, the stop codons of the remaining eleven PCGs were TAG or TAA while the start codon of 13 PCGs was ATG (Cytb, ATP8, ATP6, and CO3 genes), ATT (CO1, ND2, ND3, ND4L, ND5, and ND6 genes), and ATA (ND1, ND4, and CO2 genes), respectively. The ratio of A + T and G + C nucleotides of 13 PCGs of E. affinis mitogenome showed 63.9% and 36.1%, respectively while those ratio of the entire sequences were 65.5% and 34.5%, respectively.

Loss of the HIF pathway in a widely distributed intertidal crustacean, the copepod Tigriopus californicus

Oxygen availability is essential for development, growth, and viability of aerobic organisms. The genes in the hypoxia-inducible factor (HIF) pathway are considered master regulators of oxygen sensitivity and distribution inside cells, and they are hence highly conserved across animal groups. These genes are frequent targets of natural selection in organisms living in low-oxygen environments, such as high-altitude humans and birds. Here, we show that the abundant tidepool copepod Tigriopus californicus can withstand prolonged exposure to extreme oxygen deprivation, despite having secondarily lost key HIF-pathway members. Our results suggest the existence of alternative mechanisms of response to hypoxic stress in animals, and we show that genes involved in cuticle reorganization and ion transport may play a major role.

Hypoxia is a major physiological constraint for which multicellular eukaryotes have evolved robust cellular mechanisms capable of addressing dynamic changes in O₂ availability. In animals, oxygen sensing and regulation is primarily performed by the hypoxia-inducible factor (HIF) pathway, and the key components of this pathway are thought to be highly conserved across metazoans. Marine intertidal habitats are dynamic environments, and their inhabitants are known to tolerate wide fluctuations in salinity, temperature, pH, and oxygen. In this study, we show that an abundant intertidal crustacean, the copepod Tigriopus californicus, has lost major genetic components of the HIF pathway, but still shows robust survivorship and transcriptional response to hypoxia. Mining of protein domains across the genome, followed by phylogenetic analyses of gene families, did not identify two key regulatory elements of the metazoan hypoxia response, namely the transcription factor HIF-α and its oxygen-sensing prolyl hydroxylase repressor, EGLN. Despite this loss, phenotypic assays revealed that this species is tolerant to extremely low levels of available O₂ for at least 24 h at both larval and adult stages. RNA-sequencing (seq) of copepods exposed to nearly anoxic conditions showed differential expression of over 400 genes, with evidence for induction of glycolytic metabolism without a depression of oxidative phosphorylation. Moreover, genes involved in chitin metabolism and cuticle reorganization show categorically a consistent pattern of change during anoxia, highlighting this pathway as a potential solution to low oxygen availability in this small animal with no respiratory structures or pigment.

Spatio-temporal dynamics of Codium populations along the rocky shores of N and NW Spain

The green alga Codium fragile ssp. fragile (hereafter C. fragile) has long been assumed to outcompete and displace its native congeners via cryptic invasion. We analysed the population dynamics of the exotic C. fragile and native congeners and their relative abundance on intertidal shores in N-NW Spain. Our results did not support the existence of current competitive displacement by the exotic species. The presence of C. fragile was clearly seasonal, while the native C. tomentosum was more persistent throughout the year, due to a higher frequency of frond sprouting from perennial basal fragments. However, our results also indicated an increase in the proportion of C. fragile relative to native species towards inner areas of the Bay of Biscay, which was correlated with environmental gradients. The greater tolerance of C. fragile to environmental stress and its opportunistic abilities may favour establishment and spread of the species under a warming scenario.

Contaminant exposure effects in a changing climate: how multiple stressors can multiply exposure effects in the amphipod Hyalella azteca

Global climate change (GCC) is likely to intensify the synergistic effects between altered physicochemical parameters [of changing habitats] and other anthropogenic threats, such as water pollution, posing increased risks to aquatic biodiversity. As such, it is critical to understand how organisms will respond to changes in water temperature and salinity in the presence of contaminants. We exposed the epibenthic amphipod Hyalella azteca to a 3 × 3 factorial treatment design of three temperatures and three salinities ranging from 12 to 18 °C and 0 to 8 parts per thousand (ppt), respectively, in combination with a low-level environmentally relevant concentration of the pyrethroid insecticide bifenthrin (1 ng/L). Effects on survival and swimming behavior were evaluated after 96 h exposure. Transcription of a select suite of genes was monitored at 24, 48, and 96 h using quantitative polymerase chain reaction (qPCR). Our results not only demonstrate that the changes in salinity and temperature result in negative effects to invertebrate survival, behavior, and gene response, but that the effects were significantly more pronounced in the presence of bifenthrin. This is particularly important since greater thermal fluctuations, changes in timing and extent of glacial melt, and changes in precipitation, could result in H. azteca experiencing lower temperatures at times that coincide with increased spraying of pyrethroids. These environmentally relevant exposures using the standard test species H. azteca provide essential information for understanding effects caused by GCC in conjunction with increasing pesticide use, further highlighting the need to incorporate GCC impacts into risk assessments of contaminants of concern.

Combining niche shift and population genetic analyses predicts rapid phenotypic evolution during invasion

The rapid evolution of non-native species can facilitate invasion success, but recent reviews indicate that such microevolution rarely yields expansion of the climatic niche in the introduced habitats. However, because some invasions originate from a geographically restricted portion of the native species range and its climatic niche, it is possible that the frequency, direction, and magnitude of phenotypic evolution during invasion have been underestimated. We explored the utility of niche shift analyses in the red seaweed Gracilaria vermiculophylla, which expanded its range from the northeastern coastline of Japan to North America, Europe, and northwestern Africa within the last 100 years. A genetically informed climatic niche shift analysis indicates that native source populations occur in colder and highly seasonal habitats, while most non-native populations typically occur in warmer, less seasonal habitats. This climatic niche expansion predicts that non-native populations evolved greater tolerance for elevated heat conditions relative to native source populations. We assayed 935 field-collected and 325 common-garden thalli from 40 locations, and as predicted, non-native populations had greater tolerance for ecologically relevant extreme heat (40°C) than did Japanese source populations. Non-native populations also had greater tolerance for cold and low-salinity stresses relative to source populations. The importance of local adaptation to warm temperatures during invasion was reinforced by evolution of parallel clines: Populations from warmer, lower-latitude estuaries had greater heat tolerance than did populations from colder, higher-latitude estuaries in both Japan and eastern North America. We conclude that rapid evolution plays an important role in facilitating the invasion success of this and perhaps other non-native marine species. Genetically informed ecological niche analyses readily generate clear predictions of phenotypic shifts during invasions and may help to resolve debate over the frequency of niche conservatism versus rapid adaptation during invasion.

The Toxicogenome of Hyalella azteca: A Model for Sediment Ecotoxicology and Evolutionary Toxicology

Hyalella azteca is a cryptic species complex of epibenthic amphipods of interest to ecotoxicology and evolutionary biology. It is the primary crustacean used in North America for sediment toxicity testing and an emerging model for molecular ecotoxicology. To provide molecular resources for sediment quality assessments and evolutionary studies, we sequenced, assembled, and annotated the genome of the H. azteca U.S. Lab Strain. The genome quality and completeness is comparable with other ecotoxicological model species. Through targeted investigation and use of gene expression data sets of H. azteca exposed to pesticides, metals, and other emerging contaminants, we annotated and characterized the major gene families involved in sequestration, detoxification, oxidative stress, and toxicant response. Our results revealed gene loss related to light sensing, but a large expansion in chemoreceptors, likely underlying sensory shifts necessary in their low light habitats. Gene family expansions were also noted for cytochrome P450 genes, cuticle proteins, ion transporters, and include recent gene duplications in the metal sequestration protein, metallothionein. Mapping of differentially expressed transcripts to the genome significantly increased the ability to functionally annotate toxicant responsive genes. The H. azteca genome will greatly facilitate development of genomic tools for environmental assessments and promote an understanding of how evolution shapes toxicological pathways with implications for environmental and human health.

The Toxicogenome of Hyalella azteca: A Model for Sediment Ecotoxicology and Evolutionary Toxicology

Hyalella azteca is a cryptic species complex of epibenthic amphipods of interest to ecotoxicology and evolutionary biology. It is the primary crustacean used in North America for sediment toxicity testing and an emerging model for molecular ecotoxicology. To provide molecular resources for sediment quality assessments and evolutionary studies, we sequenced, assembled, and annotated the genome of the H. azteca U.S. Lab Strain. The genome quality and completeness is comparable with other ecotoxicological model species. Through targeted investigation and use of gene expression data sets of H. azteca exposed to pesticides, metals, and other emerging contaminants, we annotated and characterized the major gene families involved in sequestration, detoxification, oxidative stress, and toxicant response. Our results revealed gene loss related to light sensing, but a large expansion in chemoreceptors, likely underlying sensory shifts necessary in their low light habitats. Gene family expansions were also noted for cytochrome P450 genes, cuticle proteins, ion transporters, and include recent gene duplications in the metal sequestration protein, metallothionein. Mapping of differentially expressed transcripts to the genome significantly increased the ability to functionally annotate toxicant responsive genes. The H. azteca genome will greatly facilitate development of genomic tools for environmental assessments and promote an understanding of how evolution shapes toxicological pathways with implications for environmental and human health.

Introgression between ecologically distinct species following increased salinity in the Colorado Delta- Worldwide implications for impacted estuary diversity

We investigate hybridization and introgression between ecologically distinct sister species of silverside fish in the Gulf of California through combined analysis of morphological, sequence, and genotypic data. Water diversions in the past century turned the Colorado River Delta from a normal estuary to a hypersaline inverse estuary, raising concerns for the local fauna, much of which is endangered. Salinity differences are known to generate ecological species pairs and we anticipated that loss of the fresher-water historic salinity regime could alter the adaptive factors maintaining distinction between the broadly distributed Gulf-endemic Colpichthys regis and the narrowly restricted Delta-endemic Colpichthys hubbsi, the species that experienced dramatic environmental change. In this altered environmental context, these long-isolated species (as revealed by Cytochrome b sequences) show genotypic (RAG1, microsatellites) evidence of active hybridization where the species ranges abut, as well as directional introgression from C. regis into the range center of C. hubbsi. Bayesian group assignment (STRUCTURE) on six microsatellite loci and multivariate analyses (DAPC) on both microsatellites and phenotypic data further support substantial recent admixture between the sister species. Although we find no evidence for recent population decline in C. hubbsi based on mitochondrial sequence, introgression may be placing an ancient ecological species at risk of extinction. Such introgressive extinction risk should also pertain to other ecological species historically sustained by the now changing Delta environment. More broadly, salinity gradient associated ecological speciation is evident in silverside species pairs in many estuarine systems around the world. Ecological species pairs among other taxa in such systems are likely poorly understood or cryptic. As water extraction accelerates in river systems worldwide, salinity gradients will necessarily be altered, impacting many more estuary and delta systems. Such alteration of habitats will place biodiversity at risk not only from direct effects of habitat destruction, but also from the potential for the breakdown of ecological species. Thus, evolutionary response to the anthropogenic alteration of salinity gradients in estuaries merits investigation as the number of impacted systems increases around the globe, permitting parallel study of multiple systems, while also permitting a conservation management response to help preserve this little championed component of biodiversity.

Evolutionary responses to crude oil from the Deepwater Horizon oil spill by the copepod Eurytemora affinis

The BP Deepwater Horizon Oil Disaster was the most catastrophic offshore oil spill in U.S. history, yet we still have a poor understanding of how organisms could evolve in response to the toxic effects of crude oil. This study offers a rare analysis of how fitness-related traits could evolve rapidly in response to crude oil toxicity. We examined evolutionary responses of populations of the common copepod Eurytemora affinis residing in the Gulf of Mexico, by comparing crude oil tolerance of populations collected before versus after the Deepwater Horizon oil spill of 2010. In addition, we imposed laboratory selection for crude oil tolerance for ~8 generations, using an E. affinis population collected from before the oil spill. We found evolutionary increases in crude oil tolerance in the wild population following the oil spill, relative to the population collected before the oil spill. The post-oil spill population showed increased survival and rapid development time in the presence of crude oil. In contrast, evolutionary responses following laboratory selection were less clear; though, development time from metamorphosis to adult in the presence of crude oil did become more rapid after selection. We did find that the wild population, used in both experiments, harbored significant genetic variation in crude oil tolerance, upon which selection could act. Thus, our study indicated that crude oil tolerance could evolve, but perhaps not on the relatively short time scale of the laboratory selection experiment. This study contributes novel insights into evolutionary responses to crude oil, in directly examining fitness-related traits before and after an oil spill, and in observing evolutionary responses following laboratory selection.

Invasions and extinctions through the looking glass of evolutionary ecology

Invasive and endangered species reflect opposite ends of a spectrum of ecological success, yet they experience many similar eco-evolutionary challenges including demographic bottlenecks, hybridization and novel environments. Despite these similarities, important differences exist. Demographic bottlenecks are more transient in invasive species, which (i) maintains ecologically relevant genetic variation, (ii) reduces mutation load, and (iii) increases the efficiency of natural selection relative to genetic drift. Endangered species are less likely to benefit from admixture, which offsets mutation load but also reduces fitness when populations are locally adapted. Invading species generally experience more benign environments with fewer natural enemies, which increases fitness directly and also indirectly by masking inbreeding depression. Adaptive phenotypic plasticity can maintain fitness in novel environments but is more likely to evolve in invasive species encountering variable habitats and to be compromised by demographic factors in endangered species. Placed in an eco-evolutionary context, these differences affect the breadth of the ecological niche, which arises as an emergent property of antagonistic selection and genetic constraints. Comparative studies of invasions and extinctions that apply an eco-evolutionary perspective could provide new insights into the environmental and genetic basis of ecological success in novel environments and improve efforts to preserve global biodiversity.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'.

Women in evolution - highlighting the changing face of evolutionary biology

The face of science has changed. Women now feature alongside men at the forefront of many fields, and this is particularly true in evolutionary biology. This special issue celebrates the outstanding achievements and contributions of women in evolutionary biology, by highlighting a sample of their research and accomplishments. In addition to original research contributions, this collection of articles contains personal reflections to provide perspective and advice on succeeding as a woman in science. By showcasing the diversity and research excellence of women and drawing on their experiences, we wish to enhance the visibility of female scientists and provide inspiration as well as role models. These are exciting times for evolutionary biology, and the field is richer and stronger for the diversity of voices contributing to the field.