DO FRESHWATER FISHES DIVERSIFY FASTER THAN MARINE FISHES? A TEST USING STATE‐DEPENDENT DIVERSIFICATION ANALYSES AND MOLECULAR PHYLOGENETICS OF NEW WORLD SILVERSIDES (ATHERINOPSIDAE)

Freshwater habitats make up only ～0.01% of available aquatic habitat and yet harbor 40% of all fish species, whereas marine habitats comprise >99% of available aquatic habitat and have only 60% of fish species. One possible explanation for this pattern is that diversification rates are higher in freshwater habitats than in marine habitats. We investigated diversification in marine and freshwater lineages in the New World silverside fish clade Menidiinae (Teleostei, Atherinopsidae). Using a time‐calibrated phylogeny and a state‐dependent speciation–extinction framework, we determined the frequency and timing of habitat transitions in Menidiinae and tested for differences in diversification parameters between marine and freshwater lineages. We found that Menidiinae is an ancestrally marine lineage that independently colonized freshwater habitats four times followed by three reversals to the marine environment. Our state‐dependent diversification analyses showed that freshwater lineages have higher speciation and extinction rates than marine lineages. Net diversification rates were higher (but not significant) in freshwater than marine environments. The marine lineage‐through time (LTT) plot shows constant accumulation, suggesting that ecological limits to clade growth have not slowed diversification in marine lineages. Freshwater lineages exhibited an upturn near the recent in their LTT plot, which is consistent with our estimates of high background extinction rates. All sequence data are currently being archived on Genbank and phylogenetic trees archived on Treebase.     

Biogeography,habitat transitions and hybridization in a radiation of South American silverside fishes revealed by mitochondrial and genomic RAD data

Rivers and lake systems in the southern cone of South America have been widely influenced by historical glaciations, carrying important implications for the evolution of aquatic organisms, including prompting transitions between marine and freshwater habitats and by triggering hybridization among incipient species via waterway connectivity and stream capture events. Silverside fishes (Odontesthes) in the region comprise a radiation of 19 marine and freshwater species that have been hypothesized on the basis of morphological or mitochondrial DNA data to have either transitioned repeatedly into continental waters from the sea or colonized marine habitats following freshwater diversification. New double digest restriction‐site associated DNA data presented here provide a robust framework to investigate the biogeographical history of and habitat transitions in Odontesthes. We show that Odontesthes silversides originally diversified in the Pacific but independently colonized the Atlantic three times, producing three independent marine‐to‐freshwater transitions. Our results also indicate recent introgression of marine mitochondrial haplotypes into two freshwater clades, with more recurring instances of hybridization among Atlantic‐ versus Pacific‐slope species. In Pacific freshwater drainages, hybridization with a marine species appears to be geographically isolated and may be related to glaciation events. Substantial structural differences of estuarine gradients between these two geographical areas may have influenced the frequency, intensity and evolutionary effects of hybridization events.     

Out of the blue: adaptive visual pigment evolution accompanies Amazon invasion

Incursions of marine water into South America during the Miocene prompted colonization of freshwater habitats by ancestrally marine species and present a unique opportunity to study the molecular evolution of adaptations to varying environments. Freshwater and marine environments are distinct in both spectra and average intensities of available light. Here, we investigate the molecular evolution of rhodopsin, the photosensitive pigment in the eye that activates in response to light, in a clade of South American freshwater anchovies derived from a marine ancestral lineage. Using likelihood-based comparative sequence analyses, we found evidence for positive selection in the rhodopsin of freshwater anchovy lineages at sites known to be important for aspects of rhodopsin function such as spectral tuning. No evidence was found for positive selection in marine lineages, nor in three other genes not involved in vision. Our results suggest that an increased rate of rhodopsin evolution was driven by diversification into freshwater habitats, thereby constituting a rare example of molecular evolution mirroring large-scale palaeogeographic events.     

Species and shape diversification are inversely correlated among gobies and cardinalfishes (Teleostei: Gobiiformes)

Gobies and their relatives are significant components of nearshore marine, estuarine, and freshwater fish faunas in both tropical and temperate habitats worldwide. They are remarkable for their ability to adapt to and diversify in a wide range of environments. Among gobiiform clades, species diversities vary widely, ranging from two species in Kurtidae to more than 1,000 species in Gobiidae. There is also great variation in head and body shape and in environmental preferences (fresh, brackish, or marine habitats). In this study, I used a time-calibrated molecular phylogeny, coupled with morphometric and comparative analyses, to examine evolutionary rates of both speciation and morphological diversification among gobiiform lineages. Projection of the phylogeny onto a shape-derived morphospace shows that Gobioidei is morphometrically distinct from its sister taxon Apogonoidei, but that families within Gobioidei overlap in morphospace. Analysis of species diversification rates indicates that three rate shifts have occurred over the evolutionary history of Gobiiformes. Relative to the other lineages, Kurtidae has exhibited a slowdown in speciation, whereas both Apogonidae and Gobiidae?+?Gobionellidae have experienced an increase in diversification. Comparative analyses show that in Apogonidae and Gobiidae?+?Gobionellidae, increased speciation is correlated with diminished rates of morphological diversification, differently manifested in either clade and among the various sublineages. The elevation in speciation rates and diminishment in rates of morphological change in both Apogonidae and the clade Gobiidae?+?Gobionellidae are correlated with shifts to oceanic habitats from freshwater. This pattern is the complement to that seen across the global radiation of acanthomorph fishes in which a decrease in species diversification is associated with an increase in morphological disparity.     

Diverse migration strategy between freshwater and seawater habitats in the freshwater eel genus Anguilla

The freshwater eels of the genus Anguilla, which are catadromous, migrate between freshwater growth habitats and offshore spawning areas. A number of recent studies, however, found examples of the temperate species Anguilla anguilla, Anguilla rostrata, Anguilla japonica, Anguilla australis and Anguilla dieffenbachii that have never migrated into fresh water, spending their entire life history in the ocean. Furthermore, those studies found an intermediate type between marine and freshwater residents, which appear to frequently move between different environments during their growth phase. The discovery of marine and brackish-water residents Anguilla spp. suggests that they do not all have to be catadromous, and it calls into question the generalized classification of diadromous fishes. There has been little available information, however, concerning migration in tropical Anguilla spp. Anguilla marmorata, shows three fluctuation patterns: (1) continuous residence in fresh water, (2) continuous residence in brackish water and (3) residence in fresh water after recruitment, while returning to brackish water. Such migratory patterns were found in other tropical species, Anguilla bicolor bicolor and Anguilla bicolor pacifica. In A. b. bicolor collected in a coastal lagoon of Indonesia, two further patterns of habitat use were found: (1) constantly living in either brackish water or sea water with no freshwater life and (2) habitat shift from fresh water to brackish water or sea water. The wide range of environmental habitat use indicates that migratory behaviour of tropical Anguilla spp. is facultative among fresh, brackish and marine waters during their growth phases after recruitment to the coastal areas. Further, the migratory behaviours of tropical Anguilla spp. appear to differ in each habitat in response to inter and intra-specific competition. The results suggest that tropical Anguilla spp. have a flexible pattern of migration, with an ability to adapt to various habitats and salinities. The ability of anguillids to reside in environments of various salinities would be a common feature between tropical and temperate species without a latitudinal cline. Thus, the migration of Anguilla spp. into fresh water is clearly not an obligatory behaviour. This evidence of geographical variability among Anguilla spp. suggests that habitat use is determined by environmental conditions in each site.     

Multiple invasions into freshwater by pufferfishes (teleostei: tetraodontidae): a mitogenomic perspective

Pufferfishes of the Family Tetraodontidae are the most speciose group in the Order Tetraodontiformes and mainly inhabit coastal waters along continents. Although no members of other tetraodontiform families have fully discarded their marine lives, approximately 30 tetraodontid species spend their entire lives in freshwaters in disjunct tropical regions of South America, Central Africa, and Southeast Asia. To investigate the interrelationships of tetraodontid pufferfishes and thereby elucidate the evolutionary origins of their freshwater habitats, we performed phylogenetic analysis based on whole mitochondrial genome sequences from 50 tetraodontid species and closely related species (including 31 newly determined sequences). The resulting phylogenies reveal that the family is composed of four major lineages and that freshwater species from the different continents are independently nested in two of the four lineages. A monophyletic origin of the use of freshwater habitats was statistically rejected, and ancestral habitat reconstruction on the resulting tree demonstrates that tetraodontids independently entered freshwater habitats in different continents at least three times. Relaxed molecular-clock Bayesian divergence time estimation suggests that the timing of these invasions differs between continents, occurring at 0-10 million years ago (MA) in South America, 17-38 MA in Central Africa, and 48-78 MA in Southeast Asia. These timings are congruent with geological events that could facilitate adaptation to freshwater habitats in each continent.     

Fossil‐based comparative analyses reveal ancient marine ancestry erased by extinction in ray‐finned fishes

The marine‐freshwater boundary is a major biodiversity gradient and few groups have colonised both systems successfully. Fishes have transitioned between habitats repeatedly, diversifying in rivers, lakes and oceans over evolutionary time. However, their history of habitat colonisation and diversification is unclear based on available fossil and phylogenetic data. We estimate ancestral habitats and diversification and transition rates using a large‐scale phylogeny of extant fish taxa and one containing a massive number of extinct species. Extant‐only phylogenetic analyses indicate freshwater ancestry, but inclusion of fossils reveal strong evidence of marine ancestry in lineages now restricted to freshwaters. Diversification and colonisation dynamics vary asymmetrically between habitats, as marine lineages colonise and flourish in rivers more frequently than the reverse. Our study highlights the importance of including fossils in comparative analyses, showing that freshwaters have played a role as refuges for ancient fish lineages, a signal erased by extinction in extant‐only phylogenies.     

Distinct colonization waves underlie the diversification of the freshwater sculpin (Cottus gobio) in the Central European Alpine region

Ecological speciation and adaptive radiation are key processes shaping northern temperate freshwater fish diversity. Both often involve parapatric differentiation between stream and lake populations and less often, sympatric intralacustrine diversification into habitat‐ and resource‐associated ecotypes. However, few taxa have been studied, calling for studies of others to investigate the generality of these processes. Here, we test for diversification within catchments in freshwater sculpins in a network of peri‐Alpine lakes and streams. Using 8047 and 13 182 restriction site‐associated (RADseq) SNPs, respectively, we identify three deeply divergent phylogeographic lineages associated with different major European drainages. Within the Aare catchment, we observe populations from geographically distant lakes to be genetically more similar to each other than to populations from nearby streams. This pattern is consistent with two distinct colonization waves, rather than by parapatric ecological speciation after a single colonization wave. We further find two distinct depth distribution modes in three lakes of the Aare catchment, one in very shallow and one in very deep water, and significant genomewide differentiation between these in one lake. Sculpins in the Aare catchment appear to represent an early‐stage adaptive radiation involving the evolution of a lacustrine lineage distinct from parapatric stream sculpins and the repeated onset of depth‐related intralacustrine differentiation.     

Diatoms diversify and turn over faster in freshwater than marine environments*

Many clades that span the marine–freshwater boundary are disproportionately more diverse in the younger, shorter lived, and scarcer freshwater environments than they are in the marine realm. This disparity is thought to be related to differences in diversification rates between marine and freshwater lineages. However, marine and freshwaters are not ecologically homogeneous, so the study of diversification across the salinity divide should also account for other potentially interacting variables. In diatoms, freshwater and substrate‐associated (benthic) lineages are several‐fold more diverse than their marine and suspended (planktonic) counterparts. These imbalances provide an excellent system to understand whether these variables interact with diversification. Using multistate hidden‐state speciation and extinction models, we found that freshwater lineages diversify faster than marine lineages regardless of whether they inhabit the plankton or the benthos. Freshwater lineages also had higher turnover rates (speciation + extinction), suggesting that habitat transitions impact speciation and extinction rates jointly. The plankton–benthos contrast was also consistent with state‐dependent diversification, but with modest differences in diversification and turnover rates. Asymmetric and bidirectional transitions rejected hypotheses about the plankton and freshwaters as absorbing, inescapable habitats. Our results further suggest that the high turnover rate of freshwater diatoms is related to high turnover of freshwater systems themselves.     

Comparative Analysis of Japanese Three-Spined Stickleback Clades Reveals the Pacific Ocean Lineage Has Adapted to Freshwater Environments while the Japan Sea Has Not

Divergent selection and adaptive divergence can increase phenotypic diversification amongst populations and lineages. Yet adaptive divergence between different environments, habitats or niches does not occur in all lineages. For example, the colonization of freshwater environments by ancestral marine species has triggered adaptive radiation and phenotypic diversification in some taxa but not in others. Studying closely related lineages differing in their ability to diversify is an excellent means of understanding the factors promoting and constraining adaptive evolution. A well-known example of the evolution of increased phenotypic diversification following freshwater colonization is the three-spined stickleback. Two closely related stickleback lineages, the Pacific Ocean and the Japan Sea occur in Japan. However, Japanese freshwater stickleback populations are derived from the Pacific Ocean lineage only, suggesting the Japan Sea lineage is unable to colonize freshwater. Using stable isotope data and trophic morphology, we first show higher rates of phenotypic and ecological diversification between marine and freshwater populations within the Pacific Ocean lineage, confirming adaptive divergence has occurred between the two lineages and within the Pacific Ocean lineage but not in the Japan Sea lineage. We further identified consistent divergence in diet and foraging behaviour between marine forms from each lineage, confirming Pacific Ocean marine sticklebacks, from which all Japanese freshwater populations are derived, are better adapted to freshwater environments than Japan Sea sticklebacks. We suggest adaptive divergence between ancestral marine populations may have played a role in constraining phenotypic diversification and adaptive evolution in Japanese sticklebacks.     

Do habitat shifts drive diversification in teleost fishes? An example from the pufferfishes (Tetraodontidae)

Habitat shifts are implicated as the cause of many vertebrate radiations, yet relatively few empirical studies quantify patterns of diversification following colonization of new habitats in fishes. The pufferfishes (family Tetraodon‐tidae) occur in several habitats, including coral reefs and freshwater, which are thought to provide ecological opportunity for adaptive radiation, and thus provide a unique system for testing the hypothesis that shifts to new habitats alter diversification rates. To test this hypothesis, we sequenced eight genes for 96 species of pufferfishes and closely related porcupine fishes, and added 19 species from sequences available in GenBank. We time‐calibrated the molecular phylogeny using three fossils, and performed several comparative analyses to test whether colonization of novel habitats led to shifts in the rate of speciation and body size evolution, central predictions of clades experiencing ecological adaptive radiation. Colonization of freshwater is associated with lower rates of cladogenesis in pufferfishes, although these lineages also exhibit accelerated rates of body size evolution. Increased rates of cladogenesis are associated with transitions to coral reefs, but reef lineages surprisingly exhibit significantly lower rates of body size evolution. These results suggest that ecological opportunity afforded by novel habitats may be limited for pufferfishes due to competition with other species, constraints relating to pufferfish life history and trophic ecology, and other factors.     

Marine moult migration of the freshwater Scaly‐sided Merganser Mergus squamatus revealed by stable isotopes and geolocators

Scaly‐sided Mergansers Mergus squamatus breed on freshwater rivers in far eastern Russia, Korea and China, wintering in similar habitats in China and Korea, but nothing was known of their moulting habitat. To investigate the moult strategies of this species, we combined wing feather stable isotope ratios (males and females) with geolocator data (nesting females) to establish major habitat types (freshwater, brackish or saltwater) used by both sexes during wing moult. Although most Scaly‐sided Mergansers of both sexes probably moult on freshwater, some males and non‐breeding and failed breeding females appeared to undertake moult migration to brackish and marine waters. Given the previous lack of any surveys of coastal or estuarine waters for this species during the moult period, these findings suggest important survey needs for the effective conservation of the species during the flightless moult period.     

Marine-freshwater transitions are associated with the evolution of dietary diversification in terapontid grunters (Teleostei: Terapontidae)

The ecological opportunities associated with transitions across the marine-freshwater interface are regarded as an important catalyst of diversification in a range of aquatic taxa. Here, we examined the role of these major habitat transitions and trophic diversification in a radiation of Australasian fishes using a new molecular phylogeny incorporating 37 Terapontidae species. A combined mitochondrial and nuclear gene analysis yielded a well-supported tree with most nodes resolved. Ancestral terapontids appear to have been euryhaline in habitat affiliation, with a single transition to freshwater environments producing all Australasian freshwater species. Mapping of terapontid feeding modes onto the molecular phylogeny-predicted carnivorous dietary habits was displayed by ancestral terapontids, which subsequently diversified into a range of additional carnivorous, omnivorous, herbivorous and detritivorous dietary modes upon transition to freshwater habitats. Comparative analyses suggested that following the freshwater invasion, the single freshwater clade has exhibited an increased rate of diversification at almost three times the background rate evident across the rest of the family. The marine-freshwater transition within Terapontidae appears to have resulted in substantial dietary radiation in freshwater environments, as well as increased lineage diversification rates relative to euryhaline-marine habitats.     

Not going with the flow: a comprehensive time‐calibrated phylogeny of dragonflies (Anisoptera: Odonata: Insecta) provides evidence for the role of lentic habitats on diversification

Ecological diversification of aquatic insects has long been suspected to have been driven by differences in freshwater habitats, which can be classified into flowing (lotic) waters and standing (lentic) waters. The contrasting characteristics of lotic and lentic freshwater systems imply different ecological constraints on their inhabitants. The ephemeral and discontinuous character of most lentic water bodies may encourage dispersal by lentic species in turn reducing geographical isolation among populations. Hence, speciation probability would be lower in lentic species. Here, we assess the impact of habitat use on diversification patterns in dragonflies (Anisoptera: Odonata). Based on the eight nuclear and mitochondrial genes, we inferred species diversification with a model‐based evolutionary framework, to account for rate variation through time and among lineages and to estimate the impact of larval habitat on the potentially nonrandom diversification among anisopteran groups. Ancestral state reconstruction revealed lotic fresh water systems as their original primary habitat, while lentic waters have been colonized independently in Aeshnidae, Corduliidae and Libellulidae. Furthermore, our results indicate a positive correlation of speciation and lentic habitat colonization by dragonflies: speciation rates increased in lentic Aeshnidae and Libellulidae, whereas they remain mostly uniform among lotic groups. This contradicts the hypothesis of inherently lower speciation in lentic groups and suggests species with larger ranges are more likely to diversify, perhaps due to higher probability of larger areas being dissected by geographical barriers. Furthermore, larger range sizes may comprise more habitat types, which could also promote speciation by providing additional niches, allowing the coexistence of emerging species.     

Breathing air in air: in what ways might extant amphibious fish biology relate to prevailing concepts about early tetrapods, the evolution of vertebrate air breathing, and the vertebrate land transition?

The air-breathing fishes have heuristic importance as possible models for the Paleozoic evolution of vertebrate air breathing and the transition to land. A recent hypothesis about this transition suggests that the diverse assemblage of marine amphibious fishes occurring primarily in tropical, high intertidal zone habitats are analogs of early tetrapods and that the intertidal zone, not tropical freshwater lowlands, was the springboard habitat for the Devonian land transition by vertebrates. Here we argue that selection pressures imposed by life in the intertidal zone are insufficient to have resulted in the requisite aerial respiratory capacity or the degree of separation from water required for the vertebrate land transition. The extant marine amphibious fishes, which occur mainly on rocky shores or mudflats, have reached the limit of their niche expansion onto land and remain tied to water by respiratory structures that are less efficient in air and more vulnerable to desiccation than lungs. We further argue that evolutionary contingencies actuated by the Devonian origin of the tetrapods marked a critical point of divergence for a way of life in which selection pressures would operate on the physiology, morphology, and natural history of the different vertebrate groups. While chronically hypoxic and shallow water conditions in the habitats of some primitive bony fishes and some amphibians appear similar to the conditions that prevailed in the Devonian, markedly different selection pressures have operated on other amphibians and bony fishes over the 300 million years since the vertebrate land transition. For example, both egg development and larval metamorphosis in extant amphibians are geared mainly toward compensating for the uncertainty of habitat water quality or even the absence of water by minimizing the time required to develop there. In contrast, reproduction by most intertidal (and amphibious) fishes, all of which are teleosts, remains dependent on a planktonic larval phase and is characterized by specializations (brooding) that minimize overdispersal and maximize recruitment back to the littoral habitat.     

An investigation into the effects of increasing salinity on photosynthesis in freshwater unicellular cyanobacteria during the late Archaean

The oldest species of bacteria capable of oxygenic photosynthesis today are the freshwater Cyanobacteria Gloeobacter spp., belonging to the class Oxyphotobacteria. Several modern molecular evolutionary studies support the freshwater origin of cyanobacteria during the Archaean and their subsequent acquisition of salt tolerance mechanisms necessary for their expansion into the marine environment. This study investigated the effect of a sudden washout event from a freshwater location into either a brackish or marine environment on the photosynthetic efficiency of two unicellular freshwater cyanobacteria: the salt‐tolerant Chroococcidiopsis thermalis PCC7203 and the cyanobacterial phylogenetic root species, Gloeobacter violaceus PCC7421. Strains were cultured under present atmospheric levels (PAL) of CO₂ or an atmosphere containing elevated levels of CO₂ and reduced O₂ (eCO₂rO₂) in simulated shallow water or terrestrial environmental conditions. Both strains exhibited a reduction in growth rates and gross photosynthesis, accompanied by significant reductions in chlorophyll a content, in brackish water, with only C. thermalis able to grow at marine salinity levels. While the experimental atmosphere caused a significant increase in gross photosynthesis rates in both strains, it did not increase their growth rates, nor the amount of O₂ released. The differences in growth responses to increasing salinities could be attributed to genetic differences, with C. thermalis carrying additional genes for trehalose synthesis. This study demonstrates that, if cyanobacteria did evolve in a freshwater environment, they would have been capable of withstanding a sudden washout into increasingly saline environments. Both C. thermalis and G. violaceus continued to grow and photosynthesise, albeit at diminished rates, in brackish water, thereby providing a route for the evolution of open ocean‐dwelling strains, necessary for the oxygenation of the Earth's atmosphere.     

Effects of salinity on the growth and morphology of the invasive,euryhaline hydroid Cordylophora (Phylum Cnidaria,Class Hydrozoa)

The invasive, euryhaline hydroid Cordylophora sp. is a colonial cnidarian present in both freshwater and brackish water habitats. Individuals contend with osmotic stress at the tissue and cellular level. It has been suggested that this hydroid's ability to expand its range of distribution by invading new habitats is due in large part to an ability to acclimate to new salinities. The purpose of this study was to assess colony growth and morphological changes at various salinities in freshwater and brackish genotypes of Cordylophora sp. Single genotypes from a known freshwater clade (0.5 psu; Des Plaines River) and a known brackish clade (16 psu; Napa River) were cultured and gradually transitioned to 12 different salinities ranging 0.5–22 psu, and we characterized the growth rates and hydranth morphological features at each salinity. Colony growth was optimal at 0.5 psu for the freshwater genotype and 10 psu for the brackish genotype. Changes in hydranth morphology in the freshwater genotype were primarily observed at higher salinities, while morphological changes in the brackish genotype primarily occurred at lower salinities. Our results for the brackish genotype generally concur with previous work, but this study is the first to document the response of a freshwater genotype of Cordylophora sp. to various salinities. Differences in growth between these two genotypes strongly support the previously proposed existence of multiple cryptic species. Furthermore, because this hydroid is quite prevalent in freshwater and brackish systems as a fouling organism, understanding the effects of various salinities on the successful establishment of Cordylophora sp. is an important contribution to the understanding of the ecophysiology and management of this invasive hydroid.     

Do saline taxa evolve faster? Comparing relative rates of molecular evolution between freshwater and marine eukaryotes

The major branches of life diversified in the marine realm, and numerous taxa have since transitioned between marine and freshwaters. Previous studies have demonstrated higher rates of molecular evolution in crustaceans inhabiting continental saline habitats as compared with freshwaters, but it is unclear whether this trend is pervasive or whether it applies to the marine environment. We employ the phylogenetic comparative method to investigate relative molecular evolutionary rates between 148 pairs of marine or continental saline versus freshwater lineages representing disparate eukaryote groups, including bony fish, elasmobranchs, cetaceans, crustaceans, mollusks, annelids, algae, and other eukaryotes, using available protein‐coding and noncoding genes. Overall, we observed no consistent pattern in nucleotide substitution rates linked to habitat across all genes and taxa. However, we observed some trends of higher evolutionary rates within protein‐coding genes in freshwater taxa—the comparisons mainly involving bony fish—compared with their marine relatives. The results suggest no systematic differences in substitution rate between marine and freshwater organisms.     

Variations in the migratory history of the tropical catadromous eels Anguilla bicolor bicolor and A. bicolor pacifica in south-east Asian waters

Fish movements between aquatic habitats of different salinity ranges (fresh, estuarine, marine) by the tropical catadromous eels Anguilla bicolor bicolor and A. bicolor pacifica were examined by analysing the otolith strontium and calcium concentrations of yellow (immature) and silver (mature) stage eels collected in south-east Asian (Indonesia, Malaysia and Vietnam) waters. The ratios suggest that all migratory-type eels, including freshwater, brackish water and marine residents, pass the river mouth. However, the habitat preference was different among the sites (countries). In Indonesia and Vietnam, most A. bicolor bicolor and A. bicolor pacifica were either marine or brackish water residents in this study. Alternatively, most A. bicolor bicolor were freshwater residents in Malaysia; such a typical catadromous migration pattern in these eels has not been found in previous studies. The wide range of otolith Sr:Ca in both subspecies indicates that the habitat use of these tropical eels was opportunistic among fresh, brackish and marine waters during their growth phases following recruitment to coastal areas. The geographical variability of migratory histories suggests that habitat use might be determined by the inter and intraspecific competition and environmental conditions at each site.     

A Proposed Timescale for the Evolution of Armophorean Ciliates: Clevelandellids Diversify More Rapidly Than Metopids

Members of the class Armophorea occur in microaerophilic and anaerobic habitats, including the digestive tract of invertebrates and vertebrates. Phylogenetic kinships of metopid and clevelandellid armophoreans conflict with traditional morphology‐based classifications. To reconcile their relationships and understand their morphological evolution and diversification, we utilized the molecular clock theory as well as information contained in the estimated time trees and morphology of extant taxa. The radiation of the last common ancestor of metopids and clevelandellids very likely occurred during the Paleozoic and crown diversification of the endosymbiotic clevelandellids dates back to the Mesozoic. According to diversification analyses, endosymbiotic clevelandellids have higher net diversification rates than predominantly free‐living metopids. Their cladogenic success was very likely associated with sharply isolated ecological niches constituted by their hosts. Conflicts between traditional classifications and molecular phylogenies of metopids and clevelandellids very likely come from processes, leading to further diversification without extinction of ancestral lineages as well as from morphological plesiomorphies incorrectly classified as apomorphies. Our study thus suggests that diversification processes and reconstruction of ancestral morphologies improve the understanding of paraphyly which occurs in groups of organisms with an apparently long evolutionary history and when speciation prevails over extinction.