Complete Mitochondrial Genome Sequences of the South American and the Australian Lungfish: Testing of the Phylogenetic Performance of Mitochondrial Data Sets for Phylogenetic Problems in Tetrapod Relationships

Nonlethal age estimation of three threatened fish species using DNA methylation: Australian lungfish, Murray cod and Mary River cod

Age‐based demography is fundamental to management of wild fish populations. Age estimates for individuals can determine rates of change in key life‐history parameters such as length, maturity, mortality and fecundity. These age‐based characteristics are critical for population viability analysis in endangered species and for developing sustainable harvest strategies. For teleost fish, age has traditionally been determined by counting increments formed in calcified structures such as otoliths. However, the collection of otoliths is lethal and therefore undesirable for threatened species. At a molecular level, age can be predicted by measuring DNA methylation. Here, we use previously identified age‐associated sites of DNA methylation in zebrafish (Danio rerio) to develop two epigenetic clocks for three threatened freshwater fish species. One epigenetic clock was developed for the Australian lungfish (Neoceratodus forsteri) and the second for the Murray cod (Maccullochellapeelii) and Mary River cod (Maccullochellamariensis). Age estimation models were calibrated using either known‐age individuals, ages derived from otoliths or bomb radiocarbon dating of scales. We demonstrate a high Pearson's correlation between the chronological and predicted age in both the Lungfish clock (cor = .98) and Maccullochella clock (cor = .92). The median absolute error rate for both epigenetic clocks was also low (Lungfish = 0.86 years; Maccullochella = 0.34 years). This study demonstrates the transferability of DNA methylation sites for age prediction between highly phylogenetically divergent fish species. Given the method is nonlethal and suited to automation, age prediction by DNA methylation has the potential to improve fisheries and other wildlife management settings.

Physiology: An Important Tool to Assess the Welfare of Aquatic Animals

Simple Summary

Ensuring a good quality of life for animals is a matter of concern. Welfare assessment has been quite well developed for many terrestrial species, but it is less well characterized for aquatic animals. Classic methodologies, such as behavioral observation, seem unable to improve the wellbeing of aquatic animals when used alone, mainly due to the large number of species and the difficulty to obtain comparative results among taxa. For this reason, it is necessary to identify more methodologies that may be common to the main aquatic taxa of interest to humans: Fish, cephalopods, and crustaceans. Here we present a physiological framework for these taxa as a proxy to evaluate aquatic animal welfare. Physiology is a useful tool in this regard, since animals maintain their homeostasis in a range of values determined for each parameter. Changes occur depending on the type and degree of stress to which animals are subjected. Therefore, understanding the physiology of stress can offer information that helps improve the welfare of aquatic animals.

Abstract

The assessment of welfare in aquatic animals is currently under debate, especially concerning those kept by humans. The classic concept of animal welfare includes three elements: The emotional state of the organism (including the absence of negative experiences), the possibility of expressing normal behaviors, and the proper functioning of the organism. While methods for evaluating their emotions (such as fear, pain, and anguish) are currently being developed for aquatic species and understanding the natural behavior of all aquatic taxa that interact with humans is a task that requires more time, the evaluation of internal responses in the organisms can be carried out using analytical tools. This review aims to show the potential of the physiology of crustaceans, cephalopods, elasmobranchs, teleosts, and dipnoans to serve as indicators of their wellbeing. Since the classical methods of assessing welfare are laborious and time-consuming by evaluation of fear, pain, and anguish, the assessment may be complemented by physiological approaches. This involves the study of stress responses, including the release of hormones and their effects. Therefore, physiology may be of help in improving animal welfare.

Ferritins in Chordata: Potential evolutionary trajectory marked by discrete selective pressures: History and reclassification of ferritins in chordates and geological events' influence on their evolution and radiation

Ferritins (FTs) are iron storage proteins that are involved in managing iron-oxygen balance. In our work, we present a hypothesis on the putative effect of geological changes that have affected the evolution and radiation of ferritin proteins. Based on sequence analysis and phylogeny reconstruction, we hypothesize that two significant factors have been involved in the evolution of ferritin proteins: fluctuations of atmospheric oxygen concentrations, altering redox potential, and changing availability of water rich in bioavailable ferric ions. Fish, ancient amphibians, reptiles, and placental mammals developed the broadest repertoire of singular FTs, attributable to embryonic growth in aquatic environments containing low oxygen levels and abundant forms of soluble iron. In contrast, oviparous land vertebrates, like reptiles and birds, that have developed in high oxygen levels and limited levels of environmental Fe²⁺ exhibit a lower diversity of singular FTs, but display a broad repertoire of subfamilies, particularly notable in early reptiles.

The NOS/NO system in an example of extreme adaptation: The African lungfish

African dipnoi (lungfish) are aestivating fish and obligate air breathers that, throughout their complex life cycle, undergo remarkable morpho-functional organ readjustment from biochemical to morphological level. In the present review we summarize the changes of the NOS/NO (Nitric Oxide Synthase/Nitric Oxide) system occurring in lungs, gills, kidney, heart, and myotomal muscle of African lungfish of the genus Protopterus (P. dolloi and P. annectens), in relation to the switch from freshwater to aestivation, and vice-versa. In particular, the expression and localization patterns of NOS, and its protein partners Akt, Hsp-90 and HIF-1α, have been discussed, together with the apoptosis rate, evaluated by TUNEL technique. We hypothesize that all these molecular components are crucial in signalling transduction/integration networks induced by environmental challenges (temperature, dehydration, inactivity)experienced at the beginning, during, and at the end of the dry season.

Origin and diversification of the plasminogen activation system among chordates

Background

The plasminogen (PLG) activation system is composed by a series of serine proteases, inhibitors and several binding proteins, which together control the temporal and spatial generation of the active serine protease plasmin. As this proteolytic system plays a central role in human physiology and pathophysiology it has been extensively studied in mammals. The serine proteases of this system are believed to originate from an ancestral gene by gene duplications followed by domain gains and deletions. However, the identification of ancestral forms in primitive chordates supporting these theories remains elusive. In addition, evolutionary studies of the non-proteolytic members of this system are scarce.

Results

Our phylogenetic analyses place lamprey PLG at the root of the vertebrate PLG-group, while lamprey PLG-related growth factors represent the ancestral forms of the jawed-vertebrate orthologues. Furthermore, we find that the earliest putative orthologue of the PLG activator group is the hyaluronan binding protein 2 (HABP2) gene found in lampreys. The prime plasminogen activators (tissue- and urokinase-type plasminogen activator, tPA and uPA) first occur in cartilaginous fish and phylogenetic analyses confirm that all orthologues identified compose monophyletic groups to their mammalian counterparts. Cartilaginous fishes exhibit the most ancient vitronectin of all vertebrates, while plasminogen activator inhibitor 1 (PAI-1) appears for the first time in cartilaginous fishes and is conserved in the rest of jawed vertebrate clades. PAI-2 appears for the first time in the common ancestor of reptiles and mammals, and represents the latest appearing plasminogen activator inhibitor. Finally, we noted that the urokinase-type plasminogen activator receptor (uPAR)—and three-LU domain containing genes in general—occurred later in evolution and was first detectable after coelacanths.

Conclusions

This study identifies several primitive orthologues of the mammalian plasminogen activation system. These ancestral forms provide clues to the origin and diversification of this enzyme system. Further, the discovery of several members—hitherto unknown in mammals—provide new perspectives on the evolution of this important enzyme system.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1353-z) contains supplementary material, which is available to authorized users.

Regional chemoarchitecture of the brain of lungfishes based on calbindin D-28K and calretinin immunohistochemistry

Lungfishes are the closest living relatives of land vertebrates, and their neuroanatomical organization is particularly relevant for deducing the neural traits that have been conserved, modified, or lost with the transition from fishes to land vertebrates. The immunohistochemical localization of calbindin (CB) and calretinin (CR) provides a powerful method for discerning segregated neuronal populations, fiber tracts, and neuropils and is here applied to the brains of Neoceratodus and Protopterus, representing the two extant orders of lungfishes. The results showed abundant cells containing these proteins in pallial and subpallial telencephalic regions, with particular distinct distribution in the basal ganglia, amygdaloid complex, and septum. Similarly, the distribution of CB and CR containing cells supports the division of the hypothalamus of lungfishes into neuromeric regions, as in tetrapods. The dense concentrations of CB and CR positive cells and fibers highlight the extent of the thalamus. As in other vertebrates, the optic tectum is characterized by numerous CB positive cells and fibers and smaller numbers of CR cells. The so-called cerebellar nucleus contains abundant CB and CR cells with long ascending axons, which raises the possibility that it could be homologized to the secondary gustatory nucleus of other vertebrates. The corpus of the cerebellum is devoid of CB and CR and cells positive for both proteins are found in the cerebellar auricles and the octavolateralis nuclei. Comparison with other vertebrates reveals that lungfishes share most of their features of calcium binding protein distribution with amphibians, particularly with salamanders.

Acute effects of temperature and hypercarbia on cutaneous and branchial gas exchange in the South American lungfish, Lepidosiren paradoxa

The South American lungfish, Lepidosiren paradoxa inhabits seasonal environments in the Central Amazon and Paraná-Paraguay basins that undergo significant oscillations in temperature throughout the year. They rely on different gas exchange organs, such as gills and skin for aquatic gas exchange while their truly bilateral lungs are responsible for aerial gas exchange; however, there are no data available on the individual contributions of the skin and the gills to total aquatic gas exchange in L. paradoxa. Thus, in the present study we quantify the relative contributions of skin and gills on total aquatic gas exchange during warm (35°C) and cold exposure (20°C) in addition to the effects of aerial and aquatic hypercarbia on aquatic gas exchange and gill ventilation rate (f_G; 25°C), respectively. Elevated temperature (35°C) caused a significant increase in the contribution of cutaneous (from 0.61±0.13 to 1.34±0.26ml. STPD.h^-1kg^-1) and branchial (from 0.54±0.17 to 1.73±0.53ml. STPD.h^-1kg^-1) gas exchange for V̇CO₂ relative to the lower temperature (20°C), while V̇O₂ remained relatively unchanged. L. paradoxa exhibited a greater branchial contribution in relation to total aquatic gas exchange at lower temperatures (20 and 25°C) for oxygen uptake. Aerial hypercarbia decreased branchial V̇O₂ whereas branchial V̇CO₂ was significantly increased. Progressive increases in aquatic hypercarbia did not affect f_G. This response is in contrast to increases in pulmonary ventilation that may offset any increase in arterial partial pressure of CO₂ owing to CO₂ loading through the animals' branchial surface. Thus, despite their reduced contribution to total gas exchange, cutaneous and branchial gas exchange in L. paradoxa can be significantly affected by temperature and aerial hypercarbia.

The Identification of the Closest Living Relative(s) of Tetrapods: Phylogenomic Lessons for Resolving Short Ancient Internodes

Identifying the closest living relative(s) of tetrapods is an important, yet still contested question in vertebrate phylogenetics. Three hypotheses are possible and ruling out alternatives has proven difficult even with large molecular data sets due to weak phylogenetic signal coupled nonphylogenetic noise resulting from relatively rapid speciation events that occurred a long time ago ([Formula: see text]400 Ma). Here, we revisit the identity of the closest living relative of land vertebrates from a phylogenomic perspective and include new genomic data for all extant lungfish genera. RNA-seq proves to be a great alternative to genomic sequencing, which currently is technically not feasible in lungfishes due to their huge (50-130 Gb) and repetitive genomes. We examined the most important sources of systematic error, namely long-branch attraction (LBA), compositional heterogeneity and distribution of missing data and applied different correction techniques. A multispecies coalescent approach is used to account for deep coalescence that might come from the short and deep internodes separating early sarcopterygian splits. Concatenation methods favored lungfishes as the closest living relatives of tetrapods with strong statistical support. Amino acid profile mixture models can unambiguously resolve this difficult internode thanks to their ability to avoid systematic error. We assessed the performance of different site-heterogeneous models and data partitioning and compared the ability of different strategies designed to overcome LBA, including taxon manipulation, reduction of among-lineage rate heterogeneity and removal of fast-evolving or compositionally heterogeneous positions. The identification of lungfish as sister group of tetrapods is robust regarding the effects of nonstationary composition and distribution of missing data. The multispecies coalescent method reconstructed strongly supported topologies that were congruent with concatenation, despite pervasive gene tree heterogeneity. We reject alternative topologies for early sarcopterygian relationships by increasing the signal-to-noise ratio in our alignments. The analytical pipeline outlined here combines probabilistic phylogenomic inference with methods for evaluating data quality, model adequacy, and assessing systematic error, and thus is likely to help resolve similarly difficult internodes in the tree of life. [Coalescence; coelacanth; compositional heterogeneity; gene tree; long-branch attraction; lungfish; missing data; model misspecification; phylogenomic; species tree; systematic error.].

Genetic Diversity and Hybridisation between Native and Introduced Salmonidae Fishes in a Swedish Alpine Lake

Understanding the processes underlying diversification can aid in formulating appropriate conservation management plans that help maintain the evolutionary potential of taxa, particularly under human-induced activities and climate change. Here we assessed the microsatellite genetic diversity and structure of three salmonid species, two native (Arctic charr, Salvelinus alpinus and brown trout, Salmo trutta) and one introduced (brook charr, Salvelinus fontinalis), from an alpine lake in sub-arctic Sweden, Lake Ånn. The genetic diversity of the three species was similar and sufficiently high from a conservation genetics perspective: corrected total heterozygosity, H’_T = 0.54, 0.66, 0.60 and allelic richness, A_R = 4.93, 5.53 and 5.26 for Arctic charr, brown trout and brook charr, respectively. There were indications of elevated inbreeding coefficients in brown trout (G_IS = 0.144) and brook charr (G_IS = 0.129) although sibling relationships were likely a confounding factor, as a high proportion of siblings were observed in all species within and among sampling locations. Overall genetic structure differed between species, Fst = 0.01, 0.02 and 0.04 in Arctic charr, brown trout and brook charr respectively, and there was differentiation at only a few specific locations. There was clear evidence of hybridisation between the native Arctic charr and the introduced brook charr, with 6% of individuals being hybrids, all of which were sampled in tributary streams. The ecological and evolutionary consequences of the observed hybridisation are priorities for further research and the conservation of the evolutionary potential of native salmonid species.

The Lungfish Transcriptome: A Glimpse into Molecular Evolution Events at the Transition from Water to Land

Lungfish and coelacanths are the only living sarcopterygian fish. The phylogenetic relationship of lungfish to the last common ancestor of tetrapods and their close morphological similarity to their fossil ancestors make this species uniquely interesting. However their genome size, the largest among vertebrates, is hampering the generation of a whole genome sequence. To provide a partial solution to the problem, a high-coverage lungfish reference transcriptome was generated and assembled. The present findings indicate that lungfish, not coelacanths, are the closest relatives to land-adapted vertebrates. Whereas protein-coding genes evolve at a very slow rate, possibly reflecting a “living fossil” status, transposable elements appear to be active and show high diversity, suggesting a role for them in the remarkable expansion of the lungfish genome. Analyses of single genes and gene families documented changes connected to the water to land transition and demonstrated the value of the lungfish reference transcriptome for comparative studies of vertebrate evolution.

Microscleres and gemmoscleres as phylogenetic signals in Spongillida: phylogeny and biogeography of the genus Metania Gray, 1867 (Porifera, Metaniidae)

The genus Metania comprises 11 species of freshwater sponge that are distributed circumtropically: five are Neotropical, three Afrotropical, two Oriental and one Australian. Here we infer the phylogeny of the genus Metania and examine the processes that lead to the current biogeographic distribution using cladistic analysis. One matrix with 26 morphological characters was analysed using the TNT software, and resulted in two most parsimonious cladograms (strict consensus). Our results support monophyly of Metania due to two characters unique to the genus: presence of acanthoxeas and presence of spines in the shaft of the gemmoscleres. Also, the genera Drulia and Houssayella were synonymised with Metania. The family Metaniidae – allocated in the recently proposed order Spongillida – now contains three genera: Acalle Gray, 1867, Metania Gray, 1867 and Corvomeyenia Weltner, 1913. Brooks parsimony analysis of Metania resulted in a single area cladogram showing a Gondwanan pattern: (Neartic (Australian (Oriental (Afrotropical, Neotropical)))) and thus the current distribution is explained by the breakup of Gondwana.

Comparative and phylogenetic perspectives of the cleavage process in tailed amphibians

The order Caudata includes about 660 species and displays a variety of important developmental traits such as cleavage pattern and egg size. However, the cleavage process of tailed amphibians has never been analyzed within a phylogenetic framework. We use published data on the embryos of 36 species concerning the character of the third cleavage furrow (latitudinal, longitudinal or variable) and the magnitude of synchronous cleavage period (up to 3–4 synchronous cell divisions in the animal hemisphere or a considerably longer series of synchronous divisions followed by midblastula transition). Several species from basal caudate families Cryptobranchidae (Andrias davidianus and Cryptobranchus alleganiensis) and Hynobiidae (Onychodactylus japonicus) as well as several representatives from derived families Plethodontidae (Desmognathus fuscus and Ensatina eschscholtzii) and Proteidae (Necturus maculosus) are characterized by longitudinal furrows of the third cleavage and the loss of synchrony as early as the 8-cell stage. By contrast, many representatives of derived families Ambystomatidae and Salamandridae have latitudinal furrows of the third cleavage and extensive period of synchronous divisions. Our analysis of these ontogenetic characters mapped onto a phylogenetic tree shows that the cleavage pattern of large, yolky eggs with short series of synchronous divisions is an ancestral trait for the tailed amphibians, while the data on the orientation of third cleavage furrows seem to be ambiguous with respect to phylogeny. Nevertheless, the midblastula transition, which is characteristic of the model species Ambystoma mexicanum (Caudata) and Xenopus laevis (Anura), might have evolved convergently in these two amphibian orders.

Phylogenetic aspects of carbamoyl phosphate synthetase in lungfish: a transitional enzyme in transitional fishes

Carbamoyl phosphate synthetase (CPS) catalyses the formation of carbamoyl phosphate from glutamine or ammonia, bicarbonate and ATP. There are three different isoforms of CPS that play vital roles in two metabolic pathways, pyrimidine biosynthesis (CPS II) and arginine/urea biosynthesis (CPS I and CPS III). Gene duplication has been proposed as the evolutionary mechanism creating this gene family with CPS II likely giving rise to the CPS I/III clade. In the evolutionary history of this gene family it is still undetermined when CPS I diverged from CPS III on the path to terrestriality in the vertebrates. Transitional organisms such as lungfishes are of particular interest because they are capable of respiring via gills and with lungs and therefore can be found in both aquatic and terrestrial environments. Notably, enzymatic characterization of the mitochondrial CPS isoforms in this transitional group has not led to clear conclusions. In order to determine which CPS isoform is present in transitional animals, we examined partial sequences for liver CPS amplified from five species of lungfish, and a larger fragment of CPS from one lungfish species (Protopterus annectens) and compared them to CPS isoforms from other fish and mammals. Enzyme activities for P. annectens liver were also examined. While enzyme activities did not yield a clear distinction between isoforms (virtually equal activities were obtained for either CPS I or III), CPS sequences from the lungfishes formed a monophyletic clade within the CPS I clade and separate from the CPS III clade of other vertebrates. This finding implies that the mitochondrial isoform of CPS in lungfish is derived from CPS I and is likely to have a physiological function similar to CPS I. This finding is important because it supports the hypothesis that lungfish employ a urea cycle similar to terrestrial air-breathing vertebrates.

The non-evaginated secondary prosencephalon of vertebrates

The secondary prosencephalon (telencephalon plus hypothalamus) is probably the most complex area of the brain, with complicated patterning specifications. As yet, no prosomeric subdivisions have been reported and only distinct histogenetic territories have been recognized. In the present comparative study we analyzed cross-correlated expression maps in the non-evaginated territories of the secondary prosencephalon in different vertebrates throughout development, to assess the existence of comparable divisions and subdivisions in the different groups. Each division is characterized by expression of a unique combination of developmental regulatory genes, and each appears to represent a self-regulated and topologically constant histogenetic brain compartment that gives rise to a specific cell group. The non-evaginated area of the telencephalon corresponds to the preoptic region, whereas the hypothalamus, topologically rostral to the diencephalic prethalamus, includes basal (mammillary and tuberal) and alar (paraventricular and suprachiasmatic) parts. This complex area is specified by a cascade of transcription factors, among which the Dlx family members and Nkx2.1 are essential for the correct development. The only exception is found in the subdivision named termed the supraoptoparaventricular area, in which the transcription factor Orthopedia is essential in restricting the fate of multiple categories of neuroendocrine neurons, in the absence of the Dlx/Nkx2.1 combination. Our analysis, based on own data and published results by other researchers, suggests that common features are shared at least by all tetrapods and, therefore, they most likely were present in the stem tetrapods. The available data for agnathans (lampreys) and other fish groups indicate that not all subdivisions of the secondary prosencephalon were present at the origin of vertebrates, raising important questions about their evolution.

F. K. Studnička (1894): Fishes and amphibians also have the cerebral cortex

The aim of this paper is to provide translation of probably the first report (Studnička 1894) demonstrating that the telencephalon of all vertebrate taxa (including fishes and amphibians) is characterized by the presence of the cerebral cortex (pallium). This report was one of those initiating a century-long and still not fully resolved discussion concerning homologies of various pallial subdivisions in different vertebrate taxa and probably the first to draw attention to the importance of careful study of the pallium in representatives of agnathans (Cyclostomes) such as lampreys (Petromyzonts) and hagfishes (Myxinoids). This article also briefly reviews the current status of comparative research on vertebrate telencephalon, and provides historical notes which position Studnička’s report in its historical context.

Comparing the performance of multiple mitochondrial genes in the analysis of Australian freshwater fishes

In this study, four mitochondrial genes (cytochrome oxidase I, ATPase, cytochrome b and control region) were amplified from most of the fish species found in the fresh waters of south-eastern Queensland, Australia. The performance of these different gene regions was compared in terms of their ability to cluster fish families together in a neighbour-joining tree, both individually by gene and in all combinations. The relative divergence rates of each of these genes were also calculated. The three coding genes (cytochrome oxidase I, ATPase and cytochrome b) recovered similar number of families and had broadly similar divergence rates. ATPase diverged a little more quickly than cytochrome oxidase I and cytochrome b slightly more slowly than cytochrome oxidase I. All two-gene combinations recovered the same number of families. Results from the control region were much more variable, and, although generally possessing more diversity than the other regions, were sometimes less variable.

The complete mitochondrial genome of dhole Cuon alpinus: phylogenetic analysis and dating evolutionary divergence within Canidae

The dhole (Cuon alpinus) is the only existent species in the genus Cuon (Carnivora: Canidae). In the present study, the complete mitochondrial genome of the dhole was sequenced. The total length is 16672 base pairs which is the shortest in Canidae. Sequence analysis revealed that most mitochondrial genomic functional regions were highly consistent among canid animals except the CSB domain of the control region. The difference in length among the Canidae mitochondrial genome sequences is mainly due to the number of short segments of tandem repeated in the CSB domain. Phylogenetic analysis was progressed based on the concatenated data set of 14 mitochondrial genes of 8 canid animals by using maximum parsimony (MP), maximum likelihood (ML) and Bayesian (BI) inference methods. The genera Vulpes and Nyctereutes formed a sister group and split first within Canidae, followed by that in the Cuon. The divergence in the genus Canis was the latest. The divarication of domestic dogs after that of the Canis lupus laniger is completely supported by all the three topologies. Pairwise sequence divergence data of different mitochondrial genes among canid animals were also determined. Except for the synonymous substitutions in protein-coding genes, the control region exhibits the highest sequence divergences. The synonymous rates are approximately two to six times higher than those of the non-synonymous sites except for a slightly higher rate in the non-synonymous substitution between Cuon alpinus and Vulpes vulpes. 16S rRNA genes have a slightly faster sequence divergence than 12S rRNA and tRNA genes. Based on nucleotide substitutions of tRNA genes and rRNA genes, the times since divergence between dhole and other canid animals, and between domestic dogs and three subspecies of wolves were evaluated. The result indicates that Vulpes and Nyctereutes have a close phylogenetic relationship and the divergence of Nyctereutes is a little earlier. The Tibetan wolf may be an archaic pedigree within wolf subspecies. The genetic distance between wolves and domestic dogs is less than that among different subspecies of wolves. The domestication of dogs was about 1.56-1.92 million years ago or even earlier.

Vasotocin/V2-type receptor/aquaporin axis exists in African lungfish kidney but is functional only in terrestrial condition

The vasopressin/vasotocin (VT)-V2-type receptor (V2R)-aquaporin (AQP)-2 axis plays a pivotal role in renal water reabsorption in tetrapods. It is widely thought that this axis evolved with the emergence of the tetrapods, reflecting a requirement of water retention in terrestrial environment. Here we report that lungfish, the closest living relatives of tetrapods, already possess a system similar to the VT-V2R-AQP2 axis in the kidney, but the system is functional only in the terrestrial estivating condition. We cloned a novel AQP paralogous to AQP0. The water permeability of Xenopus oocytes was increased by injection with the AQP cRNA and was further facilitated by preincubation with cAMP. In the kidney of estivating lungfish, the AQP protein was localized on the apical plasma membrane of the late distal tubule and was colocalized with basolateral V2R. By contrast, we found only little expression of the AQP mRNA and protein in the kidney of lungfish in aquatic condition. The expression levels of mRNA and protein were dramatically increased during estivation and decreased again by reacclimation of estivating lungfish to water. The AQP mRNA levels positively correlated with the VT mRNA levels in the hypothalamus, suggesting that the AQP exerts tubular antidiuretic action under control of VT. Because the tetrapod AQP2/AQP5 lineage is considered to be evolved from duplication of an AQP0 gene, the paralogous AQP0 in the lungfish probably represents ancestral molecule for tetrapod AQP2.

The unusual energy metabolism of elasmobranch fishes

The unusual energy metabolism of elasmobranchs is characterized by limited or absent fatty acid oxidation in cardiac and skeletal muscle and a great reliance on ketone bodies and amino acids as oxidative fuels in these tissues. Other extrahepatic tissues in elasmobranchs rely on ketone bodies and amino acids for aerobic energy production but, unlike muscle, also appear to possess a significant capacity to oxidize fatty acids. This organization of energy metabolism is reflected by relatively low plasma levels of non-esterified fatty acids (NEFA) and by plasma levels of the ketone body ss-hydroxybutyrate that are as high as those seen in fasted mammals. The preference for ketone body oxidation rather than fatty acid oxidation in muscle of elasmobranchs under routine conditions is opposite to the situation in teleosts and mammals. Carbohydrates appear to be utilized as a fuel source in elasmobranchs, similar to other vertebrates. Amino acid- and lipid-fueled ketogenesis in the liver, the lipid storage site in elasmobranchs, sustains the demand for ketone bodies as oxidative fuels. The liver also appears to export NEFA and serves a buoyancy role. The regulation of energy metabolism in elasmobranchs and the effects of environmental factors remain poorly understood. The metabolic organization of elasmobranchs was likely present in the common ancestor of the Chondrichthyes ca. 400million years ago and, speculatively, it may reflect the ancestral metabolism of jawed vertebrates. We assess hypotheses for the evolution of the unusual energy metabolism of elasmobranchs and propose that the need to synthesize urea has influenced the utilization of ketone bodies and amino acids as oxidative fuels.

Evidence for maternal inheritance of mitochondrial DNA in allotetraploid

The complete mitochondrial DNA (mtDNA) sequences of the allotetraploid and red crucian carp were determined in this paper. We compared the complete mtDNA sequences between the allotetraploid and its female parent red crucian carp, and between the allotetraploid and its male parent common carp. The results indicated that the complete mtDNA nucleotide identity (99.7%) between the allotetraploid and its female parent red crucian carp was higher than that (89.0%) between the allotetraploid and its male parent common carp. Moreover, the analysis on the start and stop codons, overlaps and spacers, and phylogeny of the mt genomes indicated the genetic relationship between the allotetraploid and its female parent red crucian carp was closer than that between the allotetraploid and its male parent common carp. Our results indicated that the allotetraploid mt genome was strictly maternally inherited. Through maternal inheritance, the mt genome in the F(11) allotetraploid displayed extremely high similarity to that in the female parent red crucian carp after 11 generations (from F(1) to F(11) hybrids). Such results indicated that the F(11) allotetraploid possessed the stable inheritance characteristic. Thus the tetraploid stocks possessed the good base to form a new tetraploid species in the future. Since the establishment of the new tetraploid stocks has the great significance in analyzing evolutionary theory of vertebrate and in improving aquaculture industry, analysis of the mt genome and the elucidation of the variation of the mt genome in the allotetraploid and its parents proved that it was a useful genetic marker to monitor the variations in the progeny of the crosses.

Visual ecology of the Australian lungfish (Neoceratodus forsteri)

Background

The transition from water to land was a key event in the evolution of vertebrates that occurred over a period of 15–20 million years towards the end of the Devonian. Tetrapods, including all land-living vertebrates, are thought to have evolved from lobe-finned (sarcopterygian) fish that developed adaptations for an amphibious existence. However, while many of the biomechanical and physiological modifications necessary to achieve this feat have been studied in detail, little is known about the sensory adaptations accompanying this transition. In this study, we investigated the visual system and visual ecology of the Australian lungfish Neoceratodus forsteri, which is the most primitive of all the lungfish and possibly the closest living relative to the ancestors of tetrapods.

Results

Juvenile Neoceratodus have five spectrally distinct retinal visual pigments. A single type of rod photoreceptor contains a visual pigment with a wavelength of maximum absorbance (λ_max) at 540 nm. Four spectrally distinct single cone photoreceptors contain visual pigments with λ_max at 366 (UVS), 479 (SWS), 558 (MWS) and 623 nm (LWS). No double cones were found. Adult lungfish do not possess UVS cones and, unlike juveniles, have ocular media that prevent ultraviolet light from reaching the retina. Yellow ellipsoidal/paraboloidal pigments in the MWS cones and red oil droplets in the LWS cones narrow the spectral sensitivity functions of these photoreceptors and shift their peak sensitivity to 584 nm and 656 nm, respectively. Modelling of the effects of these intracellular spectral filters on the photoreceptor colour space of Neoceratodus suggests that they enhance their ability to discriminate objects, such as plants and other lungfishes, on the basis of colour.

Conclusion

The presence of a complex colour vision system based on multiple cone types and intracellular spectral filters in lungfishes suggests that many of the ocular characteristics seen in terrestrial or secondarily aquatic vertebrates, such as birds and turtles, may have evolved in shallow water prior to the transition onto land. Moreover, the benefits of spectral filters for colour discrimination apply equally to purely aquatic species as well as semi-aquatic and terrestrial animals. The visual system of the Australian lungfish resembles that of terrestrial vertebrates far more closely than that of other sarcopterygian fish. This supports the idea that lungfishes, and not the coelacanth, are the closest living relatives of the ancestors of tetrapods.

Molecular cloning, characterization, and evolutionary analysis of estrogen receptors from phylogenetically ancient fish

Estrogens are necessary for ovarian differentiation during a critical developmental stage in many vertebrates, and they promote the growth and differentiation of the adult female reproductive system. To understand the evolution of vertebrate estrogen receptors (ESRs) and to evaluate estrogen receptor-ligand interactions in phylogenetically ancient fish, we used PCR techniques to isolate the cDNA encoding ESRs from lungfish, sturgeon, and gar. Sequence analyses indicate that these fishes have two ESRs, ESR1 (ERalpha) and ESR2 (ERbeta), as previously reported for other vertebrate species, but a second type of ESR2 (ERbeta2) was not found as has been reported in a number of teleost fishes. Phylogenetic analysis of the ESR sequences indicated that the lungfish ESRs are classified to the tetrapod ESR group, not with the teleost fish ESRs as are the ESRs from gar and sturgeon. Using transient transfection assays of mammalian cells, ESR proteins from these three ancient fishes displayed estrogen-dependent activation of transcription from an estrogen-responsive-element containing promoter. We also examined the estrogenic potential of o,p'-dichloro-diphenyl-trichloroethane (o,p'-DDT) and p,p'-DDT as well as one of its common metabolites, p,p'-dichloro-diphenyl-ethylene (p,p'-DDE) on the ESRs from these fishes. Lungfish ESR1 was less sensitive to DDT/DDE than the ESR1 from the other two fishes. The response of lungfish ESR1 to these pesticides is similar to the pattern obtained from salamander ESR1. These data provide a basic tool allowing future studies examining the receptor-ligand interactions and endocrine-disrupting mechanisms in three species of phylogenetically ancient fish and also expands our knowledge of ESR evolution.

Evaluation of posttranslational processing of proopiomelanocortin in the banded houndshark pituitary by combined cDNA cloning and mass spectrometry

Proopiomelanocortin (POMC) is cleaved into small peptides, such as adrenocorticotropic hormone (ACTH), melanocyte-stimulating hormones (MSHs), and beta-endorphin (beta-END), by tissue-specific posttranslational processing in the corticotrophs of the pars distalis (PD) and melanotrophs of the neurointermediate lobe (NIL) of the pituitary. We examined the posttranslational processing of POMC in the pituitary of the banded houndshark Triakis scyllium by molecular cloning and subsequent mass spectrometric identification of the POMC-derived peptides in the pituitary extracts. One-fifth of the randomly selected clones from a Triakis pituitary cDNA library contained a cDNA encoding for POMC. Triakis prePOMC contained 4 MSHs and a single beta-END, as has been observed in case of other cartilaginous fish POMCs. These predicted hormonal segments were flanked by basic amino acid residues, which are the cleavage sites for the processing enzymes, i.e., protein convertases. Mass spectrometry was performed using PD (including most parts of the rostral and proximal PD) and NIL extracts to detect mass values corresponding to the POMC-derived peptides. Consequently, ACTH, beta-END, and the joining peptide (JP) were detected in the PD extract, while MSHs, processed beta-END, and some other POMC-derived peptides were identified in the NIL extract; however, neither acetylated alpha-MSH nor acetylated beta-END was detected in the latter. These tissue-specific POMC processing patterns are similar to those of the other vertebrate pituitaries; however, the absence of acetylated peptides suggests the lack of an acetylation system in the melanotrophs in the NIL of the Triakis pituitary.

Gondwanan break-up: legacies of a lost world?

Fierce debate surrounds the history of organisms in the southern hemisphere; did Gondwanan break-up produce ocean barriers that imposed distribution patterns on phylogenies (vicariance)? Or have organisms modified their distributions through trans-oceanic dispersal? Recent advances in biogeographical theory suggest that the current focus on vicariance versus dispersal is too narrow because it ignores 'geodispersal' (i.e. expansion of species into areas when geographical barriers disappear), extinction and sampling errors. Geodispersal produces multiple, conflicting vicariance patterns, and extinction and sampling errors destroy vicariance patterns. This perspective suggests that it is more difficult to detect vicariance than trans-oceanic dispersal and that specialized methods must be applied if an unbiased understanding of southern hemisphere biogeography is to be achieved.

Developmental plasticity and disparity in early dipnoan (lungfish) dentitions

Although the lungfish (Dipnoi) belong within the Osteichthyes, their dentitions are radically different from other osteichthyans. Lungfish dentitions also show a uniquely high structural disparity during the early evolution of the group, partly owing to the independent variation of odontogenic and odontoclastic processes that are tightly and stereotypically coordinated in other osteichthyans. We present a phylogenetic analysis of early lungfishes incorporating a novel approach to coding these process characters in preference to the resultant adult dental morphology. The results only partially resolve the interrelationships of Devonian dipnoans, but show that the widely discussed hypothesis of separate tooth-plated, dentine-plated, and denticulated lineages is unlikely to be true. The dipnoan status of Diabolepis is corroborated. Lungfish dentitions seem to have undergone extensive and nonparsimonious evolution during the early history of the group, but much of the resulting disparity can be explained by a modest number of evolutionary steps in the underlying developmental processes, those for dental formation (odontogenic) and those for the remodeling of dentine tissue (odontoclastic). Later in lungfish evolution, this disparity was lost as the group settled to a pattern of dental development that is just as stereotypic as, but completely different from, that of other osteichthyans.

Ribosomal RNA genes and deuterostome phylogeny revisited: More cyclostomes, elasmobranchs, reptiles, and a brittle star

This is an expanded study of the relationships among the deuterostome animals based on combined, nearly complete 28S and 18S rRNA genes (>3925 nt.). It adds sequences from 20 more taxa to the approximately 45 sequences used in past studies. Seven of the new taxa were sequenced here (brittle star Ophiomyxa, lizard Anolis, turtle Chrysemys, sixgill shark Hexanchus, electric ray Narcine, Southern Hemisphere lamprey Geotria, and Atlantic hagfish Myxine for 28S), and the other 13 were from GenBank and the literature (from a chicken, dog, rat, human, three lungfishes, and several ray-finned fishes, or Actinopterygii). As before, our alignments were based on secondary structure but did not account for base pairing in the stems of rRNA. The new findings, derived from likelihood-based tree-reconstruction methods and by testing hypotheses with parametric bootstrapping, include: (1) brittle star joins with sea star in the echinoderm clade, Asterozoa; (2) with two hagfishes and two lampreys now available, the cyclostome (jawless) fishes remain monophyletic; (3) Hexanchiform sharks are monophyletic, as Hexanchus groups with the frilled shark, Chlamydoselachus; (4) turtle is the sister taxon of all other amniotes; (5) bird is closer to the lizard than to the mammals; (6) the bichir Polypterus is in a monophyletic Actinopterygii; (7) Zebrafish Danio is the sister taxon of the other two teleosts we examined (trout and perch); (8) the South American and African lungfishes group together to the exclusion of the Australian lungfish. Other findings either upheld those of the previous rRNA-based studies (e.g., echinoderms and hemichordates group as Ambulacraria; orbitostylic sharks; batoids are not derived from any living lineage of sharks) or were obvious (monophyly of mammals, gnathostomes, vertebrates, echinoderms, etc.). Despite all these findings, the rRNA data still fail to resolve the relations among the major groups of deuterostomes (tunicates, Ambulacraria, cephalochordates and vertebrates) and of gnathostomes (chondrichthyans, lungfishes, coelacanth, actinopterygians, amphibians, and amniotes), partly because tunicates and lungfishes are rogue taxa that disrupt the tree. Nonetheless, parametric bootstrapping showed our RNA-gene data are only consistent with these dominant hypotheses: (1) deuterostomes consist of Ambulacraria plus Chordata, with Chordata consisting of tunicates and 'vertebrates plus cephalochordates'; and (2) lungfishes are the closest living relatives of tetrapods.

Purification and characterization of pepsinogens from the gastric mucosa of African coelacanth, Latimeria chalumnae, and properties of the major pepsins

Two major pepsinogens, PG1 and PG2, and one minor pepsinogen, PG3, were purified from the gastric mucosa of African coelacanth, Latimeria chalumnae (Actinistia). PG1 and PG2 were much less acidic than PG3. Their molecular masses were estimated by SDS-PAGE to be 37.0, 37.0 and 39.3 kD, respectively. When incubated at pH 2.0, PG1 and PG2 were converted autocatalytically to the mature pepsins through an intermediate form, whereas PG3 was converted to an intermediate form, but not to the mature pepsin autocatalytically. The N-terminal sequencing indicated that the 42 residue sequences of the propeptides of PG1 and PG2 were essentially identical with each other, but different from that of PG3. A phylogenetic tree based on the N-terminal propeptide sequences indicates that PG1 and PG2 belong to the pepsinogen A group, and PG3 to the pepsinogen C group. From the phylogenetic comparison, coelacanth PG1 and PG2 appear to be evolutionally closer to tetrapod pepsinogens A than ray-finned fish pepsinogens A, consistent with the traditional systematics. Pepsins 1 and 2 were essentially identical with each other and rather similar to mammalian pepsins A in the pH optimum toward hemoglobin (pH 2-2.5), the cleavage specificity toward oxidized insulin B chain and strong inhibition by pepstatin, except that they possessed a significant level of activity in the higher pH range unlike mammalian pepsins A.

Cloning and sequence analysis of the neuropeptide Y receptors Y5 and Y6 in the coelacanth Latimeria chalumnae

Two coelacanth species, Latimeria chalumnae and Latimeria menadoensis, the recently discovered second species, have a key evolutionary position at the divergence of bony fishes and tetrapods. Together with lungfishes, they are the only living species separating the species-rich tetrapods from the other major group of vertebrates, the ray-finned fishes. The coelacanth is therefore of great importance for comparisons of gene families that differ between these two groups, such as the neuropeptide Y (NPY) receptor family. In this work we have sequenced the full-length genes for two NPY receptors in Latimeria chalumnae. Phylogenetic analysis indicated that the two sequences are orthologs of the mammalian Y5 and Y6 receptors. The Y5 gene has been implicated in appetite stimulation in mammals but is absent from teleost fishes. The presence of the Y5 receptor in Latimeria together with phylogenetic analysis shows that Y5 existed before the separation of bony fishes and tetrapods. The Latimeria receptor has about 62% identity to tetrapod Y5 sequences and contains the extended third intracellular loop with several highly conserved motifs that may be involved in signal transduction. The Latimeria Y6 receptor has about 60% identity to tetrapod Y6 sequences. The functional role of Y6 is unclear as the gene is seemingly functional in some mammals but is non-functional in others. The Y6 receptor is also missing in teleost fishes. Our results confirm an early vertebrate origin for all NPY receptor subtypes presently found in mammals followed by differential gene loss in the different classes of vertebrates.

Mitochondrial genomes of parasitic arthropods: implications for studies of population genetics and evolution

Over 39000 species of arthropods parasitize humans, domestic animals and wildlife. Despite their medical, veterinary and economic importance, most aspects of the population genetics and evolution of the vast majority of parasitic arthropods are poorly understood. Mitochondrial genomes are a rich source of markers for studies of population genetics and evolution. These markers include (1) nucleotide sequences of each of the 37 mitochondrial genes and non-coding regions; (2) concatenated nucleotide sequences of 2 or more genes; and (3) genomic features, such as gene duplications, gene rearrangements, and changes in gene content and secondary structures of RNAs. To date, the mitochondrial genomes of over 700 species of multi-cellular animals have been sequenced entirely, however, only 24 of these species are parasitic arthropods. Of the mitochondrial genome markers, only the nucleotide sequences of 4 mitochondrial genes,cox1,cob,rrnSandrrnL, have been well explored in population genetic and evolutionary studies of parasitic arthropods whereas the sequences of the other 33 genes, and various genomic features have not. We review current knowledge of the mitochondrial genomes of parasitic arthropods, summarize applications of mitochondrial genes and genomic features in population genetic and evolutionary studies, and highlight prospects for future research.

Implementation of a Markov model for phylogenetic trees

A recently developed mathematical model for the analysis of phylogenetic trees is applied to comparative data for 48 species. The model represents a return to fundamentals and makes no hypothesis with respect to the reversibility of the process. The species have been analysed in all subsets of three, and a measure of reliability of the results is provided. The numerical results of the computations on 17,296 triples of species are made available on the Internet. These results are discussed and the development of reliable tree structures for several species is illustrated. It is shown that, indeed, the Markov model is capable of considerably more interesting predictions than has been recognized to date.

Magic bullets and golden rules: data sampling in molecular phylogenetics

Data collection for molecular phylogenetic studies is based on samples of both genes and taxa. In an ideal world, with no limitations to resources, as many genes could be sampled as deemed necessary to address phylogenetic problems. Given limited resources in the real world, inadequate (in terms of choice of genes or number of genes) sequences or restricted taxon sampling can adversely affect the reliability or information gained in phylogenetics. Recent empirical and simulation-based studies of data sampling in molecular phylogenetics have reached differing conclusions on how to deal with these problems. Some advocated sampling more genes, others more taxa. There is certainly no 'magic bullet' that will fit all phylogenetic problems, and no specific 'golden rules' have been deduced, other than that single genes may not always contain sufficient phylogenetic information. However, several general conclusions and suggestions can be made. One suggestion is that the determination of a multiple, but moderate number (e.g., 6-10) of gene sequences might take precedence over sequencing a larger set of genes and thereby permit the sampling of more taxa for a phylogenetic study.

Thyroid hormone deiodinases revisited: insights from lungfish: a review

In vertebrates, hormones released from the thyroid gland travel in the circulation to target tissues where they may be processed by deiodinating enzymes into more active or inactive iodothyronines. In mammals, there are three deiodinating enzymes described. Type1 (D1), which primarily occurs in the liver, converts reverse T3 into T2 for clearance. It also converts T4 into T3. This production of T3 is believed to contribute to the bulk of circulating T3 in mammals. The type2 (D2) enzyme may be found in many other tissues where it converts T4 to T3, which is then transferred to the receptors in the nucleus of the same cell, i.e. does not contribute to the circulating T3. The type3 (D3) enzyme converts T3 into T2. The expression of the genes for these three enzymes and/or the activity of the enzymes have been studied in several non-mammalian groups of vertebrates. From agnathans to birds, D2 and D3 appear to occur universally, with the possible exception of squamate reptiles (lack D2?). D1 has not been found in amphibians, lungfish or agnathans. All three enzymes are selenoproteins, in which a selenocysteine is found in the active centre. The nucleotide code for translation of a selenocysteine is UGA, which under normal circumstances is a stop codon. In order for UGA to code for selenocysteine, there must be a SECIS element in the 3'UTR of the mRNA. Any disruption of the SECIS will result in a truncated protein in the region of its active centre. It is suggested that such alternative splicing may be a mode of altering the expression of deiodinases in particular tissues to change the response of such tissues to thyroid hormones under differing circumstances such as stages of development.