Extensive genome duplications in sturgeons: new evidence from microsatellite data

Genome duplications and polyploidization events are thought to have played relevant roles in the early stages of vertebrate evolution, in particular near the time of divergence of the lamprey lineage. Additional genome duplications, specifically in ray‐finned fish, may have occurred before the divergence of the teleosts. The role of polyploidization in vertebrate genome evolution is a thriving area of research. Sturgeons (order Acipenseriformes) provide a unique model for the investigation of genome duplication, with existing species possessing 120, 250 or 360 chromosomes. In the present study, data from 240 sturgeon specimens representing 11 species were used for analysis of ploidy levels. Allele numbers were assessed at eleven microsatellite loci. The results provide further evidence for functional diploidy, tetraploidy and hexaploidy in species possessing 120, 250 and 360 chromosomes, respectively. The analysis also uncovered novel evidence for functional hexaploidy in the shortnose sturgeon (Acipenser brevirostrum). In conclusion, the process of functional genome reduction is demonstrated to be an on‐going process in this fish lineage.     

Microsatellite primers for the Atlantic coastal killifish,Fundulus heteroclitus,with applicability to related Fundulus species

The mummichog (Fundulus heteroclitus), a common Atlantic coastal killifish, is a model vertebrate species for the study of molecular genetic variation in natural populations and of environmental toxicology. We report the development of a set of 20 microsatellite loci in this species. Average expected heterozygosity across all loci was 0.84 (range: 0.60–0.97), revealing a high level of variability at most loci. A survey of seven additional Fundulus species yielded one or two robust amplification products in over half (63%) of the species–primer combinations tested. Therefore, many of these loci will also prove useful in studies of other members of the genus Fundulus.     

Structure and Conservation of Tandem Repeats in the Mitochondrial DNA Control Region of the Least Brook Lamprey (<Emphasis Type="Italic">Lampetra aepyptera</Emphasis>)

Tandemly repeated sequences are a common feature of vertebrate mitochondrial DNA control regions. However, questions still remain about their mode of evolution, function, and phylogenetic distribution. We report phylogenetic and geographic patterns of variation of control region repeat sequence and number in a nonparasitic lamprey, Lampetra aepyptera. A survey of populations from throughout the species’ range revealed remarkably low repeat sequence polymorphism but some interpopulation variation in repeat number. The high sequence similarity extended to repeats observed in other species in the genus Lampetra and other lamprey genera. The very low levels of variation suggest a high copy turnover. Our data are consistent with the illegitimate elongation model of repeat gain and loss and further suggest that repeat change occurs at internal copies. However, the limited variation across some species of lamprey suggests that functional constraints may further limit variation.     

Characterization of 12 microsatellite loci for the Pacific lamprey, Entosphenus tridentatus (Petromyzontidae), and cross-amplification in five other lamprey species

The Pacific lamprey (Entosphenus tridentatus) is an anadromous fish that is of conservation concern in North America and Asia. Data on Pacific lamprey population structure are scarce and conflicting, impeding conservation efforts. We optimized 12 polymorphic microsatellite loci for the Pacific lamprey. Three to 13 alleles per locus were observed in a sample of 51 fish collected from the West Fork Illinois River, Oregon. Observed heterozygosity ranged from 0.235 to 0.902 and expected heterozygosity ranged from 0.214 to 0.750. Cross-species amplification produced 8 to 12 polymorphic loci in four other Entosphenus species and in the western brook lamprey (Lampetra richardsoni). Two loci appear to be diagnostic for distinguishing Entosphenus from Lampetra. These markers will be valuable for evaluating population structure and making conservation decisions for E. tridentatus and other lamprey species.     

On the origin of the olfactory receptor family: receptor genes of the jawless fish (Lampetra fluviatilis).

In vertebrates, recognition of odorous compounds is based on a large repertoire of receptor subtypes encoded by a multigene family. Towards an understanding of the phylogenetic origin of the vertebrate olfactory receptor family, attempts have been made to identify related receptor genes in the river lampreys (Lampetra fluviatilis), which are descendants of the earliest craniates and living representatives of the most ancient vertebrates. Employing molecular cloning approaches led to the discovery of four genes encoding heptahelical receptors, which share only a rather low overall sequence identity but several of the characteristic structural hallmarks with vertebrate olfactory receptors. Furthermore, in situ hybridization studies demonstrated that the identified genes are expressed in chemosensory cells of the singular lamprey olfactory organ. Molecular phylogenetic analysis confirmed a close relationship of the lamprey receptors to vertebrate olfactory receptors and in addition demonstrated that olfactory genes of the agnathostomes diverged from the gnathostome receptor genes before those split into class I and class II receptors. The data indicate that the lamprey receptors represent the most ancient family of the hitherto identified vertebrate olfactory receptors.     

Evidence for the genetic basis and epistatic interactions underlying ocean‐ and river‐maturing ecotypes of Pacific Lamprey (Entosphenus tridentatus) returning to the Klamath River,California

Surveys of genomic variation have improved our understanding of the relationship between fitness‐related phenotypes and their underlying genetic basis. In some cases, single large‐effect genes have been found to underlie important traits; however, complex traits are expected to be under polygenic control and elucidation of multiple gene interactions may be required to fully understand the genetic basis of the trait. In this study, we investigated the genetic basis of the ocean‐ and river‐maturing ecotypes in anadromous Pacific lamprey (Entosphenus tridentatus). In Pacific lamprey, the ocean‐maturing ecotype is distinguished by advanced maturity of females (e.g., large egg mass) at the onset of freshwater migration relative to immature females of the river‐maturing ecotype. We examined a total of 219 adult Pacific lamprey that were collected at‐entry to the Klamath River over a 12‐month period. Each individual was genotyped at 308 SNPs representing known neutral and adaptive loci and measured at morphological traits, including egg mass as an indicator of ocean‐ and river‐maturing ecotype for females. The two ecotypes did not exhibit genetic structure at 148 neutral loci, indicating that ecotypic diversity exists within a single population. In contrast, we identified the genetic basis of maturation ecotypes in Pacific lamprey as polygenic, involving two unlinked gene regions that have a complex epistatic relationship. Importantly, these gene regions appear to show stronger effects when considered in gene interaction models than if just considered additive, illustrating the importance of considering epistatic effects and gene networks when researching the genetic basis of complex traits in Pacific lamprey and other species.     

Ten polymorphic microsatellite markers developed in the masson pine moth Dendrolimus punctatus Walker (Lepidoptera: Lasiocampidae)

A set of 10 polymorphic di‐ and trinucleotide microsatellite loci were developed for the forestry pest insect, masson pine moth, Dendrolimus punctatus Walker. The expected heterozygosity at these loci ranges from 0.285 to 0.859, and the observed allele numbers from five to 19. Cross species amplification of these loci in four other congeneric pine moth species indicates variable levels of loci conservation and thus cross‐applicability. Therefore, the microsatellite loci reported here should be useful for population genetic and other related studies in the masson pine moth and other closely related species.     

The Molecular Evolution of the Vertebrate Trypsinogens

We expand the already large number of known trypsinogen nucleotide and amino acid sequences by presenting additional trypsinogen sequences from the tunicate (Boltenia villosa), the lamprey (Petromyzon marinus), the pufferfish (Fugu rubripes), and the frog (Xenopus laevis). The current array of known trypsinogen sequences now spans the entire vertebrate phylogeny. Phylogenetic analysis is made difficult by the presence of multiple isozymes within species and rates of evolution that vary highly between both species and isozymes. We nevertheless present a Fitch-Margoliash phylogeny constructed from pairwise distances. We employ this phylogeny as a vehicle for speculation on the evolution of the trypsinogen gene family as well as the general modes of evolution of multigene families. Unique attributes of the lamprey and tunicate trypsinogens are noted. Received: 12 July 1997     

Evidence for a membrane-bound carbonic anhydrase in the heart of an ancient vertebrate,the sea lamprey (<Emphasis Type="Italic">Petromyzon marinus</Emphasis>)

In order to gain insight into the early evolution of carbonic-anhydrase (CA) isozymes in vertebrates, the main objective of the present study was to determine whether the hearts of an ancient vertebrate species, Petromyzon marinus, possess a membrane-bound CA isozyme. Since a significant amount of CA activity appeared to be strongly associated with the heart membrane fraction after differential centrifugation and washing, further experiments were conducted to examine the inhibitor properties of the CA from the membrane fraction in comparison with lamprey cytoplasmic CA from the red blood cell (rbc) fraction. These experiments showed that the inhibitor properties of the CA from the heart membranes were significantly different from those of the cytoplasmic CA from lamprey rbcs. A final series of experiments showed that the membrane-bound CA in the lamprey heart is not anchored via a glycosylphosphatidylinositol (GPI) linkage. Taken together, the results of these studies indicate that a membrane-bound CA does appear to be present in the hearts of lamprey, but the properties of the membrane-bound CA isozyme in these ancient vertebrates appear to differ from those in more recently evolved groups.Abbreviations Az acetazolamide - CA carbonic anhydrase - GPI glycosylphosphatidylinositol - PI-PLC phosphatidylinositol specific phospholipase C - Rbc red blood cell     

Movement of radio-tagged anadromous sea lamprey during the spawning migration in the River Mondego (Portugal)

The available spawning habitat for the anadromous sea lamprey, Petromyzon marinus L., population that enters the River Mondego has been drastically reduced in the last 20 years. The installation of a fish passage in the first impassable dam, the Açude-Ponte, would enable sea lamprey to recolonise the 34.6-km river stretch between the Açude-Ponte and Raiva dams. In order to assess the suitability of the upstream river stretches for this species, 10 radio-tagged sea lamprey were released upstream of the Açude-Ponte dam and tracked continuously throughout the entire migratory path. Lamprey were unable to pass over intact weirs that had been built for recreational purposes. Sea lamprey movements were more frequent during dusk and night than other periods. Increased river discharge at night, resulting from the operation of the Raiva power station, stimulated lamprey movements but reduced ground speeds recorded. After reaching a certain location, some of the animals maintained their position for several weeks, before undergoing a new movement. Two of the main tributaries of this river stretch were used by some sea lamprey, indicating that the animals were able to find these historical spawning grounds.     

Lactate dehydrogenase (LDH) gene duplication during chordate evolution: the cDNA sequence of the LDH of the tunicate Styela plicata

L-Lactate dehydrogenase (L-LDH, E.C. 1.1.1.27) is encoded by two or three loci in all vertebrates examined, with the exception of lampreys, which have a single LDH locus. Biochemical characterizations of LDH proteins have suggested that a gene duplication early in vertebrate evolution gave rise to Ldh-A and Ldh-B and that an additional locus, Ldh-C arose in a number of lineages more recently. Although some phylogenetic studies of LDH protein sequences have supported this pattern of gene duplication, others have contradicted it. In particular, a number of studies have suggested that Ldh-C represents the earliest divergence among vertebrate LDHs and that it may have diverged from the other loci well before the origin of vertebrates. Such hypotheses make explicit statements about the relationship of vertebrate and invertebrate LDHs, but to date, no closely related invertebrate LDH sequences have been available for comparison. We have attempted to provide further data on the timing of gene duplications leading to multiple vertebrate LDHs by determining the cDNA sequence of the LDH of the tunicate Styela plicata. Phylogenetic analyses of this and other LDH sequences provide strong support for the duplications giving rise to multiple vertebrate LDHs having occurred after vertebrates diverged from tunicates. The timing of these LDH duplications is consistent with data from a number of other gene families suggesting widespread gene duplication near the origin of vertebrates. With respect to the relationships among vertebrate LDHs, our data are not consistent with previous claims that Ldh-C represented the earliest divergence. However, the precise relationships among some of the main lineages of vertebrate LDHs were not resolved in our analyses.      

Expansion of the <Emphasis Type="Italic">Ago</Emphasis> gene family in the teleost clade

AGO proteins are universal effectors of eukaryotic small RNA-directed regulatory pathways. In this study, we used a comparative genomics approach to explore the AGO sub-family in the teleost clade. We identified five Ago homologues in teleost genomes, one more than encoded in other vertebrate clades. The additional teleost homologue was preserved most likely due to the differential retention of regulatory elements following the fish-specific genome duplication event that occurred approximately 350 million years ago. Analysis of all five Ago genomic loci in teleosts revealed that orthologues contain specific, conserved sequence elements in non-coding regions indicating that the teleost Ago paralogues are differentially regulated. This was supported by qRT-PCR analysis that showed differential expression of the zebrafish homologues across development and between adult tissues indicating stage and tissue-specific function of individual AGO proteins. Multiple sequence alignments showed not only that all teleost homologues possess critical residues for AGO function, but also that teleost homologues contain multiple orthologue-specific features, indicative of structural diversification. Notably, these are retained throughout the vertebrate lineage arguing these may be important for orthologue-specific functions.     

Early Evolution of Conserved Regulatory Sequences Associated with Development in Vertebrates

Comparisons between diverse vertebrate genomes have uncovered thousands of highly conserved non-coding sequences, an increasing number of which have been shown to function as enhancers during early development. Despite their extreme conservation over 500 million years from humans to cartilaginous fish, these elements appear to be largely absent in invertebrates, and, to date, there has been little understanding of their mode of action or the evolutionary processes that have modelled them. We have now exploited emerging genomic sequence data for the sea lamprey, Petromyzon marinus, to explore the depth of conservation of this type of element in the earliest diverging extant vertebrate lineage, the jawless fish (agnathans). We searched for conserved non-coding elements (CNEs) at 13 human gene loci and identified lamprey elements associated with all but two of these gene regions. Although markedly shorter and less well conserved than within jawed vertebrates, identified lamprey CNEs are able to drive specific patterns of expression in zebrafish embryos, which are almost identical to those driven by the equivalent human elements. These CNEs are therefore a unique and defining characteristic of all vertebrates. Furthermore, alignment of lamprey and other vertebrate CNEs should permit the identification of persistent sequence signatures that are responsible for common patterns of expression and contribute to the elucidation of the regulatory language in CNEs. Identifying the core regulatory code for development, common to all vertebrates, provides a foundation upon which regulatory networks can be constructed and might also illuminate how large conserved regulatory sequence blocks evolve and become fixed in genomic DNA.     

Bicarbonate permeability and immunological evidence for an anion exchanger-like protein in the red blood cells of the sea lamprey,Petromyzon marinus

Physiological and immuno-blotting experiments were used to determine whether the red blood cell membrane of a primitive vertebrate, the sea lamprey Petromyzon marinus, contained a counterpart similar to the vertebrate anion exchange protein known as AE1 or band 3. Results of the physiological experiments which measured CO₂ production after adding H¹⁴CO ₃ ^- to the extracellular saline, indicated significant transmembrane bicarbonate movement in lamprey blood which unlike that in most vertebrates, was insensitive to inhibition by 4,4 diisothiocyanatostilbene-2,2 disulfonic acid. The present study also showed that lamprey red blood cells possess acetazolamide-sensitive carbonic anhydrase which is an important component of CO₂ production by vertebrate red blood cells. Polyclonal immunoglobulins against a 12 amino acid domain in the C-terminus of the mouse AE1 recognized a trout red blood cell membrane protein with a relative molecular mass of 97 kDa, but failed to immunoreact with any membrane proteins from the red blood cells of lamprey. Antibodies against trout AE1 immunoreacted with trout red blood cell membrane proteins of approximately 97 kDa, 200 kDa and >200 kDa. Interestingly, only a 200-kDa membrane protein from the red blood cells of the primitive lamprey immunoreacted with the trout anti-AE1 immunoglobulin proteins. Therefore, lamprey red blood cells appear to possess an AE1-like protein that may be physiologically different than that in most other vertebrates.     

Tau-crystallin/alpha-enolase: one gene encodes both an enzyme and a lens structural protein

tau-Crystallin has been a major component of the cellular lenses of species throughout vertebrate evolution, from lamprey to birds. Immunofluorescence analysis of the embryonic turtle lens, using antiserum to lamprey tau-crystallin showed that the protein is expressed throughout embryogenesis and is present at high concentrations in all parts of the lens. Partial peptide sequence for the isolated turtle protein and deduced sequences for several lamprey peptides all revealed a close similarity to the glycolytic enzyme enolase (E.C. 4.2.1.11). A full-sized cDNA for putative duck tau- crystallin was obtained and sequenced, confirming the close relationship with alpha-enolase. Southern blot analysis showed that the duck genome contains a single alpha-enolase gene, while Northern blot analysis showed that the message for tau-crystallin/alpha-enolase is present in embryonic duck lens at 25 times the abundance found in liver. tau-Crystallin possesses enolase activity, but the activity is greatly reduced, probably because of age-related posttranslational modification. It thus appears that a highly conserved, important glycolytic enzyme has been used as a structural component of lens since the start of vertebrate evolution. Apparently the enzyme has not been recruited for its catalytic activity but for some distinct structural property. tau-Crystallin/alpha-enolase is an example of a multifunctional protein playing two very different roles in evolution but encoded by a single gene.     

Developmental anatomy of lampreys

Lampreys are a group of aquatic chordates whose relationships to hagfishes and jawed vertebrates are still debated. Lamprey embryology is of interest to evolutionary biologists because it may shed light on vertebrate origins. For this and other reasons, lamprey embryology has been extensively researched by biologists from a range of disciplines. However, many of the key studies of lamprey comparative embryology are relatively inaccessible to the modern scientist. Therefore, in view of the current resurgence of interest in lamprey evolution and development, we present here a review of lamprey developmental anatomy. We identify several features of early organogenesis, including the origin of the nephric duct, that need to be re-examined with modern techniques. The homologies of several structures are also unclear, including the intriguing subendothelial pads in the heart. We hope that this review will form the basis for future studies into the phylogenetic embryology of this interesting group of animals.     

Characterization of microsatellite loci in neotropical Heliconius butterflies

The Heliconius butterflies offer exceptional opportunities for the study of the ecology and evolution of mimicry. Despite previous reports of difficulties in the development of microsatellite loci in Lepidoptera, we characterize 15 polymorphic loci in H. erato that show promise for genetic mapping and population studies in this and other species. Levels of variation were high, in both numbers and size ranges of alleles. The loci showed broad amplification success across the genus and in two other genera. All loci that amplified in a population of H. melpomene were polymorphic.     

A Reporter Assay in Lamprey Embryos Reveals Both Functional Conservation and Elaboration of Vertebrate Enhancers

The sea lamprey is an important model organism for investigating the evolutionary origins of vertebrates. As more vertebrate genome sequences are obtained, evolutionary developmental biologists are becoming increasingly able to identify putative gene regulatory elements across the breadth of the vertebrate taxa. The identification of these regions makes it possible to address how changes at the genomic level have led to changes in developmental gene regulatory networks and ultimately to the evolution of morphological diversity. Comparative genomics approaches using sea lamprey have already predicted a number of such regulatory elements in the lamprey genome. Functional characterisation of these sequences and other similar elements requires efficient reporter assays in lamprey. In this report, we describe the development of a transient transgenesis method for lamprey embryos. Focusing on conserved non-coding elements (CNEs), we use this method to investigate their functional conservation across the vertebrate subphylum. We find instances of both functional conservation and lineage-specific functional evolution of CNEs across vertebrates, emphasising the utility of functionally testing homologous CNEs in their host species.     

Parathyroid hormone-related protein production in the lamprey <Emphasis Type="Italic">Geotria australis</Emphasis>: developmental and evolutionary perspectives

This study explored the distribution of parathyroid hormone-related protein (PTHrP) and its mRNA in tissues of the lamprey Geotria australis, a representative of one of the two surviving groups of an early and jawless stage in vertebrate evolution. For this purpose, antibodies to N-terminal and mid-molecule human PTHrP were used to determine the locations of the antigen. Sites of mRNA production were demonstrated by in situ hybridisation with a digoxigenin-labelled riboprobe to exon VI of the human PTHrP gene. The results revealed that antigen and its mRNA were widely distributed among similar sites of tissue localisation to those described for mammalian and avian species. However, some novel sites of localisation, such as in the gill and notochord, were also found. Some differences in PTHrP localisation were noted among individuals at different intervals of the life cycle, indicating that the distributions of PTHrP, and possibly its roles, change with the stage of development in this species. The widespread tissue distribution in G. australis implies diverse physiological roles for this protein. The presence of PTHrP in the lamprey, a representative of a group of vertebrates, which apparently evolved over 540 million years ago, strongly suggests that it is a protein of ancient origin. In addition, the successful use of antibodies and probes based on the human sequence in the lamprey also provides evidence that the PTHrP molecule may have been conserved from lampreys through to humans.