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PubMed2005

Genetic diversity and differentiation of central European freshwater pearl mussel (Margaritifera margaritifera L.) populations: implications for conservation and management.

Despite the fact that mollusc species play an important role in many aquatic ecosystems, little is known about their biodiversity and conservation genetics. Freshwater pearl mussel (Margaritifera margaritifera L.) populations are seriously declining all over Europe and a variety of conservation programs are being established to support the remaining endangered central European populations. In order to provide guidelines for conservation strategies and management programs, we investigated the genetic structure of 24 freshwater pearl mussel populations originating from five major central European drainages including Elbe, Danube, Rhine, Maas and Weser, representing the last and most important populations in this area. We present a nondestructive sampling method of haemolymph for DNA analyses, which is applicable for endangered bivalves. The analyses of nine microsatellite loci with different levels of polymorphism revealed a high degree of fragmented population structure and very different levels of genetic diversity within populations. These patterns can be explained by historical and demographic effects and have been enforced by anthropogenic activities. Even within drainages, distinct conservation units were detected, as revealed from high F(ST) values, private alleles and genetic distance measures. Populations sampled close to contact zones between main drainage systems showed lowest levels of correct assignment to present-day drainage systems. Populations with high priority for conservation should not only be selected by means of census population size and geographical distance to other populations. Instead, detailed genetic analyses are mandatory for revealing differentiation and diversity parameters, which should be combined with ecological criteria for sustainable conservation and recovery programs.

Animals↗
PubMed2006

Bioeconomic modeling in conservation pest management: effect of stoat control on extinction risk of an indigenous New Zealand passerine, Mohua ochrocephala.

Pest control is a key activity undertaken to conserve threatened and declining species. Although bioeconomic analysis has been used to contrast the relative efficiency of control strategies where pests affect economic resources, the same approaches have been adopted rarely in conservation settings. The Mohua (Mohoua ochrocephala) is an insectivorous passerine indigenous to beech (Nothofagus spp.) forests in New Zealand's south island. Mohua have undergone a 75% range contraction since stoats (Mustela erminea) (which prey on nests and nesting females) were introduced to the south island in the late 1800s. Mohua nests are particularly vulnerable when stoat abundance increases in response to eruptions in the density of introduced house mice (Mus musculus), which in turn respond to semiperiodic (4-6year) mass seeding (masting) of beech trees. Controlling stoats only when their abundance poses a threat to Mohua fledging success would theoretically maximize the efficiency with which Mohua are protected. To better synchronize stoat control with periods of high stoat density, control could be initiated according to (1) time since last control, (2) beech seedfall, (3) mouse abundance, or (4) stoat abundance. Monitoring the three environmental cues, however, incurs costs that should be taken into account when considering their relative efficiency I derived an empirically based stochastic model that links sequential change in beech seedfall, mouse, and stoat abundance to a simple demographic model for Mohua. I used the model to contrast the relative cost-efficiency of achieving conservation outcomes for Mohua (specified in a quasi-extinction framework), initiating stoat control according to these cues. The use of environmental cues reduced the frequency with which stoat control had to be undertaken to achieve Mohua conservation outcomes by more than 50%. For some cues, however the costs of monitoring outweighed the savings that could be achieved through reduced frequency of stoat control. The interplay between costs of monitoring environmental cues and the frequency with which stoat control had to be undertaken meant that the most efficient strategy was dependent on the conservation outcome specified for Mohua. My results demonstrate the utility of bioeconomic analysis in formulation of pest management strategies to achieve conservation outcomes.

Animals↗
PubMed2006

A graduate education framework for tropical conservation and development.

Conventional graduate training related to tropical conservation and development has typically separated the two fields, with students focusing on either conservation from the perspective of the biophysical sciences or development as an extension of the social sciences. On entering the workforce, however graduates find they are required to work beyond disciplinary boundaries to address the complex interconnectivity between biological conservation and human well-being. We devised a framework for graduate education that broadens students' skill sets to learn outside their immediate disciplines and think in terms of linked socioecological systems, work in teams, communicate in nonacademic formats, and reflect critically on their own perspectives and actions. The University of Florida's Tropical Conservation and Development program has adopted a learning and action platform that blends theory, skills, and praxis to create an intellectual, social, and professionally safe space where students, faculty, and other participants can creatively address the complex challenges of tropical conservation and development. This platform operates within a nondegree-granting program and includes core courses that are taught by a team of biophysical and social scientists. It incorporates a range of alternative learning spaces such as student-led workshops, retreats, visiting professionals, practitioner experiences, and a weekly student-led seminar that collectively encourage students and faculty to enhance their skills and systematically and thoroughly reflect on program activities. Challenges to the described approach include increased service demands on faculty, a redefinition of research excellence to include effective and equitable collaboration with host-country partners, and the trade-offs and uncertainties inherent in more collaborative, interdisciplinary research. Despite these challenges, growing interdisciplinary programs, coupled with adaptive educational approaches that emphasize learning and action networks of students, faculty, and field partners, provide the best hope for responding to the emerging challenges of tropical conservation and development.

Conservation of Natural Resources↗
PubMed2006

Transgenics and vertebrate cloning as tools for species conservation.

It has been suggested that transgenics and vertebrate cloning have a role to play in conservation. Now is the time to evaluate their risks and benefits, before these technologies are widely implemented in our field. Direct risks of transgenics include escape and introgression of transgenes into wild populations; weedy invasion by transgenic organisms; toxicity or pathogenicity of engineered organisms and their products; and human error in the field testing and tracking of transgenic organisms. Indirect risks include environmental effects of increased herbicide use; the danger that engineered organisms may aid the development of bioweapons; the likelihood that gene patenting will lead to the privatization of natural resources; and the diversion of support from less glamorous forms of conservation. Formal risk assessments are commonly used to evaluate transgenic procedures, but our incomplete understanding of both ecosystem processes and the action of transgenes renders most of these assessments scientifically and socially unjustified. Nevertheless, a few, low-risk applications of transgenics may be possible: for example, "super-sterile" ornamental cultivars. Vertebrate cloning poses little risk to the environment, but it can consume scarce conservation resources, and its chances of success in preserving species seem poor To date, the conservation benefits of transgenics and vertebrate cloning remain entirely theoretical, but many of the risks are known and documented. Conservation biologists should devote their research and energies to the established methods of conservation, none of which require transgenics or vertebrate cloning.

Animals↗
PubMed2000

Genomic organisation of the neural sex determination gene fruitless (fru) in the Hawaiian species Drosophila silvestris and the conservation of the fru BTB protein-protein-binding domain throughout evolution.

We report the cloning and sequencing of the fru gene from the Hawaiian picture-wing species Drosophila silvestris. The fru gene has seven exons spanning 15-kb encoding two transcripts with ORFs of 841 and 695 amino acids. The protein encoded by the fruA transcript is well conserved with the D. melanogaster type A protein, particularly the BTB protein-protein-binding domain, which is encoded by exons I and II and is 100% conserved. The peptide encoded by exon III has several sequence differences but these are confined mostly to regions of repetitive sequence and exons IV to VI are well conserved. The peptide encoded by exon VII is semi-conserved for the 5' end and 100% conserved for the Zinc finger domains; the rest of the peptide is virtually unconserved. The FRUA protein has a BTB domain and two zinc finger domains whereas the FRUC protein only has the BTB domain. The genomic DNA sequence encoding the BTB domain of the fru gene has been cloned from 21 species of Diptera. The protein-coding sequence is highly conserved and the amino acid sequence is identical except for two changes in the Tephritidae. The intron sequences are completely unconserved except between very closely related species such as the Hawaiian Drosophila. The phylogeny produced using the BTB exon sequences suggests that the most closely related mainland Drosophila species to the Hawaiian clade is D. moriwakii of the melanica species group. The phylogeny also shows that the Scaptomyza are closely related to the Hawaiian Drosophila so supporting a Hawaiian origin for the Scaptomyza. The genus Zaprionus is placed in the subgenus Drosophila closely related to D. immigrans along with the genera Samoaia and Liodrosophila.

Amino Acid Sequence↗
PubMed2002

Yankey's dilemma: conservation versus the people of Ghana.

The past 20 years have seen a shift in conservation approaches to realize the importance of people in conservation and wildlife management (CWM). To this extent, in most conservation circles the concept of community involvement is no longer debated. The following factors have influenced the growth of CWM, especially in Africa: (i) recent developments in postcolonial governments have made them unable to manage and control the use of natural resources in the restrictive manner mandated by the legislation of the colonial past still in place; (ii) successes, particularly in southern Africa, of approaches that involved devolution of greater access rights and responsibilities to communities have led to these approaches being used by other countries; (iii) donor agencies, encouraged by the success of these approaches, have allocated more of their resources to community-based projects; and (iv) changes in international perceptions have been heavily influenced by the growing voice of the "South" in international fora. While there has been some success, there have also been failures. In Ghana, there has been considerable effort to develop programs that incorporate community aspirations into specific objectives; one inherent problem with these programs-not exclusive to Ghana-is the tendency for conservation programs to try to fit community aspirations into conservation objectives as opposed to finding ways of using conservation to help fulfill community aspirations. When community-based programs fail to recognize this, they are generally unable to deliver on their expected outputs. Some critics have used this to dismiss the community approach, which poses a dangerous reversion to a paradigm that has significantly failed in Africa, and much of the developing world, especially in regard to wildlife outside of protected areas.

Animals↗
PubMed2004

A point mutation within conserved region VI of herpes simplex virus type 1 DNA polymerase confers altered drug sensitivity and enhances replication fidelity.

Herpes simplex virus type 1 (HSV-1) DNA polymerase contains several conserved regions within the polymerase domain. The conserved regions I, II, III, V, and VII have been shown to have functional roles in the interaction with deoxynucleoside triphosphates (dNTPs) and DNA. However, the role of conserved region VI in DNA replication has remained unclear due, in part, to the lack of a well-characterized region VI mutant. In this report, recombinant viruses containing a point mutation (L774F) within the conserved region VI were constructed. These recombinant viruses were more susceptible to aphidicolin and resistant to both foscarnet and acyclovir, compared to the wild-type KOS strain. Marker transfer experiments demonstrated that the L774F mutation conferred the altered drug sensitivities. Furthermore, mutagenesis assays demonstrated that L774F recombinant viruses containing the supF marker gene, which was integrated within the thymidine kinase locus (tk), exhibited increased fidelity of DNA replication. These data indicate that conserved region VI, together with other conserved regions, forms the polymerase active site, has a role in the interaction with deoxyribonucleotides, and regulates DNA replication fidelity. The possible effect of the L774F mutation in altering the polymerase structure and activity is discussed.

Acyclovir↗
PubMed1996

The AD1 transactivation domain of E2A contains a highly conserved helix which is required for its activity in both Saccharomyces cerevisiae and mammalian cells.

A conserved region, designated the AD1 domain, is present in a class of helix-loop-helix (HLH) proteins, E proteins, that includes E12, E47, HEB, E2-2, and a Xenopus laevis HLH protein closely related to E12. We demonstrate that the AD1 domain in E2A and the conserved region of E2-2 activate transcription in both yeast and mammalian cells. The AD1 domain contains a highly conserved putative helix that is crucial for its transactivation properties. Circular dichroism spectroscopy data show that AD1 is structured and contains distinctive helical properties. In addition, we show that a synthetic peptide corresponding to the conserved region is unstructured in aqueous solution at neutral pH but can adopt an alpha-helical conformation in the presence of the hydrophobic solvent trifluoroethanol. Amino acid substitutions that destabilize the helix abolish the transactivation ability of the AD1 domain. Both structural and functional analyses of AD1 reveal striking similarities to the acidic class of activators. Remarkably, when wild-type and mutant proteins are expressed in mammalian cells and Saccharomyces cerevisiae, identical patterns of transactivation are observed, suggesting that the target molecule is conserved between S. cerevisiae and mammals. These data show that transactivation by E proteins is mediated, in part, by a strikingly conserved peptide that has the ability to form a helix in a hydrophobic solvent. We propose that the unstructured domain may become helical upon interaction with its cellular target molecule.

Amino Acid Sequence↗
PubMed2004

Transcriptome and genome conservation of alternative splicing events in humans and mice.

Combining mRNA and EST data in splicing graphs with whole genome alignments, we discover alternative splicing events that are conserved in both human and mouse transcriptomes. 1,964 of 19,156 (10%) loci examined contain one or more such alternative splicing events, with 2,698 total events. These events represent a lower bound on the amount of alternative splicing in the human genome. Also, as these alternative splicing events are conserved between the human and mouse transcriptomes they should be enriched for functionally significant alternative splicing events, free from much of the noise found in the EST libraries. Further classification of these alternative splicing events reveals that 1,037 (38.4%) are due to exon skipping, 497 (18.4%) are due to alternative 3' splice sites, 214 (7.9%) are due to alternative 5' splice sites, 75 (2.8%) are due to intron retention and the other 875 (32.4%) are due to other, more complicated, alternative splicing events. In addition, genomic sequences nearby these alternative splicing events display increased sequence conservation. Both the alternatively spliced exons and the proximal intron show increased levels of genomic conservation relative to constitutively spliced exons. For exon skipping events both intron regions flanking the exon are conserved while for alternative 5' and 3' splicing events the conservation is greater near the alternative splice site.

Algorithms↗
PubMed1993

Identification of a human-specific epitope in a conserved region of the La/SS-B autoantigen.

Human anti-La/SS-B autoantibodies are known to react with highly conserved epitopes suggested to be functional or active sites on the La/SS-B polypeptide. This study was designed to determine whether the autoantibodies also react with poorly conserved regions of La/SS-B as predicted by an antigen-driven autoimmune response. Binding of human autoantibodies to purified human, mouse, and bovine recombinant fragments representing immunodominant regions of the La/SS-B polypeptide was compared using Western blotting and ELISA. A cross-reactive epitope was located in the highly conserved NH2-terminal region of La/SS-B. Significantly, human-specific epitopes were identified in both the conserved RNA-recognition motif and a poorly conserved COOH-terminal fragment, providing direct evidence for an autoantigen-driven response. The lack of autoantibody cross-reactivity with a conserved domain of mouse and bovine La/SS-B implies that a small number of residues in human autoepitopes may be critical for autoimmunogenicity.

Amino Acid Sequence↗
PubMed2005

Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes.

BACKGROUND: Recent advances in genome sequencing suggest a remarkable conservation in gene content of mammalian organisms. The similarity in gene repertoire present in different organisms has increased interest in studying regulatory mechanisms of gene expression aimed at elucidating the differences in phenotypes. In particular, a proximal promoter region contains a large number of regulatory elements that control the expression of its downstream gene. Although many studies have focused on identification of these elements, a broader picture on the complexity of transcriptional regulation of different biological processes has not been addressed in mammals. The regulatory complexity may strongly correlate with gene function, as different evolutionary forces must act on the regulatory systems under different biological conditions. We investigate this hypothesis by comparing the conservation of promoters upstream of genes classified in different functional categories. RESULTS: By conducting a rank correlation analysis between functional annotation and upstream sequence alignment scores obtained by human-mouse and human-dog comparison, we found a significantly greater conservation of the upstream sequence of genes involved in development, cell communication, neural functions and signaling processes than those involved in more basic processes shared with unicellular organisms such as metabolism and ribosomal function. This observation persists after controlling for G+C content. Considering conservation as a functional signature, we hypothesize a higher density of cis-regulatory elements upstream of genes participating in complex and adaptive processes. CONCLUSION: We identified a class of functions that are associated with either high or low promoter conservation in mammals. We detected a significant tendency that points to complex and adaptive processes were associated with higher promoter conservation, despite the fact that they have emerged relatively recently during evolution. We described and contrasted several hypotheses that provide a deeper insight into how transcriptional complexity might have been emerged during evolution.

Animals↗
PubMed2006

Cross-species hybridizations on a multi-species cDNA microarray to identify evolutionarily conserved genes expressed in oocytes.

BACKGROUND: Comparative genomic analysis using cDNA microarray is a new approach and a useful tool to identify important genetic sequences or genes that are conserved throughout evolution. Identification of these conserved sequences will help elucidate important molecular mechanisms or pathways common to many species. For example, the stockpiled transcripts in the oocyte necessary for successful fertilization and early embryonic development still remain relatively unknown. The objective of this study was to identify genes expressed in oocytes and conserved in three evolutionarily distant species. RESULTS: In this study we report the construction of a multi-species cDNA microarray containing 3,456 transcripts from three distinct oocyte-libraries from bovine, mouse and Xenopus laevis. Following the cross-species hybridizations, data analysis revealed that 1,541 positive hybridization signals were generated by oocytes of all three species, and 268 of these are preferentially expressed in the oocyte. Data reproducibility analyses comparing same-species to cross-species hybridization indicates that cross-species hybridizations are highly reproducible, thus increasing the confidence level in their specificity. A validation by RT-PCR using gene- and species-specific primers confirmed that cross-species hybridization allows the production of specific and reliable data. Finally, a second validation step through gene-specific microarray hybridizations further supported the validity of our cross-species microarray results. Results from these cross-species hybridizations on our multi-species cDNA microarray revealed that SMFN (Small fragment nuclease), Spin (Spindlin), and PRMT1 (Protein arginine methyltransferase 1) are transcripts present in oocytes and conserved in three evolutionarily distant species. CONCLUSION: Cross-species hybridization using a multi-species cDNA microarray is a powerful tool for the discovery of genes involved in evolutionarily conserved molecular mechanisms. The present study identified conserved genes in the oocytes of three distant species that will help understand the unique role of maternal transcripts in early embryonic development.

Animals↗
PubMed2007

Occurrence of protein structure elements in conserved sequence regions.

BACKGROUND: Conserved protein sequence regions are extremely useful for identifying and studying functionally and structurally important regions. By means of an integrated analysis of large-scale protein structure and sequence data, structural features of conserved protein sequence regions were identified. RESULTS: Helices and turns were found to be underrepresented in conserved regions, while strands were found to be overrepresented. Similar numbers of loops were found in conserved and random regions. CONCLUSION: These results can be understood in light of the structural constraints on different secondary structure elements, and their role in protein structural stabilization and topology. Strands can tolerate fewer sequence changes and nonetheless keep their specific shape and function. They thus tend to be more conserved than helices, which can keep their shape and function with more changes. Loop behavior can be explained by the presence of both constrained and freely changing loops in proteins. Our detailed statistical analysis of diverse proteins links protein evolution to the biophysics of protein thermodynamic stability and folding. The basic structural features of conserved sequence regions are also important determinants of protein structure motifs and their function.

Amino Acid Sequence↗
PubMed2002

Cellular responses to Plasmodium falciparum erythrocyte membrane protein-1: use of relatively conserved synthetic peptide pools to determine CD4 T cell responses in malaria-exposed individuals in Benin, West Africa.

BACKGROUND: Plasmodium falciparum erythrocyte membrane protein-1, a variant antigen of the malaria parasite, is potentially a target for the immune response. It would be important to determine whether there are CD4 T cells that recognise conserved regions. However, within the relatively conserved region, there is variation. It is not possible to test T cell responses from small field samples with all possible peptides. METHODS: We have aligned sequences that are relatively conserved between several PfEMP1 molecules, and chosen a representative sequence similar to most of the PfEMP1 variants. Using these peptides as pools representing CIDRalpha, CIDRbeta and DBLbeta-delta domains, DBLalpha domain, and EXON 2 domain of PfEMP1, we measured the CD4 T cell responses of malaria-exposed donors from Benin, West Africa by a FACS based assay. RESULTS: All the three peptide pools elicited a CD4 T cell response in a proportion of malaria-exposed and non-exposed donors. CD4 T cell proliferation occurs at a relatively higher magnitude to peptide pools from the DBLalpha and EXON 2 in the malaria-exposed donors living in Benin than in the UK malaria-unexposed donors. CONCLUSIONS: These findings suggest that an immunological recall response to conserved peptides of a variant antigen can be measured. Further testing of individual peptides in a positive pool will allow us to determine those conserved sequences recognised by many individuals. These types of assays may provide information on conserved peptides of PfEMP1 which could be useful for stimulating T cells to provide help to P. falciparum specific B cells.

Adolescent↗
PubMed2004

Identification of conserved gene structures and carboxy-terminal motifs in the Myb gene family of Arabidopsis and Oryza sativa L. ssp. indica.

BACKGROUND: Myb proteins contain a conserved DNA-binding domain composed of one to four repeat motifs (referred to as R0R1R2R3); each repeat is approximately 50 amino acids in length, with regularly spaced tryptophan residues. Although the Myb proteins comprise one of the largest families of transcription factors in plants, little is known about the functions of most Myb genes. Here we use computational techniques to classify Myb genes on the basis of sequence similarity and gene structure, and to identify possible functional relationships among subgroups of Myb genes from Arabidopsis and rice (Oryza sativa L. ssp. indica). RESULTS: This study analyzed 130 Myb genes from Arabidopsis and 85 from rice. The collected Myb proteins were clustered into subgroups based on sequence similarity and phylogeny. Interestingly, the exon-intron structure differed between subgroups, but was conserved in the same subgroup. Moreover, the Myb domains contained a significant excess of phase 1 and 2 introns, as well as an excess of nonsymmetric exons. Conserved motifs were detected in carboxy-terminal coding regions of Myb genes within subgroups. In contrast, no common regulatory motifs were identified in the noncoding regions. Additionally, some Myb genes with similar functions were clustered in the same subgroups. CONCLUSIONS: The distribution of introns in the phylogenetic tree suggests that Myb domains originally were compact in size; introns were inserted and the splicing sites conserved during evolution. Conserved motifs identified in the carboxy-terminal regions are specific for Myb genes, and the identified Myb gene subgroups may reflect functional conservation.

Amino Acid Motifs↗
PubMed2006

Patterns of sequence conservation in presynaptic neural genes.

BACKGROUND: The neuronal synapse is a fundamental functional unit in the central nervous system of animals. Because synaptic function is evolutionarily conserved, we reasoned that functional sequences of genes and related genomic elements known to play important roles in neurotransmitter release would also be conserved. RESULTS: Evolutionary rate analysis revealed that presynaptic proteins evolve slowly, although some members of large gene families exhibit accelerated evolutionary rates relative to other family members. Comparative sequence analysis of 46 megabases spanning 150 presynaptic genes identified more than 26,000 elements that are highly conserved in eight vertebrate species, as well as a small subset of sequences (6%) that are shared among unrelated presynaptic genes. Analysis of large gene families revealed that upstream and intronic regions of closely related family members are extremely divergent. We also identified 504 exceptionally long conserved elements (> or =360 base pairs, > or =80% pair-wise identity between human and other mammals) in intergenic and intronic regions of presynaptic genes. Many of these elements form a highly stable stem-loop RNA structure and consequently are candidates for novel regulatory elements, whereas some conserved noncoding elements are shown to correlate with specific gene expression profiles. The SynapseDB online database integrates these findings and other functional genomic resources for synaptic genes. CONCLUSION: Highly conserved elements in nonprotein coding regions of 150 presynaptic genes represent sequences that may be involved in the transcriptional or post-transcriptional regulation of these genes. Furthermore, comparative sequence analysis will facilitate selection of genes and noncoding sequences for future functional studies and analysis of variation studies in neurodevelopmental and psychiatric disorders.

Animals↗
PubMed2026

Strong phylogenetic signal from chloroplast genomes of three Barringtonia species provides the first genomic resources for their conservation.

BACKGROUND: The genus Barringtonia (Lecythidaceae) is a vital component of tropical coastal forests and mangrove ecosystems. Among its members, B. racemosa and B. fusicarpa are classified as Endangered and Vulnerable, respectively, due to habitat degradation and anthropogenic pressures, underscoring the urgent need for genetic studies to guide conservation. Chloroplast (cp.) genomes serve as essential resources for phylogenetic reconstruction and conservation genetics. However, the scarcity of cp. genome data for Barringtonia has limited comprehensive evolutionary and conservation-oriented investigations. RESULTS: We assembled and annotated the first complete cp. genomes of B. racemosa, B. fusicarpa, and B. acutangula. All three genomes exhibit the typical quadripartite structure, ranging from 158,959 bp (B. racemosa) to 159,837 bp (B. acutangula), and contain 132 genes (87 protein-coding, 37 tRNA, 8 rRNA) with a GC content of 36.68%-36.86%. Collinearity and IR boundary analyses revealed high structural conservation without large-scale rearrangements. Interspecific sequence-level variations were detected in simple sequence repeats (SSRs) and long repeats. Nucleotide diversity (π) analysis identified highly polymorphic regions, including rpl20 (π = 0.080), rpoA (π = 0.064), rps3 (π = 0.063), and ndhF (π = 0.060), which represent promising molecular markers for population genetics within the genus. Codon-based selection analyses (Ka/Ks) showed that all protein-coding genes are under strong purifying selection (mean Ka/Ks 0.32-0.37), with no evidence of positive selection. Pairwise genetic distances (p-distances) among Barringtonia species are extremely low (mean 0.0046), while distances to the related genus Bertholletia are ~ 6-fold higher, supporting their generic distinction. CONCLUSIONS: Phylogenetic analysis robustly supports Barringtonia as a monophyletic clade (bootstrap = 100%), with B. racemosa and B. fusicarpa forming a sister lineage to B. acutangula. This study provides the first high-quality cp. genome resources for the two threatened Barringtonia species, revealing strong structural and sequence conservation but no direct chloroplast genomic correlates of endangerment. The identified polymorphic regions and repeat markers lay a foundation for future population genetics, phylogeographic studies, and conservation-oriented genetic management of these ecologically important coastal plants.

Genome, Chloroplast↗
PubMed2001

Grasshopper hunchback expression reveals conserved and novel aspects of axis formation and segmentation.

While the expression patterns of segment polarity genes such as engrailed have been shown to be similar in Drosophila melanogaster and Schistocerca americana (grasshopper), the expression patterns of pair-rule genes such as even-skipped are not conserved between these species. This might suggest that the factors upstream of pair-rule gene expression are not conserved across insect species. We find that, despite this, many aspects of the expression of the Drosophila gap gene hunchback are shared with its orthologs in the grasshoppers S. americana and L. migratoria. We have analyzed both mRNA and protein expression during development, and find that the grasshopper hunchback orthologs appear to have a conserved role in early axial patterning of the germ anlagen and in the specification of gnathal and thoracic primordia. In addition, distinct stepped expression levels of hunchback in the gnathal/thoracic domains suggest that grasshopper hunchback may act in a concentration-dependent fashion (as in Drosophila), although morphogenetic activity is not set up by diffusion to form a smooth gradient. Axial patterning functions appear to be performed entirely by zygotic hunchback, a fundamental difference from Drosophila in which maternal and zygotic hunchback play redundant roles. In grasshoppers, maternal hunchback activity is provided uniformly to the embryo as protein and, we suggest, serves a distinct role in distinguishing embryonic from extra-embryonic cells along the anteroposterior axis from the outset of development - a distinction made in Drosophila along the dorsoventral axis later in development. Later hunchback expression in the abdominal segments is conserved, as are patterns in the nervous system, and in both Drosophila and grasshopper, hunchback is expressed in a subset of extra-embryonic cells. Thus, while the expected domains of hunchback expression are conserved in Schistocerca, we have found surprising and fundamental differences in axial patterning, and have identified a previously unreported domain of expression in Drosophila that suggests conservation of a function in extra-embryonic patterning.

Amino Acid Sequence↗