108 research outputs found
The effects of parameter choice on defining molecular operational taxonomic units and resulting ecological analyses of metabarcoding data
Copyright remains with the author(s) or their institution(s). Permission for reuse (free in most cases) can be obtained from RightsLink.This work was supported by a NSERC CREATE grant to M.E.C. and an Institutional Links grant 172726351 to E.L.C. under the Newton-Ungku Omar Fund, through the British Council in the UK and the Malaysian Industry-Government Group for High Technology in Malaysia. The Newton Fund is Overseas Development Assistance administered through the UK Department for Business Innovation and Skills (BIS). For further information, please visitwww.newtonfund.ac.uk
D- and L-lactate dehydrogenases during invertebrate evolution
Background: The L-lactate and D-lactate dehydrogenases, which are involved in the reduction of
pyruvate to L(-)-lactate and D(+)-lactate, belong to evolutionarily unrelated enzyme families. The
genes encoding L-LDH have been used as a model for gene duplication due to the multiple paralogs
found in eubacteria, archaebacteria, and eukaryotes. Phylogenetic studies have suggested that
several gene duplication events led to the main isozymes of this gene family in chordates, but little
is known about the evolution of L-Ldh in invertebrates. While most invertebrates preferentially
oxidize L-lactic acid, several species of mollusks, a few arthropods and polychaetes were found to
have exclusively D-LDH enzymatic activity. Therefore, it has been suggested that L-LDH and DLDH
are mutually exclusive. However, recent characterization of putative mammalian D-LDH with
significant similarity to yeast proteins showing D-LDH activity suggests that at least mammals have
the two naturally occurring forms of LDH specific to L- and D-lactate. This study describes the
phylogenetic relationships of invertebrate L-LDH and D-LDH with special emphasis on
crustaceans, and discusses gene duplication events during the evolution of L-Ldh.
Results: Our phylogenetic analyses of L-LDH in vertebrates are consistent with the general view
that the main isozymes (LDH-A, LDH-B and LDH-C) evolved through a series of gene duplications
after the vertebrates diverged from tunicates. We report several gene duplication events in the
crustacean, Daphnia pulex, and the leech, Helobdella robusta. Several amino acid sequences with
strong similarity to putative mammalian D-LDH and to yeast DLD1 with D-LDH activity were
found in both vertebrates and invertebrates.
Conclusion: The presence of both L-Ldh and D-Ldh genes in several chordates and invertebrates
suggests that the two enzymatic forms are not necessarily mutually exclusive. Although, the
evolution of L-Ldh has been punctuated by multiple events of gene duplication in both vertebrates
and invertebrates, a shared evolutionary history of this gene in the two groups is apparent.
Moreover, the high degree of sequence similarity among D-LDH amino acid sequences suggests
that they share a common evolutionary history
Complex genetic patterns in closely related colonizing invasive species
Anthropogenic activities frequently result in both rapidly changing environments and translocation of species from their native ranges (i.e., biological invasions). Empirical studies suggest that many factors associated with these changes can lead to complex genetic patterns, particularly among invasive populations. However, genetic complexities and factors responsible for them remain uncharacterized in many cases. Here, we explore these issues in the vase tunicate Ciona intestinalis (Ascidiacea: Enterogona: Cionidae), a model species complex, of which spA and spB are rapidly spreading worldwide. We intensively sampled 26 sites (N= 873) from both coasts of North America, and performed phylogenetic and population genetics analyses based on one mitochondrial fragment (cytochrome c oxidase subunit 3–NADH dehydrogenase subunit I, COX3-ND1) and eight nuclear microsatellites. Our analyses revealed extremely complex genetic patterns in both species on both coasts. We detected a contrasting pattern based on the mitochondrial marker: two major genetic groups in C. intestinalis spA on the west coast versus no significant geographic structure in C. intestinalis spB on the east coast. For both species, geo-graphically distant populations often showed high microsatellite-based genetic affinities whereas neighboring ones often did not. In addition, mitochondrial and nuclear markers provided largely inconsistent genetic patterns. Multiple factors, including random genetic drift associated with demographic changes, rapid selection due to strong local adaptation, and varying propensity for human-mediated propagule dispersal could be responsible for the observed genetic complexities
Optimization and performance testing of a sequence processing pipeline applied to detection of nonindigenous species
Genetic taxonomic assignment can be more sensitive than morphological taxonomic assignment, particularly for small, cryptic or rare species. Sequence processing is essential to taxonomic assignment, but can also produce errors because optimal parameters are not known a priori. Here, we explored how sequence processing parameters influence taxonomic assignment of 18S sequences from bulk zooplankton samples produced by 454 pyrosequencing. We optimized a sequence processing pipeline for two common research goals, estimation of species richness and early detection of aquatic invasive species (AIS), and then tested most optimal models’ performances through simulations. We tested 1,050 parameter sets on 18S sequences from 20 AIS to determine optimal parameters for each research goal. We tested optimized pipelines’ performances (detectability and sensitivity) by computationally inoculating sequences of 20 AIS into ten bulk zooplankton samples from ports across Canada. We found that optimal parameter selection generally depends on the research goal. However, regardless of research goal, we found that metazoan 18S sequences produced by 454 pyrosequencing should be trimmed to 375–400 bp and sequence quality filtering should be relaxed (1.5 ≤ maximum expected error ≤ 3.0, Phred score = 10). Clustering and denoising were only viable for estimating species richness, because these processing steps made some species undetectable at low sequence abundances which would not be useful for early detection of AIS. With parameter sets optimized for early detection of AIS, 90% of AIS were detected with fewer than 11 target sequences, regardless of whether clustering or denoising was used. Despite developments in next-generation sequencing, sequence processing remains an important issue owing to difficulties in balancing false-positive and false-negative errors in metabarcoding data
Invasion Pathway of the Ctenophore Mnemiopsis leidyi in the Mediterranean Sea
Gelatinous zooplankton outbreaks have increased globally owing to a number of human-mediated factors, including food web alterations and species introductions. The invasive ctenophore Mnemiopsis leidyi entered the Black Sea in the early 1980s. The invasion was followed by the Azov, Caspian, Baltic and North Seas, and, most recently, the Mediterranean Sea. Previous studies identified two distinct invasion pathways of M. leidyi from its native range in the western Atlantic Ocean to Eurasia. However, the source of newly established populations in the Mediterranean Sea remains unclear. Here we build upon our previous study and investigate sequence variation in both mitochondrial (Cytochrome c Oxidase subunit I) and nuclear (Internal Transcribed Spacer) markers in M. leidyi, encompassing five native and 11 introduced populations, including four from the Mediterranean Sea. Extant genetic diversity in Mediterranean populations (n = 8, Na = 10) preclude the occurrence of a severe genetic bottleneck or founder effects in the initial colonizing population. Our mitochondrial and nuclear marker surveys revealed two possible pathways of introduction into Mediterranean Sea. In total, 17 haplotypes and 18 alleles were recovered from all surveyed populations. Haplotype and allelic diversity of Mediterranean populations were comparable to populations from which they were likely drawn. The distribution of genetic diversity and pattern of genetic differentiation suggest initial colonization of the Mediterranean from the Black-Azov Seas (pairwise FST = 0.001–0.028). However, some haplotypes and alleles from the Mediterranean Sea were not detected from the well-sampled Black Sea, although they were found in Gulf of Mexico populations that were also genetically similar to those in the Mediterranean Sea (pairwise FST = 0.010–0.032), raising the possibility of multiple invasion sources. Multiple introductions from a combination of Black Sea and native region sources could be facilitated by intense local and transcontinental shipping activity, respectively
Evolutionary factors affecting Lactate dehydrogenase A and B variation in the Daphnia pulex species complex
Background: Evidence for historical, demographic and selective factors affecting enzyme evolution can be
obtained by examining nucleotide sequence variation in candidate genes such as Lactate dehydrogenase (Ldh). Two
closely related Daphnia species can be distinguished by their electrophoretic Ldh genotype and habitat. Daphnia
pulex populations are fixed for the S allele and inhabit temporary ponds, while D. pulicaria populations are fixed for
the F allele and inhabit large stratified lakes. One locus is detected in most allozyme surveys, but genome
sequencing has revealed two genes, LdhA and LdhB.
Results: We sequenced both Ldh genes from 70 isolates of these two species from North America to determine if
the association between Ldh genotype and habitat shows evidence for selection, and to elucidate the evolutionary
history of the two genes. We found that alleles in the pond-dwelling D. pulex and in the lake-dwelling D. pulicaria
form distinct groups at both loci, and the substitution of Glutamine (S) for Glutamic acid (F) at amino acid 229
likely causes the electrophoretic mobility shift in the LDHA protein. Nucleotide diversity in both Ldh genes is much
lower in D. pulicaria than in D. pulex. Moreover, the lack of spatial structuring of the variation in both genes over a
wide geographic area is consistent with a recent demographic expansion of lake populations. Neutrality tests
indicate that both genes are under purifying selection, but the intensity is much stronger on LdhA.
Conclusions: Although lake-dwelling D. pulicaria hybridizes with the other lineages in the pulex species complex,
it remains distinct ecologically and genetically. This ecological divergence, coupled with the intensity of purifying
selection on LdhA and the strong association between its genotype and habitat, suggests that experimental
studies would be useful to determine if variation in molecular function provides evidence that LDHA variants are
adaptive
Prioritizing taxa for genetic reference database development to advance inland water conservation
Biodiversity loss has accelerated over the past century and freshwater species overall are among those experiencing greatest declines. Genetic resources have the potential to help evaluate the full magnitude of this loss and represent a key tool to effectively allocate conservation resources and monitor the success of restoration efforts. The full power of genetic resources will be realized when the daunting task of referencing all DNA sequences of freshwater organisms is complete. Here, we quantified the availability and distribution of barcode and genome data for freshwater macroscopic organisms in Canada, a country rich in inland water resources and thus particularly vulnerable to aquatic species losses. Impressively, most inland water species (86 %) were represented by barcodes recorded in the BOLD Systems database, while very few had full genomes available (<4 %) in the NCBI database. We identified barcode data deficiencies in northern regions and for taxa assessed as most at risk or without sufficient information for conservation status classification. As expected, the speciose insect group had a lower-than-average number of records per species and a high proportion of data deficient species without adequate barcode coverage. This study highlights where future sequencing resources should be prioritized within initiatives such as the Canada BioGenome Project and BIOSCAN Canada and provides a workflow that could be applied internationally to inform conservation management plans and to mitigate biodiversity loss
The contribution of Nicolae Botnariuc to evolutionary biology using systems theory
Early this year, the Romanian Academy commemorated the centennial birthday of the evolutionary biologist Nicolae Botnariuc (13.03.1915 – 01.03.2011; Figure 1). The scientific contribution of Botnariuc has been well recognized within the Romanian community of biologists which fostered influential personalities like Emil G. Racovitza, Constantin Motaş and Radu Codreanu (cf. Iftimovici 1977; Negrea 2007). However, many aspects of his scientific achievements remain largely unknown beyond the Romanian academic space, likely due to publications with a restricted international distribution at the time the academic space of Eastern Europe was still constrained ideologically.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author
Daphnia pulex density long-form data for all replicates in all treatments
The nine experimental genotypes are denoted by their respective letter identifiers under the heading 'genotype', along with the 'Mixed' genotype treatment. The single (1 colonist) or many (9 colonists) quantity treatment is denoted under the 'quantity' heading. The 'replicate' heading identifies the individual replicates in each treatment (n=6 for single treatments, n=5 for many treatments, n=5 for the Mixed treatment). The density (individuals per L) values plotted in Figure 1 and used to calculate treatment effect sizes are given in the 'density(ind/L)' column
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