Dissecting the chromosome-level genome of the Asian Clam (Corbicula fluminea).

The Asian Clam (Corbicula fluminea) is a valuable commercial and medicinal bivalve, which is widely distributed in East and Southeast Asia. As a natural nutrient source, the clam is rich in protein, amino acids, and microelements. The genome of C. fluminea has not yet been characterized; therefore, genome-assisted breeding and improvements cannot yet be implemented. In this work, we present a de novo chromosome-scale genome assembly of C. fluminea using PacBio and Hi-C sequencing technologies. The assembled genome comprised 4728 contigs, with a contig N50 of 521.06 Kb, and 1,215 scaffolds with a scaffold N50 of 70.62 Mb. More than 1.51 Gb (99.17%) of genomic sequences were anchored to 18 chromosomes, of which 1.40 Gb (92.81%) of genomic sequences were ordered and oriented. The genome contains 38,841 coding genes, 32,591 (83.91%) of which were annotated in at least one functional database. Compared with related species, C. fluminea had 851 expanded gene families and 191 contracted gene families. The phylogenetic tree showed that C. fluminea diverged from Ruditapes philippinarum, ~ 228.89 million years ago (Mya), and the genomes of C. fluminea and R. philippinarum shared 244 syntenic blocks. Additionally, we identified 2 MITF members and 99 NLRP members in C. fluminea genome. The high-quality and chromosomal Asian Clam genome will be a valuable resource for a range of development and breeding studies of C. fluminea in future research.

Genetic diversity analysis of Asian clam Corbicula fluminea in the Hongze Lake based on mitochondrial cytochrome b gene.

The Asian clam Corbicula fluminea is a small bivalve with high nutritional and medical values. However, natural resources of C. fluminea have declined in many areas of China including the Hongze Lake. In this study, 119 individuals from 10 sites of this lake and 2 outgroups were analyzed using a 456 bp mitochondrial cytochrome b (cytb) gene segment. Totally, 19 polymorphic sites were detected, which defined 16 haplotypes. Polymorphism varied among the 10 populations with those at the water inlet being more polymorphic. Most FST values among these populations were below 0.15 with the overall value of 0.060 (p < .05), meanwhile, the overall gene flow was 7.67, both of which indicated the low level of population differentiation in this lake. Neutrality test and mismatch analyses indicated that population explosion may have occurred in this lake. The results obtained in this study will provide useful information for artificial breeding and resource protection of this species in the Hongze Lake.

How the fluctuations of water levels affect populations of invasive bivalve Corbicula fluminea (Müller, 1774) in a Neotropical reservoir?

Corbicula fluminea is an invasive bivalve responsible for several environmental and financial problems around the globe. Despite the invasive potential of this species, it suffers certain restrictions in lentic environments due to natural phenomena that significantly affect its population structure (e.g. water column fluctuation and sunlight exposure). The present study addresses how temporal decline of the water level in a Neotropical reservoir and exposure to sunlight affect the population structure of C. fluminea. Samplings were carried out twice in the reservoir of Furnas Hydroelectric Power Station (HPS) (Minas Gerais, Brazil), in 2011 and 2012. Population density, spatial distribution and mean shell length of C. fluminea were estimated for each year after sampling in 51 quadrats (0.0625m2) placed on three transects at different distances along the reservoir margins (0, 10 and 20 m from a fixed-point). We observed a predominance of C. fluminea in both years, with a simultaneous gradual decrease in density and richness of native species in the sampling area. Significant differences in density of C. fluminea were registered at different distances from the margin, and are related to the temporal variability of physical conditions of the sediment and water in these environments. We also registered a trend toward an increase in the density and aggregation of C. fluminea as we moved away from the margin, due to the greater stability of these areas (>10 m). The mean shell length of C. fluminea showed significant difference between the distinct distances from the margin and during the years, as well as the interaction of these factors (Distances vs.Years). These results were associated with the reproductive and invasive capacity of this species. This study reveals that these temporal events (especially water column fluctuation) may cause alterations in density, spatial distribution and mean shell length of C. fluminea and the composition of the native malacofauna in Neotropical lentic environments.

How the fluctuations of water levels affect populations of invasive bivalve Corbicula fluminea (Müller, 1774) in a Neotropical reservoir? / Como a flutuação dos níveis da água afetam as populações do bivalve invasor Corbicula fluminea (Müller, 1774) em um reservatório neotropical?

Corbicula fluminea is an invasive bivalve responsible for several environmental and financial problems around the globe. Despite the invasive potential of this species, it suffers certain restrictions in lentic environments due to natural phenomena that significantly affect its population structure (e.g. water column fluctuation and sunlight exposure). The present study addresses how temporal decline of the water level in a Neotropical reservoir and exposure to sunlight affect the population structure of C. fluminea. Samplings were carried out twice in the reservoir of Furnas Hydroelectric Power Station (HPS) (Minas Gerais, Brazil), in 2011 and 2012. Population density, spatial distribution and mean shell length of C. fluminea were estimated for each year after sampling in 51 quadrats (0.0625m2) placed on three transects at different distances along the reservoir margins (0, 10 and 20 m from a fixed-point). We observed a predominance of C. fluminea in both years, with a simultaneous gradual decrease in density and richness of native species in the sampling area. Significant differences in density of C. fluminea were registered at different distances from the margin, and are related to the temporal variability of physical conditions of the sediment and water in these environments. We also registered a trend toward an increase in the density and aggregation of C. fluminea as we moved away from the margin, due to the greater stability of these areas (>10 m). The mean shell length of C. fluminea showed significant difference between the distinct distances from the margin and during the years, as well as the interaction of these factors (Distances vs.Years). These results were associated with the reproductive and invasive capacity of this species. This study reveals that these temporal events (especially water column fluctuation) may cause alterations in density, spatial distribution and mean shell length of C. fluminea and the composition of the native malacofauna in Neotropical lentic environments.

Corbicula fluminea é um bivalve invasor, responsável por inúmeros problemas ambientais e econômicos ao redor do mundo. Apesar de sua capacidade de invasão, a espécie sofre certas restrições devido a fenômenos naturais em ambientes lênticos, afetando significativamente sua estrutura populacional (e.g. flutuação do nível da água e a exposição à luz solar). O presente trabalho avaliou como o decréscimo temporal do nível da água de um reservatório neotropical e a exposição solar, afeta a estrutura populacional de C. fluminea. Duas amostragens foram realizadas no reservatório da Usina Hidrelétrica (UHE) de Furnas (Minas Gerais, Brasil), em 2011 e 2012. A densidade populacional, o comprimento médio e a distribuição espacial da espécie para cada ano foram estimados após amostragem em 51 quadrats (0,0625m2) dispostos em três transectos em diferentes distâncias das margens do reservatório (0, 10 e 20 m em relação a um ponto fixo). Observou-se o predomínio de C. fluminea em ambos os anos, coincidindo com o decréscimo da densidade e riqueza de espécies nativas nas áreas de amostragem. Foram registradas diferenças significativas na densidade de C. fluminea entre as distâncias da margem, sendo atribuídas principalmente à variabilidade temporal do substrato e da água desses ambientes. Registrou-se também uma tendência em aumento da densidade e agregação com o aumento da distância da margem, devido à maior estabilidade dessas áreas (>10 m). Houveram diferenças significativas no tamanho médio das conchas de C. fluminea entre às distâncias da margem e durante os anos, assim como na interação desses fatores (Distâncias vs. Anos). Tais resultados foram associados à capacidade reprodutiva e invasiva da espécie. Esse estudo revelou que eventos temporais (principalmente, a flutuação do nível da água) em ambientes lênticos neotropicais provocam alterações na densidade, tamanho médio e distribuição de C. fluminea e na composição da malacofauna nativa.

Deflating trees: improving Bayesian branch-length estimates using informed priors.

Prior distributions can have a strong effect on the results of Bayesian analyses. However, no general consensus exists for how priors should be set in all circumstances. Branch-length priors are of particular interest for phylogenetics, because they affect many parameters and biologically relevant inferences have been shown to be sensitive to the chosen prior distribution. Here, we explore the use of outside information to set informed branch-length priors and compare inferences from these informed analyses to those using default settings. For both the commonly used exponential and the newly proposed compound Dirichlet prior distributions, the incorporation of relevant outside information improves inferences for data sets that have produced problematic branch- and tree-length estimates under default settings. We suggest that informed priors are worthy of further exploration for phylogenetics.

Androgenesis: a review through the study of the selfish shellfish Corbicula spp.

Among the asexual reproductive modes, androgenesis is probably one of the most astonishing and least studied mechanisms. In this 'paternal monopolization', the maternal nuclear genome fails to participate in zygote development and offspring are paternal nuclear clones. Obligate androgenesis is known in only a few organisms, including multiple species of clam in the genus Corbicula. Corbicula is a good system to review the evolutionary consequences of this 'all-male asexuality' because the cytological mechanisms of androgenetic reproduction have been described. In Corbicula, sperm are unreduced and, after fertilization, the maternal nuclear chromosomes are extruded as two polar bodies. Hermaphroditic lineages of Corbicula have a worldwide distribution and seem to reproduce through androgenesis, whereas their sexual relatives have restricted ranges. The invasive success of these androgenetic Corbicula lineages may be linked to their asexual mode of reproduction. We review the phenomenon of androgenesis, focusing on evolutionary perspectives, using the genus Corbicula as an exemplar system.

28S rDNA haplotypes of males are distinct from those of androgenetic hermaphrodites in the clam Corbicula leana.

The clam Corbicula leana exists in two forms, hermaphrodites and males. Our previous study on mitochondrial DNA suggested that the male nuclear DNA might have derived from hermaphrodite C. leana relatively recently. To clarify the origin of males in the clam, sequences of the nuclear 28S rDNA divergent domain (which is 441-444 bp long) in androgenetic hermaphrodites and males and dioecious (bisexual) species were analyzed. Unexpectedly, the nuclear 28S rDNA haplotypes of males and hermaphrodites were distinct. Haplotype network analysis indicated that males and hermaphrodites are reproductively isolated from each other without sharing the same nuclear haplotype. These results support a hypothesis that the egg nuclear genome of androgenetic hermaphrodites is replaced by the male sperm genome, and only males develop after fertilization by a male spermatozoon.

Rare gene capture in predominantly androgenetic species.

The long-term persistence of completely asexual species is unexpected. Although asexuality has short-term evolutionary advantages, a lack of genetic recombination leads to the accumulation over time of deleterious mutations. The loss of individual fitness as a result of accumulated deleterious mutations is expected to lead to reduced population fitness and possible lineage extinction. Persistent lineages of asexual, all-female clones (parthenogenetic and gynogenetic species) avoid the negative effects of asexual reproduction through the production of rare males, or otherwise exhibit some degree of genetic recombination. Another form of asexuality, known as androgenesis, results in offspring that are clones of the male parent. Several species of the Asian clam genus Corbicula reproduce via androgenesis. We compared gene trees of mitochondrial and nuclear loci from multiple sexual and androgenetic species across the global distribution of Corbicula to test the hypothesis of long-term clonality of the androgenetic species. Our results indicate that low levels of genetic capture of maternal nuclear DNA from other species occur within otherwise androgenetic lineages of Corbicula. The rare capture of genetic material from other species may allow androgenetic lineages of Corbicula to mitigate the effects of deleterious mutation accumulation and increase potentially adaptive variation. Models comparing the relative advantages and disadvantages of sexual and asexual reproduction should consider the possibility of rare genetic recombination, because such events seem to be nearly ubiquitous among otherwise asexual species.

Development of novel microsatellite markers to identify the different invasive lineages in the Corbicula complex and to assess androgenesis.

Reliable markers are needed to identify the lineages in the invasive clam genus Corbicula. Previous studies have demonstrated that mitochondrial (mt) DNA poorly resolves Corbicula phylogeny, owing to its androgenetic reproductive mode. Moreover, hybridization and mitochondrial/nuclear mismatches occur. We developed the first eleven polymorphic markers to detect these phenomena and to investigate the nuclear identity of Corbicula populations. These microsatellite loci revealed three main lineages in Western Europe. One locus allowed rapid discrimination of these three lineages on agarose gel, saving time and money. Moreover, the eleven markers were successfully cross-amplified in the invasive Corbicula lineages found in North America.

Cytogenetic and morphological characterization of Corbicula fluminalis (O. F. Müller, 1774) (Bivalvia: Veneroida: Corbiculidae): taxonomic status assessment of a freshwater clam.

Chromosomes of Corbicula fluminalis were characterized by karyotype analysis and nucleolar organizer region (NORs) localization. The triploid chromosome number was confirmed as 54; the karyotype is composed of 3 metacentric, 15 submetacentric and 36 subtelo-acrocentic chromosomes. Silver staining revealed nucleolar organizers on the telomeric regions of three subtelo-acrocentic chromosomes. This is the first study on chromosomes of C. fluminalis. The results are discussed with regards to Corbicula species as well as its relationships to other mollusc species based on cytogenetic characters and morphometric of the shells.

All-male asexuality: origin and maintenance of androgenesis in the Asian clam Corbicula.

Androgenesis is a rare form of asexual male reproduction found in disparate taxa across the Tree of Life. Phylogenetic analyses of mitochondrial genes suggest that androgenesis has arisen repeatedly in the Asian clam genus Corbicula. Two of these androgenetic species have been introduced to North America. Multiple lines of genetic evidence suggest that although nuclear recombination between these two species is rare, mitochondrial genome capture is a frequent consequence of androgenetic parasitism of heterospecific eggs. Egg parasitism may also rarely result in partial nuclear genome capture between closely related species of Corbicula, which provides a mechanism for the otherwise clonal species to avoid the deleterious effects of asexuality. Egg parasitism among congeners may explain why androgenesis has been maintained in Corbicula after fixation and has not yet led to population extinction. This mechanism also provides an explanation for the apparent multiple origins of androgenesis in Corbicula as seen on the mitochondrial DNA phylogeny. We suggest that a single androgenetic lineage may have repeatedly captured mitochondrial genomes (as well as portions of nuclear genomes) from various sexual species, resulting in several distinct androgenetic species with distantly related mtDNA genomes and divergent morphologies.

Rapid evolution of sessility in an endemic species flock of the freshwater bivalve Corbicula from ancient lakes on Sulawesi, Indonesia.

The fauna of ancient lakes frequently contains taxa with highly derived morphologies that resulted from in situ radiation of lacustrine lineages with high antiquity. We employed a molecular mtDNA phylogeny to investigate this claim for corbiculid freshwater bivalves in two ancient lake systems on the Indonesian island Sulawesi. Among the otherwise mobile corbiculid species flock, only one taxon, Posostrea anomioides, in the ancient Lake Poso exhibits a unique habit, i.e. cementing one valve to the substrate. Our data show that Corbicula on Sulawesi is polyphyletic, with the endemic riverine taxa in terminal position, and the lacustrine species flock being paraphyletic. Surprisingly, Posostrea is not confirmed as a genus distinct from Corbicula and genetic distances suggest a rather recent origin from the only other corbiculid species endemic to Lake Poso, the non-cementing Corbicula possoensis. While the cementing anomioides, despite its unique behavioural and morphological characteristics, clusters together with non-sessile Corbicula species, the latter exhibit strong genetic distances in the absence of morphological disparity and fall into several genetically rather distinct clades. These findings suggest that developmental plasticity of animals in ancient lakes rather than the antiquity of lineages might account for the unique morphology of some species.