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

Morphological and Genetic Assessment of Invasive Corbicula Lineages in Southern South America: A Case Study in Argentina

The broad global distribution of freshwater clams belonging to the genus Corbicula is driven by multiple hermaphroditic lineages. These lineages, characterized by shared morphological traits and phenotypic plasticity, pose challenges to morphological identification. Genetic markers, such as the mitochondrial COI gene, play a crucial role in delineating these lineages and their ranges. Morphotypes represent observed phenotypic variations, while lineages are defined based on genetic markers. Here, we comprehensively review Corbicula's distribution in Argentina, discriminate extant lineages based on both morphological and genetic (COI) data, and describe variations in internal and external morphologies using 15 Argentine populations. Genetic analyses identified two mitochondrial lineages: the AR morphotype (FW5 haplotype) and CS morphotype (FW17 haplotype). Strikingly, despite having similar vectors, origins, and invasive stages, Corbicula lineages exhibit virtually segregated distributions. However, mitochondrial haplotypes are found in sympatry mainly in northeastern Argentina where individuals with intermediate morphotypes exist, suggesting the presence of hybrids due to maternal genome retention. These findings contribute to the clarification of the identity and distribution of Corbicula lineages in Argentina, where the genus has been found for over half a century. Similar studies are needed in other areas to better understand the invasion patterns of this successful and adaptable group.

Sperm-dependent asexual species and their role in ecology and evolution

Sexual reproduction is the primary mode of reproduction in eukaryotes, but some organisms have evolved deviations from classical sex and switched to asexuality. These asexual lineages have sometimes been viewed as evolutionary dead ends, but recent research has revealed their importance in many areas of general biology. Our review explores the understudied, yet important mechanisms by which sperm-dependent asexuals that produce non-recombined gametes but rely on their fertilization, can have a significant impact on the evolution of coexisting sexual species and ecosystems. These impacts are concentrated around three major fields. Firstly, sperm-dependent asexuals can potentially impact the gene pool of coexisting sexual species by either restricting their population sizes or by providing bridges for interspecific gene flow whose type and consequences substantially differ from gene flow mechanisms expected under sexual reproduction. Secondly, they may impact on sexuals' diversification rates either directly, by serving as stepping-stones in speciation, or indirectly, by promoting the formation of pre- and postzygotic reproduction barriers among nascent species. Thirdly, they can potentially impact on spatial distribution of species, via direct or indirect (apparent) types of competition and Allee effects. For each such mechanism, we provide empirical examples of how natural sperm-dependent asexuals impact the evolution of their sexual counterparts. In particular, we highlight that these broad effects may last beyond the tenure of the individual asexual lineages causing them, which challenges the traditional perception that asexual lineages are short-lived evolutionary dead ends and minor sideshows. Our review also proposes new research directions to incorporate the aforementioned impacts of sperm-dependent asexuals. These research directions will ultimately enhance our understanding of the evolution of genomes and biological interactions in general.

A taxonomic reassessment of native and invasive species of Corbicula clams (Bivalvia: Cyrenidae) from the Russian Far East and Korea

Currently, the validity of many nominal bivalve species of the genus Corbicula endemic to the Russian Far East and South Korea needs a critical reassessment. In this study, we clarify the taxonomic status of Corbicula species of this area based on a combination of molecular genetic, conchological and anatomical data. According to our results, four Corbicula lineages, corresponding to the nominal species Corbicula japonica, Corbicula elatior, Corbicula leana and Corbicula fluminea, can be delineated in samples collected in the Primorye and Khabarovsk regions of Russia and South Korea. Two species endemic to the Russian Far East (i.e. Corbicula finitima and Corbicula lindholmi) are considered here as junior synonyms of the species C. japonica, which is widely distributed in estuarine habitats around the Japanese Archipelago, Sakhalin Island, southern Kurile Islands, Primorye and Khabarovsk regions, Korean Peninsula and China. Three nominal species described from the Lower Amur basin (Corbicula amurensis, Corbicula nevelskoyi and Corbicula sirotskii) appeared to be synonyms of C. elatior, whose range covers the Korean Peninsula, Primorye and Khabarovsk regions and, perhaps, China. We delineated several colour morphs of C. fluminea and C. japonica. The distinctness between these colour morphs can be attributed to both heritable and environmental factors.

Phenotype and Genotype Characterisation of the Asian Clam of the Genus Corbicula Megerle von Mϋhlfeld, 1811 (Venerida, Cyrenidae) from the East Coast of Peninsular Malaysia

The Corbicula taxonomy in Malaysia is equivocal and scarcely being reported. This study aims to characterise phenotype and genotype of the Asian clam of the genus Corbicula (Mergele Von Mühlfeld, 1811) from three locations in east coast of Peninsular Malaysia. The phenotypic characterisation of the three population of the clam was evaluated on the basis of morphometric characters, while mtDNA cytochrome b (cytb) was used to characterise the genotypes. Results of morphometric analysis showed a significant difference (p<0.05) in shell height (SH), shell width (SW) and umbo length (UL) among three locations between the evaluated population. Discriminant analysis also revealed significant difference of the characters among the study sites. However, cluster analysis revealed an overlapping of morphometric characters among evaluated C. fluminea intricate complete separation between populations. Besides, a comparison of the Corbicula with the morphotypes and holotypes had proposed the Corbicula in this region known as C. fluminea. The genotypes characterisation using mtDNA cytb verifies the existence of C. fluminea. Phylogenetic trees demonstrated polymorphism and low genetic variances although geographically separated which parallel to the phenotypic characterisation. Thus, these findings enhance the knowledge on geographical variation and elucidate the complexity of taxa.

Phylogenomic analyses confirm a novel invasive North American Corbicula (Bivalvia: Cyrenidae) lineage

The genus Corbicula consists of estuarine or freshwater clams native to temperate/tropical regions of Asia, Africa, and Australia that collectively encompass both sexual species and clonal (androgenetic) lineages. The latter have become globally invasive in freshwater systems and they represent some of the most successful aquatic invasive lineages. Previous studies have documented four invasive clonal lineages, Forms A, B, C, and Rlc, with varying known distributions. Form A (R in Europe) occurs globally, Form B is found solely in North America, mainly the western United States, Form C (S in Europe) occurs both in European watersheds and in South America, and Rlc is known from Europe. A putative fifth invasive morph, Form D, was recently described in the New World from the Illinois River (Great Lakes watershed), where it occurs in sympatry with Forms A and B. An initial study showed Form D to be conchologically distinct: possessing rust-colored rays and white nacre with purple teeth. However, its genetic distinctiveness using standard molecular markers (mitochondrial cytochrome c oxidase subunit I and nuclear ribosomal 28S RNA) was ambiguous. To resolve this issue, we performed a phylogenomic analysis using 1,699-30,027 nuclear genomic loci collected via the next generation double digested restriction-site associated DNA sequencing method. Our results confirmed Form D to be a distinct invasive New World lineage with a population genomic profile consistent with clonality. A majority (7/9) of the phylogenomic analyses recovered the four New World invasive Corbicula lineages (Forms A, B, C, and D) as members of a clonal clade, sister to the non-clonal Lake Biwa (Japan) endemic, Corbicula sandai. The age of the clonal clade was estimated at 1.49 million years (my; ± 0.401-2.955 my) whereas the estimated ages of the four invasive lineage crown clades ranged from 0.27 to 0.44 my. We recovered very little evidence of nuclear genomic admixture among the four invasive lineages in our study populations. In contrast, 2/6 C. sandai individuals displayed partial nuclear genomic Structure assignments with multiple invasive clonal lineages. These results provide new insights into the origin and maintenance of clonality in this complex system.

Identification of the Invasive Form of Corbicula Clams in Ireland

The basket clam genus, Corbicula, commonly known as the Asian clam, has become one of the most internationally high-profile and widespread aquatic invasive species. This genus is now considered to comprise a polymorphic species complex. The international invasion of Corbicula is characterised by four lineages, each fixed for one morphotype, genotype and haplotype combination: the American form (A) and European round form (R), the American form (C) and European saddle from (S), American form B, form round light colour (Rlc) and an intermediate between forms R and S known as Int. We investigated the genetic and morphometric makeup of each Irish population in order to establish which invasive lineages were present so as to identify the number of introductions to Ireland. A combination of morphometric, mitochondrial cytochrome oxidase subunit I (mtCOI) gene analysis and microsatellite markers were used to determine the invasive form at each Irish site. All Irish Corbicula samples conformed morphometrically to the invasive form A/R. All mtCOI sequences retrieved for 25 Irish individuals were identical to the international A/R form, while microsatellite markers again showed a common clustering with the international A/R forms of Corbicula. The combined approach of morphometries, total genomic DNA and microsatellite markers indicate only one form of Corbicula invaded Ireland; the international A/R form.

Androgenesis: where males hijack eggs to clone themselves

Androgenesis is a form of quasi-sexual reproduction in which a male is the sole source of the nuclear genetic material in the embryo. Two types of androgenesis occur in nature. Under the first type, females produce eggs without a nucleus and the embryo develops from the male gamete following fertilization. Evolution of this type of androgenesis is poorly understood as the parent responsible for androgenesis (the mother) gains no benefit from it. Ultimate factors driving the evolution of the second type of androgenesis are better understood. In this case, a zygote is formed between a male and a female gamete, but the female genome is eliminated. When rare, androgenesis with genome elimination is favoured because an androgenesis-determining allele has twice the reproductive success of an allele that determines sexual reproduction. Paradoxically, except in hermaphrodites, a successful androgenetic strain can drive such a male-biased sex ratio that the population goes extinct. This likely explains why androgenesis with genome elimination appears to be rarer than androgenesis via non-nucleate eggs, although both forms are either very rare or remain largely undetected in nature. Nonetheless, some highly invasive species including ants and freshwater clams are androgenetic, for reasons that are largely unexplained.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.

SmithRNAs: Could Mitochondria "Bend" Nuclear Regulation?

Typically, animal mitochondria have very compact genomes, with few short intergenic regions, and no introns. Hence, it may seem that there is little space for unknown functions in mitochondrial DNA (mtDNA). However, mtDNA can also operate through RNA interference, as small non coding RNAs (sncRNAs) produced by mtDNA have already been proposed for humans. We sequenced sncRNA libraries from isolated mitochondria of Ruditapes philippinarum (Mollusca Bivalvia) gonads, a species with doubly uniparental inheritance of mitochondria, and identified several putative sncRNAs of mitochondrial origin. Some sncRNAs are transcribed by intergenic regions that form stable stem-hairpin structures, which makes them good miRNA-like candidates. We decided to name them small mitochondrial highly-transcribed RNAs (smithRNAs). Many concurrent data support that we have recovered sncRNAs of mitochondrial origin that might be involved in gonad formation and able to affect nuclear gene expression. This possibility has been never suggested before. If mtDNA can affect nuclear gene expression through RNA interference, this opens a plethora of new possibilities for it to interact with the nucleus, and makes metazoan mtDNA a much more complex genome than previously thought.

Low Genetic Diversity and High Invasion Success of Corbicula fluminea (Bivalvia, Corbiculidae) (Müller, 1774) in Portugal

The Asian clam, Corbicula fluminea, is an invasive alien species (IAS) originally from Asia that has spread worldwide causing major ecological and economic impacts in aquatic ecosystems. Here, we evaluated C. fluminea genetic (using COI mtDNA, CYTb mtDNA and 18S rDNA gene markers), morphometric and sperm morphology variation in Portuguese freshwater ecosystems. The COI marker revealed a single haplotype, which belongs to the Asian FW5 invasive lineage, suggesting a common origin for all the 13 Portuguese C. fluminea populations analysed. Morphometric analyses showed differences between the populations colonizing the North (with the exception of the Lima River) and the Centre/South ecosystems. The sperm morphology examination revealed the presence of biflagellate sperm, a distinctive character of the invasive androgenetic lineages. The low genetic variability of the Portuguese C. fluminea populations and the pattern of sperm morphology have been illuminating for understanding the demographic history of this invasive species. We hypothesize that these populations were derived from a unique introductory event of a Corbicula fluminea FW5 invasive androgenic lineage in the Tejo River, which subsequently dispersed to other Portuguese freshwater ecosystems. The C. fluminea asexual reproductive mode may have assisted these populations to become highly invasive despite the low genetic diversity.

Genetic uniformity and long-distance clonal dispersal in the invasive androgenetic Corbicula clams

The clam genus Corbicula is an interesting model system to study the evolution of reproductive modes as it includes both sexual and asexual (androgenetic) lineages. While the sexual populations are restricted to the native Asian areas, the androgenetic lineages are widely distributed being also found in America and Europe where they form a major aquatic invasive pest. We investigated the genetic diversity of native and invasive Corbicula populations through a worldwide sampling. The use of mitochondrial and nuclear (microsatellite) markers revealed an extremely low diversity in the invasive populations with only four, undiversified, genetic lineages distributed across Europe and America. On the contrary, in the native populations, both sexual and androgenetic lineages exhibited much higher genetic diversity. Remarkably, the most abundant and widely distributed invasive forms, the so-called form A and form R found in America and Europe respectively, are fixed for the same single COI (cytochrome c oxydase subunit I) haplotype and same multilocus genotype. This suggests that form R, observed in Europe since the 1980s, derived directly from form A found in America since the 1920s. In addition, this form shares alleles with some Japanese populations, indicating a Japanese origin for this invasive lineage. Finally, our study suggests that few androgenetic Corbicula individuals successfully invaded the non-native range and then dispersed clonally. This is one striking case of genetic paradox raising the issue of invasive and evolutionary success of genetically undiversified populations.

Morphological and molecular differentiation of genus Corbicula suggests that two species are sympatrically distributed in Datong Lake in the Central Yangtze River Basin

Background

White and purple color morphs of Corbicula have been identified all over the world. Previous studies suggested that the distinct difference of inner shell color, especially for sympatric individuals, derived mainly from their different genetic constitutions, not just environmental conditions. Two color morphs of Corbicula sympatric in Datong Lake were compared by both morphometric methods (shell length, shell height, and shell width) and genetic analysis (based on the mitochondrial cytochrome c oxidase subunit I gene COI-mtCOI) to explore their taxonomic relationship.

Results

Morphological analysis showed that there were no significant differences in the values of SH/SL, SW/SL, and SW/SH (P > 0.05) between the two color morphs. Meanwhile, there were no significant differences in measurable parameters among the four mitochondrial COI haplotypes (DT-1, DT-7, DT-19, and DT-31) (P > 0.05). The sequences of four haplotypes (DT-1, DT-7, DT-19, and DT-31) were identical to FW1, FW5, FW4, and FW3, respectively. Restriction fragment length polymorphism (RFLP) analysis showed that only the sequences of haplotype DT-7 could be digested by the restriction enzyme Sac I into two fragments with 200/500 bp. Haplotype DT-31 was found only in one individual (white morph), while each of the other three haplotypes shared with both two color morphs. Phylogenetic analysis demonstrated that the four haplotypes were subdivided into two divergent clades among freshwater clades, and haplotype DT-7 was a divergent sister taxon to the other three.

Conclusions

The results indicated that there were no distinct differences on morphological measures between the two color morphs, and each color morph shared with all four mitochondrial COI haplotypes. Two species (DT-7 referred as Corbicula fluminea and DT-1, DT-19, and DT-31 as Corbicula leana) might coexisted in the Datong Lake. Therefore, a comprehensive study combining nuclear and mitochondrial data along with biological information should be performed to confirm this assumption.

On the fate of sexual traits under asexuality

Environmental shifts and life-history changes may result in formerly adaptive traits becoming non-functional or maladaptive. In the absence of pleiotropy and other constraints, such traits may decay as a consequence of neutral mutation accumulation or selective processes, highlighting the importance of natural selection for adaptations. A suite of traits are expected to lose their adaptive function in asexual organisms derived from sexual ancestors, and the many independent transitions to asexuality allow for comparative studies of parallel trait maintenance versus decay. In addition, because certain traits, notably male-specific traits, are usually not exposed to selection under asexuality, their decay would have to occur as a consequence of drift. Selective processes could drive the decay of traits associated with costs, which may be the case for the majority of sexual traits expressed in females. We review the fate of male and female sexual traits in 93 animal lineages characterized by asexual reproduction, covering a broad taxon range including molluscs, arachnids, diplopods, crustaceans and eleven different hexapod orders. Many asexual lineages are still able occasionally to produce males. These asexually produced males are often largely or even fully functional, revealing that major developmental pathways can remain quiescent and functional over extended time periods. By contrast, for asexual females, there is a parallel and rapid decay of sexual traits, especially of traits related to mate attraction and location, as expected given the considerable costs often associated with the expression of these traits. The level of decay of female sexual traits, in addition to asexual females being unable to fertilize their eggs, would severely impede reversals to sexual reproduction, even in recently derived asexual lineages. More generally, the parallel maintenance versus decay of different trait types across diverse asexual lineages suggests that neutral traits display little or no decay even after extended periods under relaxed selection, while extensive decay for selected traits occurs extremely quickly. These patterns also highlight that adaptations can fix rapidly in natural populations of asexual organisms, in spite of their mode of reproduction.

Relationship between two androgenetic clam species, Corbicula leana and Corbicula fluminea, inferred from mitochondrial cytochrome b and nuclear 28S rRNA markers

Two shell color types, yellow (type I) and brown (type II), of hermaphrodite Corbicula fluminea clams from Ritto, Shiga Prefecture, Japan, are sympatric with both male and hermaphrodite Corbicula leana. In the present study, the mitochondrial DNA (mtDNA) cytochrome b and nuclear 28S rRNA genes of C. fluminea were sequenced to construct a haplotype network in order to investigate the genetic relationship with C. leana. Ninety C. fluminea samples revealed only two cytb haplotypes; the majority (97.8%) were CB7, while the remainder were CB1. In C. leana, only CB1 was detected in hermaphrodites, but both CB1 and CB7 were detected in males. Nuclear 28S rRNA haplotypes of C. fluminea type I individuals were divergent from those of hermaphrodite C. leana. However, C. fluminea type I clams shared haplotypes with male C. leana individuals, whereas C. fluminea type II individuals shared haplotypes with both hermaphrodite and male C. leana samples. These results suggest that it may be difficult to define a clear genetic border between these species.

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.

Origin and possible role of males in hermaphroditic androgenetic Corbicula clams

Hermaphroditic Corbicula leana clams reproduce by androgenesis and have been regarded as simultaneous hermaphrodites. To date, there has been no report on the occurrence of male clams in hermaphroditic Corbicula. In an irrigation ditch in Shiga Prefecture, we found that 78.2% of C. leana specimens were males and 21.8% were hermaphrodites. Microfluorometric analysis revealed that males were diploids and hermaphrodites were triploids. All males produced nonreductional and biflagellate spermatozoa. The sequence analysis of mitochondrial DNA (cytochrome b, 621 bp) for 31 specimens of C. leana showed that four male and nine hermaphrodites shared the same H2 mtDNA haplotype; H1 was detected from 17 males and H3 was detected from one hermaphrodite. Coexisting C. fluminea clams also have haplotypes H1 and H2. Phylogenetic tree by a neighborjoining method based on the partial sequence of cytochrome b revealed that the haplotypes (H1- 3) of C. leana were evidently different from those of dioecious C. sandai (S1 and S2) and C. japonica (J1 and J2). These results suggest that males may be derived from hermaphrodite C. leana clams. The role of males in hermaphroditic populations is unknown. However, if the spermatozoon from a male is able to fertilize an egg from a hermaphrodite and the nuclear genome of the egg is expelled as polar bodies, the sperm nucleus could form a zygote nucleus. This mode of reproduction would allow the replacement of the nuclear genome.

Phylogeny and androgenesis in the invasive Corbicula clams (Bivalvia, Corbiculidae) in Western Europe

Background

The genus Corbicula is one of the most invasive groups of molluscs. It includes both sexual and androgenetic lineages. The present study re-assessed the different morphotypes and haplotypes of West European Corbicula in order to clarify their taxonomic identification and phylogenetic relationships with American and Asian Corbicula clams. We studied several populations from West European river basins (Meuse, Seine, Rhine and Rhône) through an "integrative taxonomy" approach. We combined morphology, partial mitochondrial COI and cyt b sequences and eleven microsatellite loci. Furthermore, we looked for discrepancies between mtDNA and nrDNA/morphology, indicative of androgenesis between lineages.

Results

There are three Corbicula morphotypes in Western Europe associated to three mitochondrial lineages and three genotypes. Form R shares the same COI haplotype as the American form A and the Japanese C. leana. Form S and the American form C have the same haplotype, although their morphologies seem divergent. The European form Rlc belongs to the same mitochondrial lineage as both the American form B and the Asian C. fluminea.

Interestingly, within each haplotype/genotype or lineage, no genetic diversity was found although their invasive success is high. Moreover, we detected rare mismatches between mtDNA and nrDNA/morphology, indicative of androgenesis and mitochondrial capture between form R and form S and therefore challenging the phylogenetic relatedness and the species status within this genus. The global phylogenetic analysis revealed that the sexual Corbicula lineages seem restricted to the native areas while their androgenetic relatives are widespread and highly invasive.

Conclusions

We clarified the discrepancies and incongruent results found in the literature about the European morphotypes of Corbicula and associated mitochondrial lineages. The three West European morphotypes belong to three distinct nuclear and mitochondrial lineages. However mitochondrial capture occurs in sympatric populations of forms R and S. The species status of the morphotypes therefore remains doubtful. Moreover the androgenetic lineages seem widely distributed compared to their sexual relatives, suggesting that androgenesis and invasive success may be linked in the genus Corbicula.

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.

A novel nucleo-cytoplasmic hybrid clone formed via androgenesis in polyploid gibel carp

BACKGROUND

Unisexual vertebrates have been demonstrated to reproduce by gynogenesis, hybridogenesis, parthenogenesis, or kleptogenesis, however, it is uncertain how the reproduction mode contributes to the clonal diversity. Recently, polyploid gibel carp has been revealed to possess coexisting dual modes of unisexual gynogenesis and sexual reproduction and to have numerous various clones. Using sexual reproduction mating between clone D female and clone A male and subsequent 7 generation multiplying of unisexual gynogenesis, we have created a novel clone strain with more than several hundred millions of individuals. Here, we attempt to identify genetic background of the novel clone and to explore the significant implication for clonal diversity contribution.

METHODS

Several nuclear genome markers and one cytoplasmic marker, the mitochondrial genome sequence, were used to identify the genetic organization of the randomly sampled individuals from different generations of the novel clone.

RESULTS

Chromosome number, Cot-1 repetitive DNA banded karyotype, microsatellite patterns, AFLP profiles and transferrin alleles uniformly indicated that nuclear genome of the novel clone is identical to that of clone A, and significantly different from that of clone D. However, the cytoplasmic marker, its complete mtDNA genome sequence, is same to that of clone D, and different from that of clone A.

CONCLUSIONS

The present data indicate that the novel clone is a nucleo-cytoplasmic hybrid between the known clones A and D, because it originates from the offspring of gonochoristic sexual reproduction mating between clone D female and clone A male, and contains an entire nuclear genome from the paternal clone A and a mtDNA genome (cytoplasm) from the maternal clone D. It is suggested to arise via androgenesis by a mechanism of ploidy doubling of clone A sperm in clone D ooplasm through inhibiting the first mitotic division. Significantly, the selected nucleo-cytoplasmic hybrid female still maintains its gynogenetic ability. Based on the present and previous findings, we discuss the association of rapid genetic changes and high genetic diversity with various ploidy levels and multiple reproduction modes in several unisexual and sexual complexes of vertebrates and even other invertebrates.

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.

When trees grow too long: investigating the causes of highly inaccurate bayesian branch-length estimates

A surprising number of recent Bayesian phylogenetic analyses contain branch-length estimates that are several orders of magnitude longer than corresponding maximum-likelihood estimates. The levels of divergence implied by such branch lengths are unreasonable for studies using biological data and are known to be false for studies using simulated data. We conducted additional Bayesian analyses and studied approximate-posterior surfaces to investigate the causes underlying these large errors. We manipulated the starting parameter values of the Markov chain Monte Carlo (MCMC) analyses, the moves used by the MCMC analyses, and the prior-probability distribution on branch lengths. We demonstrate that inaccurate branch-length estimates result from either 1) poor mixing of MCMC chains or 2) posterior distributions with excessive weight at long tree lengths. Both effects are caused by a rapid increase in the volume of branch-length space as branches become longer. In the former case, both an MCMC move that scales all branch lengths in the tree simultaneously and the use of overdispersed starting branch lengths allow the chain to accurately sample the posterior distribution and should be used in Bayesian analyses of phylogeny. In the latter case, branch-length priors can have strong effects on resulting inferences and should be carefully chosen to reflect biological expectations. We provide a formula to calculate an exponential rate parameter for the branch-length prior that should eliminate inference of biased branch lengths in many cases. In any phylogenetic analysis, the biological plausibility of branch-length output must be carefully considered.