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PubMedDate not supplied

Reconstructing reticulate evolution in species-theory and practice.

We present new methods for reconstructing reticulate evolution of species due to events such as horizontal transfer or hybrid speciation; both methods are based upon extensions of Wayne Maddison's approach in his seminal 1997 paper. Our first method is a polynomial time algorithm for constructing phylogenetic networks from two gene trees contained inside the network. We allow the network to have an arbitrary number of reticulations, but we limit the reticulation in the network so that the cycles in the network are node-disjoint ("galled"). Our second method is a polynomial time algorithm for constructing networks with one reticulation, where we allow for errors in the estimated gene trees. Using simulations, we demonstrate improved performance of this method over both NeighborNet and Maddison's method.

Computer Simulation↗
PubMed2026

The evolutionary origins of the parthenogenetic lizard Aspidoscelis tesselatus.

Most vertebrate species reproduce sexually. The whiptail lizards (Aspidoscelis) are a notable exception; at least 11 of the 45 recognized species are parthenogenetic. Here, we focus on one such species (Aspidoscelis tesselatus) as a case study to understand how parthenogenetic species originate and evolve. Using genome-wide sequence data and ecological niche modelling, we find that A. tesselatus likely arose from a single hybrid speciation event between A. scalaris and A. marmoratus less than 500,000 years ago. The geographic ranges of A. tesselatus and its parental species overlap currently, and niche modelling shows this zone of sympatry was even broader during the period when A. tesselatus likely formed. We additionally show evidence that A. tesselatus has a dynamic genome post-formation, with de novo mutations, introgression, and double-strand break associated events all contributing to variation within the species. These results show that asexual lineages can continue to be shaped by ongoing genomic and ecological dynamics, illuminating the processes that influence transitions in reproductive mode.

asexuality↗
PubMed2005

Reconstructing phylogenetic networks using maximum parsimony.

Phylogenies - the evolutionary histories of groups of organisms - are one of the most widely used tools throughout the life sciences, as well as objects of research within systematics, evolutionary biology, epidemiology, etc. Almost every tool devised to date to reconstruct phylogenies produces trees; yet it is widely understood and accepted that trees oversimplify the evolutionary histories of many groups of organims, most prominently bacteria (because of horizontal gene transfer) and plants (because of hybrid speciation). Various methods and criteria have been introduced for phylogenetic tree reconstruction. Parsimony is one of the most widely used and studied criteria, and various accurate and efficient heuristics for reconstructing trees based on parsimony have been devised. Jotun Hein suggested a straightforward extension of the parsimony criterion to phylogenetic networks. In this paper we formalize this concept, and provide the first experimental study of the quality of parsimony as a criterion for constructing and evaluating phylogenetic networks. Our results show that, when extended to phylogenetic networks, the parsimony criterion produces promising results. In a great majority of the cases in our experiments, the parsimony criterion accurately predicts the numbers and placements of non-tree events.

Algorithms↗
PubMedDate not supplied

Phylogenetic networks: modeling, reconstructibility, and accuracy.

Phylogenetic networks model the evolutionary history of sets of organisms when events such as hybrid speciation and horizontal gene transfer occur. In spite of their widely acknowledged importance in evolutionary biology, phylogenetic networks have so far been studied mostly for specific data sets. We present a general definition of phylogenetic networks in terms of directed acyclic graphs (DAGs) and a set of conditions. Further, we distinguish between model networks and reconstructible ones and characterize the effect of extinction and taxon sampling on the reconstructibility of the network. Simulation studies are a standard technique for assessing the performance of phylogenetic methods. A main step in such studies entails quantifying the topological error between the model and inferred phylogenies. While many measures of tree topological accuracy have been proposed, none exist for phylogenetic networks. Previously, we proposed the first such measure, which applied only to a restricted class of networks. In this paper, we extend that measure to apply to all networks, and prove that it is a metric on the space of phylogenetic networks. Our results allow for the systematic study of existing network methods, and for the design of new accurate ones.

Algorithms↗
PubMed2000

Frequency and spatial patterning of clonal reproduction in Louisiana iris hybrid populations.

The plant genera in which natural hybridization is most prevalent tend to be outcrossing perennials with some mechanism for clonal (i.e., asexual) reproduction. Although clonal reproduction in fertile, sexually reproducing hybrid populations could have important evolutionary consequences, little attention has been paid to quantifying this parameter in such populations. In the present study, we examined the frequency and spatial patterning of clonal reproduction in two Louisiana iris hybrid populations. Allozyme analysis of both populations revealed relatively high levels of genotypic diversity. However, a considerable amount of clonality was apparent. Nearly half of all genets (47%) in one population and more than half (61%) in the other had multiple ramets. Furthermore, both populations exhibited relatively high levels of genetic structuring, a pattern that resulted from the aggregation of clonal ramets. The occurrence of clonal reproduction in hybrid populations could not only facilitate introgression through an increase in the number of flowering ramets per genet and/or the survivorship of early generation hybrids, but might also influence the mating system of such populations. Any potential increase in the selfing rate due to cross-pollination among ramets of the same genet may, in turn, increase the likelihood of homoploid hybrid speciation.

Biological Evolution↗
PubMed1998

Low serum aluminum values in dialysis patients with increased bone aluminum levels.

BACKGROUND: Using an HPLC/ETAAS hybrid speciation technique we previously demonstrated iron to have a multifold effect on the binding of aluminum to transferrin by limiting the number of available binding sites and decreasing the affinity of transferrin for aluminum. Theoretically, at a 60% iron-transferrin saturation the aluminum-transferrin fraction in serum should not exceed 30 microg/l. In the present study previous experimental data were confronted with recent clinical observations in patients with either normal iron status or iron overload. PATIENTS AND RESULTS: Serum aluminum levels and iron overload: In 38 dialysis patients with a normal iron status and of whom 63% received Al(OH)3 for phosphate binding 26 (68%) had a serum aluminum level >30 microg/l. On the other hand out of 28 transfusional iron overloaded patients; 68% of them taking Al(OH)3, only 1 subject (4%) had a serum aluminum value in excess of 30 microg/l. Taking patients of both groups receiving Al(OH)3 together a significant (p = 0.001) negative correlation (r = -0.5017) was found between the iron-transferrin saturation and the serum aluminum levels. Iron status and parenteral aluminum loading: Also could a significant (p = 0.001) negative correlation (r = -0.6383) between these parameters be found in an independent group of 44 patients which were acutely intoxicated by the use of aluminum-contaminated dialysis fluids. Since in this population aluminum loading occurred parenterally and not via the gastrointestinal tract, a direct effect of iron on the transferrin binding of aluminum rather than on the element's gastrointestinal absorption must have been responsible for the inverse relationship. Bone aluminum and iron overload: Out of 22 patients with a normal iron status (mean + SD serum ferritin: 216 +/- 245 microg/l; iron-transferrin saturation 20.4 +/- 9.6%), all of them having aluminum overload (bone aluminum level >15 microg/g and/or positive Aluminon staining) none of them presented with a serum aluminum <30 microg/l (mean +/- SD: 82.2 +/- 51.6 microg/l). On the other hand out of 13 iron overloaded patients (serum ferritin >800 microg/l; iron-transferrin saturation 61.4 +/- 17.6%) 10 (77%) presented the proposed criteria of aluminum overload in the presence of a serum aluminum level <30 microg/l. CONCLUSIONS: Our data indicate that in dialysis patients with iron overload (iron-transferrin saturation >60%; serum ferritin >800 microg/l) serum aluminum levels are low (<30 microg/l) despite exposure to aluminum by the intake of Al(OH)3 or the use of aluminum-contaminated dialysis fluids. Low serum aluminum nevertheless may be associated with aluminum overload and even aluminum-related bone disease. An effect of iron on the serum aluminum speciation may at least in part explain our observations. Our findings allow a more accurate interpretation of baseline serum aluminum values.

Aluminum↗
PubMed2004

Early events in speciation: polymorphism for hybrid male sterility in Drosophila.

Capturing the process of speciation early enough to determine the initial genetic causes of reproductive isolation remains a major challenge in evolutionary biology. We have found, to our knowledge, the first example of substantial intraspecific polymorphism for genetic factors contributing to hybrid male sterility. Specifically, we show that the occurrence of hybrid male sterility in crosses between Drosophila mojavensis and its sister species, Drosophila arizonae, is controlled by factors present at different frequencies in different populations of D. mojavensis. In addition, we show that hybrid male sterility is a complex phenotype; some hybrid males with motile sperm still cannot sire offspring. Because male sterility factors in hybrids between these species are not yet fixed within D. mojavensis, this system provides an invaluable opportunity to characterize the genetics of reproductive isolation at an early stage.

Age Factors↗
PubMed2005

Contrasting views over a hybrid complex: Between speciation and evolutionary "dead-end".

The Squalius alburnoides complex, of hybrid origin, comprises diploid, triploid and tetraploid forms and has a widespread distribution in the Iberian waters. The southern populations of this complex, sympatric with S. pyrenaicus, show high genetic variability, diversity of forms and reproductive modes which create pathways that may allow for the establishment of a new species in the future. Here we report a contrasting view over the S. alburnoides complex: in the Mondego River basin (northern Portugal), nuclear "non-hybrid" and tetraploid forms are absent and a clearly impoverished genetic diversity is observed, contributing to a general scarcity of possibilities of generating novel genetic material. Moreover, the bisexual species involved in the maintenance of the complex in this basin (S. carolitertii) exhibits a considerably lower genetic variability, when compared with S. pyrenaicus. The observed differences suggest that, despite being originated by similar hybridization events and maintained by analogous reproductive mechanisms, different populations of the complex were exposed to distinct evolutionary constrains, which in some cases resulted in diversification and speciation while in others led to a compromising situation in terms of evolutionary potential. Additionally, and for the first time all forms were used in the calculation of genetic distances and diversity indices, widening the possibilities of analysis of the complex by allowing the inclusion of a large part of the available data, irrespective of ploidy level.

Animals↗
PubMed2003

Lack of mitochondrial genetic structure in hamlets (Hypoplectrus spp.): recent speciation or ongoing hybridization?

Species in the genus Hypoplectrus (hamlet fish) have been recognized primarily on the basis of colour morphology, which varies substantially. Limited differentiation in other morphological characters, however, has led to ongoing debate about their taxonomy. Our analysis of mtDNA sequences demonstrates neither reciprocal monophyly nor significant genetic differentiation among hamlet colour morphs. These data are potentially consistent with a model of recent speciation due to sexual selection on colour morphology. The presence within hamlets of two divergent mtDNA clades, however, suggests a longer history during which hybridization and gene flow have prevented the differentiation of hamlet colour morphs, at least in neutral genetic markers.

Animals↗
PubMed2006

Innovation in anti-herbivore defense systems during neopolypoloidy - the functional consequences of instantaneous speciation.

Allopolyploid hybridization instantly merges two differentially adapted genomes into one individual. Allopolyploids are often evolutionarily successful, undergoing adaptive radiations despite the genetic and physiological challenges of merging genomes. We examine a suite of induced herbivore resistance traits in three independent lines of the synthetic allopolyploid Nicotianaxmierata (Nma) and its parent species, N. miersii (Nmi) and N. attenuata (Na), to determine how a complex polygenetic adaptation fares during the early stages of neoallopolyploid formation. All species responded to Manduca sexta oral secretions (OS) with a temporally prolonged jasmonate (JA) burst. In one parent (Na), the JA burst was additionally amplified and associated with the elicitation of direct and indirect defenses. In the other parent (Nmi), OS neither amplified the JA burst nor elicited defense responses, although applied MeJA confirmed the inducibility of the defense responses. All lines of Nma retained enough aspects of Na's JA signaling to recognize OS and to accumulate sufficient direct defenses to impair the growth of Manduca larvae. Most defense-related metabolites were retained in Nma even if inherited from only one parent; however, OS-elicited volatiles, trypsin protease inhibitors (TPIs) and chlorogenic acid were lost in some lines, even though MeJA treatment elicited similar responses in all lines. Herbivore defense systems are flexibly inherited in allopolyploids, causing individuals to diverge over only a few generations; for example, line 1 of Nma could not produce TPIs after OS elicitation, whereas lines 2 and 3 could. This flexible integration of defense signaling systems with a diversity of elicited responses may explain why adaptive radiations are commonly found in allopolyploid lineages.

Adaptation, Physiological↗
PubMed2006

What does Drosophila genetics tell us about speciation?

Studies of hybrid inviability, sterility and 'speciation genes' in Drosophila have given insight into the genetic changes that result in reproductive isolation. Here, I survey some extraordinary and important advances in Drosophila speciation research. However, 'reproductive isolation' is not the same as 'speciation', and this Drosophila work has resulted in a lopsided view of speciation. In particular, Drosophila are not always well-suited to investigating ecological and other selection-driven primary causes of speciation in nature. Recent advances have made use of far less tractable, but more charismatic organisms, such as flowering plants, vertebrates and larger insects. Work with these organisms has complemented Drosophila studies of hybrid unfitness to provide a more complete understanding of speciation.

Animals↗
PubMed2003

Parasite infectivity to hybridising host species: a link between hybrid resistance and allopolyploid speciation?

Variation in host-specific infectivity was studied in monogenean polystome parasites (Protopolystoma spp.) of the interfertile, parapatric anurans Xenopus laevis laevis and Xenopus muelleri. Laboratory-raised host F1 hybrids were resistant to parasites respectively specific to each parent taxon in nature. This resistance occurred against parasite isolates from both inside and outside a host hybrid/sympatric zone (and no isolate was compatible with the foreign host species under experimental conditions). Geographical Protopolystoma xenopodis isolates showed variable infectivity to a single full-sib group of their usual host, X. l. laevis, and strains with high or low infectivity to these sibs co-occurred in spatially distant local areas (separated by 1,700 km). The host compatibility of P. xenopodis was also subject to host genotypexparasite genotype interactions. Refractoriness to some parasites or pathogens, as a consequence of hybridisation, may have conferred a selective advantage on the allopolyploid pathway by which most Xenopus spp. are believed to have evolved.

Animals↗
PubMed2006

A chloroplast genealogy of myrmecophytic Macaranga species (Euphorbiaceae) in Southeast Asia reveals hybridization, vicariance and long-distance dispersals.

Macaranga (Euphorbiaceae) includes about 280 species with a palaeotropic distribution. The genus not only comprises some of the most prominent pioneer tree species in Southeast Asian lowland dipterocarp forests, it also exhibits a substantial radiation of ant-plants (myrmecophytes). Obligate ant-plant mutualisms are formed by about 30 Macaranga species and 13 ant species of the genera Crematogaster or Camponotus. To improve our understanding of the co-evolution of the ants and their host plants, we aim at reconstructing comparative organellar phylogeographies of both partners across their distributional range. Preliminary evidence indicated that chloroplast DNA introgression among closely related Macaranga species might occur. We therefore constructed a comprehensive chloroplast genealogy based on DNA sequence data from the noncoding ccmp2, ccmp6, and atpB-rbcL regions for 144 individuals from 41 Macaranga species, covering all major evolutionary lineages within the three sections that contain myrmecophytes. A total of 88 chloroplast haplotypes were identified, and grouped into a statistical parsimony network that clearly distinguished sections and well-defined subsectional groups. Within these groups, the arrangement of haplotypes followed geographical rather than taxonomical criteria. Thus, up to six chloroplast haplotypes were found within single species, and up to seven species shared a single haplotype. The spatial distribution of the chloroplast types revealed several dispersals between the Malay Peninsula and Borneo, and a deep split between Sabah and the remainder of Borneo. Our large-scale chloroplast genealogy highlights the complex history of migration, hybridization, and speciation in the myrmecophytes of the genus Macaranga. It will serve as a guideline for adequate sampling and data interpretation in phylogeographic studies of individual Macaranga species and species groups.

Animals↗
PubMed2025

Repeatable Genomic Outcomes Along the Speciation Continuum: Insights From Pine Hybrid Zones (Genus Pinus).

Hybridization is a widespread evolutionary process and a key source of evolutionary novelty. Despite intensive study, the extent to which hybridization is deterministic and repeatable, particularly in recurrent contact events involving the same species under varying ecological conditions, remains unclear. Here, we investigated three replicated contact zones between Scots pine (Pinus sylvestris) and dwarf mountain pine (Pinus mugo) in Central Europe: two occurring in peatland habitats and one in a contrasting sandstone outcrop. Using genome-wide SNP genotyping of over 1300 individuals, we analysed genomic structure, diversity, and ancestry patterns across these zones. All sites revealed pervasive hybridization, dominated by later-generation hybrids and a notable scarcity of pure P. mugo. Across environments, hybrid populations exhibited strikingly consistent genomic compositions, with asymmetric introgression strongly biased toward P. mugo ancestry, suggesting that hybrid genome structure may follow predictable patterns under similar ecological conditions and could be shaped by cytonuclear incompatibilities. Nonetheless, we also detected site-specific differences in hybrid diversity and phenotype, highlighting the influence of local environmental selection on shared hybrid genomic backgrounds. We provide genomic evidence that Pinus uliginosa, a morphologically distinct peat bog pine traditionally regarded as a relict and endangered species is instead a partially stabilised hybrid lineage. Its genome reflects incomplete hybridization and ecological filtering, yet it lacks sufficient genetic divergence to be recognised as a distinct species. Together, these results provide evidence for the repeatability of hybridization processes, which result in the formation of phenotypes reflecting a species continuum subjected to strong environmental pressures. The findings support the simplification of taxonomic nomenclature within the Pinus mugo complex, informing adaptive conservation strategies and the genetic management of hybrid lineages.

Hybridization, Genetic↗
PubMed2005

Gamete compatibility and sperm competition affect paternity and hybridization between sympatric Asterias sea stars.

Gamete interactions may strongly influence speciation and hybridization in sympatric broadcast-spawning marine invertebrates. We examined the role of gamete compatibility in species integrity using cross-fertilization studies between sympatric Asterias sea stars from a secondary contact zone in the northwest Atlantic. In crosses between single males and single females, gametes of both species were compatible and produced viable, fertile hybrid offspring, but with considerable variation in the receptivity of eggs to heterospecific sperm. Differential compatibility of heterospecific gametes was detected in sperm competition studies in which we used a nuclear DNA marker to assign paternity to larval offspring. Several families showed conspecific sperm precedence in A. forbesi eggs, and one family showed competitive superiority of A. forbesi sperm fertilizing A. rubens eggs. Gametic interactions are an important component of prezygotic reproductive isolation in sympatric Asterias. The interaction between gametes of these closely related sea stars is consistent with the function of gamete recognition systems that are known to mediate fertilization success and speciation in other marine invertebrates.

Animals↗
PubMed2004

The normal function of a speciation gene, Odysseus, and its hybrid sterility effect.

To understand how postmating isolation is connected to the normal process of species divergence and why hybrid male sterility is often the first sign of speciation, we analyzed the Odysseus (OdsH) gene of hybrid male sterility in Drosophila. We carried out expression analysis, transgenic study, and gene knockout. The combined evidence suggests that the sterility phenotype represents a novel manifestation of the gene function rather than the reduction or loss of the normal one. The gene knockout experiment identified the normal function of OdsH as a modest enhancement of sperm production in young males. The implication of a weak effect of OdsH on the normal phenotype but a strong influence on hybrid male sterility is discussed in light of Haldane's rule of postmating isolation.

Animals↗
PubMed2006

[Effect of submerging and wetting-redrying on Cd speciation and uptake by Sorghum hybrid Sudangrass in two paddy soils under spiked Cd].

Effect of continuous submerging and wetting-redrying on cadmium speciation and uptake by Sorghum hybrid Sudangrass in a Ferric-accumulic Stagnic Anthrosol and a Tipical Hapludult collected from the Taihu Lake region and the rolling downs of Yingtan, Jiangxi, China respectively, was studied by pot experiment with Cd spike in 2003. Compared to that under wetting-redrying treatment, the MgCl2-extracted pool of Cd in Huangnitu with spiked Cd of 5mg x kg(-1) and 10mg x kg(-1) was decreased from 21.8% and 28.5% to 8.0% and 16.9% while NH2OH x HCl-extracted pool increased from 17.7% and 17.3% to28.1% and 37.5% under continuous submerging. However, in the Typical Halpudult, NaAC-extracted pool of Cd decreased from 20.8% and 29.6% to 11.6% and 12.6%. Cd uptake by Sorghum hybrid Sudangrass was found in negative correlation with the MgCl2 extracted pool of Cd. Total Cd uptake was significantly reduced by the pretreatment of continuously submerging in Huangnitu.

Adsorption↗