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PubMed2000

Phylogenetic analysis under reticulate evolution.

The usual assumption that species have evolved from a common ancestor by a simple branching process--where each branch is genetically isolated--has been challenged by the observation of frequent hybridization between species in natural populations. In fact, most plant species are thought to have hybrid origins. This reticulate pattern of species evolution has posed problems in the definition of speciation and in phylogenetic reconstruction, especially when molecular data are used. As a result, hybridization has been largely treated as an evolutionary accident or statistical error in phylogenetic analysis. In this paper, I explicitly incorporate hybridization as an evolutionary occurrence and then conduct phylogenetic reconstruction. I first examine the reticulate evolution under a pure drift model, and then extend the theory to fit a mutation model. A least-squares method is developed for reconstructing a reticulate phylogeny using gene frequency data. The efficacy of the method under the pure drift model is verified via Monte Carlo simulations.

Evolution, Molecular↗
PubMed2004

Loss-of-imprinting of Peg1 in mouse interspecies hybrids is correlated with altered growth.

Previous studies have shown that loss-of-imprinting (LOI) is a regular occurrence in interspecies hybrids of the genus Peromyscus. Furthermore, evidence was presented that indicated that LOI is involved in a placental hybrid dysgenesis effect resulting in abnormal placental growth and thus possibly in speciation. We show here that LOI of the strictly paternally expressed gene Peg1 (also called Mest) occurs in F1 hybrids between Mus musculus (MMU) and M. spretus (MSP). Peg1 LOI is correlated with increased body weight and increased weight of two of the organs tested, kidney and spleen. X-gal staining of tissues derived from Peg1(+/-) x MSP F1 mice, carrying a maternal LacZ knock-in allele of Peg1, demonstrates that LOI is stochastic in that it affects different tissues to variable extents and that, even within one tissue, not all cells are similarly affected. Furthermore, this expression from the maternal allele does not necessarily follow the endogenous paternal Peg1 expression pattern. Our results indicate that LOI occurs in interspecies hybrids in the genus Mus and that altered growth is a frequent outcome of LOI.

Animals↗
PubMed2005

Bimodal distribution of flowering time in a natural hybrid population of daylily (Hemerocallis fulva) and nightlily (Hemerocallis citrina).

Time of flower anthesis in a day is thought to evolve in response to the time of pollinator activities. We studied blooming and withering time in natural populations of daylily (Hemerocallis fulva), nightlily (Hemerocallis citrina) and their hybrids, and also in an artificially obtained array of the F1 hybrids. Blooming time of H. fulva varied from 4:30 to 7:30 and H. citrina varied from 16:30 to 20:30. In a natural hybrid population, blooming time and withering time showed discontinuous bimodal distribution in spite that morphological traits of flowers showed continuous unimodal variation. Most F1 hybrids showed diurnal flowering. These findings indicate that only a few genes have strong phenotypic effect on the determination of flowering time in Hemerocallis, and suggest that the evolution from a H. fulva-like ancestor to H. citrina was not a continuous process by accumulation of minute mutations.

Circadian Rhythm↗
PubMed2004

Relative contribution of dispersal and natural selection to the maintenance of a hybrid zone in Littorina.

Habitat preference behavior may play an important role in nonallopatric speciation. However, most examples of habitat preference contributing to differentiation within natural populations correspond to parasites or herbivores living in the discrete environments constituted by their animal or plant hosts. In the present study we investigated migration guided by habitat preference in the intertidal snail Littorina saxatilis in a hybrid zone associated with an ecotone across the shore, which is therefore a continuously varying environment. First, we found evidence for this behavior in one of the two locations studied. Second, we made reciprocal transplants to suppress the phenotypic gradient observed across the hybrid zone and measured the relative contributions of selection and migration to its regeneration. Selection played an important role at the two locations studied, but migration was only important at one, where it accounted for between a third and a half of the regenerated gradient. This overall minor effect of migration was relevant for theoretical models dealing with nonallopatric speciation, because it suggested that variation for habitat preference did not have an important role in the initiation of the differentiation process. The preference behavior observed in the hybrid zone would have evolved secondarily, as a consequence of habitat-dependent fitness differences between phenotypes.

Animals↗
PubMed1978

Satellite DNAs in eukaryotes: a non-adaptive mechanism of speciation which originated with sexual reproduction?

Satellite DNAs may have originated during evolution at the same time as sexual reproduction in order to suppress crossingover between the 2 heterogametic sex chromosomes, and may have acquired a function of sterility barriers in hybrid species during evolution. This origin of satellite DNAs appears to be reflected in different stages of speciation: partial and total heterogametic sex hybrid sterility and full hybrid sterility might correspond to subspecies, semispecies and full species.

Animals↗
PubMed2004

Testing the chromosomal speciation hypothesis for humans and chimpanzees.

Fixed differences of chromosomal rearrangements between isolated populations may promote speciation by preventing between-population gene flow upon secondary contact, either because hybrids suffer from lowered fitness or, more likely, because recombination is reduced in rearranged chromosomal regions. This chromosomal speciation hypothesis thus predicts more rapid genetic divergence on rearranged than on colinear chromosomes because the former are less porous to gene flow. A number of studies of fungi, plants, and animals, including limited genetic data of humans and chimpanzees, support the hypothesis. Here we reexamine the hypothesis for humans and chimpanzees with substantially more genomic data than were used previously. No difference is observed between rearranged and colinear chromosomes in the level of genomic DNA sequence divergence between species. The same is also true for protein sequences. When the gorilla is used as an outgroup, no acceleration in protein sequence evolution associated with chromosomal rearrangements is found. Furthermore, divergence in expression pattern between orthologous genes is not significantly different for rearranged and colinear chromosomes. These results, showing that chromosomal rearrangements did not affect the rate of genetic divergence between humans and chimpanzees, are expected if incipient species on the evolutionary lineages separating humans and chimpanzees did not hybridize.

Animals↗
PubMed2026

Untangling the Arisaema enigma: Investigating the complex evolutionary history and species relationships in North American Arisaema.

PREMISE: The evolutionary history of morphologically variable plant groups is often obscured by cryptic diversity, morphological convergence, and limited genetic data. Arisaema, a diverse genus within Araceae, exemplifies these challenges. Although some taxonomic treatments recognize only two species of North American Arisaema (A. dracontium and A. triphyllum), other studies have identified morphologically distinct groups within both taxa. Here, we reconstructed evolutionary relationships in North American Arisaema, assessed genetic structure and admixture, and tested the monophyly of proposed species. METHODS: We used 2b-RAD sequencing to generate genome-wide SNP data for 146 samples from 31 populations across the eastern United States. Phylogenetic relationships were inferred using maximum-likelihood and Bayesian approaches. Population structure and admixture were assessed using the program structure and principal component analysis (PCA). RESULTS: Both the Arisaema triphyllum and A. dracontium complexes formed well-supported monophyletic groups. Within the A. dracontium complex, we recovered three monophyletic lineages: A. dracontium, A. calciphilum, and A. macrospathum. In the A. triphyllum complex, A. quinatum, A. stewardsonii, and A. allegheniense consistently formed distinct groups. Relationships between A. pusillum and A. acuminatum, and among A. triphyllum s.s., A. purpurascens, and A. striatum were less clearly resolved, likely due to recent or incomplete divergence, gene flow, or polyploidy. CONCLUSIONS: The results support the monophyly of multiple newly proposed taxa within North American Arisaema, but additional sampling across the species' ranges is needed to fully resolve species boundaries. Our study provides the first evolutionary framework for this group, providing a foundation for future ecological, taxonomic, and conservation research in the genus.

Araceae↗
PubMed2005

Dosage balance in gene regulation: biological implications.

Classical studies in genetics involving aneuploidy and ploidy comparisons and sex-determination mechanisms indicated a balance phenomenon such that changes of individual chromosomal dosage altered the phenotype more dramatically than changes in ploidy. Recent evidence suggests that a major contributor to this balance is the behavior of molecular complexes that function in various regulatory processes affecting gene expression. In this article, we discuss the potential contribution of regulatory balance to the control of quantitative traits, hybrid vigor, genome evolution and post-zygotic speciation mechanisms.

Aneuploidy↗
PubMed2006

Genetic evidence for complex speciation of humans and chimpanzees.

The genetic divergence time between two species varies substantially across the genome, conveying important information about the timing and process of speciation. Here we develop a framework for studying this variation and apply it to about 20 million base pairs of aligned sequence from humans, chimpanzees, gorillas and more distantly related primates. Human-chimpanzee genetic divergence varies from less than 84% to more than 147% of the average, a range of more than 4 million years. Our analysis also shows that human-chimpanzee speciation occurred less than 6.3 million years ago and probably more recently, conflicting with some interpretations of ancient fossils. Most strikingly, chromosome X shows an extremely young genetic divergence time, close to the genome minimum along nearly its entire length. These unexpected features would be explained if the human and chimpanzee lineages initially diverged, then later exchanged genes before separating permanently.

Animals↗
PubMed2004

Gene duplication and speciation in Drosophila: evidence from the Odysseus locus.

The importance of gene duplication in evolution has long been recognized. Because duplicated genes are prone to diverge in function, gene duplication could plausibly play a role in species differentiation. However, experimental evidence linking gene duplication with speciation is scarce. Here, we show that a hybrid-male sterility gene, Odysseus (OdsH), arose by gene duplication in the Drosophila genome. OdsH has evolved at a very high rate, whereas its most immediate paralog, unc-4, is nearly identical among species in the Drosophila melanogaster subgroup. The disparity in their sequence evolution is echoed by the divergence in their expression patterns in both soma and reproductive tissues. We suggest that duplicated genes that have yet to evolve a stable function at the time of speciation may be candidates for "speciation genes," which is broadly defined as genes that contribute to differential adaptation between species.

Amino Acid Sequence↗
PubMed2004

Linkage-dependent gene flow in a house mouse chromosomal hybrid zone.

In the alpine valley of Valtellina there are two Robertsonian chromosomal races of house mouse, the Poschiavo (POS: 2n = 24-26) characterized by metacentric 8.12 and acrocentrics 2 and 10 and the Upper Valtellina (UV: 2n = 22-24) characterized by metacentrics 2.8 and 10.12. The races inhabit separate villages in the valley except in Sommacologna and Sondalo, where they both occur together with hybrids. A total of 179 mice from 16 villages were typed at 13 microsatellite loci. Seven of these loci were localized close to the centromeres of chromosomes 10 and 12, with the prediction that these regions on the race-specific chromosomes would be the most likely to experience a barrier to gene flow. The remaining six loci were localized at the telomeres of chromosomes 10 and 12 and at the centromeres of chromosomes that do not differ between the races. Substantial differences in allelic frequencies were found between the villages with POS and UV races at five of the loci at the centromeres of chromosomes 10 and 12 but at none of the other loci. These differences were not found to distinguish the two races in Sommacologna and Sondalo. Therefore, the centromeric regions of race-specific chromosomes do appear to experience a barrier to gene flow, although this can break down under intense interbreeding between the races. These results are considered in the context of Harrison's (1990) concept of the semipermeability of hybrid zones to gene exchange and in relation to parapatric speciation.

Animals↗
PubMed2026

Phylogenomic evidence provides insights into the phylogeny and speciation patterns in the subgenus Caloscordum (Allium, Amaryllidaceae).

Phylogenomics with abundant informative sites offers a powerful means for elucidating complex diversification history. Here, we collected 22 samples from 18 populations representing all species of subgenus Caloscordum (Allium). Using transcriptome and whole-genome resequencing data, we generated 1755 low-copy nuclear genes and 81 plastid genes. By integrating morphological and phylogenomic evidence, we clarified the subgenus's complex evolutionary histories and speciation patterns. A total of 18 morphological characteristics were analysed, with a taxonomic framework established. Our analyses resolved robust species relationships despite detecting extensive phylogenetic discordances, which were attributed to incomplete lineage sorting (ILS) and hybridization. Specifically, our results suggest that A. inutile originated via rapid budding speciation from the widespread A. tubiflorum. This process likely coincided with mid-Pleistocene glacial-interglacial cycles and may have been reinforced by geographic isolation and ecological adaptation. In contrast, the sole tetraploid species, A. peikingense, was confirmed to be of hybrid origin, derived from A. neriniflorum and A. tubiflorum. This allopolyploidization event appears to have been facilitated by secondary contact between the parent species, which was likely associated with climatic oscillations within the 35° N-45° N arid belt. Overall, our findings elucidate the intricate speciation patterns within Caloscordum and highlight how the interplay of polyploidization, ecological isolation, and tectonic uplift-driven aridification has shaped plant diversity in East Asia.

Phylogeny↗
PubMed2000

Speciation by postzygotic isolation: forces, genes and molecules.

New species arise as reproductive isolation evolves between diverging populations. Here we review recent work in the genetics of postzygotic reproductive isolation-the sterility and inviability of species hybrids. Over the last few years, research has taken two new directions. First, we have begun to learn a good deal about the population genetic forces driving the evolution of postzygotic isolation. It has, for instance, become increasingly clear that conflict-driven processes, like sexual selection and meiotic drive, may contribute to the evolution of hybrid sterility. Second, we have begun to learn something about the identity and molecular characteristics of the actual genes causing hybrid problems. Although molecular genetic data are limited, early findings suggest that "speciation genes" correspond to loci having normal functions within species and that these loci sometimes diverge as a consequence of evolution in gene regulation.

Animals↗
PubMed2002

Chromosomal and allozyme analysis of a hybrid zone between parapatric Robertsonian races of the house mouse: a case of monobrachial homology.

A detailed chromosomal and allozyme analysis of Robertsonian (Rb) populations of the house mouse in Alsace (France) was performed to evaluate the model of speciation by monobrachial centric fusions. The karyological analysis confirmed the existence of a hybrid zone between two Rb races differentiated by monobrachially homologous Rb fusions. The clinical distribution of Rb fusions showed that almost no overlap occurred between the Rb fusions specific to each race, indicating the presence of an acrocentric peak in the center of the hybrid zone. Thus, only chromosomal heterozygotes carrying one to three trivalents were present, instead of the expected highly unfit interracial hybrids, none of which were observed. The effect of karyotypic differentiation on genic divergence was tested across the hybrid zone by comparing levels of genetic structure for chromosomal and allozyme markers according to the isolation by distance model. Results confirmed the highly significant spatial structure for chromosomes, but revealed none for allozymes, indicating that genic diversity was not structured according to karyotype. These data suggest the absence of a strong chromosomal barrier to gene flow, which does not conform with predictions of the model of speciation by monobrachial centric fusions. In addition, the relatedness of these Rb races to neighboring ones, as well as the nonrandom contribution of several chromosomes to the Rb fusions, was analyzed.

Animals↗
PubMed1989

The genetics of postzygotic isolation in the Drosophila virilis group.

In a genetic study of postzygotic reproductive isolation among species of the Drosophila virilis group, we find that the X chromosome has the largest effect on male and female hybrid sterility and inviability. The X alone has a discernible effect on postzygotic isolation between closely related species. Hybridizations involving more distantly related species also show large X-effects, although the autosomes may also play a role. In the only hybridization yet subjected to such analysis, we show that hybrid male and female sterility result from the action of different X-linked loci. Our results accord with genetic studies of other taxa, and support the view that both Haldane's rule (heterogametic F1 sterility or inviability) and the large effect of the X chromosome on reproductive isolation result from the accumulation by natural selection of partially recessive or underdominant mutations. We also describe a method that allows genetic analysis of reproductive isolation between species that produce completely sterile or inviable hybrids. Such species pairs, which represent the final stage of speciation, cannot be analyzed by traditional methods. The X chromosome also plays an important role in postzygotic isolation between these species.

Animals↗
PubMed2005

Mechanisms of fungal speciation.

The objective of this review is to provide a synthesis of speciation theory, of what is known about mechanisms of speciation in fungi and from this, what is expected, and of ideas on how speciation can be elucidated in more fungal systems. The emphasis is on process rather than pattern. Phylogeographic studies in some groups, such as the agarics, demonstrate predominantly allopatric speciation, often through vicariance, as seen in many plants and animals. The variety of life history factors in fungi suggests, however, a diversity in speciation mechanisms that is borne out in comparison of some key examples. Life history features in fungi with a bearing on speciation include genetic mechanisms for intra- and interspecies interactions, haploidy as monokaryons, dikaryons, or coenocytes, distinctive types of propagules with distinctive modes of dispersal, as well as characteristic relationships to the substrate or host as specialized or generalist saprotrophs, parasites or mutualists with associated opportunities and selective pressures for hybridization. Approaches are proposed for both retrospective, phylogeographic determination of speciation mechanisms, and experimental studies with the potential for genomic applications, particularly in examining the relationship between adaptation and reproductive isolation.

Biological Evolution↗
PubMed2001

Multiplicity of infection and the evolution of hybrid incompatibility in segmented viruses.

Some viral genomes are divided into segments. When multiple viruses infect a single cell, progeny form by reassorted mixtures of genomic segments. Hybrid incompatibilities arise when a progeny virus has incompatible segments from different parental viruses. Hybrid incompatibility has been observed in influenza and in the multiparticle plant virus Dianthovirus. Hybrid incompatibility provides an opportunity to study rates of viral evolution, divergence and speciation, and the extent of epistatic interactions among components of the viral genome. This paper presents mathematical and computer simulation models to study hybrid incompatibility between diverging strains. The models identify multiplicity of infection as a key factor. When many viral particles infect each host cell, the effective ploidy of the genetic system is high. High ploidy dilutes the contribution of each locus to the phenotype, weakening the selective intensity on each locus. Weaker selection on variant alleles allows the population to maintain greater genetic diversity and to be more easily perturbed by stochastic fluctuations. Greater diversity and stochastic fluctuations explore more widely the space of epistatic interactions, causing more frequent shifts among favoured combinations of alleles. Variable ploidy of viral genetics differs from standard Mendelian genetics.

Computer Simulation↗
PubMed2005

Divergent mating systems and parental conflict as a barrier to hybridization in flowering plants.

Parental conflicts can lead to antagonistic coevolution of the sexes and of parental genomes. Within a population, the resulting antagonistic effects should balance, but crosses between populations can reveal conflict. Parental conflict is less intense in self-pollinating plants than in outcrossers because outcrossing plants are pollinated by multiple pollen donors unrelated to the seed parent, while a self-pollinating plant is primarily pollinated by one individual (itself). Therefore, in crosses between plants with differing mating systems, outcrossing parents are expected to "overpower" selfing parents. We call this the weak inbreeder/strong outbreeder (WISO) hypothesis. Prezygotically, such overpowering can alter pollination success, and we argue that our hypothesis explains a common pattern of unilateral incompatibility, in which pollen from self-incompatible populations fertilizes ovules of self-compatible individuals but the reciprocal cross fails. A postzygotic manifestation of overpowering is aberrant seed development due to parent-of-origin effects such as genomic imprinting. We evaluate evidence for the WISO hypothesis by reviewing published accounts of crosses between plants of different mating systems. Many, but not all, of such reports support our hypothesis. Since parental conflicts can perturb fertilization and development, such conflicts may strengthen reproductive barriers between populations, contributing to speciation.

Flowers↗