THE SPECIATION HISTORY OF THE PHYSCOMITRIUM—PHYSCOMITRELLA SPECIES COMPLEX

A central problem in evolutionary biology is identifying factors that promote the evolution of reproductive isolation. Among mosses, biogeographic evidence indicates that the potential for migration is great, suggesting that biological factors other than geographic isolation may be critical for speciation in this group. The moss Physcomitrella patens (Funariaceae) has long been used as a model for interspecies hybridization and has recently emerged as an important model system for comparative genomics. We report genealogical analyses of six loci from several populations of P. patens and related species in the genus Physcomitrium. These results unambiguously indicate that the so-called genus Physcomitrella arose at least three times from distinct ancestors within the genus Physcomitrium. In spite of the evidence for natural hybridization in the Physcomitrella–Physcomitrium complex, genealogical and experimental hybridization data indicate that the taxonomically defined species are reproductively isolated. However, these analyses suggest that Physcomitrium eurystomum was formed from a hybridization event between two early diverging lineages in the complex, and that the ancestral population size of these lineages was much smaller than the current population sizes. We discuss these findings in the context of the inferred mating system in the Physcomitrella–Physcomitrium complex and patterns of speciation and diversification.     

WAITING FOR SPECIATION: THE EFFECT OF POPULATION SUBDIVISION ON THE TIME TO SPECIATION

We study the time required for speciation in a species that is divided into small versus large populations. Following Dobzhansky and Muller, we assume that hybrid sterility or inviability is caused by “complementary genes,” that is, by the accumulation of genes that cause sterility or inviability when brought together in hybrids but that have no deleterious effect on their normal species genetic background. When divergence between populations is caused by genetic drift, we show that the time to speciation is independent of population subdivision: speciation occurs just as quickly in a species split into a few large populations as into many small populations. When divergence is driven by natural selection, however, the time to speciation is very sensitive to population subdivision and speciation occurs most rapidly when a species is split into two large populations. These results contradict several popular intuitions about the effect of population size on speciation.     

THE GENETICS OF AN ISOLATING MECHANISM BETWEEN TWO SIBLING SPECIES OF DROSOPHILA

Matings between Drosophila simulans females and males of the sibling species D. mauritiana are of abnormally short duration. These rapid matings interrupt the transfer of sperm, leading to substantial reproductive isolation in interspecific as compared to intraspecific copulations. Genetic analysis of this behavior shows that it is influenced much more by the male than the female genotype, with genes from D. simulans being dominant. In males, shortened copulation is caused by interspecific divergence at a minimum of three loci, with one gene on each of the major chromosomes. This is an underestimate of the true number of loci affecting the trait, which could be much larger. The two autosomes have the largest effect, whereas that of the X chromosome is much smaller. The genetic architecture of copulation duration and the larger effect of male than female genotype suggest that females can detect and discriminate against differences in male genitalia.     

SEX CHROMOSOME LINKAGE OF MATE PREFERENCE AND COLOR SIGNAL MAINTAINS ASSORTATIVE MATING BETWEEN INTERBREEDING FINCH MORPHS

Assortative mating is a key aspect in the speciation process because it is important for both initial divergence and maintenance of distinct species. However, it remains a challenge to explain how assortative mating evolves when diverging populations are undergoing gene flow (e.g., during hybridization). Here I experimentally test how assortative mating is maintained with frequent gene flow between diverged head‐color morphs of the Gouldian finch (Erythrura gouldiae). Contrary to the predominant view on the development of sexual preferences in birds, cross‐fostered offspring did not imprint on the phenotype of their conspecific (red or black morphs) or heterospecific (Bengalese finch) foster parents. Instead, the mating preferences of F₁ and F₂ intermorph‐hybrids are consistent with inheritance on the Z chromosomes, which are also the location for genes controlling color expression and the genes causing low fitness of intermorph‐hybrids. Genetic associations between color signal and preference loci on the sex chromosomes may prevent recombination from breaking down these associations when the morphs interbreed, helping to maintain assortative mating in the face of gene flow. Although sex linkage of reproductively isolating traits is theoretically expected to promote speciation, social and ecological constraints may enforce frequent interbreeding between the morphs, thus preventing complete reproductive isolation.     

GENETIC ARCHITECTURE OF ISOLATION BETWEEN TWO SPECIES OF SILENE WITH SEX CHROMOSOMES AND HALDANE'S RULE

Examination of the genetic architecture of hybrid breakdown can provide insight into the genetic mechanisms of commonly observed isolating phenomena such as Haldane's rule. We used line‐cross analysis to dissect the genetic architecture of divergence between two plant species that exhibit Haldane's rule for male sterility and rarity, Silene latifolia and Silene diclinis. We made 15 types of crosses, including reciprocal F₁, F₂, backcrosses, and later‐generation crosses, grew the seeds to flowering, and measured the number of viable ovules, proportion of viable pollen, and sex ratio. Typically, Haldane's rule for male rarity in XY animal hybrids is explained by interactions involving recessive X‐linked alleles that are deleterious when hemizygous (dominance theory), whereas sterility is explained by rapid evolution of spermatogenesis genes (faster‐male evolution). In contrast, we found that the genetic mechanisms underlying Haldane's rule between the two Silene species did not follow these conventions. Dominance theory was sufficient to explain male sterility, but male rarity likely involved faster‐male evolution. We also found an effect of the neo‐sex chromosomes of S. diclinis on the extreme rarity of some hybrid males. Our findings suggest that the genetic architecture of Haldane's rule in dioecious plants may differ from those commonly found in animals.     

SPECIATION IN THE EUROPEAN RABBIT (ORYCTOLAGUS CUNICULUS): ISLANDS OF DIFFERENTIATION ON THE X CHROMOSOME AND AUTOSOMES

Studies of gene flow between closely related taxa can provide insight into the genetic basis of speciation. To evaluate the importance of the X chromosome in reproductive isolation between subspecies of the European rabbit and to study the genomic scale over which islands of differentiation extend, we resequenced a total of 34 loci distributed along the X chromosome and chromosome 14. Previous studies based on few markers suggested that loci in centromeric regions were highly differentiated between rabbit subspecies, whereas loci in telomeric regions were less differentiated. Here, we confirmed this finding but also discovered remarkable variation in levels of differentiation among loci, with F_ST values from nearly 0 to 1. Analyses using isolation‐with‐migration models suggest that this range appears to be largely explained by differential levels of gene flow among loci. The X chromosome was significantly more differentiated than the autosomes. On chromosome 14, differentiation decayed very rapidly at increasing distances from the centromere, but on the X chromosome distinct islands of differentiation encompassing several megabases were observed both at the centromeric region and along the chromosome arms. These findings support the idea that the X chromosome plays an important role in reproductive isolation between rabbit subspecies. These results also demonstrate the mosaic nature of the genome at species boundaries.     

INTRINSIC REPRODUCTIVE ISOLATION BETWEEN TWO SISTER SPECIES OF DROSOPHILA

Drosophila santomea and D. yakuba are sister species that live on the volcanic African island of São Tomé. Previous work has revealed several barriers to gene flow, including sexual isolation, hybrid sterility, and “extrinsic” ecological isolation based on differential adaptation to and preference for temperature. Here, we describe several new “intrinsic” barriers to gene flow—barriers that do not depend on the species’ ecology. These include reduced egg number, reduced egg hatchability, and faster depletion of sperm in interspecific compared to intraspecific matings. Further, hatching interval and egg‐to‐adult development time are significantly longer in interspecific than intraspecific crosses. If a female of either species is initially mated to a heterospecific male, she lays fewer and less‐fertile eggs than if she is first mated to a conspecific male, so that heterospecific matings permanently reduce female fertility. Finally, D. santomea females mated to D. yakuba males do not live as long as virgin or conspecifically mated females. The “poisoning” effects of heterospecific ejaculates may be byproducts of antagonistic sexual selection. Although these species diverged relatively recently, they are clearly separated by many isolating barriers that act both before and after mating.     

SIGNIFICANT ROLE FOR HISTORICAL EFFECTS IN THE EVOLUTION OF REPRODUCTIVE ISOLATION: EVIDENCE FROM PATTERNS OF INTROGRESSION BETWEEN THE CYPRINID FISHES,LUXILUS CORNUTUS AND LUXILUS CHRYSOCEPHALUS

Samples of Luxilus cornutus, Luxilus chrysocephalus, and their hybrids were collected along hypothesized routes of dispersal from Pleistocene refugia to examine the significance of geographic variation in patterns of introgression between these species. Patterns of allozyme and mitochondrial DNA (mtDNA) variation were generally consistent with those from previous studies. Tests of Hardy-Weinberg equilibrium revealed significant deficiencies of heterozygotes in all samples, indicating some form of reproductive isolation. Mitochondrial DNAs of each species were not equally represented in F₁ hybrids; however, this bias was eliminated when the two largest samples were excluded from the analysis. Backcross hybrids exhibited biased mtDNA introgression, as samples from Lake Erie (eastern) and Lake Michigan (western) drainages showed significant excesses of mtDNAs from L. chrysocephalus and L. cornutus, respectively, relative to frequencies of diagnostic allozyme markers. The extent and direction of allozyme and mtDNA introgression was quantified by calculating isolation index values from morphologically “pure” individuals of each species from each locality. Analysis of variance of these measures identified limited introgression of allozyme variants with no geographic pattern, but significant differences in direction of mtDNA introgression between drainages (i.e., postglacial dispersal route). Association between patterns of mtDNA introgression and dispersal route across the latitudinal width of the contact zone is best explained by genetic divergence during past isolation of ancestral populations from these drainages. These results identify a significant role for historical effects in the evolution of reproductive isolation and the process of speciation.     

ABRUPT CLINE FOR SEX CHROMOSOMES IN A HYBRID ZONE BETWEEN TWO SPECIES OF MICE

We compared the patterns of movement of sex chromosomal and autosomal loci along a 160 km transect across a zone of hybridization between M. domesticus and M. musculus in southern Germany and western Austria using seven genetic markers. These included one Y-specific DNA sequence (YB10), two X-specific loci (DXWas68 and DXWas31), and four autosomal isozyme loci (Es-10, Es-1, Mpi-1, and Np-1). Random effects logistic regression analysis enabled us to examine the relationship between M. domesticus allele frequency and geographic distance from the western edge of the hybrid zone and allowed statistical evaluation of differences in cline midpoint and width among loci. More limited movement was observed for all three sex chromosomal markers across the zone compared with three of the four autosomal markers. If differential movement reflects fitness differences of specific alleles (or alleles at closely linked loci) on a hybrid background, then alleles that move to a limited extent across a hybrid zone may contribute to hybrid breakdown between two species. The limited flow of both X- and Y-specific alleles suggest that sex chromosomes have played an important role in Mus speciation.     

HYBRID BREAKDOWN BETWEEN TWO HAPLODIPLOID SPECIES: THE ROLE OF NUCLEAR AND CYTOPLASMIC GENES

A central question in evolutionary biology concerns the population and genetic processes by which new species arise. Here, the genetic basis of hybrid breakdown between two haplodiploid species, Nasonia vitripennis and N. giraulti is investigated. Hybridization between the two species is normally prevented by microorganisms that cause bidirectional incompatibility. However, after elimination of microorganisms, F₁ hybrids females are readily produced (due to haplodiploidy, males develop from unfertilized eggs and are therefore not hybrids). F₁ hybrid females are viable and fecund, but recombinant (haploid) F₂ male offspring suffer from severe hybrid breakdown (larval and pupal mortality). This is typically interpreted as evidence for the existence of different coadapted gene complexes in the two species, which are broken up by recombination. F₂ recombinant eggs were rescued by fertilization with the complete chromosome complement from either species, supporting the view that hybrid lethality genes tend to be recessive. Negative epistatic interactions occur between nuclear genes of the two species, and between cytoplasmically inherited factors (cytoplasmic genes) of giraulti and nuclear genes of vitripennis. Interactions between nuclear genes and cytoplasmic genes are asymmetric. Experiments clearly demonstrate that the latter incompatibility is not due to maternal-effect genes, but to cytoplasmically inherited elements. Nuclear-mitochondrial interactions are possibly involved.     

THE VARIABLE GENOMIC ARCHITECTURE OF ISOLATION BETWEEN HYBRIDIZING SPECIES OF HOUSE MICE

Studies of the genetics of hybrid zones can provide insight into the genomic architecture of species boundaries. By examining patterns of introgression of multiple loci across a hybrid zone, it may be possible to identify regions of the genome that have experienced selection. Here, we present a comparison of introgression in two replicate transects through the house mouse hybrid zone through central Europe, using data from 41 single nucleotide markers. Using both genomic and geographic clines, we found many differences in patterns of introgression between the two transects, as well as some similarities. We found that many loci may have experienced the effects of selection at linked sites, including selection against hybrid genotypes, as well as positive selection in the form of genotypes introgressed into a foreign genetic background. We also found many positive associations of conspecific alleles among unlinked markers, which could be caused by epistatic interactions. Different patterns of introgression in the two transects highlight the challenge of using hybrid zones to identify genes underlying isolation and raise the possibility that the genetic basis of isolation between these species may be dependent on the local population genetic make-up or the local ecological setting.     

FEMALE FECUNDITY IN A HYBRID ZONE BETWEEN TWO CHROMOSOME RACES OF THE SCELOPORUS GRAMMICUS COMPLEX (SAURIA,PHRYNOSOMATIDAE)

Individuals of the F5 and FM2 cytotypes of the Sceloporus grammicus complex form a narrow zone of parapatric hybridization near Tulancingo, Hidalgo, Mexico. Reproductive parameters were examined among chromosomally parental and hybrid females to assess the degree to which reduced clutch size is correlated with the level of chromosomal heterozygosity. Although clutch size in the two parental groups was highly correlated with female body size, this was not the case for females with intermediate karyotypes. These females displayed increased levels of infertility manifested as smaller clutches and as inviable embryos. F₁ females produced the smallest average clutches and suffered the most precipitous fecundity loss (up to 75%). The number of heterozygous marker chromosomes and heterozygosity at chromosome 2 had significant effects on the number of viable embryos. Analysis of embryo karyotypes revealed the production of triploid offspring and an excess number of embryos heterozygous at chromosome 1. Differences in viability, among females heterozygous for the same number of chromosomes, suggest that genetic background of the female and/or sire may be an important factor in determining reproductive success.     

A HIGH‐DENSITY SCAN OF THE Z CHROMOSOME IN FICEDULA FLYCATCHERS REVEALS CANDIDATE LOCI FOR DIVERSIFYING SELECTION

Theoretical and empirical data suggest that genes located on sex chromosomes may play an important role both for sexually selected traits and for traits involved in the build‐up of hybrid incompatibilities. We investigated patterns of genetic variation in 73 genes located on the Z chromosomes of two species of the flycatcher genus Ficedula, the pied flycatcher and the collared flycatcher. Sequence data were evaluated for signs of selection potentially related to genomic differentiation in these young sister species, which hybridize despite reduced fitness of hybrids. Seven loci were significantly more divergent between the two species than expected under neutrality and they also displayed reduced nucleotide diversity, consistent with having been influenced by directional selection. Two of the detected candidate regions contain genes that are associated with plumage coloration in birds. Plumage characteristics play an important role in species recognition in these flycatchers suggesting that the detected genes may have been involved in the evolution of sexual isolation between the species.     

THE BIOLOGY OF SPECIATION

Since Darwin published the “Origin,” great progress has been made in our understanding of speciation mechanisms. The early investigations by Mayr and Dobzhansky linked Darwin's view of speciation by adaptive divergence to the evolution of reproductive isolation, and thus provided a framework for studying the origin of species. However, major controversies and questions remain, including: When is speciation nonecological? Under what conditions does geographic isolation constitute a reproductive isolating barrier? and How do we estimate the “importance” of different isolating barriers? Here, we address these questions, providing historical background and offering some new perspectives. A topic of great recent interest is the role of ecology in speciation. “Ecological speciation” is defined as the case in which divergent selection leads to reproductive isolation, with speciation under uniform selection, polyploid speciation, and speciation by genetic drift defined as “nonecological.” We review these proposed cases of nonecological speciation and conclude that speciation by uniform selection and polyploidy normally involve ecological processes. Furthermore, because selection can impart reproductive isolation both directly through traits under selection and indirectly through pleiotropy and linkage, it is much more effective in producing isolation than genetic drift. We thus argue that natural selection is a ubiquitous part of speciation, and given the many ways in which stochastic and deterministic factors may interact during divergence, we question whether the ecological speciation concept is useful. We also suggest that geographic isolation caused by adaptation to different habitats plays a major, and largely neglected, role in speciation. We thus provide a framework for incorporating geographic isolation into the biological species concept (BSC) by separating ecological from historical processes that govern species distributions, allowing for an estimate of geographic isolation based upon genetic differences between taxa. Finally, we suggest that the individual and relative contributions of all potential barriers be estimated for species pairs that have recently achieved species status under the criteria of the BSC. Only in this way will it be possible to distinguish those barriers that have actually contributed to speciation from those that have accumulated after speciation is complete. We conclude that ecological adaptation is the major driver of reproductive isolation, and that the term “biology of speciation,” as proposed by Mayr, remains an accurate and useful characterization of the diversity of speciation mechanisms.     

GENETIC VARIATION IN CRICKET CALLING SONG ACROSS A HYBRID ZONE BETWEEN TWO SIBLING SPECIES

The sibling ground crickets Allonemobius fasciatus and A. socius meet along a mosaic hybrid zone at ≈ 40°N latitude in eastern North America. In this paper we report the findings of a genetic analysis of calling-song variation within and among six cricket populations sampled along a transect through the hybrid zone in southern New Jersey. We compared aspects of the calling song of both wild-caught and laboratory-reared crickets to test the hypothesis that population differences in song observed in the wild were genetically based. We found significant, species-level differences in all aspects of the calling song, and these differences persisted even after a generation of common-garden rearing in the laboratory, supporting the hypothesis that interspecific variation observed in the wild largely reflects genetic differentiation between the two taxa. A discriminant function analysis indicated that individual crickets could be assigned to the proper taxon with less than 10% error, supporting the premise that calling song could be used by female crickets as a mechanism for species recognition. One population, collected from within the hybrid zone and containing significant numbers of hybrid individuals, was intermediate in its calling song, presumably reflecting this population's mixed genetic makeup. In this hybrid zone population, song phenotype was highly correlated to a hybrid index score generated using species-specific alleles at four diagnostic allozyme markers, suggesting a multigenic basis to calling-song variation in these crickets as well as linkage disequilibrium between markers and song. Based on an analysis of laboratory-reared full-sib families, broad-sense heritabilities for calling-song characteristics were generally significant in the two A. socius populations, whereas many components of song showed no significant family effects in the three A. fasciatus populations. The genotypically mixed, hybrid zone population showed very high heritabilities for most calling-song components, which likely reflect the influence of interspecific gene flow on genetic variation for quantitative traits.     

两种邻域分布石鸡间的线粒体DNA渗透

采用聚合酶链式反应(PCR)和mtDNA细胞色素b基因314 bp核苷酸序列测定等方法,证明在大石鸡与山石鸡的异域种群之间存在广泛的差异.然而采自六盘山地区与山石鸡相邻分布的大石鸡种群的样本中却存在山石鸡的mtDNA基因型,这种基因型与其它大石鸡个体的基因型有4.4%核苷酸差异.在与山石鸡相邻分布的大石鸡种群中有25%的个体具有山石鸡的mtDNA基因型,而采自六盘山接触地带以西约200 km处兰州市郊的大石鸡标本中则没有发现这种基因型.此发现支持山石鸡和大石鸡之间存在或曾经有过杂交的假设.作者还提出了一种限制性内切酶分析方法,可以快速地检测这种mtDNA基因型.在此之前还没有过关于山石鸡和大石鸡之间基因流动的报道.     

SEX AND SPECIATION: GENETIC ARCHITECTURE AND EVOLUTIONARY POTENTIAL OF SEXUAL VERSUS NONSEXUAL TRAITS IN THE SIBLING SPECIES OF THE DROSOPHILA MELANOGASTER COMPLEX

Phenotypic divergence in the male reproductive system (genitalia and gonads) between species of the Drosophila melanogaster complex and their hybrids was quantified to decipher the role of these traits in species differentiation and speciation. Internal as well as external, sexual and nonsexual traits were analyzed with respect to genetic variation and trait asymmetry between strains within species, genetic divergence between species, and dominance and asymmetry in species and hybrids. The variation between strains within species was significant among sexual traits, and only external traits were less asymmetric than internal ones, which suggests that sexual traits are not strongly constrained within species. Three main findings show that sexual traits are most divergent between species: (1) testis length and area, and the area of the posterior lobe of the genital arch (sexual traits) showed the highest proportion of variation between species; (2) linear discriminant functions with the highest components associated to sexual traits were better predictors of species membership; and (3) testis length and area revealed a departure from a linear relationship between members of the species group. Examination of interspecific hybrids showed that sexual traits had higher asymmetry in species hybrids than in the parental species and that sexual traits showed additivity or dominance whereas nonsexual traits showed overdominance (with the exception of malpighian tubules length). These results suggest that sexual traits have undergone more genetic changes and, as a result, tend to show higher divergence and stronger hybrid breakdown between species than nonsexual traits. We propose that sexual selection in the broad sense, affecting all aspects of sexuality, may be responsible for the diversified appearance of sexual traits among closely related species and that the genetic architecture underlying sexual traits may be more prone to disruption during the early stages of speciation.     

THE LANGUAGE OF SPECIATION

The literature on speciation has expanded dramatically in recent years, catalyzed by the emergence of new conceptual frameworks, new theoretical approaches, and new methods for characterizing pattern and inferring process. As a consequence, the language used to describe the speciation process has become more complex. Increasing complexity may be an accurate reflection of current thinking with respect to how phenotypic differences limit gene flow, how selection results in the evolution of reproductive isolation, and genetic changes that contribute to speciation. However, increased language complexity has come at a cost; old definitions have been reconfigured and new terms have been introduced. In some instances, the introduction of new terminology has failed to recognize historical usage, leading to unnecessary ambiguity and redundancy. Although the writings of Mayr and Dobzhansky remain a reference point in the language of speciation, the last decades of the 20th century saw substantial changes in our thinking about the speciation process. During that period, the language of speciation remained relatively stable. In contrast, the first decade of the 21st century has witnessed a remarkable expansion of the language of speciation. Here, the origin and evolution of ideas about speciation are viewed through the lens of changing language use.     

两种鹪莺的种间生态位关系研究

本文研究了褐头鹪莺（Ｐｒｉｎｉａ ｓｕｂｆｌａｖａ）和黄腹鹪莺（Ｐ．ｆｌａｖｉｖｅｎｔｒｉｓ）在取食高度、取食基层和取食方法３个生态维度上的生态位宽度和生态位重叠以及它们与复合种群密度的关系。结果表明,两种鹪莺的现实生态位有较大的重叠,且种群密度变化时,生态位宽度和生态位重叠发生了显著移动,褐头鹪莺与黄腹鹪莺之 间存在着竞争;它们并没有采取生态位宽度来回避竞争,而是相反地各自扩展生态位宽度来减少重