The geography of mammalian speciation: mixed signals from phylogenies and range maps

The importance of geographic isolation in speciation has been debated since the 19th century. Since the beginning of the 20th century, the consensus has been that most speciation involves divergence in allopatry. This consensus was based largely on decades of observations by naturalists and verbal arguments against speciation without isolation. Recent attempts to quantify the importance of allopatric versus sympatric speciation using comparative methods called "age-range correlation" (ARC) suggest that allopatric speciation is more common than sympatric speciation. However, very few taxa have been studied and there are concerns about the adequacy of the methods. We propose methodological improvements including changes in the way overlap between clades is quantified and Monte Carlo methods to test the null hypothesis of no relationship between phylogenetic relatedness and geographic range overlap. We analyze 14 clades of mammals, chosen because of the availability of data and the consensus among mammalogists that speciation is routinely allopatric. Although data from a few clades clearly indicate allopatric speciation, divergence with gene flow is plausible in others and many results are inconclusive. The relative rarity of significant correlations between phylogenetic distance and range overlap may have three distinct causes: (1) post-speciation range changes, (2) relative rarity of range overlap, and (3) a mixture of geographic modes of speciation. Our results support skepticism about ARC's power for inferring the biogeography of speciation. Yet, even if few clades provide clear signals, meta-analytic approaches such as ARC may set bounds on the prevalence of alternative modes of speciation.     

Phylogenetic relationships, evolutionary origin, taxonomic status, and genetic structure of the endangered local Lower Elbe river (Germany) endemic Oenanthe conioides (Nolte ex Rchb.f.) Lange (Apiaceae): ITS and AFLP evidence

Oenanthe conioides is an endangered local endemic of the Lower Elbe river region in Germany where it is found in areas with freshwater tides. Internal transcribed spacer (ITS) and amplified fragment length polymorphism (AFLP) markers were used to investigate its phylogenetic relationships, evolutionary origin, taxonomic status, and genetic structure.Oe. conioides is most closely related to Oe. aquatica and Oe. fluviatilis, and cannot be distinguished from Oe. aquatica by ITS sequence variation. Oe. aquatica is found mainly in standing or slow-flowing freshwater habitats. The AFLP analysis indicated that Oe. conioides may constitute a monophyletic lineage nested within Oe. aquatica. Considering this result on the background of the sympatric distribution of the two species and their ecological differentiation, it is hypothesized that Oe. conioides arose sympatrically from Oe. aquatica through ecological divergence. It is concluded that Oe. conioides is best considered a subspecies of Oe. aquatica.AFLP analysis of Oe. conioides revealed low levels of genetic differentiation among populations reflecting the small geographical distance, the recent decline in population number and size, the connection of populations through the river, and their presumably high population dynamics.Considering this pattern of genetic variation, it is concluded that no individual population can be singled out as being particularly important from a genetic point of view. Also, all populations could be used as source material should the establishment of new populations or the enlargement of small populations be considered as a measure to consolidate the persistence of the species.     

The genetics and ecology of sympatric speciation: A case study

Mating occurs on the larval host plant in allRhagoletis species (Diptera: Tephritidae). We show how this attribute, when coupled with certain differences in other biological traits, strongly influences the mode of speciation. In species of thesuavis species group, host shifts have never occurred during speciation, and larvae feed in the husks of any walnut species(Juglans spp.), which are highly toxic. Taxa are allopatric or parapatric and exhibit deep phylogenetic nodes suggesting relatively ancient speciation events. Traits responsible for species and mate recognition, particularly in parapatric species, are morphologically distinct and strongly sexually dimorphic. All aspects of their biology, genetics and distribution are consistent with a slow rate of allopatric speciation followed by morphological divergence in secondary contact. In contrast, speciation in thepomonella species group has always involved a shift to a new, usually unrelated, non-toxic host, and all taxa within these groups are sympatric, monophagous and morphologically indistinguishable from one another. Phylogenetic nodes are very shallow, indicating recent sympatric speciation. Sympatric divergence is promoted by genetic variation which allows a portion of the original species to shift to a new habitat or host. Evidence suggests that changes in a few key loci responsible for host selection and fitness on a new host may initiate host shifts. By exploiting different habitats, competition for resources between diverging populations is reduced or avoided. We provide evidence that in phytophagous and parasitic insects sufficient intrinsic barriers to gene flow can evolve between sister populations as they adapt to different habitats or hosts to allow each population to establish independent evolutionary lineages in sympatry.     

Inverting the null-hypothesis of speciation: a marine snail perspective

Speciation is currently an intensely debated topic, much more so than 20–30 years ago when most biologists held the view that new species (at least of animals) were formed through the split of evolutionary lineages by the appearance of physical barriers to gene flow. Recent advances have, however, lent both theoretical and empirical support to speciation in the presence of gene flow. Nevertheless, the allopatric hypothesis of speciation is still the default model. The consequence of this is that to support sympatric and parapatric modes of speciation all allopatric alternatives must be rejected, while an allopatric explanation is usually accepted without rejecting possible non-allopatric alternatives. However, classical cases of allopatric speciation can be challenged by alternative non-allopatric explanations, and this begs for a more respectful view of how to deal with all models of speciation. An appealing approach is studying parallel evolution of reproductive barriers, which allows for comparative approaches to distinguish between allopatric and non-allopatric events, and explicit tests of a suitable null-hypothesis. Parallel evolution of reproductive isolation in a strongly polymorphic marine snail species serves as an illustrative example of such an approach. In conclusion, a more balanced debate on allopatric and non-allopatric speciation is needed and an urgent issue is to treat both allopatric and nonallopatric hypotheses critically, rather than using allopatry as the default model of speciation.     

Rejecting strictly allopatric speciation on a continental island: prolonged postdivergence gene flow between Taiwan (Leucodioptron taewanus,Passeriformes Timaliidae) and Chinese (L. canorum canorum) hwameis

Allopatry is conventionally considered the geographical mode of speciation for continental island organisms. However, strictly allopatric speciation models that assume the lack of postdivergence gene flow seem oversimplified given the recurrence of land bridges during glacial periods since the late Pliocene. Here, to evaluate whether a continental island endemic, the Taiwan hwamei (Leucodioptron taewanus, Passeriformes Timaliidae) speciated in strict allopatry, we used weighted‐regression‐based approximate Bayesian computation (ABC) to analyse the genetic polymorphism of 18 neutral nuclear loci (total length: 8500 bp) in Taiwan hwamei and its continental sister species, the Chinese hwamei (L. canorum canorum). The nonallopatry model was found to fit better with observed genetic polymorphism of the two hwamei species (posterior possibility = 0.82). We also recovered unambiguous signals of nontrivial bidirectional postdivergence gene flow (N_em » 1) between Chinese hwamei and Taiwan hwamei until 0.5 Ma. Divergence time was estimated to be 3.5 to 2 million years earlier than that estimated from mitochondrial cytochrome b sequences. Finally, using the inferred nonallopatry model to simulate genetic variation at 24 nuclear genes examined showed that the adiponectin receptor 1 gene may be under divergent adaptation. Our findings imply that the role of geographical barrier may be less prominent for the speciation of continental island endemics, and suggest a shift in speciation studies from simply correlating geographical barrier and genetic divergence to examining factors that facilitate and maintain divergence, e.g. differential selection and sexual selection, especially in the face of interpopulation gene flow.     

植物物种形成的模式与机制

物种形成是指由已有的物种通过各种进化机制进化出新物种的过程。持续不断的物种形成产生了地球上灿烂的生物物种多样性。然而,研究人员对物种形成的模式与机制的了解却非常有限。一直以来,谱系分裂被认为是最重要的物种形成模式,但在植物中,谱系融合,即通过杂交形成新物种的过程,也是一个非常重要的物种形成模式。经过几十年的研究才逐渐认识到,生殖隔离是差异适应和遗传漂变的副产品,而不是物种形成的前提。相比合子形成后隔离,合子形成前的隔离在物种形成过程中更早地发挥作用。合子形成前的隔离,尤其是生态地理的隔离是植物中最重要的隔离机制。一些基于QTLs分析的研究发现,基因组中的少数主效位点在物种形成中起了关键作用,并且这些位点往往受到自然选择的作用。适应性辐射往往发生在隆起的山脉和新形成的岛屿上,很可能与这些地方能够提供很多可利用的生态位有关。最新的物种形成理论认为,基因是物种形成的基本单位,不同的物种可以在非控制物种差异适应性状的位点上存在基因流。这一观点为植物物种形成的研究提供了新的思路。随着植物物种形成研究的深入,越来越多植物物种形成基因被分离,包括花色素苷合成通路和S-基因座上的一些关键基因,揭示了植物物种形成的分子机制。前期的研究主要集中在模式植物和农作物上,许多生态上非常有趣的非模式植物还未得到广泛的研究。在未来的研究中,还需要更多来自非模式植物的例子以全面理解植物物种形成的多样化机制。     

Divergence and hybridization in the desert plant Reaumuria soongarica

Speciation is widely accepted to be a complex and continuous process. Due to complicated evolutionary histories, desert plants are ideal model systems to understand the process of speciation along a continuum. Here, we elucidate the evolutionary history of Reaumuria soongarica (Pall.) Maxim., a typical desert plant that is wildly distributed across arid central Asia. Based on variation patterns present at nine nuclear loci in 325 individuals (representing 41 populations), we examined the demographic history, patterns of gene flow, and degree of ecological differentiation among wild R. soongarica. Our findings indicate that genetic divergence between the ancient western and eastern lineages of R. soongarica occurred approximately 0.714 Mya, probably due to the Kunlun–Yellow River tectonic movement and the Naynayxungla glaciation. Later, multiple hybridization events between the western and eastern lineages that took place between 0.287 and 0.543 Mya, and which might have been triggered by the asynchronous historical expansion of the western and eastern deserts, contributed to the formation of a hybrid northern lineage. Moreover, despite continuing gene flow into this population from its progenitors, the northern lineage maintained its genetic boundary by ecological differentiation. The northern lineage could be an incipient species, and provides an opportunity to study the continuous process of speciation. This study suggests that two opposite evolutionary forces, divergence and hybridization, coexisting in the continuous speciation of the desert plant R. soongarica in a short time. Moreover, we provide evidence that this continuous speciation process is affected by geological events, climatic change, and ecological differentiation.     

A comparative analysis of the mechanisms underlying speciation on Lord Howe Island

On Lord Howe Island, speciation is thought to have taken place in situ in a diverse array of distantly related plant taxa (Metrosideros, Howea and Coprosma; Proc. Natl Acad. Sci. USA 108 , 2011, 13188). We now investigate whether the speciation processes were driven by divergent natural selection in each genus by examining the extent of ecological and genetic divergence. We present new and extensive, ecological and genetic data for all three genera. Consistent with ecologically driven speciation, outlier loci were detected using genome scan methods. This mechanism is supported by individual‐based analyses of genotype–environment correlations within species, demonstrating that local adaptation is currently widespread on the island. Genetic analyses show that prezygotic isolating barriers within species are currently insufficiently strong to allow further population differentiation. Interspecific hybridization was found in both Howea and Coprosma, and species distribution modelling indicates that competitive exclusion may result in selection against admixed individuals. Colonization of new niches, partly fuelled by the rapid generation of new adaptive genotypes via hybridization, appears to have resulted in the adaptive radiation in Coprosma – supporting the ‘Syngameon hypothesis’.     

Genomic insights into the vulnerability of sympatric whitefish species flocks

The erosion of habitat heterogeneity can reduce species diversity directly but can also lead to the loss of distinctiveness of sympatric species through speciation reversal. We know little about changes in genomic differentiation during the early stages of these processes, which can be mediated by anthropogenic perturbation. Here, we analyse three sympatric whitefish species (Coregonus spp) sampled across two neighbouring and connected Swiss pre‐alpine lakes, which have been differentially affected by anthropogenic eutrophication. Our data set comprises 16,173 loci genotyped across 138 whitefish using restriction‐site associated DNA sequencing (RADseq). Our analysis suggests that in each of the two lakes, the population of a different, but ecologically similar, whitefish species declined following a recent period of eutrophication. Genomic signatures consistent with hybridization are more pronounced in the more severely impacted lake. Comparisons between sympatric pairs of whitefish species with contrasting ecology, where one is shallow benthic and the other one more profundal pelagic, reveal genomic differentiation that is largely correlated along the genome, while differentiation is uncorrelated between pairs of allopatric provenance with similar ecology. We identify four genomic loci that provide evidence of parallel divergent adaptation between the shallow benthic species and the two different more profundal species. Functional annotations available for two of those loci are consistent with divergent ecological adaptation. Our genomic analysis indicates the action of divergent natural selection between sympatric whitefish species in pre‐alpine lakes and reveals the vulnerability of these species to anthropogenic alterations of the environment and associated adaptive landscape.     

Reinforced postmating reproductive isolation barriers in Neurospora,an Ascomycete microfungus

Maladaptive hybridization promotes reinforcement, selection for stringent reproductive isolation barriers during speciation. Reinforcement is suspected when barriers between sympatric populations are stronger than allopatric barriers, and particularly when stronger barriers evolve in the species and sex suffering the greatest costs of hybridization. Canonically, reinforcement involves premating barriers. Selection for postmating barriers is controversial, but theoretically possible. We examined geographical patterns in reproductive isolation barriers between Neurospora crassa and Neurospora intermedia, fungi with pheromone‐mediated mate recognition and maternal care. We find that isolation is stronger between sympatric populations than allopatric populations, and stronger barriers are associated with the species (N. crassa) and mating role (maternal) suffering the greater costs of hybridization. Notably, reinforced isolation involves a postmating barrier, abortion of fruitbodies. We hypothesize that fruitbody abortion is selectively advantageous if it increases the likelihood that maternal Neurospora individuals successfully mate conspecifically after maladaptive hybrid fertilization.     

The role of allochrony in speciation

The importance of sympatric speciation – the evolution of reproductive isolation between codistributed conspecific individuals – in generating biodiversity is highly controversial. Allochrony, or differences in breeding time (phenology) between conspecific individuals, has the potential to lead to reproductive isolation and therefore speciation. We critically review the literature to test the importance of allochronic speciation over the three timescales over which allochrony can occur – over the day, between seasons or between years – and explore what is known about genomic mechanisms underlying allochrony in the diverse taxa in which it is found. We found that allochrony can be a key contributor to reproductive isolation, especially if populations have little overlap in breeding time and therefore little potential for gene flow, and may sometimes be the initial or key driver of speciation. Shifts in phenology can be caused by several factors, including a new ecological opportunity, environmental change, or reinforcement. The underlying genomic basis of allochrony has been studied mostly in insects, highlighting the need for genomic studies in other taxa; nonetheless, results to date indicate that several cases of allochrony involve changes in circadian genes. This review provides the first comprehensive discussion of the role of allochrony in speciation and demonstrates that allochrony as a contributor to divergence may be more widespread than previously thought. Understanding genomic changes and adaptations allowing organisms to breed at new times may be key in the light of phenological changes required under climate change.     

The internodal species concept: a response to 'The tree, the network, and the species'

Samadi and Barberousse attempt to provide a precise, formal definition of the species category that is faithful to the internodal species concept (Samadi S, Barberousse A. 2006. The tree, the network, and the species. Biological Journal of the Linnean Society 89: 509–521). Here, it is argued that their study is technically flawed. Most of the necessary corrections to their definitions are provided in order to accurately portray the internodal concept. It is then argued that the internodal concept is fundamentally flawed; it does not solve the 'classical problems' that Samadi and Barberousse claim it does. In particular, it does not allow for the possibility of interspecies hybridization. In addition, the proposal is unworkable in practice, and also theoretically problematic because it entails that, in many lineages, speciation events are taking place every few generations.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 865–869.     

Parallel allochronic divergence in a winter moth due to disruption of reproductive period by winter harshness

The disruption of reproductive timing by climatic harshness may result in the temporal isolation of conspecific populations and, ultimately, in speciation. However, whether temporal isolation alone can act as the force initiating speciation and how often the same type of climatic disruption results in the divergence of allochronic populations in a lineage are largely unknown. The reproductive period of the winter geometrid moth Inurois punctigera is separated into early and late winter in habitats with severe winters, but not in habitats with mild winters, suggesting that the reproductive season is disrupted by the harshness of the mid-winter period. Here, we show that sympatric pairs of early- and late-winter populations that differ in origin exist in different regions, suggesting a parallel divergence of reproductive timing. In each region, significant genetic differentiation exists between these early- and late-winter populations, suggesting that the temporal reproductive isolation has persisted. Moreover, we demonstrate that the temporal isolation, in comparison with geographic isolation, contributes greatly to the genetic differentiation among geographic and temporal populations by an analysis of molecular variance and by a comparison of genetic differentiations (F(ST) ) between geographic populations with and without difference in reproductive season. Our results suggest that adaptive divergence of allochronically reproducing populations has occurred independently in different regions, implying the generality of the role of temporal isolation in initiating speciation in a winter moth lineage.     

物种形成研究的新动态

物种形成(speciation)是遗传进化研究的一个重要的课题。近十年来一连发表了好几部有关物种形成的专著(White 1978;Grant 1981)和论文集(Atchley & Woodruff 1981; Barigozzi 1982),足见当前学者对这方面研究的重视。     

THE EVOLUTION OF LOCAL ENDEMISM IN MADAGASCAR: WATERSHED VERSUS CLIMATIC GRADIENT HYPOTHESES EVALUATED BY NULL BIOGEOGRAPHIC MODELS

Substantial insular speciation has resulted in exceptionally high levels of endemism in Madagascar, creating locally restricted species' ranges that remain poorly understood. The contributions of alternative processes that could influence patterns of local endemism—including speciation by geographic isolation or adaptation to environmental gradients—are widely debated, both for Madagascar and elsewhere. A recently proposed hypothesis (the "watershed hypothesis") suggests that allopatric speciation driven by isolation in watersheds during Quaternary climate shifts provides a general explanation for patterns of local endemism across taxa in Madagascar. Here we tested coincidence between species' distributions and areas of endemism predicted by two contrasting biogeographic hypotheses: (1) the watershed hypothesis, and (2) an alternative hypothesis driven by climatic gradients (the "current climate hypothesis"). Statistical significance of coincidence was assessed by comparing against a null model. Surprisingly, we found that extant distributions of lemurs, geckos, and chameleons reveal species patterns that are significantly coincident with the watershed and current climate hypotheses. These results strongly support local endemism developing from multiple processes, even among closely related species. Our findings thus indicate that pluralistic approaches will offer the best option both for understanding processes that generate local endemism, and for incorporating endemism within conservation priority setting.     

THE RATE TEST OF SPECIATION: ESTIMATING THE LIKELIHOOD OF NON‐ALLOPATRIC SPECIATION FROM REPRODUCTIVE ISOLATION RATES IN DROSOPHILA

Among the most debated subjects in speciation is the question of its mode. Although allopatric (geographical) speciation is assumed the null model, the importance of parapatric and sympatric speciation is extremely difficult to assess and remains controversial. Here I develop a novel approach to distinguish these modes of speciation by studying the evolution of reproductive isolation (RI) among taxa. I focus on the Drosophila genus, for which measures of RI are known. First, I incorporate RI into age‐range correlations. Plots show that almost all cases of weak RI are between allopatric taxa whereas sympatric taxa have strong RI. This either implies that most reproductive isolation (RI) was initiated in allopatry or that RI evolves too rapidly in sympatry to be captured at incipient stages. To distinguish between these explanations, I develop a new “rate test of speciation” that estimates the likelihood of non‐allopatric speciation given the distribution of RI rates in allopatry versus sympatry. Most sympatric taxa were found to have likely initiated RI in allopatry. However, two putative candidate species pairs for non‐allopatric speciation were identified (5% of known Drosophila). In total, this study shows how using RI measures can greatly inform us about the geographical mode of speciation in nature.     

PERSISTENCE OF WITHIN‐SPECIES LINEAGES: A NEGLECTED CONTROL OF SPECIATION RATES

We present a framework distinguishing three principal controls of speciation rate: rate of splitting, level of persistence, and length of speciation duration. We contend that discussions on diversification become clearer in the light of this framework, because speciation rate variation could be attributed to any of these controls. In particular, we claim that the role of persistence of within‐species lineages in controlling speciation rates has been greatly underappreciated. More emphasis on the persistence control would change expectations of the role of several biological traits and environmental factors, because they may drive speciation rate in one direction through the persistence control and in the opposite direction through the other two controls. Traits and environments have been little studied regarding their influence on speciation rate through the persistence control, with climatic fluctuations being a relatively well‐studied exception. Considering the recent advances in genomic and phylogenetic analysis, we think that the time is ripe for applying the framework in empirical research. Variation among clades and areas (and thus among traits and environments) in the importance of the three rate controls could be addressed for example by dating splitting events, detecting within‐species lineages, and scanning genomes for evidence of divergent selection.     

The relative importance of ecology and geographic isolation for speciation in anoles

The biogeographic patterns in sexually reproducing animals in island archipelagos may be interpreted as reflecting the importance of allopatric speciation. However, as the forms are allopatric, their reproductive isolation is largely untestable. A historical perspective integrating geology and molecular phylogeny reveals specific cases where ancient precursor islands coalesce, which allows the application of population genetics to critically test genetic isolation. The Anolis populations on Martinique in the Lesser Antilles are one such case where species-level populations on ancient precursor islands (ca 6-8Myr BP) have met relatively recently. The distribution of the mtDNA lineages is tightly linked to the precursor island, but the population genetic analysis of microsatellite variation in large samples shows no evidence of restricted genetic exchange between these forms in secondary contact. This tests, and rejects, the hypothesis of simple allopatric speciation in these forms. By contrast, Martinique has pronounced environmental zonation, to which anoles are known to adapt. The population genetic analysis shows restricted genetic exchange across the ecotone between xeric coastal habitat and montane rainforest. This does not indicate full ecological speciation in these forms, but it does suggest the relative importance of the role of ecology in speciation in general.     

Origin of the serpentine-endemic herb Layia discoidea from the widespread L. glandulosa (Compositae)

Phylogenetic analyses of nuclear rDNA sequences uphold Gottlieb et al.'s hypothesis that Layia discoidea, a morphologically unusual, serpentine-endemic herb of narrow distribution in central California, "budded off" recently (less than one million years ago) from a nearby lineage of the widespread L. glandulosa, which occurs on sandy soils across much of far western North America. Although L. discoidea and L. glandulosa retain complete interfertility, nuclear rDNA data for the two species are almost free of evolutionary noise, without evidence of gene flow between them; allopatric divergence of L. discoidea cannot be ruled out. Molecular data are consistent with a hypothesis of accelerated morphological evolution of L. discoidea and Gottlieb et al.'s suggestion that the closest relatives of L. discoidea are populations of L. glandulosa with yellow, rather than white, ray corollas, in accord with Clausen, Keck, and Hiesey's evidence of a gene for yellow ray coloration in the rayless L. discoidea.