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Recent genomic analyses have highlighted the prevalence of speciation with gene flow in many taxa and have underscored the importance of accounting for these reticulate evolutionary processes when constructing species trees and generating parameter estimates. This is especially important for deepening our understanding of speciation in the sea where fast-moving ocean currents, expanses of deep water, and periodic episodes of sea level rise and fall act as soft and temporary allopatric barriers that facilitate both divergence and secondary contact. Under these conditions, gene flow is not expected to cease completely while contemporary distributions are expected to differ from historical ones. Here, we conduct range-wide sampling for Pederson's cleaner shrimp (Ancylomenes pedersoni), a species complex from the Greater Caribbean that contains three clearly delimited mitochondrial lineages with both allopatric and sympatric distributions. Using mtDNA barcodes and a genomic ddRADseq approach, we combine classic phylogenetic analyses with extensive topology testing and demographic modeling (10 site frequency replicates × 45 evolutionary models × 50 model simulations/replicate = 22,500 simulations) to test species boundaries and reconstruct the evolutionary history of what was expected to be a simple case study. Instead, our results indicate a history of allopatric divergence, secondary contact, introgression, and endemic hybrid speciation that we hypothesize was driven by the final closure of the Isthmus of Panama and the strengthening of the Gulf Stream Current ~3.5 Ma. The history of this species complex recovered by model-based methods that allow reticulation differs from that recovered by standard phylogenetic analyses and is unexpected given contemporary distributions. The geologically and biologically meaningful insights gained by our model selection analyses illuminate what is likely a novel pathway of species formation not previously documented that resulted from one of the most biogeographically significant events in Earth's history. [ABSTRACT FROM AUTHOR]

Premise: Hybridization is recognized as an important mechanism in fern speciation, with many allopolyploids known among congeners, as well as evidence of ancient genome duplications. Several contemporary instances of deep (intergeneric) hybridization have been noted, invariably resulting in sterile progeny. We chose the christelloid lineage of the family Thelypteridaceae, recognized for its high frequency of both intra‐ and intergeneric hybrids, to investigate recent hybrid speciation between deeply diverged lineages. We also seek to understand the ecological and evolutionary outcomes of resulting lineages across the landscape. Methods: By phasing captured reads within a phylogenomic data set of GoFlag 408 nuclear loci using HybPhaser, we investigated candidate hybrids to identify parental lineages. We estimated divergence ages by inferring a dated phylogeny using fossil calibrations with treePL. We investigated ecological niche conservatism between one confirmed intergeneric allotetraploid and its diploid progenitors using the centroid, overlap, unfilling, and expansion (COUE) framework. Results: We provide evidence for at least six instances of intergeneric hybrid speciation within the christelloid clade and estimate up to 45 million years of divergence between progenitors. The niche quantification analysis showed moderate niche overlap between an allopolyploid species and its progenitors, with significant divergence from the niche of one progenitor and conservatism to the other. Conclusions: The examples provided here highlight the overlooked role that allopolyploidization following intergeneric hybridization may play in fern diversification and range and niche expansions. Applying this approach to other fern taxa may reveal a similar pattern of deep hybridization resulting in highly successful novel lineages. [ABSTRACT FROM AUTHOR]

Background and Aims Niche differentiation is a crucial issue in speciation. Although it has a well-known role in adaptive processes of hybrid angiosperms, it is less understood in hybrid ferns. Here, we investigate whether an intermediate ecological niche of a fern hybrid is a novel adaptation that provides insights into fern hybrid speciation. Methods Pteris fauriei (Pteridaceae) is a natural hybrid fern, occurring in environments between its parent species. The maternal Pteris minor is found in sunny areas, but the habitat of the paternal Pteris latipinna is shady. We combined data from morphology, leaf anatomy and photosynthetic traits to explore adaptation and differentiation, along with measuring the environmental features of their niches. We also performed experiments in a common garden to understand ecological plasticity. Key Results The hybrid P. fauriei was intermediate between the parent species in stomatal density, leaf anatomical features and photosynthetic characteristics in both natural habitats and a common garden. Interestingly, the maternal P. minor showed significant environmental plasticity and was more similar to the hybrid P. fauriei in the common garden, suggesting that the maternal species experiences stress in its natural habitats but thrives in environments similar to those of the hybrid. Conclusions Based on the similar niche preferences of the hybrid and parents, we propose hybrid superiority. Our results indicate that the hybrid P. fauriei exhibits greater fitness and can compete with and occupy the initial niches of the maternal P. minor. Consequently, we suggest that the maternal P. minor has experienced a niche shift, elucidating the pattern of niche differentiation in this hybrid group. These findings offer a potential explanation for the frequent occurrence of hybridization in ferns and provide new insights into fern hybrid speciation, enhancing our understanding of fern diversity. [ABSTRACT FROM AUTHOR]

Homoploid hybrid speciation is challenging to document because hybridization can lead to outcomes other than speciation. Thus, some authors have argued that establishment of homoploid hybrid speciation should include evidence that reproductive barriers isolating the hybrid neo‐species from its parental species were derived from hybridization. While this criterion is difficult to satisfy, several recent papers have successfully employed a common pipeline to identify candidate genes underlying such barriers and (in one case) to validate their function. We describe this pipeline, its application to several plant and animal species and what we have learned about homoploid hybrid speciation as a consequence. We argue that – given the ubiquity of admixture and the polygenic basis of reproductive isolation – homoploid hybrid speciation could be much more common and more protracted than suggested by earlier conceptual arguments and theoretical studies. [ABSTRACT FROM AUTHOR]

A new hybrid of primrose discovered fifteen years ago in the locality Bivacco La Plana, Pre-Alps of Bergamo, above Chignolo, a hamlet of the municipality of Oneta, later also confirmed for the crest of Mount Alben, always in the same municipality, is here described. The parental species turn out to be Primula albenensis Banfi & Ferl. and P. auricula L., the former endemic to the mountains of Bergamo (Mount Alben, Mount Aralalta group and the Ancogno Valley), the latter a European orophyte, here coexisting often together on limestone faces. The new finding shows constant morphology in its stands, and there is no evidence of either "hybrid swarming" or introgression to exclude the total sterility of the population and this occurrence should be considered result of a process of inter parentes hybrid speciation (nothospecies) deserving of taxonomic recognition. [ABSTRACT FROM AUTHOR]

This mini‐review is dedicated to a critical re‐appraisal of the putative hybrid origin of the grey‐cheeked populations of the ashy‐throated parrotbill Sinosuthora alphonsiana that was postulated based on the results of a clustering analysis using a set of five nuclear loci. However, the number of genetically admixed individuals is lower than 10% in the proposed hybrid form and largely restricted to a single population in closest vicinity of one proposed parental taxon. Based on total evidence from mitochondrial and nuclear markers the proposed hybrid taxon is indistinguishable from the second postulated parental taxon. Wide‐range allelic introgression in a broad zone of range overlap along with incomplete lineage sorting of nuclear markers is a more plausible alternative explanation for the patterns observed. So far, there is no convincing evidence of a hybrid origin of the grey‐cheeked ashy‐throated parrotbill populations. [ABSTRACT FROM AUTHOR]

Hybridization opens a unique window for observing speciation mechanisms and is a potential engine of speciation. One controversially discussed outcome of hybridization is homoploid hybrid speciation by reciprocal sorting, where a hybrid population maintains a mixed combination of the parental genetic incompatibilities, preventing further gene exchange between the newly formed population and the two parental sources. Previous work showed that, for specific linkage architectures (i.e. the genomic location and order of hybrid incompatibilities), reciprocal sorting could reliably result in hybrid speciation. Yet, the sorting of incompatibilities creates a risk of population extinction. To understand how the demographic consequences of the purging of incompatibilities interact with the formation of a hybrid species, we model an isolated hybrid population resulting from a single admixture event. We study how population size, linkage architecture, and the strength of the incompatibility affect survival of the hybrid population, resolution/purging of the genetic incompatibilities and the probability of observing hybrid speciation. We demonstrate that the extinction risk is highest for intermediately strong hybrid incompatibilities. In addition, the linkage architecture displaying the highest hybrid speciation probabilities changes drastically with population size. Overall, this indicates that population dynamics can strongly affect the outcome of hybridization and the hybrid speciation probability. [ABSTRACT FROM AUTHOR]

Hybridization can rapidly generate novel genetic variation, which can promote ecological speciation by creating novel adaptive phenotypes. However, it remains unclear how hybridization, creating novel mating phenotypes (e.g. mating season, genitalia shapes, sexual displays, mate preferences), affects speciation especially when the phenotypes do not confer adaptive advantages. Here, based on individual-based evolutionary simulations, we propose that transgressive segregation of mating traits can drive incipient hybrid speciation. Simulations demonstrated that incipient hybrid speciation occurred most frequently when the hybrid population received moderate continued immigration from parental lineages causing recurrent episodes of hybridization. Recurrent hybridization constantly generated genetic variation, which promoted the rapid stochastic evolution of mating phenotypes in a hybrid population. The stochastic evolution continued until a novel mating phenotype came to dominate the hybrid population, which reproductively isolates the hybrid population from parental lineages. However, too frequent hybridization rather hindered the evolution of reproductive isolation by inflating the variation of mating phenotypes to produce phenotypes allowing mating with parental lineages. Simulations also revealed conditions for the long-term persistence of hybrid species after their incipient emergence. Our results suggest that recurrent transgressive segregation of mating phenotypes can offer a plausible explanation for hybrid speciation and radiations that involved little adaptive ecological divergence. [ABSTRACT FROM AUTHOR]

Spiranthes Rich. (Orchidaceae) is a commonly encountered but systematically and nomenclaturally challenging component of the North American orchid flora. Here, the evolutionary history and hybrid origin of the recently described S. sheviakii Hough and Young are critically examined. The available molecular data unambiguously support a hybrid origin of S. cernua (L.) Rich. × S. ochroleuca (Rydb.) Rydb. for S. sheviakii, the same parentage as the priority name S. ×kapnosperia M.C. Pace. As hybrid formulas can have only one correct name, S. sheviakii is a synonym of S. ×kapnosperia. It is likely that S. ×kapnosperia evolved independently at least twice in at least two widely disjunct locations. [ABSTRACT FROM AUTHOR]

By hybridization and special sexual reproduction, we sequentially aggregated Zea mays, Zea perennis, and Tripsacum dactyloides in an allohexaploid, backcrossed it with maize, derived self-fertile allotetraploids of maize and Z. perennis by natural genome extraction, extended their first six selfed generations, and finally constructed amphitetraploid maize using nascent allotetraploids as a genetic bridge. Transgenerational chromosome inheritance, subgenome stability, chromosome pairings and rearrangements, and their impacts on an organism’s fitness were investigated by fertility phenotyping and molecular cytogenetic techniques genomic in situ hybridization (GISH) and fluorescence in situ hybridization (FISH). Results showed that diversified sexual reproductive methods produced highly differentiated progenies (2n = 35–84) with varying proportions of subgenomic chromosomes, of which one individual (2n = 54, MMMPT) overcame self-incompatibility barriers and produced a self-fertile nascent near-allotetraploid by preferentially eliminating Tripsacum chromosomes. Nascent near-allotetraploid progenies showed persistent chromosome changes, intergenomic translocations, and rDNA variations for at least up to the first six selfed generations; however, the mean chromosome number preferably maintained at the near-tetraploid level (2n = 40) with full integrity of 45S rDNA pairs, and a trend of decreasing variations by advancing generations with an average of 25.53, 14.14, and 0.37 for maize, Z. perennis, and T. dactyloides chromosomes, respectively. The mechanisms for three genome stabilities and karyotype evolution for formatting new polyploid species were discussed. [ABSTRACT FROM AUTHOR]

Hybrid zones can be studied by modeling clines of trait variation (e.g. morphology, genetics) over a linear transect. Yet, hybrid zones can also be spatially complex, can shift over time, and can even lead to the formation of hybrid lineages with the right combination of dispersal and vicariance. We reassessed Sibley's (1950) gradient between Collared Towhee (Pipilo ocai) and Spotted Towhee (Pipilo maculatus) in Central Mexico to test whether it conformed to a typical tension-zone cline model. By comparing historical and modern data, we found that cline centers for genetic and phenotypic traits have not shifted over the course of 70 years. This equilibrium suggests that secondary contact between these species, which originally diverged over 2 million years ago, likely dates to the Pleistocene. Given the amount of mtDNA divergence, parental ends of the cline have very low autosomal nuclear differentiation (F ST = 0.12). Dramatic and coincident cline shifts in mtDNA and throat color suggest the possibility of sexual selection as a factor in differential introgression, while a contrasting cline shift in green back color hints at a role for natural selection. Supporting the idea of a continuum between clinal variation and hybrid lineage formation, the towhee gradient can be analyzed as one population under isolation-by-distance, as a two-population cline, and as three lineages experiencing divergence with gene flow. In the middle of the gradient, a hybrid lineage has become partly isolated, likely due to forested habitat shrinking and fragmenting as it moved upslope after the last glacial maximum and a stark environmental transition. This towhee system offers a window into the potential outcomes of hybridization across a dynamic landscape including the creation of novel genomic and phenotypic combinations and incipient hybrid lineages. [ABSTRACT FROM AUTHOR]

Although more frequently discussed recently than previously, the role of ecology in homoploid hybrid and allopolyploid speciation has not been subjected to comparative analysis. We examined abiotic niche divergence of 22 assumed homoploid hybrid species and 60 allopolyploid species from that of their progenitors. Ecological niche modeling was employed in an analysis of each species' fundamental niche, and ordination methods were used in an analysis of realized niches. Both analyses utilized 100,000 georeferenced records. From estimates of niche overlap and niche breadth, we identified for both types of hybrid species four niche divergence patterns: niche novelty, niche contraction, niche intermediacy, and niche expansion. Niche shifts involving niche novelty were common and considered likely to play an important role in the establishment of both types of hybrid species, although more so for homoploid hybrid species than for allopolyploid species. Approximately 70% of homoploid hybrid species versus 37% of allopolyploid species showed shifts in the fundamental niche from their parents, and ∼86% versus ∼52%, respectively, exhibited shifts in the realized niche. Climate was shown to contribute more than soil and landform to niche shifts in both types of hybrid species. Overall, our results highlight the significance of abiotic niche divergence for hybrid speciation, especially without genome duplication. [ABSTRACT FROM AUTHOR]

Postdivergence gene flow can trigger a number of creative evolutionary outcomes, ranging from the transfer of beneficial alleles across species boundaries (i.e., adaptive introgression) to the formation of new species (i.e., hybrid speciation). Although neutral and adaptive introgression has been broadly documented in nature, hybrid speciation is assumed to be rare and the evolutionary and ecological context facilitating this phenomenon still remains controversial. Through combining genomic and phenotypic data, we evaluate the hypothesis that the dual feeding regime (based on both scrub legumes and gramineous herbs) of the taxonomically controversial grasshopper Chorthippus saulcyi algoaldensis resulted from hybridization between the sister taxa C. binotatus (that exclusively feeds on scrub legumes) and C. saulcyi (that only feeds on gramineous herbs). Genetic clustering analyses and inferences from coalescent‐based demographic simulations confirm that C. s. algoaldensis represents an independently evolving lineage and support the ancient hybrid origin of this taxon (about 1.4 Ma), which sheds light on its uncertain phylogenetic position and might explain its broader trophic niche. We propose a Pleistocene hybrid speciation model where range shifts resulting from climatic oscillations can promote the formation of hybrid swarms and facilitate their long‐term persistence through geographic isolation from parental forms in topographically complex landscapes. [ABSTRACT FROM AUTHOR]

[Display omitted] • A suspected older new taxa has been discovered. • This new taxa involves the production of a large number of hybrid offspring. • Hybridization is the main driving force of poplar evolution in Tibet Plateau. • A new hypothesis of "Hybrid Species Exterminating Their Ancestral Species" is proposed. While the diversity of species formation is broadly acknowledged, significant debate exists regarding the universal nature of hybrid species formation. Through an 18-year comprehensive study of all Populus species on the Qinghai-Tibet Plateau, 23 previously recorded species and 8 new species were identified. Based on morphological characteristics, these can be classified into three groups: species in section Leucoides , species with large leaves, and species with small leaves in section Tacamahaca. By conducting whole-genome re-sequencing of 150 genotypes from these 31 species, 2.28 million single nucleotide polymorphisms (SNPs) were identified. Phylogenetic analysis utilizing these SNPs not only revealed a highly intricate evolutionary network within the large-leaf species of section Tacamahaca but also confirmed that a new species, P. curviserrata , naturally hybridized with P. cathayana, P. szechuanica, and P. ciliata , resulting in 11 hybrid species. These findings indicate the widespread occurrence of hybrid species formation within this genus, with hybridization serving as a key evolutionary mechanism for Populus on the plateau. A novel hypothesis, "Hybrid Species Exterminating Their Ancestral Species (HSEAS)," is introduced to explain the mechanisms of hybrid species formation at three different scales: the entire plateau, the southeastern mountain region, and individual river valleys. [ABSTRACT FROM AUTHOR]

Alleles that introgress between species can influence the evolutionary and ecological fate of species exposed to novel environments. Hybrid offspring of different species are often unfit, and yet it has long been argued that introgression can be a potent force in evolution, especially in plants. Over the last two decades, genomic data have increasingly provided evidence that introgression is a critically important source of genetic variation and that this additional variation can be useful in adaptive evolution of both animals and plants. Here, we review factors that influence the probability that foreign genetic variants provide long-term benefits (so-called adaptive introgression) and discuss their potential benefits. We find that introgression plays an important role in adaptive evolution, particularly when a species is far from its fitness optimum, such as when they expand their range or are subject to changing environments. [ABSTRACT FROM AUTHOR]

Aim: Refugial isolation during glaciation is an established driver of speciation; however, the opposing role of interglacial population expansion, secondary contact, and gene flow on the diversification process remains less understood. The consequences of glacial cycling on diversity are complex and especially so for archipelago species, which experience dramatic fluctuations in connectivity in response to both lower sea levels during glacial events and increased fragmentation during glacial recession. We test whether extended refugial isolation has led to the divergence of genetically and morphologically distinct species within Holarctic ermine (Mustela erminea), a small cosmopolitan carnivore species that harbours 34 extant subspecies, 14 of which are insular endemics. Location: Holarctic. Methods: We use genetic sequences (complete mitochondrial genomes, four nuclear genes) from >100 ermine (stoats) and geometric morphometric data for >200 individuals (27 of the 34 extant subspecies) from across their Holarctic range to provide an integrative perspective on diversification and endemism across this complex landscape. Multiple species delimitation methods (iBPP, bPTP) assessed congruence between morphometric and genetic data. Results: Our results support the recognition of at least three species within the M. erminea complex, coincident with three of four genetic clades, tied to diversification in separate glacial refugia. We found substantial geographic variation within each species, with geometric morphometric results largely consistent with historical infraspecific taxonomy. Main conclusions: Phylogeographic structure mirrors patterns of diversification in other Holarctic species, with a major Nearctic‐Palearctic split, but with greater intraspecific morphological diversity. Recognition of insular endemic species M. haidarum is consistent with a deep history of refugial persistence and highlights the urgency of mindful management of island populations along North America's North Pacific Coast. Significant environmental modification (e.g. industrial‐scale logging, mining) has been proposed for a number of these islands, which may elevate the risk of extinction of insular palaeoendemics. [ABSTRACT FROM AUTHOR]

Congeneric parasites are unlikely to specialize on the same tissues of the same host species, likely because of strong multifarious selection against niche overlap. Exceptions where >1 congeneric species use the same tissues reveal important insights into ecological factors underlying the origins and maintenance of diversity. Larvae of sunflower maggot flies in the genus Strauzia feed on plants in the family Asteraceae. Although Strauzia tend to be host specialists, some species specialize on the same hosts. To resolve the origins of host sharing among these specialist flies, we used reduced representation genomic sequencing to infer the first multilocus phylogeny of genus Strauzia. Our results show that Helianthus tuberosus and Helianthus grosseserratus each host three different Strauzia species and that the flies co‐occurring on a host are not one another's closest relatives. Though this pattern implies that host sharing is most likely the result of host shifts, these may not all be host shifts in the conventional sense of an insect moving onto an entirely new plant. Many hosts of Strauzia belong to a clade of perennial sunflowers that arose 1–2 MYA and are noted for frequent introgression and hybrid speciation events. Our divergence time estimates for all of the Helianthus‐associated Strauzia are within this same time window (<1 MYA), suggesting that rapid and recent adaptive introgression and speciation in Helianthus may have instigated the diversification of Strauzia, with some flies converging upon a single plant host after their respective ancestral host plants hybridized to form a new sunflower species. [ABSTRACT FROM AUTHOR]

It is increasingly realized that homoploid hybrid speciation (HHS), which involves no change in chromosome number, is an important mechanism of speciation. HHS will likely increase in frequency as ecological and geographical barriers between species are continuing to be disrupted by human activities. HHS requires the establishment of reproductive isolation between a hybrid and its parents, but the underlying genes and genetic mechanisms remain largely unknown. In this study, we reveal by integrated approaches that reproductive isolation originates in one homoploid hybrid plant species through the inheritance of alternate alleles at genes that determine parental premating isolation. The parent species of this hybrid species are reproductively isolated by differences in flowering time and survivorship on soils containing high concentrations of iron. We found that the hybrid species inherits alleles of parental isolating major genes related to flowering time from one parent and alleles of major genes related to iron tolerance from the other parent. In this way, it became reproductively isolated from one parent by the difference in flowering time and from the other by habitat adaptation (iron tolerance). These findings and further modeling results suggest that HHS may occur relatively easily via the inheritance of alternate parental premating isolating genes and barriers. Using integrated approaches, the authors reveal that reproductive isolation originated in one homoploid hybrid plant species (Ostryopsis intermedia) through the inheritance of alternate alleles at genes that determine parental premating isolation (flowering time and habitat adaptation, i.e., iron tolerance). Their findings and further modeling results suggest that homoploid hybrid speciation can occur easily via the inheritance of alternate, pre-existing, parental reproductive isolations. [ABSTRACT FROM AUTHOR]

The Hepatica section Angulosa consists of mainly tetraploid (2n = 28) species that are distributed disjunctly throughout Eurasia. Karyological evidence proves the hybrid origin of the polyploid species of this section. Hepatica transsilvanica is a member of this species group with a conspicuous distribution restricted to the Eastern Carpathians. Based on genome size and cytotypes, the paternal parent of H. transsilvanica is described to be the only diploid species in section Angulosa, H. falconeri. The maternal species is hypothesized to be H. nobilis, a European species with entirely lobed leaves and a wider distribution area. Although the hybrid origin of H. transsilvanica is well documented by karyological evidence, the time of hybridization has never been studied. By using sequences of both the nuclear and plastid genome, we reconstructed the phylogenetic relationships and divergence times of H. transsilvanica and its parental species. The identity of the parental species is corroborated by discordant gene tree topologies of the nrITS and plastid sequences. Moreover, both gene copies of the parental species could be identified with the low-copy nuclear gene, MLH1. Divergence dating analysis using Bayesian phylogenetic methods strongly supported the long-term survival of H. transsilvanica in the Southeastern Carpathians, as the most recent common ancestor of the hybrid and parent species existed not later than the beginning of the Pleistocene, ca. 3 million years ago. These results not only highlight the biogeographic importance of the Southeastern Carpathians in the Quaternary glaciation periods, but also emphasize that Tertiary lineages could have survived in a Central European cryptic refugium. [ABSTRACT FROM AUTHOR]

Dugesia hepta Pala, Casu & Vacca, 1981 and Dugesia benazzii Lepori, 1951 are two freshwater planarian species from the islands of Corsica and Sardinia. Dugesia hepta is endemic of Sardinia and distributed in four northern hydrographic basins where it co-occurs with D. benazzii, which has a wider Tyrrhenian distribution. Although these species have been broadly studied—especially D. benazzii—as regards to their variety of reproductive patterns as well as for their karyological diversity, little is known about them from a molecular phylogenetic perspective. For the first time, we present a molecular phylogenetic tree of the two species and their populations based on two molecular markers—one mitochondrial, Cox1, and one nuclear, Dunuc12. Our results not only confirm that both species are molecularly distinct but also show that D. benazzii's Corsican and Sardinian populations could belong to separate species. Furthermore, we present the first demonstration of a natural hybridization between different species in the genus Dugesia on the basis of molecular data. [ABSTRACT FROM AUTHOR]

Summary: The wheat group offers an outstanding system to address the interplay between hybridization, chromosomal evolution and biological diversification. Most diploid wild wheats originated following hybridization between the A‐genome lineage and the B‐genome lineage some 4 Myr ago, resulting in an admixed D‐genome lineage that presented dramatic radiation accompanied by considerable changes in genome size and chromosomal rearrangements. Comparative profiling of low‐copy genes, repeated sequences and transposable elements among those divergent species characterized by different karyotypes highlights high genome dynamics and sheds new light on the processes underlying chromosomal evolution in wild wheats. One of the hybrid clades presents upsizing of metacentric chromosomes going along with the proliferation of specific repeats (i.e. 'genomic obesity'), whereas other species show stable genome size associated with increasing chromosomal asymmetry. Genetic and ecological variation in those specialized species suggest that genome restructuring was coupled with adaptive processes to support the evolution of a majority of acrocentric chromosomes. This synthesis of current knowledge on genome restructuring across the diversity of wild wheats paves the way towards surveys based on latest sequencing technologies to characterize valuable resources and address the significance of chromosomal evolution in species with complex genomes. [ABSTRACT FROM AUTHOR]

All known vertebrate clones have originated from hybridization events and some have produced distinct evolutionary lineages via hybrid speciation. Amazon mollies (Poecilia formosa) present an excellent study system to investigate how clonal species have adapted to heterogeneous environments because they are the product of a single hybridization event between male sailfin mollies (Poecilia latipinna) and female Atlantic mollies (Poecilia mexicana). Here, we ask whether the hybrid species differs from the combination of its parental species' genes in its plastic response to different environments. Using a three‐way factorial design, we exposed neonates produced by Amazon mollies and reciprocal F1 hybrid crosses to different thermal (24°C and 29°C) and salinity (0/2, 12, and 20 ppt) regimes. We measured various ontogenetic and life history characteristics across the life span of females. Our major results were as follows: (1) Reaction norms of growth and maturation to temperature and salinity are quite similar between the two hybrid crosses; (2) Amazon molly reaction norms were qualitatively different than the P. latipinna male and P. mexicana female (L×M) hybrids for the ontogenetic variables; (3) Amazon molly reaction norms in reproductive traits were also quite different from L×M hybrids; and (4) The reaction norms of net fertility were very different between Amazon mollies and L×M hybrids. We conclude that best locale for Amazon mollies is not the best locale for hybrids, which suggests that Amazon mollies are not just an unmodified mix of parental genes but instead have adapted to the variable environments in which they are found. Hybridization resulting in asexuality may represent an underappreciated mechanism of speciation because the unlikely events required to produce such hybrids rarely occur and is dependent upon the genetic distance between parental species. [ABSTRACT FROM AUTHOR]

Summary: Two major developments have made it possible to use examples of ecological radiations as model systems to understand evolution and ecology. First, the integration of quantitative genetics with ecological experiments allows detailed connections to be made between genotype, phenotype, and fitness in the field. Second, dramatic advances in molecular genetics have created new possibilities for integrating field and laboratory experiments with detailed genetic sequencing. Combining these approaches allows evolutionary biologists to better study the interplay between genotype, phenotype, and fitness to explore a wide range of evolutionary processes. Here, we present the genus Senecio (Asteraceae) as an excellent system to integrate these developments, and to address fundamental questions in ecology and evolution. Senecio is one of the largest and most phenotypically diverse genera of flowering plants, containing species ranging from woody perennials to herbaceous annuals. These Senecio species exhibit many growth habits, life histories, and morphologies, and they occupy a multitude of environments. Common within the genus are species that have hybridized naturally, undergone polyploidization, and colonized diverse environments, often through rapid phenotypic divergence and adaptive radiation. These diverse experimental attributes make Senecio an attractive model system in which to address a broad range of questions in evolution and ecology. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

[Display omitted] • Three new taxa of the sect. Leucoides were discovered. • The three new taxa all originated from distant hybridization between different sections. • The three new taxa had stronger adaptability than the ancient ancestor species. • A universal model of hybrid speciation process is proposed. Although numerous studies have been conducted on hybrid speciation, our understanding of this process remains limited. Through an 18-year systematic investigation of all taxa of Populus on the Qinghai-Tibet Plateau, we discovered three new taxa with clear characteristics of sect. Leucoides. Further evidence was gathered from morphology, whole-genome bioinformatics, biogeography, and breeding to demonstrate synthetically that they all originated from distant hybridization between sect. Leucoides and sect. Tacamahaca. P. gonggaensis originated from the hybridization of P. lasiocarpa with P. cathayana , P. butuoensis from the hybridization of P. wilsonii with P. szechuanica , and P. dafengensis from the hybridization of P. lasiocarpa with P. szechuanica. Due to heterosis, the three hybrid taxa possess greater ecological adaptability than their ancestral species. We propose a hybrid speciation process model that incorporates orthogonal, reverse, and backcrossing events. This model can adequately explain some crucial evolutionary concerns, such as the nuclear-cytoplasmic conflict on phylogeny and the extinction of ancestral species within the distribution range of hybrid species. [ABSTRACT FROM AUTHOR]

Butterfly eyes are complex organs that are composed of a diversity of proteins and they play a central role in visual signaling and ultimately, speciation, and adaptation. Here, we utilized the whole eye transcriptome to obtain a more holistic view of the evolution of the butterfly eye while accounting for speciation events that co-occur with ancient hybridization. We sequenced and assembled transcriptomes from adult female eyes of eight species representing all major clades of the Heliconius genus and an additional outgroup species, Dryas iulia. We identified 4,042 orthologous genes shared across all transcriptome data sets and constructed a transcriptome-wide phylogeny, which revealed topological discordance with the mitochondrial phylogenetic tree in the Heliconius pupal mating clade. We then estimated introgression among lineages using additional genome data and found evidence for ancient hybridization leading to the common ancestor of Heliconius hortense and Heliconius clysonymus. We estimated the K a/ K s ratio for each orthologous cluster and performed further tests to demonstrate genes showing evidence of adaptive protein evolution. Furthermore, we characterized patterns of expression for a subset of these positively selected orthologs using qRT-PCR. Taken together, we identified candidate eye genes that show signatures of adaptive molecular evolution and provide evidence of their expression divergence between species, tissues, and sexes. Our results demonstrate: 1) greater evolutionary changes in younger Heliconius lineages, that is, more positively selected genes in the cydno – melpomene – hecale group as opposed to the sara – hortense – erato group, and 2) suggest an ancient hybridization leading to speciation among Heliconius pupal-mating species. [ABSTRACT FROM AUTHOR]

Since the 1970s, an apomictic tetraploid beech fern (genus Phegopteris (C. Presl) Fée) has been known in northeastern North America. Previously published isozyme data suggest that this lineage is of allopolyploid origin involving long beech fern (P. connectilis (Michx.) Watt.) but not broad beech fern (P. hexagonoptera (Michx.) Fée), as originally hypothesized. Its second progenitor remains unknown. We performed a principal components analysis of the apomict and its North American congeners to elucidate morphological differences between them. We recognize the apomictic tetraploid at specific rank as P. excelsior N. R. Patel & A. V. Gilman and provide an illustration, a range map, a list of exsiccatae, and a key to Phegopteris species of North America. [ABSTRACT FROM AUTHOR]

Nothoscordum bonariense (2 n = 26; 22M + 4A) is a hexaploid species morphologically related to other species of section Nothoscordum. Its meiotic behaviour and that of its hybrids suggests an allopolyploid origin. Here, we investigate the origin of N. bonariense and its relationships with most closely related species based on cytological and molecular data. Cytogenetic analyses included chromosome number and morphology, distribution of ribosomal DNA (rDNA) sites, genomic in situ hybridization (GISH) and nuclear genome size. Molecular phylogenetic analyses were based on nuclear ITS and the plastid trnG intron and the atpB - rbcL and trnL - trnF spacer sequences. Nothoscordum bonariense and South American samples of N. bivalve formed a clade sister to N. gaudichaudianum, whereas N. montevidense was recovered in a different clade. Molecular phylogenetic relationships, congruent genome size variation, 35S and 5S rDNA sites distribution and GISH suggest that N. bonariense is a hybrid. Different types of reduced or unreduced gametes (2 x or 3 x) or somatic doubling in a hybrid may have led to the formation of N. bonariense karyotype. Genomic DNA of N. gaudichaudianum hybridized the x = 4 subgenome of N. bonariense more strongly than that of N. montevidense, suggesting that the former species is one of N. bonariense progenitors, instead of the latter. Genomic DNA of N. gaudichaudianum also revealed a x = 4 subgenome in one N. bivalve (2 n = 18, 14M + 4A) accession, revealing that this species may have an allopolyploid origin. However, the non-monophyly of its accessions and the variability of chromosome number and rDNA composition reported here suggest that this species needs an extensive taxonomic, biogeographic and phylogenetic revision. Allopolyploidization involving progenitors with two different basic chromosome numbers (x = 4 and x = 5) and the remarkable 5S and 35S rDNA variation described here provide further evidence of rapid karyotype evolution in section Nothoscordum. [ABSTRACT FROM AUTHOR]

Hybridization can induce transposons to jump into new genomic positions, which may result in their accumulation across the genome. Alternatively, transposon copy numbers may increase through nonallelic (ectopic) homologous recombination in highly repetitive regions of the genome. The relative contribution of transposition bursts versus recombination‐based mechanisms to evolutionary processes remains unclear because studies on transposon dynamics in natural systems are rare. We assessed the genomewide distribution of transposon insertions in a young hybrid lineage ("invasive Cottus", n = 11) and its parental species Cottus rhenanus (n = 17) and Cottus perifretum(n = 9) using a reference genome assembled from long single molecule pacbio reads. An inventory of transposable elements was reconstructed from the same data and annotated. Transposon copy numbers in the hybrid lineage increased in 120 (15.9%) out of 757 transposons studied here. The copy number increased on average by 69% (range: 10%–197%). Given the age of the hybrid lineage, this suggests that they have proliferated within a few hundred generations since admixture began. However, frequency spectra of transposon insertions revealed no increase in novel and rare insertions across assembled parts of the genome. This implies that transposons were added to repetitive regions of the genome that remain difficult to assemble. Future studies will need to evaluate whether recombination‐based mechanisms rather than genomewide transposition may explain the majority of the recent transposon proliferation in the hybrid lineage. Irrespectively of the underlying mechanism, the observed overabundance in repetitive parts of the genome suggests that gene‐rich regions are unlikely to be directly affected. [ABSTRACT FROM AUTHOR]

The evolution of reproductive isolation following hybridization is a major obstacle that may limit the prevalence of hybrid speciation among specific groups of organisms. Here, we use a flea beetle system to offer a behavioral hypothesis for why there are so few examples of homoploid hybrid speciation among insects. Specifically, we examined cuticular hydrocarbon (CHC) mating signals and mate-choice decisions of Altica fragariae and A. viridicyanea to test whether the signals produced by hybrids cause prezygotic reproductive isolation. Although hybrids of A. fragariae and A. viridicyanea had unique CHC profiles as compared to the parental species, mate-choice trials indicated that these differences were insufficient to prevent gene flow between hybrids and parental species. We found that mate-choice decisions and CHC signals were not correlated. Considering the ubiquity of CHC signaling molecules in insects, we propose that decoupling of CHC signals and mate choice may be a general mechanism limiting hybrid speciation in insects. [ABSTRACT FROM AUTHOR]

Hybridization has recently gained considerable interest both as a unique opportunity for observing speciation mechanisms and as a potential engine for speciation. The latter remains a controversial topic. It was recently hypothesized that the reciprocal sorting of genetic incompatibilities from parental species could result in hybrid speciation, when the hybrid population maintains a mixed combination of the parental incompatibilities that prevents further gene exchange with both parental populations. However, the specifics of the purging/sorting process of multiple incompatibilities have not been examined theoretically. We here investigate the allele-frequency dynamics of an isolated hybrid population that results from a single hybridization event. Using models of two or four loci, we investigate the fate of one or two genetic incompatibilities of the Dobzhansky-Muller type (DMIs). We study how various parameters affect both the sorting/purging of the DMIs and the probability of observing hybrid speciation by reciprocal sorting. We find that the probability of hybrid speciation is strongly dependent on the linkage architecture (i.e. the order and recombination rate between loci along chromosomes), the population size of the hybrid population, and the initial relative contributions of the parental populations to the hybrid population. We identify a Goldilocks zone for specific linkage architectures and intermediate recombination rates, in which hybrid speciation becomes highly probable. Whereas an equal contribution of parental populations to the hybrid population maximizes the hybrid speciation probability in the Goldilocks zone, other linkage architectures yield unintuitive asymmetric maxima. We provide an explanation for this pattern, and discuss our results both with respect to the best conditions for observing hybrid speciation in nature and their implications regarding patterns of introgression in hybrid zones. [ABSTRACT FROM AUTHOR]

Hybrid speciation is rare in vertebrates, and reproductive isolation arising from hybridization is infrequently demonstrated. Here, we present evidence supporting a hybrid-speciation event involving the genetic admixture of the snow-capped (Lepidothrix nattereri) and opal-crowned (Lepidothrix iris) manakins of the Amazon basin, leading to the formation of the hybrid species, the golden-crowned manakin (Lepidothrix vilasboasi). We used a genome-wide SNP dataset together with analysis of admixture, population structure, and coalescent modeling to demonstrate that the golden-crowned manakin is genetically an admixture of these species and does not represent a hybrid zone but instead formed through ancient genetic admixture. We used spectrophotometry to quantify the coloration of the species-specific male crown patches. Crown patches are highly reflective white (snow-capped manakin) or iridescent whitish-blue to pink (opal-crowned manakin) in parental species but are a much less reflective yellow in the hybrid species. The brilliant coloration of the parental species results from nanostructural organization of the keratin matrix feather barbs of the crown. However, using electron microscopy, we demonstrate that the structural organization of this matrix is different in the two parental species and that the hybrid species is intermediate. The intermediate nature of the crown barbs, resulting from past admixture appears to have rendered a duller structural coloration. To compensate for reduced brightness, selection apparently resulted in extensive thickening of the carotenoid-laden barb cortex, producing the yellow crown coloration. The evolution of this unique crown-color signal likely culminated in premating isolation of the hybrid species from both parental species. [ABSTRACT FROM AUTHOR]

Background: The unisexual Amazon molly (Poecilia formosa) originated from a hybridization between two sexual species, the sailfin molly (Poecilia latipinna) and the Atlantic molly (Poecilia mexicana). The Amazon molly reproduces clonally via sperm-dependent parthenogenesis (gynogenesis), in which the sperm of closely related species triggers embryogenesis of the apomictic oocytes, but typically does not contribute genetic material to the next generation. We compare for the first time the gonadal transcriptome of the Amazon molly to those of both ancestral species, P. mexicana and P. latipinna. Results: We sequenced the gonadal transcriptomes of the P. formosa and its parental species P. mexicana and P. latipinna using Illumina RNA-sequencing techniques (paired-end, 100 bp). De novo assembly of about 50 million raw read pairs for each species was performed using Trinity, yielding 106,922 transcripts for P. formosa, 115,175 for P. latipinna and 133,025 for P. mexicana after eliminating contaminations. On the basis of sequence similarity comparisons to other teleost species and the UniProt databases, functional annotation and differential expression analysis, we demonstrate the similarity of the transcriptomes among the three species. More than 40% of the transcripts for each species were functionally annotated and about 70% were assigned to orthologous genes of a closely related species. Differential expression analysis between the sexual and unisexual species uncovered 2035 up-regulated and 564 down-regulated genes in P. formosa. This was exemplary validated for six genes by qRT-PCR. Conclusions: We identified more than 130 genes related to meiosis and reproduction within the apomictically reproducing P. formosa. Overall expression of these genes seems to be down-regulated in the P. formosa transcriptome compared to both ancestral species (i.e., 106 genes down-regulated, 29 up-regulated). A further 35 meiosis and reproduction related genes were not found in the P. formosa transcriptome, but were only expressed in the sexual species. Our data support the hypothesis of general down-regulation of meiosis-related genes in the apomictic Amazon molly. Furthermore, the obtained dataset and identified gene catalog will serve as a resource for future research on the molecular mechanisms behind the reproductive mode of this unisexual species. [ABSTRACT FROM AUTHOR]

Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with "non-coding" DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called "non-coding" RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations. [ABSTRACT FROM AUTHOR]

Molecular phylogenetics is a valuable approach not only for discovering previously undetected plant diversity at the species level, but also for inferring the underlying processes of diversification. In southern Africa, two species of the woody genus Memecylon have been recognised, viz. M. natalense and M. bachmannii , with the range of M. natalense reportedly extending to northern Mozambique and southern Malawi. We investigated the evolutionary relationships of southern African Memecylon with population-level sampling and comparative sequencing of two fast-evolving DNA regions (nuclear rDNA ITS and 5′ ETS). Within M. natalense sensu lato, analyses revealed three geographically outlying populations representing distinct, semi-cryptic lineages (in forests of Maputaland and on the Soutpansberg and Mount Mulanje, respectively). Another sample from the Lindi region (southeastern Tanzania) produced an ITS sequence close to that of Kenyan M. fragrans while the ETS sequence was placed nearer to those of Mozambican M. torrei and M. natalense sensu stricto. This case of phylogenetic incongruence is taken to indicate the presence of an undescribed, homoploid hybrid species in the Rovuma region of southern Tanzania and northern Mozambique, although this hypothesis needs additional study. In KwaZulu-Natal and the Eastern Cape, rDNA spacer sequences were found to be identical or nearly so amongst samples of M. natalense and M. bachmannii , a surprising result given the clear morphological and ecological differences between these species. The minimal sequence variation would seem to indicate recent divergence or perhaps introgressive hybridisation. Further study is needed of the species boundary between M. natalense and M. bachmannii . [ABSTRACT FROM AUTHOR]

Evolutionary dynamics of structural genetic variation in lineages of hybrid origin is not well explored, although structural mutations may increase in controlled hybrid crosses. We therefore tested whether structural variants accumulate in a fish of recent hybrid origin, invasive Cottus, relative to both parental species Cottus rhenanus and Cottus perifretum. Copy-number variation in exons of 10,979 genes was assessed using comparative genome hybridization arrays. Twelve genes showed significantly higher copy numbers in invasive Cottus compared to both parents. This coincided with increased expression for three genes related to vision, detoxification and muscle development, suggesting possible gene dosage effects. Copy number increases of putative transposons were assessed by comparative mapping of genomic DNA reads against a de novo assembly of 1,005 repetitive elements. In contrast to exons, copy number increases of repetitive elements were common (20.7%) in invasive Cottus, whereas decrease was very rare (0.01%). Among the increased repetitive elements, 53.8% occurred at higher numbers in C. perifretum compared to C. rhenanus, while only 1.4% were more abundant in C. rhenanus. This implies a biased mutational process that amplifies genetic material from one ancestor. To assess the frequency of de novo mutations through hybridization, we screened 64 laboratory-bred F2 offspring between the parental species for copy-number changes at five candidate loci. We found no evidence for new structural variants, indicating that they are too rare to be detected given our sampling scheme. Instead, they must have accumulated over more generations than we observed in a controlled cross. [ABSTRACT FROM AUTHOR]

Reticulate speciation caused by interspecific hybridization is now recognized as an important mechanism in the creation of biological diversity. However, depicting the patterns of phylogenetic networks for lineages that have undergone interspecific gene flow is challenging., Here we sequenced 25 taxa representing natural diversity in the genus Actinidia with an average mapping depth of 26× on the reference genome to reconstruct their reticulate history., We found evidence, including significant gene tree discordance, cytonuclear conflicts, and changes in genome-wide heterozygosity across taxa, collectively supporting extensive reticulation in the genus. Furthermore, at least two separate parental species pairs were involved in the repeated origin of the hybrid lineages, in some of which a further phase of syngameon was triggered. On the basis of the elucidated hybridization relationships, we obtained a highly resolved backbone phylogeny consisting of taxa exhibiting no evidence of hybrid origin. The backbone taxa have distinct demographic histories and are the product of recent rounds of rapid radiations via sorting of ancestral variation under variable climatic and ecological conditions., Our results suggest a mode for consecutive plant diversification through two layers of radiations, consisting of the rapid evolution of backbone lineages and the formation of hybrid swarms derived from these lineages. [ABSTRACT FROM AUTHOR]

The establishment of hybrid taxa relies on reproductive isolation from the parental forms, typically achieved by ecological differentiation. Here, we present an alternative mechanism, in which shifts in the strength and location of dispersal barriers facilitate diversification by hybridisation. Our case study concerns the highly diverse, stenotopic rock-dwelling cichlids of the African Great Lakes, many of which display geographic colour pattern variation. The littoral habitat of these fish has repeatedly been restructured in the course of ancient lake level fluctuations. Genetic data and an experimental cross support the hybrid origin of a distinct yellow-coloured variant of Tropheus moorii from ancient admixture between two allopatric, red and bluish variants. Deficient assortative mating preferences imply that reproductive isolation continues to be contingent on geographic separation. Linking paleolimnological data with the establishment of the hybrid variant, we sketch a selectively neutral diversification process governed solely by rearrangements of dispersal barriers. [ABSTRACT FROM AUTHOR]

Modes and mechanisms of speciation are best studied in young species pairs. In older taxa, it is increasingly difficult to distinguish what happened during speciation from what happened after speciation. Lake Victoria cichlids in the genus Pundamilia encompass a complex of young species and polymorphic populations. One Pundamilia species pair, P. pundamilia and P. nyererei, is particularly well suited to study speciation because sympatric population pairs occur with different levels of phenotypic differentiation and reproductive isolation at different rocky islands within the lake. Genetic distances between allopatric island populations of the same nominal species often exceed those between the sympatric species. It thus remained unresolved whether speciation into P. nyererei and P. pundamilia occurred once, followed by geographical range expansion and interspecific gene flow in local sympatry, or if the species pair arose repeatedly by parallel speciation. Here, we use genomic data and demographic modelling to test these alternative evolutionary scenarios. We demonstrate that gene flow plays a strong role in shaping the observed patterns of genetic similarity, including both gene flow between sympatric species and gene flow between allopatric populations, as well as recent and early gene flow. The best supported model for the origin of P. pundamilia and P. nyererei population pairs at two different islands is one where speciation happened twice, whereby the second speciation event follows shortly after introgression from an allopatric P. nyererei population that arose earlier. Our findings support the hypothesis that very similar species may arise repeatedly, potentially facilitated by introgressed genetic variation. [ABSTRACT FROM AUTHOR]

This article is a Commentary on Nürk et al. 224: 518–531. [ABSTRACT FROM AUTHOR]

[Display omitted] • Multiple genetic breaks were observed and six independent species could be recognized in the Paradoxornis webbianus species complex. • P. a. ganluoensis genetically is not the intermediate between the rest of P. alphonsianus and P. webbianus despite the seemingly intermediate morphology. • P. alphonsianus most likely origins from hybridization between its currently recognized subspecies P. a. ganluoensis and P. webbianus. • The late Pliocene and Pleistocene climatic changes have most likely contributed to these speciation events in the complex. Various environmental factors impact the distribution, population structure, demography and evolutionary trajectory of a bird species, leading to genetic and morphological divergences between populations across its distribution. The Paradoxornis webbianus species complex is found throughout much of East Asia, where its geographically distinct populations exhibit dramatic morphological variation. This has resulted in a hotly debated taxonomy. This study intended to identify genetic divergence patterns and their underlying contributing factors for this species complex. We collected 243 birds, whose data was combined with those available in GenBank to perform phylogeographic analyses using one mitochondrial and six nuclear loci. Six mitochondrial clades were observed in the species complex, while individual-based Bayesian clustering using nuclear markers showed multiple congruent breaks. Overall, the six molecular lineages could be recognized as independent species under the lineage species concept in view of genetic divergence, clade-specific morphological changes and distribution: P. webbianus, P. w. bulomachus, P. alphonsianus, P. a. ganluoensis, P. brunneus brunneus and P. b. ricketti. The estimated divergence times range from 0.46 to 3.36 million years ago, suggesting it was likely impacted by paleoclimatic changes. Interestingly, P. alphonsianus carries two divergent mitochondrial lineages shared with P. webbianus and P. a. ganluoensis, respectively, and analyses based on nuclear loci found a similar pattern. We discussed the various hypotheses for this pattern and argued that P. alphonsianus was likely the result of hybridization between P. webbianus and P. a. ganluoensis. Further data on genome, transcriptome and breeding ecology are needed to address the hypothesis of hybrid speciation and its underlying mechanisms. [ABSTRACT FROM AUTHOR]

The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution; symbiogenetic fusions forming eukaryotic cells with multiple genome compartments; horizontal organelle, virus and DNA transfers; functional organization of proteins as systems of interacting domains subject to rapid evolution by exon shuffling and exonization; distributed genome networks integrated by mobile repetitive regulatory signals; and regulation of multicellular development by non-coding lncRNAs containing repetitive sequence components. Rather than single gene traits, all phenotypes involve coordinated activity by multiple interacting cell molecules. Genomes contain abundant and functional repetitive components in addition to the unique coding sequences envisaged in the early days of molecular biology. Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess "Read--Write Genomes" they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification. [ABSTRACT FROM AUTHOR]

Aim Speciation can either proceed as gradual divergence, mostly in allopatry or parapatry, or by duplication of chromosome sets: polyploidization. Hybrid-origin or allopolyploidization is an important mechanism of hybrid speciation with strong, although often incomplete, postzygotic reproductive barriers between the polyploid hybrid and its diploid parents. Allopolyploids often present novel phenotypes that exceed the ranges of their ancestral lineages, leading to the hypothesis that niche shifts could be supportive of hybrid speciation. Although polyploidy is phylogenetically widespread in animals, ecological niches of diploid ancestral and derived allopolyploids have been rarely comparatively examined. Here, we do so for five species of Palaearctic green toads ( Bufo viridis subgroup), involving three ploidy levels. Location Central Asia, High Asia. Methods We gathered distributional records of genotyped toads, covering the whole range of the five toad species. We then used similarity and equivalency tests and examined whether bioclimatic (Grinellian) niches of allopolyploids are intermediate to those of the extant diploid relatives of their ancestral forms or whether they are transgressive (beyond those of both ancestors). Results We found evidence for both transgressive and conservative niches in allopolyploids. Allotetraploids ( Bufo pewzowi, B. oblongus) showed transgressive niche evolution; they inhabited environments that were harsher (more arid and with colder winters) than both of their parental species. In contrast, the allotriploid B. baturae exhibited a conserved niche, similar to an ancestral lineage that provided two-thirds of its hybrid genome. For most comparisons, niches of extant diploid ancestral lineages were significantly different from each other. Main conclusion We conclude that allopolyploidization in amphibians leads potentially but not a necessarily to transgressive niche evolution, and may facilitate hybrid speciation by allowing newly formed hybrids to colonize novel habitats and thus escape their parental lineages. [ABSTRACT FROM AUTHOR]

Polyploidization is a rare yet sometimes successful way for animals to rapidly create geno- and phenotypes that may colonize new habitats and quickly adapt to environmental changes. In this study, we use water frogs of the Pelophylax esculentus complex, comprising two species ( Pelophylax lessonae, genotype LL; Pelophylax ridibundus, RR) and various diploid ( LR) and triploid ( LLR, LRR) hybrid forms, summarized as P. esculentus, as a model for studying recent hybridization and polyploidization in the context of speciation. Specifically, we compared the geographic distribution and genetic diversity of diploid and triploid hybrids across Europe to understand their origin, maintenance and potential role in hybrid speciation. We found that different hybrid and parental genotypes are not evenly distributed across Europe. Rather, their genetic diversity is structured by latitude and longitude and the presence/absence of parental species but not of triploids. Highest genetic diversity was observed in central and eastern Europe, the lowest in the northwestern parts of Europe. This gradient can be explained by the decrease in genetic diversity during postglacial expansion from southeastern glacial refuge areas. Genealogical relationships calculated on the basis of microsatellite data clearly indicate that hybrids are of multiple origin and include a huge variety of parental genomes. Water frogs in mixed-ploidy populations without any parental species (i.e. all-hybrid populations) can be viewed as evolutionary units that may be on their way towards hybrid speciation. Maintenance of such all-hybrid populations requires a continuous exchange of genomes between diploids and triploids, but scenarios for alternative evolutionary trajectories are discussed. [ABSTRACT FROM AUTHOR]

Homoploid hybrid speciation ( HHS) requires reproductive barriers between hybrid and parent species, despite incomplete reproductive isolation ( RI) between the parents. Novel secondary sexual trait values in hybrids may cause prezygotic isolation from both parents, whereas signals inherited by the hybrid from one parent species may cause prezygotic isolation with the other. Here we investigate whether differences in male plumage function as a premating barrier between the hybrid Italian sparrow and one of its parent species, the house sparrow, in a narrow Alpine hybrid zone. Italian sparrow male plumage is a composite mosaic of the parental traits, with its head plumage most similar to its other parent, the Spanish sparrow. We use geographical cline analysis to examine selection on three plumage traits, 75 nuclear single nucleotide polymorphisms ( SNPs) and hybrid indices based on these SNPs. Several SNPs showed evidence of restricted introgression in the Alps, supporting earlier findings. Crown colour exhibited the narrowest plumage cline, representing a 37% (range 4-65%) drop in fitness. The cline was too narrow to be due to neutral introgression. Only crown colour was significantly bimodal in the hybrid zone. Bimodality may be due to RI or a major QTL, although fitness estimates suggest that selection contributes to the pattern. We discuss the implications with respect to HHS and the species status of the Italian sparrow. [ABSTRACT FROM AUTHOR]

Speciation is regarded primarily as a bifurcation from an ancestral species into two distinct taxonomic units, but gene flow can create complex signals of phylogenetic relationships, especially among different loci. We evaluated several hypotheses that could account for phylogenetic discord between mitochondrial DNA (mt DNA) and nuclear DNA (nu DNA) within Hawaiian duck ( Anas wyvilliana), including stochastic lineage sorting, mt DNA capture and widespread genomic introgression. Our results best support the hypothesis that the contemporary Hawaiian duck is descended from an ancient hybridization event between the mallard ( Anas platyrhynchos) and Laysan duck ( Anas laysanensis). Whereas mt DNA clearly shows a sister relationship between Hawaiian duck and mallard, nu DNA is consistent with a genetic mosaic with nearly equal contributions from Laysan duck and mallard. In addition, coalescent analyses suggest that gene flow from either mallard or Laysan duck, depending on the predefined tree topology, is necessary to explain contemporary genetic diversity in Hawaiian ducks, and these estimates are more consistent with ancient, rather than contemporary, hybridization. Time since divergence estimates suggest that the genetic admixture event occurred around the Pleistocene-Holocene boundary, which is further supported by circumstantial evidence from the Hawaiian subfossil record. Although the extent of reproductive isolation from either putative parental taxon is not currently known, these species are phenotypically, genetically and ecologically different, and they meet primary criteria used in avian taxonomy for species designation. Thus, the available data are consistent with an admixed origin and support the hypothesis that the Hawaiian duck may represent a young hybrid species. [ABSTRACT FROM AUTHOR]

The genetic structure of tetraploid (4x = 44) North American species ofPrimulasubgenusAuriculastrum:P. suffrutescens,P. parryi,P. rusbyi, andP. angustifoliawas analyzed at seven enzyme loci and compared with that of the related diploidP. cuneifoliaandP. nipponica. The studied tetraploid species showed fixed or almost fixed heterozygosity at various loci, indicating a hybrid origin. About half of their alleles were shared withCuneifoliataxa sampled, suggesting that they arose from crosses involving a maternalCuneifolia-like ancestor. A preliminary survey of their possible paternal species, as inferred from their genotypes, was carried out among differentPrimulagroups. Several paternal alleles expected were observed in subgenusAleuritia, particularly among taxa of sect.Crystallophlomis(e.g.,P. chionantha,P. minor, andP. nivalis xanthobasis). However, none of these taxa proved to be a suitable paternal species. Hybridization events that originatedP. suffrutescens,P. parryi,P. rusbyi, andP. angustifoliapresumably occurred during Pleistocene secondary contacts in Beringia and involved a maternalCuneifolia-like ancestor and at least two paternal species, for sect.SuffrutescensandParryi, respectively. Further studies, involving a genetic survey ofAleuritiataxa from Siberia will be needed to detect such paternal species, if not extinct. [ABSTRACT FROM AUTHOR]

The article presents the authors' study of the plant species belonging to the taxonomic group Boechera fendleri sensu lato. Topics discussed include an overview of the plant specimens collected from various herbaria for the case study, the use of genetic sequencing techniques and the statistical tool AWCLUST in the analysis of the acquired plant specimens, and a comprehensive analysis of the results.

The triploid perennial Helianthus x multiflorus L. is a beloved garden ornamental, but its phylogenetic origin has long been a source of discussion. Sequence comparison of genes involved in the biosynthesis of the sesquiterpene lactones was used to identify the common sunflower Helianthus annuus L. and the diploid taxon Helianthus decapetalus L. as the most likely parental combination in the origin of the triploid hybrid species. A pair of deletions (22 and 26 bp in length) in an intron part of the germacrene A synthase 1 gene differentiated the diploid from the tetraploid karyotype of H. decapetalus . The same deletion was found in one of the two alleles (299 bp in length) in H. x multiflorus , whereas a second allele (350 bp in length) showed a very high similarity with the sequence found in H. annuus . Quantification of the two amplification products in H. x multiflorus showed a higher concentration of the larger amplicon thus suggesting that H. annuus has contributed an unreduced genome to the hybrid. Comparison of variable regions of the cpDNA showed highest identity of H. x multiflorus with cpDNA sequences of the diploid H. decapetalus . This suggests that H. decapetalus served as the maternal parent in a cross with H. annuus to produce H. x multiflorus . [ABSTRACT FROM AUTHOR]

Hybridization has played an important role in Saxifraga evolution causing reticulation and a high number of described hybrids, but little is known about how hybrid speciation had occurred in the genus. We focus on a group of closely related Saxifraga species of the subsection Triplinervium from Pyrenees, the phylogenetic relationships of which remain unsolved. Trying to unmask cryptic (or ancient) hybridization processes, we analyze one nuclear (ITS) and three plastid regions ( rpl32- trnL, trnS- trnG- trnG, and 3′trnV-ndhC), as well as nuclear DNA content. Pollen and seed morphology and viability studies were carried out to evaluate the status of spontaneous hybrids. DNA ploidy levels were also inferred for the two Madeiran taxa (of the same Saxifraga subsection), where recent hybridization processes are not expected. Molecular markers revealed multiple reticulation events, which, as suggested by DNA content and chromosome numbers, have occurred in homoploidy (without genome doubling after hybridization). In addition, autopolyploidy has occurred in some species or populations, especially in the Madeiran archipelago colonization. Chromosome number variation appears to be related to centric fission events, which also could lead to the formation of the B chromosomes inferred in some taxa. Spontaneous hybrids do not produce viable seeds and this could be due to differences in parental chromosome numbers. Hybrid speciation has probably been successful by chromosomal arrangements, which also generated new, more or less intermediate, chromosomal numbers in this group of taxa. [ABSTRACT FROM AUTHOR]