Comparison of gene flow among species that occur within the same geographic locations versus gene flow among populations within species reveals introgression among several Elymus species

One of the challenges in evolutionary biology is to understand the evolution of speciation with incomplete reproductive isolation as many taxa have continued gene flow both during and after speciation. Comparison of population structure between sympatric and allopatric populations can reveal specific introgression and determine if introgression occurs in a unidirectional or bidirectional manner. Simple sequence repeat markers were used to characterize sympatric and allopatric population structure of plant species, Elymus alaskanus (Scribn. and Merr.) Löve, E. caninus L., E. fibrosus (Schrenk) Tzvel., and E. mutabilis (Drobov) Tzvelev. Our results showed that genetic diversity (H_E) at species level is E. caninus (0.5355) > E. alaskanus (0.4511) > E. fibrosus (0.3924) > E. mutabilis (0.3764), suggesting that E. caninus and E. alaskanus are more variable than E. fibrosus and E. mutabilis. Gene flow between species that occurs within the same geographic locations versus gene flow between populations within species was compared to provide evidence of introgression. Our results indicated that gene flow between species that occur within the same geographic location is higher than that between populations within species, suggesting that gene flow resulting from introgressive hybridization might have occurred among the sympatric populations of these species, and may play an important role in partitioning of genetic diversity among and within populations. The migration rate from E. fibrosus to E. mutabilis is highest (0.2631) among the four species studied. Asymmetrical rates of gene flow among four species were also observed. The findings highlight the complex evolution of these four Elymus species.     

Widespread gene flow between oceans in a pelagic seabird species complex

Global‐scale gene flow is an important concern in conservation biology as it has the potential to either increase or decrease genetic diversity in species and populations. Although many studies focus on the gene flow between different populations of a single species, the potential for gene flow and introgression between species is understudied, particularly in seabirds. The only well‐studied example of a mixed‐species, hybridizing population of petrels exists on Round Island, in the Indian Ocean. Previous research assumed that Round Island represents a point of secondary contact between Atlantic (Pterodroma arminjoniana) and Pacific species (Pterodroma neglecta and Pterodroma heraldica). This study uses microsatellite genotyping and tracking data to address the possibility of between‐species hybridization occurring outside the Indian Ocean. Dispersal and gene flow spanning three oceans were demonstrated between the species in this complex. Analysis of migration rates estimated using bayesass revealed unidirectional movement of petrels from the Atlantic and Pacific into the Indian Ocean. Conversely, structure analysis revealed gene flow between species of the Atlantic and Pacific oceans, with potential three‐way hybrids occurring outside the Indian Ocean. Additionally, geolocation tracking of Round Island petrels revealed two individuals travelling to the Atlantic and Pacific. These results suggest that interspecific hybrids in Pterodroma petrels are more common than was previously assumed. This study is the first of its kind to investigate gene flow between populations of closely related Procellariiform species on a global scale, demonstrating the need for consideration of widespread migration and hybridization in the conservation of threatened seabirds.     

Using nuclear haplotypes with microsatellites to study gene flow between recently separated Cichlid species

When populations or species have recently separated they often share genetic variation. However, it can be difficult to determine whether shared polymorphisms are the result of gene flow, the result of the persistence of variation in both populations since the time of common ancestry, or both of these factors. We have developed an empirical protocol for using loci that include unique nuclear DNA sequence haplotypes together with linked microsatellites or short tandem repeats (STRs). These 'HapSTRs' offer the potentially high resolution associated with the high mutation rate of STRs, together with the advantages of low homoplasy of unique sequence DNA. We also describe a new procedure for estimating the likelihood of HapSTR data under an Isolation with Migration model. An example using Cichlid fishes from Lake Malawi is described. The analysis suggests that the species have been exchanging genes since the time they began to diverge.     

Associations between physical isolation and geographical variation within three species of Neotropical birds

We studied effects of physical isolation on geographical variation in mtDNA RFLP polymorphisms and a suite of morphological characters within three species of neotropical forest birds; the crimson-backed tanager Ramphocelus dimidiatus, the blue-gray tanager Thraupis episcopus, and the streaked saltator Saltator albicollis. Variation among populations within continuous habitat on the Isthmus of Panama was compared with that among island populations isolated for about 10000 years. Putative barriers to dispersal were influential, but apparent isolation effects varied by species, geographical scale, and whether molecular or morphological traits were being assessed. We found no geographical structuring among the contiguous, mainland sampling sites. Migration rates among the islands appeared sufficient to maintain homogeneity in mtDNA haplotype frequencies. In contrast, variation in external morphology among islands was significant within two of three species. For all species, we found significant variation in genetic and morphological traits between the island (collectively) and mainland populations. Interspecific variation in the effects of isolation was likely related to differential vagility. These data generally corroborate other studies reporting relatively great geographical structuring within tropical birds over short distances. Behaviourally based traits - low vagility and high ‘sensitivity’ to geographical barriers - may underlie extensive diversification within neotropical forest birds, but more extensive ecological and phylogeographic information are needed on a diverse sample of species.     

Ancient hybridization and mitochondrial capture between two species of chipmunks

Models that posit speciation in the face of gene flow are replacing classical views that hybridization is rare between animal species. We use a multilocus approach to examine the history of hybridization and gene flow between two species of chipmunks ( Tamias ruficaudus and T. amoenus ). Previous studies have shown that these species occupy different ecological niches and have distinct genital bone morphologies, yet appear to be incompletely isolated reproductively in multiple areas of sympatry. We compared data from four sequenced nuclear loci and from seven microsatellite loci to published cytochrome b sequences. Interspecific gene flow was primarily restricted to introgression of the T. ruficaudus mitochondrial genome into a sympatric subspecies of T. amoenus , T. a. canicaudus , with the four sequenced nuclear loci showing little to no interspecific allele sharing. Microsatellite data were consistent with high levels of differentiation between the species and also showed no current gene flow between broadly sympatric populations of T. a. canicaudus and T. ruficaudus . Coalescent analyses date the mtDNA introgression event from the mid-Pleistocene to late Pliocene. Overall, these data indicate that introgression has had a minimal impact on the nuclear genomes of T. amoenus and T. ruficaudus despite multiple independent hybridization events. Our findings challenge long-standing assumptions on patterns of reproductive isolation in chipmunks and suggest that there may be other examples of hybridization among the 23 species of Tamias that occur in western North America.     

Ring species as demonstrations of the continuum of species formation

In the mid‐20th century, Ernst Mayr (1942) and Theodosius Dobzhansky (1958) championed the significance of ‘circular overlaps’ or ‘ring species’ as the perfect demonstration of the gradual nature of species formation. As an ancestral species expands its range, wrapping around a geographic barrier, derived taxa within the ring display interactions typical of populations, such as genetic and morphological intergradation, while overlapping taxa at the terminus of the ring behave largely as sympatric, reproductively isolated species. Are ring species extremely rare or are they just difficult to detect? What conditions favour their formation? Modelling studies have attempted to address these knowledge gaps by estimating the biological parameters that result in stable ring species (Martins et al. 2013), and determining the necessary topographic parameters of the barriers encircled (Monahan et al. 2012). However, any generalization is undermined by a major limitation: only a handful of ring species are known to exist in nature. In addition, many of them have been broken into multiple species presumed to be evolving independently, usually obscuring the evolutionary dynamics that generate diversity. A paper in this issue of Molecular Ecology by Fuchs et al. (2015), focused on the entire genealogy of a bulbul (Alophoixus) species complex, offers key insights into the evolutionary processes underlying diversification of this Indo‐Malayan bird. Their findings fulfil most of the criteria that can be expected for ring species (Fig.  1 ): an ancestor has colonized the mainland from Sundaland, expanded along the forested habitat wrapping around Thailand's lowlands, adjacent taxa intergrade around the ring distribution, and terminal taxa overlap at the ring closure. Although it remains unclear whether ring divergence has resulted in restrictive gene flow relative to that observed around the ring, their results suggest that circular overlaps might be more common in nature than currently recognized in the literature. Most importantly, this work shows that the continuum of species formation that Mayr and Dobzhansky praised in circular overlaps is found in biological systems currently described as ‘rings of species’, in addition to the idealized ‘ring species’.     

Barriers to gene flow and ring species formation

Ring species are groups of organisms that dispersed along a ring‐shaped region in such a way that the two ends of the population that meet after many generations are reproductively isolated. They provide a rare opportunity to understand the role of spatial structuring in speciation. Here, we simulate the evolution of ring species assuming that individuals become sexually isolated if the genetic distance between them is above a certain threshold. The model incorporates two forms of dispersal limitation: exogenous geographic barriers that limit the population range and endogenous barriers that result in genetic structuring within the population range. As expected, species' properties that reduce gene flow within the population range facilitate the evolution of reproductive isolation and ring species formation. However, if populations are confined to narrow ranges by geographic barriers, ring species formation increases when local mating is less spatially restricted. Ring species are most likely to form if a population expands while confined to a quasi‐unidimensional range but preserving high mobility in the direction of the range expansion. These conditions are unlikely to be met or persist in real populations and may explain why ring species are rare.     

Phylogeographic structure, gene flow and species status in blue grouse (Dendragapus obscurus)

We investigated the genetic population structure and species status of a relatively sedentary bird that is a permanent resident of western North American forests, the blue grouse (Dendragapus obscurus). Phylogenetic analysis of complete mitochondrial control region DNA sequences resulted in the identification of three basal clades of haplotypes that were largely congruent with well-known biogeographical regions. These clades corresponded to the parapatric sooty (D. o. fuliginosus) and dusky (D. o. obscurus) subspecies groups of blue grouse plus a previously unrecognized division between northern and southern dusky grouse populations; the latter does not correspond closely to any currently recognized subspecies boundary. Approximately 66% of the total genetic variation was distributed among these three regions. Maximum likelihood estimates of gene flow between the regions were low or asymmetric; gene flow has been insufficient to prevent genetic divergence between dusky and sooty grouse. Estimates of gene flow among populations within sooty grouse were large except across the Columbia River valley. Among populations of dusky grouse, estimates of gene flow were heterogeneous and asymmetrical, reflecting large-scale fragmentation of the distribution due to landscape features and associated vegetation. Genetic, morphological and behavioural evidence suggest that sooty and dusky grouse are species-level taxa; the specific status of a third clade remains ambiguous.     

Recent advances in assessing gene flow between diverging populations and species

The evolutionary process of divergence, which ultimately leads to the generation of new species, is thought to occur usually without any gene exchange between the diverging populations. However, until the recent growth of multi-locus datasets, and the development of new population genetic methods, it has been very difficult to assess whether or not closely related species have, or have not, exchanged genes during their divergence. Several recent studies have found significant signals of gene flow during species formation, calling into question the conventional wisdom that gene flow is absent during speciation.     

Extremely divergent host plant acceptance with gene flow between sympatric host races of the phytophagous ladybird beetle Henosepilachna diekei

Ecological divergence alone can prevent the majority of gene flow in the absence of other forms of reproductive isolation. Although the importance of ecological divergence in promoting reproductive isolation has been broadly recognized, its net impact on speciation has rarely been estimated in the wild. The phytophagous ladybird beetle Henosepilachna diekei Jadwiszczak & Wegrzynowicz includes two sympatric host races that are reproductively isolated solely by extreme specialization to either of the host plants Mikania micrantha Kunth (Asteraceae) or Leucas lavandulifolia Sm. (Lamiaceae) in West Java, Indonesia. To investigate the impact of differential host use as an isolating barrier, we carried out adult host acceptance tests and molecular population genetic analyses based on mitochondrial ND2 and nucleic ITS2 gene sequences using 13 wild populations of the host races, including four sympatric population pairs. Almost all individuals of these host races persistently accepted only the original host plant. We detected restricted but a degree of gene flow between these host races. A migration event occurred only in very recent time compared to their divergence time, indicating recent secondary contact of these host races in the surveyed area. These results reveal the remarkably large impact of host‐plant shift over almost the entire process of speciation and illustrate that ecological divergence has been maintained even under the presence of a certain degree of gene flow.     

Genomic differentiation and patterns of gene flow between two long‐tailed tit species (Aegithalos)

Patterns of heterogeneous genomic differentiation have been well documented between closely related species, with some highly differentiated genomic regions (“genomic differentiation islands”) spread throughout the genome. Differential levels of gene flow are proposed to account for this pattern, as genomic differentiation islands are suggested to be resistant to gene flow. Recent studies have also suggested that genomic differentiation islands could be explained by linked selection acting on genomic regions with low recombination rates. Here, we investigate genomic differentiation and gene‐flow patterns for autosomes using RAD‐seq data between two closely related species of long‐tailed tits (Aegithalos bonvaloti and A. fuliginosus) in both allopatric and contact zone populations. The results confirm recent or ongoing gene flow between these two species. However, there is little evidence that the genomic regions that were found to be highly differentiated between the contact zone populations are resistant to gene flow, suggesting that differential levels of gene flow is not the cause of the heterogeneous genomic differentiation. Linked selection may be the cause of genomic differentiation islands between the allopatric populations with no or very limited gene flow, but this could not account for the heterogeneous genomic differentiation between the contact zone populations, which show evidence of recent or ongoing gene flow.     

Reproductive isolation between oviparous and viviparous lineages of the Eurasian common lizard Zootoca vivipara in a contact zone

Contact zones between two evolutionary lineages are often useful for understanding the process of speciation because the observed genetic pattern reflects the history of differentiation. The Eurasian lacertid lizard Zootoca vivipara is a potentially interesting model for studying the role of reproductive mode in the speciation of squamate reptiles because it has both oviparous (Zootoca vivipara carniolica) and viviparous (Zootoca vivipara vivipara) populations that have recently been shown to be genetically distinct. We studied a newly‐discovered syntopic area of these two Zootoca subspecies in the central Italian Alps using genetic markers to investigate the level of introgression between them. Patterns of genetic differentiation in a fragment of the mitochondrial DNA cytb gene and a set of nuclear microsatellites show that the speciation process is complete in this area, with no evidence of recent introgression. Phylogenetic and genotypic divergence suggests that the two subspecies have experienced long independent evolutionary histories, during which genetic and phenotypic differences evolved. The possible roles of biogeography, reproductive mode, and cytogenetic differentiation in this speciation process are discussed. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 566–573.     

Restricted gene flow between two social forms in the ant Formica truncorum

We studied genetic differentiation between two social forms (M-type: single queen, independent nest founding; P-type: multiple queens, dependent nest founding, building of colonial networks) of the ant Formica truncorum in a locality where the social types characterize two sympatric populations. The genetic results indicate restricted gene flow between the social forms. Female gene flow between the forms appears to be absent as they did not share mitochondrial haplotypes. Significant nuclear differentiation and the distribution of private alleles suggest that male gene flow between the forms is weak. However, the assignment analysis indicates some gene flow with P males mating with M females. The results have potentially important implications concerning social evolution within the forms but they need to be confirmed in other localities before they can be generalized. The colonies in the M-type population have earlier been shown to produce split sex ratios, depending on the mating frequency of the queens. The inferred gene flow from the P to the M type means that the split sex ratio is partly suboptimal, possibly because the P populations are not long-lived enough to influence the behavioural decisions in the M colonies.     

Gene flow between species of Lake Victoria haplochromine fishes

The haplochromine cichlid fishes of Lake Victoria (LV), East Africa, are a textbook example of adaptive radiation-a rapid divergence of multiple morphologically distinguishable forms from a few founding lineages. The forms are generally believed to constitute a "flock" of several hundred reproductively isolated species in a dozen or so genera. This belief has, until now, not been subjected to a test, however. Here, we compare genetic variation at 11 loci in 10 haplochromine populations of 6 different species. Although the genetic diversity in the populations is quite high, using a variety of statistical tests, we find no evidence of genetic differentiation among the populations of LV haplochromines. On genetic distance trees, populations of the same species intermingle with those of different species. At the molecular level, the species are indistinguishable from one another. Genetic comparisons with closely related species in 2 crater lakes indicate that the species within LV continue exchanging genes. These observations have important implications for phylogenetic reconstruction. The approach used in this study is applicable to other instances of adaptive radiation.     

Maintenance of species boundaries in a Neotropical radiation of Begonia

A major goal of evolutionary biology is to determine the mechanisms generating biodiversity. In Begonia, one of the largest plant genera (1900+ species), it has been postulated that the high number of endemic species is a by‐product of low gene flow among populations, which predisposes the group to speciation. However, this model of divergence requires that reproductive barriers accumulate rapidly among diverging species that overlap in their geographic ranges, otherwise speciation will be opposed by homogenizing gene flow in zones of secondary contact. Here, we test the outcomes of secondary contact in Begonia by genotyping multiple sympatric sites with 12 nuclear and seven plastid loci. We show that three sites of secondary contact between B. heracleifolia and B. nelumbiifolia are highly structured, mostly containing parental genotypes, with few F1 hybrids. A sympatric site between B. heracleifolia and B. sericoneura contains a higher proportion of F1s, but little evidence of introgression. The lack of later‐generation hybrids contrasts with that documented in many other plant taxa, where introgression is extensive. Our results, in conjunction with previous genetic work, show that Begonia demonstrate properties making them exceptionally prone to speciation, at multiple stages along the divergence continuum. Not only are populations weakly connected by gene flow, promoting allopatric speciation, but species often show strong reproductive barriers in secondary contact. Whether similar mechanisms contribute to diversification in other large genera remains to be tested.