Barriers To Gene Flow Research Articles

Differential effects of landscape‐level environmental features on genetic structure in three codistributed tree species in Central America

Landscape genetic studies use spatially explicit population genetic information to determine the physical and environmental causes of population genetic structure on regional scales. Comparative studies that identify common barriers to gene flow across multiple species within a community are important to both understand the evolutionary trajectories of populations and prioritize habitat conservation. Here, we use a comparative landscape genetic approach to ask whether gradients in temperature or precipitation seasonality structure genetic variation across three codistributed tree species in Central America, or whether a simpler (geographic distance) or more complex, species-specific environmental niche model is necessary to individually explain population genetic structure. Using descriptive statistics and causal modelling, we find that different factors best explain genetic distance in each of the three species: environmental niche distance in Bursera simaruba, geographic distance in Ficus insipida and historical barriers to gene flow or cryptic reproductive barriers for Brosimum alicastrum. This study confirms suggestions from previous studies of Central American tree species that imply that population genetic structure of trees in this region is determined by complex interactions of both historical and current barriers to gene flow.

Genetic diversity and structure in the annual vernal pool endemic Limnanthes vinculans Ornduff (Limnanthaceae): implications of breeding system and restoration practices

Many California vernal pool plants are endangered requiring information on genetic diversity and structure to inform conservation efforts. We determined the temporal, and range-wide population genetic status of the outcrossing endangered vernal pool forb Limnanthes vinculans, endemic to Sonoma and Napa Counties with 10 microsatellite markers. Allelic diversity was threefold higher than in an endangered self-pollinating congener. Most populations showed heterozygote deficiency indicating past bottlenecks, inbreeding or genetic drift. Analysis of molecular variance and Bayesian ordination revealed genetic distinction at the county scale (F CT = 0.158); within Sonoma County, population genetic distinctions were lower (F SC = 0.043). Eight gene flow barriers demarcated most natural populations (F ST > 0.05). We found temporal genetic structure among six natural populations (F ST = 0.07). We conclude that breeding system and natural, anthropogenic, and temporal seed inputs combined to influence the patterns of genetic variation we found in natural and created populations informing conservation of the species.

Interspecific hybridization in sympatric species of Daphnia inhabiting lakes in northeastern Poland

Abstract Populations of three sympatric species (Daphnia cucullata, Daphnia galeata, and Daphnia hyalina (Daphnia longispina complex)) inhabiting three lakes in northeastern Poland (Roś, Mikołajskie, Wigry) were checked for interspecific hybrids. Hybrid Daphnia coexisting with parental individuals were detected in each of the investigated lakes. Several classes of hybrids (F1, F2, backcrosses), including D. cucullata×galeata×hyalina individuals, have been detected. Hybrids constituted a substantial (13%–38%) part of the total abundance of individuals of the D. longispina complex. Deficiency of heterozygotes (hybrids) detected may indicate the existence of barriers for gene flow between the sympatric Daphnia taxa.

Taxonomic delimitation and drivers of speciation in the Ibero‐North African Carex sect. Phacocystis river‐shore group (Cyperaceae)

The Ibero-North African Carex sect. Phacocystis river-shore group is a set of perennial helophytic species with poorly defined taxonomic boundaries. In the present study, we delimited the different taxonomic units, addressed the phylogeographic history, and evaluated the drivers of differentiation that have promoted diversification of these plants. We analyzed molecular data using statistical parsimony for plastid sequences (26 samples from 26 populations) and principal coordinate analysis, neighbor joining, and Bayesian analysis of population structure for AFLPs (186 samples from 26 populations). Chromosome numbers from 14 samples (9 populations) are newly reported. Three species can be distinguished (C. acuta, C. elata, and C. reuteriana). Unexpectedly for rhizome-growing helophytes, the vegetative reproduction detected was incidental. The widespread C. elata was found to be a genetically poorly differentiated taxon, whereas the local C. reuteriana displayed geographical structuring. Geographical factors seem to be the main driver of differentiation for both taxa. Despite apparent morphological and ecological similarities, C. elata and C. reuteriana have disparate genetic structures and evolutionary histories, which may have originated from small ecological differences. Carex elata is broadly distributed throughout Europe, and its northern populations were recently founded, probably after the last glacial maximum. In contrast, C. reuteriana is an Ibero-North African endemic, with long-standing populations affected by isolation and limited gene flow. It is likely that high-density blocking effects and different gene-flow barriers act together to delimit its distribution and promote its relatively high population differentiation.

Maintenance of sympatric floral tube-length variation in a Cape irid

Transition zones between morphologically different individuals of the same species provide insights into the evolution and maintenance of gene-flow barriers. Here we investigate Tritoniopsis revoluta, which has geographically variable tube lengths, thought to be adaptations to insects with different proboscis lengths. We found a narrow transition zone between plants differing by three-fold in perianth tube length. We determined whether strong gene-flow barriers result from assortative mating arising from different pollinators, a high prevalence of selfing, or post-pollination incompatibilities between plants with different tube lengths. We found that there was little evidence to support assortative mating through different pollinators. Both short- and long-tubed plants were mainly visited by bees with short proboscides. Selfing is unlikely to contribute significantly to seed set, plants with different tube lengths were interfertile and hybrid plants were fertile. We conclude that the contact zone is unstable because these ecotypes have not accrued enough allopatric differences to translate into strong gene-flow barriers, or, alternatively, bimodality is not a consequence of secondary contact but the result of a novel mutation for short tubes spreading through a long-tubed population. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104, 129‐137. ADDITIONAL KEYWORDS: adaptive peaks ‐ assortative mating ‐ bimodal tube length ‐ gene-flow barriers ‐ hybrid zone ‐ pollination ‐ pollinator ecotypes.

The Influence of Historical Geneflow, Bathymetry and Distribution Patterns on the Population Genetics of Morphologically Diverse Galápagos’ Opuntia echios

Throughout history, remote archipelagos have repeatedly been designated natural laboratories to study evolutionary processes. The extensive, geographically structured, morphological variation within Galápagos' Opuntia cacti has been presumed to be another example of how such processes shape diversity. However, recent genetic studies on speciation and potential effects of plasticity within this system failed to confirm earlier classification and hypothesized radiation on both global and single island levels. Detailed population genetic information, however, is crucial in conserving these semi-arid ecosystem keystone species. In this article, we re-evaluate the genetics of Opuntia echios inhabiting one of the most taxon rich places on the archipelago: Santa Cruz and its surrounding satellite islands, using microsatellite data. Our analysis revealed high genetic variability within all sampled locations, providing little support for the hypothesis of clonal reproduction. Inter-island gene flow patterns appear to be largely influenced by bathymetry and sea levels during last ice ages. Although O. echios from Seymour Norte are morphologically recognized as being a separate taxon, Daphné Major's cacti are the most differentiated. In addition, we found a potential barrier for gene flow along the ring-like distribution of Opuntias at the western side of Santa Cruz, suggesting potential links with geology.

Phylogeography and gene diversity of the gall-forming aphid <i>Aploneura lentisci</i> in the Mediterranean basin

Pistacia lentiscus L. (Anacardiaceae) is a common shrub in the Mediterranean vegetation. Throughout its distribution area, this species is the obligate host of the kidney-shaped gall-forming aphid Aploneura lentisci (Homoptera: Fordinae). Despite the wide distribution of Pistacia lentiscus in diverse habitats along a climatic gradient in Israel, our previous study did not reveal any pattern of ecologically related genetic differentiation. Here we examined changes in gall density and genetic diversity of the gall-forming aphid A. lentisci along its distribution gradient in Israel, in the neighboring island of Cyprus, and in Tunisia, North Africa. Gall density and mass differed significantly among the Israeli populations and were positively correlated with annual precipitation and plants' annual growth. Gene diversity of A. lentisci was very low in all populations and, as with its host plant, the genetic similarity was high within and among the Israeli populations and between the Israeli and Cyprian populations. To conclude, we found no evidence for any gene flow barrier and genetic differentiation among the aphid populations.

English

  The fundamental molecular basis for phenotypic and genetic similarities among many described cases of plant hybrid necrosis has not been fully described. Plants can be good models for studying the basis of such gene flow barriers which occur between species. Many studies in prezygotic barriers like stigma recognition of pollen, environmental adaptation differences and pollinator preferences which can reduce the chances of species mating success have been done. Also studied are post zygotic barriers in gene flow like lack of ecosystem adaptation of hybrids which may include failure of pollinators from being attracted to floral parts due to developmental changes and gene or chromosome incompatibility resulting in genetic isolation. Polyploidy has also been recognized as an isolating force although it might not be the only post zygotic genome isolating force; other forces may also contribute hindrances in the gene flow after zygote formation. Here, papers which have tended to pinpoint the increasing evidence of epigenetic polymorphisms as causes of genomic conflicts which cause barriers to the gene flow resulting in hybrid necrosis in plants were reviewed. Explorations into the mechanisms which unlock hybrid necrosis can help plant breeders to avoid genetic and epigenetic incompatibilities during crop improvement programs.   Key words: Hybrid necrosis, heterosis, epigenetic, hybrid sterility, RNAi. 

Population genetic structure of the Antarctic ascidian Aplidium falklandicum from Scotia Arc and South Shetland Islands

In sessile marine organisms, gene flow between populations depends mainly on free-living reproductive stages (such as larvae and gametes), and usually the strength of genetic structure is related to the time spent in the plankton and physical factors as oceanographic conditions. In Antarctica, abyssal depths that surround the continent and the Polar Front are considered strong barriers for benthic marine fauna, keeping the continent isolated from other shelves. The only available shallow water habitats between South America and the Antarctic continent are those around the Scotia Arc Islands; there are no shallow water habitats between the other southern continents and Antarctica. In this work, ISSRs-PCR markers were used to study the genetic structure of populations of Aplidium falklandicum, a compound ascidian with short-lived lecitotrophic larvae. A highly significant genetic differentiation (ΦST = 0.405; P < 0.05) and a pattern of isolation by distance were found. A genetic landscape approach identified a discontinuity in genetic diversity, coincident with the southernmost registered position of the Polar Front. For A. falklandicum, a species with presumably low capacity of long distance dispersal, the abyssal depths together with the large geographic distances create a barrier for gene flow.

Historical biogeography of the land snail Cornu aspersum: a new scenario inferred from haplotype distribution in the Western Mediterranean basin

BackgroundDespite its key location between the rest of the continent and Europe, research on the phylogeography of north African species remains very limited compared to European and North American taxa. The Mediterranean land mollusc Cornu aspersum (= Helix aspersa) is part of the few species widely sampled in north Africa for biogeographical analysis. It then provides an excellent biological model to understand phylogeographical patterns across the Mediterranean basin, and to evaluate hypotheses of population differentiation. We investigated here the phylogeography of this land snail to reassess the evolutionary scenario we previously considered for explaining its scattered distribution in the western Mediterranean, and to help to resolve the question of the direction of its range expansion (from north Africa to Europe or vice versa). By analysing simultaneously individuals from 73 sites sampled in its putative native range, the present work provides the first broad-scale screening of mitochondrial variation (cyt b and 16S rRNA genes) of C. aspersum.ResultsPhylogeographical structure mirrored previous patterns inferred from anatomy and nuclear data, since all haplotypes could be ascribed to a B (West) or a C (East) lineage. Alternative migration models tested confirmed that C. aspersum most likely spread from north Africa to Europe. In addition to Kabylia in Algeria, which would have been successively a centre of dispersal and a zone of secondary contacts, we identified an area in Galicia where genetically distinct west and east type populations would have regained contact.ConclusionsVicariant and dispersal processes are reviewed and discussed in the light of signatures left in the geographical distribution of the genetic variation. In referring to Mediterranean taxa which show similar phylogeographical patterns, we proposed a parsimonious scenario to account for the "east-west" genetic splitting and the northward expansion of the western (B) clade which roughly involves (i) the dispersal of ancestral (eastern) types through Oligocene terranes in the Western Mediterranean (ii) the Tell Atlas orogenesis as gene flow barrier between future west and east populations, (iii) the impact of recurrent climatic fluctuations from mid-Pliocene to the last ice age, (iv) the loss of the eastern lineage during Pleistocene northwards expansion phases.

Population genetic structure of long-tailed pygmy rice rats (Oligoryzomys longicaudatus) from Argentina and Chile based on the mitochondrial control region

The rodent Oligoryzomys longicaudatus (Bennett, 1832) (Rodentia, Cricetidae) inhabits southern forests of Argentina and Chile, a region severely affected by glaciations during the Pleistocene–Holocene periods. We evaluate here the diversity of the mitochondrial control region to characterize the genetic structure of this species from forests and bushy areas of seven populations from Argentina and four populations from Chile. Statistical analyses showed shallow haplotype trees and mismatch distributions compatible with recent range expansions. The presence of “private” haplotypes indicates that current levels of gene flow among populations of each country would be low to moderate. Significant differences in haplotype frequencies were detected between eastern and western populations, indicating that the Andes mountains would be an effective geographic barrier for gene flow despite the existing valleys that could act as corridors for dispersion. A single clade containing all the haplotypes was recovered in the phylogenetic trees, suggesting postglacial dispersion from a single refugium during the Last Glacial Maximum. The higher effective size and levels of polymorphism in populations from Chile suggest that the refugium was located in this country. The asymmetric gene flow from Chile to Argentina may reflect a recent colonization of the eastern populations.

Genetic structure of Podocarpus nubigena (Podocarpaceae) provides evidence of Quaternary and ancient historical events

Evolution of ancient lineages inhabiting austral latitudes of the southern Andes has taken place in response to historical processes occurring at distinct spatial and temporal scales. We tested the hypothesis that distribution patterns of genetic polymorphisms within Podocarpus nubigena Lindl. (Podocarpaceae) were shaped by contemporary events acting at local scales such as Quaternary glaciations as well as pre-Quaternary palaeogeographical features of the landscape. We predict that such cold hardy species was able to survive locally in refugia during ice ages. As a result of local long-lasting persistence, its gene pool may also reflect the pre-Quaternary palaeogeography of southern South America. We collected fresh leaves from 30 randomly selected individuals at 14 populations. Leaf tissue was analyzed by isozyme electrophoresis using 12 putative loci most of which (92%) were polymorphic in at least one population. Elevated total genetic diversity was recorded H T = 0.275 which was similarly high throughout populations with an overall significant mean among-population isolation ( F ST = 18%). Multivariate cluster and Bayesian analyses yielded significant latitudinal divergence at 43°S associated to a palaeobasin that produced a barrier for gene flow. Populations south of 43°S and those growing in lowland areas on Quaternary substrates of the North Patagonian Massif (Q NPM) present the highest genetic diversity suggesting long-lasting persistence. In contrast, northern mountain populations on pre-Quaternary substrates (pre-Q NPM) hold reduced genetic variation due to altitudinal movements in response to climate shifts. We suggest that palaeogeography of southern South America in addition to Neogene glaciations have shaped the genetic makeup of such ancient lineage as Podocarpus.

Strait of Gibraltar: an effective gene‐flow barrier for wind‐pollinated Carex helodes (Cyperaceae) as revealed by DNA sequences, AFLP, and cytogenetic variation

The Strait of Gibraltar is the most important barrier disconnecting the landmasses of Europe and Africa on the western Mediterranean extreme. Carex helodes is a wind-pollinated species endemic to the western Mediterranean. Because molecular and cytogenetic data allow the inference of its evolutionary history, we analyzed variations in chromosome number, including meiotic chromosome behavior, amplified fragment length polymorphism (AFLP) fingerprints, and nucleotide substitutions in plastid and nuclear DNA sequences. Cytogeographic results showed that the African populations have stabilized at a single chromosome number of 2n = 74, whereas the most frequent cytotype in Iberia is 2n = 72. Phylogenetic reconstructions of 17 sequences from nine closely related species revealed that C. helodes is monophyletic and that the Moroccan populations are embedded in the Iberian lineages. The haplotype network is also consistent with a European origin of the northern African haplotype. AFLP analysis also revealed hierarchical levels of genetic variation compatible with a founder effect process responsible for the African populations. All sources of evidence support the hypothesis that the Strait of Gibraltar has been an effective gene-flow barrier, generating two isolated evolutionary lineages after their dispersal. Recent connections between the two lineages appear unlikely, whereas active gene flow occurs among populations within the two lineages.

Landscape features affect gene flow of Scottish Highland red deer (Cervus elaphus)

Landscape features have been shown to strongly influence dispersal and, consequently, the genetic population structure of organisms. Studies quantifying the effect of landscape features on gene flow of large mammals with high dispersal capabilities are rare and have mainly been focused at large geographical scales. In this study, we assessed the influence of several natural and human-made landscape features on red deer gene flow in the Scottish Highlands by analysing 695 individuals for 21 microsatellite markers. Despite the relatively small scale of the study area (115 x 87 km), significant population structure was found using F-statistics (F(ST) = 0.019) and the program structure, with major differentiation found between populations sampled on either side of the main geographical barrier (the Great Glen). To assess the effect of landscape features on red deer population structure, the ArcMap GIS was used to create cost-distance matrices for moving between populations, using a range of cost values for each of the landscape features under consideration. Landscape features were shown to significantly affect red deer gene flow as they explained a greater proportion of the genetic variation than the geographical distance between populations. Sea lochs were found to be the most important red deer gene flow barriers in our study area, followed by mountain slopes, roads and forests. Inland lochs and rivers were identified as landscape features that might facilitate gene flow of red deer. Additionally, we explored the effect of choosing arbitrary cell cost values to construct least cost-distance matrices and described a method for improving the selection of cell cost values for a particular landscape feature.

Autoimmunity: A Barrier to Gene Flow in Plants?

Autoimmunity: A Barrier to Gene Flow in Plants?

Autoimmune Response as a Mechanism for a Dobzhansky-Muller-Type Incompatibility Syndrome in Plants

Epistatic interactions between genes are a major factor in evolution. Hybrid necrosis is an example of a deleterious phenotype caused by epistatic interactions that is observed in many intra- and interspecific plant hybrids. A large number of hybrid necrosis cases share phenotypic similarities, suggesting a common underlying mechanism across a wide range of plant species. Here, we report that approximately 2% of intraspecific crosses in Arabidopsis thaliana yield F1 progeny that express necrosis when grown under conditions typical of their natural habitats. We show that several independent cases result from epistatic interactions that trigger autoimmune-like responses. In at least one case, an allele of an NB-LRR disease resistance gene homolog is both necessary and sufficient for the induction of hybrid necrosis, when combined with a specific allele at a second locus. The A. thaliana cases provide insights into the molecular causes of hybrid necrosis, and serve as a model for further investigation of intra- and interspecific incompatibilities caused by a simple epistatic interaction. Moreover, our finding that plant immune-system genes are involved in hybrid necrosis suggests that selective pressures related to host–pathogen conflict might cause the evolution of gene flow barriers in plants.

The Himalayas as a Directional Barrier to Gene Flow

High-resolution Y-chromosome haplogroup analyses coupled with Y-short tandem repeat (STR) haplotypes were used to (1) investigate the genetic affinities of three populations from Nepal--including Newar, Tamang, and people from cosmopolitan Kathmandu (referred to as "Kathmandu" subsequently)--as well as a collection from Tibet and (2) evaluate whether the Himalayan mountain range represents a geographic barrier for gene flow between the Tibetan plateau and the South Asian subcontinent. The results suggest that the Tibetans and Nepalese are in part descendants of Tibeto-Burman-speaking groups originating from Northeast Asia. All four populations are represented predominantly by haplogroup O3a5-M134-derived chromosomes, whose Y-STR-based age (+/-SE) was estimated at 8.1+/-2.9 thousand years ago (KYA), more recent than its Southeast Asian counterpart. The most pronounced difference between the two regions is reflected in the opposing high-frequency distributions of haplogroups D in Tibet and R in Nepal. With the exception of Tamang, both Newar and Kathmandu exhibit considerable similarities to the Indian Y-haplogroup distribution, particularly in their haplogroup R and H composition. These results indicate gene flow from the Indian subcontinent and, in the case of haplogroup R, from Eurasia as well, a conclusion that is also supported by the admixture analysis. In contrast, whereas haplogroup D is completely absent in Nepal, it accounts for 50.6% of the Tibetan Y-chromosome gene pool. Coalescent analyses suggest that the expansion of haplogroup D derivatives--namely, D1-M15 and D3-P47 in Tibet--involved two different demographic events (5.1+/-1.8 and 11.3+/-3.7 KYA, respectively) that are more recent than those of D2-M55 representatives common in Japan. Low frequencies, relative to Nepal, of haplogroup J and R lineages in Tibet are also consistent with restricted gene flow from the subcontinent. Yet the presence of haplogroup O3a5-M134 representatives in Nepal indicates that the Himalayas have been permeable to dispersals from the east. These genetic patterns suggest that this cordillera has been a biased bidirectional barrier.

Hybrid necrosis: autoimmunity as a potential gene-flow barrier in plant species

Ecological factors, hybrid sterility and differences in ploidy levels are well known for contributing to gene-flow barriers in plants. Another common postzygotic incompatibility, hybrid necrosis, has received comparatively little attention in the evolutionary genetics literature. Hybrid necrosis is associated with a suite of phenotypic characteristics that are similar to those elicited in response to various environmental stresses, including pathogen attack. The genetic architecture is generally simple, and complies with the Bateson-Dobzhansky-Muller model for hybrid incompatibility between species. We survey the extensive literature on this topic and present the hypothesis that hybrid necrosis can result from autoimmunity, perhaps as a pleiotropic effect of evolution of genes that are involved in pathogen response.

The genetic structure of hawthorn‐infestingRhagoletis pomonellapopulations in Mexico: implications for sympatric host race formation

The genetic origins of species may not all trace to the same time and place as the proximate cause(s) for population divergence. Moreover, inherent gene-flow barriers separating populations may not all have evolved under the same geographical circumstances. These considerations have lead to a greater appreciation of the plurality of speciation: that one geographical mode for divergence may not always be sufficient to describe a speciation event. The apple maggot fly, Rhagoletis pomonella, a model system for sympatric speciation via host-plant shifting, has been a surprising contributor to the concept of speciation mode plurality. Previous studies have suggested that past introgression of inversion polymorphism from a hawthorn-fly population in the trans-Mexican volcanic belt (EVTM) introduced diapause life-history variation into a more northern fly population that subsequently contributed to sympatric host race formation and speciation in the United States (US). Here, we report results from a microsatellite survey implying (i) that volcanic activity in the eastern EVTM may have been responsible for the initial geographical isolation of the Mexican and northern hawthorn-fly populations c. 1.57 mya; and (ii) that flies in the Sierra Madre Oriental Mountains (SMO) likely served as a conduit for past gene flow from the EVTM into the US. Indeed, the microsatellite data suggest that the current US population may represent a range expansion from the northern SMO. We discuss the implications of these findings for sympatric race formation in Rhagoletis and speciation theory.

Unexpected species diversity of Malagasy primates (Lepilemur spp.) in the same biogeographical zone: a morphological and molecular approach with the description of two new species.

BackgroundThe lemurs of Madagascar provide an excellent mammalian radiation to explore mechanisms and processes favouring species diversity and evolution. Species diversity, in particular of nocturnal species, increased considerably during the last decade. However, the factors contributing to this high diversity are not well understood. We tested predictions derived from two existing biogeographic models by exploring the genetic and morphological divergence among populations of a widely distributed lemur genus, the sportive lemur (Lepilemur ssp.) along a 560 km long transect from western to northern Madagascar.ResultsBy using the phylogenetic analyses of mtDNA sequence data, molecular diagnostic sites and phenotypic morphometric traits, we uncovered two previously undetected species whose distributions contradict the two existing biogeographic models. Brief species descriptions are provided and a new biogeographic model is proposed (the ”large river model“).ConclusionAccording to the ”large river model“, large rivers in north and northwestern Madagascar acted as geographical barriers for gene flow and facilitated speciation events on a much smaller spatial scale than previously thought. Thereby, this study does not only show that species diversity in nocturnal Malagasy primates is continuously underestimated but aims to emphasize the need for conservation actions if those species with small ranges shall not face extinction in the near future.