Amount Of Introgression Research Articles

Genetic analysis of hybridization between white-handed (Hylobates lar) and pileated (Hylobates pileatus) gibbons in a contact zone in Khao Yai National Park, Thailand.

Natural hybridization has played various roles in the evolutionary history of primates. Its consequences range from genetic introgression between taxa, formation of hybrid zones, and formation of new lineages. Hylobates lar, the white-handed gibbon, and Hylobates pileatus, the pileated gibbon, are largely allopatric species in Southeast Asia with a narrow contact zone in Khao Yai National Park, Thailand, which contains both parental types and hybrids. Hybrid individuals in the zone are recognizable by their intermediate pelage and vocal patterns, but have not been analyzed genetically. We analyzed mitochondrial and microsatellite DNA of 52 individuals to estimate the relative genetic contributions of the parental species to each individual, and the amount of introgression into the parental species. We obtained fecal samples from 33 H. lar, 15 H. pileatus and four phenotypically intermediate individuals in the contact zone. Both mitochondrial and microsatellite markers confirmed distinct differences between these taxa. Both H. lar and H. pileatus contributed to the maternal lineages of the hybrids based on mitochondrial analysis; hybrids were viable and present in socially normal reproductive pairs. The microsatellite analysis identified ten admixed individuals, four F1 hybrids, which corresponded to phenotypic hybrids, and six H. lar-like backcrosses. All 15 H. pileatus samples were identified as originating from genetically H. pileatus individuals with no H. lar admixture; hence, backcrossing is biased toward H. lar. A relatively low number of phenotypic hybrids and backcrossed individuals along with a high number of parental types indicates a bimodal hybrid zone, which suggests relatively strong bias in mate selection between the species.

Hybridization and introgression during density-dependent range expansion: European wildcats as a case study.

Interbreeding between historically allopatric species with incomplete reproductive barriers may result when species expand their range. The genetic consequences of such hybridization depend critically on the dynamics of the range expansion. Hybridization models during range expansion have been developed but assume dispersal to be independent from neighboring population densities. However, organisms may disperse because they are attracted by conspecifics or because they prefer depopulated areas. Here, through spatially explicit simulations, we assess the effect of various density‐dependent dispersal modes on the introgression between two species. We find huge introgression from the local species into the invasive one with all dispersal modes investigated, even when the hybridization rate is relatively low. This represents a general expectation for neutral genes even if the dispersal modes differ in colonization times and amount of introgression. Invasive individuals attracted by conspecifics need more time to colonize the whole area and are more introgressed by local genes, whereas the opposite is found for solitary individuals. We applied our approach to a recent expansion of European wildcats in the Jura Mountains and the hybridization with domestic cats. We show that the simulations explained better the observed level of introgression at nuclear, mtDNA, and Y chromosome markers, when using solitary dispersal for wildcats instead of random or gregarious dispersal, in accordance with ecological knowledge. Thus, use of density‐dependent dispersal models increases the predictive power of the approach.

A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes.

Hybridization is increasingly recognized as a significant evolutionary process, in particular because it can lead to introgression of genes from one species to another. A striking pattern of discordance in the amount of introgression between mitochondrial and nuclear markers exists such that substantial mitochondrial introgression is often found in combination with no or little nuclear introgression. Multiple mechanisms have been proposed to explain this discordance, including positive selection for introgressing mitochondrial variants, several types of sex-biases, drift, negative selection against introgression in the nuclear genome, and spatial expansion. Most of these hypotheses are verbal, and have not been quantitatively evaluated so far. We use individual-based, multilocus, computer simulations of secondary contact under a wide range of demographic and genetic scenarios to evaluate the ability of the different mechanisms to produce discordant introgression. Sex-biases and spatial expansions fail to produce substantial mito-nuclear discordance. Drift and nuclear selection can produce strong discordance, but only under a limited range of conditions. In contrast, selection on the mitochondrial genome produces strong discordance, particularly when dispersal rates are low. However, commonly used statistical tests have little power to detect this selection. Altogether, these results dismiss several popular hypotheses, and provide support for adaptive mitochondrial introgression.

Loss of genetic diversity and reduction of genetic distance among lake trout Salvelinus namaycush ecomorphs, Lake Superior 1959 to 2013

North America's northern lakes are undergoing major changes. Lake Superior is the coldest and northernmost of the Laurentian Great Lakes. Here, we present an extension of a long-term data set that monitors genetic and phenotypic diversity of lake trout Salvelinus namaycush in Lake Superior. Hypotheses were investigated pertaining to loss of genetic diversity and genetic homogenization among three lake trout ecomorphs in Lake Superior during their recovery several decades after a major fishery collapse in the early 1960s. Comparison of a contemporary (2004–2013) microsatellite DNA data set to a previously published, post-collapse recovery period data set (1995–1999) indicated substantive losses in genetic diversity. Allelic richness decreased by 5.7%, 12.3%, and 6.8% at Isle Royale, Stannard Rock, and Klondike Reef, respectively. A 60.7% reduction in genetic distance among ecomorphs since the 1990s was detected. Comparisons with a third data set of samples collected during the fishery collapse (1959) indicated an overall 18.2% loss in allelic richness at Isle Royale. The amount of introgression among ecomorphs has likely increased over time. Apparent losses in genetic diversity could be a consequence of historical fishery harvests (early 1900s) exacerbated by intensive stocking (1950s–1980s) and invasions of non-native species (1960s–1990s). Overlap in foraging and breeding areas may have contributed to increasing levels of hybridization among ecomorphs. Knowledge of these processes will help to identify impediments and strategies for the maintenance of lake trout biodiversity in northern Great Lakes, and their re-establishment in the Laurentian Great Lakes.

Genetic diversity and hybridization in the two species Inga ingoides and Inga edulis: potential applications for agroforestry in the Peruvian Amazon

Slash and burn practices affect tropical forests. Our results showed strong introgression between Inga ingoides and Inga edulis in the species contact area. Interspecific hybridization could be sought to improve yield and tolerance to flooding and further increase the economic potential of the poorly drained Amazonian soils and minimize deforestation. Inga species are important components of tropical American forests, as well as a local food source. Little is known about the genetic structure of these species; in particular the amount of introgression among species remains unknown. We assessed the degree of genetic divergence and introgression among populations of I. ingoides (Rich.) Willd. and I. edulis Mart. (Fabaceae) from three Peruvian Amazon tributary rivers. Using microsatellite markers we determined the genetic structure of populations using an analysis of molecular variance and a Bayesian analysis of population structure in areas affected by seasonal river fluctuations and in ‘terra firme’ forests. Overall genetic differentiation was weak. The degree of genetic variation was similar in the two species. A putatively strong introgression was detected between the two species and an intense gene flow was identified among populations. This indicates that an intense gene flow had happened in the past, leading also to a small differentiation among populations within species. Selection of natural hybrids or artificial hybridization between I. edulis and I. ingoides could be applied to improve legume size and yield in the later species, while maintaining tolerance to flooding. Improved I. ingoides could be used in multipurpose agroforestry on open areas along the rivers, instead of using the usual slash and burn practice to create inland open areas.

Shaping species with ephemeral boundaries: the distribution and genetic structure of desert tortoise (Gopherus morafkai) in the Sonoran Desert region

AbstractAimWe examine the role biogeographical features played in the evolution of Morafka's desert tortoise (Gopherus morafkai) and test the hypothesis that G. morafkai maintains genetically distinct lineages associated with different Sonoran Desert biomes. Increased knowledge of the past and present distribution of the Sonoran Desert region's biota provides insight into the forces that drive and maintain its biodiversity.LocationSonoran Desert biogeographical region; Sonora and Sinaloa, Mexico and Arizona, USA.MethodsWe examined wild tortoises from Mexico (n = 155) and Arizona (n = 78), spanning their known distribution. We used mtDNA sequences to reconstruct matrilineal relationships and 25 microsatellite (STR) loci for Bayesian analyses of gene flow. We performed clinal analyses on both mtDNA and STR loci to determine the position and amount of introgression where lineages co‐occur. We used GIS to assess the association of genetic structuring with ecological features. We used these data in a hypothesis‐driven approach to assess different models of how genetic diversity is maintained and distributed in G. morafkai.ResultsGopherus morafkai was found to comprise genetically and geographically distinct ‘Sonoran’ and ‘Sinaloan’ lineages. Both lineages occurred in a relatively narrow zone of overlap in Sinaloan thornscrub, where it transitions into Sonoran desertscrub. Limited introgression occurred at the contact zone. The best‐fit model suggests that these lineages diverged in parapatry where the distribution of genotypes is environment‐dependent and introgression is inhibited by exogenous selection.Main conclusionsThe historically shifting ecotone between tropical deciduous forest and Sonoran desertscrub appears to be a boundary that fostered divergence between parapatric lineages of tortoises. The sharp genetic cline between the two lineages suggests that periods of isolation in temporary refugia due to Pleistocene climatic cycling influenced divergence. Despite incomplete reproductive isolation, the Sonoran and Sinaloan lineages of G. morafkai are on separate evolutionary trajectories.

Genetic evidence for human-mediated introduction of Anatolian water frogs (Pelophylax cf. bedriagae) to Cyprus (Amphibia: Ranidae)

We found in two water frogs captured in Cyprus, the distribution area of P. cypriensis, nuclear alleles and mitochondrial haplotypes that are characteristic of Anatolian water frogs, Pelophylax cf. bedriagae. Mitochondrial and nuclear DNA data strongly indicate that the ancestors of these two frogs did not arrive on Cyprus via a land bridge or overseas dispersal but were unintentionally introduced by humans, most probably together with carp fingerlings. Both individuals exhibited recombined nuclear genomes characteristic of backcross hybrids. Further investigations are needed to estimate the amount of introgression of allochthonous alleles into the gene pool of P. cypriensis.

Common bean (Phaseolus vulgaris L.) landraces in Catalonia, a Mesoamerican germplasm hotspot to be preserved

SummarySeveral landraces of common bean with high organoleptic value have resisted the rapid expansion of improved cultivars in Catalonia, in north-eastern Spain. To establish strategies for their preservation and use, we employed RAPD and AFLP markers to investigate the genetic variability within 15 landraces and to identify their original gene pools. A higher percentage of Mesoamerican landraces was found in Catalonia (40%) than in the rest of the Iberian Peninsula, or in Europe (approx. 20%). This is probably due to the exclusion of Catalonia from early trade with the American colonies and stronger commercial links with the Caribbean during the nineteenth century. Our results confirm that Catalan consumers prefer white-seeded common bean varieties of Mesoamerican origin. The landrace ‘Castellfollit del Boix’ showed 69.6% polymorphic RAPD primers, with 53.2% polymorphic bands, while at the other extreme ‘Tavella Brisa’ showed 47.8% polymorphic primers with 25.3% polymorphic bands. An AFLP approach yielded similar results. The high genetic variability found in ‘Castellfollit del Boix’, one of the landraces most threatened, suggests a considerable amount of introgression from improved inbreds.

Amount of introgression in flycatcher hybrid zones reflects regional differences in pre and post‐zygotic barriers to gene exchange

Introgression is the incorporation of alleles from one species or semispecies into the gene pool of another through hybridization and backcrossing. The rate at which this occurs depends on the frequency of hybridization and the fitness of hybrids and backcrosses compared to 'pure' individuals. The collared flycatcher (Ficedula albicollis) and the pied flycatcher (F. hypoleuca) co-exist and hybridize at low to moderate frequencies in a clinal hybrid zone in Central Europe and on the islands of Gotland and Oland off the Swedish east coast. Data on hatching success suggest that hybrids are less fertile in Central Europe compared to on the islands. Direct fitness estimates using molecular markers to infer paternity are consistent with the demographic data. Applying a tag-array-based minisequencing assay to genotype interspecific substitutions and single nucleotide polymorphisms we demonstrate that the amount of introgression from the pied to the collared flycatcher is higher in the two island populations (Gotland and Oland) than in two geographically distinct areas from the Central European hybrid zone (Czech Republic and Hungary). In all areas the amount of introgression from collared to pied flycatchers is very low or seemingly absent. The different patterns of introgression are consistent with regional differences in rates of hybridization and fitness of hybrids. We suggest that barriers to gene exchange may have been partly broken down on the islands due to asymmetric gene flow from allopatry. Alternatively, or in addition, more pronounced reinforcement of prezygotic isolation in Central Europe might have increased post-zygotic isolation through hitchhiking, since genes affecting pre and post-zygotic isolation are both sex-linked in these birds. One of our genetic markers appears to introgress from pied to collared flycatchers at a much higher rate than the other markers. We discuss the possibility that the introgressed marker may be linked to a gene which is under positive selection in the novel genetic background.

Factors influencing gene introgression into the allotetraploidCoffea arabicaL. from its diploid relatives

Factors controlling gene introgression into cultivated arabica coffee (Coffea arabica L.) were investigated. Interspecific triploid hybrid plants between the tetraploid species C. arabica (2n = 44) and a diploid species (2n = 22), either Coffea canephora or Coffea eugenioides, were backcrossed to C. arabica (male parent). Flow cytometric analysis of the nuclear DNA content revealed that most of the BC(1) individuals derived from triploid hybrids involving C. eugenioides were tetraploid or nearly tetraploid. Among the gametes produced by the interspecific triploid hybrids, those possessing approximately 22 chromosomes appeared strongly favored. The amount of introgression in BC(1) individuals (21 and 43 for the BC(1) progenies involving C. canephora and C. eugenioides, respectively) was estimated using species-specific microsatellite markers. A large number of introgressed markers was observed in all BC(1) individuals. Nevertheless, while the frequency of introgressed markers seemed as expected, assuming random chromosome segregation and diploid gamete formation, in the BC(1) derived from triploid hybrids involving C. canephora, this frequency appeared significantly lower in the BC(1) derived from triploid hybrids involving C. eugenioides. Furthermore, the comparison of reciprocal progenies between C. arabica and triploid interspecific hybrids (C. arabica x C. canephora) used as male or female parent revealed a very strong effect of the backcross direction.

Phenotypic and Molecular Evaluation of Interspecific Peanut (Arachis) Lines

Abstract Peanut breeders are constantly in search of new sources of genes that confer tolerance or resistance to biotic and abiotic stresses to improve the production and quality. The objective of this study was to evaluate peanut lines generated from interspecific crosses for amounts of wild species introgression, including genes for resistance to peanut root-knot nematodes, tomato spotted wilt virus and leaf spot diseases. Nine diploid Arachis species were crossed with peanut breeding lines and 130 different interspecific hybrid lines were developed. These lines were evaluated for the amount of introgression using RFLP analyses, plant morphology, and disease resistant phenotypes. Based on RFLPs, 41 lines showed measurable introgression and 12 hexaploid-derived lines were polymorphic for at least four probes. Greenhouse and field evaluations indicated that resistance was not present in the lines tested for tomato spotted wilt virus, early leaf spot, or Cylindrocladium black rot. However, resistance approaching that of the wild species was found for the peanut root-knot nematode (Meloidogyne arenaria) among lines derived from crosses with Arachis diogoi, A. correntina, A. batizocoi, and A. cardenasii. Introgression lines were resistant (disease ratings of 1.5 to 4.5 and lesion numbers 8 to 63) compared to Southern Runner (ratings of 5.5 to 6 and lesion numbers of nearly 500) for late leaf spot (Cercosporidium personation) in field evaluations performed in Gainesville, FL over 2 yr. The greatest resistance was found among lines from crosses with A. batizocoi, A. duranensis, A. stenosperma, A. magma, and A. diogoi. Results indicate that it should be possible to identify molecular markers to tag resistance genes for use in conventional breeding programs and stack these genes in highly productive peanut cultivars.

Intrapopulation and Interpopulation Genetic Variation of Quercus in Denmark

Native Danish oak stands are fragmented and decreasing because of the extensive use of foreign seed sources. Therefore, the population structure of natural Danish oak stands was analysed by means of six polymorphic enzyme loci. A total of 17 stands of Quercus robur L. (including an ''outgroup'' sample from The Netherlands), seven Quercus petraea [Matt.] Liebl. and two putative hybrid stands were included in the study. The average genetic diversity was similar for the two species as well as for the putative hybrid stands: 0.25 for Q. robur, 0.27 for Q. petraea and 0.26 for the hybrid stands. The genotypic proportions at two (Pgm and Mnr) of the six loci showed many significant deviations from Hardy-Weinberg expectations, always with an excess of homozygotes, whereas the remaining four loci accorded to Hardy-Weinberg proportions, suggesting a low level of inbreeding. The differentiation of the Q. petraea and Q. robur populations was quantified with Wright's F-statistics. The within-species component was low, 0.022, reflecting the wind-pollinated reproductive mode of the two species. The betweenspecies component was 10-fold higher, 0.235, indicating two separate groups. A phylogenetic tree estimated from allele frequencies also supported the presence of these two groups. Despite the two well-separated groups in the tree, it was not possible to assign all individuals to the species to which they supposedly belonged. In total, 10% of the Q. robur individuals and 14% of the Q. petraea individuals were assigned to the other species, suggesting a limited amount of introgression between the two species.

Frequency of interspecific matings and of hybrid offspring in sympatric populations of Viviparus ater andV. contectus (Mollusca: Prosobranchia)

In species pairs able to produce fertile hybrids, the amount of introgression can be limited by the frequency of interspecific copulations. We investigated the frequency of interspecific copulations between Viviparus ater and V. contectus and the proportion of hybrid offspring of V. ater females in natural populations in northern Italy. Although there was significant assortative mating, the frequency of interspecific copulations was substantial. At sites where V. contectus was rare, 5.9% of all matings, and up to 73% of matings in which V. contectus was involved, were interspecific. At sites where both species were abundant 14.8% of all matings were interspecific. Male–male matings occurred in approximately 3% of copulations. In 1993, 12 out of 325 V. ater females collected from 10 sympatric populations and held in isolation for two to five months gave birth to 25 hybrid offspring, out of a total of 2548 offspring produced by all females. The proportion of hybrid offspring (ranging from 0 to 2.3% depending on the site) was positively related to the proportion of V. contectus in the population. Since interspecific copulations are frequent and hybrid offspring are produced in nature, we conclude that assortative mating is not an effective isolating mechanism between V. ater and V. contectus.

Frequency of interspecific matings and of hybrid offspring in sympatric populations of Viviparus ater and V. contectus (Mollusca: Prosobranchia)

In species pairs able to produce fertile hybrids, the amount of introgression can be limited by the frequency of interspecific copulations. We investigated the frequency of interspecific copulations between Kviparus ater and V. contectus and the proportion of hybrid offspring of V. ater females in natural populations in northern Italy. Although there was significant assortative mating, the frequency of interspecific copulations was substantial. At sites where V. contectus was rare, 5.9% of all matings, and up to 73% of matings in which V. contectus was involved, were interspecific. At sites where both species were abundant 14.8% of all matings were interspecific. Male-male matings occurred in approximately 3% of copulations. In 1993, 12 out of 325 V. ater females collected from 10 sympatric populations and held in isolation for two to five months gave birth to 25 hybrid offspring, out of a total of 2548 offspring produced by all females. The proportion of hybrid offspring (ranging from 0 to 2.3% depending on the site) was positively related to the proportion of V. contectus in the population. Since interspecific copulations are frequent and hybrid offspring are produced in nature, we conclude that assortative mating is not an effective isolating mechanism between V. ater and V. contectus.

NATURAL HYBRIDIZATION BETWEEN <i>PLATICHTHYS</i> <i>STELLATUS</i> AND <i>KAREIUS BICOLORATUS</i>

Allelic isozymes were examined in Platichthys stellatus and Kareius bicoloratus collected in Sendai Bay. Of the 32 genetic loci examined, the 9 loci were divergent and the other loci were non-divergent and polymorphic. With one exception, all of these divergent loci were polymorphic in P. stellatus but the commonest alleles were different from these homozygous in K. bicoloratus. The secondary alleles of these loci were identical to those homozygous in K. bicoloratus.A comparison was made between biochemical and morphological characters to detect natural hybrides in fish populations. The dextral fishes of P. stellatus showed hybrid patterns in all of the 9 divergent loci, indicating that they were F1 hybrids between P. stellatus and K. bicoloratus. From the distribution and frequencies of the secondary alleles in P. stellatus population, an amount of introgression between both species can be estimated.

Protein Variation in Several Species of Hyla

Case, S. M., Haneline, P. G., and M. F. Smith (Museum of Vertebrate Zoology, University of California, Berkeley, California 94720) 1975. Protein variation in several species of Hyla. Syst. Zool. 24:281-295.-Allelic variation at fourteen loci coding for ten enzymes was studied in seventeen populations of Hyla regilla and in H. eximia, H. wrightorum, H. cadaverina, and H. euphorbiacea. Heterozygote deficiencies were found at several loci in several populations of H. regilla and possible reasons are suggested. The proportion of polymorphic loci and average individual heterozygosity were typical of other vertebrates with some exceptions: (1) the Lee's Camp, Oregon population; (2) the Santa Cruz Island population; (3) the three San Diego Co. populations; (4) the Sierra San Pedro Martyr population; and (5) the three populations in southern Baja California. Measures of genetic similarity (S) and genetic distance (D), as well as patterns of variation in allele frequencies at PGI and IDH-2, suggested three groups within Hyla regilla. These were: (1) the four Oregon populations; (2) the three central California populations; and (3) the ten southern California and Baja populations. The proportion of major alleles shared indicated Hyla eximia and H. wrightorum, are very closely related and that H. wrightorum is not a subspecies of H. regilla; H. eximia and H. wrightorum are also closely related to H. euphorbiacea. Hyla regilla and H. cadaverina are more closely allied to each other than they are to the other three forms. A strong correlation (r = 0.93) between genetic relatedness as measured by immunological comparisons of albumin and that measured by electrophoretic studies of many proteins was found, although immunological techniques cannot be used to study taxa which are very closely related (D = 0.25 or less). [Proteins; genetics; Hylidae] Since the pioneering work of Lewontin & Hubby (1966) attention has been focused on the amount and significance of genic variation in local populations. Subsequently electrophoresis has been used to study various aspects of local population genetics and the relationships among species (see Selander & Johnson, 1973 for a review). A number of electrophoretic studies of anurans have been conducted (Dessauer & Nevo, 1969; Gartside, 1972; Guttman & Wilson, 1973; Maxson & Wilson, 1974a; Platz & Platz, 1973; Rogers, 1973a and b; Salthe, 1969; Salthe & Nevo, 1969). The scope of these works is wide, ranging from an analysis of variation at a few loci as a method of assessing amounts of introgression to a survey of variation at a large number of loci in an effort to determine the overall level ' California Academy of Sciences, San Francisco, California; Present address: Department of Amiphibians and Reptiles, Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138. of genic variation and to examine genetic relationships between two or more forms. No detailed study of the latter type has been done with any members of the genus Hyla. The main purpose of this study was to determine the amount of genic variation within and the genetic distance between populations of Hyla regilla. This is of particular interest since this species ranges from British Columbia to the tip of Baja California and has been divided into ten subspecies by Jameson, et al. (1966) on the basis of a discriminate analysis of morphological characters. Maxson & Wilson (1974b) have compared the serum albumins of eight of these subspecies using the method of microcomplement fixation. Electrophoretic estimates of genetic distance can provide an independent method for detecting subgroups within this wide-ranging species. In addition, several other members of the Hyla eximia group, in which H. regilla