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PubMed1993

Challenges and opportunities for integrating genetically modified animals into traditional animal breeding plans.

Techniques have been developed to introduce specific genes from one species into the germplasm of another, including livestock. This paper reviews reports on evaluation, selection, and breeding procedures for introduction and multiplication of transgenes in breeding populations of livestock. Before transgenes are introduced and multiplied in commercial breeding populations, it is necessary to test transgenics extensively for both favorable and unfavorable transgene effects. Parent stock used to produce transgenic founder animals should be selected to excel in polygenic breeding value for economically important traits, especially if founder animals or their sons are to be used directly by AI in commercial populations. However, polygenic breeding value of founder transgenic animals and inbreeding depression are of negligible importance if a transgene is introgressed into a selection nucleus population from three or four generations of backcrossing. Transgenic development should be economically viable for traits with major effects on net merit, especially in the dairy industry, where transgenic sires can be used extensively by AI. A minimum effect of about 10% of the mean (or one phenotypic standard deviation) is a reasonable approximation of the minimum transgene effect that would be necessary to justify introgression into a nucleus swine population. A transgene effect of 10 to 20% of the mean would be required for most economic traits in beef cattle.

Animals↗

PubMed2025

Whole Genome Development of Specific Alien-Chromosome Oligo (SAO) Markers for Wild Peanut Chromosomes Based on Chorus2.

The cultivated peanut (Arachis hypogaea L.) is a globally important oilseed and economic crop, but its narrow genetic base limits breeding progress. Wild Arachis species represent valuable genetic resources for enhancing the resilience of the peanut cultigen. While wild species from section Arachis are widely used in breeding programs, the detection of alien chromosomes in hybrids remains challenging due to limited molecular tools. In this study, a cost-effective and efficient system was established for generating species-specific molecular markers using low-coverage next-generation sequencing data, bypassing the need for whole-genome assembly. Utilizing the Chorus2 software, specific alien-chromosome oligo (SAO) markers were developed for four wild species, A. duranensis (accession A19), A. pusilla (A10), A. appresipilla (A33), and A. glabrata (G2 and G3). A total of 1166 primer pairs were designed, resulting in 220 SAO markers specific to A. duranensis, 77 to A. pusilla, 112 to A. appresipilla, 69 to A. glabrata G2, and 59 to A. glabrata G3, with the highest development efficiency observed in A. duranensis (55.0%). These markers span all chromosomes of the five wild accessions. Genome-wide, chromosome-specific SAO markers enable the efficient detection of introgressed alien chromosomes and provide insight into syntenic relationships among homoeologous chromosomes. These markers offer an effective tool for identifying favorable genes and facilitating targeted introgression for the genetic improvement of the cultivated peanut.

Chorus2↗

PubMed2026

Evaluating three alternative scenarios for the origin of a disjunct Arctium tomentosum population in the Pyrenees.

BACKGROUND: Disjunctions in species distributions offer natural experiments for investigating the mechanisms underlying distributional breaks, such as range contraction, long-distance pollen transport, or long-distance seed dispersal. Here, we document and characterise a floristic novelty in the Pyrenean and Iberian regions, and use it as a case study to investigate the processes underlying disjunct species distributions. Our analysis focuses on Arctium L. (burdocks), a genus native to Eurasia comprising several cosmopolitan weedy species. It is characterised by hooked capitula that facilitate epizoochorous dispersal. METHODS: To clarify the taxonomic identity of a previously undocumented Pyrenean population resembling A. tomentosum, we adopted an integrative approach, combining distribution information, morphology, genome size, repetitive DNA analysis and chloroplast data across the four known European species. Additionally, we conducted a comparative study of functional capitulum traits, predispersal fruit predation, and associated entomofauna for the newly discovered population and nearby A. minus populations. RESULTS: The discovered population constitutes a floristic novelty for the region and is identified as A. tomentosum, exhibiting signatures of past introgression from A. minus, as indicated by cytonuclear discordance. We evaluated three alternative scenarios to explain its origin: (i) persistence as a relict from a previously wider distribution, (ii) long-distance pollination by migrating insects, and (iii) long-distance seed dispersal from an A. tomentosum population with a history of past introgression. Of these, only the third is consistent with the available evidence. These results highlight the complexity of interpreting disjunct species distributions and underscore the value of integrative approaches for resolving population identity, origin, dispersal, and persistence across environments.

Arctium↗

PubMed1997

[Gene diffusion in hybrid populations of green frogs Rana esculenta L., 1758 complex (Amphibia, Ranidae) from the Dnepr Basin].

Population-genetic analysis of hybrid populations of green frogs from the Dnepr basin demonstrated limited gene introgression in diploid hybrids in addition to semiclonal reproduction, which is typical for Rana esculenta hybrids. Introgression is largely confined to the Ldh-B locus: the gene of R. lessonae is introduced into the R. ridibunda genome. This phenomenon is unstable as it is geographically restricted and absent in populations of the E-L type.

Animals↗

PubMed1998

Paternal directional mating in two Amerindian subpopulations located at different altitudes in northwestern Argentina.

We used mitochondrial DNA (mtDNA) and Y-chromosome DNA polymorphisms to analyze the ethnic origin of maternal and paternal lineages in two Amerindian subpopulations from northwestern Argentina. One of the subpopulations was from San Salvador de Jujuy, located 1200 m above sea level. The second subpopulation inhabits the Quebrada de Humahuaca area at altitudes ranging from 2500 to 3500 m. Both subpopulations have the same ethnic background. All mtDNA haplotypes were identified as Amerindian with a frequency of 64.6% of the B form (9-bp deletion in mtDNA region V). Because all Central Andean Amerindian populations studied so far exhibit high frequencies of the B haplotype, we propose that they probably are derived from a common ancestral population that inhabited the Central Andes 6000-8000 years B.P. The presence of paternal directional mating (asymmetric contribution of one parental lineage to interethnic gene mixtures) was demonstrated by the finding of an average introgression of 40.5% Spanish Y chromosomes into our Amerindian sample. This introgression was more evident at low altitude than at high altitude, with frequencies of 64.3% in San Salvador de Jujuy (low altitude) and 27.6% in Quebrada de Humahuaca (high altitude) (p < 0.05). The San Salvador de Jujuy subpopulation also showed a significantly higher Y-chromosome gene variability than the Quebrada de Humahuaca subpopulation. These findings are in good agreement with historical reports indicating that the colonization of South America was undertaken by men who usually practiced polygamous unions with Amerindian women and that San Salvador de Jujuy was the main northwestern Argentinian region of European to Amerindian gene admixture. We found 16.7% of cases with Spanish Y chromosomes and Amerindian family names, and the same percentage with Amerindian Y chromosomes and Hispanic names. The former group probably is the result of unions between Hispanic men, who transmitted the Y chromosome, and Amerindian women, who transmitted the family name to the progeny. The latter group likely illustrates the practice of changing names from Amerindian to Hispanic during the baptism of native Americans in colonial times.

Adult↗

PubMed2026

Phylotranscriptomics Allows Distinguishing Major Gene Flow Events from Incomplete Lineage Sorting in Rapidly Diversifying Mimetic Orchids (Genus Ophrys).

Ophrys orchids (or bee orchids) provide an outstanding example of a plant adaptive radiation. Over the last 5 million years, this genus has diversified into hundreds of taxa as a result of its unconventional pollination strategy, known as "sexual swindling". However, the rapid and substantial diversification of this genus, combined with its capacity for hybridization and large genome size, poses significant challenges in addressing its systematics. We used phylotranscriptomics as a genome complexity reduction technique to infer the phylogenetic relationships among Ophrys main lineages. More than seven thousand gene trees enabled us to determine the relative contributions of gene flow and incomplete lineage sorting (ILS) in Ophrys evolution. First, we propose a new phylogenetic hypothesis for the genus with an unprecedented resolution that largely confirms the relationships between the main Ophrys lineages, but also provides new insights within each subgenera. By combining phylogenetic network inference with introgression analyzes based on gene tree topologies and branch lengths, we then show that the numerous phylogenetic incongruences among gene tree topologies result from a pervasive background of ILS, over which stand out several well-supported, ancient and potentially adaptive gene flow events between lineages. These major gene flow events provide a new perspective on the evolution of the Ophrys genus and its pollination, questioning previous hypotheses inferred without considering its reticulate evolution, and providing a better understanding of discrepancies observed among previous phylogenetic studies of the genus.

Orchidaceae↗

PubMed2025

Pleistocene island connectivity did not enhance dispersal or impact population size change in Galápagos geckos.

Patterns of biodiversity on remote archipelagos are largely shaped by intra-archipelago colonization followed by in situ diversification. Pleistocene sea-level fluctuations purportedly enhanced gene flow among terrestrial organisms by increasing connectivity during periods of lower sea level. Furthermore, changes in sea-level are hypothesized to impact population sizes as a result of fluctuations in island sizes. Here, we used genomic data to test the role of Pleistocene island connectivity on the diversification and demographics of leaf-toed geckos (Phyllodactylus) endemic to the Galápagos. Consistent with previous studies, we found that present diversity of Galápagos Phyllodactylus stems from three independent dispersal events. Contrary to the hypothesis of Pleistocene-driven diversification, we found no correspondence between lineage divergence and island connectivity. Furthermore, we found no evidence of introgression; demographic modelling indicated that all species increased rapidly in effective population size in the period 20-150 ka, and these inferred demographic expansions were largely asynchronous and apparently unassociated with species or island age. Collectively, these results indicate that more complex abiotic and/or biotic factors may better explain the recent demographic history of Phyllodactylus and underscore the need for additional population genomic studies of terrestrial taxa to understand the impact of past climate cycles on Galápagos island communities.

Animals↗

PubMed2025

Mapping Species Birth Across the Recombination Landscapes of Marine Snails.

Understanding the drivers of heterogeneous genomic divergence is essential for uncovering the mechanisms that generate and constrain biodiversity. The extent to which adaptation and speciation are facilitated by reorganisation of the recombination landscape remains untested in many systems. Marine ecosystems, with their dynamic and fluid habitats, offer a compelling context to investigate genomic divergence. In this study, we mapped genomic divergence and selection across recombination landscapes of parapatric marine snail sister species that we show have recently undergone secondary contact. Regions of reduced recombination were enriched for genes exhibiting signatures of negative selection, whereas regions of high recombination were associated with genes under putative positive selection. Notably, the recombination landscape of the population in parapatry of one species (Scurria viridula) differs markedly from that of the other population within this same species, highlighting the role of introgression in reshaping recombination landscapes. In the other species (Scurria zebrina), conservation of the recombination landscape and divergent selection among populations suggest trapping of beneficial allele combinations in regions of low recombination maintains the identity of this species. Among species, signals of divergence with gene flow consistently cluster within specific genomic regions characterised by high recombination rate variation among the populations of S. viridula. These results challenge traditional theoretical expectations of recombination evolution by showing that the causes of genomic divergence can be population-specific. This study demonstrates that recombination landscapes are key modulators of genomic divergence, with contemporary evolutionary shifts that could enable populations to adapt to distinct environments. Our findings provide new insights into the interplay between recombination, selection, and gene flow during speciation, underscoring the complexity of evolutionary trajectories in marine systems.

Genetic Introgression↗

PubMed2025

Repeatable Genomic Outcomes Along the Speciation Continuum: Insights From Pine Hybrid Zones (Genus Pinus).

Hybridization is a widespread evolutionary process and a key source of evolutionary novelty. Despite intensive study, the extent to which hybridization is deterministic and repeatable, particularly in recurrent contact events involving the same species under varying ecological conditions, remains unclear. Here, we investigated three replicated contact zones between Scots pine (Pinus sylvestris) and dwarf mountain pine (Pinus mugo) in Central Europe: two occurring in peatland habitats and one in a contrasting sandstone outcrop. Using genome-wide SNP genotyping of over 1300 individuals, we analysed genomic structure, diversity, and ancestry patterns across these zones. All sites revealed pervasive hybridization, dominated by later-generation hybrids and a notable scarcity of pure P. mugo. Across environments, hybrid populations exhibited strikingly consistent genomic compositions, with asymmetric introgression strongly biased toward P. mugo ancestry, suggesting that hybrid genome structure may follow predictable patterns under similar ecological conditions and could be shaped by cytonuclear incompatibilities. Nonetheless, we also detected site-specific differences in hybrid diversity and phenotype, highlighting the influence of local environmental selection on shared hybrid genomic backgrounds. We provide genomic evidence that Pinus uliginosa, a morphologically distinct peat bog pine traditionally regarded as a relict and endangered species is instead a partially stabilised hybrid lineage. Its genome reflects incomplete hybridization and ecological filtering, yet it lacks sufficient genetic divergence to be recognised as a distinct species. Together, these results provide evidence for the repeatability of hybridization processes, which result in the formation of phenotypes reflecting a species continuum subjected to strong environmental pressures. The findings support the simplification of taxonomic nomenclature within the Pinus mugo complex, informing adaptive conservation strategies and the genetic management of hybrid lineages.

Hybridization, Genetic↗

PubMed2026

A Cis-Regulatory Duplication in a Hox Hotspot Implicated in Mimetic Convergence in the Bumble Bee Bombus flavifrons.

Several species of North American bumble bees spanning the Pacific Coastal and Rocky Mountain regions converge onto distinct mimetic abdominal colour forms for each region by switching abdominal coloration from black to red. Previous genome-wide association studies (GWAS) of red and black transitions in two mimics (Bombus melanopygus and Bombus vancouverensis) revealed that black forms were generated by independently deleting a portion of the same cis-regulatory region near the Hox gene Abdominal-B (Abd-B). Here, we test the genetic basis of these mimetic colour forms in a third co-mimic, Bombus flavifrons, that has continuous variation in red and black that is shifted posteriorly one segment compared to its co-mimics. Using genome-wide association of red and black forms, we identified a structural variant < 50 bp away from the deletions in B. melanopygus and B. vancouverensis that was strongly associated with the colour phenotype. Sequencing across mimicry zones and closely related taxa revealed that all red forms of B. flavifrons and monomorphic red close relative Bombus centralis have a 319 bp tandem duplication at this locus that has extensive modification to the duplicated copy. Black forms of B. flavifrons from the Cascades also have this duplication but without the modifications, while black forms in the western Rockies mostly lack this duplication, similar to ancestral black forms. This suggests independent mechanisms may regulate the black phenotypes in different populations and that ancestral sorting of variation and/or adaptive introgression generated these phenotypes. This study strengthens support for this Abd-B cis-regulatory region being a hotspot for regulating abdominal coloration in bumble bees, and features the role of regulatory region duplication in creating novel phenotypes.

Animals↗

PubMed1997

Confirmation and location of the hybrid zone between wild populations of Macaca tonkeana and Macaca hecki in central Sulawesi, Indonesia.

Reports of hybridization between Macaca tonkeana and Macaca hecki were investigated in Central Sulawesi, Indonesia. We defined sets of morphological traits that were diagnostic for M. tonkeana and M. hecki and then located an areas where animals had intermediate or mosaic features. Hybridization as indicated by morphology was detected between M. tonkeana and M. hecki. The hybrid zone appeared to be strongly centered at the road that crosses the isthmus of Central Sulawesi from Tawaeli to Toboli. Macaques in this region were not morphologically uniform; animals from the western area of the Tawaeli-Toboli road resembled M. hecki, while animals from the eastern area resembled M. tonkeana. The hybrid zone was found to be smaller than previously thought, with maximum dimensions of approximately 15 and 7.5 km. Clines for diagnostic morphological features were broadly coincident, suggesting that the hybrid zone originated by secondary contact. Analysis of three museum specimens collected in 1916 provided evidence that the hybrid zone has been in existence since at least then. The narrow width of the hybrid zone, along with its age, suggested that some prezygotic or postzygotic barrier must exist to full introgression between M. tonkeana and M. hecki.

Animals↗

PubMed1995

Polymerase chain reaction-based assays for the characterisation of plant genetic resources.

Plant genetic resources are an important component of biodiversity and provide the basic genetic variability that allow new and improved cultivars to be developed. Numerous germplasm collections have been established and it is important to established that such collections are representative and accessible to breeders and biotechnologists. Molecular markers provide the best estimate of genetic diversity since they are independent of the confounding effects of environmental factors. Assays based on the polymerase chain reaction (PCR) are considered to meet both the technical and genetical requirements for the characterisation of plant and animal genetic resources. Two main approaches are described, based on anonymous and defined primers. The use of both randomly amplified polymorphic DNA (RAPD) and microsatellites or simple sequence repeats (SSR) for the characterisation of perennial tree species, and distribution of variability within gene pools is reported. The detection of interspecific gene introgression between coffee species with RAPD markers is described together with the use of microsatellites to genotype potato. The use of PCR-based assays will facilitate the evaluation and utilisation of plant genetic resources.

Base Sequence↗

PubMed1995

Polymorphism at VNTR locus 3 to the apolipoprotein B gene in a Tunisian population: difference from other ethnic groups.

The Hypervariable region (HVR) detected at the 3' end of the apolipoprotein B (Apo B) locus has been the subject of numerous studies. As for many VNTR (variable number of tandem repeat), this locus is highly polymorphic and until now about 20 alleles have been described. The genotype distribution in all populations follows the Hardy-Weinberg predictions. A bimodal pattern of allele frequency distribution is apparent in all Caucasoid populations. We have analyzed the frequencies of different alleles in a Tunisian population (123 individuals) by the polymerase chain reaction technique and compared our results to those obtained in several ethnic groups. It appears that the distributions of the allele frequencies are very different: for Caucasoid populations, there are two peaks of frequencies for alleles with 36 and 48 repeats, but alleles of intermediate lengths are more frequent. Hixson et al. [(1993) Hum Genet 91:475-479] have shown a similar difference between black and white American populations. We found the same results in a black African group. Some of the repeat units of this HVR contain a Ssp I restriction site and digestion of the PCR products by this enzyme gives different patterns on gradient acrylamide gel [Desmarais et al., 1993, Nucleic Acids Res 21:2179-2184.] The DNA of African individuals (42) has been analyzed to discover the origin of this new allele. Preliminary results indicate that these particular alleles probably arose by introgression from the African population into the Tunisian one.

Alleles↗

PubMed1998

Olfactory preferences in two strains of wild mice, Mus musculus musculus and Mus musculus domesticus, and their hybrids.

We studied olfactory preferences of two strains of mice, Mus musculus musculus and Mus musculus domesticus (considered here to be subspecies), and their hybrids, to examine the possible role of odours as a behavioural, premating mechanism that could explain the characteristics of their natural hybrid zone. We used a choice test with the bedding material of animals of the opposite sex from the animal tested and from both subspecies. Male and female M. m. domesticus showed no preference either for their own subspecies' odours or for the other subspecies' odours. In contrast, M. m. musculus individuals and three types of hybrids (all the female hybrids and males from crosses between an M. m. musculus female and an M. m. domesticus male) sniffed for longer at materials from the musculus source than from the domesticus source. We interpreted the results as a preference for musculus odours. Differences between the two subspecies in their response towards consubspecific and heterosubspecific odours could explain the asymmetrical introgression observed in the hybrid zone.Copyright 1998 The Association for the Study of Animal Behaviour

Journal Article↗

PubMed1998

Linkage analysis and construction of a congenic strain for a blood pressure QTL on rat chromosome 9.

A blood pressure quantitative trait locus was found (LOD = 5.0) on rat chromosome 9 using a large F2 population (N = 233) derived from Dahl salt-sensitive (S) and Dahl salt-resistant (R) rats. The F2 rats were fed 8% NaCl diet for 8 weeks. A congenic strain introgressing the R low-blood-pressure QTL allele on chromosome 9 into the S strain was constructed. The congenic strain, designated S.R(chr 9), had a lower blood pressure (19 mm Hg, P < 0.0001) and lower heart weight (112 mg, P < 0.0001) than S rats (2% NaCl diet for 24 days), proving the existence of a blood pressure QTL in the congenic region of about 21 cM.

Animals↗

PubMed1995

Phylogeny of six Sciurus aberti subspecies based on nucleotide sequences of cytochrome b.

The tassel-eared squirrel, Sciurus aberti, is separated into six subspecies which occupy restricted and comparable habitats in ponderosa pine forests in the south-western United States and Mexico. These forests and squirrel populations are currently isolated by large arid areas and, as such, S. aberti appears to offer an example of incipient speciation. We sequenced the complete mitochondrial cytochrome b gene to construct a molecular phylogeny for S. aberti and to determine whether subspecific genetic structure and geographic patterns are correlative. Twenty alleles were identified among 612 squirrels throughout the species' range. Nucleotide divergence between alleles ranged from 0.009 to 0.0233, whereas average sequence divergence between S. aberti and an outgroup species, Sciurus niger, was 0.1823. Neighbor-joining and maximum parsimony analyses identified three major genetic assemblages composed of the following subspecies groups: (1) barberi and durangi; (2) aberti and kaibabensis; and (3) ferreus. The chuscensis samples were the only population with divergent sequences; one sequence was identical to an aberti sequence and a second unique sequence clustered with the ferreus sequences. The presence of divergent sequences in the chuscensis population, coupled with its central geographic position between aberti and ferreus, suggests a relatively recent influx of aberti mtDNA. Estimates of the times separating sequences in subspecies within different groups ranged from 0.94 to 1.52 x 10(6) years, based on a rate estimate of 7.15 x 10(-9) substitutions/year/site. The limited divergence observed between (1) aberti and kaibabensis as well as (2) barberi and durangi suggests relatively recent separations of subspecies within each assemblage. In fact, populations defined morphologically and geographically as ferreus exhibited greater sequence divergence than the aforementioned groups, identifying ferreus as the subspecies with the greatest genetic substructuring. The levels of cytochrome b divergence observed for the three distinct groups argues against a significant role for late Pleistocene glaciation in dispersal of this particular species; however, the proposed intermixing of aberti and chuscensis populations may well have been associated with such glacial events. Nucleotide diversity within subspecies ranked chuscensis >> aberti > barberi approximately kaibabensis approximately ferreus subpopulations; the relatively high level of diversity of chuscensis samples likely results from the apparent introgression of an aberti haplotype. The comparative levels of diversity in the aberti, barberi, kaibabensis, and ferreus sample populations do not correlate with respective habitat size (and presumably population size), suggesting that relatively recent forces, e.g., glaciation and inconsistent timber harvests, may have influenced diversity in these populations without apparent alterations in population size.

Amino Acid Sequence↗

PubMed1995

Phylogenetic analysis of Pacific salmon (genus Oncorhynchus) based on mitochondrial DNA sequence data.

Previous phylogenetic analyses of the fishes belonging to the genus Oncorhynchus based on mitochondrial DNA data have produced conflicting trees. This is especially true with respect to the relationships among the three most derived Pacific salmon species, the pink salmon (Oncorhynchus gorbuscha), sockeye salmon (Oncorhynchus nerka), and chum salmon (Oncorhynchus keta). Smith (Syst. Biol. 41(1): 41-57, 1992) suggested that introgression in opposite directions on either side of the Pacific ocean may account for some of the conflicting data. The ATPase 6 and ND3 mitochondrial genes were sequenced from Asian and North American representatives of several species of Pacific salmon and the aligned sequences were analyzed along with other data on these genes. Analysis of the ATPase 6 and ND3 sequence data and RFLP data gives strong support for a sister relationship between pink salmon and chum salmon.

Adenosine Triphosphatases↗

PubMed1997

Phylogenetic relationships within genus Leuciscus (Pisces, Cyprinidae) in Portuguese fresh waters, based on mitochondrial DNA cytochrome b sequences.

To investigate phylogenetic relationships among Leuciscus species occurring in Portuguese inland waters, the cytochrome b gene was sequenced from representatives of the main rivers. This study supports the recognition of the species level for L. pyrenaicus, including populations from the southern Portuguese drainages (Tejo, Sado, and Guadiana drainages), and for L. carolitertii, including populations from the northern Portuguese drainages. The existence of two new species occurring in the extreme southwestern drainages of Mira and Arade is also suggested. The present results support the monophyly of the Mira and the Arade populations, as well as an early divergence of these two lineages. The present-day distribution of Leuciscus species is seen as a consequence of Pliocene and Pleistocene events, such as river disjunctions and posterior confluence in epicontinental seas and river captures. A mixture of haplotypes was observed in the Mondego and the Tejo drainages, which could be a consequence of ancient river captures, with a possible mitochondrial DNA introgression in the Tejo drainage and a recent introduction by man in the Mondego drainage. The pattern of differentiation among mtDNA haplotypes and their geographic distribution is discussed in terms of evolutionary aspects.

Animals↗