Literatura académica sobre el tema "Ancestral introgression"

The importance of introgressive hybridization in plant evolution has long been recognized. Nevertheless, information on gene flow between allopolyploids and their diploid relatives is very limited, even though gene flow could play a major role in polyploid establishment and evolution. Here, we investigated the processes governing hybrid formation and introgression between the allotetraploid Coffea arabica and one of its ancestral diploid progenitors, C. canephora, in a sympatric zone of New Caledonia. The occurrence of a large assortment of hybridization events between the 2 coffee species is clearly established. First-generation hybrids (F1) and post-F1 hybrids were characterized. The involvement of unreduced gametes of C. canephora is suggested, because tetraploid F1 hybrid plants were detected. Moreover, although bidirectional mating was observed, only unidirectional gene flow from C. canephora to C. arabica was noted in post-F1 hybrids. Most of the collected post-F1 hybrid plants exhibited a high level of introgression, and the frequency of introgression observed among the different analyzed loci was homogeneous, suggesting no significant counterselection against introgressions from C. canephora. Overall, the New Caledonian central mountains appear to be a highly favourable environment for introgressive hybridization and a genetic diversity center for C. arabica.

While often deleterious, hybridization can also be a key source of genetic variation and pre-adapted haplotypes, enabling rapid evolution and niche expansion. Here we evaluate these opposing selection forces on introgressed ancestry between maize (Zea mays ssp. mays) and its wild teosinte relative, mexicana (Zea mays ssp. mexicana). Introgression from ecologically diverse teosinte may have facilitated maize’s global range expansion, in particular to challenging high elevation regions (> 1500 m). We generated low-coverage genome sequencing data for 348 maize and mexicana individuals to evaluate patterns of introgression in 14 sympatric population pairs, spanning the elevational range of mexicana, a teosinte endemic to the mountains of Mexico. While recent hybrids are commonly observed in sympatric populations and mexicana demonstrates fine-scale local adaptation, we find that the majority of mexicana ancestry tracts introgressed into maize over 1000 generations ago. This mexicana ancestry seems to have maintained much of its diversity and likely came from a common ancestral source, rather than contemporary sympatric populations, resulting in relatively low FST between mexicana ancestry tracts sampled from geographically distant maize populations. Introgressed mexicana ancestry in maize is reduced in lower-recombination rate quintiles of the genome and around domestication genes, consistent with pervasive selection against introgression. However, we also find mexicana ancestry increases across the sampled elevational gradient and that high introgression peaks are most commonly shared among high-elevation maize populations, consistent with introgression from mexicana facilitating adaptation to the highland environment. In the other direction, we find patterns consistent with adaptive and clinal introgression of maize ancestry into sympatric mexicana at many loci across the genome, suggesting that maize also contributes to adaptation in mexicana, especially at the lower end of its elevational range. In sympatric maize, in addition to high introgression regions we find many genomic regions where selection for local adaptation maintains steep gradients in introgressed mexicana ancestry across elevation, including at least two inversions: the well-characterized 14 Mb Inv4m on chromosome 4 and a novel 3 Mb inversion Inv9f surrounding the macrohairless1 locus on chromosome 9. Most outlier loci with high mexicana introgression show no signals of sweeps or local sourcing from sympatric populations and so likely represent ancestral introgression sorted by selection, resulting in correlated but distinct outcomes of introgression in different contemporary maize populations.

The genomic era has made clear that introgression, or the movement of genetic material between species, is a common feature of evolution. Examples of both adaptive and deleterious introgression exist in a variety of systems. What is unclear is how the fitness of an introgressing haplotype changes as species diverge or as the size of the introgressing haplotype changes. In a simple model, we show that introgression may more easily occur into parts of the genome which have not diverged heavily from a common ancestor. The key insight is that alleles from a shared genetic background are likely to have positive epistatic interactions, increasing the fitness of a larger introgressing block. In regions of the genome where few existing substitutions are disrupted, this positive epistasis can be larger than incompatibilities with the recipient genome. Further, we show that early in the process of divergence, introgression of large haplotypes can be favored more than introgression of individual alleles. This model is consistent with observations of a positive relationship between recombination rate and introgression frequency across the genome; however, it generates several novel predictions. First, the model suggests that the relationship between recombination rate and introgression may not exist, or may be negative, in recently diverged species pairs. Furthermore, the model suggests that introgression that replaces existing derived variation will be more deleterious than introgression at sites carrying ancestral variants. These predictions are tested in an example of introgression in Drosophila melanogaster, with some support for both. Finally, the model provides a potential alternative explanation to asymmetry in the direction of introgression, with expectations of higher introgression from rapidly diverged populations into slowly evolving ones.

Introgression is a common evolutionary phenomenon that results in shared genetic material across non-sister taxa. Existing statistical methods such as Patterson’s D statistic can detect introgression by measuring an excess of shared derived alleles between populations. The D statistic is effective to detect genome-wide patterns of introgression but can give spurious inferences of introgression when applied to local regions. We propose a new statistic, D+, that leverages both shared ancestral and derived alleles to infer local introgressed regions. Incorporating both shared derived and ancestral alleles increases the number of informative sites per region, improving our ability to identify local introgression. We use a coalescent framework to derive the expected value of this statistic as a function of different demographic parameters under an instantaneous admixture model and use coalescent simulations to compute the power and precision of D+. While the power of D and D+ is comparable, D+ has better precision than D. We apply D+ to empirical data from the 1000 Genome Project and Heliconius butterflies to infer local targets of introgression in humans and in butterflies.

Recent studies suggest that admixture with archaic hominins played an important role in facilitating biological adaptations to new environments. For example, interbreeding with Denisovans facilitated the adaptation to high-altitude environments on the Tibetan Plateau. Specifically, the EPAS1 gene, a transcription factor that regulates the response to hypoxia, exhibits strong signatures of both positive selection and introgression from Denisovans in Tibetan individuals. Interestingly, despite being geographically closer to the Denisova Cave, East Asian populations do not harbor as much Denisovan ancestry as populations from Melanesia. Recently, two studies have suggested two independent waves of Denisovan admixture into East Asians, one of which is shared with South Asians and Oceanians. Here, we leverage data from EPAS1 in 78 Tibetan individuals to interrogate which of these two introgression events introduced the EPAS1 beneficial sequence into the ancestral population of Tibetans, and we use the distribution of introgressed segment lengths at this locus to infer the timing of the introgression and selection event. We find that the introgression event unique to East Asians most likely introduced the beneficial haplotype into the ancestral population of Tibetans around 48,700 (16,000–59,500) y ago, and selection started around 9,000 (2,500–42,000) y ago. Our estimates suggest that one of the most convincing examples of adaptive introgression is in fact selection acting on standing archaic variation.

Hybridization has the potential to transfer beneficial alleles across species boundaries, and there are a growing number of examples in which this has apparently occurred. Recent studies suggest that Heliconius butterflies have transferred wing pattern mimicry alleles between species via hybridization, but ancestral polymorphism could also produce a signature of shared ancestry around mimicry genes. To distinguish between these alternative hypotheses, we measured DNA sequence divergence around putatively introgressed mimicry loci and compared this with the rest of the genome. Our results reveal that putatively introgressed regions show strongly reduced sequence divergence between co-mimetic species, suggesting that their divergence times are younger than the rest of the genome. This is consistent with introgression and not ancestral variation. We further show that this signature of introgression occurs at sites throughout the genome, not just around mimicry genes.

Human activities have precipitated a rise in the levels of introgressive gene flow among animals. The investigation of conspecific populations at different time points may shed light on the magnitude of human-mediated introgression. We used the red junglefowl Gallus gallus, the wild ancestral form of the chicken, as our study system. As wild junglefowl and domestic chickens readily admix, conservationists fear that domestic introgression into junglefowl may compromise their wild genotype. By contrasting the whole genomes of 51 chickens with 63 junglefowl from across their natural range, we found evidence of a loss of the wild genotype across the Anthropocene. When comparing against the genomes of junglefowl from approximately a century ago using rigorous ancient-DNA protocols, we discovered that levels of domestic introgression are not equal among and within modern wild populations, with the percentage of domestic ancestry around 20–50%. We identified a number of domestication markers in which chickens are deeply differentiated from historic junglefowl regardless of breed and/or geographic provenance, with eight genes under selection. The latter are involved in pathways dealing with development, reproduction and vision. The wild genotype is an allelic reservoir that holds most of the genetic diversity of G. gallus, a species which is immensely important to human society. Our study provides fundamental genomic infrastructure to assist in efforts to prevent a further loss of the wild genotype through introgression of domestic alleles.

Hybridization frequently occurs in plant species. With repeated backcross, the introgression may influence evolutionary trajectories through the entry of foreign genes. However, the genetic admixture via hybridization events is often confused with the ancestral polymorphism, especially in closely related species that have experienced similar evolutionary events. In Taiwan, two independent-originated endemic snakebark maples have contrasted postglacial range expansion routes: northward and upward expansion in Acer caudatifolium and downward expansion in A. morrisonense. The range expansion causes the current parapatric distribution, increasing the possibility of introgression. This study elucidates how their genetic variation reflects introgression and historical demography. With 17 EST-SSR markers among the intensely sampled 657 individuals, we confirmed that the genetic admixture between species mainly was attributed to recent introgression instead of common ancestral polymorphism. The secondary contact scenario inferred by approximate Bayesian computation suggested that A. morrisonense received more genetic variations from A. caudatifolium. Introgression occurred in colonized Taiwan around the early Last Glacial Period. Furthermore, the demography of A. caudatifolium was more severely affected by introgression than A. morrisonense, especially in the wavefront populations with high altitude range expansion, implying an altitude-related adaptive introgression. In contrast, A. morrisonense exhibited ubiquitous introgression independent of postglacial expansion, suggesting that introgression in A. morrisonense was neutral. In terms of different genetic consequences, introgression had different demographic impacts on species with different altitude expansion directions even under the same climate-change conditions within an island.

Species within the genus Quercus (oak) hybridize in complex patterns that have yet to be fully explored with phylogenomic data. Analyses to date have recovered reasonable divergent patterns, suggesting that the impact of introgression may not always be obvious in inferred oak phylogenies. We explore this phenomenon using RADseq data for 136 samples representing 54 oak species by conducting phylogenetic analyses designed to distinguish signals of lineage diversification and hybridization, focusing on the lobed-leaf species Quercus gambelii, Q. lobata, and Q. garryana in the context of a broad sampling of allied white oaks (Quercus section Quercus), and particularly the midwestern Q. macrocarpa. We demonstrate that historical introgressive hybridization between once sympatric species affects phylogeny estimation. Historical range expansion during periods of favorable climate likely explains our observations; analyses support genetic exchange between ancestral populations of Q. gambelii and Q. macrocarpa. We conclude that the genomic consequences of introgression caused the attraction of distant lineages in phylogenetic tree space, and that introgressive and divergent signals can be disentangled to produce a robust estimate of the phylogenetic history of the species.

Abstract Baobabs (Adansonia) are a cohesive group of tropical trees with a disjunct distribution in Australia, Madagascar, and continental Africa, and diverse flowers associated with two pollination modes. We used custom-targeted sequence capture in conjunction with new and existing phylogenetic comparative methods to explore the evolution of floral traits and pollination systems while allowing for reticulate evolution. Our analyses suggest that relationships in Adansonia are confounded by reticulation, with network inference methods supporting at least one reticulation event. The best supported hypothesis involves introgression between Adansonia rubrostipa and core Longitubae, both of which are hawkmoth pollinated with yellow/red flowers, but there is also some support for introgression between the African lineage and Malagasy Brevitubae, which are both mammal-pollinated with white flowers. New comparative methods for phylogenetic networks were developed that allow maximum-likelihood inference of ancestral states and were applied to study the apparent homoplasy in floral biology and pollination mode seen in Adansonia. This analysis supports a role for introgressive hybridization in morphological evolution even in a clade with highly divergent and geographically widespread species. Our new comparative methods for discrete traits on species networks are implemented in the software PhyloNetworks. [Comparative methods; Hyb-Seq; introgression; network inference; population trees; reticulate evolution; species tree inference; targeted sequence capture.]

L'étude de la distribution de la variation génétique au sein des populations et entre elles permet de mieux comprendre l'histoire évolutive d'une espèce. De plus, l'accès à de grands ensembles de données génomiques permet d'étudier les processus évolutifs qui façonnent la variation ségrégative de l'espèce. Dans ce travail, nous retraçons l'histoire évolutive de l'espèce Saccharomyces cerevisiae par la détection et la classification de polymorphismes partagés avec son espèce sœur Saccharomyces paradoxus. Nous identifions des polymorphismes partagés acquis par hybridation suivie d'introgression et des polymorphismes qui persistent à travers le processus de spéciation et de diversification résultant en des cas de triage incomplet des lignées (ILS).Nous définissons un ensemble de données de polymorphismes nucléotidiques simples diagnostiques bialléliques entre Saccharomyces cerevisiae et Saccharomyces paradoxus que nous utilisons comme marqueur diagnostique pour décrire la composition génomique de 1,673 S. cerevisiae, pour lesquels un séquençage à lecture courte du génome entier était publiquement disponible. Nous développons une méthode basée sur les marqueurs pour la détection et la classification des marqueurs de diagnostic organisés soit en 1) blocs de marqueurs S. paradoxus consécutifs, soit en 2) marqueurs S. paradoxus isolés à l'échelle du génome.Pour les blocs, nous décrivons les limites, et la distribution dans la collection S. cerevisiae et nous retraçons l'origine de S. paradoxus par comparaison de séquences avec des assemblages de génomes entiers télomère à télomère des principales populations de S. paradoxus. Pour un événement récurrent, nous avons effectué un test pour évaluer l'effet sur la condition physique de porter un haplotype S. paradoxus à un locus unique englobant une paire de gènes impliqués dans la dégradation de composés toxiques pour la levure. Nous avons démontré que l'haplotype S. paradoxus confère un avantage par rapport à l'haplotype S. cerevisiae dans des conditions environnementales caractéristiques de la niche habitée par la population S. cerevisiae.Pour les marqueurs isolés, nous appliquons une méthode classique de détection des signatures d'un tri lignager incomplet, qui peut expliquer l'excès de marqueurs S. paradoxus distribués à l'échelle du génome dans certaines populations de S. cerevisiae. Nous montrons des preuves convaincantes de la rétention d'allèles ancestraux dans une seule population sauvage de S. cerevisiae qui se trouve à la racine de l'espèce. Nous émettons l'hypothèse que la persistance d'une telle variation ancestrale est due à la possibilité réduite de croisement avec d'autres populations de S. cerevisiae dans la nature, en raison du nombre réduit de générations et des goulets d'étranglement moins spectaculaires qu'ont connu les autres lignées au cours de la dispersion et de la domestication. Dans l'ensemble, nous avons retracé l'histoire de la divergence et des contacts secondaires entre les populations de S. cerevisiae et de S. paradoxus et dévoilé un cas convaincant d'introgression interespèces avec un résultat fonctionnel
The study of the distribution of the genetic variation within and across populations provides insights into the evolutionary history of a species. Moreover, the access to large genomic datasets allows the investigation of the evolutionary processes that shape the species' segregating variation. In this work, we retrace the evolutionary history of the species Saccharomyces cerevisiae through the detection and classification of shared polymorphisms with its sister species Saccharomyces paradoxus. We identify shared polymorphisms acquired because hybridization followed by introgression and polymorphisms that persist across the process of speciation and diversification resulting in instances of incomplete lineage sorting (ILS). We define a dataset of biallelic diagnostic single nucleotide polymorphisms between Saccharomyces cerevisiae and Saccharomyces paradoxus that we use as diagnostic marker to describe the genomic composition of 1,673 S. cerevisiae, for which short-read whole-genome sequencing were publicly available. We develop a marker-based method for the detection and classification of diagnostic markers organized either in 1) blocks of consecutive S. paradoxus markers or in 2) genome-wide isolated S. paradoxus markers. For the blocks, we describe the boundaries, the distribution across the S. cerevisiae collection and we retrace the S. paradoxus origin by sequence comparison with telomere-to-telomere whole genome assemblies of the main S. paradoxus populations. For a recurrent event, we performed an assay to evaluate the fitness effect of carrying a S. paradoxus haplotype at a single locus encompassing a gene-pair involved in the degradation of toxic compounds for the yeast. We demonstrate that the S. paradoxus haplotype confers an advantage over the S. cerevisiae haplotype in environmental conditions that are characteristic of the niche that the S. cerevisiae population inhabits. For the isolated markers, we apply a classical method for detecting signatures of incomplete lineage sorting, which can explain the excess of genome-wide distributed S. paradoxus markers in certain populations of S. cerevisiae. We show convincing evidence of retention of ancestral alleles in a single wild S. cerevisiae population that stands at the root of the species. We speculate about the persistence of such ancestral variation because of reduced possibility of outcrossing with other S. cerevisiae populations into the wild due to fewer generations and less dramatic bottlenecks that were instead experienced by the other lineages during dispersal and domestication. Overall, we retraced histories of divergence and secondary contacts across S. cerevisiae and S. paradoxus populations and unveiled a compelling case of interspecies introgression with a functional outcome

Global population is expected to rise to 9 billion in another 40 years and changing climatic conditions coupled with various other abiotic and biotic stress factor have posed challenges for crop cultivars globally. Cereals like wheat, rice and maize have a central place in the human diet and require immediate attention in terms of improving yield in order to satiate the global food demand. This demand can be fulfilled by improving crop yield by exploiting natural variation in modern wheat by conventional breeding method like wheat ancestral introgression. One of the key traits that can be exploited such hybrids would be photosynthesis, ongoing debate and researcher have suggested that improving photosynthesis would be an attempt towards enhancing biomass and yield in crops like wheat and rice. In this project two different approaches were used to create interspecific hybrid, these hybrid were amphidiploids, which were created by chromosome doubling of haploid chromosome from wheat and wild relatives of wheat. First, a set of wild relatives were crossed bread wheat such as Highbury, Paragon, Chinese spring mutant, Chinese spring mutant and Pavon 76) and the amphidiploids created through these crosses where exploited for photosynthetic traits and other related physiological traits under glasshouse conditions. Second, amphidiploids created by cross using a wild relative Thinopyrum bessarabicum with durum wheat and tested in field conditions in India. Techniques like infra-red gas exchange, chlorophyll were used to assess photosynthetic performance in the glasshouse in optimal conditions and in the field under challenging environmental conditions. Along with the amphidiploids in the field conditions, a panel of 30 Indian genotypes were tested for natural variation in photosynthesis in field conditions. Almost similar set Indian genotypes were tested in glasshouse conditions in UK, to exploit the natural variation in photosynthesis. Initially, these Indian genotypes and amphidiploids grown in glasshouse as well as field conditions were screened for variation in photosynthesis. Promising lines derived from these instantaneous measurements were investigated for detailed photosynthetic measurements to understand the underlying biochemical mechanism that regulates photosynthesis and also were investigated leaf morphological and anatomical features for increased photosynthetic capacity. Here we show natural variation in photosynthesis in the amphidiploid population in both field and glasshouse conditions and range parameters that regulates photosynthetic rate in introgressed lines.

Wheat is the third most widely consumed crop after rice and maize globally. The Green Revolution increased the Indian wheat production tremendously since the 1960s using semi-dwarf wheat varieties and subsequent trait-based breeding under non-hostile soils. In addition to grain yield, wheat is an important source of dietary zinc (Zn) and other mineral elements in many countries. Dietary Zn deficiency is widespread, especially in developing countries, and there are wide scale efforts to breed wheat with increased grain Zn concentrations in South Asia. It is not clear if further grain yield and quality traits such as grain Zn concentration improvements can be sustained due to 1) narrow genetic diversity in modern wheat, and 2) limited land availability e.g., many soils are marginal due to salinity, alkalinity, acidity and mineral nutrient imbalances. The first aim of this thesis was to quantify grain yield and yield components, including juvenile root traits, and grain Zn concentration of a panel of 36 Indian diverse wheat genotypes to explore the potential for site specific trait selection for hostile soils and characterise the baseline effect of genotype (G), site (E), and genotype x site interaction (G*E) under a wide range of soil conditions. Mean grain yields ranged from 1.0 to 5.5 t ha-1 at hostile and non-hostile sites, respectively. G*E interactions affected many yield and component traits, which support the value of site-specific traits selection for hostile soils. The mean grain Zn concentration of 36 genotypes ranged from 25 to 35 mg kg-1. Despite a relatively small overall contribution of G to the overall variation in grain Zn concentration, biofortifying wheat through breeding is likely to be effective at scale given that some genotypes (e.g. Kharchia 65) performed consistently across diverse soil types. Root angle and lateral root traits were associated with grain yield and some mineral composition traits. The second aim of this thesis was to study the performance of eight amphidiploids derived from Thinopyrum bessarabicum, a tall wheat grass, for yield, yield components and grain Zn concentration under saline soils. Reduction in GYD in amphidiploids were less than in Indian genotypes under saline soils and grain Zn concentration ranged from 36-43 mg kg-1. The third aim of this thesis was to explore wild wheat relatives, non-relatives and their derivatives to increase the genetic diversity for grain Zn concentration. The mean grain Zn concentration of 225 wild wheat accession ranged from 47 to 178 mg kg-1. Notably, Amblyopyrum muticum, derived amphidiploids and double haploid lines could be useful sources of grain Zn variation that can be used in breeding programmes to increase the grain Zn concentration in modern wheat varieties to alleviate the dietary Zn deficiency.

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Animais híbridos representam um desafio à taxonomia e sistemática, pois correpondem a unidades evolutivas sem clara delimitação morfológica, comportamental e molecular. Híbridos podem ser morfologicamente intermediários aos parentais ou, devido à introgressão e retrocruzamentos, suas características podem se misturar tornando difícil a identificação. No entanto, resultados conflitantes entre dados moleculares provenientes do DNA mitocondrial (DNAmt) e DNA nuclear (DNAn) podem ser devido ao sorteamento incompleto de polimorfismos ancestrais (ILS). Em localidades do Espírito Santo, Brasil, foram coletados indivíduos de morfologia distinta de Trachycephalus mesophaeus e T. nigromaculatus, que são as únicas espécies do gênero conhecidas para esse estado. Porém, estudos piloto usando o gene mitocondrial COI agruparam esses espécimes com amostras de T. typhonius. Devido a estas incongruências, foram sequenciados fragmentos de dois genes mitocondriais (COI e ND2) e um exon nuclear (tirosinase) de 173 indivíduos de Trachycephalus, de forma a clarificar as identificações taxonômicas e investigar a correspondência entre caracteres morfológicos e genéticos nesta linhagem, na sua área de ocorrência As filogenias moleculares, divergências genéticas, redes de haplótipos e polimorfismos de nucleotídeos únicos (SNPs) confirmaram as três espécies acima mencionadas como linhagens evolutivas distintas e revelaram mais sete indivíduos potencialmente híbridos, mas morfologicamente assinalados a uma espécie. Devido à taxa de evolução lenta da tirosinase, as espécies mais recentes T. typhonius e T. nigromaculatus parecem não terem sido sorteadas completamente nesse gene. Já T. mesophaeus é a espécie mais antiga das três e foi recuperada inequivocamente em todas as análises. De forma inédita, as análises moleculares evidenciaram a ocorrência de introgressão bidirecional entre T. nigromaculatus e T. typhonius e entre T. nigromaculatus e T. mesophaeus, sendo que há indícios de indivíduos F1. A utilização do gene ND2 mostrou-se mais eficiente do que o gene COI nas filogenias e, apesar da tirosinase ser um gene nuclear de evolução lenta, contribuiu para a identificação de incongruências citonucleares. Nossos resultados mostram que a história filogenética de Trachycephalus é complexa e que o uso de marcadores nucleares de evolução mais rápida e ampliação dessas análises para outras espécies do gênero podem revelar eventos de hibridação.

Humans have migrated from their ancestral homelands in Africa to nearly every part of the world. Human migration is characterized by a recurrent process of physical isolation and genetic diversification followed by admixture, whereby previously isolated populations come together and exchange genes. Admixture results in the introgression of alleles from ancestral source populations into hybrid admixed populations, and introgression can facilitate rapid, adaptive evolution by introducing beneficial alleles at intermediate frequencies. We provide examples of adaptive introgression between archaic and modern human populations and for admixed populations in the Americas, which were formed relatively recently via admixture among African, European, and Indigenous American ancestral populations. Adaptive introgression has had an outsized effect on the human immune system. In light of the ubiquity of admixture in human evolution, we propose that adaptive introgression is a fundamentally important mechanism for driving rapid, adaptive evolution in human populations.

<em>Abstract</em>.—Since the 1970s, the only known naturally reproducing population of native Gulf of Mexico (Gulf ) striped bass <em>Morone saxatilis</em> occurs in the Apalachicola–Chattahoochee–Flint River system (ACF) in Florida, Georgia, and Alabama.To augment its depleted population, low numbers of fry and fingerlings of Atlantic coast ancestry were released into the ACF between 1965 and 1976.Restoration of Gulf striped bass was initiated in 1980 when putative Gulf fingerlings spawned from Apalachicola River (Gulf ) broodfish were stocked back into the ACF. Since the initial stocking, approximately 10 million phase-I (25–50 mm) and 900,000 phase-II (150–250 mm) fingerlings have been released into Lake Seminole and the Apalachicola River, with hundreds of thousands more released into upstream reservoirs. Low levels of successful natural reproduction in the ACF were documented in 9 of the 10 years that natural reproduction was evaluated. Marked stocked fish have typically comprised 75–100% of fall age-0 samples. After stocking was initiated, striped bass harvest estimates increased as much as 10-fold during peak-season creel surveys conducted in the tailrace of Jim Woodruff Lock and Dam. A comparison of Atlantic-origin and Gulf striped bass co-stocked into an adjacent river-reservoir system over a 5-year period indicated no consistent differences in relative survival or growth through age 4. Gulf striped bass occupied coolwater thermal refuges during summer. Enhancement of thermal refuge habitats was successful, but results were short-lived. Small populations of Gulf striped bass, dependent on stocking of hatchery fish, now exist in several Gulf of Mexico tributary systems where adequate habitat is present.Genetic analysis of both mitochondrial and nuclear genomes revealed that a high percentage of fish from the ACF exhibit mitochondrial DNA (mtDNA) haplotypes and nuclear DNA (nDNA) alleles that are absent in Atlantic populations.However, significant introgression of Atlantic nDNA alleles was documented in the extant population. Knowledge of the life history of Gulf striped bass was improved as a result of this multi-state collaboration as well as a large stocking program, new Gulf broodfish repositories, extensive genetic cataloged database,and expanded trophy fisheries. ACF Gulf striped bass restoration goals and objectives were defined, adjusted, and revised throughout the collaborative process to meet the concerns and management needs of all participating agencies.