Genetic Swamping Research Articles

Climate‐Mediated Hybridisation and the Future of Andean Forests

ABSTRACTThe tropical Andes face unprecedented warming and shifting precipitation patterns due to climate change and land‐use alteration, challenging the future of Andean forests. During the Quaternary, many Andean trees responded to climate change through upslope migrations but, while there is evidence of such ongoing migrations in many species, they are at rates far below what is needed to remain in equilibrium with the current climate. Similarly, given the number of generations required for adaptation and the long lifespans of many tropical trees, it is unlikely that most species will be able to adapt fast enough. This synthesis explores the role of migration‐induced secondary contact and hybridisation as potential mechanisms for accelerating the adaptive response of Andean forests. Hybridisation, historically underappreciated in tropical trees, is increasingly recognised as an important driver of speciation and ecological diversity. It may facilitate gene flow and introgression, providing novel genetic combinations that enhance species resilience to climate change. This process can generate new allelic diversity, allowing species to adapt more rapidly than through mutation or selection on standing variation alone. However, hybridisation can also lead to negative outcomes like genetic swamping and outbreeding depression. Conservation strategies should consider the potential benefits and risks of hybridisation in maintaining biodiversity under changing environmental conditions. As habitat fragmentation and deforestation exacerbate the challenges faced by these forests, preserving habitat connectivity will be crucial to facilitate migration and gene flow, potentially aiding the survival of many Andean tree species in the Anthropocene.

Surviving the extinction vortex? Discovering remnant stands of Senecio hercynicus (Compositae, Senecioneae) evading genetic swamping by its congener S. ovatus in the Bavarian and Bohemian Forest region

Surviving the extinction vortex? Discovering remnant stands of Senecio hercynicus (Compositae, Senecioneae) evading genetic swamping by its congener S. ovatus in the Bavarian and Bohemian Forest region

Long-read de novo assembly of the red-legged partridge (Alectoris rufa) genome

The red-legged partridge (Alectoris rufa) is a popular game bird species that is in decline in several regions of southwestern Europe. The introduction of farm-reared individuals of a distinct genetic make-up in hunting reserves can result in genetic swamping of wild populations. Here we present a de novo genome assembly for the red-legged partridge based on long-read sequencing technology. The assembled genome size is 1.14 Gb, with scaffold N50 of 37.6 Mb and contig N50 of 29.5 Mb. Our genome is highly contiguous and contains 97.06% of complete avian core genes. Overall, the quality of this genome assembly is equivalent to those available for other close relatives such as the Japanese quail or the chicken. This genome assembly will contribute to the understanding of genetic dynamics of wild populations of red-legged partridges with releases of farm-reared reinforcements and to appropriate management decisions of such populations.

Divergent ecological selection maintains species boundaries despite gene flow in a rare endemic tree, Quercus acerifolia (maple-leaf oak).

Strong gene flow from outcrossing relatives tends to blur species boundaries, while divergent ecological selection can counteract gene flow. To better understand how these two forces affect the maintenance of species boundaries, we focused on a species complex including a rare species, maple-leaf oak (Quercus acerifolia), which is found in only four disjunct ridges in Arkansas. Its limited range and geographic proximity to co-occurring close relatives create the possibility for genetic swamping. In this study, we gathered genome-wide single nucleotide polymorphisms (SNPs) using restriction-site-associated DNA sequencing (RADseq) from 190 samples of Q. acerifolia and three of its close relatives, Q. shumardii, Q. buckleyi, and Q. rubra. We found that Q. shumardii and Q. acerifolia are reciprocally monophyletic with low support, suggesting incomplete lineage sorting, introgression between Q. shumardii and Q. acerifolia, or both. Analyses that model allele distributions demonstrate that admixture contributes strongly to this pattern. Populations of Q. acerifolia experience gene flow from Q. shumardii and Q. rubra, but we found evidence that divergent selection is likely maintaining species boundaries: 1) ex situ collections of Q. acerifolia have a higher proportion of hybrids compared to the mature trees of the wild populations, suggesting ecological selection against hybrids at the seed/seedling stage; 2) ecological traits co-vary with genomic composition; and 3) Q. acerifolia shows genetic differentiation at loci hypothesized to influence tolerance of radiation, drought, and high temperature. Our findings strongly suggest that in maple-leaf oak, selection results in higher divergence at regions of the genome despite gene flow from close relatives.

Widespread gene flow from Betula tianshanica and Betula pendula to Betula microphylla: a rare species from Northwest China

Widespread gene flow from <i>Betula tianshanica</i> and <i>Betula pendula</i> to <i>Betula microphylla</i>: a rare species from Northwest China

Distinct Island Lineages of Binturong (Arctictis binturong) from Indonesia and Its Conservation Implications

Binturong (Arctictis binturong) is a threatened carnivore that inhabits the forests of South and Southeast Asia. Despite its wide range, binturong is relatively scarce across its habitat distribution and is currently under the threat of poaching and illegal trade. Captive breeding has unfortunately been conducted rather haphazardly with a lack of origin record maintained, implicating potential risks to the management such as inbreeding or genetic swamping. This study thus aims to characterise the phylogenetic relationship of Indonesian binturong within the context of Southeast Asian binturong and further probe the distinctness of lineages originating from Java, Sumatra, Indonesian Borneo, and Bangka using Cytochrome B (CytB) and Cytochrome C Oxidase Subunit 1 (CO1). Genetic distance, phylogram topology, and haplotype analysis of both encoding genes further corroborate the distinctness of Java, Borneo, and Bangka binturong from other binturong from Indochinese regions such as India, Laos, and Myanmar. Search for prospective single nucleotide polymorphism markers to discriminate island lineages consistently found that each Java, Bangka, and Bornean binturong be distinct from each other and other lineages, especially when assessed using haplotype-based clustering. Assigning binturong originated from Sumatra is nonetheless more complicated, suggesting the possibility. Our findings substantiated the much-needed systematic research of Southeast Asian binturong as ex-situ insurance population management grows in Indonesia and other parts of the world to protect the diversity of binturong lineages and their corresponding unique evolutionary history.

Hatchery-Imposed Selection Does Not Impact the Genetic Diversity of Australian Farmed Blue Mussels (Mytilus spp.)

Australian blue mussels (Mytilus spp.) are an increasingly important sustainable product of the Australian aquaculture industry. Although important for commercial fisheries, aquaculture may have adverse environmental and ecological impacts. This study assessed the impact of standard hatchery-imposed selection practices on the genetic diversity of farmed blue mussels. Using microsatellite markers, relatedness and genetic structure analyses showed that hatchery-reared larvae have high levels of genetic diversity without a significant decline as they move through the hatchery rearing process. Selection and/or genetic drift does appear to be operating during the hatchery rearing process, however, evidenced by an increase in relatedness among larvae over time. Significant shifts in allele frequency as well as genetic clusters provides further evidence that selection is acting on larvae due to the selection practice applied at the hatchery. Comparison of the level of genetic diversity and genetic differentiation of adults from wild and farmed populations provided no evidence that farmed mussels have lower diversity, or that they are genetically swamping local natural populations. The data suggest that careful design and implementation of mussel breeding programs can maintain high genetic diversity among larvae that does not lead to genetic swamping of natural mussel populations in the surrounding area.

Eclipta thermalis, a previously common weed, threatened by the expansion of the exotic congener E. alba in Japanese rice paddies

AbstractRice paddies are wetland ecosystems recognized as important habitats for many organisms; however, the hybridization‐related extinction risk of native plant species has not been investigated in this system so far. Eclipta L. (Compositae) is a common paddy weed in Japan; however, its genetic composition might be altered due to the hybridization between the native E. thermalis and the closely related exotic E. alba. We examined Eclipta's genetic composition using 12 microsatellite markers (612 samples collected from 109 populations) and found (i) widespread geographical distribution of E. alba in Japan, (ii) hybridization with E. thermalis, and a large number of later‐generation hybrids, and (iii) widely varying situations among regions and populations. Eclipta alba appears to have invaded an open niche in northern Japan but has not yet reached southern Japan. Both E. alba and E. thermalis were found in central Japan; however, the latter had become rare due to hybridization‐mediated processes such as competition, and demographic and genetic swamping. Notably, endogenous and exogenous selection plays an important role in the invasion of E. alba, but to varying degrees among different areas. In summary, considering the genetic variability in E. thermalis, the genetic cluster of mainland Japan is in a highly critical situation due to the invasion of E. alba.

Genetic swamping of the critically endangered Scottish wildcat was recent and accelerated by disease

The European wildcat population in Scotland is considered critically endangered as a result of hybridization with introduced domestic cats,1,2 though the time frame over which this gene flow has taken place is unknown. Here, using genome data from modern, museum, and ancient samples, we reconstructed the trajectory and dated the decline of the local wildcat population from viable to severely hybridized. We demonstrate that although domestic cats have been present in Britain for over 2,000 years,3 the onset of hybridization was only within the last 70 years. Our analyses reveal that the domestic ancestry present in modern wildcats is markedly over-represented in many parts of the genome, including the major histocompatibility complex (MHC). We hypothesize that introgression provides wildcats with protection against diseases harbored and introduced by domestic cats, and that this selection contributes to maladaptive genetic swamping through linkage drag. Using the case of the Scottish wildcat, we demonstrate the importance of local ancestry estimates to both understand the impacts of hybridization in wild populations and support conservation efforts to mitigate the consequences of anthropogenic and environmental change.

Scientific evidence does not support the translocation of guanacos in Argentina

AbstractThe Argentinian Ministry of Environment has approved the translocation of 45 guanacos from Southern Patagonia to the Pampas region, a distance of 1500 km, as the initial phase toward future translocations into a National Park located in the Chaco region, another 1600 km further North. This decision raises concerns about the technical and ethical aspects of the translocation. Firstly, there is a lack of proper evaluation and scientific evidence to support the need, opportunity, and feasibility of this translocation. The guanaco population is currently over one million and is increasing, and genetic differences exist among local populations. The translocation could produce anthropogenic‐driven admixed populations, leading to genetic swamping and disrupting evolutionary processes. Second, there are ethical conflicts around managing wild species populations that prioritize private objectives and disregard local, publicly funded science. Rewilding projects require a deep understanding of interacting ecosystem processes, and of the socio‐economic context. This management decision violates guiding principles for rewilding and should have followed proper scientific evaluation and transparent local consultation.

A common statement on anthropogenic hybridization of the European wildcat (Felis silvestris)

Preserving natural genetic diversity and ecological function of wild species is a central goal in conservation biology. As such, anthropogenic hybridization is considered a threat to wild populations, as it can lead to changes in the genetic makeup of wild species and even to the extinction of wild genomes. In European wildcats, the genetic and ecological impacts of gene flow from domestic cats are mostly unknown at the species scale. However, in small and isolated populations, it is known to include genetic swamping of wild genomes. In this context, it is crucial to better understand the dynamics of hybridization across the species range, to inform and implement management measures that maintain the genetic diversity and integrity of the European wildcat. In the present paper, we aim to provide an overview of the current scientific understanding of anthropogenic hybridization in European wildcats, to clarify important aspects regarding the evaluation of hybridization given the available methodologies, and to propose guidelines for management and research priorities.

Is hybridisation with non‐native congeneric species a threat to the UK native bluebell Hyacinthoides non‐scripta?

Societal Impact StatementHybridisation is an important evolutionary force in plants, but it can potentially lead to genetic swamping and extinction of one or both parental species. The threat of extinction is of particular concern if hybridisation occurs between native and introduced species, especially when the native is of national importance. The widespread occurrence of non‐native bluebells in the United Kingdom has raised concerns that the iconic native bluebell could be at risk due to extinction by hybridisation from introduced non‐native bluebells. This study determines the taxonomic identity of non‐natives and investigates the amount of hybridisation occurring in natural and semi‐natural UK bluebell populations.Summary The widespread occurrence of a non‐native bluebell taxon in the UK has raised concerns that the iconic native bluebell H. non‐scripta (Asparagaceae) could be at risk due to extinction by hybridisation from introduced non‐native congeners. Understanding the nature of this threat requires quantification of the extent of hybridisation between the native and non‐native taxa. An additional complication is taxonomic uncertainty regarding the identity of the non‐native bluebells in the United Kingdom that are colloquially referred to as the ‘Spanish’ bluebell (H. hispanica). We collected 501 bluebell samples from 56 populations in the United Kingdom (H. non‐scripta and non‐natives) and the Iberian Peninsula (H. hispanica). The samples were assayed for variation at 1871 nuclear and 17 plastid single nucleotide polymorphisms. Our genetic analyses demonstrated that non‐native bluebells in the United Kingdom are not H. hispanica but the hybrid between H. hispanica and H. non‐scripta. Moreover, they supported the hypothesis that Portugal is the country of origin of the first H. hispanica introductions to the United Kingdom. The frequency of hybrids was about 16%. Backcrosses between the (hybrid) non‐native bluebell and the native H. non‐scripta were primarily found in public parks. Of the sampled individuals for H. non‐scripta from natural habitats, only 2% showed evidence of introgression. Although hybridisation might be frequent in locations where non‐native bluebells have been introduced, we found no evidence of large‐scale introgression in natural H. non‐scripta populations. Therefore, our results do not support concerns of an ‘extinction by hybridisation’ scenario.

Translocation precipitates natural hybridisation and pervasive introgression between marine gastropods with divergent developmental modes

Translocation precipitates natural hybridisation and pervasive introgression between marine gastropods with divergent developmental modes

Genomic diversity and signals of selection processes in wild and farm-reared red-legged partridges (Alectoris rufa)

Genomic diversity and signals of selection processes in wild and farm-reared red-legged partridges (Alectoris rufa)

Comparison of plastid genomes and ITS of two sister species in Gentiana and a discussion on potential threats for the endangered species from hybridization

BackgroundGentiana rigescens Franchet is an endangered medicinal herb from the family Gentianaceae with medicinal values. Gentiana cephalantha Franchet is a sister species to G. rigescens possessing similar morphology and wider distribution. To explore the phylogeny of the two species and reveal potential hybridization, we adopted next-generation sequencing technology to acquire their complete chloroplast genomes from sympatric and allopatric distributions, as along with Sanger sequencing to produce the nrDNA ITS sequences.ResultsThe plastid genomes were highly similar between G. rigescens and G. cephalantha. The lengths of the genomes ranged from 146,795 to 147,001 bp in G. rigescens and from 146,856 to 147,016 bp in G. cephalantha. All genomes consisted of 116 genes, including 78 protein-coding genes, 30 tRNA genes, four rRNA genes and four pseudogenes. The total length of the ITS sequence was 626 bp, including six informative sites. Heterozygotes occurred intensively in individuals from sympatric distribution. Phylogenetic analysis was performed based on chloroplast genomes, coding sequences (CDS), hypervariable sequences (HVR), and nrDNA ITS. Analysis based on all the datasets showed that G. rigescens and G. cephalantha formed a monophyly. The two species were well separated in phylogenetic trees using ITS, except for potential hybrids, but were mixed based on plastid genomes. This study supports that G. rigescens and G. cephalantha are closely related, but independent species. However, hybridization was confirmed to occur frequently between G. rigescens and G. cephalantha in sympatric distribution owing to the lack of stable reproductive barriers. Asymmetric introgression, along with hybridization and backcrossing, may probably lead to genetic swamping and even extinction of G. rigescens.ConclusionG. rigescens and G. cephalantha are recently diverged species which might not have undergone stable post-zygotic isolation. Though plastid genome shows obvious advantage in exploring phylogenetic relationships of some complicated genera, the intrinsic phylogeny was not revealed because of matrilineal inheritance here; nuclear genomes or regions are hence crucial for uncovering the truth. As an endangered species, G. rigescens faces serious threats from both natural hybridization and human activities; therefore, a balance between conservation and utilization of the species is extremely critical in formulating conservation strategies.

The evolutionary outcomes of climate-change-induced hybridization in insect populations.

The evolutionary outcomes of climate-change-induced hybridization in insect populations.

Evidence of hybrid breakdown among invasive hybrid cattails (Typha × glauca).

Interspecific hybridization has varied consequences for offspring fitness, with implications for the maintenance of species integrity. Hybrid vigour, when it occurs, can peak in first-generation (F1) hybrids and then decline in advanced-generation (F2+) hybrids. This hybrid breakdown, together with the processes affecting patterns of hybridization and hybrid fitness, determine the evolutionary stability of hybrid zones. An extensive hybrid zone in North America involving the cattails Typha latifolia, T. angustifolia, and their invasive hybrid T. × glauca is characterized by hybrid vigour among F1s, but the fitness of advanced-generation hybrids has not been studied. We compared seed germination and plant growth of T. latifolia (parental L), F1 T. × glauca (F1), hybrid backcrosses to T. angustifolia (bcA) and T. latifolia (bcL), and advanced-generation (F2) hybrids. Consistent with expectations under hybrid breakdown, we found reduced plant growth for F2 hybrids in comparison with F1s (plant height and above-ground biomass) and parental Ls (above-ground biomass). Backcrossed hybrids had intermediate measures of plant growth and bcLs were characterized by reduced seed germination in comparison with parental Ls. Hybrid breakdown could make the formation of F1s in North America finite because (1) hybridization among cattails is asymmetric, with T. angustifolia but not T. latifolia subject to genetic swamping, and (2) T. angustifolia is less common and subject to competitive displacement by F1s. Hybrid breakdown is therefore expected to reduce hybrid frequencies over time, contributing to the long-term maintenance of T. latifolia - the only native cattail in the study region.

Pollen competition in hybridizing Cakile species: How does a latecomer win the race?

PremiseHybridization between cross‐compatible species depends on the extent of competition between alternative mates. Even if stigmatic compatibility allows for hybridization, hybridization requires the heterospecific pollen to be competitive. Here, we determined whether conspecific pollen has an advantage in the race to fertilize ovules and the potential handicap to be overcome by heterospecific pollen in invasive Cakile species.MethodsWe used fluorescence microscopy to measure pollen tube growth after conspecific and heterospecific hand‐pollination treatments. We then determined siring success in the progeny relative to the timing of heterospecific pollen arrival on the stigma using CAPS markers.ResultsIn the absence of pollen competition, pollination time and pollen recipient species had a significant effect on the ratio of pollen tube growth. In long‐styled C. maritima (outcrosser), pollen tubes grew similarly in both directions. In short‐styled C. edentula (selfer), conspecific and heterospecific pollen tubes grew differently. Cakile edentula pollen produced more pollen tubes, revealing the potential for a mating asymmetry whereby C. edentula pollen had an advantage relative to C. maritima. In the presence of pollen competition, siring success was equivalent when pollen deposition was synchronous. However, a moderate 1‐h advantage in the timing of conspecific pollination resulted in almost complete assortative mating, while an equivalent delay in conspecific pollination resulted in substantial hybrid formation.ConclusionsHybridization can aid the establishment of invasive species through the transfer of adaptive alleles from cross‐compatible species, but also lead to extinction through demographic or genetic swamping. Time of pollen arrival on the stigma substantially affected hybridization rate, pointing to the importance of pollination timing in driving introgression and genetic swamping.

Consequences of Hybridization in Mammals: A Systematic Review.

Hybridization, defined as breeding between two distinct taxonomic units, can have an important effect on the evolutionary patterns in cross-breeding taxa. Although interspecific hybridization has frequently been considered as a maladaptive process, which threatens species genetic integrity and survival via genetic swamping and outbreeding depression, in some cases hybridization can introduce novel adaptive variation and increase fitness. Most studies to date focused on documenting hybridization events and analyzing their causes, while relatively little is known about the consequences of hybridization and its impact on the parental species. To address this knowledge gap, we conducted a systematic review of studies on hybridization in mammals published in 2010–2021, and identified 115 relevant studies. Of 13 categories of hybridization consequences described in these studies, the most common negative consequence (21% of studies) was genetic swamping and the most common positive consequence (8%) was the gain of novel adaptive variation. The total frequency of negative consequences (49%) was higher than positive (13%) and neutral (38%) consequences. These frequencies are biased by the detection possibilities of microsatellite loci, the most common genetic markers used in the papers assessed. As negative outcomes are typically easier to demonstrate than positive ones (e.g., extinction vs hybrid speciation), they may be over-represented in publications. Transition towards genomic studies involving both neutral and adaptive variation will provide a better insight into the real impacts of hybridization.

Hybridization: a ‘double-edged sword’ for Neotropical plant diversity

AbstractHybridization can facilitate both evolutionary diversification and extinction and has had a critical role in plant evolution, with c. 25% of species known to hybridize in some temperate floras. However, in the species-rich Neotropical flora, the role of hybridization in the evolution of diversity remains unclear. Our review examines studies of hybridization in seed plants from across the Neotropics and explores its outcomes on Neotropical plant evolution. We review studies on a per-biome basis and a spectrum of evolutionary outcomes from hybridization are evident across Neotropical biomes and taxa. These range from short-term impacts, such as the broadening of ecological amplitude in hybrid progeny with transgressive phenotypes and genetic swamping, through to long term impacts, such as the generation of new lineages. Among these studies certain themes emerge, such as the pervasive hybridization among species-rich plant radiations from the Andean páramos, suggesting a role for hybridization in rapid diversification events. Finally, we highlight that hybridization is relatively understudied in the Neotropical flora, despite its remarkable species richness. The advent of genomic techniques can facilitate the study of hybridization and its effects in understudied biomes and plant groups. The increasing availability of genomic resources will eventually allow comparisons between tropical and temperate floras and therefore shed light on the evolutionary impacts of hybridization across the latitudinal biodiversity gradient.