SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal.Bioinformatics 2019 Nov;35(21):4480-4483. 5488121. 10.1093/bioinformatics/btz311. PMC6821363. 12-05-2019
Currat M, Arenas M, Quilodràn CS, Excoffier L, Ray N
SPLATCHE3 simulates genetic data under a variety of spatially explicit evolutionary scenarios, extending previous versions of the framework. The new capabilities include long-distance migration, spatially and temporally heterogeneous short-scale migrations, alternative hybridization models, simulation of serial samples of genetic data and a large variety of DNA mutation models. These implementations have been applied independently to various studies, but grouped together in the current version.
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, while 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. Using density-dependent dispersal models thus increase the predictive power of the approach. This article is protected by copyright. All rights reserved.
Human-induced habitat changes may lead to the breakdown of reproductive barriers between distantly related species. This phenomenon may result in fertile first-generation hybrids (F ) that exclude the genome of one parental species during gametogenesis, thus disabling introgression. The species extinction risk associated with hybridization with genome exclusion is largely underappreciated because the phenomenon produces only F hybrid phenotype, leading to the misconception that hybrids are sterile and potentially of minor conservation concern. We used a simulation model that integrates the main genetic, demographic, and ecological processes to examine the dynamics of hybridization with genome exclusion. We showed that this mode of hybridization may lead to extremely rapid extinction when the process of genome exclusion is unbalanced between the interbreeding species and when the hybridization rate is not negligible. The coexistence of parental species was possible in some cases of asymmetrical genome exclusion, but show this equilibrium was highly vulnerable to environmental variation. Expanding the exclusive habitat of the species at risk allowed its persistence. Our results highlight the extent of possible extinction risk due to hybridization with genome exclusion and suggest habitat management as a promising conservation strategy. In anticipation of serious threats to biodiversity due to hybridization with genome exclusion, we recommend a detailed assessment of the reproductive status of hybrids in conservation programs. We suggest such assessments include the inspection of genetic content in hybrid gametes.
The dispersal of non-native genes due to hybridization is a form of cryptic invasion with growing concern in evolution and conservation. This includes the spread of transgenic genes and antibiotic resistance. To investigate how genes and phenotypes are transmitted, we developed a general model that, for the first time, considers concurrently: multiple loci, quantitative and qualitative gene expression, assortative mating, dominance/recessivity inheritance and density-dependent demographic effects. Selection acting on alleles or genotypes can also be incorporated. Our results reveal that the conclusions about how hybridization threatens a species can be biased if they are based on single-gene models, while considering two or more genes can correct this bias. We also show that demography can amplify or balance the genetic effects, evidencing the need of jointly incorporating both processes. By implementing our model in a real case, we show that mallard ducks introduced in New Zealand benefit from hybridization to replace native grey-ducks. Total displacement can take a few generations and occurs by interspecific competition and by competition between hybrids and natives, demonstrating how hybridization may facilitate biological invasions. We argue that our general model represents a powerful tool for the study of a wide range of biological and societal questions.
Understanding the processes that drive population genetic divergence in the Amazon is challenging because of the vast scale, the environmental richness and the outstanding biodiversity of the region. We addressed this issue by determining the genetic structure of the widespread Amazonian common sardine fish Triportheus albus (Characidae). We then examined the influence, on this species, of all previously proposed population-structuring factors, including isolation-by-distance, isolation-by-barrier (the Teotônio Falls) and isolation-by-environment using variables that describe floodplain and water characteristics. The population genetics analyses revealed an unusually strong structure with three geographical groups: Negro/Tapajós rivers, Lower Madeira/Central Amazon, and Upper Madeira. Distance-based redundancy analyses showed that the optimal model for explaining the extreme genetic structure contains all proposed structuring factors and accounts for up to 70% of the genetic structure. We further quantified the contribution of each factor via a variance-partitioning analysis. Our results demonstrate that multiple factors, often proposed as individual drivers of population divergence, have acted in conjunction to divide T. albus into three genetic lineages. Because the conjunction of multiple long-standing population-structuring processes may lead to population reproductive isolation, that is, the onset of speciation, we suggest that the multifactorial population-structuring processes highlighted in this study could account for the high speciation rate characterising the Amazon Basin.
Modelling interspecific hybridization with genome exclusion to identify conservation actions: the case of native and invasive Pelophylax waterfrogs.Evol Appl 2015 Feb;8(2):199-210. 10.1111/eva.12245. PMC4319866. 17-02-2015
Interspecific hybridization occurs in nature but can also be caused by human actions. It often leads to infertile or fertile hybrids that exclude one parental genome during gametogenesis, escaping genetic recombination and introgression. The threat that genome-exclusion hybridization might represent on parental species is poorly understood, especially when invasive species are involved. Here, we show how to assess the effects of genome-exclusion hybridization and how to elaborate conservation actions by simulating scenarios using a model of nonintrogressive hybridization. We examine the case of the frog Pelophylax ridibundus, introduced in Western Europe, which can hybridize with the native Pelophylax lessonae and the pre-existing hybrid Pelophylax esculentus, maintained by hybridogenesis. If translocated from Southern Europe, P. ridibundus produces new sterile hybrids and we show that it mainly threatens P. esculentus. Translocation from Central Europe leads to new fertile hybrids, threatening all native waterfrogs. Local extinction is demographically mediated via wasted reproductive potential or via demographic flow through generations towards P. ridibundus. We reveal that enlarging the habitat size of the native P. lessonae relative to that of the invader is a promising conservation strategy, avoiding the difficulties of fighting the invader. We finally stress that nonintrogressive hybridization is to be considered in conservation programmes.
Models of hybridization during range expansions and their application to recent human evolutionIn book: Cultural Developments in the Eurasian Paleolithic and the Origin of Anatomically Modern Humans, Publisher: Derevianko, AP; Shunkov, M, pp.122-137 31-12-2014
The simulated presence of conspecifics has been proposed to attract territorial songbirds to protect nesting areas when the habitat is being disturbed by human activities. We studied the effects of conspecifics on the nest-site selection of the Thorn-tailed Rayadito (Aphrastura spinicauda; Furnariidae), a forest songbird that depends on cavities for nesting.Plantations represent usable habitat for foraging, but the scarcity of cavities restricts their use during the breeding period. The use of nest boxes is a documented measure to mitigate the negative effect of plantations on cavity users. We installed nest boxes in a plantation ofPinus radiata in south-central Chile, using the simulated presence of conspecifics as a potential tool to attract rayaditos to new available sites to nest. We simulated the presence of conspecifics through playback during 45 days prior nest building. Our results showed two contrasting outcomes. Firstly, conspecific simulation attracts rayaditos, by increasing their density before playback experiments by 75%. Secondly, rayaditos tended to avoid playback treatment sites as nesting started. The establishment of nests occurred 71%of the time and started 20 days earlier in control sites compared to playback treatment. Other secondary cavity-nesting birds, such as the House Wren (Troglodytes aedon;Troglodytidae) andWhite-throated Tree runner (Pygarrhichas albogularis; Furnariidae), also avoided playback plots as nesting sites. The scarcity of cavities in pine plantations may increase the aggressive defense of breeding territories, making cavity-nesting birds move to other previously known vacant sites to nest when they listen other birds in the nesting site. It is highly recommended to assess the behavioral response to conspecific and heterospecific birds before the establishment of a management measure aiming to attract or discourage the presence of a target species.
A general model of distant hybridization reveals the conditions for extinction in Atlantic salmon and brown trout.PLoS ONE 2014 ;9(7):e101736. 10.1371/journal.pone.0101736. PONE-D-14-07667. PMC4086968. 09-07-2014
Interspecific hybridization is common in nature but can be increased in frequency or even originated by human actions, such as species introduction or habitat modification, which may threaten species persistence. When hybridization occurs between distantly related species, referred to as "distant hybridization," the resulting hybrids are generally infertile or fertile but do not undergo chromosomal recombination during gametogenesis. Here, we present a model describing this frequent but poorly studied interspecific hybridization to assess its consequences on parental species and to anticipate the conditions under which they can reach extinction. Our general model fully incorporates three important processes: density-dependent competition, dominance/recessivity inheritance of traits and assortative mating. We demonstrate its use and flexibility by assessing population extinction risk between Atlantic salmon and brown trout in Norway, whose interbreeding has recently increased due to farmed fish releases into the wild. We identified the set of conditions under which hybridization may threaten salmonid species. Thanks to the flexibility of our model, we evaluated the effect of an additional risk factor, a parasitic disease, and showed that the cumulative effects dramatically increase the extinction risk. The consequences of distant hybridization are not genetically, but demographically mediated. Our general model is useful to better comprehend the evolution of such hybrid systems and we demonstrated its importance in the field of conservation biology to set up management recommendations when this increasingly frequent type of hybridization is in action.
Understanding the factors that determine waterfowl nesting site selection is an essential tool for wetland management, but, unfortunately, this information is lacking for most species in the Southern Hemisphere. During the 2007 breeding season, reproductive biology and nesting habitat selection of the Red Shoveler (Anas platalea) were investigated in a wetland of Central Chile. Red Shoveler nests were clumped, primarily in scrubby meadows, containing an average of 8.56 ± 1 eggs (n = 2 3). Nesting microhabitat was characterized by well-covered ground and an intermediate height of the rich herbaceous layer close to the water. Hatching success was 80 ± 20% and was negatively associated with the number of cattle dung piles and the proportion of dry vegetation, but positively explained by herbaceous height and the distance to watercourse. Results suggest that the risk of predation, the access to food, and cattle disturbance would affect the selection of breeding sites and nest success of Red Shoveler. Management should focus on increasing diversity the herbaceous layer, ensuring easy access to water sources, and decreasing livestock pressure during the nesting period.
We installed nest boxes for Thorn-tailed Rayaditos (Aphrastrura spinicauda) and monitored their use in a Monterrey pine (Pinus radiata) plantation in the Maule Region, south central Chile. Thirty-four breeding pairs built nests in boxes, of which 75% began laying eggs. Nest establishment began in early September and construction lasted 12.8 ± 4.9 days (n = 23). Rayaditos used mainly pine needles, together with mosses, epiphytes, herbs, and animal hair in their nests. Clutch size ranged from two to four eggs (mode = 3) that were incubated for 15.8 ± 1.2 days. Brood size negatively affected mass of nestlings, but was positively related to mass of the parents. Adults had higher body mass and built larger nests than those reported previously for the species on Chiloé Island, where broods are larger and the incubation period is shorter. The provision of artificial cavities allowed Thorn-tailed Rayaditos to nest in the pine plantation. Nest boxes combined with other management tools, such as maintaining snags and understory enhancement, may be important factors in mitigation of negative effects of pine plantations on secondary cavity-nesting birds.
Natural hybridization has played an important role in the evolution of many plant and animal taxa. However, when hybridization is caused by anthropogenic factors, it may lead to serious consequences for biological conservation. This is particularly true in native rare or threatened species, because if the population size is too small we expect a gradual replacement of their genotype by hybrids.
This research project aims to model the impact of anthropogenic changes on the genetic integrity of organisms due to interspecific hybridization. We will highlight the potential effects of exotic invasive species and habitat modifications, due in particular to global climate change. Global warming will impact rainfall regimes and result in a reduction of river flow, especially in small tributaries and headwaters. As a consequence, freshwater organisms will be forced to respond with downstream population displacements, leading to new interactions among populations and species. The fish of the family Cyprinidae are used as model organisms as they represent most of the fish biodiversity in European continental waters and because they are particularly subject to interspecific hybridization.
In the first part of this project we will develop a simple model based on two well-studied species inhabiting the Rhône basin that display natural and viable hybrids: Rutilus rutilus x Abramis brama. In the second part, the influence of non-native invasive species that can hybridize with local species will be added to the model.
The final goal of this project is to estimate under which conditions the increasing rate of hybridization can affect the extinction risk of freshwater organisms and to provide guidance concerning the kind of data required to propose potential conservation strategies.