scholarly journals The Spatial Mixing of Genomes in Secondary Contact Zones

2015 ◽  
Author(s):  
Alisa Sedghifar ◽  
Yaniv Brandvain ◽  
Peter L. Ralph ◽  
Graham Coop
Keyword(s):  
Contact Zone ◽  
Dispersal Distance ◽  
Secondary Contact ◽  
Zone Model ◽  
Demographic Model ◽  
Contact Zones ◽  
Geographic Space ◽  
Indonesian Archipelago ◽  
Population Genomic ◽  
Genomic Studies

Recent genomic studies have highlighted the important role of admixture in shaping genome-wide patterns of diversity. Past admixture leaves a population genomic signature of linkage disequilibrium (LD), reflecting the mixing of parental chromosomes by segregation and recombination. The extent of this LD can be used to infer the timing of admixture. However, the results of inference can depend strongly on the assumed demographic model. Here, we introduce a theoretical framework for modeling patterns of LD in a geographic contact zone where two differentiated populations are diffusing back together. We derive expressions for the expected LD and admixture tract lengths across geographic space as a function of the age of the contact zone and the dispersal distance of individuals. We develop an approach to infer age of contact zones using population genomic data from multiple spatially sampled populations by fitting our model to the decay of LD with recombination distance. We use our approach to explore the fit of a geographic contact zone model to three human population genomic datasets from populations along the Indonesian archipelago, populations in Central Asia and populations in India.

scholarly journals Mitochondrial Ecophysiology: Assessing the Evolutionary Forces That Shape Mitochondrial Variation

2019 ◽  
Vol 59 (4) ◽  
pp. 925-937 ◽  
Author(s):  
Jessica L McKenzie ◽  
Dillon J Chung ◽  
Timothy M Healy ◽  
Reid S Brennan ◽  
Heather J Bryant ◽  
...  
Keyword(s):  
Adaptive Evolution ◽  
Mitochondrial Function ◽  
Fundulus Heteroclitus ◽  
Secondary Contact ◽  
Mitochondrial Genomes ◽  
Evolutionary Forces ◽  
Population Genomic ◽  
Genomic Studies

Abstract The mitonuclear species concept hypothesizes that incompatibilities between interacting gene products of the nuclear and mitochondrial genomes are a major factor establishing and maintaining species boundaries. However, most of the data available to test this concept come from studies of genetic variation in mitochondrial DNA, and clines in the mitochondrial genome across contact zones can be produced by a variety of forces. Here, we show that using a combination of population genomic analyses of the nuclear and mitochondrial genomes and studies of mitochondrial function can provide insight into the relative roles of neutral processes, adaptive evolution, and mitonuclear incompatibility in establishing and maintaining mitochondrial clines, using Atlantic killifish (Fundulus heteroclitus) as a case study. There is strong evidence for a role of secondary contact following the last glaciation in shaping a steep mitochondrial cline across a contact zone between northern and southern subspecies of killifish, but there is also evidence for a role of adaptive evolution in driving differentiation between the subspecies in a variety of traits from the level of the whole organism to the level of mitochondrial function. In addition, studies are beginning to address the potential for mitonuclear incompatibilities in admixed populations. However, population genomic studies have failed to detect evidence for a strong and pervasive influence of mitonuclear incompatibilities, and we suggest that polygenic selection may be responsible for the complex patterns observed. This case study demonstrates that multiple forces can act together in shaping mitochondrial clines, and illustrates the challenge of disentangling their relative roles.

scholarly journals Landscape resistance constrains hybridization across contact zones in a reproductively and morphologically polymorphic salamander

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Guillermo Velo-Antón ◽  
André Lourenço ◽  
Pedro Galán ◽  
Alfredo Nicieza ◽  
Pedro Tarroso
Keyword(s):  
Contact Zone ◽  
Environmental Heterogeneity ◽  
Evolutionary Dynamics ◽  
Morphological Differentiation ◽  
Phenotypic Traits ◽  
Hybrid Zones ◽  
Landscape Resistance ◽  
Phenotypic Differentiation ◽  
Contact Zones

AbstractExplicitly accounting for phenotypic differentiation together with environmental heterogeneity is crucial to understand the evolutionary dynamics in hybrid zones. Species showing intra-specific variation in phenotypic traits that meet across environmentally heterogeneous regions constitute excellent natural settings to study the role of phenotypic differentiation and environmental factors in shaping the spatial extent and patterns of admixture in hybrid zones. We studied three environmentally distinct contact zones where morphologically and reproductively divergent subspecies of Salamandra salamandra co-occur: the pueriparous S. s. bernardezi that is mostly parapatric to its three larviparous subspecies neighbours. We used a landscape genetics framework to: (i) characterise the spatial location and extent of each contact zone; (ii) assess patterns of introgression and hybridization between subspecies pairs; and (iii) examine the role of environmental heterogeneity in the evolutionary dynamics of hybrid zones. We found high levels of introgression between parity modes, and between distinct phenotypes, thus demonstrating the evolution to pueriparity alone or morphological differentiation do not lead to reproductive isolation between these highly divergent S. salamandra morphotypes. However, we detected substantial variation in patterns of hybridization across contact zones, being lower in the contact zone located on a topographically complex area. We highlight the importance of accounting for spatial environmental heterogeneity when studying evolutionary dynamics of hybrid zones.

scholarly journals What could be the fate of secondary contact zones between closely related plant species?

2020 ◽  
Vol 43 (2) ◽  
Author(s):  
Carolina K. Schnitzler ◽  
Caroline Turchetto ◽  
Marcelo C. Teixeira ◽  
Loreta B. Freitas
Keyword(s):  
Plant Species ◽  
Secondary Contact ◽  
Contact Zones ◽  
Related Plant

Extensive hybridization between two Andean warbler species with shallow divergence in mtDNA

The Auk ◽  
2021 ◽  
Vol 138 (1) ◽  
Author(s):  
Laura N Céspedes-Arias ◽  
Andrés M Cuervo ◽  
Elisa Bonaccorso ◽  
Marialejandra Castro-Farias ◽  
Alejandro Mendoza-Santacruz ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Contact Zone ◽  
Hybrid Zone ◽  
Secondary Contact ◽  
Tropical Andes ◽  
Phenotypic Data ◽  
Geographic Ranges ◽  
Intermediate Phenotypes ◽  
Ecological Barriers

Abstract Studying processes acting on differentiated populations upon secondary contact, such as hybridization, is important to comprehensively understand how species are formed and maintained over time. However, avian speciation studies in the tropical Andes have largely focused on the role of topographic and ecological barriers promoting divergence in allopatry, seldom examining hybridization and introgression. We describe a hybrid zone involving 2 closely related Andean warblers (Parulidae), the Golden-fronted Redstart (Myioborus ornatus), and the Spectacled Redstart (Myioborus melanocephalus). Geographic ranges of these species abut near the Colombia-Ecuador border and many specimens from the region exhibit intermediate phenotypes, but a formal description of phenotypic variation in the contact zone was heretofore lacking. We collected specimens across a transect encompassing the area where ranges abut and areas where only “pure” parental phenotypes of M. ornatus chrysops and M. melanocephalus ruficoronatus occur. We described variation in plumage traits including patterns of head and ventral coloration and tail markings based on 321 specimens. To describe genetic variation in the contact zone and over a broader phylogeographic context, we used sequences of the mitochondrial ND2 gene for 219 individuals across the transect and the entire range of both species, including all subspecies, from Venezuela to Bolivia. We documented a hybrid zone ~200 km wide based on head coloration, where intermediate plumage phenotypes are most common and “pure” forms do not overlap geographically, consistent with extensive hybridization. Across the range of the M. ornatus–M. melanocephalus complex, mitochondrial genetic structure was shallow, with genetic breaks only coinciding clearly with one topographic feature. Such a low genetic structure is striking given the high diversity in plumage phenotypes and the current taxonomy of the group. Our phenotypic data suggest that barriers to hybridization are not strong, and allow us to postulate hypotheses to be tested using forthcoming genomic data.

The distribution and biogeography of slow worms (Anguis, Squamata) across the Western Palearctic, with an emphasis on secondary contact zones

2021 ◽  
pp. 1-12
Author(s):  
Daniel Jablonski ◽  
Neftalí Sillero ◽  
Oleksandra Oskyrko ◽  
Adriana Bellati ◽  
Andris Čeirāns ◽  
...  
Keyword(s):  
Natural History ◽  
Genetic Data ◽  
Secondary Contact ◽  
Hybrid Zones ◽  
Grey Zone ◽  
Contact Zones ◽  
Distribution Maps ◽  
Western Palearctic ◽  
Southern Balkans

Abstract The slow-worm lizards (Anguis) comprise five species occurring throughout most of the Western Palearctic. Although these species are relatively uniform morphologically – with the exception of A. cephallonica, which exhibits a quite unique morphology – they are genetically deeply divergent. Here, we provide detailed distribution maps for each species and discuss their biogeography and conservation based on updated genetic data and a robust distribution database. We pay particular attention to the so called ‘grey zone’, which typically represents secondary contact zones and in some cases confirmed or presumed hybrid zones. Four of the five species live in parapatry, while only two species, A. cephallonica and A. graeca from the southern Balkans occur in partial sympatry. Further research should focus on the eco-evolutionary interactions between species in contact, including their hybridization rates, to reveal deeper details of the slow-worm evolutionary and natural history.

Evolution and Adaptation of Forest and Crop Pathogens in the Anthropocene

2020 ◽  
pp. PHYTO-08-20-035
Author(s):  
Pauline Hessenauer ◽  
Nicolas Feau ◽  
Upinder Gill ◽  
Benjamin Schwessinger ◽  
Gurcharn S. Brar ◽  
...  
Keyword(s):  
Population Genomics ◽  
Production Systems ◽  
Management Strategies ◽  
Forest Trees ◽  
Forest Production ◽  
Population Genomic ◽  
Genomic Studies ◽  
Pathogen Populations ◽  
Different Characteristics ◽  
Global Food

Anthropocene marks the era when human activity is making a significant impact on earth, its ecological and biogeographical systems. The domestication and intensification of agricultural and forest production systems have had a large impact on plant and tree health. Some pathogens benefitted from these human activities and have evolved and adapted in response to the expansion of crop and forest systems, resulting in global outbreaks. Global pathogen genomics data including population genomics and high-quality reference assemblies are crucial for understanding the evolution and adaptation of pathogens. Crops and forest trees have remarkably different characteristics, such as reproductive time and the level of domestication. They also have different production systems for disease management with more intensive management in crops than forest trees. By comparing and contrasting results from pathogen population genomic studies done on widely different agricultural and forest production systems, we can improve our understanding of pathogen evolution and adaptation to different selection pressures. We find that in spite of these differences, similar processes such as hybridization, host jumps, selection, specialization, and clonal expansion are shaping the pathogen populations in both crops and forest trees. We propose some solutions to reduce these impacts and lower the probability of global pathogen outbreaks so that we can envision better management strategies to sustain global food production as well as ecosystem services.

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