scholarly journals Genomic signatures of sympatric speciation with historical and contemporary gene flow in a tropical anthozoan (Hexacorallia: Actiniaria)

2019 ◽  
Vol 28 (15) ◽  
pp. 3572-3586 ◽  
Author(s):  
Benjamin M. Titus ◽  
Paul D. Blischak ◽  
Marymegan Daly
Keyword(s):  
Gene Flow ◽  
Sympatric Speciation ◽  
Genomic Signatures ◽  
Contemporary Gene Flow

scholarly journals Genomic signatures of sympatric speciation with historical and contemporary gene flow in a tropical anthozoan

2018 ◽  
Author(s):  
Benjamin M. Titus ◽  
Paul D. Blischak ◽  
Marymegan Daly
Keyword(s):  
Gene Flow ◽  
Cryptic Species ◽  
Species Complex ◽  
Sympatric Speciation ◽  
Sea Anemone ◽  
Secondary Contact ◽  
Marine Habitats ◽  
Contemporary Gene Flow ◽  
Cryptic Species Complex ◽  
Tropical Sea

AbstractSympatric diversification is increasingly thought to have played an important role in the evolution of biodiversity around the globe. However, an in situ sympatric origin for co-distributed taxa is difficult to demonstrate empirically because different evolutionary processes can lead to similar biogeographic outcomes-especially in ecosystems with few hard barriers to dispersal that can facilitate allopatric speciation followed by secondary contact (e.g. marine habitats). Here we use a genomic (ddRADseq), model-based approach to delimit a cryptic species complex of tropical sea anemones that are co-distributed on coral reefs throughout the Tropical Western Atlantic. We use coalescent simulations in fastsimcoal2 to test competing diversification scenarios that span the allopatric-sympatric continuum. We recover support that the corkscrew sea anemone Bartholomea annulata (Le Sueur, 1817) is a cryptic species complex, co-distributed throughout its range. Simulation and model selection analyses suggest these lineages arose in the face of historical and contemporary gene flow, supporting a sympatric origin, but an alternative secondary contact model also receives appreciable model support. Leveraging the genome of Exaiptasia pallida we identify five loci under divergent selection between cryptic B. annulata lineages that fall within mRNA transcripts or CDS regions. Our study provides a rare empirical, genomic example of sympatric speciation in a tropical anthozoan-a group that includes reef-building corals. Finally, these data represent the first range-wide molecular study of any tropical sea anemone, underscoring that anemone diversity is under described in the tropics, and highlighting the need for additional systematic studies into these ecologically and economically important species.

scholarly journals Genetic structure and historical and contemporary gene flow of Astyanaxmexicanus in the Gulf of Mexico slope: a microsatellite-based analysis

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10784
Author(s):  
Rodolfo Pérez-Rodríguez ◽  
Sarai Esquivel-Bobadilla ◽  
Adonaji Madeleine Orozco-Ruíz ◽  
José Luis Olivas-Hernández ◽  
Francisco Javier García-De León
Keyword(s):  
Gene Flow ◽  
Gulf Of Mexico ◽  
Microsatellite Loci ◽  
Evolutionary History ◽  
Population Analysis ◽  
Morphological Variability ◽  
High Capacity ◽  
Genetic Population ◽  
Contemporary Gene Flow ◽  
Taxonomic Uncertainty

Background Astyanax mexicanus from the river basins of the Gulf of Mexico slope are small freshwater fish that usually live in large groups in different freshwater environments. The group is considered successful due to its high capacity for dispersal and adaptation to different habitats, and the species present high morphological variability throughout their distribution in Mexico. This has produced the most extreme morphotype of the group; the hypogeous or troglobite, which has no eyes or coloration, and is probably the cause of taxonomic uncertainty in the recognition of species across the entire range. Most studies of A. mexicanus have mainly focused on cave individuals, as well as their adjacent surface locations, providing an incomplete evolutionary history, particularly in terms of factors related to dispersal and the potential corridors used, barriers to gene flow, and distribution of genetic variability. The aim of the present study is to determine the population structure and the degree and direction of genetic flow in this complex taxonomic group, incorporating geographic locations not previously included in analyses using microsatellite loci. Our aim is to contribute to the knowledge of the intricate evolutionary history of A. mexicanus throughout most of its range. Methods The present study included a set of several cave and surface locations of A. mexicanus, which have been widely sampled along the Gulf of Mexico slope, in a genetic population analysis using 10 microsatellite loci. Results Ten genetic populations or lineages were identified. In these populations, gene flow was recorded at two time periods. Historical gene flow, both inter and intra-basin, was observed among surface populations, from surface to cave populations, and among cave populations, whereas recording of contemporary gene flow was limited to intra-basin exchanges and observed among surface populations, surface to cave populations, and cave populations.

scholarly journals Fine-scale landscape genetics unveiling contemporary asymmetric movement of red panda (Ailurus fulgens) in Kangchenjunga landscape, India

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Supriyo Dalui ◽  
Hiren Khatri ◽  
Sujeet Kumar Singh ◽  
Shambadeb Basu ◽  
Avijit Ghosh ◽  
...  
Keyword(s):  
Gene Flow ◽  
Landscape Connectivity ◽  
Anthropogenic Activities ◽  
Clustering Algorithms ◽  
Area Network ◽  
Fine Scale ◽  
Contemporary Gene Flow ◽  
Red Panda ◽  
Population Structuring ◽  
Ailurus Fulgens

Abstract Wildlife management in rapid changing landscapes requires critical planning through cross cutting networks, and understanding of landscape features, often affected by the anthropogenic activities. The present study demonstrates fine-scale spatial patterns of genetic variation and contemporary gene flow of red panda (Ailurus fulgens) populations with respect to landscape connectivity in Kangchenjunga Landscape (KL), India. The study found about 1,309.54 km2 area suitable for red panda in KL—India, of which 62.21% area fell under the Protected Area network. We identified 24 unique individuals from 234 feces collected at nine microsatellite loci. The spatially explicit and non-explicit Bayesian clustering algorithms evident to exhibit population structuring and supported red panda populations to exist in meta-population frame work. In concurrence to the habitat suitability and landscape connectivity models, gene flow results supported a contemporary asymmetric movement of red panda by connecting KL—India in a crescent arc. We demonstrate the structural-operational connectivity of corridors in KL—India that facilitated red panda movement in the past. We also seek for cooperation in Nepal, Bhutan and China to aid in preparing for a comprehensive monitoring plan for the long-term conservation and management of red panda in trans-boundary landscapes.

scholarly journals Host races in plant–feeding insects and their importance in sympatric speciation

2002 ◽  
Vol 357 (1420) ◽  
pp. 471-492 ◽  
Author(s):  
Michele Drès ◽  
James Mallet
Keyword(s):  
Linkage Disequilibrium ◽  
Gene Flow ◽  
Natural Selection ◽  
Reproductive Isolation ◽  
Sympatric Speciation ◽  
Accurate Information ◽  
Sympatric Populations ◽  
New Host ◽  
Host Races ◽  
Plant Feeding

The existence of a continuous array of sympatric biotypes—from polymorphisms, through ecological or host races with increasing reproductive isolation, to good species—can provide strong evidence for a continuous route to sympatric speciation via natural selection. Host races in plant–feeding insects, in particular, have often been used as evidence for the probability of sympatric speciation. Here, we provide verifiable criteria to distinguish host races from other biotypes: in brief, host races are genetically differentiated, sympatric populations of parasites that use different hosts and between which there is appreciable gene flow. We recognize host races as kinds of species that regularly exchange genes with other species at a rate of more than ca . 1% per generation, rather than as fundamentally distinct taxa. Host races provide a convenient, although admittedly somewhat arbitrary intermediate stage along the speciation continuum. They are a heuristic device to aid in evaluating the probability of speciation by natural selection, particularly in sympatry. Speciation is thereby envisaged as having two phases: (i) the evolution of host races from within polymorphic, panmictic populations; and (ii) further reduction of gene flow between host races until the diverging populations can become generally accepted as species. We apply this criterion to 21 putative host race systems. Of these, only three are unambiguously classified as host races, but a further eight are strong candidates that merely lack accurate information on rates of hybridization or gene flow. Thus, over one–half of the cases that we review are probably or certainly host races, under our definition. Our review of the data favours the idea of sympatric speciation via host shift for three major reasons: (i) the evolution of assortative mating as a pleiotropic by–product of adaptation to a new host seems likely, even in cases where mating occurs away from the host; (ii) stable genetic differences in half of the cases attest to the power of natural selection to maintain multilocus polymorphisms with substantial linkage disequilibrium, in spite of probable gene flow; and (iii) this linkage disequilibrium should permit additional host adaptation, leading to further reproductive isolation via pleiotropy, and also provides conditions suitable for adaptive evolution of mate choice (reinforcement) to cause still further reductions in gene flow. Current data are too sparse to rule out a cryptic discontinuity in the apparently stable sympatric route from host–associated polymorphism to host–associated species, but such a hiatus seems unlikely on present evidence. Finally, we discuss applications of an understanding of host races in conservation and in managing adaptation by pests to control strategies, including those involving biological control or transgenic parasite–resistant plants.

scholarly journals Contrasting signatures of genomic divergence during sympatric speciation

Nature ◽  
2020 ◽  
Vol 588 (7836) ◽  
pp. 106-111 ◽  
Author(s):  
Andreas F. Kautt ◽  
Claudius F. Kratochwil ◽  
Alexander Nater ◽  
Gonzalo Machado-Schiaffino ◽  
Melisa Olave ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Architecture ◽  
Single Species ◽  
Sympatric Speciation ◽  
Ecological Performance ◽  
Genome Wide ◽  
Genomic Divergence ◽  
Empirical Tests ◽  
Selected Traits ◽  
Stable Genome

AbstractThe transition from ‘well-marked varieties’ of a single species into ‘well-defined species’—especially in the absence of geographic barriers to gene flow (sympatric speciation)—has puzzled evolutionary biologists ever since Darwin1,2. Gene flow counteracts the buildup of genome-wide differentiation, which is a hallmark of speciation and increases the likelihood of the evolution of irreversible reproductive barriers (incompatibilities) that complete the speciation process3. Theory predicts that the genetic architecture of divergently selected traits can influence whether sympatric speciation occurs4, but empirical tests of this theory are scant because comprehensive data are difficult to collect and synthesize across species, owing to their unique biologies and evolutionary histories5. Here, within a young species complex of neotropical cichlid fishes (Amphilophus spp.), we analysed genomic divergence among populations and species. By generating a new genome assembly and re-sequencing 453 genomes, we uncovered the genetic architecture of traits that have been suggested to be important for divergence. Species that differ in monogenic or oligogenic traits that affect ecological performance and/or mate choice show remarkably localized genomic differentiation. By contrast, differentiation among species that have diverged in polygenic traits is genomically widespread and much higher overall, consistent with the evolution of effective and stable genome-wide barriers to gene flow. Thus, we conclude that simple trait architectures are not always as conducive to speciation with gene flow as previously suggested, whereas polygenic architectures can promote rapid and stable speciation in sympatry.

scholarly journals Understanding Historical Demographic Processes to Inform Contemporary Conservation of an Arid Zone Specialist: The Yellow-Footed Rock-Wallaby

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 154
Author(s):  
Sally Potter ◽  
Linda E. Neaves ◽  
Mark Lethbridge ◽  
Mark D. B. Eldridge
Keyword(s):  
Gene Flow ◽  
Control Region ◽  
Arid Zone ◽  
Genetic Research ◽  
Mitochondrial Control Region ◽  
Genetic Connectivity ◽  
Mountain Range ◽  
Contemporary Gene Flow ◽  
Region Data ◽  
Demographic Processes

Little genetic research has been undertaken on mammals across the vast expanse of the arid biome in Australia, despite continuing species decline and need for conservation management. Here, we evaluate the contemporary and historical genetic connectivity of the yellow-footed rock-wallaby, Petrogale xanthopus xanthopus, a threatened macropodid which inhabits rocky outcrops across the disconnected mountain range systems of the southern arid biome. We use 17 microsatellite loci together with mitochondrial control region data to determine the genetic diversity of populations and the evolutionary processes shaping contemporary population dynamics on which to base conservation recommendations. Our results indicate the highly fragmented populations have reduced diversity and limited contemporary gene flow, with most populations having been through population bottlenecks. Despite limited contemporary gene flow, the phylogeographic relationships of the mitochondrial control region indicate a lack of structure and suggests greater historical connectivity. This is an emerging outcome for mammals across this arid region. On the basis of our results, we recommend augmentation of populations of P. x. xanthopus, mixing populations from disjunct mountain range systems to reduce the chance of continued diversity loss and inbreeding depression, and therefore maximize the potential for populations to adapt and survive into the future.

A temporal perspective on population structure and gene flow in Atlantic salmon (Salmo salar) in Newfoundland, Canada

2010 ◽  
Vol 67 (2) ◽  
pp. 225-242 ◽  
Author(s):  
Friso P. Palstra ◽  
Daniel E. Ruzzante
Keyword(s):  
Population Dynamics ◽  
Population Structure ◽  
Gene Flow ◽  
Atlantic Salmon ◽  
Salmo Salar ◽  
Environmental Changes ◽  
Population Connectivity ◽  
Temporal Perspective ◽  
Atlantic Salmon Salmo Salar ◽  
Contemporary Gene Flow

Studying population structure and gene flow patterns on temporal scales facilitates an evaluation of the consequences of demographic, physical, and environmental changes on the stability and persistence of populations. Here, we examine temporal genetic variation within and among Atlantic salmon ( Salmo salar ) rivers in Newfoundland and Labrador, Canada, using samples collected over a period of six decades (1951–2004). Our objective was to evaluate temporal changes in population connectivity associated with the closure of a commercial marine fishery. Despite demographic instability, we find that population structure remained temporally stable over more than 50 years. However, age structure can affect results when not taken into consideration, particularly in populations of large effective size where genetic drift is not strong. Where weak signals of genetic differentiation did not complicate analyses, contemporary migration was often asymmetric, yet low, suggesting patterns of intermittent gene flow. Nevertheless, we find some links between changes in population dynamics and contemporary gene flow. These findings may therefore imply that management decisions impacting the contemporary population dynamics of individual Atlantic salmon rivers can also affect the genetic stability of this species as a whole.

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