Is Niagara Falls a barrier to gene flow in riverine fishes? A test using genome‐wide SNP data from seven native species

2020 ◽  
Vol 29 (7) ◽  
pp. 1235-1249 ◽  
Author(s):  
Nathan K. Lujan ◽  
Jason T. Weir ◽  
Brice P. Noonan ◽  
Nathan R. Lovejoy ◽  
Nicholas E. Mandrak
Keyword(s):  
Gene Flow ◽  
Native Species ◽  
Niagara Falls ◽  
Snp Data ◽  
Genome Wide

scholarly journals Genetic analysis of Sephardic ancestry in the Iberian Peninsula

2018 ◽  
Author(s):  
Miguel Martín Álvarez-Álvarez ◽  
Neil Risch ◽  
Christopher R. Gignoux ◽  
Scott Huntsman ◽  
Elad Ziv ◽  
...  
Keyword(s):  
Gene Flow ◽  
Iberian Peninsula ◽  
Eastern Mediterranean ◽  
Genetic Data ◽  
North African ◽  
Religious Persecution ◽  
South Italy ◽  
Target Populations ◽  
Snp Data ◽  
Genome Wide

AbstractThe Sephardim are a major Jewish ethnic division whose origins can be traced back to the Iberian Peninsula. We used genome-wide SNP data to investigate the degree of Sephardic admixture in seven populations from the Iberian Peninsula and surrounding regions in the aftermath of their religious persecution starting in the late 14th century. To this end, we used Eastern Mediterranean (from South Italy, Greece and Israel) and North African (Tunisian and Moroccan) populations as proxies for the major ancestral components found in the target populations and carried out unlinked- and linked-marker analyses on the available genetic data. We report evidence of Sephardic ancestry in some of our Iberian samples, as well as in North Italy and Tunisia. We find the Sephardic admixture to be more recent relative to the Berber admixture following an out-of-Iberia geographic dispersal, suggesting Sephardic gene flow from Spain outwards. We also report some of the challenges in assigning Sephardic ancestry to potentially admixed individuals due to the lack of a clear genetic signature.

scholarly journals Genome-wide single nucleotide polymorphism scan suggests adaptation to urbanization in an important pollinator, the red-tailed bumblebee ( Bombus lapidarius L.)

2018 ◽  
Vol 285 (1877) ◽  
pp. 20172806 ◽  
Author(s):  
Panagiotis Theodorou ◽  
Rita Radzevičiūtė ◽  
Belinda Kahnt ◽  
Antonella Soro ◽  
Ivo Grosse ◽  
...  
Keyword(s):  
Gene Flow ◽  
Native Species ◽  
Sampling Site ◽  
Urban Land Use ◽  
Genomic Diversity ◽  
Genetic Structuring ◽  
Single Nucleotide ◽  
Insect Pollinator ◽  
Genome Wide ◽  
German Cities

Urbanization is considered a global threat to biodiversity; the growth of cities results in an increase in impervious surfaces, soil and air pollution, fragmentation of natural vegetation and invasion of non-native species, along with numerous environmental changes, including the heat island phenomenon. The combination of these effects constitutes a challenge for both the survival and persistence of many native species, while also imposing altered selective regimes. Here, using 110 314 single nucleotide polymorphisms generated by restriction-site-associated DNA sequencing, we investigated the genome-wide effects of urbanization on putative neutral and adaptive genomic diversity in a major insect pollinator, Bombus lapidarius , collected from nine German cities and nine paired rural sites. Overall, genetic differentiation among sites was low and there was no obvious genome-wide genetic structuring, suggesting the absence of strong effects of urbanization on gene flow. We nevertheless identified several loci under directional selection, a subset of which was associated with urban land use, including the percentage of impervious surface surrounding each sampling site. Overall, our results provide evidence of local adaptation to urbanization in the face of gene flow in a highly mobile insect pollinator.

scholarly journals Riverscape genomics of cichlid fishes in the lower Congo: Uncovering mechanisms of diversification in an extreme hydrological regime

2021 ◽  
Author(s):  
Naoko Kurata ◽  
Michael Hickerson ◽  
Sandra Hoffberg ◽  
Ned Gardiner ◽  
Melanie L.J. Stiassny ◽  
...  
Keyword(s):  
Gene Flow ◽  
Spatial Scales ◽  
Hydrological Regime ◽  
High Energy ◽  
Ecological Specialization ◽  
Cichlid Fishes ◽  
Heterogeneous Habitats ◽  
Snp Data ◽  
Genome Wide ◽  
Physical Barriers

Rivers provide excellent models to understand how species diversity is generated and maintained across heterogeneous habitats. The lower Congo River (LCR) consists of a dynamic hydroscape exhibiting extraordinary aquatic biodiversity, endemicity, and ecological specialization. Previous studies have suggested that the numerous high-energy rapids throughout the LCR form physical barriers to gene flow, thus facilitating diversification and speciation, and generating ichthyofaunal diversity. However, this hypothesis has not been fully explored using genome-wide SNPs for fish species distributed across the LCR. In this study, we examined four species of lamprologine cichlids endemic to the LCR, of which three are sequentially distributed along the LCR without range overlap. Using genome-wide SNP data, we tested the hypotheses that high-energy rapids serve as physical barriers to gene flow that generate genetic divergence at inter- and intraspecific levels, and that gene flow occurs primarily in a downstream direction. Our results are consistent with the prediction that the rapids sometimes serve to reduce gene flow, but also suggest that at certain temporal and spatial scales, they may also act as promoters of gene flow. Furthermore, we detected both upstream and downstream gene flow between some populations of Lamprologus tigripictilis as well as hybridization between congeneric species. These results suggest that powerful high-energy rapids may therefore provide occasional multidirectional dispersal opportunities for riverine cichlid fishes, highlighting the complexity of factors driving evolutionary processes in the LCR.

scholarly journals Denisovan Ancestry in East Eurasian and Native American Populations.

2015 ◽  
Author(s):  
Pengfei Qin ◽  
Mark Stoneking
Keyword(s):  
Native American ◽  
Gene Flow ◽  
New Guinea ◽  
Modern Human ◽  
Common Source ◽  
Human Populations ◽  
Snp Data ◽  
Genome Wide ◽  
Or Gene ◽  
The Relationship

Although initial studies suggested that Denisovan ancestry was found only in modern human populations from island Southeast Asia and Oceania, more recent studies have suggested that Denisovan ancestry may be more widespread. However, the geographic extent of Denisovan ancestry has not been determined, and moreover the relationship between the Denisovan ancestry in Oceania and that elsewhere has not been studied. Here we analyze genome-wide SNP data from 2493 individuals from 221 worldwide populations, and show that there is a widespread signal of a very low level of Denisovan ancestry across Eastern Eurasian and Native American (EE/NA) populations. We also verify a higher level of Denisovan ancestry in Oceania than that in EE/NA; the Denisovan ancestry in Oceania is correlated with the amount of New Guinea ancestry, but not the amount of Australian ancestry, indicating that recent gene flow from New Guinea likely accounts for signals of Denisovan ancestry across Oceania. However, Denisovan ancestry in EE/NA populations is equally correlated with their New Guinea or their Australian ancestry, suggesting a common source for the Denisovan ancestry in EE/NA and Oceanian populations. Our results suggest that Denisovan ancestry in EE/NA is derived either from common ancestry with, or gene flow from, the common ancestor of New Guineans and Australians, indicating a more complex history involving East Eurasians and Oceanians than previously suspected.

scholarly journals What is a dingo – origins, hybridisation and identity

2021 ◽  
Author(s):  
Kylie M Cairns
Keyword(s):  
Native Species ◽  
Evolutionary Relationship ◽  
Domestic Dog ◽  
Ongoing Debate ◽  
Dna Test ◽  
Southeastern Australia ◽  
Snp Data ◽  
Genome Wide ◽  
Future Work ◽  
The Impact

ABSTRACT Controversy about the nomenclature and taxonomy of dingoes has sparked interest in their complex identity. At the root of taxonomy debates are differences in the species concepts employed, differing opinions about the domestication status of dingoes (and their ancestors) and a simplistic handling of the complex evolutionary relationship between wolves, dingoes and domestic dogs. I explore the relationship of dingoes to village dogs, modern breed dogs and wolves using genome-wide SNP data and discuss the implications of these findings to the ongoing debate about dingo identity and nomenclature. Importantly, despite controversy about what to call dingoes and whether they are a full species, these animals represent an important, distinct and unique evolutionary unit worthy of high conservation priority, as a native species. There is growing concern about the spread of domestic dog genes into dingo populations, particularly in southeastern Australia, and the impact this has on conservation goals. However, the discovery of biogeographic subdivision within dingoes raises questions about the accuracy of the current methods used for estimating dog vs dingo ancestry. I caution scientists and wildlife managers to carefully consider the limitations of current ancestry estimate methods when assessing DNA test results. Future work using genome-wide DNA technology to improve dingo ancestry estimates will be fundamental to ongoing debate about what dingoes are, how to identify dingoes and how to conserve them.

scholarly journals Genome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kyung Seok Kim ◽  
Kevin J. Roe
Keyword(s):  
Phylogenetic Analyses ◽  
Freshwater Mussel ◽  
Conservation Strategies ◽  
Nucleotide Polymorphisms ◽  
Conservation Units ◽  
Genetic Structuring ◽  
The North ◽  
Snp Data ◽  
Genome Wide ◽  
Significant Difference

AbstractDetailed information on species delineation and population genetic structure is a prerequisite for designing effective restoration and conservation strategies for imperiled organisms. Phylogenomic and population genomic analyses based on genome-wide double digest restriction-site associated DNA sequencing (ddRAD-Seq) data has identified three allopatric lineages in the North American freshwater mussel genus Cyprogenia. Cyprogenia stegaria is restricted to the Eastern Highlands and displays little genetic structuring within this region. However, two allopatric lineages of C. aberti in the Ozark and Ouachita highlands exhibit substantial levels (mean uncorrected FST = 0.368) of genetic differentiation and each warrants recognition as a distinct evolutionary lineage. Lineages of Cyprogenia in the Ouachita and Ozark highlands are further subdivided reflecting structuring at the level of river systems. Species tree inference and species delimitation in a Bayesian framework using single nucleotide polymorphisms (SNP) data supported results from phylogenetic analyses, and supports three species of Cyprogenia over the currently recognized two species. A comparison of SNPs generated from both destructively and non-destructively collected samples revealed no significant difference in the SNP error rate, quality and amount of ddRAD sequence reads, indicating that nondestructive or trace samples can be effectively utilized to generate SNP data for organisms for which destructive sampling is not permitted.

scholarly journals Genome-wide SNP data unravel the ancestry and signatures of divergent selection in Ghurrah pigs of India

2021 ◽  
pp. 104587
Author(s):  
Arnav Mehrotra ◽  
Bharat Bhushan ◽  
Karthikeyan A ◽  
Akansha Singh ◽  
Snehasmita Panda ◽  
...  
Keyword(s):  
Divergent Selection ◽  
Snp Data ◽  
Genome Wide

scholarly journals On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Gabriele Senczuk ◽  
Salvatore Mastrangelo ◽  
Paolo Ajmone-Marsan ◽  
Zsolt Becskei ◽  
Paolo Colangelo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Diversity Indices ◽  
Melting Pot ◽  
Cattle Breeds ◽  
Snp Data ◽  
Early Migration ◽  
Genome Wide ◽  
European Colonization ◽  
Approximate Bayesian ◽  
European Cattle

Abstract Background During the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so-called Podolian trunk, the history of which is still not well established. Here, we used genome-wide single nucleotide polymorphism (SNP) data on 806 individuals belonging to 36 breeds to reconstruct the origin and diversification of Podolian cattle and to provide a reliable scenario of the European colonization, through an approximate Bayesian computation random forest (ABC-RF) approach. Results Our results indicate that European Podolian cattle display higher values of genetic diversity indices than both African taurine and Asian indicine breeds. Clustering analyses show that Podolian breeds share close genomic relationships, which suggests a likely common genetic ancestry. Among the simulated and tested scenarios of the colonization of Europe from taurine cattle, the greatest support was obtained for the model assuming at least two waves of diffusion. Time estimates are in line with an early migration from the domestication centre of non-Podolian taurine breeds followed by a secondary migration of Podolian breeds. The best fitting model also suggests that the Italian Podolian breeds are the result of admixture between different genomic pools. Conclusions This comprehensive dataset that includes most of the autochthonous cattle breeds belonging to the so-called Podolian trunk allowed us not only to shed light onto the origin and diversification of this group of cattle, but also to gain new insights into the diffusion of European cattle. The most well-supported scenario of colonization points to two main waves of migrations: with one that occurred alongside with the Neolithic human expansion and gave rise to the non-Podolian taurine breeds, and a more recent one that favoured the diffusion of European Podolian. In this process, we highlight the importance of both the Mediterranean and Danube routes in promoting European cattle colonization. Moreover, we identified admixture as a driver of diversification in Italy, which could represent a melting pot for Podolian cattle.

Sign in / Sign up

Export Citation Format

Share Document