Population genetic divergence corresponds with species-level biodiversity patterns in the large genusBegonia

Liriodendron is a Tertiary period relic tree genus with a typical East Asian and North American disjunction distribution pattern. As an angiosperm base group of trees, Liriodendron provides a valuable resource for the study of evolution processes. Here, we reconstruct the phylogeny and population genetic structure of Liriodendron based on the restriction site-associated DNA sequencing (RAD-Seq) of a wide collection of individuals from 16 populations. Our results reveal a clear phylogenetic break between L. chinense and L. tulipifera and obvious genetic divergence between the eastern and western populations of L. chinense, which are consistent with the patterns of geographical distributions. The phylogeographic history and long-term geographical isolation of the genus may be responsible for this pattern. Furthermore, a closer relationship was found between L. tulipifera and the eastern populations of L. chinense, indicating the ancient phylogeny of L. chinense in this area. The results of this study will aid in the development of scientific strategies for the conservation and utilization of the Liriodendron germplasm.

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Population Genetic Divergence and Environment Influence the Gut Microbiome in Oregon Threespine Stickleback

Genes ◽

10.3390/genes10070484 ◽

2019 ◽

Vol 10 (7) ◽

pp. 484 ◽

Cited By ~ 6

Author(s):

Steury ◽

Currey ◽

Cresko ◽

Bohannan

Keyword(s):

Gut Microbiome ◽

Genetic Divergence ◽

Population Genetic ◽

Host Population ◽

Threespine Stickleback ◽

Wild Host ◽

Microbiome Research ◽

Host Genetic ◽

Combine Population ◽

Natural Ecology

Much of animal-associated microbiome research has been conducted in species for which little is known of their natural ecology and evolution. Microbiome studies that combine population genetic, environment, and geographic data for wild organisms can be very informative, especially in situations where host genetic variation and the environment both influence microbiome variation. The few studies that have related population genetic and microbiome variation in wild populations have been constrained by observation-based kinship data or incomplete genomic information. Here we integrate population genomic and microbiome analyses in wild threespine stickleback fish distributed throughout western Oregon, USA. We found that gut microbiome diversity and composition partitioned more among than within wild host populations and was better explained by host population genetic divergence than by environment and geography. We also identified gut microbial taxa that were most differentially abundant across environments and across genetically divergent populations. Our findings highlight the benefits of studies that investigate host-associated microbiomes in wild organisms.

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Population genetic divergence of bonnethead sharks Sphyrna tiburo in the western North Atlantic: Implications for conservation

Aquatic Conservation Marine and Freshwater Ecosystems ◽

10.1002/aqc.3434 ◽

2020 ◽

Author(s):

Píndaro Díaz‐Jaimes ◽

Natalia J. Bayona‐Vásquez ◽

Elena Escatel‐Luna ◽

Manuel Uribe‐Alcocer ◽

Carlo Pecoraro ◽

...

Keyword(s):

North Atlantic ◽

Genetic Divergence ◽

Population Genetic ◽

Sphyrna Tiburo

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Post-Glacial Expansion and Population Genetic Divergence of Mangrove Species Avicennia germinans (L.) Stearn and Rhizophora mangle L. along the Mexican Coast

PLoS ONE ◽

10.1371/journal.pone.0093358 ◽

2014 ◽

Vol 9 (4) ◽

pp. e93358 ◽

Cited By ~ 26

Author(s):

Eduardo Sandoval-Castro ◽

Richard S. Dodd ◽

Rafael Riosmena-Rodríguez ◽

Luis Manuel Enríquez-Paredes ◽

Cristian Tovilla-Hernández ◽

...

Keyword(s):

Genetic Divergence ◽

Population Genetic ◽

Rhizophora Mangle ◽

Avicennia Germinans ◽

Mangrove Species ◽

Glacial Expansion

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Isolation by resistance across a complex coral reef seascape

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2015.1217 ◽

2015 ◽

Vol 282 (1812) ◽

pp. 20151217 ◽

Cited By ~ 20

Author(s):

Luke Thomas ◽

W. Jason Kennington ◽

Michael Stat ◽

Shaun P. Wilkinson ◽

Johnathan T. Kool ◽

...

Keyword(s):

Gene Flow ◽

Genetic Structure ◽

Genetic Divergence ◽

Larval Dispersal ◽

Population Genetic ◽

Spatial Genetic Structure ◽

Spatial Scales ◽

Genetic Data ◽

Genetic Structure Of Populations ◽

Seascape Genetics

A detailed understanding of the genetic structure of populations and an accurate interpretation of processes driving contemporary patterns of gene flow are fundamental to successful spatial conservation management. The field of seascape genetics seeks to incorporate environmental variables and processes into analyses of population genetic data to improve our understanding of forces driving genetic divergence in the marine environment. Information about barriers to gene flow (such as ocean currents) is used to define a resistance surface to predict the spatial genetic structure of populations and explain deviations from the widely applied isolation-by-distance model. The majority of seascape approaches to date have been applied to linear coastal systems or at large spatial scales (more than 250 km), with very few applied to complex systems at regional spatial scales (less than 100 km). Here, we apply a seascape genetics approach to a peripheral population of the broadcast-spawning coral Acropora spicifera across the Houtman Abrolhos Islands, a high-latitude complex coral reef system off the central coast of Western Australia. We coupled population genetic data from a panel of microsatellite DNA markers with a biophysical dispersal model to test whether oceanographic processes could explain patterns of genetic divergence. We identified significant variation in allele frequencies over distances of less than 10 km, with significant differentiation occurring between adjacent sites but not between the most geographically distant ones. Recruitment probabilities between sites based on simulated larval dispersal were projected into a measure of resistance to connectivity that was significantly correlated with patterns of genetic divergence, demonstrating that patterns of spatial genetic structure are a function of restrictions to gene flow imposed by oceanographic currents. This study advances our understanding of the role of larval dispersal on the fine-scale genetic structure of coral populations across a complex island system and applies a methodological framework that can be tailored to suit a variety of marine organisms with a range of life-history characteristics.

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Evaluating the utility of the female-specific mitochondrialf-orfgene for population genetic, phylogeographic and systematic studies in freshwater mussels (Bivalvia: Unionida)

PeerJ ◽

10.7717/peerj.5007 ◽

2018 ◽

Vol 6 ◽

pp. e5007 ◽

Cited By ~ 3

Author(s):

Brent M. Robicheau ◽

Emily E. Chase ◽

Walter R. Hoeh ◽

John L. Harris ◽

Donald T. Stewart ◽

...

Keyword(s):

Population Genetic ◽

Freshwater Mussels ◽

Mitochondrial Protein ◽

Species Level ◽

Uniparental Inheritance ◽

Genome Sequences ◽

Doubly Uniparental Inheritance ◽

Protein Coding ◽

Coding Regions ◽

Female Specific

Freshwater mussels (order: Unionida) represent one of the most critically imperilled groups of animals; consequently, there exists a need to establish a variety of molecular markers for population genetics and systematic studies in this group. Recently, two novel mitochondrial protein-coding genes were described in unionoids with doubly uniparental inheritance of mtDNA. These genes are thef-orfin female-transmitted mtDNA and them-orfin male-transmitted mtDNA. In this study, whole F-type mitochondrial genome sequences of two morphologically similarLampsilisspp. were compared to identify the most divergent protein-coding regions, including thef-orfgene, and evaluate its utility for population genetic and phylogeographic studies in the subfamily Ambleminae. We also tested whether thef-orfgene is phylogenetically informative at the species level. Our preliminary results indicated that thef-orfgene could represent a viable molecular marker for population- and species-level studies in freshwater mussels.

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KoT: an automatic implementation of the K/θ method for species delimitation

10.1101/2021.08.17.454531 ◽

2021 ◽

Author(s):

Yann Spöri ◽

Fabio Stoch ◽

Simon Dellicour ◽

C. William Birky ◽

Jean-François Flot

Keyword(s):

Genetic Diversity ◽

Species Delimitation ◽

Population Genetic ◽

Average Distance ◽

Species Level ◽

Species Boundaries ◽

Fasta File ◽

Genetic Theory ◽

Putative Species ◽

The Impact

K/θ is a method to delineate species that rests on the calculation of the ratio between the average distance K separating two putative species-level clades and the genetic diversity θ of these clades. Although this method is explicitly rooted in population genetic theory, it was never benchmarked due to the absence of a program allowing automated analyses. For the same reason, its application by hand was limited to small datasets of a few tens of sequences. We present an automatic implementation of the K/θ method, dubbed KoT (short for "K over Theta"), that takes as input a FASTA file, builds a neighbour-joining tree, and returns putative species boundaries based on a user-specified K/θ threshold. This automatic implementation avoids errors and makes it possible to apply the method to datasets comprising many sequences, as well as to test easily the impact of choosing different K/θ threshold ratios. KoT is implemented in Haxe, with a javascript webserver interface freely available at https://eeg-ebe.github.io/KoT/ .

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