Speciation in the presence of gene flow: population genomics of closely related and diverging Eucalyptus species

AbstractPopulation genomic approaches can characterise dispersal across a single generation through to many generations in the past, bridging the gap between individual movement and intergenerational gene flow. These approaches are particularly useful when investigating dispersal in recently altered systems, where they provide a way of inferring long-distance dispersal between newly established populations and their interactions with existing populations. Human-mediated biological invasions represent such altered systems which can be investigated with appropriate study designs and analyses. Here we apply temporally-restricted sampling and a range of population genomic approaches to investigate dispersal in a 2004 invasion of Aedes albopictus (the Asian tiger mosquito) in the Torres Strait Islands (TSI) of Australia. We sampled mosquitoes from 13 TSI villages simultaneously and genotyped 373 mosquitoes at genome-wide single nucleotide polymorphisms (SNPs): 331 from the TSI, 36 from Papua New Guinea (PNG), and 4 incursive mosquitoes detected in uninvaded regions. Within villages, spatial genetic structure varied substantially but overall displayed isolation by distance and a neighbourhood size of 232–577. Close kin dyads revealed recent movement between islands 31–203 km apart, and deep learning inferences showed incursive Ae. albopictus had travelled to uninvaded regions from both adjacent and non-adjacent islands. Private alleles and a coancestry matrix indicated direct gene flow from PNG into nearby islands. Outlier analyses also detected four linked alleles introgressed from PNG, with the alleles surrounding 12 resistance-associated cytochrome P450 genes. By treating dispersal as both an intergenerational process and a set of discrete events, we describe a highly interconnected invasive system.

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Gene Flow Between Introduced and Native Eucalyptus Species: Morphological Analysis of Tri-Species and Backcross Hybrids Involving E. nitens

Silvae Genetica ◽

10.1515/sg-2007-0019 ◽

2007 ◽

Vol 56 (1-6) ◽

pp. 127-133 ◽

Cited By ~ 7

Author(s):

C. Barbour ◽

B. M. Potts ◽

R. E. Vaillancourt

Keyword(s):

Gene Flow ◽

Second Generation ◽

Current Work ◽

F1 Hybrids ◽

Morphological Identification ◽

Eucalyptus Species ◽

Pure Species ◽

Backcross Hybrids ◽

In The Wild ◽

Species Hybrids

Summary Morphometric analyses were conducted on second-generation tri-species and backcross hybrids in Eucalyptus. These hybrids were all produced using pollen from two E. nitens x cordata F1 hybrids and controlled pollination techniques. Tri-species hybrids were created with E. gunnii, E. ovata and E. viminalis as females, while backcrosses were produced with E. cordata. Multivariate analysis of seedling characteristics indicated that eighty percent of the backcross hybrids fell within the morphological range of E. cordata. All three cross combinations of the tri-species hybrids were biased away from E. nitens and towards their maternal parent and E. cordata. The inclusion of data for first-generation (F1) hybrids between the pure parental species in the current work showed the F1’s to be easily distinguishable from pure species, compared to second-generation hybrids. The use of morphology for detecting second-generation hybridisation involving exotic plantation species and native eucalypt populations will therefore be unreliable, and identifies a need for preventing second-generation hybrids from establish in the wild. The current work, nevertheless, provides further demonstration of the effectiveness of morphological identification of F1 hybrids. The easy recognition of F1 hybrids will be useful in identifying sites and species at risk of exotic gene flow and enable the development of weeding programs that focus on removing exotic hybrids in the wild.

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Gene flow between introduced and native Eucalyptus species: crossability of native Tasmanian species with exotic E. nitens

Australian Journal of Botany ◽

10.1071/bt05021 ◽

2005 ◽

Vol 53 (5) ◽

pp. 465 ◽

Cited By ~ 15

Author(s):

R. C. Barbour ◽

B. M. Potts ◽

R. E. Vaillancourt

Keyword(s):

Gene Flow ◽

Native Species ◽

Seed Set ◽

Pollen Competition ◽

F1 Hybrids ◽

Eucalyptus Species ◽

F1 Hybrid ◽

Genetic Pollution ◽

Morphometric Analyses ◽

Natural Hybridisation

Eucalyptus nitens (Deane & Maiden) Maiden has been extensively introduced to the island of Tasmania for plantation purposes. Natural hybridisation with two native species has already been confirmed and this study aimed to determine which other Tasmanian native species could potentially hybridise with E. nitens. Controlled and supplementary pollinations with E. nitens pollen were undertaken on all Tasmanian native species that are potentially at risk of exotic gene flow and hence genetic pollution. Across the seven species tested by using controlled pollinations, seed set per flower, following E. nitens pollinations, was significantly less than for intraspecific outcross pollinations. No significant differences were evident in the percentage of seed that germinated or the percentage of germinants that grew into healthy seedlings in the glasshouse. Hybridity was verified by morphometric analyses and F1 hybrid seedlings were clearly differentiated from parental species and generally intermediate in morphology. Supplementary E. nitens pollination of open-pollinated native flowers was conducted to simulate natural pollination where pollen competition would occur. Seven of the fifteen species tested produced F1 hybrids in this case; however, further crossing is required to verify failed cross combinations. Although E. nitens can potentially hybridise with many native species, the results from both supplementary and controlled pollinations suggest the presence of post-pollination barriers of varying strength that need to be considered in assessing the risk of exotic gene flow from plantations.

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Population genomics data supports introgression between western Iberian Squalius freshwater fish species

10.1101/585687 ◽

2019 ◽

Author(s):

Sofia L. Mendes ◽

Maria M. Coelho ◽

Vitor C. Sousa

Keyword(s):

Gene Flow ◽

Freshwater Fish ◽

Population Genomics ◽

Genotyping By Sequencing ◽

Population Divergence ◽

Freshwater Species ◽

Genomic Approach ◽

Demographic Modelling ◽

Paraphyletic Group ◽

First Time

AbstractIn freshwater fish, processes of population divergence and speciation are often linked to the geomorphology of rivers and lakes that isolate populations. However, current geographical isolation does not necessarily imply total absence of gene flow during the divergence process. Here, we focused on four species of the genus Squalius in Portuguese rivers: S. carolitertii, S. pyrenaicus, S. aradensis and S. torgalensis. Previous studies based on eight nuclear and mitochondrial markers revealed incongruent patterns, with nuclear loci suggesting that S. pyrenaicus was a paraphyletic group since its northern populations were genetically closer to S. carolitertii than to its southern populations. For the first time, we successfully applied a genomic approach to the study of the relationship between these species, using a Genotyping by Sequencing (GBS) approach. Our results revealed a species tree with two main lineages: (i) S. carolitertii and S. pyrenaicus; (ii) S. torgalensis and S. aradensis. Regarding S. carolitertii and S. pyrenaicus, we found evidence for past introgression between the two in the northern part of S. pyrenaicus distribution. This introgression reconciles previous mitochondrial and nuclear incongruent results and explains the apparent paraphyly of S. pyrenaicus. Our demographic modelling estimates are consistent across models, suggesting that the northern populations of S. pyrenaicus received a contribution of approximately 90% from S. carolitertii and 10% from southern S. pyrenaicus. This illustrates that even in freshwater species currently allopatric, we are able to detect past gene flow events in present-day genomes, suggesting speciation is more complex than simply allopatric.

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Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2020.1960 ◽

2020 ◽

Vol 287 (1938) ◽

pp. 20201960

Author(s):

Matheus E. Bianconi ◽

Luke T. Dunning ◽

Emma V. Curran ◽

Oriane Hidalgo ◽

Robyn F. Powell ◽

...

Keyword(s):

Gene Flow ◽

Population Genomics ◽

Nuclear Genome ◽

Its Region ◽

Grass Species ◽

Region Of Origin ◽

Ploidy Levels ◽

Lower Elevation ◽

Limited Dispersal ◽

Genome Analyses

C 4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this species encompasses C 4 and non-C 4 populations. Using phylogenomics and population genomics, we infer the history of dispersal and secondary gene flow before, during and after photosynthetic divergence in A. semialata . We further analyse the genome composition of individuals with varied ploidy levels to establish the origins of polyploids in this species. Detailed organelle phylogenies indicate limited seed dispersal within the mountainous region of origin and the emergence of a C 4 lineage after dispersal to warmer areas of lower elevation. Nuclear genome analyses highlight repeated secondary gene flow. In particular, the nuclear genome associated with the C 4 phenotype was swept into a distantly related maternal lineage probably via unidirectional pollen flow. Multiple intraspecific allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types. Overall, our results show that limited dispersal and isolation allowed lineage divergence, with photosynthetic innovation happening after migration to new environments, and pollen-mediated gene flow led to the rapid spread of the derived C 4 physiology away from its region of origin.

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Population genomics of Cryptosporidium hominis across five continents identifies two subspecies that have diverged and recombined during 500 years of evolution

10.1101/2021.09.09.459610 ◽

2021 ◽

Author(s):

Swapnil Tichkule ◽

Simone M. Cacciò ◽

Guy Robinson ◽

Rachel M. Chalmers ◽

Ivo Mueller ◽

...

Keyword(s):

Gene Flow ◽

Low Income ◽

Population Genomics ◽

Balancing Selection ◽

Public Health Problem ◽

High Income ◽

Secondary Contact ◽

Middle Income ◽

Middle Income Countries ◽

Low And Middle Income

AbstractCryptosporidium is a significant public health problem and one of the primary causes of diarrhoea in humans, particularly in very young children living in low- and middle-income countries. While the zoonotic Cryptosporidium parvum and anthroponotic C. hominis species collectively account for most cases globally, the latter is predominant in low- and middle-income countries. Here, we present a comprehensive whole genome study of C. hominis, comprising 114 isolates from 16 countries within five continents. We detect two highly diverged lineages with a distinct biology and demography that have diverged circa 500 years ago. We consider these lineages as two subspecies, and provisionally propose the names C. hominis hominis (clade 1) and C. hominis aquapotentis (clade 2 or gp60 subtype IbA10G2). C. h. hominis is mostly found in low-income countries in Africa and Asia, and it appears to have recently undergone population contraction. In marked contrast, C. h. aquapotentis was found in high-income countries, mainly in Europe, North America and Oceania, and we reveal a signature of population expansion. Moreover, we detected genomic regions of introgression representing gene flow after a secondary contact between the subspecies from low- and high-income countries. We demonstrate that this gene flow resulted in genomic island of high diversity and divergence, and that this diversity at potential virulence genes is maintained by balancing selection, suggesting that they are involved in a coevolutionary arms race.

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Genetic Population Structure in Blue Crabs (Callinectes sapidus): High Resolution Population Genomics of a High Gene Flow Species

Authorea ◽

10.22541/au.158532006.65921878 ◽

2020 ◽

Author(s):

Joseph Neigel ◽

Sophie Plouviez ◽

Timothy Sullivan ◽

Bree Yednock ◽

Vanessa Rashbrook

Keyword(s):

Population Structure ◽

Gene Flow ◽

High Resolution ◽

Population Genomics ◽

Callinectes Sapidus ◽

Genetic Population Structure ◽

Blue Crabs ◽

Genetic Population ◽

High Gene Flow ◽

High Gene

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Spatial Genetic Structure of the Insect-Vectored Conifer Pathogen Leptographium wageneri Suggests Long Distance Gene Flow Among Douglas-fir Plantations in Western Oregon

Frontiers in Forests and Global Change ◽

10.3389/ffgc.2021.695981 ◽

2021 ◽

Vol 4 ◽

Author(s):

Patrick I. Bennett ◽

Javier F. Tabima ◽

Anna L. Leon ◽

John Browning ◽

Michael J. Wingfield ◽

...

Keyword(s):

Population Structure ◽

Gene Flow ◽

Bark Beetles ◽

Population Genomics ◽

Spatial Genetic Structure ◽

Douglas Fir ◽

Insect Vector ◽

Long Distance ◽

Tree Disease ◽

Genetic Clustering

Many fungi in the Ophiostomatales are vectored by bark beetles that introduce these fungi directly into their tree hosts. Most of these fungal associates have little effect on their hosts, but some can cause serious diseases. One such fungus, Leptographium wageneri, causes an economically and ecologically important tree disease known as black stain root disease (BSRD). For this study, 159 full genome sequences of L. wageneri were analyzed using a population genomics approach to investigate the epidemiology, dispersal capabilities, and reproductive biology of this fungus. Analyses were performed with SNP haplotypes from 155 isolates of L. wageneri var. pseudotsugae collected in 16 Douglas-fir stands in Oregon and 4 isolates of L. wageneri var. wageneri collected in pinyon pine stands in southern California. These two host-specific varieties appear to be evolutionarily divergent, likely due a combination of factors such as host differentiation and geographic isolation. We analyzed gene flow and population structure within and among Douglas-fir plantations in western Oregon to infer the relative importance of local vs. long distance dispersal in structuring populations of L. wageneri var. pseudotsugae. Long-distance gene flow has occurred between Douglas-fir plantations, contributing to diversity and population structure within stands, and likely reflecting the behavior of an important insect vector. Genetic clustering analyses revealed the presence of unique local clusters within stands and plantations in addition to those common among multiple stands or plantations. Although populations of L. wageneri var. pseudotsugae are primarily asexual, two mating types were present in many stands, suggesting that recombination is at least possible and may contribute to genetic diversity.

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Population genomics perspectives on convergent adaptation

10.1101/503284 ◽

2018 ◽

Author(s):

Kristin M Lee ◽

Graham Coop

Keyword(s):

Gene Flow ◽

Conceptual Framework ◽

Quantitative Genetics ◽

Molecular Basis ◽

Population Genomics ◽

Evolutionary Change ◽

Fitness Advantage ◽

Standing Variation ◽

Independent Replication ◽

Genetics And Genomics

Convergent adaptation is the independent evolution of similar traits conferring a fitness advantage in two or more lineages. Cases of convergent adaptation inform our ideas about the ecological and molecular basis of adaptation. In judging the degree to which putative cases of convergent adaptation provide independent replication of the process of adaptation, it is necessary to establish the degree to which the evolutionary change is unexpected under null models and to show that selection has repeatedly, independently driven these changes. Here, we discuss the issues that arise from these questions particularly for closely-related populations, where gene flow and standing variation add additional layers of complexity. We outline a conceptual framework to guide intuition as to the extent to which evolutionary change represents the independent gain of information due to selection and show that this is a measure of how surprised we should be by convergence. Additionally, we summarize the ways population and quantitative genetics and genomics may help us address questions related to convergent adaptation, as well as open new questions and avenues of research.

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