Population genomics indicate three different modes of divergence and speciation with gene flow in the green-winged teal duck complex

The processes leading to divergence and speciation can differ broadly among taxa with different life histories. We examine these processes in a small clade of ducks with historically uncertain relationships and species limits. The green-winged teal (Anas crecca) complex is a Holarctic species of dabbling duck currently categorized as three subspecies (Anas crecca crecca, A. c. nimia, and A. c. carolinensis) with a close relative, the yellow-billed teal (Anas flavirostris) from South America. We examined divergence and speciation patterns in this group, determining their phylogenetic relationships and the presence and levels of gene flow among lineages using both mitochondrial and genome-wide nuclear DNA obtained from 1,393 ultraconserved element (UCE) loci. Phylogenetic relationships using nuclear DNA among these taxa showed A. c. crecca, A. c. nimia, and A. c. carolinensis clustering together to form one polytomous clade, with A. flavirostris sister to this clade. This relationship can be summarized as (crecca, nimia, carolinensis)(flavirostris). However, whole mitogenomes revealed a different phylogeny: (crecca, nimia)(carolinensis, flavirostris). The best demographic model for key pairwise comparisons supported divergence with gene flow as the probable speciation mechanism in all three contrasts (crecca−nimia, crecca−carolinensis, and carolinensis−flavirostris). Given prior work, gene flow was expected among the Holarctic taxa, but gene flow between North American carolinensis and South American flavirostris (M ~0.1 - 0.4 individuals/generation), albeit low, was not expected. Three geographically oriented modes of divergence are likely involved in the diversification of this complex: heteropatric (crecca−nimia), parapatric (crecca−carolinensis), and (mostly) allopatric (carolinensis−flavirostris). Ultraconserved elements are a powerful tool for simultaneously studying systematics and population genomics in systems like this.

Download Full-text

Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event

10.7287/peerj.preprints.27035 ◽

2018 ◽

Author(s):

Kevin Winker ◽

Travis C Glenn ◽

Brant C Faircloth

Keyword(s):

Gene Flow ◽

Population Genomics ◽

Divergence Time ◽

Demographic Model ◽

Nucleotide Polymorphisms ◽

Effective Population ◽

Ultraconserved Elements ◽

Genomic Markers ◽

Allelic Differences ◽

Analytical Approaches

Using a large, consistent set of loci shared by descent (orthologous) to study relationships among taxa would revolutionize among-lineage comparisons of divergence and speciation processes. Ultraconserved elements (UCEs), highly conserved regions of the genome, offer such genomic markers. The utility of UCEs for deep phylogenetics is clearly established and there are mature analytical frameworks available, but fewer studies apply UCEs to recent evolutionary events, creating a need for additional example datasets and analytical approaches. We used UCEs to study population genomics in snow and McKay’s buntings (Plectrophenax nivalis and P. hyperboreus). Prior work suggested divergence of these sister species during the last glacial maximum (~18-74 Kya). With a sequencing depth of ~30× from four individuals of each species, we used a series of analysis tools to genotype both alleles, obtaining a complete dataset of 2,635 variable loci (~3.6 single nucleotide polymorphisms [SNPs]/locus) and 796 invariable loci. We found no fixed allelic differences between the lineages, and few loci had large allele frequency differences. Nevertheless, individuals were 100% diagnosable to species, and the two taxa were different genetically (FST = 0.034; P = 0.03). The demographic model best fitting the data was one of divergence with gene flow. Estimates of demographic parameters differed from published mtDNA research, with UCE data suggesting lower effective population sizes (~92,500 - 240,500 individuals), a deeper divergence time (~241,000 yrs), and lower gene flow (2.8-5.2 individuals per generation). Our methods provide a framework for future population studies using UCEs, and our results provide additional evidence that UCEs are useful for answering questions at shallow evolutionary depths.

Download Full-text

Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event

10.7287/peerj.preprints.27035v1 ◽

2018 ◽

Author(s):

Kevin Winker ◽

Travis C Glenn ◽

Brant C Faircloth

Keyword(s):

Gene Flow ◽

Population Genomics ◽

Divergence Time ◽

Demographic Model ◽

Nucleotide Polymorphisms ◽

Effective Population ◽

Ultraconserved Elements ◽

Genomic Markers ◽

Allelic Differences ◽

Analytical Approaches

Download Full-text

Population structure and phylogenetic relationships of Ceutorhynchus neglectus (Coleoptera: Curculionidae)

The Canadian Entomologist ◽

10.4039/n05-046 ◽

2005 ◽

Vol 137 (6) ◽

pp. 672-684 ◽

Cited By ~ 9

Author(s):

R. D. Laffin ◽

L. M. Dosdall ◽

F.A.H. Sperling

Keyword(s):

Population Structure ◽

Gene Flow ◽

North America ◽

Phylogenetic Relationships ◽

Nuclear Dna ◽

Isolation By Distance ◽

Coi Gene ◽

Restricted Gene Flow ◽

Species Variation ◽

Internal Transcribed Spacer Region

AbstractCeutorhynchus neglectus Blatchley is a weevil that is native to, and widely distributed in, North America. It has life-history characteristics similar to its alien invasive congener, Ceutorhynchus obstrictus (Marsham), the cabbage seedpod weevil. Our study was undertaken to compare the population structure of C. neglectus in North America to that of C. obstrictus, which, in contrast, was introduced only recently to North America and might be expected to have a simpler population structure. We also compared the population structure of C. neglectus to that of Pissodes strobi (Peck), which is known to possess high levels of intraspecific variation and is also a Nearctic weevil. We sequenced a 790-bp fragment of mtDNA (cytochrome oxidase I (COI) gene) and a 117-bp fragment of nuclear DNA (internal transcribed spacer region 1 (ITS1)). Nested clade analysis inferred contiguous range expansion and restricted gene flow with isolation by distance. Analysis of molecular variance also supported restricted gene flow between geographically distant populations. However, within-species variation in C. neglectus was lower than that for other weevil species including C. obstrictus. We also examined DNA divergences and phylogenetic relationships among 10 species of Ceutorhynchus using parsimony analysis of a 2.3-kb fragment of mtDNA (COI–COII) and a 541-bp fragment of nuclear DNA (elongation factor 1α).

Download Full-text

Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event

PeerJ ◽

10.7717/peerj.5735 ◽

2018 ◽

Vol 6 ◽

pp. e5735 ◽

Cited By ~ 14

Author(s):

Kevin Winker ◽

Travis C. Glenn ◽

Brant C. Faircloth

Keyword(s):

Gene Flow ◽

Population Genomics ◽

Divergence Time ◽

Demographic Model ◽

Nucleotide Polymorphisms ◽

Effective Population ◽

Ultraconserved Elements ◽

Genomic Markers ◽

Allelic Differences ◽

Analytical Approaches

Using a large, consistent set of loci shared by descent (orthologous) to study relationships among taxa would revolutionize among-lineage comparisons of divergence and speciation processes. Ultraconserved elements (UCEs), highly conserved regions of the genome, offer such genomic markers. The utility of UCEs for deep phylogenetics is clearly established and there are mature analytical frameworks available, but fewer studies apply UCEs to recent evolutionary events, creating a need for additional example datasets and analytical approaches. We used UCEs to study population genomics in snow and McKay’s buntings (Plectrophenax nivalis and P. hyperboreus). Prior work suggested divergence of these sister species during the last glacial maximum (∼18–74 Kya). With a sequencing depth of ∼30× from four individuals of each species, we used a series of analysis tools to genotype both alleles, obtaining a complete dataset of 2,635 variable loci (∼3.6 single nucleotide polymorphisms/locus) and 796 invariable loci. We found no fixed allelic differences between the lineages, and few loci had large allele frequency differences. Nevertheless, individuals were 100% diagnosable to species, and the two taxa were different genetically (FST = 0.034; P = 0.03). The demographic model best fitting the data was one of divergence with gene flow. Estimates of demographic parameters differed from published mtDNA research, with UCE data suggesting lower effective population sizes (∼92,500–240,500 individuals), a deeper divergence time (∼241,000 years), and lower gene flow (2.8–5.2 individuals per generation). Our methods provide a framework for future population studies using UCEs, and our results provide additional evidence that UCEs are useful for answering questions at shallow evolutionary depths.

Download Full-text

Faculty Opinions recommendation of Genomic evidence for divergence with gene flow in host races of the larch budmoth.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1017881.204351 ◽

2004 ◽

Author(s):

Mohamed Noor

Keyword(s):

Gene Flow ◽

Host Races ◽

Divergence With Gene Flow

Download Full-text

Phylogenetic relationships and taxonomic issues in Gastridium (Poaceae) inferred from plastid and nuclear DNA sequence analysis

Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology ◽

10.1080/11263504.2020.1753845 ◽

2020 ◽

Vol 154 (6) ◽

pp. 947-960

Author(s):

Anna Scoppola ◽

Simone Cardoni ◽

Mariangela Pellegrino ◽

Javier López-Tirado ◽

Marco Cosimo Simeone

Keyword(s):

Sequence Analysis ◽

Dna Sequence ◽

Phylogenetic Relationships ◽

Nuclear Dna ◽

Dna Sequence Analysis

Download Full-text

Geographic Structure of Mitochondrial and Nuclear Gene Polymorphisms in Australian Green Turtle Populations and Male-Biased Gene Flow

Genetics ◽

10.1093/genetics/147.4.1843 ◽

1997 ◽

Vol 147 (4) ◽

pp. 1843-1854 ◽

Cited By ~ 8

Author(s):

Nancy N FitzSimmons ◽

Craig Moritz ◽

Colin J Limpus ◽

Lisa Pope ◽

Robert Prince

Keyword(s):

Gene Flow ◽

Genetic Structure ◽

Green Turtle ◽

Nuclear Dna ◽

Nuclear Gene ◽

Chelonia Mydas ◽

Single Copy ◽

Microsatellite Data ◽

Ecological Data ◽

Infinite Allele Model

Abstract The genetic structure of green turtle (Chelonia mydas) rookeries located around the Australian coast was assessed by (1) comparing the structure found within and among geographic regions, (2) comparing microsatellite loci vs. restriction fragment length polymorphism analyses of anonymous single copy nuclear DNA (ascnDNA) loci, and (3) comparing the structure found at nuclear DNA markers to that of previously analyzed mitochondrial (mtDNA) control region sequences. Significant genetic structure was observed over all regions at both sets of nuclear markers, though the microsatellite data provided greater resolution in identifying significant genetic differences in pairwise tests between regions. Inferences about population structure and migration rates from the microsatellite data varied depending on whether statistics were based on the stepwise mutation or infinite allele model, with the latter being more congruent with geography. Estimated rates of gene flow were generally higher than expected for nuclear DNA (nDNA) in comparison to mtDNA, and this difference was most pronounced in comparisons between the northern and southern Great Barrier Reef (GBR). The genetic data combined with results from physical tagging studies indicate that the lack of nuclear gene divergence through the GBR is likely due to the migration of sGBR turtles through the courtship area of the nGBR population, rather than male-biased dispersal. This example highlights the value of combining comparative studies of molecular variation with ecological data to infer population processes.

Download Full-text

Shallow genetic divergence and distinct phenotypic differences between two Andean hummingbirds: Speciation with gene flow?

The Auk ◽

10.1093/auk/ukz046 ◽

2019 ◽

Vol 136 (4) ◽

Cited By ~ 3

Author(s):

Catalina Palacios ◽

Silvana García-R ◽

Juan Luis Parra ◽

Andrés M Cuervo ◽

F Gary Stiles ◽

...

Keyword(s):

Gene Flow ◽

Genetic Differentiation ◽

Incomplete Lineage Sorting ◽

Lineage Sorting ◽

Phenotypic Differences ◽

Adaptive Mechanisms ◽

The Face ◽

Gloger’S Rule ◽

Divergence With Gene Flow ◽

Neutral Markers

Abstract Ecological speciation can proceed despite genetic interchange when selection counteracts the homogenizing effects of migration. We tested predictions of this divergence-with-gene-flow model in Coeligena helianthea and C. bonapartei, 2 parapatric Andean hummingbirds with marked plumage divergence. We sequenced putatively neutral markers (mitochondrial DNA [mtDNA] and nuclear ultraconserved elements [UCEs]) to examine genetic structure and gene flow, and a candidate gene (MC1R) to assess its role underlying divergence in coloration. We also tested the prediction of Gloger’s rule that darker forms occur in more humid environments, and examined morphological variation to assess adaptive mechanisms potentially promoting divergence. Genetic differentiation between species was low in both ND2 and UCEs. Coalescent estimates of migration were consistent with divergence with gene flow, but we cannot reject incomplete lineage sorting reflecting recent speciation as an explanation for patterns of genetic variation. MC1R variation was unrelated to phenotypic differences. Species did not differ in macroclimatic niches but were distinct in morphology. Although we reject adaptation to variation in macroclimatic conditions as a cause of divergence, speciation may have occurred in the face of gene flow driven by other ecological pressures or by sexual selection. Marked phenotypic divergence with no neutral genetic differentiation is remarkable for Neotropical birds, and makes C. helianthea and C. bonapartei an appropriate system in which to search for the genetic basis of species differences employing genomics.

Download Full-text