scholarly journals Population Structure and Mitochondrial Polyphyly in North American Gadwalls (Anas Strepera)

The Auk ◽  
2007 ◽  
Vol 124 (2) ◽  
pp. 444-462 ◽  
Author(s):  
Jeffrey L. Peters ◽  
Kevin E. Omland
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
North America ◽  
North American ◽  
Incomplete Lineage Sorting ◽  
Population Expansion ◽  
Lineage Sorting ◽  
Clade B ◽  
Base Pair Fragment ◽  
Anas Strepera

Abstract We examined population genetic structure in Gadwalls (Anas strepera) to test the prediction that female philopatry and fidelity to migratory flyways have contributed to the partitioning of mitochondrial variation across North America. Sequencing a 658–659 base-pair fragment of the mitochondrial DNA (mtDNA) control region from 348 Gadwalls, we found two distinct clades that were broadly intermixed across both breeding and nonbreeding populations. Clade A was abundant in North America as well as among published sequences from Eurasia. Clade B was sequenced from 5.5% of North American Gadwalls and was more similar to Asian Falcated Duck (A. falcata) haplotypes than to clade A haplotypes. Maximum likelihood indicated that Gadwall clade B haplotypes were a monophyletic group nested within Falcated Duck haplotypes, which suggests mtDNA introgression of clade B into Gadwalls. However, that topology was weakly supported, and we could not reject topologies that were consistent with incomplete lineage-sorting as the cause of mitochondrial polyphyly. Migratory flyways did not contribute significantly to population structure and, in general, we found a lack of genetic structure among most populations. However, Gadwalls sampled in Alaska and Washington were well differentiated from other populations. Coalescent analyses supported a historical population expansion for clade A, and this expansion could have contributed to the high genetic similarity among some populations but the strong differentiation of others. Female-mediated gene flow, along with both historical and contemporary population and range expansions, has likely contributed to the overall weak mtDNA structure in North American Gadwalls. Estructura Poblacional y Polifilia Mitocondrial en Anas strepera

scholarly journals The choices we make and the impacts they have: Machine learning and species delimitation in North American box turtles (Terrapene spp.)

2020 ◽  
Author(s):  
Bradley T. Martin ◽  
Tyler K. Chafin ◽  
Marlis R. Douglas ◽  
John S. Placyk ◽  
Roger D. Birkhead ◽  
...  
Keyword(s):  
Machine Learning ◽  
North American ◽  
Species Delimitation ◽  
Species Concept ◽  
Incomplete Lineage Sorting ◽  
Signal To Noise Ratio ◽  
Lineage Sorting ◽  
Biogeographic History ◽  
Box Turtles ◽  
A Minor

AbstractModel-based approaches that attempt to delimit species are hampered by computational limitations as well as the unfortunate tendency by users to disregard algorithmic assumptions. Alternatives are clearly needed, and machine-learning (M-L) is attractive in this regard as it functions without the need to explicitly define a species concept. Unfortunately, its performance will vary according to which (of several) bioinformatic parameters are invoked. Herein, we gauge the effectiveness of M-L-based species-delimitation algorithms by parsing 64 variably-filtered versions of a ddRAD-derived SNP dataset involving North American box turtles (Terrapene spp.). Our filtering strategies included: (A) minor allele frequencies (MAF) of 5%, 3%, 1%, and 0% (=none), and (B) maximum missing data per-individual/per-population at 25%, 50%, 75%, and 100% (=none). We found that species-delimitation via unsupervised M-L impacted the signal-to-noise ratio in our data, as well as the discordance among resolved clades. The latter may also reflect biogeographic history, gene flow, incomplete lineage sorting, or combinations thereof (as corroborated from previously observed patterns of differential introgression). Our results substantiate M-L as a viable species-delimitation method, but also demonstrate how commonly observed patterns of phylogenetic discord can seriously impact M-L-classification.

scholarly journals Genetic Diversity in the mtDNA control region and population structure of Chrysichthys nigrodigitatus from selected Nigerian rivers: Implications for conservation and aquaculture

2016 ◽  
Vol 24 (2) ◽  
pp. 85-97 ◽  
Author(s):  
Sylvanus A. Nwafili ◽  
Tian-Xiang Gao
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Control Region ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Mitochondrial Control Region ◽  
Recent Population Expansion ◽  
Base Pair Fragment ◽  
Population Structures ◽  
High Level

Abstract The genetic diversity and population structure of Chrysichthys nigrodigitatus were evaluated using a 443 base pair fragment of the mitochondrial control region. Among the eight populations collected comprising 129 individuals, a total of 89 polymorphic sites defined 57 distinct haplotypes. The mean haplotype diversity and nucleotide diversity of the eight populations were 0.966±0.006 and 0.0359±0.004, respectively. Analysis of molecular variance showed significant genetic differentiation among the eight populations (FST =0.34; P < 0.01). The present results revealed that C. nigrodigitatus populations had a high level of genetic diversity and distinct population structures. We report the existence of two monophyletic matrilineal lineages with mean genetic distance of 10.5% between them. Non-significant negative Tajima’s D and Fu’s Fs for more than half the populations suggests that the wild populations of C. nigrodigitatus underwent a recent population expansion, although a weak one since the late Pleistocene.

Population structure of Heterobasidion annosum from North America and Europe

1993 ◽  
Vol 71 (8) ◽  
pp. 1064-1071 ◽  
Author(s):  
William J. Otrosina ◽  
Thomas E. Chase ◽  
Fields W. Cobb Jr. ◽  
Kari Korhonen
Keyword(s):  
Population Structure ◽  
North America ◽  
North American ◽  
Forest Tree ◽  
Heterobasidion Annosum ◽  
Evolutionary Relationships ◽  
The North ◽  
Isozyme Loci ◽  
Intersterility Groups ◽  
European Populations

Isolates of Heterobasidion annosum (Fr.) Bref. representing North American S and P and European S, P, and F intersterility groups were subjected to isozyme analysis. European S, P, and F groups had more variability than the North American S and P groups in expected hterozygosity, number of alleles per locus, and percent polymorphic loci. In contrast with the North American S and P groups, the European intersterility groups could not be distinguished from each other on the basis of individual isozyme loci, although significant differences in allele frequencies exist between European S and P groups. This suggests that evolution proceeded at different rates in the intersterility groups, or intersterility barriers appeared later in the European populations relative to the North American populations of H. annosum. Changes in climate and host species associations during the Tertiary may have been a major factor in evolution of H. annosum intersterility groups. Key words: allozymes, forest tree hosts, playnological events, evolutionary relationships, Hymenomycetes, root disease.

scholarly journals Genomic insights into adaptive divergence and speciation among malaria vectors of the Anopheles nili group

2016 ◽  
Author(s):  
Caroline Fouet ◽  
Colince Kamdem ◽  
Stephanie Gamez ◽  
Bradley J. White
Keyword(s):  
Population Structure ◽  
Large Scale ◽  
Incomplete Lineage Sorting ◽  
Snp Markers ◽  
Malaria Vectors ◽  
Adaptive Divergence ◽  
Nucleotide Polymorphisms ◽  
Lineage Sorting ◽  
Interspecific Gene Flow ◽  
Scale Control

AbstractOngoing speciation in most African malaria vectors gives rise to cryptic populations, which differ remarkably in their behaviour, ecology and capacity to vector malaria parasites. Understanding the population structure and the drivers of genetic differentiation among mosquitoes is critical for effective disease control because heterogeneity within species contribute to variability in malaria cases and allow fractions of vector populations to escape control efforts. To examine the population structure and the potential impacts of recent large-scale control interventions, we have investigated the genomic patterns of differentiation in mosquitoes belonging to the Anopheles nili group, a large taxonomic group that diverged ∼3-Myr ago. Using 4343 single nucleotide polymorphisms (SNPs), we detected strong population structure characterized by high FST values between multiple divergent populations adapted to different habitats within the Central African rainforest. Delineating the cryptic species within the Anopheles nili group is challenging due to incongruence between morphology, ribosomal DNA and SNP markers consistent with incomplete lineage sorting and/or interspecific gene flow. A very high proportion of loci are fixed (FST = 1) within the genome of putative species, which suggests that ecological and/or reproductive barriers are maintained by strong selection on a substantial number of genes.

scholarly journals Phylogenomic Analyses Clarify True Species within the Butterfly Genus Speyeria despite Evidence of a Recent Adaptive Radiation

Insects ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 209
Author(s):  
Erin Thompson ◽  
Jason Baumsteiger ◽  
Ryan I. Hill
Keyword(s):  
Adaptive Radiation ◽  
North American ◽  
Incomplete Lineage Sorting ◽  
Legal Protection ◽  
Evolutionary Model ◽  
Morphological Characters ◽  
Anthropogenic Factors ◽  
Lineage Sorting ◽  
The North ◽  
Phylogenetic Resolution

When confronted with an adaptive radiation, considerable evidence is needed to resolve the evolutionary relationships of these closely related lineages. The North American genus Speyeria is one especially challenging radiation of butterflies due to potential signs of incomplete lineage sorting, ongoing hybridization, and similar morphological characters between species. Previous studies have found species to be paraphyletic and have been unable to disentangle taxa, often due to a lack of data and/or incomplete sampling. As a result, Speyeria remains unresolved. To achieve phylogenetic resolution of the genus, we conducted phylogenomic and population genomic analyses of all currently recognized North American Speyeria species, as well as several subspecies, using restriction-site-associated DNA sequencing (RADseq). Together, these analyses confirm the 16 canonical species, and clarify many internal relationships. However, a few relationships within Speyeria were poorly supported depending on the evolutionary model applied. This lack of resolution among certain taxa corroborates Speyeria is experiencing an ongoing adaptive radiation, with incomplete lineage sorting and lack of postzygotic reproductive barriers contributing to hybridization and further ambiguity. Given that many Speyeria taxa are under duress from anthropogenic factors, their legal protection must be viewed cautiously and on a case by case basis in order to properly conserve the diversity being generated.

scholarly journals Peeling Back the Layers: the Complex Dynamics Shaping the Evolution of the Ledebouriinae (Scilloideae, Asparagaceae)

2020 ◽  
Author(s):  
Cody Coyotee Howard ◽  
Andrew A. Crowl ◽  
Timothy S. Harvey ◽  
Nico Cellinese
Keyword(s):  
Complex Dynamics ◽  
Incomplete Lineage Sorting ◽  
Sub Saharan Africa ◽  
Lineage Sorting ◽  
East African ◽  
Historical Factors ◽  
Clade B ◽  
Phylogenetic Framework ◽  
Sub Saharan ◽  
Probe Set

AbstractThe Ledebouriinae (Scilloideae, Asparagaceae) are a widespread group of bulbous geophytes found predominantly throughout seasonal climates in sub-Saharan Africa, with a handful of taxa in Madagascar, the Middle East, India and Sri Lanka. An understanding of the phylogenetic relationships within the group have been historically difficult to reconstruct, however. Here, we provide the first phylogenomic perspective into the Ledebouriinae. We use this renewed phylogenetic framework to hypothesize historical factors that have resulted in the topology recovered. Using the Angiosperms353 targeted enrichment probe set, we consistently recovered four major clades (i.e. two Ledebouria clades, Drimiopsis, and Resnova). The two Ledebouria clades closely align with geography, either consisting almost entirely of sub-Saharan African taxa (Ledebouria Clade A), or East African and non-African taxa (Ledebouria Clade B). Our results also suggest that the Ledebouriinae underwent a rapid radiation leading to rampant incomplete lineage sorting. [Asparagaceae; Drimiopsis; geophytes; Ledebouria; monocots; Resnova; Scilloideae.]

scholarly journals Highly replicated evolution of parapatric ecotypes

2020 ◽  
Author(s):  
Maddie E. James ◽  
Henry Arenas-Castro ◽  
Jeffery S. Groh ◽  
Jan Engelstädter ◽  
Daniel Ortiz-Barrientos
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Incomplete Lineage Sorting ◽  
Parallel Evolution ◽  
Geographic Location ◽  
Lineage Sorting ◽  
Colonization History ◽  
Multiple Origins ◽  
History Of ◽  
Neutral Markers

AbstractParallel evolution of ecotypes occurs when selection independently drives the evolution of similar traits across similar environments. The multiple origin of ecotypes is often inferred on the basis of a phylogeny which clusters populations according to geographic location and not by the environment they occupy. However, the use of phylogenies to infer parallel evolution in closely related populations is problematic due to the potential for gene flow and incomplete lineage sorting to uncouple the genetic structure at neutral markers from the colonization history of populations. Here, we demonstrate multiple origins within ecotypes of an Australian wildflower, Senecio lautus. We observed strong genetic structure as well as phylogenetic clustering by geography, and show this is unlikely due to gene flow between parapatric ecotypes, which is surprisingly low. We further confirm this analytically by demonstrating that phylogenetic distortion due to gene flow often requires higher levels of migration than those observed in S. lautus. Our results imply that selection can repeatedly create similar phenotypes despite the perceived homogenizing effects of gene flow.

scholarly journals Phylogenetic incongruence and the origins of cardenolide-resistant forms of Na+, K+- ATPase in North American Danaus butterflies

2016 ◽  
Author(s):  
Matthew L. Aardema ◽  
Peter Andolfatto
Keyword(s):  
North American ◽  
Host Plants ◽  
Incomplete Lineage Sorting ◽  
Danaus Plexippus ◽  
Orthologous Gene ◽  
Transcriptome Data ◽  
Lineage Sorting ◽  
Rapid Radiation ◽  
Sodium Potassium ◽  
Phylogenetic Incongruence

AbstractRapid species radiations can obscure phylogenetic relationships between even distantly related species and lead to incorrect evolutionary inferences. For this reason, we examined evolutionary relationships among the three North American milkweed butterflies, Danaus plexippus, D. gilippus and D. eresimus using >400 orthologous gene sequences assembled from transcriptome data. Contrary to previous phylogenetic assessments, our results indicate that D. plexippus and D. eresimus are the sister taxa among these species. This result explains many previously noted phylogenetic incongruences such as an amino acid substitution in the sodium-potassium pump (Na+,K+-ATPase) of D. eresimus and D. plexippus, which increases resistance to the toxins found in these butterflies’ host plants. In accordance with a rapid radiation of Danaus butterflies, we also find evidence that both incomplete lineage sorting and post-speciation genetic exchange have contributed significantly to the evolutionary histories of these species. Furthermore, our findings suggest that D. plexippus is highly derived both morphologically and behaviorally.

scholarly journals Population genetics of the Amazonian tortoises, Chelonoidis denticulata and C. carbonaria, (Cryptodira: Testudinidae) in an area of sympatry

2007 ◽  
Vol 28 (3) ◽  
pp. 357-365 ◽  
Author(s):  
Izeni Pires Farias ◽  
Afrânio Melo ◽  
Marcio Martins ◽  
Adriano Jerozolimski ◽  
Maria das Neves Viana ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Incomplete Lineage Sorting ◽  
Population Expansion ◽  
Deciduous Forests ◽  
Lineage Sorting ◽  
Population Genetic Analysis ◽  
Humid Forest ◽  
Natural Processes ◽  
Low Levels ◽  
Suitable Habitats

AbstractWe conducted a population genetic analysis of the two Amazonian tortoises, Chelonoidis denticulata (n = 40) and Chelonoidis carbonaria (n = 39) in a region of sympatry within the Xingú River basin. High levels of gene flow among sampled localities indicated lack of population structure for both species. Genetic parameters indicated a moderate level of genetic diversity in C. denticulata and neutrality tests suggested that populations of this species were in demographic equilibrium with respect to mitochondrial DNA. On the other hand, C. carbonaria presented low levels of genetic diversity and a signal of population expansion. Most records of C. denticulata are from areas of humid forest while those for C. carbonaria are from areas of semi-deciduous forests and transitional areas between humid and semi-deciduous forests. Therefore, the demographic expansion observed in C. carbonaria population could reflect an increase in the availability of suitable habitats for this species due to anthropogenic or natural processes. Additionally, we observed haplotype sharing between these two tortoise species indicating hybridization or incomplete lineage sorting.

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