Genetic diversity, paraphyly and incomplete lineage sorting of mtDNA, ITS2 and microsatellite flanking region in closely related Heliopora species (Octocorallia)

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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Genetic diversity and species limits in Veltheimia (Asparagaceae: Scilloideae): insights from noncoding cpDNA sequence data

Phytotaxa ◽

10.11646/phytotaxa.429.3.6 ◽

2020 ◽

Vol 429 (3) ◽

pp. 239-247

Author(s):

NIGEL P. BARKER ◽

TAMIKA FELLOWS ◽

NTOMBIFIKILE PHALISO ◽

JOHN ROURKE

Keyword(s):

Genetic Diversity ◽

Bayesian Analysis ◽

Southern Africa ◽

Sequence Data ◽

Incomplete Lineage Sorting ◽

Summer Rainfall ◽

Coastal Forests ◽

Lineage Sorting ◽

Dna Sequence Data ◽

Cpdna Sequence

Veltheimia is a genus of two species of bulbous flowering angiosperms restricted to southern Africa. Both parsimony and Bayesian analysis of 1829 nucleotides of DNA sequence data, from three non-coding chloroplast regions from multiple samples of both species, indicates that specimens of V. bracteata form a monophyletic clade together with three specimens named as V. capensis. This clade receives low support and is embedded within a paraphyletic grade of specimens of V. capensis. A Median Joining Network analysis of a subset of samples revealed nine haplotypes, the relationships of which mirrored the relationships resolved by the Bayesian analysis. With the exception of the V. capensis members of the V. bracteata clade, the remaining specimens are from the summer rainfall thicket and coastal forests. The samples of the basal V. capensis grade are found in the winter rainfall regions of southern Africa. These results indicate that there is limited genetic diversity within the genus, and there is no clear distinction between these two species based on plastid non-coding DNA data. This may be due to their recent divergence and incomplete lineage sorting, or recent or ongoing hybridisation and / or introgression.

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Recent and Historical Gene Flow in Cultivars, Landraces, and a Wild Taxon of Cucurbita pepo in Mexico

Frontiers in Ecology and Evolution ◽

10.3389/fevo.2021.656051 ◽

2021 ◽

Vol 9 ◽

Author(s):

Carmina Martínez-González ◽

Gabriela Castellanos-Morales ◽

Josué Barrera-Redondo ◽

Guillermo Sánchez-de la Vega ◽

Helena S. Hernández-Rosales ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Evolutionary Biology ◽

Management Practices ◽

Incomplete Lineage Sorting ◽

Genetic Material ◽

Genotyping By Sequencing ◽

Wild Relative ◽

Lineage Sorting ◽

Evolutionary Trajectory

Gene flow among crops and their wild relatives is an active study area in evolutionary biology and horticulture, because genetic exchange between them may impact their evolutionary trajectories and increase the genetic variation of the cultivated lineages. Mexico is a center of diversity for the genus Cucurbita that includes pumpkins, squash and gourds. Gene flow between domesticated and wild species has been reported as common in Cucurbita; but gene flow among populations of C. pepo ssp. pepo from Mexico and its wild relative has not been studied. We used 2,061 SNPs, derived from tunable genotyping by sequencing (tGBS) to estimate gene flow among 14 Mexican traditional landraces of C. pepo ssp. pepo, also including individuals from five improved cultivars of C. pepo ssp. pepo and C. pepo ssp. ovifera var. ovifera, and individuals of their wild relative C. pepo ssp. fraterna. We found moderate to high levels of genetic diversity, and low to moderate genetic differentiation. In the test of introgression between lineages, we found that all possible arrangements for ancestral and derived sites between the lineages showed similar frequencies; thus, incomplete lineage sorting, but also gene flow, might be taking place in C. pepo. Overall, our results suggest that gene flow between these subspecies and cultigens, incomplete lineage sorting and the retention of ancestral characters shaped the evolutionary trajectory of C. pepo in its area of origin and diversification. In addition, we found evidence of the use of Mexican landraces as genetic material for the improvement of commercial cultivars. The landraces of Mexico are an important source of genetic diversity for C. pepo, which has been preserved both by management practices of small farmers and by the natural gene flow that exists between the different crop fields of the region.

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Faculty Opinions recommendation of Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting.

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

10.3410/f.1052717.504629 ◽

2006 ◽

Author(s):

Artyom Kopp

Keyword(s):

Incomplete Lineage Sorting ◽

Species Tree ◽

Gene Trees ◽

Lineage Sorting

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The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales

Systematic Biology ◽

10.1093/sysbio/syaa083 ◽

2020 ◽

Author(s):

Liming Cai ◽

Zhenxiang Xi ◽

Emily Moriarty Lemmon ◽

Alan R Lemmon ◽

Austin Mast ◽

...

Keyword(s):

Gene Flow ◽

Incomplete Lineage Sorting ◽

Estimation Error ◽

Gene Tree ◽

Species Tree ◽

Flowering Plant ◽

Estimation Methods ◽

Lineage Sorting ◽

Tree Estimation ◽

Perfect Storm

Abstract The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent (MSC) model and improved gene tree estimation methods can better accommodate gene tree heterogeneity caused by incomplete lineage sorting (ILS) and gene tree estimation error stemming from the short internal branches. However, the relative influence of these factors in species tree inference is not well understood. Using anchored hybrid enrichment, we generated a data set including 423 single-copy loci from 64 taxa representing 39 families to infer the species tree of the flowering plant order Malpighiales. This order includes nine of the top ten most unstable nodes in angiosperms, which have been hypothesized to arise from the rapid radiation during the Cretaceous. Here, we show that coalescent-based methods do not resolve the backbone of Malpighiales and concatenation methods yield inconsistent estimations, providing evidence that gene tree heterogeneity is high in this clade. Despite high levels of ILS and gene tree estimation error, our simulations demonstrate that these two factors alone are insufficient to explain the lack of resolution in this order. To explore this further, we examined triplet frequencies among empirical gene trees and discovered some of them deviated significantly from those attributed to ILS and estimation error, suggesting gene flow as an additional and previously unappreciated phenomenon promoting gene tree variation in Malpighiales. Finally, we applied a novel method to quantify the relative contribution of these three primary sources of gene tree heterogeneity and demonstrated that ILS, gene tree estimation error, and gene flow contributed to 10.0%, 34.8%, and 21.4% of the variation, respectively. Together, our results suggest that a perfect storm of factors likely influence this lack of resolution, and further indicate that recalcitrant phylogenetic relationships like the backbone of Malpighiales may be better represented as phylogenetic networks. Thus, reducing such groups solely to existing models that adhere strictly to bifurcating trees greatly oversimplifies reality, and obscures our ability to more clearly discern the process of evolution.

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Morphological, Ecological, and Molecular Divergence of Conogethes pinicolalis from C. punctiferalis (Lepidoptera: Crambidae)

Insects ◽

10.3390/insects12050455 ◽

2021 ◽

Vol 12 (5) ◽

pp. 455

Author(s):

Na Ra Jeong ◽

Min Jee Kim ◽

Sung-Soo Kim ◽

Sei-Woong Choi ◽

Iksoo Kim

Keyword(s):

Phylogenetic Analysis ◽

First Generation ◽

Incomplete Lineage Sorting ◽

Divergence Time ◽

Sequence Divergence ◽

Lineage Sorting ◽

Mitochondrial Coi ◽

Feeding Type ◽

Pine Trees ◽

Yellow Peach Moth

Conogethes pinicolalis has long been considered as a Pinaceae-feeding type of the yellow peach moth, C. punctiferalis, in Korea. In this study, the divergence of C. pinicolalis from the fruit-feeding moth C. punctiferalis was analyzed in terms of morphology, ecology, and genetics. C. pinicolalis differs from C. punctiferalis in several morphological features. Through field observation, we confirmed that pine trees are the host plants for the first generation of C. pinicolalis larvae, in contrast to fruit-feeding C. punctiferalis larvae. We successfully reared C. pinicolalis larvae to adults by providing them pine needles as a diet. From a genetic perspective, the sequences of mitochondrial COI of these two species substantially diverged by an average of 5.46%; moreover, phylogenetic analysis clearly assigned each species to an independent clade. On the other hand, nuclear EF1α showed a lower sequence divergence (2.10%) than COI. Overall, EF1α-based phylogenetic analysis confirmed each species as an independent clade, but a few haplotypes of EF1α indicated incomplete lineage sorting between these two species. In conclusion, our results demonstrate that C. pinicolalis is an independent species according to general taxonomic criteria; however, analysis of the EF1α sequence revealed a short divergence time.

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Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere

Systematic Biology ◽

10.1093/sysbio/syaa099 ◽

2020 ◽

Author(s):

Fernando Lopes ◽

Larissa R Oliveira ◽

Amanda Kessler ◽

Yago Beux ◽

Enrique Crespo ◽

...

Keyword(s):

Incomplete Lineage Sorting ◽

Gene Tree ◽

Molecular Data ◽

Species Tree ◽

Gene Trees ◽

Lineage Sorting ◽

Data Types ◽

High Coverage ◽

Sea Lions ◽

The Family

Abstract The phylogeny and systematics of fur seals and sea lions (Otariidae) have long been studied with diverse data types, including an increasing amount of molecular data. However, only a few phylogenetic relationships have reached acceptance because of strong gene-tree species tree discordance. Divergence times estimates in the group also vary largely between studies. These uncertainties impeded the understanding of the biogeographical history of the group, such as when and how trans-equatorial dispersal and subsequent speciation events occurred. Here we used high-coverage genome-wide sequencing for 14 of the 15 species of Otariidae to elucidate the phylogeny of the family and its bearing on the taxonomy and biogeographical history. Despite extreme topological discordance among gene trees, we found a fully supported species tree that agrees with the few well-accepted relationships and establishes monophyly of the genus Arctocephalus. Our data support a relatively recent trans-hemispheric dispersal at the base of a southern clade, which rapidly diversified into six major lineages between 3 to 2.5 Ma. Otaria diverged first, followed by Phocarctos and then four major lineages within Arctocephalus. However, we found Zalophus to be non-monophyletic, with California (Z. californianus) and Steller sea lions (Eumetopias jubatus) grouping closer than the Galapagos sea lion (Z. wollebaeki) with evidence for introgression between the two genera. Overall, the high degree of genealogical discordance was best explained by incomplete lineage sorting resulting from quasi-simultaneous speciation within the southern clade with introgresssion playing a subordinate role in explaining the incongruence among and within prior phylogenetic studies of the family.

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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.

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Disentangling Incomplete Lineage Sorting and Introgression to Refine Species-Tree Estimates for Lake Tanganyika Cichlid Fishes

Systematic Biology ◽

10.1093/sysbio/syw069 ◽

2016 ◽

pp. syw069 ◽

Cited By ~ 12

Author(s):

Britta S. Meyer ◽

Michael Matschiner ◽

Walter Salzburger

Keyword(s):

Lake Tanganyika ◽

Incomplete Lineage Sorting ◽

Species Tree ◽

Lineage Sorting ◽

Cichlid Fishes

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Impact of Ghost Introgression on Coalescent-based Species Tree Inference and Estimation of Divergence Time

10.1101/2022.01.11.475787 ◽

2022 ◽

Author(s):

XiaoXu Pang ◽

Da-Yong Zhang

Keyword(s):

Incomplete Lineage Sorting ◽

Divergence Time ◽

Species Tree ◽

Gene Trees ◽

Species Trees ◽

Lineage Sorting ◽

Multispecies Coalescent ◽

Tree Inference ◽

Tree Methods ◽

The Impact

The species studied in any evolutionary investigation generally constitute a very small proportion of all the species currently existing or that have gone extinct. It is therefore likely that introgression, which is widespread across the tree of life, involves "ghosts," i.e., unsampled, unknown, or extinct lineages. However, the impact of ghost introgression on estimations of species trees has been rarely studied and is thus poorly understood. In this study, we use mathematical analysis and simulations to examine the robustness of species tree methods based on a multispecies coalescent model under gene flow sourcing from an extant or ghost lineage. We found that very low levels of extant or ghost introgression can result in anomalous gene trees (AGTs) on three-taxon rooted trees if accompanied by strong incomplete lineage sorting (ILS). In contrast, even massive introgression, with more than half of the recipient genome descending from the donor lineage, may not necessarily lead to AGTs. In cases involving an ingroup lineage (defined as one that diverged no earlier than the most basal species under investigation) acting as the donor of introgression, the time of root divergence among the investigated species was either underestimated or remained unaffected, but for the cases of outgroup ghost lineages acting as donors, the divergence time was generally overestimated. Under many conditions of ingroup introgression, the stronger the ILS was, the higher was the accuracy of estimating the time of root divergence, although the topology of the species tree is more prone to be biased by the effect of introgression.

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