scholarly journals Diagnosis of the mechanisms of different types of discordances between phylogenies inferred from nuclear and mitochondrial markers

2020 ◽  
Vol 24 (4) ◽  
pp. 420-426
Author(s):  
A. A. Poroshina ◽  
D. Y. Sherbakov ◽  
T. E. Peretolchina
Keyword(s):  
Phylogenetic Trees ◽  
Environmental Changes ◽  
Incomplete Lineage Sorting ◽  
Adaptive Dynamics ◽  
Introgressive Hybridization ◽  
Sister Species ◽  
Complex Case ◽  
Special Focus ◽  
Large Species ◽  
Lineage Sorting

In ancient freshwater lakes, an abnormally large species diversity is observed. The mechanisms that g nerated extremely high biodiversity in the ancient lakes have not been sufficiently studied and remain only partially known. Sequences of environmental changes in highly complex ecosystems such as Lake Baikal, may induce sophisticated combinations of microevolutionary processes. These processes are likely to result in unusual “patterns” of genetic variability of species. The most unusual patterns include the ones when speciation is followed by incomplete lineage sorting as well as mitochondrial or nuclear introgression. All these phenomena are diagnosed by comparing the topologies of phylogenetic trees inferred from molecular markers of evolution located in mitochondria and nuclei. Mitochondrial and nuclear introgression is a particularly interesting and complex case, which is the process of incorporating the gene alleles of one species into the gene pool of a sister species due to interspecific hybridization (introgressive hybridization). In many cases, existing methods for molecular phylogenetic analysis do not automatically allow the observed patterns of polymorphism to be explained and, therefore, cannot provide hypotheses that would explain the mechanisms which resulted to these patterns. Here we use adaptive dynamics models to study neutral molecular evolution under various scenarios of interaction between sister species and the environment. We propose and justify a set of criteria for detecting how two evolutionary trees may differ, with a special focus on comparing a tree inferred from nuclear DNA to one from mitochondrial DNA. The criteria react to branching pattern and branch lengths, including relative distances from ancestral lineages. Simulations show that the criteria allow fast and automated detection of various types of introgression, secondary breaches of reproductive barriers, and incomplete lineage sorting.

scholarly journals Comparative Performance of Popular Methods for Hybrid Detection using Genomic Data

2020 ◽  
Author(s):  
Sungsik Kong ◽  
Laura S. Kubatko
Keyword(s):  
Statistical Power ◽  
Evolutionary Dynamics ◽  
Mean Squared Error ◽  
Incomplete Lineage Sorting ◽  
Introgressive Hybridization ◽  
Genomic Data ◽  
Lineage Sorting ◽  
Comparative Performance ◽  
Pattern Frequency ◽  
Hybrid Detection

AbstractInterspecific hybridization is an important evolutionary phenomenon that generates genetic variability in a population and fosters species diversity in nature. The availability of large genome scale datasets has revolutionized hybridization studies to shift from the examination of the presence or absence of hybrids in nature to the investigation of the genomic constitution of hybrids and their genome-specific evolutionary dynamics. Although a handful of methods have been proposed in an attempt to identify hybrids, accurate detection of hybridization from genomic data remains a challenging task. The available methods can be classified broadly as site pattern frequency based and population genetic clustering approaches, though the performance of the two classes of methods under different hybridization scenarios has not been extensively examined. Here, we use simulated data to comparatively evaluate the performance of four tools that are commonly used to infer hybridization events: the site pattern frequency based methods HyDe and the D-statistic (i.e., the ABBA-BABA test), and the population clustering approaches structure and ADMIXTURE. We consider single hybridization scenarios that vary in the time of hybridization and the amount of incomplete lineage sorting (ILS) for different proportions of parental contributions (γ); introgressive hybridization; multiple hybridization scenarios; and a mixture of ancestral and recent hybridization scenarios. We focus on the statistical power to detect hybridization, the false discovery rate (FDR) for the D-statistic and HyDe, and the accuracy of the estimates of γ as measured by the mean squared error for HyDe, structure, and ADMIXTURE. Both HyDe and the D-statistic demonstrate a high level of detection power in all scenarios except those with high ILS, although the D-statistic often has an unacceptably high FDR. The estimates of γ in HyDe are impressively robust and accurate whereas structure and ADMIXTURE sometimes fail to identify hybrids, particularly when the proportional parental contributions are asymmetric (i.e., when γ is close to 0). Moreover, the posterior distribution estimated using structure exhibits multimodality in many scenarios, making interpretation difficult. Our results provide guidance in selecting appropriate methods for identifying hybrid populations from genomic data.

scholarly journals Disentangling Population History and Character Evolution among Hybridizing Lineages

2020 ◽  
Vol 37 (5) ◽  
pp. 1295-1305 ◽  
Author(s):  
Sean P Mullen ◽  
Nicholas W VanKuren ◽  
Wei Zhang ◽  
Sumitha Nallu ◽  
Evan B Kristiansen ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
De Novo ◽  
Balancing Selection ◽  
Incomplete Lineage Sorting ◽  
Introgressive Hybridization ◽  
Character Evolution ◽  
Population History ◽  
Lineage Sorting ◽  
Evolutionary Origins ◽  
Whole Genome Resequencing

Abstract Understanding the origin and maintenance of adaptive phenotypic novelty is a central goal of evolutionary biology. However, both hybridization and incomplete lineage sorting can lead to genealogical discordance between the regions of the genome underlying adaptive traits and the remainder of the genome, decoupling inferences about character evolution from population history. Here, to disentangle these effects, we investigated the evolutionary origins and maintenance of Batesian mimicry between North American admiral butterflies (Limenitis arthemis) and their chemically defended model (Battus philenor) using a combination of de novo genome sequencing, whole-genome resequencing, and statistical introgression mapping. Our results suggest that balancing selection, arising from geographic variation in the presence or absence of the unpalatable model, has maintained two deeply divergent color patterning haplotypes that have been repeatedly sieved among distinct mimetic and nonmimetic lineages of Limenitis via introgressive hybridization.

scholarly journals Cytonuclear discordance in the crowned-sparrows, Zonotrichia atricapilla and Zonotrichia leucophrys: a mitochondrial selective sweep?

2020 ◽  
Author(s):  
Rebecca S. Taylor ◽  
Ashley C. Bramwell ◽  
Rute Clemente-Carvalho ◽  
Nicholas A. Cairns ◽  
Frances Bonier ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Environmental Changes ◽  
Incomplete Lineage Sorting ◽  
Mitochondrial Gene ◽  
Nuclear Gene ◽  
Phylogeographic Structure ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Reciprocal Monophyly ◽  
Mitochondrial Introgression

ABSTRACTThe golden-crowned (Zonotrichia atricapilla) and white-crowned (Z. leucophrys) sparrows have been presented as a compelling case for rapid speciation. They display divergence in song and plumage with overlap in their breeding ranges implying reproductive isolation, but have almost identical mitochondrial genomes. Previous research proposed hybridization and subsequent mitochondrial introgression as an alternate explanation, but lacked robust nuclear gene trees to distinguish between introgression and incomplete lineage sorting. We test for signatures of these processes between Z. atricapilla and Z. leucophrys, and investigate the relationships among Z. leucophrys subspecies, using mitochondrial sequencing and a reduced representation nuclear genomic dataset. Contrary to the paraphyly evident in mitochondrial gene trees, we confirmed the reciprocal monophyly of Z. atricapilla and Z. leucophrys using large panels of single nucleotide polymorphism (SNPs). The pattern of cytonuclear discordance is consistent with limited, historical hybridization and mitochondrial introgression, rather than a recent origin and incomplete lineage sorting between recent sister species. We found evidence of nuclear phylogeographic structure within Z. leucophrys with two distinct clades. Altogether, our results support the true species status of Z. atricapilla and Z. leucophrys, and indicate deeper divergences between the two species than inferred using mitochondrial markers. Our results demonstrate the limitations of relying solely on mitochondrial DNA for taxonomy, and raise questions about the possibility of selection on the mitochondrial genome during temperature oscillations (e.g. during the Pleistocene). Historical mitochondrial introgression facilitated by past environmental changes could cause erroneous dating of lineage splitting in other taxa when based on mitochondrial DNA alone.

scholarly journals Rapid phenotypic evolution during incipient speciation in a continental avian radiation

2011 ◽  
Vol 279 (1734) ◽  
pp. 1847-1856 ◽  
Author(s):  
Leonardo Campagna ◽  
Pilar Benites ◽  
Stephen C. Lougheed ◽  
Darío A. Lijtmaer ◽  
Adrián S. Di Giacomo ◽  
...  
Keyword(s):  
Phenotypic Diversity ◽  
Incomplete Lineage Sorting ◽  
Introgressive Hybridization ◽  
Molecular Data ◽  
Species Group ◽  
Adult Males ◽  
Lineage Sorting ◽  
Male Plumage ◽  
Recent Group ◽  
Genetic Signatures

Adaptive radiations have helped shape how we view animal speciation, particularly classic examples such as Darwin's finches, Hawaiian fruitflies and African Great Lakes cichlids. These ‘island’ radiations are comparatively recent, making them particularly interesting because the mechanisms that caused diversification are still in motion. Here, we identify a new case of a recent bird radiation within a continentally distributed species group; the capuchino seedeaters comprise 11 Sporophila species originally described on the basis of differences in plumage colour and pattern in adult males. We use molecular data together with analyses of male plumage and vocalizations to understand species limits of the group. We find marked phenotypic variation despite lack of mitochondrial DNA monophyly and few differences in other putatively neutral nuclear markers. This finding is consistent with the group having undergone a recent radiation beginning in the Pleistocene, leaving genetic signatures of incomplete lineage sorting, introgressive hybridization and demographic expansions. We argue that this apparent uncoupling between neutral DNA homogeneity and phenotypic diversity is expected for a recent group within the framework of coalescent theory. Finally, we discuss how the ecology of open habitats in South America during the Pleistocene could have helped promote this unique and ongoing radiation.

scholarly journals Plastid phylogenomics of Pleurothallidinae (Orchidaceae): Conservative plastomes, new variable markers, and comparative analyses of plastid, nuclear, and mitochondrial data

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0256126
Author(s):  
Anna Victoria Silvério R. Mauad ◽  
Leila do Nascimento Vieira ◽  
Valter Antônio de Baura ◽  
Eduardo Balsanelli ◽  
Emanuel Maltempi de Souza ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Incomplete Lineage Sorting ◽  
Introgressive Hybridization ◽  
Single Copy ◽  
Nuclear Ribosomal Dna ◽  
Molecular Characteristics ◽  
Lineage Sorting ◽  
Variable Regions ◽  
Mutational Hotspots ◽  
Phylogenomic Analyses

We present the first comparative plastome study of Pleurothallidinae with analyses of structural and molecular characteristics and identification of the ten most-variable regions to be incorporated in future phylogenetic studies. We sequenced complete plastomes of eight species in the subtribe and compared phylogenetic results of these to parallel analyses of their nuclear ribosomal DNA operon (26S, 18S, and 5.8S plus associated spacers) and partial mitochondrial genome sequences (29–38 genes and partial introns). These plastomes have the typical quadripartite structure for which gene content is similar to those of other orchids, with variation only in the composition of the ndh genes. The independent loss of ndh genes had an impact on which genes border the inverted repeats and thus the size of the small single-copy region, leading to variation in overall plastome length. Analyses of 68 coding sequences indicated the same pattern of codon usage as in other orchids, and 13 protein-coding genes under positive selection were detected. Also, we identified 62 polymorphic microsatellite loci and ten highly variable regions, for which we designed primers. Phylogenomic analyses showed that the top ten mutational hotspots represent well the phylogenetic relationships found with whole plastome sequences. However, strongly supported incongruence was observed among plastid, nuclear ribosomal DNA operon, and mitochondrial DNA trees, indicating possible occurrence of incomplete lineage sorting and/or introgressive hybridization. Despite the incongruence, the mtDNA tree retrieved some clades found in other analyses. These results, together with performance in recent studies, support a future role for mitochondrial markers in Pleurothallidinae phylogenetics.

scholarly journals The Legacy of Recurrent Introgression during the Radiation of Hares

2020 ◽  
Author(s):  
Mafalda S Ferreira ◽  
Matthew R Jones ◽  
Colin M Callahan ◽  
Liliana Farelo ◽  
Zelalem Tolesa ◽  
...  
Keyword(s):  
Incomplete Lineage Sorting ◽  
Introgressive Hybridization ◽  
Lineage Sorting ◽  
Whole Exome ◽  
Extant Species ◽  
The Last Glacial Maximum ◽  
Shared Genetic ◽  
The Last Glacial ◽  
Shared Variation

Abstract Hybridization may often be an important source of adaptive variation, but the extent and long-term impacts of introgression have seldom been evaluated in the phylogenetic context of a radiation. Hares (Lepus) represent a widespread mammalian radiation of 32 extant species characterized by striking ecological adaptations and recurrent admixture. To understand the relevance of introgressive hybridization during the diversification of Lepus, we analyzed whole exome sequences (61.7 Mb) from 15 species of hares (1- 4 individuals per species), spanning the global distribution of the genus, and two outgroups. We used a coalescent framework to infer species relationships and divergence times, despite extensive genealogical discordance. We found high levels of allele sharing among species and show that this reflects extensive incomplete lineage sorting and temporally layered hybridization. Our results revealed recurrent introgression at all stages along the Lepus radiation, including recent gene flow between extant species since the last glacial maximum, but also pervasive ancient introgression occurring since near the origin of the hare lineages. We show that ancient hybridization between northern hemisphere species has resulted in shared variation of potential adaptive relevance to highly seasonal environments, including genes involved in circadian rhythm regulation, pigmentation, and thermoregulation. Our results illustrate how the genetic legacy of ancestral hybridization may persist across a radiation, leaving a long-lasting signature of shared genetic variation that may contribute to adaptation.

scholarly journals Phylogenetic Trees and Networks Can Serve as Powerful and Complementary Approaches for Analysis of Genomic Data

2019 ◽  
Vol 69 (3) ◽  
pp. 593-601 ◽  
Author(s):  
Christopher Blair ◽  
Cécile Ané
Keyword(s):  
Gene Flow ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Phylogenetic Network ◽  
Genomic Data ◽  
Point Of View ◽  
Phylogenetic Networks ◽  
Lineage Sorting

Abstract Genomic data have had a profound impact on nearly every biological discipline. In systematics and phylogenetics, the thousands of loci that are now being sequenced can be analyzed under the multispecies coalescent model (MSC) to explicitly account for gene tree discordance due to incomplete lineage sorting (ILS). However, the MSC assumes no gene flow post divergence, calling for additional methods that can accommodate this limitation. Explicit phylogenetic network methods have emerged, which can simultaneously account for ILS and gene flow by representing evolutionary history as a directed acyclic graph. In this point of view, we highlight some of the strengths and limitations of phylogenetic networks and argue that tree-based inference should not be blindly abandoned in favor of networks simply because they represent more parameter rich models. Attention should be given to model selection of reticulation complexity, and the most robust conclusions regarding evolutionary history are likely obtained when combining tree- and network-based inference.

A “complex” problem: delimiting sibling species boundaries in black flies (Diptera: Simuliidae)

2012 ◽  
Vol 144 (2) ◽  
pp. 323-336 ◽  
Author(s):  
Ida M. Conflitti ◽  
Gerald F. Shields ◽  
Douglas C. Currie
Keyword(s):  
Sibling Species ◽  
Incomplete Lineage Sorting ◽  
Introgressive Hybridization ◽  
Complex Problem ◽  
Genetic Distances ◽  
Species Boundaries ◽  
Lineage Sorting ◽  
Reciprocal Monophyly ◽  
Coi Barcoding ◽  
Species Groups

AbstractRapid and recent lineage radiations pose challenges to systematists. Using members of the highly diverse Simulium arcticum Malloch complex, we tested whether the cytochrome c oxidase subunit I (COI) barcoding gene can differentiate black fly sibling species. Members of the S. arcticum complex were monophyletic in relation to two morphospecies and two cryptic species of the Simulium malyschevi Dorogostaisky et al. and Simulium noelleri Friederichs species-groups, respectively. Of five S. arcticum sibling species analysed, only Simulium negativum Adler et al. was monophyletic. No other members of the complex could be distinguished using COI barcodes. The inability to resolve S. arcticum sibling species resulted because (1) haplotypes were shared between species and (2) the distribution of interspecific genetic distances completely overlapped the range of variation within species. Potential sources of incongruence between barcode data and species boundaries include imperfect taxonomy, inadequate genetic information, incomplete lineage sorting, and/or introgressive hybridization. We ruled out imperfect taxonomy because chromosomal, ecological, and distributional evidence support the validity of S. arcticum sibling species. Therefore, current nomenclature should be maintained pending further study. We conclude that one or more of the latter three sources of incongruence could be responsible for the lack of reciprocal monophyly among species of the S. arcticum complex.

scholarly journals The legacy of recurrent introgression during the radiation of hares

2020 ◽  
Author(s):  
Mafalda S. Ferreira ◽  
Matthew R. Jones ◽  
Colin M. Callahan ◽  
Liliana Farelo ◽  
Zelalem Tolesa ◽  
...  
Keyword(s):  
Incomplete Lineage Sorting ◽  
Introgressive Hybridization ◽  
Lineage Sorting ◽  
Whole Exome ◽  
Extant Species ◽  
The Last Glacial Maximum ◽  
Shared Genetic ◽  
The Last Glacial ◽  
Shared Variation

AbstractHybridization may often be an important source of adaptive variation, but the extent and long-term impacts of introgression have seldom been evaluated in the phylogenetic context of a radiation. Hares (Lepus) represent a widespread mammalian radiation of 32 extant species characterized by striking ecological adaptations and recurrent admixture. To understand the relevance of introgressive hybridization during the diversification of Lepus, we analyzed whole exome sequences (61.7 Mb) from 15 species of hares (1- 4 individuals per species), spanning the global distribution of the genus, and two outgroups. We used a coalescent framework to infer species relationships and divergence times, despite extensive genealogical discordance. We found high levels of allele sharing among species and show that this reflects extensive incomplete lineage sorting and temporally layered hybridization. Our results revealed recurrent introgression at all stages along the Lepus radiation, including recent gene flow between extant species since the last glacial maximum, but also pervasive ancient introgression occurring since near the origin of the hare lineages. We show that ancient hybridization between northern hemisphere species has resulted in shared variation of potential adaptive relevance to highly seasonal environments, including genes involved in circadian rhythm regulation, pigmentation, and thermoregulation. Our results illustrate how the genetic legacy of ancestral hybridization may persist across a radiation, leaving a long-lasting signature of shared genetic variation that may contribute to adaptation within and among species.

scholarly journals When species trees disagree: an approach consistent with the coalescent that quantifies phylogenomic support for contentious relationships

2020 ◽  
Author(s):  
Richard G.J. Hodel ◽  
Joseph F. Walker ◽  
L. Lacey Knowles ◽  
Stephen A. Smith
Keyword(s):  
Phylogenetic Trees ◽  
Incomplete Lineage Sorting ◽  
Current Method ◽  
Species Trees ◽  
Lineage Sorting ◽  
True Tree ◽  
Valuable Complement ◽  
Phylogenomic Analyses ◽  
Edge Based ◽  
Inference Methods

AbstractPhylogenies inferred using both concatenation- and coalescent-based analyses typically render highly congruent trees. However, when they disagree, they often differ with respect to historically contentious and evolutionarily important relationships. These relationships may also involve etiolated lineages where increased sampling is not possible. Recently, methods aimed at interrogating single relationships or trees have emerged as promising investigative tools to examine these cases. Although recent methods such as “Edge-based Phylogenomic Support analYsis” (EPSY) led to insights into both systematic error and real biological signal, whether they are consistent with the coalescent in cases with high Incomplete Lineage Sorting (ILS) has yet to be characterized. Here, we use simulations and an empirical dataset to test the performance of EPSY, concatenation, and coalescent-based summary analyses under high levels of ILS. We focused on high-ILS scenarios because these represent the typical difficult cases that researchers often face due to the prevalence of ILS in phylogenomic datasets. ILS is known to be a major cause of phylogenomic conflict, which confounds many biological conclusions that depend on a resolved phylogeny, such as inferring ancestral character states, biogeographic reconstructions, and domestication histories. Our study found that EPSY was consistent with the coalescent in a high-ILS empirical dataset. In high-ILS simulations EPSY infers the correct edge more than half the time, whereas coalescent based methods and concatenation methods inferred the actual tree 37.8% and 25% of the time, respectively. All methods have conditions under which they generate the most accurate inferences. Given the levels of ILS in simulations, 26.2% of the time no method recovered the true tree. This zone where no current method can infer the true topology is likely due to properties of the species tree, such as the length of internal edges adjacent to a conflict and/or the length of the shortest branch. Nevertheless, the EPSY approach proves to be a valuable complement to phylogenomic analyses for interrogating regions of the tree with conflicting hypotheses generated from past studies or alternative inference methods. Our analyses highlight that robust phylogenetic trees may not be possible under some scenarios regardless of method and data source.

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