scholarly journals Significant cross-species gene flow detected in the Tamias quadrivittatus group of North American chipmunks

2021 ◽  
Author(s):  
Jiayi Ji ◽  
Donavan J. Jackson ◽  
Adam D. Leaché ◽  
Ziheng Yang
Keyword(s):  
Gene Flow ◽  
Sequence Data ◽  
Nuclear Genome ◽  
Likelihood Method ◽  
Recent Analysis ◽  
The Past ◽  
Rapid Speciation ◽  
Full Likelihood ◽  
Nuclear Loci ◽  
Robust Evidence

In the past two decades genomic data have been widely used to detect historical gene flow between species in a variety of plants and animals. The Tamias quadrivittatus group of North America chipmunks, which originated through a series of rapid speciation events, are known to undergo massive amounts of mitochondrial introgression. Yet in a recent analysis of targeted nuclear loci from the group, no evidence for cross-species introgression was detected, indicating widespread cytonuclear discordance. The study used heuristic methods that analyze summaries of the multilocus sequence data to detect gene flow, which may suffer from low power. Here we use the full likelihood method implemented in the Bayesian program BPP to reanalyze these data. We take a stepwise approach to constructing an introgression model by adding introgression events onto a well-supported binary species tree. The analysis detected robust evidence for multiple ancient introgression events affecting the nuclear genome, with introgression probabilities reaching 65%. We estimate population parameters and highlight the fact that species divergence times may be seriously underestimated if ancient cross-species gene flow is ignored in the analysis. Our analyses highlight the importance of using adequate statistical methods to reach reliable biological conclusions concerning cross-species gene flow.

scholarly journals Measuring the degree of starshape in genealogies – summary statistics and demographic inference

2009 ◽  
Vol 91 (4) ◽  
pp. 281-292 ◽  
Author(s):  
KONRAD LOHSE ◽  
JEROME KELLEHER
Keyword(s):  
Sequence Data ◽  
Simple Algorithm ◽  
Likelihood Estimation ◽  
Likelihood Method ◽  
Summary Statistics ◽  
Full Likelihood ◽  
Tests Of Neutrality ◽  
History Of ◽  
Neutrality Tests ◽  
Demographic Inference

SummaryThe degree of starshape of a genealogy is readily detectable using summary statistics and can be taken as a surrogate for the effect of past demography and other non-neutral forces. Summary statistics such as Tajima's D and related measures are commonly used for this. However, it is well known that because of their neglect of the genealogy underlying a sample such neutrality tests are far from ideal. Here, we investigate the properties of two types of summary statistics that are derived by considering the genealogy: (i) genealogical ratios based on the number of mutations on the rootward branches, which can be inferred from sequence data using a simple algorithm and (ii) summary statistics that use properties of a perfectly star-shaped genealogy. The power of these measures to detect a history of exponential growth is compared with that of standard summary statistics and a likelihood method for the single and multi-locus case. Statistics that depend on pairwise measures such as Tajima's D have comparatively low power, being sensitive to the random topology of the underlying genealogy. When analysing multi-locus data, we find that the genealogical measures are most powerful. Provided reliable outgroup information is available they may constitute a useful alternative to full likelihood estimation and standard tests of neutrality.

scholarly journals The Impact of Cross-Species Gene Flow on Species Tree Estimation

2020 ◽  
Vol 69 (5) ◽  
pp. 830-847 ◽  
Author(s):  
Xiyun Jiao ◽  
Tomáš Flouri ◽  
Bruce Rannala ◽  
Ziheng Yang
Keyword(s):  
Gene Flow ◽  
Sequence Data ◽  
Majority Vote ◽  
Gene Tree ◽  
Species Tree ◽  
Likelihood Method ◽  
Estimation Methods ◽  
Vote Method ◽  
Multispecies Coalescent ◽  
Tree Estimation

Abstract Recent analyses of genomic sequence data suggest cross-species gene flow is common in both plants and animals, posing challenges to species tree estimation. We examine the levels of gene flow needed to mislead species tree estimation with three species and either episodic introgressive hybridization or continuous migration between an outgroup and one ingroup species. Several species tree estimation methods are examined, including the majority-vote method based on the most common gene tree topology (with either the true or reconstructed gene trees used), the UPGMA method based on the average sequence distances (or average coalescent times) between species, and the full-likelihood method based on multilocus sequence data. Our results suggest that the majority-vote method based on gene tree topologies is more robust to gene flow than the UPGMA method based on coalescent times and both are more robust than likelihood assuming a multispecies coalescent (MSC) model with no cross-species gene flow. Comparison of the continuous migration model with the episodic introgression model suggests that a small amount of gene flow per generation can cause drastic changes to the genetic history of the species and mislead species tree methods, especially if the species diverged through radiative speciation events. Estimates of parameters under the MSC with gene flow suggest that African mosquito species in the Anopheles gambiae species complex constitute such an example of extreme impact of gene flow on species phylogeny. [IM; introgression; migration; MSci; multispecies coalescent; species tree.]

scholarly journals Early history of Neanderthals and Denisovans

2017 ◽  
Vol 114 (37) ◽  
pp. 9859-9863 ◽  
Author(s):  
Alan R. Rogers ◽  
Ryan J. Bohlender ◽  
Chad D. Huff
Keyword(s):  
Gene Flow ◽  
Dna Sequence ◽  
Evolutionary History ◽  
Sequence Data ◽  
Early History ◽  
Middle Pleistocene ◽  
Dna Sequence Data ◽  
The Past ◽  
History Of

Extensive DNA sequence data have made it possible to reconstruct human evolutionary history in unprecedented detail. We introduce a method to study the past several hundred thousand years. Our results show that (i) the Neanderthal–Denisovan lineage declined to a small size just after separating from the modern lineage, (ii) Neanderthals and Denisovans separated soon thereafter, and (iii) the subsequent Neanderthal population was large and deeply subdivided. They also (iv) support previous estimates of gene flow from Neanderthals into modern Eurasians. These results suggest an archaic human diaspora early in the Middle Pleistocene.

scholarly journals Complex introgression history of the erato-sara clade of Heliconius butterflies

2021 ◽  
Author(s):  
Yuttapong Thawornwattana ◽  
Fernando A. Seixas ◽  
Ziheng Yang ◽  
James Mallet
Keyword(s):  
Gene Flow ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Hybrid Origin ◽  
Ancestral Population ◽  
Ancestral Gene ◽  
Species Phylogeny ◽  
Full Likelihood ◽  
History Of

AbstractIntrogression plays a key role in adaptive evolution and species diversification in many groups of species including Heliconius butterflies. However, frequent hybridization and subsequent gene flow between species makes estimation of the species phylogeny challenging. Here, we infer species phylogeny and introgression events from whole-genome sequence data of six members of the erato-sara clade of Heliconius using a multispecies coalescent model with introgression (MSci) and an isolation-with-migration (IM) model. These approaches probabilistically capture the genealogical heterogeneity across the genome due to introgression and incomplete lineage sorting in a full likelihood framework. We detect robust signals of introgression across the genome, and estimate the direction, timing and magnitude of each introgression event. The results clarify several processes of speciation and introgression in the erato-sara group. In particular, we confirm ancestral gene flow between the sara clade and an ancestral population of H. telesiphe, a hybrid origin of H. hecalesia, and gene flow between the sister species H. erato and H. himera. The ability to confidently infer the presence, timing and magnitude of introgression events using genomic sequence data is helpful for understanding speciation in the presence of gene flow and will be useful for understanding the adaptive consequences of introgressed regions of the genome. Our analysis serves to highlight the power of full likelihood methods under the MSci model to the history of species divergence and cross-species introgression from genome-scale data.

scholarly journals Resolving Recalcitrant Clades in the Pantropical Ochnaceae: Insights From Comparative Phylogenomics of Plastome and Nuclear Genomic Data Derived From Targeted Sequencing

2021 ◽  
Vol 12 ◽  
Author(s):  
Julio V. Schneider ◽  
Juraj Paule ◽  
Tanja Jungcurt ◽  
Domingos Cardoso ◽  
André Márcio Amorim ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
De Novo ◽  
Sequence Data ◽  
Plastid Dna ◽  
Targeted Sequencing ◽  
Recent Analysis ◽  
Target Sequence ◽  
Uniparental Inheritance ◽  
Plastid Genomes ◽  
Nuclear Loci

Plastid DNA sequence data have been traditionally widely used in plant phylogenetics because of the high copy number of plastids, their uniparental inheritance, and the blend of coding and non-coding regions with divergent substitution rates that allow the reconstruction of phylogenetic relationships at different taxonomic ranks. In the present study, we evaluate the utility of the plastome for the reconstruction of phylogenetic relationships in the pantropical plant family Ochnaceae (Malpighiales). We used the off-target sequence read fraction of a targeted sequencing study (targeting nuclear loci only) to recover more than 100 kb of the plastid genome from the majority of the more than 200 species of Ochnaceae and all but two genera using de novo and reference-based assembly strategies. Most of the recalcitrant nodes in the family’s backbone were resolved by our plastome-based phylogenetic inference, corroborating the most recent classification system of Ochnaceae and findings from a phylogenomic study based on nuclear loci. Nonetheless, the phylogenetic relationships within the major clades of tribe Ochnineae, which comprise about two thirds of the family’s species diversity, received mostly low support. Generally, the phylogenetic resolution was lowest at the infrageneric level. Overall there was little phylogenetic conflict compared to a recent analysis of nuclear loci. Effects of taxon sampling were invoked as the most likely reason for some of the few well-supported discords. Our study demonstrates the utility of the off-target fraction of a target enrichment study for assembling near-complete plastid genomes for a large proportion of samples.

scholarly journals The Impact of Cross-Species Gene Flow on Species Tree Estimation

2019 ◽  
Author(s):  
Xiyun Jiao ◽  
Thomas Flouris ◽  
Bruce Rannala ◽  
Ziheng Yang
Keyword(s):  
Gene Flow ◽  
Sequence Data ◽  
Majority Vote ◽  
Gene Tree ◽  
Species Tree ◽  
Likelihood Method ◽  
Estimation Methods ◽  
Vote Method ◽  
Tree Estimation ◽  
The Impact

ABSTRACTRecent analyses of genomic sequence data suggest cross-species gene flow is common in both plants and animals, posing challenges to species tree inference. We examine the levels of gene flow needed to mislead species tree estimation with three species and either episodic introgressive hybridization or continuous migration between an outgroup and one ingroup species. Several species tree estimation methods are examined, including the majority-vote method based on the most common gene tree topology (with either the true or reconstructed gene trees used), the UPGMA method based on the average sequence distances (or average coalescent times) between species, and the full-likelihood method based on multi-locus sequence data. Our results suggest that the majority-vote method is more robust to gene flow than the UPGMA method and both are more robust than likelihood assuming a multispecies coalescent (MSC) model with no cross-species gene flow. A small amount of introgression or migration can mislead species tree methods if the species diverged through speciation events separated by short time intervals. Estimates of parameters under the MSC with gene flow suggest the Anopheles gambia African mosquito species complex is an example where gene flow greatly impacts species phylogeny.

Children’s Lives and Deaths in Merovingian Gaul

2020 ◽  
pp. 185-213
Author(s):  
Émilie Perez
Keyword(s):  
Social Identity ◽  
Age Groups ◽  
New Method ◽  
Recent Analysis ◽  
Age And Gender ◽  
The Past ◽  
And Gender ◽  
Grave Goods

The role of children in Merovingian society has long been downplayed, and the study of their graves and bones has long been neglected. However, during the past fifteen years, archaeologists have shown growing interest in the place of children in Merovingian society. Nonetheless, this research has not been without challenges linked to the nature of the biological and material remains. Recent analysis of 315 children’s graves from four Merovingian cemeteries in northern Gaul (sixth to seventh centuries) allows us to understand the modalities of burial ritual for children. A new method for classifying children into social age groups shows that the type, quality, quantity, and diversity of grave goods were directly correlated with the age of the deceased. They increased from the age of eight and particularly around the time of puberty. This study discusses the role of age and gender in the construction and expression of social identity during childhood in the Merovingian period.

Association of variants m.T16172C and m.T16519C in whole mtDNA sequences with high altitude pulmonary edema in Han Chinese lowlanders

2021 ◽  
Author(s):  
Yan Wang ◽  
Xuewen Huang ◽  
Fujun Peng ◽  
Huiling Han ◽  
Yanan Gu ◽  
...  
Keyword(s):  
Pulmonary Edema ◽  
High Altitude ◽  
Sequence Data ◽  
Nuclear Genome ◽  
Han Chinese ◽  
Mtdna Sequences ◽  
Reactive Protein ◽  
Arterial Blood ◽  
High Altitude Pulmonary Edema ◽  
Systolic Arterial Blood Pressure

Abstract Background: High altitude pulmonary edema (HAPE) is a hypoxia-induced non-cardiogenic pulmonary edema that typically occurred in un-acclimatized lowlanders, which inevitably leads to life-threatening consequences. Apart from multiple factors involved, the genetic factors also play an important role in the pathogenesis of HAPE. So far, researchers put more energy into the nuclear genome and HAPE, and ignored the relationship between the mitochondrion DNA (mtDNA) variants and HAPE susceptibility. Methods: We recruited a total of 366 individuals including 181 HAPE patients and 185 healthy or non-HAPE populations through two times. The first time, 49 HAPE patients and 58 non-HAPE cases were performed through whole mtDNA sequences to search the mutations and haplogroups, which were associated with the HAPE. The second time, 132 HAPE patients and 127 non-HAPE subjects were collected to apply of verifying these variants and haplogroups of mtDNA with routine PCR method. Results: We analyzed and summarized the clinical characteristics and sequence data for 49 HAPE patients and 58 non-HAPE cases. We found that a series of routine blood indexes including systolic arterial blood pressure (SBP), heart rate (HR), white blood cell (WBC) and C-reactive protein (CRP) in HAPE group presented higher and displayed the significant differences compared with those in non-HAPE group. Though the average numbers of variants in different regions and groups samples were not statistically significant (P > 0.05), the mutation densities of different region in the internal group shown the significant differences. Then we found that two mutations (T16172C and T16519C) associated with the HAPE susceptibility, and the T16172C mutation increased the risk of HAPE, and the T16519C mutation decreased the HAPE rating. Furthermore, the two mutations were demonstrated with 132 HAPE cases and 127 non-HAPE individuals. Unfortunately, all the haplogroups were not associated with the HAPE haplogroups.Conclusions: We provided the evidence of differences in mtDNA polymorphism frequencies between HAPE and non-HAPE Han Chinese. Genotypes of mtDNA 16172C and 16519C were correlated with HAPE susceptibility, which indicated that the role in mitochondrial genome in the pathogenesis of HAPE.

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