scholarly journals Phylogeography of Canada Geese (Branta Canadensis) in Western North America

The Auk ◽  
2003 ◽  
Vol 120 (3) ◽  
pp. 889-907
Author(s):  
Kim T. Scribner ◽  
Sandra L. Talbot ◽  
John M. Pearce ◽  
Barbara J. Pierson ◽  
Karen S. Bollinger ◽  
...  
Keyword(s):  
North America ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Molecular Genetic ◽  
Sequence Divergence ◽  
Branta Canadensis ◽  
Canada Geese ◽  
Western North America ◽  
Gene Trees ◽  
Lineage Sorting

Abstract Using molecular genetic markers that differ in mode of inheritance and rate of evolution, we examined levels and partitioning of genetic variation for seven nominal subspecies (11 breeding populations) of Canada Geese (Branta canadensis) in western North America. Gene trees constructed from mtDNA control region sequence data show that subspecies of Canada Geese do not have distinct mtDNA. Large and small-bodied forms of Canada Geese were highly diverged (0.077 average sequence divergence) and represent monophyletic groups. A majority (65%) of 20 haplotypes resolved were observed in single breeding locales. However, within both large and small-bodied forms certain haplotypes occurred across multiple subspecies. Population trees for both nuclear (microsatellites) and mitochondrial markers were generally concordant and provide resolution of population and subspecific relationships indicating incomplete lineage sorting. All populations and subspecies were genetically diverged, but to varying degrees. Analyses of molecular variance, nested-clade and coalescencebased analyses of mtDNA suggest that both historical (past fragmentation) and contemporary forces have been important in shaping current spatial genetic distributions. Gene flow appears to be ongoing though at different rates, even among currently recognized subspecies. The efficacy of current subspecific taxonomy is discussed in light of hypothesized historical vicariance and current demographic trends of management and conservation concern.

Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment

Zootaxa ◽  
2020 ◽  
Vol 4750 (3) ◽  
pp. 328-348 ◽  
Author(s):  
DAVID A. GRAY ◽  
DAVID B. WEISSMAN ◽  
JEFFREY A. COLE ◽  
EMILY MORIARTY LEMMON
Keyword(s):  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
The United States ◽  
Field Cricket ◽  
Future Research ◽  
Gene Trees ◽  
Lineage Sorting ◽  
The Bahamas ◽  
Field Crickets ◽  
Anchored Hybrid Enrichment

We present the first comprehensive molecular phylogeny of Gryllus field cricket species found in the United States and Canada, select additional named Gryllus species found in Mexico and the Bahamas, plus the European field cricket G. campestris Linnaeus and the Afro-Eurasian cricket G. bimaculatus De Geer. Acheta, Teleogryllus, and Nigrogryllus were used as outgroups. Anchored hybrid enrichment was used to generate 492,531 base pairs of DNA sequence from 563 loci. RAxML analysis of concatenated sequence data and Astral analysis of gene trees gave broadly congruent results, especially for older branches and overall tree structure. The North American Gryllus are monophyletic with respect to the two Old World taxa; certain sub-groups show rapid recent divergence. This is the first Anchored Hybrid Enrichment study of an insect group done for closely related species within a single genus, and the results illustrate the challenges of reconstructing the evolutionary history of young rapidly diverged taxa when both incomplete lineage sorting and probable hybridization are at play. Because Gryllus field crickets have been used extensively as a model system in evolutionary ecology, behavior, neuro-physiology, speciation, and life-history and life-cycle evolution, these results will help inform, interpret, and guide future research in these areas. 

PHYLOGEOGRAPHY OF CANADA GEESE (BRANTA CANADENSIS) IN WESTERN NORTH AMERICA

The Auk ◽  
2003 ◽  
Vol 120 (3) ◽  
pp. 889 ◽  
Author(s):  
Kim T. Scribner ◽  
Sandra L. Talbot ◽  
John M. Pearce ◽  
Barbara J. Pierson ◽  
Karen S. Bollinger ◽  
...  
Keyword(s):  
North America ◽  
Branta Canadensis ◽  
Canada Geese ◽  
Western North America

scholarly journals Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone

2019 ◽  
Vol 68 (6) ◽  
pp. 937-955 ◽  
Author(s):  
Alison Cloutier ◽  
Timothy B Sackton ◽  
Phil Grayson ◽  
Michele Clamp ◽  
Allan J Baker ◽  
...  
Keyword(s):  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Estimation Error ◽  
Gene Tree ◽  
Species Tree ◽  
Tree Topology ◽  
Whole Genome ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Genome Analyses

Abstract Palaeognathae represent one of the two basal lineages in modern birds, and comprise the volant (flighted) tinamous and the flightless ratites. Resolving palaeognath phylogenetic relationships has historically proved difficult, and short internal branches separating major palaeognath lineages in previous molecular phylogenies suggest that extensive incomplete lineage sorting (ILS) might have accompanied a rapid ancient divergence. Here, we investigate palaeognath relationships using genome-wide data sets of three types of noncoding nuclear markers, together totaling 20,850 loci and over 41 million base pairs of aligned sequence data. We recover a fully resolved topology placing rheas as the sister to kiwi and emu + cassowary that is congruent across marker types for two species tree methods (MP-EST and ASTRAL-II). This topology is corroborated by patterns of insertions for 4274 CR1 retroelements identified from multispecies whole-genome screening, and is robustly supported by phylogenomic subsampling analyses, with MP-EST demonstrating particularly consistent performance across subsampling replicates as compared to ASTRAL. In contrast, analyses of concatenated data supermatrices recover rheas as the sister to all other nonostrich palaeognaths, an alternative that lacks retroelement support and shows inconsistent behavior under subsampling approaches. While statistically supporting the species tree topology, conflicting patterns of retroelement insertions also occur and imply high amounts of ILS across short successive internal branches, consistent with observed patterns of gene tree heterogeneity. Coalescent simulations and topology tests indicate that the majority of observed topological incongruence among gene trees is consistent with coalescent variation rather than arising from gene tree estimation error alone, and estimated branch lengths for short successive internodes in the inferred species tree fall within the theoretical range encompassing the anomaly zone. Distributions of empirical gene trees confirm that the most common gene tree topology for each marker type differs from the species tree, signifying the existence of an empirical anomaly zone in palaeognaths.

scholarly journals Recent Progress on Methods for Estimating and Updating Large Phylogenies

2021 ◽  
Author(s):  
Paul Zaharias ◽  
Tandy Warnow
Keyword(s):  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Divide And Conquer ◽  
Estimation Methods ◽  
Gene Trees ◽  
Species Trees ◽  
Lineage Sorting ◽  
Multiple Sequence ◽  
Large Gene ◽  
Large Trees

With the increased availability of sequence data and even of fully sequenced and assembled genomes, phylogeny estimation of very large trees (even of hundreds of thousands of sequences) is now a goal for some biologists. Yet, the construction of these phylogenies is a complex pipeline presenting analytical and computational challenges, especially when the number of sequences is very large. In the last few years, new methods have been developed that aim to enable highly accurate phylogeny estimations on these large datasets, including divide-and-conquer techniques for multiple sequence alignment and/or tree estimation, methods that can estimate species trees from multi-locus datasets while addressing heterogeneity due to biological processes (e.g., incomplete lineage sorting and gene duplication and loss), and methods to add sequences into large gene trees or species trees. Here we present some of these recent advances and discuss opportunities for future improvements.

scholarly journals Plastome data reveal multiple geographic origins of Quercus Group Ilex

2015 ◽  
Author(s):  
Marco Cosimo Simeone ◽  
Guido W Grimm ◽  
Alessio Papini ◽  
Federico Vessella ◽  
Simone Cardoni ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Nuclear Genome ◽  
Sequence Divergence ◽  
Geographic Area ◽  
Geographic Region ◽  
Tectonic Activity ◽  
Lineage Sorting ◽  
Distribution Ranges

Nucleotide sequences from the plastome are currently the main source for assessing taxonomic and phylogenetic relationships in flowering plants and their historical biogeography at all hierarchical levels. One exception is the large and economically important genus Quercus (oaks). Whereas differentiation patterns of the nuclear genome are in agreement with morphology and the fossil record, diversity patterns in the plastome are at odds with established taxonomic and phylogenetic relationships. However, the extent and evolutionary implications of this incongruence has yet to be fully uncovered. The DNA sequence divergence of four Euro-Mediterranean Group Ilex oak species (Quercus ilex L., Q. coccifera L., Q. aucheri Jaub. & Spach., Q. alnifolia Poech.) was explored at three chloroplast markers (rbcL, trnK-matK, trnH-psbA). Phylogenetic relationships were reconstructed including worldwide members of additional 55 species representing all Quercus subgeneric groups. Family and order sequence data were harvested from gene banks to better frame the observed divergence in larger taxonomic contexts. We found a strong geographic sorting in the focal group and the genus in general that is entirely decoupled from species boundaries. Main plastid haplotypes shared by distinct oak lineages from the same geographic region and high plastid diversity in members of Group Ilex are indicative for a polyphyletic origin of their plastomes. The results suggest that incomplete lineage sorting and repeated phases of unidirectional introgression among ancestral lineages of Group Ilex and two other main Groups of Eurasian oaks (Cyclobalanopsis and Cerris) caused this complex pattern. Comparison with the current phylogenetic synthesis also suggests an initial high- versus mid-latitude biogeographic split within Quercus. High plastome plasticity of Group Ilex reflects geographic area disruptions, possibly linked with high tectonic activity of past and modern distribution ranges, that did not leave imprints in the nuclear genome of modern species and infrageneric lineages.

scholarly journals MetaCurator: A hidden Markov model-based toolkit for extracting and curating sequences from taxonomically-informative genetic markers

2019 ◽  
Author(s):  
Rodney T. Richardson ◽  
Douglas B. Sponsler ◽  
Harper McMinn-Sauder ◽  
Reed M. Johnson
Keyword(s):  
Markov Models ◽  
Sequence Data ◽  
Hidden Markov ◽  
Incomplete Lineage Sorting ◽  
Genetic Material ◽  
Sequence Divergence ◽  
Reference Sequence ◽  
Sequence Classification ◽  
Lineage Sorting ◽  
Link Type

SummaryThe community-level analysis of samples containing diverse genetic material, via metabarcoding and metagenomic approaches, is increasingly popular. While the production of sequence data for such studies has become straightforward, questions remain about how best to analyze and taxonomically characterize sequence data. For many sequence classification approaches, an important component of the workflow involves the curation of reference sequences. Ideally, this involves trimming away extraneous sequence at the 3 prime and 5 prime ends of the target marker of interest, as well as the removal of reference sequence duplicates. Here, we present MetaCurator, a software package written in Python, designed for automated reference sequence curation and highly generalizable across markers and study systems. MetaCurator is organized in a modular fashion, so users can implement tools individually in addition to utilizing the automated and flexible MetaCurator parental code. Aside from modules used to organize and format taxonomic lineage data, MetaCurator contains two signature tools. IterRazor utilizes profile hidden Markov models and an iterative search framework to exhaustively identify and extract the precise amplicon marker of interest from available reference sequence data. DerepByTaxonomy then facilitates sequence dereplication using a taxonomically aware approach, removing duplicates only when they belong to the same taxon. This is important for cases of incomplete lineage sorting between species and for highly conserved markers, such as plantrbcLandtrnL, which often display no sequence divergence across taxa, even at the genus level.Availability and implementationMetaCurator is supported on OSX and Linux (RedHat/CentOS) and is freely available under a GPL v3.0 license athttps://github.com/RTRichar/[email protected] informationCode associated with this work is available athttps://github.com/RTRichar/MetabarcodeDBsV2and additional analysis is presented in supplementary files.

scholarly journals Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix

2013 ◽  
Author(s):  
Rebecca T Kimball ◽  
Edward L Braun
Keyword(s):  
Japanese Quail ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Model Systems ◽  
Data Matrix ◽  
Bootstrap Support ◽  
Published Data ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Individual Gene

The resolution of rapid evolutionary radiations or “bushes” in the tree of life has been one of the most difficult and interesting problems in phylogenetics. The avian order Galliformes appears to have undergone several rapid radiations that have limited the resolution of prior studies and obscured the position of taxa important both agriculturally and as model systems (chicken, turkey, Japanese quail). Here we present analyses of a multi-locus data matrix comprising over 15,000 sites, primarily from nuclear introns but also including three mitochondrial regions, from 46 galliform taxa with all gene regions sampled for all taxa. The increased sampling of unlinked nuclear genes provided strong bootstrap support for all but a small number of relationships. Coalescent-based methods to combine individual gene trees and analyses of datasets independent of published data indicated that this well-supported topology is likely to reflect the galliform species tree. Some of the key findings include support for a second major clade within the core phasianids that includes the chicken and Japanese quail and clarification of the phylogenetic relationships of turkey. Jackknifed datasets suggested that there is an advantage to sampling many independent regions across the genome rather than obtaining long sequences for a small number of loci, possibly reflecting the differences among gene trees that differ due to incomplete lineage sorting. Despite the novel insights we obtained using this increased sampling of gene regions, some nodes remain unresolved, likely due to periods of rapid diversification. Resolving these remaining groups will likely require sequencing a very large number of gene regions, but our analyses now appear to support a robust backbone for this order.

scholarly journals Recent Progress on Methods for Estimating and Updating Large Phylogenies

2022 ◽  
Author(s):  
Paul Zaharias ◽  
Tandy Warnow
Keyword(s):  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Divide And Conquer ◽  
Estimation Methods ◽  
Gene Trees ◽  
Species Trees ◽  
Lineage Sorting ◽  
Multiple Sequence ◽  
Large Gene ◽  
Large Trees

With the increased availability of sequence data and even of fully sequenced and assembled genomes, phylogeny estimation of very large trees (even of hundreds of thousands of sequences) is now a goal for some biologists. Yet, the construction of these phylogenies is a complex pipeline presenting analytical and computational challenges, especially when the number of sequences is very large. In the last few years, new methods have been developed that aim to enable highly accurate phylogeny estimations on these large datasets, including divide-and-conquer techniques for multiple sequence alignment and/or tree estimation, methods that can estimate species trees from multi-locus datasets while addressing heterogeneity due to biological processes (e.g., incomplete lineage sorting and gene duplication and loss), and methods to add sequences into large gene trees or species trees. Here we present some of these recent advances and discuss opportunities for future improvements.

scholarly journals Plastome data reveal multiple geographic origins ofQuercusGroup Ilex

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1897 ◽  
Author(s):  
Marco Cosimo Simeone ◽  
Guido W. Grimm ◽  
Alessio Papini ◽  
Federico Vessella ◽  
Simone Cardoni ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Nuclear Genome ◽  
Sequence Divergence ◽  
Geographic Area ◽  
Tectonic Activity ◽  
Lineage Sorting ◽  
Geographic Origins ◽  
Distribution Ranges

Nucleotide sequences from the plastome are currently the main source for assessing taxonomic and phylogenetic relationships in flowering plants and their historical biogeography at all hierarchical levels. One major exception is the large and economically important genusQuercus(oaks). Whereas differentiation patterns of the nuclear genome are in agreement with morphology and the fossil record, diversity patterns in the plastome are at odds with established taxonomic and phylogenetic relationships. However, the extent and evolutionary implications of this incongruence has yet to be fully uncovered. The DNA sequence divergence of four Euro-Mediterranean Group Ilex oak species (Quercus ilexL.,Q. cocciferaL.,Q. aucheriJaub. & Spach.,Q. alnifoliaPoech.) was explored at three chloroplast markers (rbcL, trnK/matK, trnH-psbA). Phylogenetic relationships were reconstructed including worldwide members of additional 55 species representing allQuercussubgeneric groups. Family and order sequence data were harvested from gene banks to better frame the observed divergence in larger taxonomic contexts. We found a strong geographic sorting in the focal group and the genus in general that is entirely decoupled from species boundaries. High plastid divergence in members ofQuercusGroup Ilex, including haplotypes shared with related, but long isolated oak lineages, point towards multiple geographic origins of this group of oaks. The results suggest that incomplete lineage sorting and repeated phases of asymmetrical introgression among ancestral lineages of Group Ilex and two other main Groups of Eurasian oaks (Cyclobalanopsis and Cerris) caused this complex pattern. Comparison with the current phylogenetic synthesis also suggests an initial high- versus mid-latitude biogeographic split withinQuercus. High plastome plasticity of Group Ilex reflects geographic area disruptions, possibly linked with high tectonic activity of past and modern distribution ranges, that did not leave imprints in the nuclear genome of modern species and infrageneric lineages.

scholarly journals Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix

2013 ◽  
Author(s):  
Rebecca T Kimball ◽  
Edward L Braun
Keyword(s):  
Japanese Quail ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Model Systems ◽  
Data Matrix ◽  
Bootstrap Support ◽  
Published Data ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Individual Gene

The resolution of rapid evolutionary radiations or “bushes” in the tree of life has been one of the most difficult and interesting problems in phylogenetics. The avian order Galliformes appears to have undergone several rapid radiations that have limited the resolution of prior studies and obscured the position of taxa important both agriculturally and as model systems (chicken, turkey, Japanese quail). Here we present analyses of a multi-locus data matrix comprising over 15,000 sites, primarily from nuclear introns but also including three mitochondrial regions, from 46 galliform taxa with all gene regions sampled for all taxa. The increased sampling of unlinked nuclear genes provided strong bootstrap support for all but a small number of relationships. Coalescent-based methods to combine individual gene trees and analyses of datasets independent of published data indicated that this well-supported topology is likely to reflect the galliform species tree. Some of the key findings include support for a second major clade within the core phasianids that includes the chicken and Japanese quail and clarification of the phylogenetic relationships of turkey. Jackknifed datasets suggested that there is an advantage to sampling many independent regions across the genome rather than obtaining long sequences for a small number of loci, possibly reflecting the differences among gene trees that differ due to incomplete lineage sorting. Despite the novel insights we obtained using this increased sampling of gene regions, some nodes remain unresolved, likely due to periods of rapid diversification. Resolving these remaining groups will likely require sequencing a very large number of gene regions, but our analyses now appear to support a robust backbone for this order.

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