scholarly journals Rapid ecological specialization despite constant population sizes

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6476 ◽  
Author(s):  
Andrinajoro R. Rakotoarivelo ◽  
Paul O’Donoghue ◽  
Michael W. Bruford ◽  
Yoshan Moodley
Keyword(s):  
East Africa ◽  
Nuclear Dna ◽  
Incomplete Lineage Sorting ◽  
Demographic History ◽  
12S Rrna ◽  
Surprising Result ◽  
Ecological Specialization ◽  
Lineage Sorting ◽  
Mt Dna ◽  
Data Set

Background The bushbuck, Tragelaphus scriptus, is a widespread and ecologically diverse ungulate species complex within the spiral-horned antelopes. This species was recently found to consist of two genetically divergent but monophyletic lineages, which are paraphyletic at mitochondrial (mt)DNA owing to an ancient interspecific hybridization event. The Scriptus lineage (T. s. scriptus) inhabits the north-western half of the African continent while Sylvaticus (T. s. sylvaticus) is found in the south-eastern half. Here we test hypotheses of historical demography and adaptation in bushbuck using a higher-resolution framework, with four nuclear (MGF, PRKCI, SPTBN, and THY) and three new mitochondrial markers (cytochrome b, 12S rRNA, and 16S rRNA). Methods Genealogies were reconstructed for the mitochondrial and nuclear data sets, with the latter dated using fossil calibration points. We also inferred the demographic history of Scriptus and Sylvaticus using coalescent-based methods. To obtain an overview of the origins and ancestral colonisation routes of ancestral bushbuck sequences across geographic space, we conducted discrete Bayesian phylogeographic and statistical dispersal-vicariance analyses on our nuclear DNA data set. Results Both nuclear DNA and mtDNA support previous findings of two genetically divergent Sylvaticus and Scriptus lineages. The three mtDNA loci confirmed 15 of the previously defined haplogroups, including those with convergent phenotypes. However, the nuclear tree showed less phylogenetic resolution at the more derived parts of the genealogy, possibly due to incomplete lineage sorting of the slower evolving nuclear genome. The only exception to this was the montane Menelik’s bushbuck (Sylvaticus) of the Ethiopian highlands, which formed a monophyletic group at three of four nuclear DNA loci. We dated the coalescence of the two lineages to a common ancestor ∼2.54 million years ago. Both marker sets revealed similar demographic histories of constant population size over time. We show that the bushbuck likely originated in East Africa, with Scriptus dispersing to colonise suitable habitats west of the African Rift and Sylvaticus radiating from east of the Rift into southern Africa via a series of mainly vicariance events. Discussion Despite lower levels of genetic structure at nuclear loci, we confirmed the independent evolution of the Menelik’s bushbuck relative to the phenotypically similar montane bushbuck in East Africa, adding further weight to previous suggestions of convergent evolution within the bushbuck complex. Perhaps the most surprising result of our analysis was that both Scriptus and Sylvaticus populations remained relatively constant throughout the Pleistocene, which is remarkable given that this was a period of major climatic and tectonic change in Africa, and responsible for driving the evolution of much of the continent’s extant large mammalian diversity.

scholarly journals Rapid ecological specialization despite constant population sizes

2018 ◽  
Author(s):  
Andrinajoro R Rakotoarivelo ◽  
Paul O'Donoghue ◽  
Michael W Bruford ◽  
Yoshan Moodley
Keyword(s):  
East Africa ◽  
Nuclear Dna ◽  
Incomplete Lineage Sorting ◽  
Demographic History ◽  
Secondary Contact ◽  
12S Rrna ◽  
Surprising Result ◽  
Ecological Specialization ◽  
Data Set ◽  
North East

Background. The bushbuck, Tragelaphus scriptus, is the most widespread and ecologically diverse ungulate species complex within the spiral-horned antelopes. This species was recently found to consist of two genetically divergent but monophyletic Scriptus and Sylvaticus lineages, which are paraphyletic at mitochondrial (mt)DNA owing to an ancient interspecific hybridization event. The Scriptus lineage inhabits the north-western half of the African continent while Sylvaticus is found in the south-eastern half. Here we test hypotheses of historical demography and adaptation in bushbuck using a higher-resolution framework, with four nuclear (MGF, PRKCI, SPTBN, and THY) and three new mitochondrial markers (cytochrome b, 12S rRNA, and 16S rRNA). Methods. Genealogies were reconstructed for the mitochondrial and nuclear data sets, with the latter dated using fossil calibration points. We also inferred the demographic history of Scriptus and Sylvaticus using coalescent-based methods. To obtain an overview of the origins and ancestral colonisation routes of ancestral bushbuck sequences across geographic space, we conducted a discrete Bayesian phylogeographic analysis on our nuclear DNA data set. Results. Both nDNA and mtDNA support previously findings of two genetically divergent Sylvaticus and Scriptus lineages, with no allele sharing despite coming into secondary contact at several geographic locations. The three mtDNA loci confirmed 15 of the previously defined ecotypes, including those with convergent phenotypes. However, the nuclear tree showed less phylogenetic resolution at the more derived parts of the genealogy, possibly due to incomplete lineage sorting of the slower evolving nuclear genome. The only exception to this was the montane ecotype meneliki (Sylvaticus) of the Ethiopian highlands, which formed a monophyletic group at three of four nDNA loci. We dated the coalescence of the two lineages to a common ancestor ∼2.54 million years ago. Both marker sets revealed similar demographic histories of constant population size over time. We show that the bushbuck likely originated in North-East Africa, with Scriptus colonising suitable habitats towards west of the rift and Sylvaticus diffusing from east of the rift into southern Africa. Discussion. Despite lower levels of genetic structure at nuclear loci, we confirmed the independent evolution of the Menelik’s bushbuck relative to the phenotypically similar montane ecotypes in East Africa, adding further weight to previous suggestions of convergent evolution within the bushbuck complex. Perhaps the most surprising result of our analysis was that both Scriptus and Sylvaticus populations remained relatively constant throughout the Pleistocene, which is remarkable given that this was a period of major climatic and tectonic change in Africa, and responsible for driving the evolution of much of the continents extant large mammal diversity.

scholarly journals Rapid ecological specialization despite constant population sizes

2018 ◽  
Author(s):  
Andrinajoro R Rakotoarivelo ◽  
Paul O'Donoghue ◽  
Michael W Bruford ◽  
Yoshan Moodley
Keyword(s):  
East Africa ◽  
Nuclear Dna ◽  
Incomplete Lineage Sorting ◽  
Demographic History ◽  
Secondary Contact ◽  
12S Rrna ◽  
Surprising Result ◽  
Ecological Specialization ◽  
Data Set ◽  
North East

Background. The bushbuck, Tragelaphus scriptus, is the most widespread and ecologically diverse ungulate species complex within the spiral-horned antelopes. This species was recently found to consist of two genetically divergent but monophyletic Scriptus and Sylvaticus lineages, which are paraphyletic at mitochondrial (mt)DNA owing to an ancient interspecific hybridization event. The Scriptus lineage inhabits the north-western half of the African continent while Sylvaticus is found in the south-eastern half. Here we test hypotheses of historical demography and adaptation in bushbuck using a higher-resolution framework, with four nuclear (MGF, PRKCI, SPTBN, and THY) and three new mitochondrial markers (cytochrome b, 12S rRNA, and 16S rRNA). Methods. Genealogies were reconstructed for the mitochondrial and nuclear data sets, with the latter dated using fossil calibration points. We also inferred the demographic history of Scriptus and Sylvaticus using coalescent-based methods. To obtain an overview of the origins and ancestral colonisation routes of ancestral bushbuck sequences across geographic space, we conducted a discrete Bayesian phylogeographic analysis on our nuclear DNA data set. Results. Both nDNA and mtDNA support previously findings of two genetically divergent Sylvaticus and Scriptus lineages, with no allele sharing despite coming into secondary contact at several geographic locations. The three mtDNA loci confirmed 15 of the previously defined ecotypes, including those with convergent phenotypes. However, the nuclear tree showed less phylogenetic resolution at the more derived parts of the genealogy, possibly due to incomplete lineage sorting of the slower evolving nuclear genome. The only exception to this was the montane ecotype meneliki (Sylvaticus) of the Ethiopian highlands, which formed a monophyletic group at three of four nDNA loci. We dated the coalescence of the two lineages to a common ancestor ∼2.54 million years ago. Both marker sets revealed similar demographic histories of constant population size over time. We show that the bushbuck likely originated in North-East Africa, with Scriptus colonising suitable habitats towards west of the rift and Sylvaticus diffusing from east of the rift into southern Africa. Discussion. Despite lower levels of genetic structure at nuclear loci, we confirmed the independent evolution of the Menelik’s bushbuck relative to the phenotypically similar montane ecotypes in East Africa, adding further weight to previous suggestions of convergent evolution within the bushbuck complex. Perhaps the most surprising result of our analysis was that both Scriptus and Sylvaticus populations remained relatively constant throughout the Pleistocene, which is remarkable given that this was a period of major climatic and tectonic change in Africa, and responsible for driving the evolution of much of the continents extant large mammal diversity.

scholarly journals Rapid ecological specialization despite constant population sizes

2018 ◽  
Author(s):  
Andrinajoro R Rakotoarivelo ◽  
Yoshan Moodley
Keyword(s):  
Incomplete Lineage Sorting ◽  
Molecular Dating ◽  
Sub Saharan Africa ◽  
Dna Polymorphisms ◽  
Secondary Contact ◽  
12S Rrna ◽  
Ecological Specialization ◽  
Lineage Sorting ◽  
Mt Dna ◽  
Data Set

Background. The bushbuck, Tragelaphus scriptus, is the most widespread and ecologically diverse ungulate species complex within the spiral-horned antelopes, occurring in approximately 73% of the total land area of sub-Saharan Africa. This species was found to consist of two genetically divergent lineages based on the mitochondrial (mt)DNA control region. One lineage inhabited the north-western half of the African continent (T. scriptus) while the other lineage (T. sylvaticus) was found in the south-eastern half. The complex was also found to comprise an unprecedented example of 23 phylogenetically distinct groups (‘ecotypes’), with montane and desert phenotypes potentially resulting from convergent evolution. The current study aim to test hypotheses regarding historical demography and adaptation of bushbuck using a higher-resolution framework, with faster evolving nuclear markers(MGF, PRKCI, SPTBN, and THY) as well as three further mitochondrial markers (cytochrome b, 12S rRNA, and 16S rRNA). Methods. Genealogies were reconstructed for the nuclear and mitochondrial data sets and for each gene independently to test the non-monphyly of the bushbuck complexe in a multi loci framework. In addition, we reconstruct the phylogeographic history of the bushbuck complex by a Bayesian discrete phylogeographic approach of our nucDNA data set to investigate its geographic diffusion and ancestral sequence location. Results. We uncovered two evolutionarily divergent lineages and geographically restricted lineages (Sylvaticus and Scriptus) of bushbuck using phylogenetics. Molecular dating indicates that these lineages last shared a common ancestor ∼2.54 million years ago. Summary statistics and analysis of the frequency distributions of DNA polymorphisms do not have any support for expanding population. Both BSPs and EBSPs indicate that the Scriptus and Sylvaticus lineages have remained relatively stable during the last 225-450Kya. Discussion. Both nucDNA and mtDNA support previously findings of two genetically divergent Sylvaticus and Scriptus lineages, despite them coming into secondary contact in several geographic regions. The three mtDNA loci confirmed 15 of the previously defined ecotypes, including those with convergent phenotypes. However, the nuclear tree showed less phylogenetic resolution at the more derived parts of the genealogy, possibly due to incomplete lineage sorting of the slower evolving nuclear genome. The only exception to this was the montane ecotype meneliki of the Ethiopian highlands, which formed a monophyletic group at three of the four nucDNA loci. The independent evolution of this group relative to phenotypically similar montane ecotypes in Africa confirm previously suggestions of convergence within the bushbuck complex.

Phylogeny and evolution of the green lizards, Lacerta spp. (Squamata: Lacertidae) based on mitochondrial and nuclear DNA sequences

2005 ◽  
Vol 26 (3) ◽  
pp. 271-285 ◽  
Author(s):  
D. James Harris ◽  
Nuno Ferrand ◽  
Eduardo Crespo ◽  
Raquel Godinho
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Nuclear Dna ◽  
Incomplete Lineage Sorting ◽  
Bird Species ◽  
Rrna Genes ◽  
12S Rrna ◽  
Lineage Sorting ◽  
Extant Species ◽  
Mitochondrial Cytochrome B

AbstractPartial DNA sequences from three mitochondrial (cytochrome b, 12S rRNA and 16S rRNA) and two nuclear (β-fibrinogen intron 7 and C-mos) genes were used to estimate the phylogenetic relationships among all eight extant species of green lizards, Lacerta sensu stricto, and many currently recognized subspecies. All eight species form a monophyletic group. L. agilis, L. schreiberi and L. strigata are genetically well differentiated species. L. trilineata and L. pamphylica are not monophyletic units based on analyses of the β-fibrinogen intron 7. Lacerta media is closely related to some Lacerta trilineata. L. bilineata and L. viridis are closely related, and recognition of L. bilineata as a distinct species makes L. viridis paraphyletic also. For both L. bilineata and L. viridis, some subspecies appear to remain in their southern glacial refugia, while a single genetic entity shows successfully postglacial expansion. The topology derived from C-mos variation is concordant with that derived from mtDNA, with substitutions occurring at a similar rate to that of transversions in the rRNA genes. Although C-mos is typically used at deeper taxonomic levels it is also phylogenetically informative within green lizards. β-fibrinogen intron 7, typically used for assessing phylogenetic relationships among bird species, is a useful phylogenetic marker for reptiles also, showing considerable variation between species. There is not complete concordance between estimates of relationships derived from the mtDNA and nuclear markers, probably because rapid diversification led to incomplete lineage sorting in the green lizards. Introgression could also be occuring between some species.

scholarly journals Excluding spatial sampling bias does not eliminate over-splitting in DNA-based species delimitation analyses

2021 ◽  
Author(s):  
Daniel Lukic ◽  
Jonas Eberle ◽  
Jana Thormann ◽  
Carolus Holzschuh ◽  
Dirk Ahrens
Keyword(s):  
Dna Barcoding ◽  
Species Delimitation ◽  
Incomplete Lineage Sorting ◽  
Sampling Bias ◽  
Lineage Sorting ◽  
Data Set ◽  
Dna Taxonomy ◽  
Operational Taxonomic Units ◽  
And Performance ◽  
Single Locality

DNA-barcoding and DNA-based species delimitation are major tools in DNA taxonomy. Sampling has been a central debate in this context, because the geographical composition of samples affect the accuracy and performance of DNA-barcoding. Performance of complex DNA-based species delimitation is to be tested under simpler conditions in absence of geographic sampling bias. Here, we present an empirical data set sampled from a single locality in a Southeast-Asian biodiversity hotspot (Laos: Phou Pan mountain). We investigate the performance of various species delimitation approaches on a megadiverse assemblage of herbivore chafer beetles (Coleoptera: Scarabaeidae) to infer whether species delimitation suffers in the same way from exaggerate infraspecific variation despite the lack of geographic genetic variation that led to inconsistencies between entities from DNA-based and morphology-based species inference in previous studies. For this purpose, a 658 bp fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) was analysed for a total of 186 individuals of 56 morphospecies. Tree based and distance based species delimitation methods were used. All approaches showed a rather limited match ratio (max. 77%) with morphospecies. PTP and TCS prevailingly over-splitted morphospecies, while 3% clustering and ABGD also lumped several species into one entity. ABGD revealed the highest congruence between molecular operational taxonomic units (MOTUs) and morphospecies. Disagreements between morphospecies and MOTUs were discussed in the context of historically acquired geographic genetic differentiation, incomplete lineage sorting, and hybridization. The study once again highlights how important morphology still is in order to correctly interpret the results of molecular species delimitation.

scholarly journals Detecting destabilizing species in the phylogenetic backbone of Potentilla (Rosaceae) using low-copy nuclear markers

AoB Plants ◽  
2020 ◽  
Vol 12 (3) ◽  
Author(s):  
Nannie L Persson ◽  
Ingrid Toresen ◽  
Heidi Lie Andersen ◽  
Jenny E E Smedmark ◽  
Torsten Eriksson
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Data Sets ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Nuclear Markers ◽  
Data Set ◽  
Multispecies Coalescent ◽  
Single Marker ◽  
Named Groups

Abstract The genus Potentilla (Rosaceae) has been subjected to several phylogenetic studies, but resolving its evolutionary history has proven challenging. Previous analyses recovered six, informally named, groups: the Argentea, Ivesioid, Fragarioides, Reptans, Alba and Anserina clades, but the relationships among some of these clades differ between data sets. The Reptans clade, which includes the type species of Potentilla, has been noticed to shift position between plastid and nuclear ribosomal data sets. We studied this incongruence by analysing four low-copy nuclear markers, in addition to chloroplast and nuclear ribosomal data, with a set of Bayesian phylogenetic and Multispecies Coalescent (MSC) analyses. A selective taxon removal strategy demonstrated that the included representatives from the Fragarioides clade, P. dickinsii and P. fragarioides, were the main sources of the instability seen in the trees. The Fragarioides species showed different relationships in each gene tree, and were only supported as a monophyletic group in a single marker when the Reptans clade was excluded from the analysis. The incongruences could not be explained by allopolyploidy, but rather by homoploid hybridization, incomplete lineage sorting or taxon sampling effects. When P. dickinsii and P. fragarioides were removed from the data set, a fully resolved, supported backbone phylogeny of Potentilla was obtained in the MSC analysis. Additionally, indications of autopolyploid origins of the Reptans and Ivesioid clades were discovered in the low-copy gene trees.

scholarly journals Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l

2020 ◽  
Author(s):  
Diego F Morales-Briones ◽  
Gudrun Kadereit ◽  
Delphine T Tefarikis ◽  
Michael J Moore ◽  
Stephen A Smith ◽  
...  
Keyword(s):  
Network Inference ◽  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Phylogenetic Network ◽  
Species Tree ◽  
Data Sets ◽  
Species Trees ◽  
Lineage Sorting ◽  
Data Set ◽  
Gene Tree Discordance

Abstract Gene tree discordance in large genomic data sets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we test a hypothesis of ancient hybridization events within the plant family Amaranthaceae s.l. that was previously supported by morphological, ecological, and Sanger-based molecular data. The data set included seven genomes and 88 transcriptomes, 17 generated for this study. We examined gene-tree discordance using coalescent-based species trees and network inference, gene tree discordance analyses, site pattern tests of introgression, topology tests, synteny analyses, and simulations. We found that a combination of processes might have generated the high levels of gene tree discordance in the backbone of Amaranthaceae s.l. Furthermore, we found evidence that three consecutive short internal branches produce anomalous trees contributing to the discordance. Overall, our results suggest that Amaranthaceae s.l. might be a product of an ancient and rapid lineage diversification, and remains, and probably will remain, unresolved. This work highlights the potential problems of identifiability associated with the sources of gene tree discordance including, in particular, phylogenetic network methods. Our results also demonstrate the importance of thoroughly testing for multiple sources of conflict in phylogenomic analyses, especially in the context of ancient, rapid radiations. We provide several recommendations for exploring conflicting signals in such situations. [Amaranthaceae; gene tree discordance; hybridization; incomplete lineage sorting; phylogenomics; species network; species tree; transcriptomics.]

scholarly journals Terraces in Gene Tree Reconciliation-Based Species Tree Inference

2020 ◽  
Author(s):  
Michael J. Sanderson ◽  
Michelle M. McMahon ◽  
Mike Steel
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Solution Space ◽  
Species Tree ◽  
Gene Trees ◽  
Species Trees ◽  
Lineage Sorting ◽  
Data Set ◽  
Tree Reconciliation ◽  
The Impact

AbstractTerraces in phylogenetic tree space are sets of trees with identical optimality scores for a given data set, arising from missing data. These were first described for multilocus phylogenetic data sets in the context of maximum parsimony inference and maximum likelihood inference under certain model assumptions. Here we show how the mathematical properties that lead to terraces extend to gene tree - species tree problems in which the gene trees are incomplete. Inference of species trees from either sets of gene family trees subject to duplication and loss, or allele trees subject to incomplete lineage sorting, can exhibit terraces in their solution space. First, we show conditions that lead to a new kind of terrace, which stems from subtree operations that appear in reconciliation problems for incomplete trees. Then we characterize when terraces of both types can occur when the optimality criterion for tree search is based on duplication, loss or deep coalescence scores. Finally, we examine the impact of assumptions about the causes of losses: whether they are due to imperfect sampling or true evolutionary deletion.

scholarly journals Divergence estimation in the presence of incomplete lineage sorting and migration

2017 ◽  
Author(s):  
Graham Jones
Keyword(s):  
Incomplete Lineage Sorting ◽  
Simulated Data ◽  
Species Tree ◽  
Lineage Sorting ◽  
Data Set ◽  
Migration Rates ◽  
Isolation With Migration ◽  
Multispecies Coalescent ◽  
Tree Inference ◽  
And Migration

AbstractThis paper focuses on the problem of estimating a species tree from multilocus data in the presence of incomplete lineage sorting and migration. We develop a mathematical model similar to IMa2 (Hey 2010) for the relevant evolutionary processes which allows both the the population size parameters and the migration rates between pairs of species tree branches to be integrated out. We then describe a BEAST2 package DENIM which based on this model, and which uses an approximation to sample from the posterior. The approximation is based on the assumption that migrations are rare, and it only samples from certain regions of the posterior which seem likely given this assumption. The method breaks down if there is a lot of migration. Using simulations, Leaché et al 2014 showed migration causes problems for species tree inference using the multispecies coalescent when migration is present but ignored. We re-analyze this simulated data to explore DENIM’s performance, and demonstrate substantial improvements over *BEAST. We also re-analyze an empirical data set. [isolation-with-migration; incomplete lineage sorting; multispecies coalescent; species tree; phylogenetic analysis; Bayesian; Markov chain Monte Carlo]

scholarly journals Practical Aspects of Phylogenetic Network Analysis Using PhyloNet

2019 ◽  
Author(s):  
Zhen Cao ◽  
Xinhao Liu ◽  
Huw A. Ogilvie ◽  
Zhi Yan ◽  
Luay Nakhleh
Keyword(s):  
Incomplete Lineage Sorting ◽  
Phylogenetic Network ◽  
Synthetic Data ◽  
Simulated Data ◽  
Single Species ◽  
Phylogenetic Networks ◽  
Lineage Sorting ◽  
Data Set ◽  
Types Of Information ◽  
Analyze Data

AbstractPhylogenetic networks extend trees to enable simultaneous modeling of both vertical and horizontal evolutionary processes. PhyloNet is a software package that has been under constant development for over 10 years and includes a wide array of functionalities for inferring and analyzing phylogenetic networks. These functionalities differ in terms of the input data they require, the criteria and models they employ, and the types of information they allow to infer about the networks beyond their topologies. Furthermore, PhyloNet includes functionalities for simulating synthetic data on phylogenetic networks, quantifying the topological differences between phylogenetic networks, and evaluating evolutionary hypotheses given in the form of phylogenetic networks.In this paper, we use a simulated data set to illustrate the use of several of PhyloNet’s functionalities and make recommendations on how to analyze data sets and interpret the results when using these functionalities. All inference methods that we illustrate are incomplete lineage sorting (ILS) aware; that is, they account for the potential of ILS in the data while inferring the phylogenetic network. While the models do not include gene duplication and loss, we discuss how the methods can be used to analyze data in the presence of polyploidy.The concept of species is irrelevant for the computational analyses enabled by PhyloNet in that species-individuals mappings are user-defined. Consequently, none of the functionalities in PhyloNet deals with the task of species delimitation. In this sense, the data being analyzed could come from different individuals within a single species, in which case population structure along with potential gene flow is inferred (assuming the data has sufficient signal), or from different individuals sampled from different species, in which case the species phylogeny is being inferred.

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