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Sara Ruane, Robert W. Bryson, Jr. Alexander Pyron, Frank T. Both gene-tree discordance and unrecognized diversity are sources of error for accurate estimation of species trees, and can affect downstream diversification analyses by obscuring the correct of nodes, their density, and the lengths of the branches subtending them. Although the theoretical impact of gene-tree discordance on evolutionary analyses has been examined ly, the effect of unsampled and cryptic diversity has not.

Here, we examine how delimitation of ly unrecognized diversity in the milksnake Lampropeltis triangulum and use of a species-tree approach affects both estimation of the Lampropeltis phylogeny and comparative analyses with respect to the timing of diversification.

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Coalescent species delimitation indicates that L. Both genealogical and temporal discordance occurs between gene trees and the species tree, with evidence that mitochondrial DNA mtDNA introgression is a main factor. This discordance is further manifested in the preferred models of diversification, where the concatenated gene tree strongly supports an early burst of speciation during the Miocene, in contrast to species-tree estimates where diversification follows a birth—death model and speciation occurs mostly in the Pliocene and Pleistocene.

This study highlights the crucial interaction among coalescent-based phylogeography and species delimitation, systematics, and species diversification analyses. The description, diagnosis, and delimitation of species is essential across all Looking for Fort Smith Arkansas ruane of biology and is necessary for studies conducted within a phylogenetic framework, as missing taxa are known to decrease accuracy in inferring taxonomic relationships, estimating models of evolution, and calculating divergence times Hillis; Graybeal ; Poe ; Pollock and Bruno ; Pollock et al.

Species may be missing from phylogenies because samples from known species were not available or included by researchers, or due to unrecognized diversity. For many groups, new species are still being discovered using traditional morphological data and techniques e.

One major problem associated with unsampled species in phylogenetic reconstruction is the impact of missing taxa on comparative analyses. Incomplete sampling may result in an increase in the overall divergence-time estimates due to an oversampling of deep nodes Cusimano and Renner Measures that quantify diversification will then incorrectly indicate that rates of speciation have decreased toward the present Pybus and Harvey ; Rabosky and Lovette ; Cusimano and Renner ; Smith et al.

The use of gene trees also adds to the problem of divergence-time overestimation McCormack et al. Because gene divergences predate species divergences, gene-tree methods will incorrectly yield estimates of older branching times relative to species divergences Edwards and Beerli ; Carstens and Knowles ; Burbrink and Pyron This has been demonstrated empirically in Aphelocoma jays, where the dates generated using concatenated data sets are older than those from multi-locus species trees McCormack et al.

For taxa used in studies examining the timing and tempo of speciation, a basic understanding of species s and species-tree phylogeny is thus crucial. A key example is the milksnake Lampropeltis triangulumone of the most well-known New World snakes owing to its vivid red, black, and yellow tri-color patterns.

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Despite its use in comparative phylogenetic studies Pyron and Burbrink a ; Burbrink and Pyron ; Burbrink et al. The 25 currently recognized subspecies of milksnake following Williams range from southeastern Canada, across the United States to the Rocky Mountains, and south to Ecuador, making the inter-continental distribution of the milksnake one of the largest of any squamate Williams These dramatic ecological and phenotypic differences, consistent with predictions of the general lineage species concept followed here; de Queiroz, suggest that L.

Recent molecular studies within the tribe Lampropeltini, which include many commonly known snakes such as kingsnakes e. Within Lampropeltis alone, two distinct species have recently been found to contain cryptic taxa, resulting in the recognition of seven rather than two species L. Several of these studies also indicate that the milksnake may not form a monophyletic group with respect to other species of Lampropeltis ; gene trees reconstructed from mitochondrial DNA mtDNA and single-copy nuclear DNA markers scnDNA result in differing topological placement of milksnake within Lampropeltis Bryson et al.

These studies further suggest that there may be multiple distinct lineages within L. However, none of these studies focused on the milksnake specifically, all included a limited and distribution of samples, and all relied on gene trees rather than species trees. Diversification analyses of Lampropeltini have found that, unlike many other North American taxa Rand ; Avise ; Johnson and Cicerospeciation in this tribe occurred mostly during the Miocene Looking for Fort Smith Arkansas ruane Pliocene and slowed toward the present, with few species originating during the Pleistocene Pyron and Burbrink d ; Burbrink and Pyron However, these studies did not include the most recently elevated species within Lampropeltis and relied on the topology and branch lengths from concatenated gene trees.

The combination of unsampled taxa and gene-tree based approaches may be especially problematic for prior analyses that included Lampropeltis and relied potentially on inaccurate divergence times and branch lengths. Here, we address the following questions: 1 Is the milksnake a single, wide-ranging species or multiple, independently evolving species? To examine species diversity and timing of diversification in Lampropeltiswe use data collected from 11 nuclear loci and individuals spanning the geographic range of L. We also include representatives from all species in Lampropeltis to then infer a species tree for the genus.

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We delimit species using coalescent methods based on guide trees from both a mitochondrial gene tree and from a population structure analysis. from our study demonstrate the need to explicitly delimit taxa for species-tree analyses, and underscores the importance of including all species to properly understand the tempo of species diversification and other downstream comparative analyses. The four subspecies of milksnake not included in our study L.

We also note that L. For aCytb milksnake clades are indicated by colored lineages, followed by the clade name in parentheses and the corresponding delimited species name; names and colors correspond with the Cytb-lineage map c. For the species tree bthe delimited milksnake species are indicated by colored branches, with the lineage name in parentheses; names and colors correspond with the species-tree map d.

Where applicable, colors and names are conserved between the Cytb and species trees, although it should be noted that there are fewer delimitable species than there are Cytb clades for milksnakes, as some Cytb clades are collapsed within the species delimitation. Note that all L. DNA was extracted using Qiagen DNeasy kits tissue protocol from samples of shed skin, liver, muscle tissue, or whole blood. We optimized the amplification and sequencing protocols for 1 mtDNA gene cytochrome b ; Cyt b and 11 scnDNAs, including 5 anonymous loci developed using the protocol from Noonan and Yoder Details for loci, primers, and polymerase chain reaction PCR protocols are listed in Appendix 1.

No gaps were found in any of the protein-coding genes.

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For all genes and subsequent analyses, we determined the most appropriate substitution model using Bayesian Information Criterion in the program jModeltest Table 1 ; Posada Note: The length in base pairs, the model of evolution, of variable sites, and total of sequences for each locus are listed.

Additional details for each locus and PCR protocols are listed in Appendix 2. in the form of posterior probability distributions PP indicate whether two or more predefined lineages can be differentiated from each other ing for coalescent uncertainty. To test species hypotheses for the milksnake, we constructed guide trees in two ways.

First, with both the mtDNA and scnDNA data set the mtDNA data set was reduced to the same individuals used in the scnDNA data set for all subsequent analyses, see online Appendix 1we Looking for Fort Smith Arkansas ruane the program Structurama Huelsenbeck and Andolfatto to infer groups and as individuals to these groups. Structurama uses a Dirichlet process prior for a random of k populations with the initial concentration parameter of populations set to 5 to estimate the of groups and asment of individuals with the highest probability.

The appropriate value of k was chosen as the one with the highest posterior probability value. Second, we inferred a gene tree for Cytb using all samples as the basis for a second guide tree. For all guide trees, BPP was run using the algorithm 0, and we adjusted the fine-tuning parameters to ensure swapping rates ranged between 0. Zhang et al. We ran all of these analyses using the two different guide trees. Following Burbrink et al. Species-delimitation programs such as BPP Yang and Rannala only assess error due to incomplete lineage sorting, meaning migration between lineages may violate assumptions Zhang et al.

Assessing gene-flow, or a lack thereof, can also provide support as to whether lineages should be treated as independent species. As such, we examined rates of migration to develop a better understanding of how much gene flow occurs among the resulting geographically adjacent milksnake species using Migrate-n v. We also included L. A mean generation time for Lampropeltis of 2.

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Each run was repeated four times with different starting seeds to ensure consistency between runs. We also constructed a combined scnDNA network for resulting lineages using Splitstree v. Networks can further help visualize reticulate relationships among taxa and possible mixed ancestry or hybrid individuals. This method uses a multispecies coalescent model to estimate the species tree from multiple genes and multiple individuals per species, while taking into incomplete lineage sorting.

For this analysis, we used the scnDNA data set consisting of the milksnake lineages recovered in the BPP analyses and all other currently recognized species in the genus Lampropeltis. Because of the possibility of mtDNA introgression discussed laterwhich violates assumptions of no admixture, we ran the species-tree analysis without the Cytb data.

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Individuals were ased to species based on the from the BPP analyses. For the species tree and divergence-time estimation, we used an uncorrelated lognormal tree prior with a Yule speciation-process prior and calibrated the tree using two appropriate fossil constraints. From Holmanthe two calibrations are as follows: 1 The divergence time between the genera Lampropeltis and Cemophora was given a mean date of The analysis was run four times to ensure consistency among.

To explore the difference in divergence times between gene trees and species trees, we ran BEAST using the concatenated scnDNA data set with one representative for the same terminal taxa used in the species-tree estimation. We then calculated the Robinson—Foulds distance Robinson and Foulds between the species tree and concatenated tree using R in the package PHANGORN Schliep ; this metric measures the of bipartitions found in one tree but not the other, indicating the amount of topological discordance between trees.

presented here discussed later and in a study Bryson et al. To determine whether introgression has occurred within Lampropeltiswe used the program JML v. JML tests whether the minimum genetic distance between the sequences of two species is smaller than expected under a scenario that does not for hybridization i. JML simulates new data for the locus of interest using the information contained in the species trees e.

The program then compares the minimum pairwise sequence distance between the species for all simulated data sets with the original data. The output files from JML indicate which, if any, species show introgression.

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