Does evolutionary relatedness predict ecological similarity?

Paleobiology ◽  
2020 ◽  
pp. 1-17
Author(s):  
Judith A. Sclafani ◽  
Curtis R. Congreve ◽  
Mark E. Patzkowsky
Keyword(s):  
Phylogenetic Trees ◽  
Evolutionary Model ◽  
Branch Length ◽  
Pairwise Distance ◽  
Phylogenetic Distance ◽  
Environmental Preferences ◽  
Occurrence Data ◽  
Evolutionary Relatedness ◽  
Species Pairs ◽  
Ecological Difference

Abstract A fundamental question in paleobiology is whether ecology is correlated with evolutionary history. By combining time-calibrated phylogenetic trees with genus occurrence data through time, we can understand how environmental preferences are distributed on a tree and evaluate support for models of ecological similarity. Exploring parameters that lend support to each evolutionary model will help address questions that lie at the nexus of the evolutionary and ecological sciences. We calculated ecological difference and phylogenetic distance between species pairs for 83 taxa used in recent phylogenetic revisions of the brachiopod order Strophomenida. Ecological difference was calculated as the pairwise distance along gradients of water depth, carbonate, and latitudinal affinity. Phylogenetic distance was calculated as the pairwise branch length between tips of the tree. Our results show no relationship between ecological affinity and phylogeny. Instead results suggest an ecological burst during the initial radiation of the clade. This pattern likely reflects scaling at the largest macroevolutionary and macroecological scales preserved in the fossil record. Hierarchical scaling of ecological and evolutionary processes is complex, but phylogenetic paleoecology is an avenue for better evaluating these questions.

scholarly journals Predicting the Impact of Describing New Species on Phylogenetic Patterns

2019 ◽  
Vol 1 (1) ◽  
Author(s):  
D C Blackburn ◽  
G Giribet ◽  
D E Soltis ◽  
E L Stanley
Keyword(s):  
New Species ◽  
Phylogenetic Trees ◽  
Branch Length ◽  
Length Variation ◽  
Tree Shape ◽  
Branch Lengths ◽  
Taxonomic History ◽  
Ecological Patterns ◽  
The Impact ◽  
Incomplete Sampling

Abstract Although our inventory of Earth’s biodiversity remains incomplete, we still require analyses using the Tree of Life to understand evolutionary and ecological patterns. Because incomplete sampling may bias our inferences, we must evaluate how future additions of newly discovered species might impact analyses performed today. We describe an approach that uses taxonomic history and phylogenetic trees to characterize the impact of past species discoveries on phylogenetic knowledge using patterns of branch-length variation, tree shape, and phylogenetic diversity. This provides a framework for assessing the relative completeness of taxonomic knowledge of lineages within a phylogeny. To demonstrate this approach, we use recent large phylogenies for amphibians, reptiles, flowering plants, and invertebrates. Well-known clades exhibit a decline in the mean and range of branch lengths that are added each year as new species are described. With increased taxonomic knowledge over time, deep lineages of well-known clades become known such that most recently described new species are added close to the tips of the tree, reflecting changing tree shape over the course of taxonomic history. The same analyses reveal other clades to be candidates for future discoveries that could dramatically impact our phylogenetic knowledge. Our work reveals that species are often added non-randomly to the phylogeny over multiyear time-scales in a predictable pattern of taxonomic maturation. Our results suggest that we can make informed predictions about how new species will be added across the phylogeny of a given clade, thus providing a framework for accommodating unsampled undescribed species in evolutionary analyses.

scholarly journals Is cytochrome c oxidase subunit I (COI) the right DNA barcoding marker for the Chaetopteryx villosa group?

2021 ◽  
Vol 4 ◽  
Author(s):  
Dalila Destanović ◽  
Lejla Ušanović ◽  
Lejla Lasić ◽  
Jasna Hanjalić ◽  
Belma Kalamujić Stroil
Keyword(s):  
Phylogenetic Trees ◽  
Pairwise Distance ◽  
Zoological Museum ◽  
Species Determination ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Software Analysis ◽  
Group Data ◽  
Species Specific ◽  
The Right

Chaetopteryx villosa (Fabricius, 1798) is a caddisfly species distributed throughout Europe, except in the Balkan and Apennine Peninsula. However, phylogenetically close species belonging to the C. villosa group are widespread throughout entire Europe. Species of this group (C. villosa, C. gessneri, C. fusca, C. sahlbergi, C. atlantica, C. bosniaca, C. vulture, and C. trinacriae) have distinct distributions with some overlaps. Adult forms of these species are morphologically similar, whereas larval morphology is only known for some species. There are also indications of species hybridization (e.g., C. villosa x fusca). Presumably, the molecular approach for the species determination of this group would be highly beneficial. In the BOLD database, there are 154 specimens with COI-5P barcodes of C. villosa species. Out of the remaining species, C. sahlbergi has 27 specimens with a barcode, C. fusca 20, C. gessneri 5, C. bosniaca 5, and C. atlantica 1, whereas sequences from the species C. vulture and C. trinacriae are missing. Therefore, we tested the power of discrimination of the COI-5P marker in the C. villosa group, as the most common barcoding markers for species identification in animals. Only sequences from public records originating from experienced research groups or taxonomists and containing a specimen photograph were taken as input. A total of 75 sequences from the BOLD database were obtained. Out of these sequences, 11 belonged to C. fusca, 5 to C. gessneri, 52 to C. villosa, 5 to C. bosniaca, and 2 to C. sahlbergi. For the generation of overview trees, COI-5P barcodes of Rhyacophila fasciata and Rh. nubila were used as outgroups. All sequences were trimmed at 5’ and 3’ ends, resulting in a final alignment length of 516 base pairs. Multiple sequence alignments and editing were done in the MEGA-X software. Analysis of nucleotide polymorphism was done in DNASP6 software. MEGA-X was used to calculate the pairwise distance and overall mean p-distance, and to construct the overview trees. Analysis of DNA polymorphism revealed 14 haplotypes of C. villosa, 3 haplotypes of C. fusca, 2 haplotypes of C. gessneri, and one for species C. bosniaca and C. sahlbergi. There were no significant interspecific and intraspecific differences among haplotypes based on pairwise distances. The p-distance between one of the haplotypes of C. fusca and C. villosa was 0.000, whereas the p-distance among haplotypes of C. villosa varied from 0.001 to about 0.055. The mean overall p-distance among haplotypes of all species equaled 0.03. No species-specific clusters were observed when phylogenetic trees were constructed except for C. gessneri, regardless of the method used (i.e., NJ, UPGMA, ML, ME, or MP). To minimize the possibility of species misidentification, we used only records submitted by NTNU-Norwegian University of Science and Technology (Norway), SNSB-Zoologische Staatssammlung Muenchen (Germany), Zoologisches Forschungsmuseum Alexander Koenig (Germany), University of Oulu, Zoological Museum (Finland), prof Hans Malicky and prof Mladen Kučinić. No records identified as hybrids were included in the analyses. With the exception of C. gessneri, COI-5P marker failed to separate the species of the C. villosa group. However, it is highly unlikely that poor species determination was the basis for such a result. To enable the comprehensive and unbiased evaluation of the relationships within this group, data coverage in BOLD database for most of the studied species should be enhanced, encompassing different geographical distribution of samples. Further studies are needed to detect the array of molecular markers suitable for the species delineation in a complex group such as C. villosa.

A DIMENSIONLESS FIT MEASURE FOR PHYLOGENETIC DISTANCE TREES

2005 ◽  
Vol 03 (06) ◽  
pp. 1429-1440 ◽  
Author(s):  
MANUEL GIL ◽  
CHRISTOPHE DESSIMOZ ◽  
GASTON H. GONNET
Keyword(s):  
Phylogenetic Trees ◽  
Distance Matrix ◽  
Phylogenetic Distance ◽  
Linear Transformations ◽  
Relative Measure ◽  
Absolute Measure ◽  
Distance Matrices ◽  
Fit Index

We present a dimensionless fit index for phylogenetic trees that have been constructed from distance matrices. It is designed to measure the quality of the fit of the data to a tree in absolute terms, independent of linear transformations on the distance matrix. The index can be used as an absolute measure to evaluate how well a set of data fits to a tree, or as a relative measure to compare different methods that are expected to produce the same tree. The usefulness of the index is demonstrated in three examples.

scholarly journals Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats

mBio ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Se Jin Song ◽  
Jon G. Sanders ◽  
Frédéric Delsuc ◽  
Jessica Metcalf ◽  
Katherine Amato ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Cost Benefit ◽  
Phylogenetic Distance ◽  
Strong Correlations ◽  
Evolutionary Relatedness ◽  
Host Diet ◽  
Comprehensive Survey ◽  
Taxonomic Range ◽  
Host Phylogeny ◽  
The Cost

ABSTRACT Diet and host phylogeny drive the taxonomic and functional contents of the gut microbiome in mammals, yet it is unknown whether these patterns hold across all vertebrate lineages. Here, we assessed gut microbiomes from ∼900 vertebrate species, including 315 mammals and 491 birds, assessing contributions of diet, phylogeny, and physiology to structuring gut microbiomes. In most nonflying mammals, strong correlations exist between microbial community similarity, host diet, and host phylogenetic distance up to the host order level. In birds, by contrast, gut microbiomes are only very weakly correlated to diet or host phylogeny. Furthermore, while most microbes resident in mammalian guts are present in only a restricted taxonomic range of hosts, most microbes recovered from birds show little evidence of host specificity. Notably, among the mammals, bats host especially bird-like gut microbiomes, with little evidence for correlation to host diet or phylogeny. This suggests that host-gut microbiome phylosymbiosis depends on factors convergently absent in birds and bats, potentially associated with physiological adaptations to flight. Our findings expose major variations in the behavior of these important symbioses in endothermic vertebrates and may signal fundamental evolutionary shifts in the cost/benefit framework of the gut microbiome. IMPORTANCE In this comprehensive survey of microbiomes of >900 species, including 315 mammals and 491 birds, we find a striking convergence of the microbiomes of birds and animals that fly. In nonflying mammals, diet and short-term evolutionary relatedness drive the microbiome, and many microbial species are specific to a particular kind of mammal, but flying mammals and birds break this pattern with many microbes shared across different species, with little correlation either with diet or with relatedness of the hosts. This finding suggests that adaptation to flight breaks long-held relationships between hosts and their microbes.

Basic chromosome number in Boronia (Rutaceae)—competing hypotheses examined

2006 ◽  
Vol 54 (7) ◽  
pp. 681 ◽  
Author(s):  
Fucheng Shan ◽  
Guijun Yan ◽  
Julie A. Plummer
Keyword(s):  
Chromosome Number ◽  
Phylogenetic Trees ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Negative Relationship ◽  
Branch Length ◽  
Critical Issue ◽  
Basic Chromosome Number ◽  
Arbitrary Primers ◽  
Basic Chromosome

Rutaceae have attracted considerable attention because of the wide chromosome-number variation. Cytoevolution of the genus Boronia, with n = 7–36, has been controversial. The critical issue is whether the base chromosome number is x = 18 or x = 9 in this genus and in the family Rutaceae. Phylogenetic analysis based on random amplified polymorphic DNA (RAPD) markers was used to evaluate the hypothesis. Twenty decamer arbitrary primers were used to produce RAPD markers in 25 accessions of 18 Boronia species and a total of 559 DNA fragments was generated. UPGMA distance analysis and Wagner parsimony analysis on the DNA data produced two phylogenetic trees with very similar topology. The two trees generally supported the present classification of Boronia species. The exception was B. tenuis, which may be better treated as a new section or genus. Chromosome numbers of all the genotypes used in the analysis were counted with n = 7, 8, 9, 11, 16–36. Evolutionary distances between species were determined on the basis of branch length of the Wagner cladogram. Regression analysis indicated that Boronia chromosome number has a significant negative relationship with evolutionary distance. Chromosome number in Boronia evolved from higher to lower. The basic chromosome number for Boronia is suggested to be 18.

scholarly journals Ecological speciation in European whitefish is driven by a large-gaped predator

2019 ◽  
Author(s):  
Gunnar Öhlund ◽  
Mats Bodin ◽  
Karin A. Nilsson ◽  
Sven-Ola Öhlund ◽  
Kenyon B. Mobley ◽  
...  
Keyword(s):  
Evolutionary Model ◽  
Ecological Speciation ◽  
Northern Pike ◽  
Model Systems ◽  
Coregonus Lavaretus ◽  
Habitat Specificity ◽  
Species Pairs ◽  
Gape Size ◽  
Using Data ◽  
Gill Raker

AbstractLake-dwelling fish that form species pairs/flocks characterized by body size divergence are important model systems for speciation research. While several sources of divergent selection have been identified in these systems, their importance for driving the speciation process remains elusive. A major problem is that in retrospect, we cannot distinguish selection pressures that initiated divergence from those acting later in the process. To address this issue, we reconstructed the initial stages of speciation in European whitefish (Coregonus lavaretus) using data from 357 populations of varying age (26-10 000 years). We find that whitefish speciation is driven by a large-growing predator, the northern pike (Esox lucius). Pike initiates divergence by causing a largely plastic differentiation into benthic giants and pelagic dwarfs; ecotypes that will subsequently develop partial reproductive isolation and heritable differences in gill raker number. Using an eco-evolutionary model, we demonstrate how pike’s habitat specificity and large gape size are critical for imposing a between-habitat trade-off, causing prey to mature in a safer place or at a safer size. Thereby, we propose a novel mechanism for how predators may cause dwarf/giant speciation in lake-dwelling fish species.

scholarly journals speciesgeocodeR: An R package for linking species occurrences, user-defined regions and phylogenetic trees for biogeography, ecology and evolution

2015 ◽  
Author(s):  
Alexander Zizka ◽  
Alexandre Antonelli
Keyword(s):  
Data Quality ◽  
Phylogenetic Trees ◽  
Large Scale ◽  
Data Cleaning ◽  
R Package ◽  
Species Occurrence ◽  
Occurrence Data ◽  
User Friendly ◽  
Species Occurrences

1. Large-scale species occurrence data from geo-referenced observations and collected specimens are crucial for analyses in ecology, evolution and biogeography. Despite the rapidly growing availability of such data, their use in evolutionary analyses is often hampered by tedious manual classification of point occurrences into operational areas, leading to a lack of reproducibility and concerns regarding data quality. 2. Here we present speciesgeocodeR, a user-friendly R-package for data cleaning, data exploration and data visualization of species point occurrences using discrete operational areas, and linking them to analyses invoking phylogenetic trees. 3. The three core functions of the package are 1) automated and reproducible data cleaning, 2) rapid and reproducible classification of point occurrences into discrete operational areas in an adequate format for subsequent biogeographic analyses, and 3) a comprehensive summary and visualization of species distributions to explore large datasets and ensure data quality. In addition, speciesgeocodeR facilitates the access and analysis of publicly available species occurrence data, widely used operational areas and elevation ranges. Other functionalities include the implementation of minimum occurrence thresholds and the visualization of coexistence patterns and range sizes. SpeciesgeocodeR accompanies a richly illustrated and easy-to-follow tutorial and help functions.

scholarly journals Markov Katana: a Novel Method for Bayesian Resampling of Parameter Space Applied to Phylogenetic Trees

2018 ◽  
Author(s):  
Stephen T. Pollard ◽  
Kenji Fukushima ◽  
Zhengyuan O. Wang ◽  
Todd A. Castoe ◽  
David D. Pollock
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Statistical Approach ◽  
Evolutionary Model ◽  
Complex Model ◽  
Tree Topology ◽  
Added Value ◽  
General Idea ◽  
Branch Lengths ◽  
Tree Space

ABSTRACTPhylogenetic inference requires a means to search phylogenetic tree space. This is usually achieved using progressive algorithms that propose and test small alterations in the current tree topology and branch lengths. Current programs search tree topology space using branch-swapping algorithms, but proposals do not discriminate well between swaps likely to succeed or fail. When applied to datasets with many taxa, the huge number of possible topologies slows these programs dramatically. To overcome this, we developed a statistical approach for proposal generation in Bayesian analysis, and evaluated its applicability for the problem of searching phylogenetic tree space. The general idea of the approach, which we call ‘Markov katana’, is to make proposals based on a heuristic algorithm using bootstrapped subsets of the data. Such proposals induce an unintended sampling distribution that must be determined and removed to generate posterior estimates, but the cost of this extra step can in principle be small compared to the added value of more efficient parameter exploration in Markov chain Monte Carlo analyses. Our prototype application uses the simple neighbor-joining distance heuristic on data subsets to propose new reasonably likely phylogenetic trees (including topologies and branch lengths). The evolutionary model used to generate distances in our prototype was far simpler than the more complex model used to evaluate the likelihood of phylogenies based on the full dataset. This prototype implementation indicates that the Markov katana approach could be easily incorporated into existing phylogenetic search programs and may prove a useful alternative in conjunction with existing methods. The general features of this statistical approach may also prove useful in disciplines other than phylogenetics. We demonstrate that this method can be used to efficiently estimate a Bayesian posterior.

scholarly journals DNA Barcoding of the Solanaceae Family in Puerto Rico Including Endangered and Endemic Species

2019 ◽  
Vol 144 (5) ◽  
pp. 363-374 ◽  
Author(s):  
Lumariz Hernandez Rosario ◽  
Juan O. Rodríguez Padilla ◽  
Desiree Ramos Martínez ◽  
Alejandra Morales Grajales ◽  
Joel A. Mercado Reyes ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Puerto Rico ◽  
Dna Barcoding ◽  
Endemic Species ◽  
Phylogenetic Trees ◽  
Dna Barcode ◽  
Pairwise Distance ◽  
Greater Antilles ◽  
Solanaceae Species ◽  
Solanaceae Family

The Solanaceae family is one of the largest and well-distributed plant families in the world. It contains species of agricultural and economical importance, such as Solanum tuberosum, Solanum melongena, Solanum lycopersicum, Nicotiana tabacum, and Capsicum annuum. In Puerto Rico, there are ≈46 species of Solanaceae of which six are endemic: Brunfelsia densifolia, Brunfelsia lactea, Brunfelsia portoricensis, Goetzea elegans, Solanum ensifolium, and Solanum woodburyi. Our objective was to use DNA barcoding to identify the Solanaceae species in Puerto Rico, including the endemics, and to assess the species relationships between them. To accomplish our objective, two chloroplast regions (psbA-trnH and matK) and a nuclear region [internal transcribed spacer (ITS)] were assessed. Pairwise distance and phylogenetic analysis demonstrate that DNA barcoding can be used to discriminate at the species level among these taxa in Puerto Rico. For all three markers, the genus that showed the highest pairwise distance between represented species was Solanum, whereas the genus that displayed the least was Capsicum. Phylogenetic trees of single and concatenated regions were generated from sequences obtained in this study and from data downloaded from the National Center for Biotechnology Information database. Our results show that this technique can be used to identify species with one, two, or three combinations of DNA barcode markers depending on the taxon. In addition, this is the first study to include the endemic species S. woodburyi in a molecular phylogenetic analysis, and it was found to have a close relationship with S. ensifolium, also endemic to Puerto Rico, and to Solanum bahamense from the Bahamas and Greater Antilles. Therefore, we suggest that S. woodburyi might be part of the Bahamense clade.

scholarly journals Conditions under which distributions of edge length ratios on phylogenetic trees can be used to order evolutionary events

2021 ◽  
Author(s):  
Edward Susko ◽  
Mike Steel ◽  
Andrew J. Roger
Keyword(s):  
Molecular Clock ◽  
Phylogenetic Trees ◽  
Branch Length ◽  
Edge Length ◽  
Eukaryotic Cells ◽  
High Profile ◽  
Large Sets ◽  
Different Origins ◽  
Alternative Set ◽  
Strict Molecular Clock

AbstractTwo recent high profile studies have attempted to use edge (branch) length ratios from large sets of phylogenetic trees to determine the relative ages of genes of different origins in the evolution of eukaryotic cells. This approach can be straightforwardly justified if substitution rates are constant over the tree for a given protein. However, such strict molecular clock assumptions are not expected to hold on the billion-year timescale. Here we propose an alternative set of conditions under which comparisons of edge length distributions from multiple sets of phylogenies of proteins with different origins can be validly used to discern the order of their origins. We also point out scenarios where these conditions are not expected to hold and caution is warranted.

Sign in / Sign up

Export Citation Format

Share Document