scholarly journals Complex Ecological Phenotypes on Phylogenetic Trees: A Markov Process Model for Comparative Analysis of Multivariate Count Data

2020 ◽  
Vol 69 (6) ◽  
pp. 1200-1211
Author(s):  
Michael Grundler ◽  
Daniel L Rabosky
Keyword(s):  
Count Data ◽  
Ecological Niche ◽  
Phylogenetic Trees ◽  
Process Model ◽  
Evolutionary Dynamics ◽  
Categorical Variables ◽  
Individual Species ◽  
Niche Evolution ◽  
Ecological Traits ◽  
Sampling Variation

Abstract The evolutionary dynamics of complex ecological traits—including multistate representations of diet, habitat, and behavior—remain poorly understood. Reconstructing the tempo, mode, and historical sequence of transitions involving such traits poses many challenges for comparative biologists, owing to their multidimensional nature. Continuous-time Markov chains are commonly used to model ecological niche evolution on phylogenetic trees but are limited by the assumption that taxa are monomorphic and that states are univariate categorical variables. A necessary first step in the analysis of many complex traits is therefore to categorize species into a predetermined number of univariate ecological states, but this procedure can lead to distortion and loss of information. This approach also confounds interpretation of state assignments with effects of sampling variation because it does not directly incorporate empirical observations for individual species into the statistical inference model. In this study, we develop a Dirichlet-multinomial framework to model resource use evolution on phylogenetic trees. Our approach is expressly designed to model ecological traits that are multidimensional and to account for uncertainty in state assignments of terminal taxa arising from effects of sampling variation. The method uses multivariate count data across a set of discrete resource categories sampled for individual species to simultaneously infer the number of ecological states, the proportional utilization of different resources by different states, and the phylogenetic distribution of ecological states among living species and their ancestors. The method is general and may be applied to any data expressible as a set of observational counts from different categories. [Comparative methods; Dirichlet multinomial; ecological niche evolution; macroevolution; Markov model.]

scholarly journals Complex ecological phenotypes on phylogenetic trees: a hidden Markov model for comparative analysis of multivariate count data

2019 ◽  
Author(s):  
Michael C. Grundler ◽  
Daniel L. Rabosky
Keyword(s):  
Markov Model ◽  
Hidden Markov Model ◽  
Resource Use ◽  
Count Data ◽  
Phylogenetic Trees ◽  
Hidden Markov ◽  
Categorical Variables ◽  
Individual Species ◽  
Ecological Traits ◽  
Sampling Variation

ABSTRACTThe evolutionary dynamics of complex ecological traits – including multistate representations of diet, habitat, and behavior – remain poorly understood. Reconstructing the tempo, mode, and historical sequence of transitions involving such traits poses many challenges for comparative biologists, owing to their multidimensional nature and intraspecific variability. Continuous-time Markov chains (CTMC) are commonly used to model ecological niche evolution on phylogenetic trees but are limited by the assumption that taxa are monomorphic and that states are univariate categorical variables. Thus, a necessary first step when using standard CTMC models is to categorize species into a pre-determined number of ecological states. This approach potentially confounds interpretation of state assignments with effects of sampling variation because it does not directly incorporate empirical observations of resource use into the statistical inference model. The neglect of sampling variation, along with univariate representations of true multivariate phenotypes, potentially leads to the distortion and loss of information, with substantial implications for downstream macroevolutionary analyses. In this study, we develop a hidden Markov model using a Dirichlet-multinomial framework to model resource use evolution on phylogenetic trees. Unlike existing CTMC implementations, states are unobserved probability distributions from which observed data are sampled. Our approach is expressly designed to model ecological traits that are intra-specifically variable and to account for uncertainty in state assignments of terminal taxa arising from effects of sampling variation. The method uses multivariate count data for individual species to simultaneously infer the number of ecological states, the proportional utilization of different resources by different states, and the phylogenetic distribution of ecological states among living species and their ancestors. The method is general and may be applied to any data expressible as a set of observational counts from different categories.

scholarly journals Evolutionary Dynamics of rDNA Clusters in Chromosomes of Five Clam Species Belonging to the Family Veneridae (Mollusca, Bivalvia)

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Concepción Pérez-García ◽  
Ninoska S. Hurtado ◽  
Paloma Morán ◽  
Juan J. Pasantes
Keyword(s):  
Phylogenetic Trees ◽  
Evolutionary Dynamics ◽  
5S Rdna ◽  
Gene Clusters ◽  
Ruditapes Philippinarum ◽  
Ruditapes Decussatus ◽  
Rdna Cluster ◽  
Single Chromosome ◽  
Molecular Phylogenetic ◽  
Chromosomal Changes

The chromosomal changes accompanying bivalve evolution are an area about which few reports have been published. To improve our understanding on chromosome evolution in Veneridae, ribosomal RNA gene clusters were mapped by fluorescentin situhybridization (FISH) to chromosomes of five species of venerid clams (Venerupis corrugata,Ruditapes philippinarum,Ruditapes decussatus,Dosinia exoleta, andVenus verrucosa). The results were anchored to the most comprehensive molecular phylogenetic tree currently available for Veneridae. While a single major rDNA cluster was found in each of the five species, the number of 5S rDNA clusters showed high interspecies variation. Major rDNA was either subterminal to the short arms or intercalary to the long arms of metacentric or submetacentric chromosomes, whereas minor rDNA signals showed higher variability. Major and minor rDNAs map to different chromosome pairs in all species, but inR. decussatusone of the minor rDNA gene clusters and the major rDNA cluster were located in the same position on a single chromosome pair. This interspersion of both sequences was confirmed by fiber FISH. Telomeric signals appeared at both ends of every chromosome in all species. FISH mapping data are discussed in relation to the molecular phylogenetic trees currently available for Veneridae.

Using ecological niche modeling for quantitative biogeographic analysis: a case study of Miocene and Pliocene Equinae in the Great Plains

Paleobiology ◽  
2009 ◽  
Vol 35 (4) ◽  
pp. 587-611 ◽  
Author(s):  
Kaitlin Clare Maguire ◽  
Alycia L. Stigall
Keyword(s):  
Great Plains ◽  
Late Miocene ◽  
Ecological Niche ◽  
Middle Miocene ◽  
Ecological Niche Modeling ◽  
Environmental Parameters ◽  
Geographic Range ◽  
Individual Species ◽  
Geographic Ranges ◽  
Speciation Rates

The subfamily Equinae in the Great Plains region of North America underwent a dramatic radiation and subsequent decline as climate changed from warm and humid in the middle Miocene to cooler and more arid conditions during the late Miocene. Here we use ecological niche modeling (ENM), specifically the GARP (Genetic Algorithm using Rule-set Prediction) modeling system, to reconstruct the geographic distribution of individual species during two time slices from the middle Miocene through early Pliocene. This method combines known species occurrence points with environmental parameters inferred from sedimentological variables to model each species' fundamental niche. The geographic range of each species is then predicted to occupy the geographic area within the study region wherever the set of environmental parameters that constrain the fundamental niche occurs. We analyze changes in the predicted distributions of individual species between time slices in relation to Miocene/Pliocene climate change. Specifically, we examine and compare distribution patterns for two time slices that span the period from the mid-Miocene (Barstovian) Climatic Optimum into the early Pliocene (Blancan) to determine whether habitat fragmentation led to speciation within the clade and whether species survival was related to geographic range size. Patchy geographic distributions were more common in the middle Miocene when speciation rates were high. During the late Miocene, when speciation rates were lower, continuous geographic ranges were more common. Equid species tracked their preferred habitat within the Great Plains region as well as regionally throughout North America. Species with larger predicted ranges preferentially survived the initial cooling event better than species with small geographic ranges. As climate continued to deteriorate in the late Miocene, however, range size became irrelevant to survival, and extinction rates increased for species of all range sizes. This is the first use of ENM and GARP in the continental fossil record. This powerful quantitative biogeographic method offers great promise for studies of other taxa and geologic intervals.

Stratigraphic tests of cladistic hypotheses

Paleobiology ◽  
1995 ◽  
Vol 21 (2) ◽  
pp. 153-178 ◽  
Author(s):  
Peter J. Wagner
Keyword(s):  
Confidence Intervals ◽  
Fossil Record ◽  
Evolutionary Dynamics ◽  
Test Group ◽  
Individual Species ◽  
Stratigraphic Record ◽  
Long Time ◽  
Morphologic Evolution ◽  
Phylogenetic Hypotheses ◽  
Stratigraphic Ranges

Cladograms predict the order in which fossil taxa appeared and, thus, make predictions about general patterns in the stratigraphic record. Inconsistencies between cladistic predictions and the observed stratigraphic record reflect either inadequate sampling of a clade's species, incomplete estimates of stratigraphic ranges, or homoplasy producing an incorrect phylogenetic hypothesis. A method presented in this paper attempts to separate the effects of homoplasy from the effects of inadequate sampling. Sampling densities of individual species are used to calculate confidence intervals on their stratigraphic ranges. The method uses these confidence intervals to test the order of branching predicted by a cladogram. The Lophospiridae (“Archaeogastropoda”) of the Ordovician provide a useful test group because the clade has a good fossil record and it produced species over a long time. Confidence intervals reject several cladistic hypotheses that postulate improbable “ghost lineages.” Other hypotheses are acceptable only with explicit ancestor-descendant relationships. The accepted cladogram is the shortest one that stratigraphic data cannot reject. The results caution against evaluating phylogenetic hypotheses of fossil taxa without considering both stratigraphic data and the possible presence of ancestral species, as both factors can affect interpretations of a clade's evolutionary dynamics and its patterns of morphologic evolution.

scholarly journals Avian Influenza Viruses in Wild Birds: Virus Evolution in a Multihost Ecosystem

2018 ◽  
Vol 92 (15) ◽  
Author(s):  
Divya Venkatesh ◽  
Marjolein J. Poen ◽  
Theo M. Bestebroer ◽  
Rachel D. Scheuer ◽  
Oanh Vuong ◽  
...  
Keyword(s):  
Avian Influenza ◽  
Host Species ◽  
Phylogenetic Trees ◽  
Evolutionary Dynamics ◽  
Natural Host ◽  
Influenza Viruses ◽  
Seasonal Migration ◽  
The Black Sea ◽  
Avian Influenza Viruses ◽  
Stopover Site

ABSTRACTWild ducks and gulls are the major reservoirs for avian influenza A viruses (AIVs). The mechanisms that drive AIV evolution are complex at sites where various duck and gull species from multiple flyways breed, winter, or stage. The Republic of Georgia is located at the intersection of three migratory flyways: the Central Asian flyway, the East Africa/West Asia flyway, and the Black Sea/Mediterranean flyway. For six complete study years (2010 to 2016), we collected AIV samples from various duck and gull species that breed, migrate, and overwinter in Georgia. We found a substantial subtype diversity of viruses that varied in prevalence from year to year. Low-pathogenic AIV (LPAIV) subtypes included H1N1, H2N3, H2N5, H2N7, H3N8, H4N2, H6N2, H7N3, H7N7, H9N1, H9N3, H10N4, H10N7, H11N1, H13N2, H13N6, H13N8, and H16N3, and two highly pathogenic AIVs (HPAIVs) belonging to clade 2.3.4.4, H5N5 and H5N8, were found. Whole-genome phylogenetic trees showed significant host species lineage restriction for nearly all gene segments and significant differences in observed reassortment rates, as defined by quantification of phylogenetic incongruence, and in nucleotide sequence diversity for LPAIVs among different host species. Hemagglutinin clade 2.3.4.4 H5N8 viruses, which circulated in Eurasia during 2014 and 2015, did not reassort, but analysis after their subsequent dissemination during 2016 and 2017 revealed reassortment in all gene segments except NP and NS. Some virus lineages appeared to be unrelated to AIVs in wild bird populations in other regions, with maintenance of local AIVs in Georgia, whereas other lineages showed considerable genetic interrelationships with viruses circulating in other parts of Eurasia and Africa, despite relative undersampling in the area.IMPORTANCEWaterbirds (e.g., gulls and ducks) are natural reservoirs of avian influenza viruses (AIVs) and have been shown to mediate the dispersal of AIVs at intercontinental scales during seasonal migration. The segmented genome of influenza viruses enables viral RNA from different lineages to mix or reassort when two viruses infect the same host. Such reassortant viruses have been identified in most major human influenza pandemics and several poultry outbreaks. Despite their importance, we have only recently begun to understand AIV evolution and reassortment in their natural host reservoirs. This comprehensive study illustrates AIV evolutionary dynamics within a multihost ecosystem at a stopover site where three major migratory flyways intersect. Our analysis of this ecosystem over a 6-year period provides a snapshot of how these viruses are linked to global AIV populations. Understanding the evolution of AIVs in the natural host is imperative to mitigating both the risk of incursion into domestic poultry and the potential risk to mammalian hosts, including humans.

scholarly journals The role of ecological niche evolution on diversification patterns of birds distinctly distributed between the Amazonia and Atlantic rainforests

PLoS ONE ◽  
2020 ◽  
Vol 15 (10) ◽  
pp. e0238729
Author(s):  
Ricardo Ribeiro da Silva ◽  
Bruno Vilela ◽  
Daniel Paiva Silva ◽  
André Felipe Alves de Andrade ◽  
Pablo Vieira Cerqueira ◽  
...  
Keyword(s):  
Ecological Niche ◽  
Niche Evolution

scholarly journals A null biogeographical test for assessing ecological niche evolution

2016 ◽  
Vol 44 (6) ◽  
pp. 1331-1343 ◽  
Author(s):  
Laura A. Nunes ◽  
Richard G. Pearson
Keyword(s):  
Ecological Niche ◽  
Niche Evolution

scholarly journals Interspecies variation of larval locomotion kinematics in the genus Drosophila and its relation to habitat temperature

2020 ◽  
Author(s):  
Yuji Matsuo ◽  
Akinao Nose ◽  
Hiroshi Kohsaka
Keyword(s):  
Bayesian Inference ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Evolutionary Rate ◽  
Phylogenetic Analyses ◽  
The Body ◽  
Quantitative Relation ◽  
Individual Species ◽  
Habitat Temperature ◽  
History Of

AbstractSpeed and trajectory of locomotion are characteristic traits of individual species. During evolution, locomotion kinematics is likely to have been tuned for survival in the habitats of each species. Although kinematics of locomotion is thought to be influenced by habitats, the quantitative relation between the kinematics and environmental factors has not been fully revealed. Here, we performed comparative analyses of larval locomotion in 11 Drosophila species. We found that larval locomotion kinematics are divergent among the species. The diversity is not correlated to the body length but is correlated instead to the minimum habitat temperature of the species. Phylogenetic analyses using Bayesian inference suggest that the evolutionary rate of the kinematics is diverse among phylogenetic trees. The results of this study imply that the kinematics of larval locomotion has diverged in the evolutionary history of the genus Drosophila and evolved under the effects of the minimum ambient temperature of habitats.

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