scholarly journals Predicting long pendant edges in model phylogenies, with applications to biodiversity and tree inference

2021 ◽  
Author(s):  
Sergey Bocharov ◽  
Simon Harris ◽  
Emma Kominek ◽  
Arne O Mooers ◽  
Mike Steel
Keyword(s):  
Diversity Indices ◽  
Edge Length ◽  
Extinction Rate ◽  
Yule Process ◽  
Extant Species ◽  
Constant Rate ◽  
Branch Lengths ◽  
Tree Inference ◽  
Number Of Leaves ◽  
Complete Tree

In the simplest phylodynamic model (the pure-birth Yule process), lineages split independently at a constant rate λ for time t. The length of a randomly chosen edge (either interior or pendant) in the resulting tree has an expected value that rapidly converges to 1/(2λ) as t grows, and thus is essentially independent of t. However, the behaviour of the length L of the longest pendant edge reveals remarkably different behaviour: L converges to t/2 as the expected number of leaves grows. Extending this model to allow an extinction rate μ (where μ<λ), we also establish a similar result for birth--death trees, except that t/2 is replaced by t/2 x (1-μ/λ). This 'complete' tree may contain subtrees that have died out before time t; for the 'reduced tree' that just involves the leaves present at time t and their direct ancestors, the longest pendant edge length L again converges to t/2. Thus, there is likely to be at least one extant species whose associated pendant branch attaches to the tree approximately half-way back in time to the origin of the entire clade. We also briefly consider the length of the shortest edges. Our results are relevant to phylogenetic diversity indices in biodiversity conservation, and to questions concerning the length of aligned sequences required to correctly infer a tree. We compare our theoretical results with simulations, and with the branch lengths from a recent phylogenetic tree of all mammals.

scholarly journals A new method of inference of ancestral nucleotide and amino acid sequences.

Genetics ◽  
1995 ◽  
Vol 141 (4) ◽  
pp. 1641-1650 ◽  
Author(s):  
Z Yang ◽  
S Kumar ◽  
M Nei
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Sequences ◽  
New Method ◽  
Maximum Likelihood Estimates ◽  
Parsimony Method ◽  
Ancestral Sequences ◽  
Extant Species ◽  
Branch Lengths ◽  
A Site

Abstract A statistical method was developed for reconstructing the nucleotide or amino acid sequences of extinct ancestors, given the phylogeny and sequences of the extant species. A model of nucleotide or amino acid substitution was employed to analyze data of the present-day sequences, and maximum likelihood estimates of parameters such as branch lengths were used to compare the posterior probabilities of assignments of character states (nucleotides or amino acids) to interior nodes of the tree; the assignment having the highest probability was the best reconstruction at the site. The lysozyme c sequences of six mammals were analyzed by using the likelihood and parsimony methods. The new likelihood-based method was found to be superior to the parsimony method. The probability that the amino acids for all interior nodes at a site reconstructed by the new method are correct was calculated to be 0.91, 0.86, and 0.73 for all, variable, and parsimony-informative sites, respectively, whereas the corresponding probabilities for the parsimony method were 0.84, 0.76, and 0.51, respectively. The probability that an amino acid in an ancestral sequence is correctly reconstructed by the likelihood analysis ranged from 91.3 to 98.7% for the four ancestral sequences.

scholarly journals Can clade age alone explain the relationship between body size and diversity?

2012 ◽  
Vol 2 (2) ◽  
pp. 170-179 ◽  
Author(s):  
Rampal S. Etienne ◽  
Sara N. de Visser ◽  
Thijs Janzen ◽  
Jeanine L. Olsen ◽  
Han Olff ◽  
...  
Keyword(s):  
Body Size ◽  
Size Dependence ◽  
Allometric Scaling ◽  
The Body ◽  
Scaling Exponent ◽  
Extinction Rate ◽  
Extinction Rates ◽  
Constant Rate ◽  
Wide Range ◽  
Birth Death

One of the most striking patterns observed among animals is that smaller-bodied taxa are generally much more diverse than larger-bodied taxa. This observation seems to be explained by the mere fact that smaller-bodied taxa tend to have an older evolutionary origin and have therefore had more time to diversify. A few studies, based on the prevailing null model of diversification (i.e. the stochastic constant-rate birth–death model), have suggested that this is indeed the correct explanation, and body-size dependence of speciation and extinction rates does not play a role. However, there are several potential shortcomings to these studies: a suboptimal statistical procedure and a relatively narrow range of body sizes in the analysed data. Here, we present a more coherent statistical approach, maximizing the likelihood of the constant-rate birth–death model with allometric scaling of speciation and extinction rates, given data on extant diversity, clade age and average body size in each clade. We applied our method to a dataset compiled from the literature that includes a wide range of Metazoan taxa (range from midges to elephants). We find that the higher diversity among small animals is indeed, partly, caused by higher clade age. However, it is also partly caused by the body-size dependence of speciation and extinction rates. We find that both the speciation rate and extinction rate decrease with body size such that the net diversification rate is close to 0. Even more interestingly, the allometric scaling exponent of speciation and extinction rates is approximately −0.25, which implies that the per generation speciation and extinction rates are independent of body size. This suggests that the observed relationship between diversity and body size pattern can be explained by clade age alone, but only if clade age is measured in generations rather than years. Thus, we argue that the most parsimonious explanation for the observation that smaller-bodied taxa are more diverse is that their evolutionary clock ticks faster.

An analysis of primordium initiation in Avalon winter wheat crops with different sowing dates and at nine sites in England and Scotland

1987 ◽  
Vol 109 (1) ◽  
pp. 123-134 ◽  
Author(s):  
E. J. M. Kirby ◽  
J. R. Porter ◽  
W. Day ◽  
Jill S. Adam ◽  
Margaret Appleyard ◽  
...  
Keyword(s):  
Winter Wheat ◽  
Thermal Time ◽  
Rapid Rate ◽  
Leaf Initiation ◽  
Sowing Dates ◽  
Constant Rate ◽  
Number Of Leaves

SummaryThe initiation of leaf and spikelet primordia was studied at sites ranging in latitude from Newton Abbot (50·6°N) to Aberdeen (57·2°N) in crops sown in the middle of September, October and November 1983. The rate of primordium initiation tended to decrease from south to north but there were also marked differences between quite close sites.The rate of leaf initiation increased with temperature but photoperiod had little effect; the rate of spikelet initiation was affected both by temperature and by photoperiod. There were differences in the total number of leaves initiated which were only partlyexplained by differences in vernalization.Expressing leaf and spikelet initiation rates in terms of thermal and photo-thermal time respectively showed a constant rate of leaf initiation and a constant and more rapid rate of spikelet initiation.

scholarly journals Comprehensive taxon sampling and vetted fossils help clarify the time tree of shorebirds (Aves, Charadriiformes)

2021 ◽  
Author(s):  
David Černý ◽  
Rossy Natale
Keyword(s):  
Divergence Time ◽  
Morphological Characters ◽  
Total Evidence ◽  
Fossil Calibration ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Early Diversification ◽  
Extant Species ◽  
Tree Inference ◽  
The Impact

Shorebirds (Charadriiformes) are a globally distributed clade of modern birds and, due to their ecological and morphological disparity, a frequent subject of comparative studies. While molecular phylogenies have been instrumental to resolving the suprafamilial backbone of the charadriiform tree, several higher-level relationships, including the monophyly of plovers (Charadriidae) and the phylogenetic positions of several monotypic families, have remained unclear. The timescale of shorebird evolution also remains uncertain as a result of extensive disagreements among the published divergence dating studies, stemming largely from different choices of fossil calibrations. Here, we present the most comprehensive non-supertree phylogeny of shorebirds to date, based on a total-evidence dataset comprising 336 ingroup taxa (89\% of all extant species), 24 loci (15 mitochondrial and 9 nuclear), and 69 morphological characters. Using this phylogeny, we clarify the charadriiform evolutionary timeline by conducting a node-dating analysis based on a subset of 8 loci tested to be clock-like and 16 carefully selected, updated, and vetted fossil calibrations. Our concatenated, species-tree, and total-evidence analyses consistently support plover monophyly and are generally congruent with the topologies of previous studies, suggesting that the higher-level relationships among shorebirds are largely settled. However, several localized conflicts highlight areas of persistent uncertainty within the gulls (Laridae), true auks (Alcinae), and sandpipers (Scolopacidae). At shallower levels, our phylogenies reveal instances of genus-level nonmonophyly that suggest changes to currently accepted taxonomies. Our node-dating analyses consistently support a mid-Paleocene origin for the Charadriiformes and an early diversification for most major subclades. However, age estimates for more recent divergences vary between different relaxed clock models, and we demonstrate that this variation can affect phylogeny-based macroevolutionary studies. Our findings demonstrate the impact of fossil calibration choice on the resulting divergence time estimates, and the sensitivity of diversification rate analyses to the modeling assumptions made in time tree inference.

scholarly journals Renewed diversification following Miocene landscape turnover in a Neotropical butterfly radiation

2017 ◽  
Author(s):  
Nicolas Chazot ◽  
Keith R. Willmott ◽  
Gerardo Lamas ◽  
André V. L. Freitas ◽  
Florence Piron-Prunier ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Complex Dynamics ◽  
Negative Impact ◽  
Neotropical Region ◽  
Diversification Rate ◽  
Sudden Increase ◽  
Extinction Rate ◽  
The Andes ◽  
Extant Species ◽  
Peer Community

Abstract“This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100032)”The Neotropical region has experienced a dynamic landscape evolution throughout the Miocene, with the large wetland Pebas occupying western Amazonia until 11-8 my ago and continuous uplift of the Andes mountains along the western edge of South America. Although the complex dynamics between the Andes and Amazonia may have strongly affected the trajectory of Neotropical biodiversity, there is little evidence for such an influence from time-calibrated phylogenies of groups that diversified during this period. Here, we generate one of the most comprehensive time-calibrated molecular phylogenies of a group of Neotropical insects: the butterfly tribe Ithomiini. Our tree includes 340 species (87% of extant species), spanning 26 million years of diversification in the Neotropics. We investigate temporal and spatial patterns of diversification, focusing on the influence of Miocene landscape tranformations on the dynamics of speciation, extinction and biotic interchanges at the Amazonia/Andes interface. We find that Ithomiini likely began diversifying at the interface between the Andes and the Amazonia around 26.4 my ago. Five subtribes with a very low extant diversity started diversifying early in western Amazonia, but a rapid decrease in diversification rate due to increased extinction rate between 20 and 10 my ago suggests a negative impact of the Pebas wetland system on these early lineages. By contrast, the clade containing the five most species-rich subtribes (85% of extant species) was characterized by a high, positive net diversification rate. This clade diversified exclusively in the Central Andes from 20 to 10 my ago. After the demise of the Pebas system (11-8 my ago), we found a sudden increase of interchanges with the Northern Andes and Amazonia, followed by local diversification, which led to a substantial renewal of diversification. In general, ecological turnovers throughout the Miocene strongly determined the dynamics of speciation, and extinction and interchanges, and appear as a key driving force shaping the region’s current extraordinary biodiversity.

Occurrence and biogeographic significance of Heliaster (Echinodermata: Asteroidea) from the Pliocene of southwest Florida

1988 ◽  
Vol 62 (01) ◽  
pp. 126-132 ◽  
Author(s):  
Douglas S. Jones ◽  
Roger W. Portell
Keyword(s):  
Central American ◽  
Eastern Pacific ◽  
Whole Body ◽  
Marine Fauna ◽  
Western Atlantic ◽  
Southwest Florida ◽  
Extant Species ◽  
Geologic Record ◽  
Central American Isthmus

Whole body asteroid fossils are rare in the geologic record and previously unreported from the Cenozoic of Florida. However, specimens of the extant species,Heliaster microbrachiusXantus, were recently discovered in upper Pliocene deposits. This marks the first reported fossil occurrence of the monogeneric Heliasteridae, a group today confined to the eastern Pacific. This discovery provides further non-molluscan evidence of the close similarities between the Neogene marine fauna of Florida and the modern fauna of the eastern Pacific. The extinction of the heliasters in the western Atlantic is consistent with the pattern of many other marine groups in the region which suffered impoverishment following uplift of the Central American isthmus.

Constant-Rate Feed Device. A Reply to Comment

1950 ◽  
Vol 22 (7) ◽  
pp. 956-956 ◽  
Author(s):  
Lester Lundsted
Keyword(s):  
Constant Rate ◽  
Feed Device

Thysanoptera diversity associated with Mexican lemon (Citrus aurantifolia Christm.)

2020 ◽  
Vol 13 (9) ◽  
Author(s):  
Francisco Javier Avendaño-Gutiérrez ◽  
Salvador Aguirre Paleo ◽  
Alejandro Morales Hernández ◽  
Venecia Quesadas-Béjar
Keyword(s):  
Biosphere Reserve ◽  
Simple Random Sampling ◽  
Diversity Indices ◽  
Diaphorina Citri ◽  
Program Calculation ◽  
Homogeneous Relation ◽  
Candidatus Liberibacter ◽  
Scirtothrips Citri ◽  
Species Richness And Abundance ◽  
First Time

Objective: To calculate the monthly relative abundance of Thysanoptera species, according to the Margalef, Simpson and Shannon-Wiener diversity indices. Design / Methodology / Approach: The work was carried out in three geographic units with conventional management, during January-December, 2019 in the Reserva de la Biosfera Zicuirán-Infiernillo (Biosphere Reserve), Michoacán, Mexico. In each unit, 10 trees were selected through simple random sampling. Thrips counts were performed on ten shoots per tree every 15 d, for a total of 7200 shoots in the three geographic units. Thysanoptera individuals were placed in entomological jars. The variables were: number of thrips collected per shoot in sampled tree and geographic unit (orchard). To estimate the specific richness and structure of species, the program "calculation of diversity indices DIVERS" was used. Results: In the three geographical units studied, the recorded presence of Thysanoptera accounted for 12 to 17 species. For Nueva Italia 12 recorded species, two were permanent (16.66%), five abundant (41.66%), one scarce (8.3%) and four rare (33.33%). In Zicuirán, three species were permanent (17.64%), six abundant (35.29%), two scarce (11.76%) and six rare (35.29%). In Los Hoyos, four species were permanent (26.66%), four abundant (26.66%) and seven rare (46.66%). The abundance of species was represented by the genus Frankliniella and the species Scolothrips sexmaculatus and Scirtothrips citri. The highest species richness and abundance was found from January to May. In October and November, the value of the calculated indices was zero, which shows less richness and abundance of individuals. The best species uniformity was recorded during January and December, which meant a more stable and homogeneous relation. Study limitations/Implications. Pest resurgence, presence of Candidatus Liberibacter spp. and its vector Diaphorina citri. Findings / Conclusions: in Nueva Italia, 12 species were taxonomically determined; in Los Hoyos 15, and in Zicuirán 17 species, which are reported for the first time in the state of Michoacán, Mexico. At the geographic unit "Los Hoyos" diversity was higher, uniform and stable.

Climate resilience through natural regeneration in degraded natural forests of south-eastern hilly region of Bangladesh

2019 ◽  
Vol 48 (3) ◽  
pp. 417-425
Author(s):  
Md Khayrul Alam Bhuiyan ◽  
Md Akhter Hossain ◽  
Abdul Kadir Ibne Kamal ◽  
Mohammed Kamal Hossain ◽  
Mohammed Jashimuddin ◽  
...  
Keyword(s):  
Tree Species ◽  
Natural Regeneration ◽  
Diversity Indices ◽  
Acacia Auriculiformis ◽  
Quantitative Structure ◽  
Natural Forests ◽  
Climate Resilience ◽  
Hilly Region ◽  
Major Cluster ◽  
Ecological Dominance

A study was conducted by using 5m × 5m sized 179 quadrates following multistage random sampling method for comparative regenerating tree species, quantitative structure, diversity, similarity and climate resilience in the degraded natural forests and plantations of Cox's Bazar North and South Forest Divisions. A total of 70 regenerating tree species were recorded representing maximum (47 species) from degraded natural forests followed by 43 species from 0.5 year 39 species from 1.5 year and 29 species from 2.5 year old plantations. Quantitative structure relating to ecological dominance indicated dominance of Acacia auriculiformis, Grewia nervosa and Lithocarpus elegans seedlings in the plantations whereas seedlings of Aporosa wallichii, Suregada multiflora and Grewia nervosa in degraded natural forests. The degraded natural forests possess higher natural regeneration potential as showed by different diversity indices. The dominance-based cluster analysis showed 2 major cluster of species under one of which multiple sub-clusters of species exists. Poor plant diversity and presence of regenerating exotic species in the plantations indicated poor climate resilience of forest ecosystem in terms of natural regeneration.

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