scholarly journals A Simulation-Based Evaluation of Tip-Dating Under the Fossilized Birth–Death Process

2019 ◽  
Vol 69 (2) ◽  
pp. 325-344 ◽  
Author(s):  
Arong Luo ◽  
David A Duchêne ◽  
Chi Zhang ◽  
Chao-Dong Zhu ◽  
Simon Y W Ho
Keyword(s):  
Morphological Characters ◽  
Nucleotide Sequences ◽  
Tree Topology ◽  
Molecular Dating ◽  
Morphological Data ◽  
Death Process ◽  
Joint Analysis ◽  
Nucleotide Sequence Data ◽  
Wide Range ◽  
Birth Death

Abstract Bayesian molecular dating is widely used to study evolutionary timescales. This procedure usually involves phylogenetic analysis of nucleotide sequence data, with fossil-based calibrations applied as age constraints on internal nodes of the tree. An alternative approach is tip-dating, which explicitly includes fossil data in the analysis. This can be done, for example, through the joint analysis of molecular data from present-day taxa and morphological data from both extant and fossil taxa. In the context of tip-dating, an important development has been the fossilized birth–death process, which allows non-contemporaneous tips and sampled ancestors while providing a model of lineage diversification for the prior on the tree topology and internal node times. However, tip-dating with fossils faces a number of considerable challenges, especially, those associated with fossil sampling and evolutionary models for morphological characters. We conducted a simulation study to evaluate the performance of tip-dating using the fossilized birth–death model. We simulated fossil occurrences and the evolution of nucleotide sequences and morphological characters under a wide range of conditions. Our analyses of these data show that the number and the maximum age of fossil occurrences have a greater influence than the degree of among-lineage rate variation or the number of morphological characters on estimates of node times and the tree topology. Tip-dating with the fossilized birth–death model generally performs well in recovering the relationships among extant taxa but has difficulties in correctly placing fossil taxa in the tree and identifying the number of sampled ancestors. The method yields accurate estimates of the ages of the root and crown group, although the precision of these estimates varies with the probability of fossil occurrence. The exclusion of morphological characters results in a slight overestimation of node times, whereas the exclusion of nucleotide sequences has a negative impact on inference of the tree topology. Our results provide an overview of the performance of tip-dating using the fossilized birth–death model, which will inform further development of the method and its application to key questions in evolutionary biology.

scholarly journals A Simulation-Based Evaluation of Total-Evidence Dating Under the Fossilized Birth-Death Process

2018 ◽  
Author(s):  
Arong Luo ◽  
David A. Duchêne ◽  
Chi Zhang ◽  
Chao-Dong Zhu ◽  
Simon Y.W. Ho
Keyword(s):  
Morphological Characters ◽  
Nucleotide Sequences ◽  
Tree Topology ◽  
Molecular Dating ◽  
Total Evidence ◽  
Morphological Data ◽  
Death Process ◽  
Nucleotide Sequence Data ◽  
Wide Range ◽  
Birth Death

AbstractBayesian molecular dating is widely used to study evolutionary timescales. This procedure usually involves phylogenetic analysis of nucleotide sequence data, with fossil-based calibrations applied as age constraints on internal nodes of the tree. An alternative approach is Bayesian total-evidence dating, which involves the joint analysis of molecular data from present-day taxa and morphological data from both extant and fossil taxa. Part of its appeal stems from the fossilized birth-death process, which provides a model of lineage diversification for the prior on the tree topology and node times. However, total-evidence dating faces a number of considerable challenges, especially those associated with fossil sampling and evolutionary models for morphological characters. We conducted a simulation study to evaluate the performance of total-evidence dating with the fossilized birth-death model. We simulated fossil occurrences and the evolution of nucleotide sequences and morphological characters under a wide range of conditions. Our analyses show that fossil occurrences have a greater influence than the degree of among-lineage rate variation or the number of morphological characters on estimates of node times and the tree topology. Total-evidence dating generally performs well in recovering the relationships among extant taxa, but has difficulties in correctly placing fossil taxa in the tree and identifying the number of sampled ancestors. The method yields accurate estimates of the origin time of the fossilized birth-death process and the ages of the root and crown group, although the precision of these estimates varies with the probability of fossil occurrence. The exclusion of morphological characters results in a slight overestimation of node times, whereas the exclusion of nucleotide sequences has a negative impact on inference of the tree topology. Overall, our results provide a detailed view of the performance of total-evidence dating, which will inform further development of the method and its application to key questions in evolutionary biology.

A new skink of the genus Scincella Mittleman, 1950 (Squamata: Scincidae) from Ba Den Mountain, Tay Ninh Province, southern Vietnam

Zootaxa ◽  
2019 ◽  
Vol 4648 (2) ◽  
pp. 273-286
Author(s):  
SANG NGOC NGUYEN ◽  
VU DANG HOANG NGUYEN ◽  
LUAN THANH NGUYEN ◽  
ROBERT W. MURPHY
Keyword(s):  
New Species ◽  
Endemic Species ◽  
Morphological Characters ◽  
Nucleotide Sequences ◽  
Morphological Data ◽  
Medium Size ◽  
Southern Vietnam ◽  
Males And Females ◽  
Coi Sequences ◽  
Dorsal Pattern

Ba Den is an isolated mountain in southern Vietnam and home to two endemic species of lizards. Herein, we describe another endemic species, a new skink of the genus Scincella Mittleman, 1950, from the area based on morphological data, including hemipenial characters and nucleotide sequences of COI. The following morphological characters diagnose Scincella badenensis sp. nov.: medium size in adults (snout-vent length up to 64.4 mm); toes reach to fingers when limbs adpressed; midbody scale rows 32–36, smooth; paravertebral scales 67–71; dorsal scales not enlarged; ventral scale rows 68–74; supraoculars four; prefrontals in broad contact with one another; loreal scales two; tympanum deeply sunk, without auricular lobules; two enlarged anterior temporal scales; smooth lamellae beneath toe IV 18–20; pair of enlarged precloacal scales; hemipenes short, smooth and forked near the tip with two short lobes and two small terminal papillae; no dorsal pattern in males; and females with black interruptive vertebral line. The new species differs from its congeners by at least 10.4% uncorrected p-distance in COI sequences. 

Morphologic variation in the USDA/ARS rhubarb germplasm collection

2009 ◽  
Vol 8 (1) ◽  
pp. 35-41 ◽  
Author(s):  
Alberto Pantoja ◽  
Joseph C. Kuhl
Keyword(s):  
Germplasm Collection ◽  
Morphological Characters ◽  
Morphological Data ◽  
Skin Colour ◽  
Base Thickness ◽  
Flesh Colour ◽  
Combining Data ◽  
Wide Range ◽  
Morphologic Variation ◽  
The Mean

Rhubarb includes approximately 60 species in the genusRheum. It has been utilized for thousands of years for medicinal purposes, but only recently identified for its culinary use. In the mid 1700s, edible petioles were discovered on seedlings from rhubarb species. Hundreds of cultivars have since been identified for a wide range of uses from tarts to wine. Unfortunately, propagation by seed and irregular naming has resulted in a plethora of similarly named cultivars and multitude of phenotypes. Fifteen morphological characters were evaluated to differentiate rhubarb cultivars in the USDA, ARSRheumcollection in Palmer, Alaska. Two years of morphological data, focusing on horticultural characteristics indicated variation between the years. To improve cultivar resolution, the results suggest using 1 year's data instead of combining data from different years. The mean °Brix observed was 3.8, with a range from 2.2 to 6.1. Flesh colour and basal skin colour were poorly correlated (R2 = 0.462); overall skin colour was more red at the base than in the middle of the petiole. Rhubarb character categories, in particular petiole number and petiole base thickness, need to be modified to better anticipate the range of expected values, and thereby contribute improved reproducibility and reliability to separate cultivars based on morphological characters.

scholarly journals Craniodental morphology and phylogeny of marsupials

2021 ◽  
Author(s):  
Robin M. D. Beck ◽  
Robert Voss ◽  
Sharon Jansa
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Future Research ◽  
Data Types ◽  
Wide Range ◽  
Morphological And Molecular Data ◽  
Dense Sampling

The current literature on marsupial phylogenetics includes numerous studies based on analyses of morphological data with relatively limited sampling of Recent and fossil taxa, and many studies based on analyses of molecular data that include a dense sampling of Recent taxa, but relatively few that combine both data types. Another dichotomy in the marsupial phylogenetic literature is between studies that focus on New World taxa, others that focus on Sahulian taxa. To date, there has been no attempt to assess the phylogenetic relationships of the global marsupial fauna, based on combined analyses of morphology and molecular sequences, for a dense sampling of Recent and fossil taxa. For this report, we compiled morphological and molecular data from an unprecedented number of Recent and fossil marsupials. Our morphological data consist of 180 craniodental characters that we scored for 97 species representing every currently recognized Recent genus, 42 additional ingroup (crown-clade marsupial) taxa represented by well-preserved fossils, and 5 outgroups (non-marsupial metatherians). Our molecular data comprise 24.5 kb of DNA sequences from whole-mitochondrial genomes and six nuclear loci (APOB, BRCA1, GHR, RAG1, RBP3 and VWF) for 97 marsupial terminals (the same Recent taxa scored for craniodental morphology) and several placental and monotreme outgroups. The results of separate and combined analyses of these data using a wide range of phylogenetic methods support many currently accepted hypotheses of ingroup (marsupial) relationships, but they also underscore the difficulty of placing fossils with key missing data (e.g., †Evolestes), and the unique difficulty of placing others that exhibit mosaics of plesiomorphic and autapomorphic traits (e.g., †Yalkaparidon). Unique contributions of our study are (1) critical discussions and illustrations of marsupial craniodental morphology, including descriptions and illustrations of some features never previously coded for phylogenetic analysis; (2) critical assessments of relative support for many suprageneric clades; (3) estimates of divergence times derived from tip-and-node dating based on uniquely taxon-dense analyses; and (4) a revised, higher-order classification of marsupials accompanied by lists of supporting craniodental synapomorphies. Far from the last word on these topics, this report lays the foundation for future research that may be enabled by the discovery of new fossil taxa, better-preserved material of previously described taxa, novel morphological characters, and improved methods of phylogenetic analysis.

scholarly journals Probabilities of Unranked and Ranked Anomaly Zones under Birth–Death Models

2019 ◽  
Vol 37 (5) ◽  
pp. 1480-1494 ◽  
Author(s):  
Anastasiia Kim ◽  
Noah A Rosenberg ◽  
James H Degnan
Keyword(s):  
Gene Tree ◽  
Species Tree ◽  
Tree Topology ◽  
Death Process ◽  
Gene Trees ◽  
Species Trees ◽  
Multispecies Coalescent ◽  
Speciation Rates ◽  
Tree Topologies ◽  
Birth Death

Abstract A labeled gene tree topology that is more probable than the labeled gene tree topology matching a species tree is called “anomalous.” Species trees that can generate such anomalous gene trees are said to be in the “anomaly zone.” Here, probabilities of “unranked” and “ranked” gene tree topologies under the multispecies coalescent are considered. A ranked tree depicts not only the topological relationship among gene lineages, as an unranked tree does, but also the sequence in which the lineages coalesce. In this article, we study how the parameters of a species tree simulated under a constant-rate birth–death process can affect the probability that the species tree lies in the anomaly zone. We find that with more than five taxa, it is possible for species trees to have both anomalous unranked and ranked gene trees. The probability of being in either type of anomaly zone increases with more taxa. The probability of anomalous gene trees also increases with higher speciation rates. We observe that the probabilities of unranked anomaly zones are higher and grow much faster than those of ranked anomaly zones as the speciation rate increases. Our simulation shows that the most probable ranked gene tree is likely to have the same unranked topology as the species tree. We design the software PRANC, which computes probabilities of ranked gene tree topologies given a species tree under the coalescent model.

A new species of Ahaetulla Link, 1807 (Squamata: Colubridae) from the Mekong Delta, Vietnam

Zootaxa ◽  
2021 ◽  
Vol 4966 (3) ◽  
pp. 290-304
Author(s):  
NGON QUANG LAM ◽  
TRAN THI ANH THU ◽  
LUAN THANH NGUYEN ◽  
ROBERT W. MURPHY ◽  
SANG NGOC NGUYEN
Keyword(s):  
New Species ◽  
Mekong Delta ◽  
Morphological Characters ◽  
Nucleotide Sequences ◽  
Morphological Data ◽  
White Stripe ◽  
Southern Vietnam ◽  
Bright Green ◽  
Red Eyes ◽  
A New Species

A new vine snake, genus Ahaetulla, from Soc Trang Province, southern Vietnam is described based on morphological data and nucleotide sequences from COI and Cytb. Ahaetulla rufusoculara sp. nov. is diagnosed by the following morphological characters: bright red eyes; snout without dermal appendage; internasal separated from supralabial by loreal; body scale rows 15-15-13; ventrals 186–190 in males and 182–185 in females; subcaudals 143–153 in males and 128 or 129 in females; 8 (rarely 9) supralabials, fourth and fifth or fourth to sixth entering orbit; 12–14 maxillary teeth; hemipenis short, reaching 6th or 7th SC; cloacal plate divided; dorsum bright green; and yellow or white stripe along the lower flank. The new species differs from its congeners by an uncorrected p-distance in COI and Cytb sequences of at least 7.7% and 7.5%, respectively. 

A review of species recognition in the Phenacoccus aceris species-group (Hemiptera: Coccomorpha: Pseudococcidae) using molecular and morphological data

Zootaxa ◽  
2017 ◽  
Vol 4319 (3) ◽  
pp. 483
Author(s):  
XU-BO WANG ◽  
SAN-AN WU
Keyword(s):  
Sequence Data ◽  
Species Recognition ◽  
Morphological Characters ◽  
Species Group ◽  
Morphological Data ◽  
Character State ◽  
Relative Width ◽  
Nucleotide Sequence Data ◽  
Putative Species ◽  
Species Separation

The maple mealybug, Phenacoccus aceris (Signoret) (Hemiptera: Pseudococcidae), is a widespread polyphagous pest. The taxonomy of P. aceris and some congeners is controversial. This study utilized molecular analysis of one mitochondrial (cytochrome oxidase I) and two nuclear (EF-1α and 28S D2D3) genes, and morphological data, to investigate the P. aceris species-group based on 120 individuals collected from 16 localities in China. Analyses of the nucleotide sequence data recovered four well-supported clades that enabled us to reassess the taxonomic utility of some morphological characters used for species recognition in the P. aceris species-group, such as the number, location and width of circuli, and the distribution pattern of oral-collar tubular ducts on the dorsum. Polymorphism in the number of circuli indicated that this character-state alone is unreliable for species separation, but a combination of the number, location and relative width of the circuli provides a significant taxonomic character. The distribution of oral-collar tubular ducts on dorsal segments of the cephalothorax can be used also for species separation. In addition, specimens that keyed morphologically to P. aceris contained three putative species that are not separated by host-plant preferences. These putative species are genetically and morphologically different from P. aceris in France (the type locality of P. aceris) and are thus probably new to science. A network analysis of the COI haplotypes showed that the hosts Fraxinus spp. (Oleaceae) and Zanthoxylum bungeanum (Rutaceae) in North China are attacked by both P. aceris and P. azaleae, so previous identifications of this group based on the identity of these host plants is misleading. The taxonomic confusion in the P. aceris species-group may be due to the co-occurrence of multiple putative species. 

scholarly journals Mistreating birth-death models as priors in phylogenetic analysis compromises our ability to compare models

2021 ◽  
Author(s):  
Michael R May ◽  
Carl Rothfels
Keyword(s):  
Prior Distribution ◽  
Phylogenetic Trees ◽  
Model Comparison ◽  
Marginal Likelihood ◽  
Death Process ◽  
Wide Range ◽  
Tree Models ◽  
Extinction Events ◽  
Lineage Diversification ◽  
Birth Death

Time-calibrated phylogenetic trees are fundamental to a wide range of evolutionary studies. Typically, these trees are inferred in a Bayesian framework, with the phylogeny itself treated as a parameter with a prior distribution (a "tree prior"). This prior distribution is often a variant of the stochastic birth-death process, which models speciation events, extinction events, and sampling events (of extinct and/or extant lineages). However, the samples produced by this process are observations, so their probability should be viewed as a likelihood rather than a prior probability. We show that treating the samples as part of the prior results in incorrect marginal likelihood estimates and can result in model-comparison approaches disfavoring the best model within a set of candidate models. The ability to correctly compare the fit of competing tree models is critical to accurate phylogenetic estimates, especially of divergence times, and also to studying the processes that govern lineage diversification. We outline potential remedies, and provide guidance for researchers interested in comparing the fit of competing tree models.

scholarly journals Morphological and molecular studies of three species of Boerhavia L. from Ile-Ife, Nigeria

2020 ◽  
Vol 22 (2) ◽  
pp. 225-236
Author(s):  
S.O. Azeez ◽  
J.O. Matthew ◽  
E.A. Olaoluwa ◽  
G.B. Adegboyega ◽  
I.O. Akinyoola
Keyword(s):  
Cluster Analysis ◽  
Phylogenetic Relationship ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Pollen Grains ◽  
Morphological Characters ◽  
Morphological Data ◽  
Group Method ◽  
Wide Range ◽  
High Level

A wide range of plasticity and polymorphism have been documented in the genus Boerhavia. More so, the possible presence of natural hybrids  among the species of the genus has made species identification more difficult. This study employed morphological characters, pollen parameters as well as Random Amplified Polymorphic DNA (RAPD) to identify and elucidate the phylogenetic relationship that exists among the three species of Boerhavia distributed in Ile-Ife, Nigeria. Qualitative and quantitative morphological characters were observed and measured respectively. The acetolysis of the pollen grains was carried out according to Erdtman method. Fresh and young leaves of the Boerhavia species studied were  collected for genomic DNA extraction using modified Dellarpota procedure. The quality and concentration of DNA was assessed by gel electrophoresis on 2% agarose with known concentrations of undigested lambda DNA. Subsequently, the DNA quantification was done according to standard measurement. The Principal Components Analysis of the morphological traits and the pollen grain studies indicated that the three Boerhavia species studied have a very high level of relationship. However, the Single Linkage Cluster Analysis of the morphological data and the unweighted pair group method with arithmetic mean (UPGMA) cluster analysis of RAPD data revealed that B. erecta is distantly related to B. coccinea and B. diffusa. Despite the fact that the three Boerhavia species studied possess high level of similarity, they can still be distinguished from each other. In conclusion, B. coccinea and B. diffusa are more closely related to each other than B. erecta. Key words: RAPD marker, Pollen grains, Phylogenetic relationship, Polymorphism

scholarly journals Species delimitation and inter-specific gene flow in Tamarix L. (Tamaricaceae)

Hacquetia ◽  
2019 ◽  
Vol 18 (2) ◽  
pp. 313-322
Author(s):  
Masoud Sheidai ◽  
Tahmineh Shagholi ◽  
Maryam Keshavarzi ◽  
Fahimeh Koohdar ◽  
Habibollah Ijbari
Keyword(s):  
Gene Flow ◽  
Molecular Phylogeny ◽  
Species Delimitation ◽  
Morphological Characters ◽  
Morphological Data ◽  
Specific Gene ◽  
Closely Related Species ◽  
Specific Hybridization ◽  
Wide Range ◽  
Semnan Province

Abstract Tamarix L. play important role in preventing deforestation in Iran. Tamarix species exhibit wide range of morphological variation therefore, the species delimitation become difficult. This is further complicated due to similarity of morphological characters in closely related species and the occurrence of inter-specific hybridization. The present study was performed to identify Tamarix species and their potential hybrids in Semnan Province of Iran. We used ITS and ISSR and 42 morphological characters for our investigation. Molecular phylogeny of the studied species and their relationship was not in agreement with the species tree of morphological characters and with taxonomic treatment of the genus. HGT tree of ITS and morphological data obtained revealed the occurrence of inter-specific hybridization or introgression between Tamarix species.

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