scholarly journals Dating the origin and diversification of Pan-Chelidae (Testudines, Pleurodira) under multiple molecular clock approaches

2020 ◽  
Vol 89 (2) ◽  
pp. 146-174 ◽  
Author(s):  
J. Alfredo Holley ◽  
Juliana Sterli ◽  
Néstor G. Basso
Keyword(s):  
Molecular Structure ◽  
Phylogenetic Analysis ◽  
South America ◽  
Sister Group ◽  
Molecular Data ◽  
Total Evidence ◽  
Morphological Data ◽  
South American ◽  
Morphological And Molecular Data ◽  
The Individual

Pan-Chelidae (Testudines, Pleurodira) is a group of side-necked turtles with a currently disjointed distribution in South America and Australasia and characterized by two morphotypes: the long-necked and the short-necked chelids. Both geographic groups include both morphotypes, but different phylogenetic signals are obtained from morphological and molecular data, suggesting the monophyly of the long-necked chelids or the independent evolution of this trait in both groups. In this paper, we addressed this conflict by compiling and editing available molecular and morphological data for Pan-Chelidae, and performing phylogenetic and dating analyses over the individual and the combined datasets. Our total-evidence phylogenetic analysis recovered the clade Chelidae as monophyletic and as sister group of a clade of South American extinct chelids; furthermore Chelidae retained inside the classical molecular structure with the addition of extinct taxa in both the Australasian and the South American clades. Our dating results suggest a Middle Jurassic origin for the total clade Pan-Chelidae, an Early Cretaceous origin for Chelidae, a Late Cretaceous basal diversification of both geographic clades with the emergence of long-necked lineages, and an Eocene diversification at genera level, with the emergence of some species before the final breakup of Southern Gondwana and the remaining species after this event.

Phylogenetic Analysis of the New World Family Heterothripidae (Thysanoptera, Terebrantia) based on Morphological and Molecular Evidence

2019 ◽  
Vol 50 (5) ◽  
pp. 702-716 ◽  
Author(s):  
Veronica Pereyra ◽  
Adriano Cavalleri ◽  
Claudia Szumik ◽  
Christiane Weirauch
Keyword(s):  
Phylogenetic Analysis ◽  
New World ◽  
Sister Group ◽  
Molecular Data ◽  
Species Level ◽  
Total Evidence ◽  
Molecular Evidence ◽  
Large Genus ◽  
Morphological And Molecular Data

The New World family Heterothripidae (~90 spp., four genera) comprises flower-feeding and ectoparasitic thrips. The monophyly of the group has remained untested and species-level relationships were unknown. Morphological (123 characters) and molecular (28S rDNA D2 and D3-D5, H3, and partial COI) data were compiled to reconstruct phylogenetic relationships of this group. The ingroup was represented by 65 species of the four recognized Heterothripidae genera (Aulacothrips Hood, Heterothrips Hood, Lenkothrips De Santis & Sureda, and Scutothrips Stannard). The monophyly of Heterothripidae was recovered in the total evidence and molecular data only analyses with the ectoparasitic Aulacothrips placed as the sister group of the remaining Heterothripidae. The large genus Heterothrips (>80% of the species-level diversity), which was thoroughly sampled in our analyses (56 species), was recovered as paraphyletic with respect to Scutothrips and Lenkothrips. We conclude that additional morphological and molecular data would be desirable before revising the classification of Heterothripidae

Combining morphological and molecular data resolves the phylogeny of Squilloidea (Crustacea : Malacostraca)

2019 ◽  
Author(s):  
Cara Van Der Wal ◽  
Shane T. Ahyong ◽  
Simon Y. W. Ho ◽  
Luana S. F. Lins ◽  
Nathan Lo
Keyword(s):  
Phylogenetic Analysis ◽  
Adaptive Radiation ◽  
Phylogenetic Relationships ◽  
Morphological Characters ◽  
Molecular Data ◽  
Total Evidence ◽  
Morphological Data ◽  
Mantis Shrimp ◽  
Generic Groups ◽  
Morphological And Molecular Data

The mantis shrimp superfamily Squilloidea, with over 185 described species, is the largest superfamily in the crustacean order Stomatopoda. To date, phylogenetic relationships within this superfamily have been comprehensively analysed using morphological data, with six major generic groupings being recovered. Here, we infer the phylogeny of Squilloidea using a combined dataset comprising 75 somatic morphological characters and four molecular markers. Nodal support is low when the morphological and molecular datasets are analysed separately but improves substantially when combined in a total-evidence phylogenetic analysis. We obtain a well resolved and strongly supported phylogeny that is largely congruent with previous estimates except that the Anchisquilloides-group, rather than the Meiosquilla-group, is the earliest-branching lineage in Squilloidea. The splits among the Anchisquilloides- and Meiosquilla-groups are followed by those of the Clorida-, Harpiosquilla-, Squilla- and Oratosquilla-groups. Most of the generic groups are recovered as monophyletic, with the exception of the Squilla- and Oratosquilla-groups. However, many genera within the Oratosquilla-group are not recovered as monophyletic. Further exploration with more extensive molecular sampling will be needed to resolve relationships within the Oratosquilla-group and to investigate the adaptive radiation of squilloids. Overall, our results demonstrate the merit of combining morphological and molecular datasets for resolving phylogenetic relationships.

The American Proteaceae

1998 ◽  
Vol 11 (4) ◽  
pp. 287 ◽  
Author(s):  
Ghillean T. Prance ◽  
Vanessa Plana
Keyword(s):  
South America ◽  
Molecular Data ◽  
Central American ◽  
General Distribution ◽  
South American ◽  
Land Bridge ◽  
Eastern Brazil ◽  
The Family ◽  
Single Genus ◽  
Morphological And Molecular Data

The American Proteaceae are outliers from the main centres of diversity of the family in Australia and South Africa. There are about 83 species in eight genera which all belong to the monophyletic subfamily Grevilleoideae. Three genera, Embothrium, Oreocallis and Lomatia, are placed in the tribe Embothrieae (sensu Johnson and Briggs), four Euplassa, Gevuina, Panopsis and Roupala in the Macadamieae and the single genus Orites in the Oriteae. There are five genera endemic to America and three also have species in Australia and New Guinea (Gevuina, Lomatia and Orites). The Proteaceae appear to have arrived in South America via two routes. The larger genera Euplassa, Panopsis and Roupala, which are all endemic to America and have a general distribution in northern South America and south-eastern Brazil, are derived from Gondwanaland before it separated from South America. The remaining genera are distributed either in temperate South America or in the high Andes and appear to have arrived more recently via the Australia–Antarctica–South American connection. Three of these genera have species in both regions. The centres of species diversity of Euplassa, Panopsis and Roupala fall outside hypothesised forest refugia, indicating that they are not true rainforest species but species of seasonal habitats like those achieved at higher altitudes where they are commonly found. Two genera,Panopsis and Roupala, have reached Central America after the central American land bridge was formed six million years ago. The exact relationship to genera on other continents is still unclear and there is a need for a cladistic biogeographic analysis of the group based on both morphological and molecular data.

scholarly journals Cretaceous origin and repeated tertiary diversification of the redefined butterflies

2011 ◽  
Vol 279 (1731) ◽  
pp. 1093-1099 ◽  
Author(s):  
Maria Heikkilä ◽  
Lauri Kaila ◽  
Marko Mutanen ◽  
Carlos Peña ◽  
Niklas Wahlberg
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Sister Group ◽  
Morphological Characters ◽  
Molecular Data ◽  
Bayesian Approaches ◽  
The Family ◽  
Family Level ◽  
Morphological And Molecular Data

Although the taxonomy of the ca 18 000 species of butterflies and skippers is well known, the family-level relationships are still debated. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the superfamilies Papilionoidea, Hesperioidea and Hedyloidea to date based on morphological and molecular data. We reconstructed their phylogenetic relationships using parsimony and Bayesian approaches. We estimated times and rates of diversification along lineages in order to reconstruct their evolutionary history. Our results suggest that the butterflies, as traditionally understood, are paraphyletic, with Papilionidae being the sister-group to Hesperioidea, Hedyloidea and all other butterflies. Hence, the families in the current three superfamilies should be placed in a single superfamily Papilionoidea. In addition, we find that Hedylidae is sister to Hesperiidae, and this novel relationship is supported by two morphological characters. The families diverged in the Early Cretaceous but diversified after the Cretaceous–Palaeogene event. The diversification of butterflies is characterized by a slow speciation rate in the lineage leading to Baronia brevicornis , a period of stasis by the skippers after divergence and a burst of diversification in the lineages leading to Nymphalidae, Riodinidae and Lycaenidae.

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 Synergistic effects of combining morphological and molecular data in resolving the phylogeny of butterflies and skippers

2005 ◽  
Vol 272 (1572) ◽  
pp. 1577-1586 ◽  
Author(s):  
Niklas Wahlberg ◽  
Michael F Braby ◽  
Andrew V.Z Brower ◽  
Rienk de Jong ◽  
Ming-Min Lee ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Synergistic Effects ◽  
Strong Support ◽  
Sister Group ◽  
Morphological Characters ◽  
Molecular Data ◽  
Total Evidence ◽  
Data Matrix ◽  
Morphological Data ◽  
Combined Analysis

Phylogenetic relationships among major clades of butterflies and skippers have long been controversial, with no general consensus even today. Such lack of resolution is a substantial impediment to using the otherwise well studied butterflies as a model group in biology. Here we report the results of a combined analysis of DNA sequences from three genes and a morphological data matrix for 57 taxa (3258 characters, 1290 parsimony informative) representing all major lineages from the three putative butterfly super-families (Hedyloidea, Hesperioidea and Papilionoidea), plus out-groups representing other ditrysian Lepidoptera families. Recently, the utility of morphological data as a source of phylogenetic evidence has been debated. We present the first well supported phylogenetic hypothesis for the butterflies and skippers based on a total-evidence analysis of both traditional morphological characters and new molecular characters from three gene regions ( COI , EF-1α and wingless ). All four data partitions show substantial hidden support for the deeper nodes, which emerges only in a combined analysis in which the addition of morphological data plays a crucial role. With the exception of Nymphalidae, the traditionally recognized families are found to be strongly supported monophyletic clades with the following relationships: (Hesperiidae+(Papilionidae+(Pieridae+(Nymphalidae+(Lycaenidae+Riodinidae))))). Nymphalidae is recovered as a monophyletic clade but this clade does not have strong support. Lycaenidae and Riodinidae are sister groups with strong support and we suggest that the latter be given family rank. The position of Pieridae as the sister taxon to nymphalids, lycaenids and riodinids is supported by morphology and the EF-1α data but conflicted by the COI and wingless data. Hedylidae are more likely to be related to butterflies and skippers than geometrid moths and appear to be the sister group to Papilionoidea+Hesperioidea.

scholarly journals Comparative Osteology, Phylogeny and Classification of the Eastern South American Catfish Genus Trichomycterus (Siluriformes: Trichomycteridae)

Taxonomy ◽  
2021 ◽  
Vol 1 (2) ◽  
pp. 160-191
Author(s):  
Wilson J. E. M. Costa
Keyword(s):  
Phylogenetic Analysis ◽  
South America ◽  
Morphological Diversity ◽  
Molecular Data ◽  
Total Evidence ◽  
Valid Species ◽  
Character State ◽  
Data Set ◽  
Long Time ◽  
Osteological Characters

Trichomycterus has been considered for a long time to be the most problematic genus of the diverse neotropical subfamily Trichomycterinae. Recently, Trichomycterus was restricted to a clade from eastern South America supported by molecular data, but no unique morphological character state was found to distinguish it, making it difficult to allocate new species based on morphology alone. The objectives of this study were to conduct an osteological comparative analysis comprising a large sample of valid species of Trichomycterus, to conduct a total evidence phylogenetic analysis, combining osteological characters and a multigene database, and to propose an intrageneric classification based on the results of the phylogenetic analysis. Fifty-two osteological characters were combined with a multigene molecular data set of 2974 bp for 44 species of Trichomycterus, and 21 outgroups generated a well-supported phylogenetic tree, making it possible to delimit and diagnose intrageneric lineages, of which six subgenera are recognized. The high morphological diversity of osteological structures herein first reported for Trichomycterus from eastern South America is possibly related to some ecological specializations. This study shows that osteological characters combined with molecular data may be useful to consistently delimit and distinguish between trichomycterines, shedding light on the still persistent problems in trichomycterine systematics.

Phylogenetic analysis of Micracidini bark beetles (Coleoptera: Curculionidae) demonstrates a single trans-Atlantic disjunction and inclusion ofCactopinusin the New World clade

2016 ◽  
Vol 149 (1) ◽  
pp. 8-25 ◽  
Author(s):  
Bjarte H. Jordal ◽  
Johanna Kaidel
Keyword(s):  
Phylogenetic Analysis ◽  
Bark Beetles ◽  
New World ◽  
Sister Group ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Similarity ◽  
External Data ◽  
Group Relationships ◽  
Morphological And Molecular Data

AbstractMicracidini (Coleoptera: Curculionidae: Scolytinae) is an unusual tribe of mainly bigynous bark beetles found in dry forests and scrublands in Afrotropical and Neotropical regions. Their phylogenetic relationship to other bark beetle groups is poorly known with few clues from external morphology. Hence, a phylogenetic analysis of five genes (COI, EF-1a, 28S, CAD, ArgK) and morphological (internal and external) data was conducted to test potential sister group relationships, including 56 outgroup genera in 22 tribes, and 18 species in 10 genera of Micracidini.CactopinusSchwarz – a genus with many cactus feeding species – was nested within a clade of all Neotropical and Nearctic genera. The New World was colonised by an Afrotropical ancestor about 75–85 million years ago, where cactus feeding inCactopinusevolved much later. All analyses indicated a paraphyletic clade of Afrotropical micracidines, strongly supporting inclusion of the Ipini genusDendrochilusSchedl inAfromicracisSchedl. Hypoborini appear to be one of the more plausible sistergroup candidates to Micracidini, and revealed morphological similarity in protibial and proventricular characters. Most phylogenetic results were supported independently by morphological and molecular data and therefore document the power of thorough examination of morphological characters analysed properly in a phylogenetic context.

On the New World spiders previously misplaced in Leptopholcus: molecular and morphological analyses and descriptions of four new species (Araneae : Pholcidae)

2014 ◽  
Vol 28 (4) ◽  
pp. 432 ◽  
Author(s):  
Bernhard A. Huber ◽  
Leonardo S. Carvalho ◽  
Suresh P. Benjamin
Keyword(s):  
New Species ◽  
Puerto Rican ◽  
New World ◽  
Sister Group ◽  
Molecular Data ◽  
Morphological Data ◽  
Sister Group Relationship ◽  
South American ◽  
World Species ◽  
American Clade

The generic placement of New World pholcids assigned to the genus Leptopholcus Simon, 1893 has long been questioned and recent molecular data have shown that Caribbean (Hispaniolan) representatives are more closely related to the Old World genus Micropholcus Deeleman-Reinhold & Prinsen, 1987 than to ‘true’ African Leptopholcus (Dimitrov, Astrin and Huber 2013, Cladistics 29: 132–146). Here we provide new molecular (16S, 18S, 28S, COI, H3, WNT1) and morphological data about Caribbean (Cuban, Puerto Rican) and South American (Brazilian) representatives, supporting the sister-group relationship with Micropholcus and suggesting a monophyletic New World clade that in turn consists of a Caribbean and a South American clade. The ten New World species previously assigned to Leptopholcus are thus transferred to Micropholcus for which an emended diagnosis is provided: M. baoruco (Huber, 2006), comb. nov.; M. brazlandia (Huber, Pérez & Baptista, 2005), comb. nov.; M. dalei (Petrunkevitch, 1929), comb. nov.; M. delicatulus (Franganillo, 1930), comb. nov.; M. evaluna (Huber, Pérez & Baptista, 2005), comb. nov.; M. hispaniola (Huber, 2000), comb. nov.; M. jamaica (Huber, 2000), comb. nov.; M. kiskeya (Huber & Wunderlich, 2006), comb. nov.; M. pataxo (Huber, Pérez & Baptista, 2005), comb. nov.; M. toma (Huber, 2006), comb. nov. Four Brazilian species are newly described: M. piaui, sp. nov.; M. piracuruca, sp. nov.; M. crato, sp. nov.; M. ubajara, sp. nov. Natural history data are provided for M. piaui and M. ubajara.

A revision of the Dwarf Geckos, genus Lygodactylus (Squamata: Gekkonidae), from Angola, with the description of three new species

Zootaxa ◽  
2020 ◽  
Vol 4853 (3) ◽  
pp. 301-352 ◽  
Author(s):  
MARIANA P. MARQUES ◽  
LUIS M. P. CERÍACO ◽  
MATTHEW D. BUEHLER ◽  
SUZANA A. BANDEIRA ◽  
JOYCE M. JANOTA ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Taxonomic Revision ◽  
Molecular Data ◽  
Morphological Data ◽  
Mitochondrial Marker ◽  
Number Of Species ◽  
Voucher Specimens ◽  
Morphological And Molecular Data ◽  
Three New Species

At present the genus Lygodactylus is represented by three species in Angola confirmed by voucher specimens—L. angolensis, L. bradfieldi, and L. capensis—and two others believed to be present, but without specimens with precise localities, L. chobiensis and L. lawrencei. We present a detailed taxonomic revision of the group in Angola and describe three new species, Lygodactylus baptistai sp. nov. L. nyaneka sp. nov. and Lygodactylus tchokwe sp. nov. Phylogenetic analysis using the mitochondrial marker ND2, as well as morphological data support the recognition of the new species. In addition, data suggest that specimens historically assigned to L. capensis in Angola represent misidentifications of L. nyaneka sp. nov. and L. tchokwe sp. nov. We revisit the identity of Lygodactylus laurae, a junior synonym of L. angolensis. We also present the first confirmed record of L. lawrencei in the country, using both morphological and molecular data. The description of the new species and the revision of the taxonomic identity of the Angolan populations of the genus, raises the number of species occurring in the country to five. A key to the Angolan species is presented. 

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