scholarly journals Phylogenetic analysis of a new morphological dataset elucidates the evolutionary history of Crocodylia and resolves the long-standing gharial problem

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12094
Author(s):  
Jonathan P. Rio ◽  
Philip D. Mannion
Keyword(s):  
Molecular Data ◽  
Morphological Data ◽  
Sister Taxon ◽  
Last Common Ancestor ◽  
South American ◽  
Biogeographic History ◽  
History Of ◽  
Gavialis Gangeticus ◽  
Divergence Timing ◽  
Early Paleogene

First appearing in the latest Cretaceous, Crocodylia is a clade of semi-aquatic, predatory reptiles, defined by the last common ancestor of extant alligators, caimans, crocodiles, and gharials. Despite large strides in resolving crocodylian interrelationships over the last three decades, several outstanding problems persist in crocodylian systematics. Most notably, there has been persistent discordance between morphological and molecular datasets surrounding the affinities of the extant gharials, Gavialis gangeticus and Tomistoma schlegelii. Whereas molecular data consistently support a sister taxon relationship, in which they are more closely related to crocodylids than to alligatorids, morphological data indicate that Gavialis is the sister taxon to all other extant crocodylians. Here we present a new morphological dataset for Crocodylia based on a critical reappraisal of published crocodylian character data matrices and extensive firsthand observations of a global sample of crocodylians. This comprises the most taxonomically comprehensive crocodylian dataset to date (144 OTUs scored for 330 characters) and includes a new, illustrated character list with modifications to the construction and scoring of characters, and 46 novel characters. Under a maximum parsimony framework, our analyses robustly recover Gavialis as more closely related to Tomistoma than to other extant crocodylians for the first time based on morphology alone. This result is recovered regardless of the weighting strategy and treatment of quantitative characters. However, analyses using continuous characters and extended implied weighting (with high k-values) produced the most resolved, well-supported, and stratigraphically congruent topologies overall. Resolution of the gharial problem reveals that: (1) several gavialoids lack plesiomorphic features that formerly drew them towards the stem of Crocodylia; and (2) more widespread similarities occur between species traditionally divided into tomistomines and gavialoids, with these interpreted here as homology rather than homoplasy. There remains significant temporal incongruence regarding the inferred divergence timing of the extant gharials, indicating that several putative gavialids (‘thoracosaurs’) are incorrectly placed and require future re-appraisal. New alligatoroid interrelationships include: (1) support for a North American origin of Caimaninae in the latest Cretaceous; (2) the recovery of the early Paleogene South American taxon Eocaiman as a ‘basal’ alligatoroid; and (3) the paraphyly of the Cenozoic European taxon Diplocynodon. Among crocodyloids, notable results include modifications to the taxonomic content of Mekosuchinae, including biogeographic affinities of this clade with latest Cretaceous–early Paleogene Asian crocodyloids. In light of our new results, we provide a comprehensive review of the evolutionary and biogeographic history of Crocodylia, which included multiple instances of transoceanic and continental dispersal.

scholarly journals Systematic placement of an enigmatic Southeast Asian taxon Eupetes macrocerus and implications for the biogeography of a main songbird radiation, the Passerida

2007 ◽  
Vol 3 (3) ◽  
pp. 323-326 ◽  
Author(s):  
Knud A Jønsson ◽  
Jon Fjeldså ◽  
Per G.P Ericson ◽  
Martin Irestedt
Keyword(s):  
South African ◽  
Plate Tectonics ◽  
Molecular Data ◽  
Sister Taxon ◽  
Long Distance ◽  
Biogeographic History ◽  
Basal Group ◽  
History Of ◽  
Biogeographic Regions ◽  
Wallace’S Line

Biogeographic connections between Australia and other continents are still poorly understood although the plate tectonics of the Indo-Pacific region is now well described. Eupetes macrocerus is an enigmatic taxon distributed in a small area on the Malay Peninsula and on Sumatra and Borneo. It has generally been associated with Ptilorrhoa in New Guinea on the other side of Wallace's Line, but a relationship with the West African Picathartes has also been suggested. Using three nuclear markers, we demonstrate that Eupetes is the sister taxon of the South African genus Chaetops , and their sister taxon in turn being Picathartes , with a divergence in the Eocene. Thus, this clade is distributed in remote corners of Africa and Asia, which makes the biogeographic history of these birds very intriguing. The most parsimonious explanation would be that they represent a relictual basal group in the Passerida clade established after a long-distance dispersal from the Australo-Papuan region to Africa. Many earlier taxonomic arrangements may have been based on assumptions about relationships with similar-looking forms in the same, or adjacent, biogeographic regions, and revisions with molecular data may uncover such cases of neglect of ancient relictual patterns reflecting past connections between the continents.

scholarly journals The taxonomic history of Indo-Papuan groundsnakes, genus Stegonotus Duméril et al., 1854 (Colubridae), with some taxonomic revisions and the designation of a neotype for S. parvus (Meyer, 1874)

Zootaxa ◽  
2018 ◽  
Vol 4512 (1) ◽  
pp. 1
Author(s):  
CHRISTINE M. KAISER ◽  
HINRICH KAISER ◽  
MARK O’SHEA
Keyword(s):  
New Guinea ◽  
Molecular Data ◽  
The Philippines ◽  
Morphological Data ◽  
Valid Species ◽  
Museum Specimens ◽  
Type Specimens ◽  
History Of ◽  
Original Species ◽  
Species Specific

Since its conceptualization in 1854, 29 species of the colubrid genus Stegonotus have been recognized or described, of which 15 (admiraltiensis, batjanensis, borneensis, cucullatus, derooijae, diehli, florensis, guentheri, iridis, heterurus, melanolabiatus, modestus, muelleri, parvus, poechi) are still considered valid today. Original species descriptions for the members of this genus were published in Dutch, English, French, German, and Italian and, perhaps as a consequence of these polyglot origins, there has been a considerable amount of confusion over which species names should be applied to which populations of Stegonotus throughout its range across Borneo, the Philippines, Wallacea, New Guinea, Australia, and associated archipelagos. In addition, the terminology used to notate characteristics in the descriptions of these forms was not uniform and may have added to the taxonomic confusion. In this paper, we trace in detail the history of the type specimens, the species, and the synonyms currently associated with the genus Stegonotus and provide a basic, species-specific listing of their characteristics, derived from our examination of over 1500 museum specimens. Based on our data, we are able to limit the distribution of S. modestus to the islands of Ambon, Buru, and Seram in the central Moluccas of Indonesian Wallacea. We correct the type locality of S. cucullatus to the Manokwari area on the Bird’s Head Peninsula of West Papua, Indonesian New Guinea and designate a neotype for S. parvus, a species likely to be a regional endemic in the Schouten Archipelago of Cenderawasih Bay (formerly Geelvink Bay), Indonesian New Guinea. We unequivocally identify and explain the problematic localities of the type specimens of S. muelleri and Lycodon muelleri, which currently reside in the same specimen jar. We remove L. aruensis and L. lividum from the synonymy of S. modestus and recognize them as S. aruensis n. comb. and S. lividus n. comb., respectively. We remove S. keyensis and Zamenophis australis from the synonymy of S. cucullatus and recognize them as S. keyensis n. comb. and S. australis n. comb., respectively. We further remove S. reticulatus from the synonymy of S. cucullatus, S. dorsalis from the synonymy of S. diehli, and S. sutteri from the synonymy of S. florensis. We designate lectotypes for S. guentheri, S. heterurus, S. lividus, and S. reticulatus. Lastly, we introduce S. poechi, a valid species not mentioned in the scientific literature since its description in 1924. This brings the diversity in the genus Stegonotus to 22 species. We also caution that in a complex group of organisms like Stegonotus any rush to taxonomic judgment on the basis of molecular and incomplete morphological data sets may perpetuate errors and introduce incongruities. Only through the careful work of connecting type material with museum specimens and molecular data can the taxonomy and nomenclature of complex taxa be stabilized. 

scholarly journals Evolution of Philodendron (Araceae) species along Neotropical biomes

2016 ◽  
Author(s):  
Leticia Loss-Oliveira ◽  
Cassia CMS Sakuragui ◽  
Maria de Lourdes Soares ◽  
Carlos G Schrago
Keyword(s):  
Morphological Diversity ◽  
Neotropical Region ◽  
Last Common Ancestor ◽  
Amazon Forest ◽  
Ancestral Reconstruction ◽  
Biogeographic History ◽  
Early Diversification ◽  
Sister Clade ◽  
History Of ◽  
Wide Geographic Distribution

Philodendron is the second most diverse genus of the Araceae, a tropical monocot family with significant morphological diversity along its wide geographic distribution in the Neotropics. Although evolutionary studies of Philodendron were conducted in recent years, the phylogenetic relationship among its species remains unclear. Additionally, analyses conducted to date suggested the inclusion of all American representatives of a closely related genus, Homalomena, within the Philodendron clade. A thorough evaluation of the phylogeny and timescale of these lineages is thus necessary to elucidate the tempo and mode of evolution of this large Neotropical genus and to unveil the biogeographic history of Philodendron evolution along the Amazonian and Atlantic Rain Forests, as well as open dry forests of South America. To this end, we have estimated the molecular phylogeny for 68 Philodendron species, which consists of the largest sampling assembled to date aiming the study of the evolutionary affinities. We have also performed ancestral reconstruction of species distribution along biomes. Finally, we contrasted these results with the inferred timescale of Philodendron and Homalomena lineage diversification. Our estimates indicate that American Homalomena is the sister clade to Philodendron. The early diversification of Philodendron took place in the Amazon Forest from Early to Middle Miocene, followed by colonization of the Atlantic Forest and the savanna-like landscapes, respectively. Based on the age of the last common ancestor of Philodendron, the species of this genus diversified by rapid radiations, leading to its wide extant distribution in the Neotropical region.

Arcanumophis, a new genus and generic allocation for Erythrolamprus problematicus (Myers 1986), Xenodontinae (Colubridae) from the Cordillera de Carabaya, southern Peru

Zootaxa ◽  
2019 ◽  
Vol 4671 (1) ◽  
pp. 129-138 ◽  
Author(s):  
CHRISTOPHER R. SMAGA ◽  
ALEX TTITO ◽  
ALESSANDRO CATENAZZI
Keyword(s):  
New Genus ◽  
Original Description ◽  
Molecular Data ◽  
Sister Taxon ◽  
South American ◽  
Single Specimen ◽  
Snake Species ◽  
Southern Peru ◽  
The Status ◽  
Morphological And Molecular Data

The systematics of South American Xenodontinae snakes has experienced large changes and improvements as a result of recent studies employing molecular data. Herein we assess the status of the rare Peruvian snake species, Erythrolamprus problematicus (Dipsadidae, Xenodontinae, Xenodontini), previously known from a single specimen collected in 1950. Based on new morphological and molecular data from a second specimen that we collected, we confirmed the presence of a crease in the rostral scale, mentioned in the original description (a unique trait among the Xenodontini), and recovered E. problematicus as the sister-taxon of all other Xenodontini, instead of nested among the current Erythrolamprus. Therefore, our phylogenetic results justify the erection of a new genus to accommodate the species. 

scholarly journals Phylogenetic relationships of the neon tetras Paracheirodon spp. (Characiformes: Characidae: Stethaprioninae), including comments on Petitella georgiae and Hemigrammus bleheri

2020 ◽  
Vol 18 (2) ◽  
Author(s):  
Pedro Senna Bittencourt ◽  
Valéria Nogueira Machado ◽  
Bruce Gavin Marshall ◽  
Tomas Hrbek ◽  
Izeni Pires Farias
Keyword(s):  
Phylogenetic Relationships ◽  
Species Complex ◽  
Molecular Data ◽  
Morphological Data ◽  
Sister Taxon ◽  
Taxonomic History ◽  
Relationship Of

ABSTRACT Neon tetras (Paracheirodon spp.) are three colorful characid species with a complicated taxonomic history, and relationships among the species are poorly known. Molecular data resolved the relationships among the three neon tetras, and strongly supported monophyly of the genus and its sister taxon relationship to Brittanichthys. Additionally, the sister-taxon relationship of the rummy-nose tetras Hemigrammus bleheri and Petitella georgiae was strongly supported by molecular and morphological data. Therefore, we propose to transfer the rummy-nose tetras H. bleheri and H. rhodostomus to the genus Petitella. Furthermore, Petitella georgiae is likely to be a species complex comprised of at least two species.

scholarly journals The tribe Scrophularieae (Scrophulariaceae): A Review of Phylogenetic Studies

Hacquetia ◽  
2019 ◽  
Vol 18 (2) ◽  
pp. 337-347 ◽  
Author(s):  
Mehrshid Riahi ◽  
Farrokh Ghahremaninejad
Keyword(s):  
Phylogenetic Relationships ◽  
Molecular Data ◽  
Morphological Data ◽  
Hybrid Speciation ◽  
The North ◽  
Phylogenetic Studies ◽  
Phylogenetic Reconstructions ◽  
Data Collection And Analysis ◽  
History Of ◽  
Review Reports

Abstract Molecular data have been increasingly used to study the phylogenetic relationships among many taxa, including scrophs. Sometimes they have provided phylogenetic reconstructions that are in conflict with morphological data leading to a re-evaluation of long-standing evolutionary hypotheses. In this paper, we review reports of the recent knowledge of the phylogenetic relationships within Scrophularieae (2011–2017). The results of these analyses led to the following conclusions. (1) Species of Scrophularia have undergone one or more Miocene migration events occurred from eastern Asia to the North America with subsequent long dispersal and diversification in three main directions. (2) Allopolyploid and aneuploid hybrid speciation between Scrophularia species can occur, so hybridization and polyploidy have an important role for history of diversification. (3) The ancestral staminode type for the genus Scrophularia seems to be a large staminode. (4) Monophyly of the genus Verbascum with respect to the genus Scrophularia is strongly supported. (5) Oreosolen, is not monophyletic, because all accessions of Oreosolen were nested within Scrophularia. We discuss methods of data collection and analysis, and we describe the areas of conflict and agreement between molecular phylogenies.

The “Cobra-preta” of São Tomé Island, Gulf of Guinea, is a new species of Naja Laurenti, 1768 (Squamata: Elapidae)

Zootaxa ◽  
2017 ◽  
Vol 4324 (1) ◽  
pp. 121 ◽  
Author(s):  
LUIS M. P. CERÍACO ◽  
MARIANA P. MARQUES ◽  
ANDREAS SCHMITZ ◽  
AARON M. BAUER
Keyword(s):  
New Species ◽  
Conservation Status ◽  
Molecular Data ◽  
Oceanic Islands ◽  
Gulf Of Guinea ◽  
Biogeographic History ◽  
History Of ◽  
Morphological And Molecular Data ◽  
Taxonomic Groups ◽  
A New Species

The Cobra-Preta (black snake in Portuguese) of Sao Tomé Island in the Gulf of Guinea has historically been referred to as Naja (Boulengerina) melanoleuca (Squamata: Elapidae). Its presence on the island has been traditionally explained as an introduction from the mainland by Portuguese settlers, supposedly to control the rat population. This explanation has been widely accepted by local authorities and even international conservation agencies. The taxonomic identity of this snake has remained undisputed by all taxonomists who have published about it, with the exception of L. Capocaccia in 1961. Arguments supporting the human introduction hypothesis are weak and are contradicted by historical, morphological and molecular data. Further, the biogeographic history of the Gulf of Guinea oceanic islands and recent insights on the taxonomic identity and evolutionary history of other taxonomic groups occurring there suggest that the Cobra-Preta, in fact, represents a distinct lineage of the melanoleuca group, endemic to São Tomé. We here describe the Cobra Preta as a new species. The new species differs from N. (B.) melanoleuca, its sister species, by a distinct coloration ventral pattern and the type of contact of the sublingual scales. Data on the toxicology, distribution, ecology, folklore and conservation status of the new species are presented. 

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.

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