4.7 Article

A comprehensive molecular phylogeny of Afrotropical white -eyes (Aves: Zosteropidae) highlights prior underestimation of mainland diversity and complex colonisation history

Journal

MOLECULAR PHYLOGENETICS AND EVOLUTION
Volume 149, Issue -, Pages -

Publisher

ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ympev.2020.106843

Keywords

-

Funding

  1. NERC [NE/G523612/1]
  2. Systematics Research Fund
  3. Swedish Research Council [621-2014-5113]

Ask authors/readers for more resources

Authors

I am an author on this paper
Click your name to claim this paper and add it to your profile.

Reviews

Primary Rating

4.7
Not enough ratings

Secondary Ratings

Novelty
-
Significance
-
Scientific rigor
-
Rate this paper

Recommended

Article Evolutionary Biology

Geographical differentiation and cryptic diversity in the monocled cobra, Naja kaouthia (Elapidae), from Thailand

Napat Ratnarathorn, Pongchai Harnyuttanakorn, Lawan Chantiome, Susan E. Evans, Julia J. Day

ZOOLOGICA SCRIPTA (2019)

Article Ecology

Contrasting trajectories of morphological diversification on continents and islands in the Afrotropical white-eye radiation

Julia J. Day, Frederico C. Martins, Joseph A. Tobias, David J. Murrell

JOURNAL OF BIOGEOGRAPHY (2020)

Editorial Material Biochemistry & Molecular Biology

The toad's warts: Discordance creates bumpy expectations of mitochondrial-nuclear evolution between species

Jeffrey W. Streicher, Julia J. Day

MOLECULAR ECOLOGY (2020)

Article Evolutionary Biology

The roles of vicariance and isolation by distance in shaping biotic diversification across an ancient archipelago: evidence from a Seychelles caecilian amphibian

Simon T. Maddock, Ronald A. Nussbaum, Julia J. Day, Leigh Latta, Mark Miller, Debra L. Fisk, Mark Wilkinson, Sara Rocha, David J. Gower, Michael E. Pfrender

BMC EVOLUTIONARY BIOLOGY (2020)

Article Multidisciplinary Sciences

Adaptation of the carbamoyl-phosphate synthetase enzyme in an extremophile fish

Lewis J. White, Gemma Sutton, Asilatu Shechonge, Julia J. Day, Kanchon K. Dasmahapatra, Mary E. Pownall

ROYAL SOCIETY OPEN SCIENCE (2020)

Article Biochemistry & Molecular Biology

Molecular phylogenetics of sub-Saharan African natricine snakes, and the biogeographic origins of the Seychelles endemic Lycognathophis seychellensis

V Deepak, Simon T. Maddock, Rhiannon Williams, Zoltan T. Nagy, Werner Conradie, Sara Rocha, D. James Harris, Ana Perera, Vaclav Gvozdik, Thomas M. Doherty-Bone, Rachunliu G. Kamei, Michele Menegon, Jim Labisko, Charles Morel, Natalie Cooper, Julia J. Day, David J. Gower

Summary: The phylogenetic relationships of sub-Saharan African natricine snakes, including the Seychelles endemic Lycognathophis seychellensis, are not well-understood. Genetic analysis suggests a close relationship between L. seychellensis and mainland sub-Saharan natricines, with low genetic variation. The lineage of L. seychellensis is estimated to have dispersed to the Seychelles from mainland Africa approximately 43-25 million years ago, challenging the idea that it is a Gondwanan relic.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2021)

Article Ecology

MAMMALS IN PORTUGAL: A data set of terrestrial, volant, and marine mammal occurrences in Portugal

Clara Grilo, Beatriz C. Afonso, Filipe Afonso, Marta Alexandre, Sara Aliacar, Ana Almeida, Ivan Prego Alonso, Francisco Alvares, Paulo Alves, Paulo Celio Alves, Pedro Alves, Anabela Amado, Vitor Amendoeira, Francisco Amorim, Guilherme da Silva Aparicio, Ricardo Araujo, Fernando Ascensao, Margarida Augusto, Victor Bandeira, A. Marcia Barbosa, Soraia Barbosa, Sergio Barbosa, Silvia Barreiro, Paulo Barros, Tania Barros, Filomena Barros, Mafalda Basto, Joana Bernardino, Sara Bicho, Luis Eduardo Biedma, Marta Borges, Luis Braz, Jose Carlos Brito, Tiago Brito, Joao Alexandre Cabral, Javier Calzada, Claudia Camarinha, Mafalda Carapuco, Paulo Cardoso, Mario Carmo, Carlos Carrapato, Mailis da Silva Carrilho, Diogo Filipe T. C. S. Carvalho, Filipe Carvalho, Joao Carvalho, Diana Castro, Guilherme Castro, Joana Castro, Luis Roma Castro, Filipe Xavier Catry, Ana M. Cerveira, Andre Cid, Rafael Clarke, Conceicao Conde, Jose Conde, Jorge Costa, Mafalda Costa, Pedro Costa, Cristina Costa, Andre Pedro do Couto, Joao Craveiro, Marta Dias, Sofia Dias, Beatriz Duarte, Virginia Duro, Claudia Encarnacao, Sofia Eufrazio, Antonio Fael, Joao Salvador Fale, Sandra Faria, Carlos Fernandes, Margarida Fernandes, Goncalo Ferrao da Costa, Clara Ferreira, Diogo F. Ferreira, Eduardo Ferreira, Joaquim Pedro Ferreira, Joao Ferreira, Diana Ferreira, Carlos Fonseca, Ines Fontes, Ricardo Fragoso, Claudia Franco, Tamira Freitas, Sofia I. Gabriel, Rory Gibb, Patricia Gil, Carla Patricia Jorge Gomes, Pedro Horta, Pedro Gomes, Veronica Gomes, Filipa Grilo, Americo Guedes, Filipa Guilherme, Ivan Gutierrez, Henry Harper, Jose M. Herrera, Dario Hipolito, Samuel Infante, Jose Jesus, Kate E. Jones, Marina I. Laborde, Luis Lamas de Oliveira, Ines Leitao, Rita Lemos, Catia Lima, Paloma Linck, Hugo Lopes, Susana Lopes, Adria Lopez-Baucells, Armando Loureiro, Filipa Loureiro, Rui Lourenco, Sofia Lourenco, Paula Lucas, Ana Magalhaes, Cristina Maldonado, Fabio Marcolin, Sara Marques, J. Tiago Marques, Carina Marques, Paulo Marques, Pedro Caetano Marrecas, Frederico Martins, Raquel Martins, Miguel Mascarenhas, Vanessa A. Mata, Ana Rita Mateus, Milene Matos, Denis Medinas, Tiago Mendes, Gabriel Mendes, Frederico Mestre, Catarina Milhinhas, Antonio Mira, Rita I. Monarca, Norberto Monteiro, Barbara Monteiro, Pedro Monterroso, Monia Nakamura, Nuno Negroes, Eva K. Nobrega, Miguel Novoa, Manuel Nunes, Nuno Jardim Nunes, Flavio Oliveira, Jose Miguel Oliveira, Jorge M. Palmeirim, Joao Pargana, Anabela Paula, Joana Pauperio, Nuno M. Pedroso, Guilherme Pereira, Pedro F. Pereira, Jose Pereira, Maria Joao Ramos Pereira, Francisco Petrucci-Fonseca, Miguel Pimenta, Sara Pinto, Nuno Pinto, Rosa Pires, Ricardo Pita, Carlos Pontes, Marisa Quaresma, Joao Queiros, Luis Queiros, Ana Rainho, Maria da Graca Ramalhinho, Patricia Ramalho, Helena Raposeira, Francisco Rasteiro, Hugo Rebelo, Frederico Tata Regala, Dyana Reto, Sergio Bruno Ribeiro, Helena Rio-Maior, Ricardo Rocha, Rita Gomes Rocha, Luisa Rodrigues, Jacinto Roman, Sara Roque, Luis Miguel Rosalino, Ines T. do Rosario, Mariana Rossa, Danilo Russo, Pedro Sa, Helena Sabino-Marques, Vania Salgueiro, Helena Santos, Joana Santos, Joao P. V. Santos, Nuno Santos, Sara Santos, Carlos Pedro Santos, Margarida Santos-Reis, Ana Serronha, Pablo Sierra, Bruno Silva, Carla S. G. M. Silva, Clara Silva, Diogo Silva, Luis P. da Silva, Ricardo Silva, Carmen Silva, Flavio Manoel Rodrigues da Silva Junior, Pedro Sousa, Diana Sousa-Guedes, Giulia Spadoni, Joaquim T. Tapisso, Daniela Teixeira, Sergio Teixeira, Nuno Teixeira, Rita T. Torres, Paulo Travassos, Helia Vale-Goncalves, Nuno Cidraes-Vieira, Sophie von Merten, Maria da Luz Mathias

ECOLOGY (2022)

Article Paleontology

How to date a crocodile: estimation of neosuchian clade ages and a comparison of four time-scaling methods

Sebastian S. Groh, Paul Upchurch, Paul M. Barrett, Julia J. Day

Summary: The ages of clades within the crocodylomorph clade Neosuchia have been controversial. This study compared four time calibration methods to estimate clade ages based on morphological data. The results suggest that Neosuchia originated in the Late Triassic or Early Jurassic, with major extant eusuchian groups appearing by the end of the Late Cretaceous. The number of lineages before the K/Pg boundary remains uncertain. The study highlights the importance of understanding phylogenetic relationships, tree reconstruction methods, and taxonomic coverage in dating analyses.

PALAEONTOLOGY (2022)

Article Biochemistry & Molecular Biology

A near-complete species-level phylogeny of uropeltid snakes harnessing historical museum collections as a DNA source

Filipa L. Sampaio, Julia J. Day, L. J. Mendis Wickramasinghe, Vivek P. Cyriac, Anna Papadopoulou, Selina Brace, Albert Rajendran, Cornelia Simon-Nutbrown, Tomas Flouris, Paschalia Kapli, Dulan Ranga Vidanapathirana, Ramachandran Kotharambath, Ullasa Kodandaramaiah, David J. Gower

Summary: Uropeltidae is a clade of small snakes endemic to peninsular India and Sri Lanka. Through genome-wide shotgun sequencing and field sampling, a near-complete multilocus species-level phylogeny was established, supporting the monophyly of all genera and providing a platform for future taxonomic revision. The study also suggests that Sri Lankan uropeltids may have experienced a single colonization event and raises questions about the phylogenetic position of Rhinophis goweri.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2023)

Article Biochemistry & Molecular Biology

Exceptional levels of species discovery ameliorate inferences of the biogeography and diversification of an Afrotropical catfish family

Julia J. Day, Elizabeth M. Steell, Thomas R. Vigliotta, Lewis A. Withey, Roger Bills, John P. Friel, Martin J. Genner, Melanie L. J. Stiassny

Summary: The use of DNA molecular sequence data has greatly aided in the discovery of new species, particularly cryptic species. This study generated a species-level family tree of Afrotropical Mochokidae catfishes and discovered a large number of new species, particularly in the genus Chiloglanis. The results highlight the potential hotspot of undescribed and cryptic species diversity in fast-flowing lotic freshwaters, but emphasize the urgent need to explore and conserve the biodiversity of tropical freshwaters, as many freshwater fishes are currently threatened with extinction.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2023)

Article Ecology

Sympatric and allopatric Alcolapia soda lake cichlid species show similar levels of assortative mating

Michael R. M. Lawson, Michael G. B. Hayle, Asilatu H. Shechonge, Wanja Dorothy Nyingi, Antonia G. P. Ford, Joseph I. Hoffman, Julia J. Day, George F. Turner, Kanchon K. Dasmahapatra

Summary: Characterizing reproductive barriers within evolutionary radiations is crucial for understanding speciation. In this study, we focus on assortative mating among Alcolapia species, which are well-known for their adaptive radiations. We observed assortative mating both among the sympatric Natron species and between allopatric species from Natron and Magadi. However, a substantial proportion of disassortative matings was also found, indicating that additional reproductive barriers may contribute to genetic isolation in nature.

FRONTIERS IN ECOLOGY AND EVOLUTION (2023)

Article Developmental Biology

Exploring the Expression of Cardiac Regulators in a Vertebrate Extremophile: The Cichlid Fish Oreochromis (Alcolapia) alcalica

Gemma Sutton, Lewis J. White, Antonia G. P. Ford, Asilatu Shechonge, Julia J. Day, Kanchon K. Dasmahapatra, Mary E. Pownall

JOURNAL OF DEVELOPMENTAL BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Paraphyly and cryptic diversity unveils unexpected challenges in the naked lichens (Calvitimela, Lecanoromycetes, Ascomycota)

Markus Osaland Fjelde, Einar Timdal, Reidar Haugan, Mika Bendiksby

Summary: This study investigated the taxonomy of the crustose lichen genus Calvitimela using molecular phylogenetics and morphological observations. The results revealed evolutionarily old and deeply divergent lineages within Calvitimela, with overlapping morphological characters between different subgenera. Chemical characters were informative at the level of subgenera but often homoplastic at the species level. A practical taxonomy of Calvitimela was proposed based on these findings.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2024)

Article Biochemistry & Molecular Biology

Diversification of freshwater crabs on the sky islands in the Hengduan Mountains Region, China

Bo-Yang Shi, Da Pan, Kang-Qin Zhang, Tian-Yu Gu, Darren C. J. Yeo, Peter K. L. Ng, Neil Cumberlidge, Hong-Ying Sun

Summary: This study investigates the evolutionary history and speciation mechanisms of montane potamids in the Hengduan Mountains Region. The results suggest that the vicariance events of these crabs are correlated with the emergence of sky islands due to the uplift of the mountains. The mountain ridges provided corridors for their dispersal and past climatic conditions played a crucial role in their evolutionary history. The mechanisms isolating sky islands are reinforced by the climatic features of dry-hot valleys and continue to affect local diversification.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2024)

Article Biochemistry & Molecular Biology

Evolutionary history and systematics of European blind mole rats (Rodentia: Spalacidae: Nannospalax): Multilocus phylogeny and species delimitation in a puzzling group

Attila Nemeth, Edvard Mizsei, Levente Laczko, David Czaban, Zsolt Hegyeli, Szabolcs Lengyel, Gabor Csorba, Gabor Sramko

Summary: Species delimitation of European blind mole rats is challenging due to their small morphological differences and complex chromosomal evolution. This study provides a comprehensive framework to improve understanding of their evolutionary history and revise their taxonomy. The results reveal the presence of multiple superspecies and species, with distinct geographic patterns and rapid chromosomal evolution.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2024)

Article Biochemistry & Molecular Biology

Phylogenomic analyses reveal a single deep-water colonisation in Patellogastropoda

Ying Qi, Zhaoyan Zhong, Xu Liu, Xing He, Yadong Zhou, Lili Zhang, Chong Chen, Katrin Linse, Jian-Wen Qiu, Jin Sun

Summary: This study investigates the phylogenetic relationships among patellogastropod families using mitochondrial and phylogenomic data. The results show that the mitochondrial phylogeny recovers monophyly of most families, but the relationships among families are still contentious. However, a more robust family-level topology consistent with morphology is achieved by phylogenomics. Additionally, the mainly deep-water families are found to be monophyletic, suggesting a single colonization of the deep water during the Jurassic.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2024)

Article Biochemistry & Molecular Biology

A model of hybrid speciation process drawn from three new poplar species originating from distant hybridization between sections

Yu-Jie Shi, Jin -Liang Huang, Jia-Xuan Mi, Jing Li, Fan-Yu Meng, Yu Zhong, Fang He, Fei -Fei Tian, Fan Zhang, Liang-Hua Chen, Han-Bo Yang, Hong-Lin Hu, Xue-Qin Wan

Summary: Despite numerous studies on hybrid speciation, our understanding of this process remains limited. In this study, we conducted an 18-year systematic investigation on Populus taxa on the Qinghai-Tibet Plateau and discovered three new taxa that originated from distant hybridization between two different sections. These hybrid taxa demonstrate greater ecological adaptability than their ancestral species due to heterosis. We propose a hybrid speciation process model that can explain important evolutionary concerns.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2024)

Article Biochemistry & Molecular Biology

Phylogenomic position of genetically diverse phagotrophic stramenopile flagellates in the sediment-associated MAST-6 lineage and a potentially halotolerant placididean

Anna Cho, Denis Tikhonenkov, Gordon Lax, Kristina I. Prokina, Patrick J. Keeling

Summary: Unlike conspicuous ochrophytes, many small and overlooked flagellates belonging to basally branching stramenopiles remain poorly characterized at the cellular or genomic level. This study describes four new species, including two new genera, of sediment-dwelling MAST-6 and provides updated phylogenomic tree of stramenopiles. The characterization of these flagellates is important due to their phylogenetic diversity and abundance in various environments.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2024)

Article Biochemistry & Molecular Biology

Phylogenomic conflict analyses of the plastid and mitochondrial genomes via deep genome skimming highlight their independent evolutionary histories: A case study in the cinquefoil genus Potentilla sensu lato (Potentilleae, Rosaceae)

Tian-Tian Xue, Steven B. Janssens, Bin-Bin Liu, Sheng-Xiang Yu

Summary: Phylogenomic conflicts are widespread among genomic data, with most previous studies primarily focusing on nuclear datasets instead of organellar genomes. In this study, we investigated the phylogenetic conflicts within and between plastid and mitochondrial genomes using Potentilla as a case study. We found that both plastid and mitochondrial genomes divided Potentilla into eight highly supported clades, with two newly identified clades. Our results demonstrate that mitochondrial genes can fully resolve phylogenetic relationships among major clades of Potentilla and are not always linked with plastomes in evolutionary history.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2024)

Article Biochemistry & Molecular Biology

Co-phylogeny of a hyper-symbiotic system: Endosymbiotic bacteria (Gammaproteobacteria), chewing lice (Insecta: Phthiraptera) and birds (Passeriformes)

Alexandra A. Grossi, Chunpo Tian, Mengjiao Ren, Fasheng Zou, Daniel R. Gustafsson

Summary: This study suggests that the coevolutionary relationships between chewing lice, endosymbiotic bacteria, and birds are not independent, but the patterns vary depending on the analysis method used. Additionally, louse host-switching does not seem to affect bacterial strains.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2024)

Article Biochemistry & Molecular Biology

Hyper-Cryptic radiation of a tropical montane plant lineage

Ingrid Olivares, Sergio Tusso, Maria Jose Sanin, Marylaure de La Harpe, Oriane Loiseau, Jonathan Rolland, Nicolas Salamin, Michael Kessler, Kentaro K. Shimizu, Margot Paris

Summary: Traditionally, differences between species have been associated with morphological variation. However, the discovery of cryptic diversity suggests that the evolution of distinct lineages can occur without morphological differences. Through genetic analysis, we found that a tropical montane plant lineage is composed of numerous unrecognized genetic groups that are not morphologically distinct. Geographic distance and topography play a crucial role in determining the genetic divergence of these groups.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2024)