Article
Zoology
Mariana Neves Moura, Danon Clemes Cardoso, Maykon Passos Cristiano
Summary: The study estimated genome sizes of 99 ant species, with the mean GS of Formicidae being 0.38 pg and an AT/GC ratio of 62.40/37.60. Phylogenetic reconstruction indicated significant differences in GS between subfamilies sampled. The evolution of GS in Formicidae was suggested to occur through loss and accumulation of non-coding regions, mainly transposable elements, and occasionally by whole genome duplication.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2021)
Article
Biochemical Research Methods
Milos Musil, Rayyan Tariq Khan, Andy Beier, Jan Stourac, Hannes Konegger, Jiri Damborsky, David Bednar
Summary: Researchers are increasingly interested in improving the stability of proteins, and ancestral sequence reconstruction has been proven to be an effective method for designing stable proteins. FireProt(ASR) offers a fully automated workflow to help users obtain ancestral sequences based on just a sequence query.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biology
Xiao-Qian Li, Xiao-Guo Xiang, Qiang Zhang, Florian Jabbour, Rosa del C. Ortiz, Andrey S. Erst, Zhen-Yu Li, Wei Wang
Summary: This study investigates the immigration dynamics of tropical and subtropical Southeast Asian karst floras using Gesneriaceae as a proxy. The study reveals the timing and locations of immigration into these regions, with peak periods occurring in the Early Miocene and Late Eocene. The research also highlights the presence of immigrant pre-adapted lineages and descendants from local acid soil ancestors in Southeast Asian karst biodiversity. This study advances our understanding of the historical assembly of Southeast Asian karst floras.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Microbiology
Jin-Chen Li, Hai-Xia Wu, Yuying Li, Xin-Hao Li, Jia-Yu Song, Nakarin Suwannarach, Nalin N. Wijayawardene
Summary: The members of Phyllachora are biotrophic, obligate plant parasitic fungi with a high degree of host specificity and species richness. This study discovered four new species in Shanxi and Shaanxi Provinces, China, and analyzed their morphology, genetics, and host relationships.
Article
Biochemistry & Molecular Biology
Huan-Wen Peng, Kun-Li Xiang, Andrey S. Erst, Tatyana V. Erst, Florian Jabbour, Rosa Del C. Ortiz, Wei Wang
Summary: This study provides a comprehensive analysis of the diversification patterns in the subfamily Fumarioideae of the Papaveraceae family. The results suggest that the subfamily originated in Asia during the Late Cretaceous and dispersed to other regions in the Cenozoic era. The study also identifies two periods of rapid diversification in certain species, which coincided with changes in habitat and life history.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Patrick C. F. Buchholz, Bert van Loo, Bernard D. G. Eenink, Erich Bornberg-Bauer, Juergen Pleiss
Summary: Protein family evolutionary relationships can be characterized either by networks or by trees. Ancestral protein sequences in networks act as bridges and share close similarity with extant sequences. Some reconstructed ancestor sequences can also be interpreted as yet-to-be-identified homologues or consensus sequences.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2021)
Article
Microbiology
Fernando Javier Ureta Suelgaray, Viviana Monica Chiocchio, Federico Ciolfi, Mario Carlos Nazareno Saparrat
Summary: Dark septate endophytes (DSE) are pigmented fungi that colonize plant roots and have a key position in the evolution of the order Chaetothyriales. The order has representatives with diverse lifestyles, but all taxa have the phenotypic characteristic of being highly melanized, which allows them to tolerate extreme or toxic environmental conditions. This study analyzes the contribution of the DSE habit to the diversification of Chaetothyriales and reports its distribution among the main families and/or clades within the order.
ARCHIVES OF MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Hiroki Kise, Maria Eduarda Alves Santos, Chloe Julie Lois Fourreau, Akira Iguchi, Ryutaro Goto, James Davis Reimer
Summary: Symbioses play important roles in forming marine diversity, and understanding how interspecies interactions through symbioses contribute to biodiversity is essential. Host switching is considered a main driver of diversification in symbiotic systems, but its process and patterns in the marine realm are poorly investigated. This study provides insight into the patterns of host switching and the diversification history of zoantharians, highlighting the role of symbioses in the morphological and ecological evolution of marine invertebrates.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Teiji Sota, Yasuoki Takami, Hiroshi Ikeda, Hongbin Liang, Gayane Karagyan, Clarke Scholtz, Michio Hori
Summary: Carabinae beetles, a group of flightless underground insects, are widely distributed on all continents except Antarctica. Through DNA analysis, researchers have found that Carabinae originated in the Americas and diversified into four tribes. The ancestral Carabinae had wings, but three of the tribes lost their wings and flight capability during evolution. The study also revealed a higher speciation rate of Carabinae in Eurasia.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Plant Sciences
Raul Ernesto Pozner, Leigh A. Johnson, Silvia Suyai Denham
Summary: Calyceraceae, a small South American family sister to Asteraceae, has been taxonomically rearranged into eight genera based on phylogenetic analyses. Flower morphology is diverse but provides limited diagnostic features, reflecting likely selection for pollination or fruit dispersal rather than phylogenetic affinity.
Article
Zoology
Dennis Hazerli, Christoph Gert Hoepel, Stefan Richter
Summary: Portunoidea is a taxonomic group of true crabs known for their swimming ability. This study combines molecular and morphological data to determine the phylogenetic positioning of some members of Portunoidea. The researchers found that the morphology of swimming crabs is more diverse than previously believed. The ancestral state reconstruction suggests that the swimming crab morphology appeared in the ancestors of Portunoidea, but with less effective swimming compared to the current species. Some extant species have reversed the swimming crab morphology.
FRONTIERS IN ZOOLOGY
(2022)
Article
Biodiversity Conservation
Jenny A. Hodgson, Zoe Randle, Chris R. Shortall, Tom H. Oliver
Summary: There is little empirical evidence on how the configuration of habitat affects expansion at species' cool range margins. This study analyzed colonization events of southerly distributed moths in Britain and found that habitat configuration influences contemporary range shifts. Woodland species' colonization was predicted by woodland habitat conductance, regardless of dispersal distances and habitat needs. For species associated with farmland or suburban habitats, colonization was slower in landscapes with high variance in elevation and/or temperature.
GLOBAL CHANGE BIOLOGY
(2022)
Article
Agriculture, Multidisciplinary
Thomas Fartmann, Dominik Poniatowski, Lisa Holtmann
Summary: Land use change and climate warming are the major drivers of shifts in grasshopper assemblages in the agricultural landscape of NW-German Lowland. Loss of grassland patches due to cultivation of maize has led to landscape homogenization, while grassland verges are becoming increasingly important as both dispersal corridors and refuges for biodiversity.
AGRICULTURE ECOSYSTEMS & ENVIRONMENT
(2021)
Article
Microbiology
Yanmei Wang, Jia Feng, Junping Lv, Qi Liu, Fangru Nan, Xudong Liu, Shulian Xie
Summary: This study constructed a phylogenetic tree of green euglenophytes based on the 18S rRNA gene, reconstructed ancestral states, clarified the phylogenetic relationships of green euglenophytes, and provided a basis for the study of the origin of these plants.
JOURNAL OF EUKARYOTIC MICROBIOLOGY
(2021)
Article
Ecology
Mark J. McKone, Daniel L. Hernandez
Summary: Climate change poses a threat to highly fragmented habitats like North American tallgrass prairie. To address this, it is recommended to incorporate assisted migration into new prairie plantings, introducing species that can adapt to changing climates to increase biodiversity. Based on future climate projections, the species richness of future prairie plantings in Minnesota could be significantly enhanced.
RESTORATION ECOLOGY
(2021)
Correction
Multidisciplinary Sciences
Quentin Carradec, Julie Poulain, Emilie Boissin, Benjamin C. C. Hume, Christian R. Voolstra, Maren Ziegler, Stefan Engelen, Corinne Cruaud, Serge Planes, Patrick Wincker
Summary: The paper has been amended and the revised version can be accessed through a link at the top of the paper.
SCIENTIFIC REPORTS
(2021)
Article
Ecology
Danielle Davenport, Paul Butcher, Sara Andreotti, Conrad Matthee, Andrew Jones, Jennifer Ovenden
Summary: Monitoring breeding population size of white sharks in east Australia-New Zealand over a few years shows stable and comparable effective breeding number values using genetic estimators, providing insight into conservation effectiveness.
ECOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Lauric Reynes, Thierry Thibaut, Stephane Mauger, Aurelie Blanfune, Florian Holon, Corinne Cruaud, Arnaud Couloux, Myriam Valero, Didier Aurelle
Summary: The study identified genomic signatures of partial clonality in the deep water kelp species Laminaria rodriguezii and compared them with a closely related species Laminaria digitata. The findings showed distinct genetic distributions and different impacts of clonality and genetic drift on population diversity. These results provide insights into the genetic study of asexuality in natural populations and highlight potential applications of RAD-sequencing in investigating partial clonality in various non-model species.
Article
Biology
Elise J. Gay, Jessica L. Soyer, Nicolas Lapalu, Juliette Linglin, Isabelle Fudal, Corinne Da Silva, Patrick Wincker, Jean-Marc Aury, Corinne Cruaud, Anne Levrel, Jocelyne Lemoine, Regine Delourme, Thierry Rouxel, Marie-Helene Balesdent
Summary: This study analyzed the gene expression at different stages of the interaction between Leptosphaeria maculans and Brassica napus, revealing that about 9% of the fungus genes are highly expressed during interactions with the host plant. These highly expressed genes are distributed into eight clusters, enriched in effector genes, with one cluster specific to the saprophytic lifestyle. The study suggests that genes involved in niche adaptation may be located in heterochromatic regions of the genome, providing a plasticity of expression that could be targeted for plant disease control.
Article
Multidisciplinary Sciences
Francisco Latorre, Ina M. Deutschmann, Aurelie Labarre, Aleix Obiol, Anders K. Krabberod, Eric Pelletier, Michael E. Sieracki, Corinne Cruaud, Olivier Jaillon, Ramon Massana, Ramiro Logares
Summary: The research reveals significant differences in distribution and genomic content among the oceanic unicellular eukaryotic predator MAST-4, suggesting potential correlation with adaptation to temperature and prey type.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Fisheries
Robin S. Waples, Pierre Feutry
Summary: Research has found that genetic methods and close-kin mark-recapture methods differ in estimating population size, but combining the two can provide a better assessment of both ecological and evolutionary processes.
FISH AND FISHERIES
(2022)
Article
Biochemistry & Molecular Biology
Belen Jimenez-Mena, Hugo Flavio, Romina Henriques, Alice Manuzzi, Miguel Ramos, Dorte Meldrup, Janette Edson, Snaebjorn Palsson, Gudbjorg Asta Olafsdottir, Jennifer R. Ovenden, Einar Eg Nielsen
Summary: This research presents specific guidelines and considerations for designing capture sequencing experiments for population genetics, focusing on neutral genomic regions and regions subject to selection. The bait design process for three fish species was described, and the performance of the approach was evaluated across historical and modern samples. The supeRbaits R-package, which implements the workflow used for designing the bait sets, is user-friendly and versatile.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Genetics & Heredity
Chen Wang, Tinghe Lai, Peiyuan Ye, Yunrong Yan, Pierre Feutry, Binyuan He, Zhongjian Huang, Ting Zhu, Junjie Wang, Xiao Chen
Summary: In this study, the complete mitogenome of the Japanese topeshark was determined for the first time, revealing a novel non-coding region and gene rearrangements. Phylogenetic analysis based on mitogenomic data provided further insights into the evolution and phylogeny of shark mitogenomes.
Article
Fisheries
Giulia Anderson, Jed Macdonald, Joanne Potts, Pierre Feutry, Peter M. Grewe, Marion Boutigny, Campbell R. Davies, Jeff A. Muir, Francois Roupsard, Caroline Sanchez, Simon J. Nicol
Summary: Cross-contamination is a widespread issue in genetics and genomics, especially in the context of managing marine resources using molecular methods. An experiment on wild-caught bigeye tuna was conducted to assess cross-contamination risk under different tissue sampling treatments. Adjustments to current tissue sampling protocols were shown to significantly reduce cross-contamination risk for downstream genetic analyses on tunas and potentially on other species and fisheries.
ICES JOURNAL OF MARINE SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Natacha Nikolic, Floriaan Devloo-Delva, Diane Bailleul, Ekaterina Noskova, Clement Rougeux, Chrystelle Delord, Philippe Borsa, Cathy Liautard-Haag, Mohamad Hassan, Amandine D. Marie, Pierre Feutry, Peter Grewe, Campbell Davies, Jessica Farley, Daniel Fernando, Sebastian Biton-Porsmoguer, Francois Poisson, Denham Parker, Agostino Leone, Jorden Aulich, Matt Lansdell, Francis Marsac, Sophie Arnaud-Haond
Summary: The blue shark is a widely distributed top predator, classified as Critically Endangered in the Mediterranean Sea and Near Threatened globally. Genetic studies have previously suggested a single global population. However, this study used a genome-wide approach and revealed two main groups, the Mediterranean Sea and northern Atlantic samples differentiated from Indo-west Pacific samples. Within the Atlantic Ocean, further genetic differentiation was observed, as well as between the Atlantic Ocean and the Mediterranean Sea. The results highlight the importance of considering genetic population structure and demographic history in the management and conservation strategies of the blue shark.
Article
Multidisciplinary Sciences
Toby A. Patterson, Richard M. Hillary, Peter M. Kyne, Richard D. Pillans, Rasanthi M. Gunasekera, James R. Marthick, Grant J. Johnson, Pierre Feutry
Summary: By using sibling pairs, the abundance and connectivity of adult sharks in two river systems in Australia were estimated. The results showed male philopatry in the Adelaide River and high connectivity of males in the Alligator Rivers with the Adelaide River. This method allows simultaneous assessment of abundance and connectivity in rare and threatened species.
Article
Evolutionary Biology
Luke R. Lloyd-Jones, Matthew L. Brien, Pierre Feutry, Emma Lawrence, Paul Beri, Simon Booth, Steven Coulson, Shane M. Baylis, Kira Villiers, Laurence E. Taplin, David A. Westcott
Summary: Effective management of protected species requires understanding of appropriate evolutionary and geographic population boundaries, as well as knowledge of how the physical environment and life-history traits shape population structure and connectivity. A study on saltwater crocodiles in Queensland, Australia revealed significant genetic structure with six broad populations correlated with geographical location. Gene flow was found to be higher along the east coast compared to the west, indicating limited dispersal and reproductive philopatry. Management and conservation interventions should be considered at regional and state-wide scales due to limited dispersal, lack of suitable habitat, low crocodile densities, and a high proportion of immature individuals.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Ecology
Floriaan Devloo-Delva, Christopher P. Burridge, Peter M. Kyne, Juerg M. Brunnschweiler, Demian D. Chapman, Patricia Charvet, Xiao Chen, Geremy Cliff, Ryan Daly, J. Marcus Drymon, Mario Espinoza, Daniel Fernando, Laura Garcia Barcia, Kerstin Glaus, Blanca I. Gonzalez-Garza, Michael I. Grant, Rasanthi M. Gunasekera, Sebastian Hernandez, Susumu Hyodo, Rima W. Jabado, Sebastien Jaquemet, Grant Johnson, James T. Ketchum, Helene Magalon, James R. Marthick, Frederik H. Mollen, Stefano Mona, Gavin J. P. Naylor, John E. G. Nevill, Nicole M. Phillips, Richard D. Pillans, Bautisse D. Postaire, Amy F. Smoothey, Katsunori Tachihara, Bree J. Tillet, Jorge A. Valerio-Vargas, Pierre Feutry
Summary: In this study, the population structure of the Bull Shark was assessed globally for the first time. The results revealed reproductive isolation between and across ocean basins, with distinct island populations in Japan and Fiji. The Bull Sharks maintain gene flow through shallow coastal waters as dispersal corridors, but large oceanic distances and historical land-bridges act as barriers. Protecting these insular populations of Bull Sharks is crucial for ecosystem stability and functioning.
ECOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Luke R. R. Lloyd-Jones, Mark V. V. Bravington, Kyle N. N. Armstrong, Emma Lawrence, Pierre Feutry, Christopher M. M. Todd, Annabel Dorrestein, Justin A. A. Welbergen, John M. M. Martin, Karrie Rose, Jane Hall, David N. N. Phalen, Isabel Peters, Shane M. M. Baylis, Nicholas A. A. Macgregor, David A. A. Westcott
Summary: Reliable population size information is crucial for managing threatened species. In this study, we applied the close-kin mark-recapture method to estimate the abundance of the critically endangered Christmas Island flying-fox (CIFF). Our findings provide the most robust understanding of the CIFF population status and have important implications for conservation initiatives.
SCIENTIFIC REPORTS
(2023)
Article
Microbiology
Shi-Zhen Wang, Corinne Cruaud, Jean-Marc Aury, David Vallenet, Julie Poulain, Benoit Vacherie, Anne Zaparucha, Carine Vergne-Vaxelaire
Summary: Pseudomonas marincola YsY11 and Pseudomonas oleovorans T9AD were isolated from marine environments in the Pacific Ocean, and their whole-genome sequences were reported. YsY11 has a single 4.77 Mb chromosome, while T9AD has a 5.57 Mb chromosome and a 2.8 kb plasmid.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
