UCE phylogenomics, biogeography, and classification of long-horned bees (Hymenoptera: Apidae: Eucerini), with insights on using specimens with extremely degraded DNA
Freitas, Felipe V; Branstetter, Michael G; Franceschini-Santos, Vinícius Het al.
CURE; ddBD; MCMCtree; museomics; UCE curation; Ecology, Evolution, Behavior and Systematics; Animal Science and Zoology; Developmental Biology; Insect Science
Abstract :
[en] Long-horned bees (Apidae, Eucerini) are found in different biomes worldwide and include some important crop pollinators. In the Western Hemisphere, Eucerini received extensive taxonomic study during the twentieth century, resulting in several revisions of its genera. In contrast, progress on eucerine phylogenetic research and the genus-level classification has been slow, primarily due to the relatively homogeneous external morphology within the tribe and the rarity of many of its species in collections. Here, we present a comprehensive phylogenetic study of Eucerini based on ultraconserved elements, including 153 species from nearly all genera and subgenera and from all biogeographic regions where they occur. Many of these specimens are from museums and were collected as far back as 1909. We discuss the challenges of working with specimens with highly degraded DNA, present insights into improving phylogenetic results for both species-tree and concatenation approaches, and present a new pipeline for UCE curation (Curation of UltraconseRved Elements - CURE). Our results show the existence of seven main lineages in Eucerini and most of the genera and subgenera to be reciprocally monophyletic. Using a comprehensive and up-to-date phylogenetic framework, we: (1) propose taxonomic changes, including a new subtribal classification and reorganized generic and subgeneric limits; (2) estimate divergence times; and (3) conduct a detailed exploration of historical biogeography of long-horned bees. We find that eucerine lineages expanded their range onto most continents only after their initial diversification in southern South America during the Eocene.
Disciplines :
Entomology & pest control
Author, co-author :
Freitas, Felipe V ; Laboratório de Biologia Comparada e Abelhas (LBCA), Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras, Universidade de São Paulo, Ribeirão Preto, Brazil ; U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pollinating Insects Research Unit, Utah State University, Logan, United States ; Departamento de Ciências Biológicas, Instituto de Biociências, Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista 'Júlio de Mesquita Filho' (UNESP), Brazil ; Department of Entomology, Washington State University, Pullman, United States
Branstetter, Michael G ; U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pollinating Insects Research Unit, Utah State University, Logan, United States
Franceschini-Santos, Vinícius H ; Laboratório de Biologia Comparada e Abelhas (LBCA), Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras, Universidade de São Paulo, Ribeirão Preto, Brazil ; Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
Dorchin, Achik ; Université de Mons - UMONS > Faculté des Sciences > Service de Zoologie ; Department of Biology - Invertebrates, Royal Museum for Central Africa, Tervuren, Belgium
Wright, Karen W; Plant Protection Division, Washington State Department of Agriculture, Yakima, United States ; Sevilleta Long-Term Ecological Research, University of New Mexico, Albuquerque, United States
López-Uribe, Margarita M ; Department of Entomology, The Pennsylvania State University, University Park, United States
Griswold, Terry; U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pollinating Insects Research Unit, Utah State University, Logan, United States
Silveira, Fernando A; Laboratório de Sistemática de Insetos, Departamento de Zoologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
Almeida, Eduardo A. B ; Laboratório de Biologia Comparada e Abelhas (LBCA), Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras, Universidade de São Paulo, Ribeirão Preto, Brazil
Language :
English
Title :
UCE phylogenomics, biogeography, and classification of long-horned bees (Hymenoptera: Apidae: Eucerini), with insights on using specimens with extremely degraded DNA
This article is dedicated to Professor Fernando A. Silveira, mentor of the junior and senior authors. Fernando had an active role in the development of this research, especially in the proposal of a revised subtribal classification of Eucerini, but sadly passed away months before the submission of the manuscript. We are grateful to Antonio J. C. Aguiar (Universidade de Brasília, Brazil), Christophe Praz (Université de Neuchâtel, Switzerland), Jerome G. Rozen Jr. (American Museum of Natural History, USA), Carlos Roberto F. Brandão (Museu de Zoologia da Universidade de São Paulo, Brazil), Laurence Packer (York University, Canada), Maximilian Schwarz (Ansfelden, Austria), and Seán G. Brady (US National Museum of Natural History—Smithsonian Institution, USA) for generously providing specimens or tissue samples, essential for our broad taxonomic sampling. We are thankful to Gabriel A.R. Melo for kindly discussing some key aspects of the taxonomy of Neotropical Eucerini, and to three anonymous reviewers and the associate editor of Insect Systematics and Diversity, Jessica Gillung, for their valuable suggestions that helped improve the manuscript. We are grateful to Adriana Tiba, Julio Pupin, Laurence Packer, Sergio Jansen-Gonzalez, Javier Gross, and Shan Gui for allowing the use of their beautiful photographs of eucerine bee. This study was supported by USDA-ARS, and NSF (Project No. 2080-21000-019-00-D, and grant DEB-2127744, respectively) to M.G.B.; by grants #2018/09666-5, #2019/09215-6, and #2021/02196-6, São Paulo Research Foundation (FAPESP) to E.A.B.A. and F.V.F.; by the Brazilian National Council for Scientific and Technological Development (CNPq grants #310111/2019-6 and #422019/2018-6) to E.A.B.A. and F.V.F.; and by Coordenacão de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)—Brazil (Finance Code 001). USDA is an equal opportunity provider and employer.
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