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Dagallier LPMJ, Condamine FL, Couvreur TLP. Sequential diversification with Miocene extinction and Pliocene speciation linked to mountain uplift explains the diversity of the African rain forest clade Monodoreae (Annonaceae). ANNALS OF BOTANY 2024; 133:677-696. [PMID: 37659091 PMCID: PMC11082524 DOI: 10.1093/aob/mcad130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/29/2023] [Indexed: 09/04/2023]
Abstract
BACKGROUND AND AIMS Throughout the Cenozoic, Africa underwent several climatic and geological changes impacting the evolution of tropical rain forests (TRFs). African TRFs are thought to have extended from east to west in a 'pan-African' TRF, followed by several events of fragmentation during drier climate periods. During the Miocene, climate cooling and mountain uplift led to the aridification of tropical Africa and open habitats expanded at the expense of TRFs, which probably experienced local extinctions. However, in plants, these drivers were previously inferred using limited taxonomic and molecular data. Here, we tested the impact of climate and geological changes on diversification within the diverse clade Monodoreae (Annonaceae) composed of 90 tree species restricted to African TRFs. METHODS We reconstructed a near-complete phylogenetic tree, based on 32 nuclear genes, and dated using relaxed clocks and fossil calibrations in a Bayesian framework. We inferred the biogeographical history and the diversification dynamics of the clade using multiple birth-death models. KEY RESULTS Monodoreae originated in East African TRFs ~25 million years ago (Ma) and expanded toward Central Africa during the Miocene. We inferred range contractions during the middle Miocene and document important connections between East and West African TRFs after 15-13 Ma. Our results indicated a sudden extinction event during the late Miocene, followed by an increase in speciation rates. Birth-death models suggested that African elevation change (orogeny) is positively linked to speciation in this clade. CONCLUSION East Africa is inferred as an important source of Monodoreae species, and possibly for African plant diversity in general. Our results support a 'sequential scenario of diversification' in which increased aridification triggered extinction of TRF species in Monodoreae. This was quickly followed by fragmentation of rain forests, subsequently enhancing lagged speciation resulting from vicariance and improved climate conditions. In contrast to previous ideas, the uplift of East Africa is shown to have played a positive role in Monodoreae diversification.
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Affiliation(s)
- Léo-Paul M J Dagallier
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY 10458, USA
| | - Fabien L Condamine
- CNRS, Institut des Sciences de l’Evolution de Montpellier (Université de Montpellier), Place Eugène Bataillon, 34095 Montpellier, France
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2
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McCabe LM, Chesshire P, Cobb NS. Forest habitats and plant communities strongly predicts Megachilidae bee biodiversity. PeerJ 2023; 11:e16145. [PMID: 37904844 PMCID: PMC10613436 DOI: 10.7717/peerj.16145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/30/2023] [Indexed: 11/01/2023] Open
Abstract
Megachilidae is one of the United States' most diverse bee families, with 667 described species in 19 genera. Unlike other bee families, which are primarily ground nesters, most megachilid bees require biotic cavities for nesting (i.e., wood, pithy stems, etc.). For this group, the availability of woody-plant species may be as important as nectar/pollen resources in maintaining populations. We studied Megachilidae biodiversity in the continental United States. We confirmed that the highest species richness of Megachilidae was in the southwestern United States. We examined the relationship between species richness and climate, land cover, tree species richness, and flowering plant diversity. When examining environmental predictors across the conterminous United States, we found that forested habitats, but not tree diversity, strongly predicted Megachilidae richness. Additionally, Megachilidae richness was highest in areas with high temperature and low precipitation, however this was not linearly correlated and strongly positively correlated with flowering plant diversity. Our research suggests that the availability of nesting substrate (forested habitats), and not only flowering plants, is particularly important for these cavity-nesting species. Since trees and forested areas are particularly susceptible to climate change, including effects of drought, fire, and infestations, nesting substrates could become a potential limiting resource for Megachilidae populations.
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Affiliation(s)
- Lindsie M. McCabe
- USDA-ARS Pollinating Insects Research Unit, Logan, Utah, United States
- Department of Biological Science, Northern Arizona University, Flagstaff, Arizona, United States
| | - Paige Chesshire
- Department of Biological Science, Northern Arizona University, Flagstaff, Arizona, United States
| | - Neil S. Cobb
- Biodiversity Outreach Network, Flagstaff, AZ, United States
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3
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Labandeira CC, Wappler T. Arthropod and Pathogen Damage on Fossil and Modern Plants: Exploring the Origins and Evolution of Herbivory on Land. ANNUAL REVIEW OF ENTOMOLOGY 2023; 68:341-361. [PMID: 36689301 DOI: 10.1146/annurev-ento-120120-102849] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The use of the functional feeding group-damage type system for analyzing arthropod and pathogen interactions with plants has transformed our understanding of herbivory in fossil plant assemblages by providing data, analyses, and interpretation of the local, regional, and global patterns of a 420-Myr history. The early fossil record can be used to answer major questions about the oldest evidence for herbivory, the early emergence of herbivore associations on land plants, and later expansion on seed plants. The subsequent effects of the Permian-Triassic ecological crisis on herbivore diversity, the resulting formation of biologically diverse herbivore communities on gymnosperms, and major shifts in herbivory ensuing from initial angiosperm diversification are additional issues that need to be addressed. Studies ofherbivory resulting from more recent transient spikes and longer-term climate trends provide important data that are applied to current global change and include herbivore community responses to latitude, altitude, and habitat. Ongoing paleoecological themes remaining to be addressed include the antiquity of modern interactions, differential herbivory between ferns and angiosperms, and origins of modern tropical forests. The expansion of databases that include a multitude of specimens; improvements in sampling strategies; development of new analytical methods; and, importantly, the ability to address conceptually stimulating ecological and evolutionary questions have provided new impetus in this rapidly advancing field.
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Affiliation(s)
- Conrad C Labandeira
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA;
- Department of Entomology, University of Maryland, College Park, Maryland, USA
- College of Life Sciences and Academy for Multidisciplinary Studies, Capital Normal University, Beijing, China
| | - Torsten Wappler
- Natural History Department, Hessisches Landesmuseum, Darmstadt, Germany;
- Paleontology Section, Institute of Geosciences, Rheinische Friedrich-Wilhelms Universität Bonn, Bonn, Germany
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4
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Haran J, Procheş Ş, Benoit L, Kergoat GJ. From monocots to dicots: host shifts in Afrotropical derelomine weevils shed light on the evolution of non-obligatory brood pollination mutualism. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Weevils from the tribe Derelomini (Curculionidae: Curculioninae) are specialized brood pollinators engaged in mutualistic relationships with several angiosperm lineages. In brood pollination systems, reproductive plant tissues are used for the development of insect larval stages, whereas adult insects pollinate their plant hosts as a reward. The evolutionary history of derelomines in relationship to their hosts is poorly understood and potentially contrasts with other brood pollination systems, wherein a pollinator lineage is usually associated with a single host plant family. In the case of Afrotropical Derelomini, host records indicate a diverse host repertoire consisting of several families of monocot and dicot plants. In this study, we investigate their phylogenetic relationships, timing of diversification and evolution of host use. Our results suggest that derelomine lineages started their diversification ~40 Mya. Reconstructions of host use evolution support an ancestral association with the monocotyledonous palm family (Arecaceae), followed by several shifts towards other plant families in Afrotropical lineages, especially to dicotyledonous plants from the family Ebenaceae (on the genus Euclea L.). Some level of phylogenetic conservatism of host use is recovered for the lineages associated with either palms or Euclea. Multiple instances of sympatric weevil assemblages on the same plant are also unravelled, corresponding to either single or independent colonization events. Overall, the diversity of hosts colonized and the frequency of sympatric assemblages highlighted in non-obligatory plant–derelomine brood pollination systems contrast with what is generally expected from plant–insect brood pollination systems.
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Affiliation(s)
- Julien Haran
- CBGP, CIRAD, INRAE, IRD, Institut Agro, Univ. Montpellier , Montpellier , France
| | - Şerban Procheş
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal , Durban , South Africa
| | - Laure Benoit
- CBGP, CIRAD, INRAE, IRD, Institut Agro, Univ. Montpellier , Montpellier , France
| | - Gael J Kergoat
- CBGP, INRAE, CIRAD, IRD, Montpellier Institut Agro, Univ. Montpellier , Montpellier , France
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5
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Davis RB, Õunap E, Tammaru T. A supertree of Northern European macromoths. PLoS One 2022; 17:e0264211. [PMID: 35180261 PMCID: PMC8856531 DOI: 10.1371/journal.pone.0264211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/05/2022] [Indexed: 11/19/2022] Open
Abstract
Ecological and life-history data on the Northern European macromoth (Lepidoptera: Macroheterocera) fauna is widely available and ideal for use in answering phylogeny-based research questions: for example, in comparative biology. However, phylogenetic information for such studies lags behind. Here, as a synthesis of all currently available phylogenetic information on the group, we produce a supertree of 114 Northern European macromoth genera (in four superfamilies, with Geometroidea considered separately), providing the most complete phylogenetic picture of this fauna available to date. In doing so, we assess those parts of the phylogeny that are well resolved and those that are uncertain. Furthermore, we identify those genera for which phylogenetic information is currently too poor to include in such a supertree, or entirely absent, as targets for future work. As an aid to studies involving these genera, we provide information on their likely positions within the macromoth tree. With phylogenies playing an ever more important role in the field, this supertree should be useful in informing future ecological and evolutionary studies.
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Affiliation(s)
- Robert B. Davis
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Erki Õunap
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Toomas Tammaru
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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6
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St Laurent RA, Carvalho APS, Earl C, Kawahara AY. Food Plant Shifts Drive the Diversification of Sack-Bearer Moths. Am Nat 2021; 198:E170-E184. [PMID: 34648399 DOI: 10.1086/716661] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractLepidoptera are a highly diverse group of herbivorous insects; however, some superfamilies have relatively few species. Two alternative hypotheses for drivers of Lepidoptera diversity are shifts in food plant use or shifts from concealed to external feeding as larvae. Many studies address the former hypothesis but with bias toward externally feeding taxa. One of the most striking examples of species disparity between sister lineages in Lepidoptera is between the concealed-feeding sack-bearer moths (Mimallonoidea), which contain about 300 species, and externally feeding Macroheterocera, which have over 74,000 species. We provide the first dated tree of Mimallonidae to understand the diversification dynamics of these moths in order to fill a knowledge gap pertaining to drivers of diversity within an important concealed-feeding clade. We find that Mimallonidae is an ancient Lepidoptera lineage that originated in the Cretaceous ∼105 million years ago and has had a close association with the plant order Myrtales for the past 40 million years. Diversification dynamics are tightly linked with food plant usage in this group. Reliance on Myrtales may have influenced diversification of Mimallonidae because clades that shifted away from the ancestral condition of feeding on Myrtales have the highest speciation rates in the family.
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Aduse-Poku K, van Bergen E, Sáfián S, Collins SC, Etienne RS, Herrera-Alsina L, Brakefield PM, Brattström O, Lohman DJ, Wahlberg N. Miocene Climate and Habitat Change Drove Diversification in Bicyclus, Africa's Largest Radiation of Satyrine Butterflies. Syst Biol 2021; 71:570-588. [PMID: 34363477 PMCID: PMC9016770 DOI: 10.1093/sysbio/syab066] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/02/2021] [Accepted: 08/04/2021] [Indexed: 11/14/2022] Open
Abstract
Compared to other regions, the drivers of diversification in Africa are poorly understood. We studied a radiation of insects with over 100 species occurring in a wide range of habitats across the Afrotropics to investigate the fundamental evolutionary processes and geological events that generate and maintain patterns of species richness on the continent. By investigating the evolutionary history of Bicyclus butterflies within a phylogenetic framework, we inferred the group's origin at the Oligo-Miocene boundary from ancestors in the Congolian rainforests of central Africa. Abrupt climatic fluctuations during the Miocene (ca. 19-17 Ma) likely fragmented ancestral populations, resulting in at least eight early-divergent lineages. Only one of these lineages appears to have diversified during the drastic climate and biome changes of the early Miocene, radiating into the largest group of extant species. The other seven lineages diversified in forest ecosystems during the late Miocene and Pleistocene when climatic conditions were more favourable-warmer and wetter. Our results suggest changing Neogene climate, uplift of eastern African orogens, and biotic interactions might have had different effects on the various subclades of Bicyclus, producing one of the most spectacular butterfly radiations in Africa.
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Affiliation(s)
- Kwaku Aduse-Poku
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, UK.,Biology Department, University of Richmond, Richmond, 138 UR Drive, USA.,Department of Life and Earth Sciences, Perimeter College, Georgia State University, USA
| | - Erik van Bergen
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, UK.,Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Szabolcs Sáfián
- Institute of Silviculture and Forest Protection, University of Sopron, Sopron, Hungary
| | - Steve C Collins
- African Butterfly Research Institute, P.O. Box 14308, 0800 Westlands, Nairobi, Kenya
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, 9700 CC Groningen, The Netherlands
| | | | - Paul M Brakefield
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, UK
| | - Oskar Brattström
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, UK.,African Butterfly Research Institute, P.O. Box 14308, 0800 Westlands, Nairobi, Kenya.,University of Glasgow, School of Life Sciences, Glasgow, Scotland, UK.,University of Glasgow, Institute of Biodiversity, Animal Health and Comparative Medicine, Glasgow, Scotland, UK
| | - David J Lohman
- Biology Department, City College of New York, City University of New York, USA.,Ph.D. Program in Biology, Graduate Center, City University of New York, NY, USA.,Entomology Section, National Museum of Natural History, Manila, 1000, Philippines
| | - Niklas Wahlberg
- Department of Biology, Lund University, Sölvegatan35, SE-223, 62 Lund, Sweden
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8
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A novel reference dated phylogeny for the genus Spodoptera Guenée (Lepidoptera: Noctuidae: Noctuinae): new insights into the evolution of a pest-rich genus. Mol Phylogenet Evol 2021; 161:107161. [PMID: 33794395 DOI: 10.1016/j.ympev.2021.107161] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 03/16/2021] [Accepted: 03/23/2021] [Indexed: 02/03/2023]
Abstract
The noctuid genus Spodoptera currently consists of 31 species with varied host plant breadths, ranging from monophagous and oligophagous non-pest species to polyphagous pests of economic importance. Several of these pest species have become major invaders, colonizing multiple continents outside their native range. Such is the case of the infamous fall armyworm, Spodoptera frugiperda (J.E. Smith), which includes two recognized host strains that have not been treated as separate species. Following its accidental introduction to Africa in 2016, it quickly spread through Africa and Asia to Australia. Given that half the described Spodoptera species cause major crop losses, comparative genomics studies of several Spodoptera species have highlighted major adaptive changes in genetic architecture, possibly relating to their pest status. Several recent population genomics studies conducted on two species enable a more refined understanding of their population structures, migration patterns and invasion processes. Despite growing interest in the genus, the taxonomic status of several Spodoptera species remains unstable and evolutionary studies suffer from the absence of a robust and comprehensive dated phylogenetic framework. We generated mitogenomic data for 14 Spodoptera taxa, which are combined with data from 15 noctuoid outgroups to generate a resolved mitogenomic backbone phylogeny using both concatenation and multi-species coalescent approaches. We combine this backbone with additional mitochondrial and nuclear data to improve our understanding of the evolutionary history of the genus. We also carry out comprehensive dating analyses, which implement three distinct calibration strategies based on either primary or secondary fossil calibrations. Our results provide an updated phylogenetic framework for 28 Spodoptera species, identifying two well-supported ecologically diverse clades that are recovered for the first time. Well-studied larvae in each of these clades are characterized by differences in mandibular shape, with one clade's being more specialized on silica-rich C4 grasses. Interestingly, the inferred timeframe for the genus suggests an earlier origin than previously thought for the genus: about 17-18 million years ago.
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9
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Allio R, Nabholz B, Wanke S, Chomicki G, Pérez-Escobar OA, Cotton AM, Clamens AL, Kergoat GJ, Sperling FAH, Condamine FL. Genome-wide macroevolutionary signatures of key innovations in butterflies colonizing new host plants. Nat Commun 2021; 12:354. [PMID: 33441560 PMCID: PMC7806994 DOI: 10.1038/s41467-020-20507-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 12/03/2020] [Indexed: 01/29/2023] Open
Abstract
The mega-diversity of herbivorous insects is attributed to their co-evolutionary associations with plants. Despite abundant studies on insect-plant interactions, we do not know whether host-plant shifts have impacted both genomic adaptation and species diversification over geological times. We show that the antagonistic insect-plant interaction between swallowtail butterflies and the highly toxic birthworts began 55 million years ago in Beringia, followed by several major ancient host-plant shifts. This evolutionary framework provides a valuable opportunity for repeated tests of genomic signatures of macroevolutionary changes and estimation of diversification rates across their phylogeny. We find that host-plant shifts in butterflies are associated with both genome-wide adaptive molecular evolution (more genes under positive selection) and repeated bursts of speciation rates, contributing to an increase in global diversification through time. Our study links ecological changes, genome-wide adaptations and macroevolutionary consequences, lending support to the importance of ecological interactions as evolutionary drivers over long time periods.
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Affiliation(s)
- Rémi Allio
- CNRS, IRD, EPHE, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France.
| | - Benoit Nabholz
- CNRS, IRD, EPHE, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20b, 01062, Dresden, Germany
| | - Guillaume Chomicki
- Department of Bioscience, Durham University, Stockton Road, Durham, DH1 3LE, UK
| | | | - Adam M Cotton
- 86/2 Moo 5, Tambon Nong Kwai, Hang Dong, Chiang Mai, Thailand
| | - Anne-Laure Clamens
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier, Montpellier, France
| | - Gaël J Kergoat
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier, Montpellier, France
| | - Felix A H Sperling
- Department of Biological Sciences, University of Alberta, Edmonton, T6G 2E9, AB, Canada
| | - Fabien L Condamine
- CNRS, IRD, EPHE, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France.
- Department of Biological Sciences, University of Alberta, Edmonton, T6G 2E9, AB, Canada.
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10
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Halali S, van Bergen E, Breuker CJ, Brakefield PM, Brattström O. Seasonal environments drive convergent evolution of a faster pace-of-life in tropical butterflies. Ecol Lett 2020; 24:102-112. [PMID: 33099881 DOI: 10.1111/ele.13626] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/22/2020] [Accepted: 09/22/2020] [Indexed: 01/16/2023]
Abstract
New ecological niches that may arise due to climate change can trigger diversification, but their colonisation often requires adaptations in a suite of life-history traits. We test this hypothesis in species-rich Mycalesina butterflies that have undergone parallel radiations in Africa, Asia, and Madagascar. First, our ancestral state reconstruction of habitat preference, using c. 85% of extant species, revealed that early forest-linked lineages began to invade seasonal savannahs during the late Miocene-Pliocene. Second, rearing replicate pairs of forest and savannah species from the African and Malagasy radiation in a common garden experiment, and utilising published data from the Asian radiation, demonstrated that savannah species consistently develop faster, have smaller bodies, higher fecundity with an earlier investment in reproduction, and reduced longevity, compared to forest species across all three radiations. We argue that time-constraints for reproduction favoured the evolution of a faster pace-of-life in savannah species that facilitated their persistence in seasonal habitats.
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Affiliation(s)
- Sridhar Halali
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - Erik van Bergen
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK.,Research Centre of Ecological Change, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Casper J Breuker
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Paul M Brakefield
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - Oskar Brattström
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK.,School of Health and Life Sciences, University of West Scotland, Paisley, PA1 2BE, Scotland
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11
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Molecular Clocks without Rocks: New Solutions for Old Problems. Trends Genet 2020; 36:845-856. [PMID: 32709458 DOI: 10.1016/j.tig.2020.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 06/02/2020] [Accepted: 06/11/2020] [Indexed: 02/07/2023]
Abstract
Molecular data have been used to date species divergences ever since they were described as documents of evolutionary history in the 1960s. Yet, an inadequate fossil record and discordance between gene trees and species trees are persistently problematic. We examine how, by accommodating gene tree discordance and by scaling branch lengths to absolute time using mutation rate and generation time, multispecies coalescent (MSC) methods can potentially overcome these challenges. We find that time estimates can differ - in some cases, substantially - depending on whether MSC methods or traditional phylogenetic methods that apply concatenation are used, and whether the tree is calibrated with pedigree-based mutation rates or with fossils. We discuss the advantages and shortcomings of both approaches and provide practical guidance for data analysis when using these methods.
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12
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Halali S, Brakefield PM, Collins SC, Brattström O. To mate, or not to mate: The evolution of reproductive diapause facilitates insect radiation into African savannahs in the Late Miocene. J Anim Ecol 2020; 89:1230-1241. [DOI: 10.1111/1365-2656.13178] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 11/27/2019] [Indexed: 01/19/2023]
Affiliation(s)
- Sridhar Halali
- Department of Zoology University of Cambridge Cambridge UK
| | | | | | - Oskar Brattström
- Department of Zoology University of Cambridge Cambridge UK
- African Butterfly Research Institute (ABRI) Nairobi Kenya
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13
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Condamine FL, Rolland J, Morlon H. Assessing the causes of diversification slowdowns: temperature‐dependent and diversity‐dependent models receive equivalent support. Ecol Lett 2019; 22:1900-1912. [DOI: 10.1111/ele.13382] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/20/2019] [Accepted: 08/12/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Fabien L. Condamine
- CNRS, UMR 5554 Institut des Sciences de l'Evolution de Montpellier Place Eugène Bataillon 34095Montpellier France
- CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique) route de Saclay 91128Palaiseau France
| | - Jonathan Rolland
- CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique) route de Saclay 91128Palaiseau France
- Department of Computational Biology, Biophore University of Lausanne Lausanne 1015Switzerland
- Department of Zoology University of British Columbia University Blvd #4200‐6270Vancouver B.C Canada
| | - Hélène Morlon
- CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique) route de Saclay 91128Palaiseau France
- IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University F‐75005Paris France
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