1
|
Matthews AE, Wijeratne AJ, Sweet AD, Hernandes FA, Toews DPL, Boves TJ. Dispersal-Limited Symbionts Exhibit Unexpectedly Wide Variation in Host Specificity. Syst Biol 2023; 72:802-819. [PMID: 36960591 DOI: 10.1093/sysbio/syad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 02/08/2023] [Accepted: 03/21/2023] [Indexed: 03/25/2023] Open
Abstract
A fundamental aspect of symbiotic relationships is host specificity, ranging from extreme specialists associated with only a single host species to generalists associated with many different species. Although symbionts with limited dispersal capabilities are expected to be host specialists, some are able to associate with multiple hosts. Understanding the micro- and macro-evolutionary causes of variations in host specificity is often hindered by sampling biases and the limited power of traditional evolutionary markers. Here, we studied feather mites to address the barriers associated with estimates of host specificity for dispersal-limited symbionts. We sampled feather mites (Proctophyllodidae) from a nearly comprehensive set of North American breeding warblers (Parulidae) to study mite phylogenetic relationships and host-symbiont codiversification. We used pooled-sequencing (Pool-Seq) and short-read Illumina technology to interpret results derived from a traditional barcoding gene (cytochrome c oxidase subunit 1) versus 11 protein-coding mitochondrial genes using concatenated and multispecies coalescent approaches. Despite the statistically significant congruence between mite and host phylogenies, mite-host specificity varies widely, and host switching is common regardless of the genetic marker resolution (i.e., barcode vs. multilocus). However, the multilocus approach was more effective than the single barcode in detecting the presence of a heterogeneous Pool-Seq sample. These results suggest that presumed symbiont dispersal capabilities are not always strong indicators of host specificity or of historical host-symbiont coevolutionary events. A comprehensive sampling at fine phylogenetic scales may help to better elucidate the microevolutionary filters that impact macroevolutionary processes regulating symbioses, particularly for dispersal-limited symbionts. [Codiversification; cophylogenetics; feather mites; host switching; pooled sequencing; species delineation; symbiosis, warblers.].
Collapse
Affiliation(s)
- Alix E Matthews
- College of Sciences and Mathematics and Molecular Biosciences Program, Arkansas State University, Jonesboro, AR, USA
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, USA
| | - Asela J Wijeratne
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, USA
| | - Andrew D Sweet
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, USA
| | - Fabio A Hernandes
- Department of Ecology and Zoology, CCB/ECZ, Federal University of Santa Catarina (UFSC), Trindade, Florianópolis, Santa Catarina, Brazil
| | - David P L Toews
- Department of Biology, Pennsylvania State University, State College, PA, USA
| | - Than J Boves
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, USA
| |
Collapse
|
2
|
Nelson CM, Ord TJ. Identifying potential cues of species identity in complex animal signals. Anim Behav 2022. [DOI: 10.1016/j.anbehav.2022.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
3
|
Hu AQ, Gale SW, Liu ZJ, Fischer GA, Saunders RMK. Diversification Slowdown in the Cirrhopetalum Alliance ( Bulbophyllum, Orchidaceae): Insights From the Evolutionary Dynamics of Crassulacean Acid Metabolism. FRONTIERS IN PLANT SCIENCE 2022; 13:794171. [PMID: 35185977 PMCID: PMC8851032 DOI: 10.3389/fpls.2022.794171] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/10/2022] [Indexed: 05/17/2023]
Abstract
Evolutionary slowdowns in diversification have been inferred in various plant and animal lineages. Investigation based on diversification models integrated with environmental factors and key characters could provide critical insights into this diversification trend. We evaluate diversification rates in the Cirrhopetalum alliance (Bulbophyllum, Orchidaceae subfam. Epidendroideae) using a time-calibrated phylogeny and assess the role of Crassulacean acid metabolism (CAM) as a hypothesised key innovation promoting the spectacular diversity of orchids, especially those with an epiphytic habit. An explosive early speciation in the Cirrhopetalum alliance is evident, with the origin of CAM providing a short-term advantage under the low atmospheric CO2 concentrations (pCO2) associated with cooling and aridification in the late Miocene. A subsequent slowdown of diversification in the Cirrhopetalum alliance is possibly explained by a failure to keep pace with pCO2 dynamics. We further demonstrate that extinction rates in strong CAM lineages are ten times higher than those of C3 lineages, with CAM not as evolutionarily labile as previously assumed. These results challenge the role of CAM as a "key innovation" in the diversification of epiphytic orchids.
Collapse
Affiliation(s)
- Ai-Qun Hu
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Division of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Kadoorie Farm and Botanic Garden, Tai Po, Hong Kong SAR, China
| | - Stephan W. Gale
- Kadoorie Farm and Botanic Garden, Tai Po, Hong Kong SAR, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | | | - Richard M. K. Saunders
- Division of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| |
Collapse
|
4
|
de Alencar LRV, Quental TB. Linking population-level and microevolutionary processes to understand speciation dynamics at the macroevolutionary scale. Ecol Evol 2021; 11:5828-5843. [PMID: 34141187 PMCID: PMC8207422 DOI: 10.1002/ece3.7511] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 03/17/2021] [Indexed: 11/05/2022] Open
Abstract
Although speciation dynamics have been described for several taxonomic groups in distinct geographic regions, most macroevolutionary studies still lack a detailed mechanistic view on how or why speciation rates change. To help partially fill this gap, we suggest that the interaction between the time taken by a species to geographically expand and the time populations take to evolve reproductive isolation should be considered when we are trying to understand macroevolutionary patterns. We introduce a simple conceptual index to guide our discussion on how demographic and microevolutionary processes might produce speciation dynamics at macroevolutionary scales. Our framework is developed under different scenarios: when speciation is mediated by geographical or resource-partitioning opportunities, and when diversity is limited or not. We also discuss how organismal intrinsic properties and different overall geographical settings can influence the tempo and mode of speciation. We argue that specific conditions observed at the microscale might produce a pulse in speciation rates even without a pulse in either climate or physical barriers. We also propose a hypothesis to reconcile the apparent inconsistency between speciation measured at the microscale and macroscale, and emphasize that diversification rates are better seen as an emergent property. We hope to bring the reader's attention to interesting mechanisms to be further studied, to motivate the development of new theoretical models that connect microevolution and macroevolution, and to inspire new empirical and methodological approaches to more adequately investigate speciation dynamics either using neontological or paleontological data.
Collapse
Affiliation(s)
| | - Tiago Bosisio Quental
- Departamento de EcologiaInstituto de BiociênciasUniversidade de São PauloSão PauloBrazil
| |
Collapse
|
5
|
Love J, Goller F. Processes underlying complex patterns of song trait evolution in a Setophaga hybrid zone. Ecol Evol 2021; 11:7264-7277. [PMID: 34188811 PMCID: PMC8216987 DOI: 10.1002/ece3.7559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 03/22/2021] [Accepted: 03/25/2021] [Indexed: 11/12/2022] Open
Abstract
During secondary contact between two species when hybrids are less fit than parents, mating signals are expected to diverge, while aggressive signals are expected to converge. If a single signal trait is used in both mating and aggression, then the dynamics between these two forces could influence the evolutionary trajectory of that trait. We studied such a situation in an avian hybrid zone between two Setophaga species, where birdsong is used in both mate attraction and territory defense. We hypothesized that song modules of the two species will show separate and distinct geographic patterns due to the influence of selective pressures for effective territorial aggression and for effective mate attraction. We conducted geographic cline analyses and playback experiments across this hybrid zone. We found an unexpected geographic pattern of asymmetric introgression of song rhythm, which may be explained by results of the playback experiments that suggest that differences in song rhythm serve a greater role in mate attraction than in territory defense. In contrast, differences in syllable morphology show little evidence of importance in mate attraction or territorial defense. Song features converge in the hybrid zone, yet patterns of trait change suggest that the song production modules may vary in their modes of development and inheritance. Syringeal motor gesturing, which gives rise to syllable morphology, shows a nonclinal mosaic pattern, suggesting that this trait may be predominantly learned. In contrast, respiratory patterning, which forms song rhythm, shows a clinal geographic transition, suggesting that this trait could be more innate. The results indicate that opposing forces act independently on song via distinct modules of the song production mechanism, driving complex patterns of song trait evolution.
Collapse
Affiliation(s)
- Jay Love
- University of UtahSalt Lake CityUTUSA
| | - Franz Goller
- University of UtahSalt Lake CityUTUSA
- University of MünsterMünsterGermany
| |
Collapse
|
6
|
Simpson RK, Wilson DR, Mistakidis AF, Mennill DJ, Doucet SM. Sympatry drives colour and song evolution in wood-warblers (Parulidae). Proc Biol Sci 2021; 288:20202804. [PMID: 33434456 DOI: 10.1098/rspb.2020.2804] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Closely related species often exhibit similarities in appearance and behaviour, yet when related species exist in sympatry, signals may diverge to enhance species recognition. Prior comparative studies provided mixed support for this hypothesis, but the relationship between sympatry and signal divergence is likely nonlinear. Constraints on signal diversity may limit signal divergence, especially when large numbers of species are sympatric. We tested the effect of sympatric overlap on plumage colour and song divergence in wood-warblers (Parulidae), a speciose group with diverse visual and vocal signals. We also tested how number of sympatric species influences signal divergence. Allopatric species pairs had overall greater plumage and song divergence compared to sympatric species pairs. However, among sympatric species pairs, plumage divergence positively related to the degree of sympatric overlap in males and females, while male song bandwidth and syllable rate divergence negatively related to sympatric overlap. In addition, as the number of species in sympatry increased, average signal divergence among sympatric species decreased, which is likely due to constraints on warbler perceptual space and signal diversity. Our findings reveal that sympatry influences signal evolution in warblers, though not always as predicted, and that number of sympatric species can limit sympatry's influence on signal evolution.
Collapse
Affiliation(s)
- Richard K Simpson
- Department of Integrative Biology, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - David R Wilson
- Department of Integrative Biology, University of Windsor, Windsor, Ontario N9B 3P4, Canada.,Department of Psychology, Memorial University of Newfoundland, St John's, Newfoundland A1B 3X9, Canada
| | - Allison F Mistakidis
- Department of Integrative Biology, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Daniel J Mennill
- Department of Integrative Biology, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Stéphanie M Doucet
- Department of Integrative Biology, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| |
Collapse
|
7
|
Ford BM, Cornellas A, Leonard JA, Weir RD, Russello MA. Spatiotemporal analyses suggest the role of glacial history and the ice-free corridor in shaping American badger population genetic variation. Ecol Evol 2020; 10:8345-8357. [PMID: 32788984 PMCID: PMC7417222 DOI: 10.1002/ece3.6541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 06/03/2020] [Accepted: 06/10/2020] [Indexed: 11/07/2022] Open
Abstract
Recurring glacial cycles through the Quaternary period drastically altered the size and distribution of natural populations of North American flora and fauna. The "southerly refugia model" has been the longstanding framework for testing the effects of glaciation on contemporary genetic patterns; however, insights from ancient DNA have contributed to the reconstruction of more complex histories for some species. The American badger, Taxidea taxus, provides an interesting species for exploring the genetic legacy of glacial history, having been hypothesized to have postglacially emerged from a single, southerly refugium to recolonize northern latitudes. However, previous studies have lacked genetic sampling from areas where distinct glacial refugia have been hypothesized, including the Pacific Northwest and American Far North (Yukon, Alaska). In order to further investigate the phylogeographic history of American badgers, we collected mitochondrial DNA sequence data from ancient subfossil material collected within the historical range (Alaska, Yukon) and combined them with new and previously published data from across the species' contemporary distribution (n = 1,207). We reconstructed a mostly unresolved phylogenetic tree and star-like haplotype network indicative of emergence from a largely panmictic glacial refugium and recent population expansion, the latter further punctuated by significantly negative Tajima's D and Fu's Fs values. Although directionality of migration cannot be unequivocally inferred, the moderate to high levels of genetic variation exhibited by American badgers, alongside the low frequency of haplotypes with indels in the Midwest, suggest a potential recolonization into central North America after the hypothesized ice-free corridor reopened ~13,000 years ago. Overall, the expanded reconstruction of phylogeographic history of American badgers offers a broader understanding of contemporary range-wide patterns and identifies unique genetic units that can likely be used to inform conservation of at-risk populations at the northern periphery.
Collapse
Affiliation(s)
- Brett M. Ford
- Department of BiologyUniversity of British ColumbiaKelownaBCCanada
| | - Anna Cornellas
- Conservation and Evolutionary Genetics GroupEstación Biológica de Doñana (EBD‐CSIC)SevilleSpain
| | - Jennifer A. Leonard
- Conservation and Evolutionary Genetics GroupEstación Biológica de Doñana (EBD‐CSIC)SevilleSpain
| | - Richard D. Weir
- British Columbia Ministry of Environment and Climate Change StrategyVictoriaBCCanada
| | | |
Collapse
|
8
|
McEntee JP, Burleigh JG, Singhal S. Dispersal Predicts Hybrid Zone Widths across Animal Diversity: Implications for Species Borders under Incomplete Reproductive Isolation. Am Nat 2020; 196:9-28. [PMID: 32552108 DOI: 10.1086/709109] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Hybrid zones occur as range boundaries for many animal taxa. One model for how hybrid zones form and stabilize is the tension zone model, a version of which predicts that hybrid zone widths are determined by a balance between random dispersal into hybrid zones and selection against hybrids. Here, we examine whether random dispersal and proxies for selection against hybrids (genetic distances between hybridizing pairs) can explain variation in hybrid zone widths across 131 hybridizing pairs of animals. We show that these factors alone can explain ∼40% of the variation in zone width among animal hybrid zones, with dispersal explaining far more of the variation than genetic distances. Patterns within clades were idiosyncratic. Genetic distances predicted hybrid zone widths particularly well for reptiles, while this relationship was opposite tension zone predictions in birds. Last, the data suggest that dispersal and molecular divergence set lower bounds on hybrid zone widths in animals, indicating that there are geographic restrictions on hybrid zone formation. Overall, our analyses reinforce the fundamental importance of dispersal in hybrid zone formation and more generally in the ecology of range boundaries.
Collapse
|
9
|
Simpson RK, Mistakidis AF, Doucet SM. Natural and sexual selection shape the evolution of colour and conspicuousness in North American wood-warblers (Parulidae). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Natural and sexual selection drive colour evolution in animals. However, these different selective forces are often studied independently or without considering environmental variation. We evaluated the roles of natural and sexual selection together on colour evolution in 15 sympatric wood-warbler species, while considering the influence of variation in the light environment and visual background. We tested the influence of each selective pressure on male and female coloration and contrast against the background using avian visual models in phylogenetically controlled analyses. We found natural and sexual selection simultaneously driving cryptic and conspicuous plumage in males by acting on different body regions. For example, we found that ground-nesting species had males with conspicuous under-body plumage and cryptic upper-body plumage, showing how natural and sexual selection can drive colour evolution concordantly. We also found interesting relationships with female plumage, such as nest predation positively covarying with female contrast against the background, suggesting a cost to female conspicuousness. Our findings here showcase the complexity of selection on coloration and illustrate the importance of: (1) accounting for environmental variation when assessing how natural and sexual selection drive colour evolution; and (2) testing how multiple selection pressures are shaping colour diversity among species.
Collapse
Affiliation(s)
- Richard K Simpson
- Department of Biological Sciences, University of Windsor, 401 Sunset Avenue, Windsor, Ontario, Canada
| | - Allison F Mistakidis
- Department of Biological Sciences, University of Windsor, 401 Sunset Avenue, Windsor, Ontario, Canada
| | - Stéphanie M Doucet
- Department of Biological Sciences, University of Windsor, 401 Sunset Avenue, Windsor, Ontario, Canada
| |
Collapse
|
10
|
Smissen PJ, Rowe KC. Repeated biome transitions in the evolution of Australian rodents. Mol Phylogenet Evol 2018; 128:182-191. [DOI: 10.1016/j.ympev.2018.07.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 06/26/2018] [Accepted: 07/16/2018] [Indexed: 12/31/2022]
|
11
|
Maliet O, Gascuel F, Lambert A. Ranked Tree Shapes, Nonrandom Extinctions, and the Loss of Phylogenetic Diversity. Syst Biol 2018; 67:1025-1040. [DOI: 10.1093/sysbio/syy030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 04/08/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Odile Maliet
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
- ED 227, Sorbonne Universités, Paris, France
| | - Fanny Gascuel
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
- ED 227, Sorbonne Universités, Paris, France
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France
| | - Amaury Lambert
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France
- Laboratoire Probabilités, Statistique et Modélisation (LPSM), Sorbonne Université, CNRS, Paris, France
| |
Collapse
|
12
|
Sun Z, Pan T, Hu C, Sun L, Ding H, Wang H, Zhang C, Jin H, Chang Q, Kan X, Zhang B. Rapid and recent diversification patterns in Anseriformes birds: Inferred from molecular phylogeny and diversification analyses. PLoS One 2017; 12:e0184529. [PMID: 28892502 PMCID: PMC5593203 DOI: 10.1371/journal.pone.0184529] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/25/2017] [Indexed: 11/29/2022] Open
Abstract
The Anseriformes is a well-known and widely distributed bird order, with more than 150 species in the world. This paper aims to revise the classification, determine the phylogenetic relationships and diversification patterns in Anseriformes by exploring the Cyt b, ND2, COI genes and the complete mitochondrial genomes (mito-genomes). Molecular phylogeny and genetic distance analyses suggest that the Dendrocygna species should be considered as an independent family, Dendrocygnidae, rather than a member of Anatidae. Molecular timescale analyses suggests that the ancestral diversification occurred during the Early Eocene Climatic Optimum (58 ~ 50 Ma). Furthermore, diversification analyses showed that, after a long period of constant diversification, the median initial speciation rate was accelerated three times, and finally increased to approximately 0.3 sp/My. In the present study, both molecular phylogeny and diversification analyses results support that Anseriformes birds underwent rapid and recent diversification in their evolutionary history, especially in modern ducks, which show extreme diversification during the Plio-Pleistocene (~ 5.3 Ma). Therefore, our study support that the Plio-Pleistocene climate fluctuations are likely to have played a significant role in promoting the recent diversification for Anseriformes.
Collapse
Affiliation(s)
- Zhonglou Sun
- School of Life Sciences, Anhui Key Laboratory of Eco-engineering and Bio-technique, Anhui University, Hefei, Anhui, China
| | - Tao Pan
- School of Life Sciences, Anhui Key Laboratory of Eco-engineering and Bio-technique, Anhui University, Hefei, Anhui, China
| | - Chaochao Hu
- School of Life Science, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Lu Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Hengwu Ding
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Hui Wang
- School of Life Sciences, Anhui Key Laboratory of Eco-engineering and Bio-technique, Anhui University, Hefei, Anhui, China
| | - Chenling Zhang
- Faculty of Life Science and Chemical Engineering, Jiangsu Second Normal University, Nanjing, Jiangsu, China
| | - Hong Jin
- School of Life Science, Nanjing Normal University, Nanjing, Jiangsu, China
- Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Qing Chang
- School of Life Science, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Xianzhao Kan
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Baowei Zhang
- School of Life Sciences, Anhui Key Laboratory of Eco-engineering and Bio-technique, Anhui University, Hefei, Anhui, China
| |
Collapse
|
13
|
Zink RM, Gardner AS. Glaciation as a migratory switch. SCIENCE ADVANCES 2017; 3:e1603133. [PMID: 28948216 PMCID: PMC5606702 DOI: 10.1126/sciadv.1603133] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 08/28/2017] [Indexed: 06/07/2023]
Abstract
Migratory behavior in birds is evolutionarily plastic, but it is unclear how this behavior responded during glacial cycles. One view is that at glacial maxima, species simply shifted their breeding ranges south of glacial ice and remained migratory. To test this hypothesis, we constructed ecological niche models for breeding and wintering ranges of 56 species, finding that 70% of currently long-distance North American migrant species likely lacked suitable breeding habitat in North America at the Last Glacial Maximum (LGM), and we hypothesized that they reverted to the ancestral state of being tropical sedentary residents. A smaller percentage of short-distance migrants (27%) experienced altered migratory behavior at the LGM, although the ranges of all species were shifted southward, as traditionally envisioned. We suggest that many species oscillate between sedentary and migratory strategies with each glacial cycle acting as an adaptive switch. Thus, range shifts occur more frequently than speciation events and are inadequately depicted by phylogenetic reconstructions. We suggest that reconstructing the evolutionary history of traits, such as migratory behavior, is best served by using ranges at glacial maxima. A phylogeny of warblers strongly predicted LGM, but not present distributions, and suggested that migration was re-expressed from three tropical centers of warbler diversity. Understanding of evolutionary history will be improved when reconstructions use distributions relevant to the time of character transitions.
Collapse
Affiliation(s)
- Robert M. Zink
- School of Natural Resources, School of Biological Sciences, and University of Nebraska State Museum, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Aubrey S. Gardner
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108, USA
| |
Collapse
|
14
|
Herrera JP. Testing the adaptive radiation hypothesis for the lemurs of Madagascar. ROYAL SOCIETY OPEN SCIENCE 2017; 4:161014. [PMID: 28280597 PMCID: PMC5319363 DOI: 10.1098/rsos.161014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 12/12/2016] [Indexed: 05/12/2023]
Abstract
Lemurs, the diverse, endemic primates of Madagascar, are thought to represent a classic example of adaptive radiation. Based on the most complete phylogeny of living and extinct lemurs yet assembled, I tested predictions of adaptive radiation theory by estimating rates of speciation, extinction and adaptive phenotypic evolution. As predicted, lemur speciation rate exceeded that of their sister clade by nearly twofold, indicating the diversification dynamics of lemurs and mainland relatives may have been decoupled. Lemur diversification rates did not decline over time, however, as predicted by adaptive radiation theory. Optimal body masses diverged among dietary and activity pattern niches as lineages diversified into unique multidimensional ecospace. Based on these results, lemurs only partially fulfil the predictions of adaptive radiation theory, with phenotypic evolution corresponding to an 'early burst' of adaptive differentiation. The results must be interpreted with caution, however, because over the long evolutionary history of lemurs (approx. 50 million years), the 'early burst' signal of adaptive radiation may have been eroded by extinction.
Collapse
Affiliation(s)
- James P. Herrera
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
- Division of Paleontology, American Museum of Natural History, New York, NY 10024, USA
- Richard Gilder Graduate School, American Museum of Natural History, New York, NY 10024, USA
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
- Author for correspondence: James P. Herrera e-mail:
| |
Collapse
|
15
|
Toews D, Taylor S, Vallender R, Brelsford A, Butcher B, Messer P, Lovette I. Plumage Genes and Little Else Distinguish the Genomes of Hybridizing Warblers. Curr Biol 2016; 26:2313-8. [DOI: 10.1016/j.cub.2016.06.034] [Citation(s) in RCA: 250] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 04/13/2016] [Accepted: 06/15/2016] [Indexed: 01/04/2023]
|
16
|
Rabosky DL, Title PO, Huang H. Minimal effects of latitude on present-day speciation rates in New World birds. Proc Biol Sci 2016; 282:20142889. [PMID: 26019156 DOI: 10.1098/rspb.2014.2889] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The tropics contain far greater numbers of species than temperate regions, suggesting that rates of species formation might differ systematically between tropical and non-tropical areas. We tested this hypothesis by reconstructing the history of speciation in New World (NW) land birds using BAMM, a Bayesian framework for modelling complex evolutionary dynamics on phylogenetic trees. We estimated marginal distributions of present-day speciation rates for each of 2571 species of birds. The present-day rate of speciation varies approximately 30-fold across NW birds, but there is no difference in the rate distributions for tropical and temperate taxa. Using macroevolutionary cohort analysis, we demonstrate that clades with high tropical membership do not produce species more rapidly than temperate clades. For nearly any value of present-day speciation rate, there are far more species in the tropics than the temperate zone. Any effects of latitude on speciation rate are marginal in comparison to the dramatic variation in rates among clades.
Collapse
Affiliation(s)
- Daniel L Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pascal O Title
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Huateng Huang
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
17
|
Alhajeri BH, Schenk JJ, Steppan SJ. Ecomorphological diversification following continental colonization in muroid rodents (Rodentia: Muroidea). Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12695] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Bader H. Alhajeri
- Department of Biological Science; Florida State University; Tallahassee FL 32306-4295 USA
- Department of Biological Sciences; Kuwait University; Safat 13110 Kuwait
| | - John J. Schenk
- Department of Biological Science; Florida State University; Tallahassee FL 32306-4295 USA
- Department of Ecology and Evolutionary Biology; Tulane University; New Orleans LA 70118-5698 USA
| | - Scott J. Steppan
- Department of Biological Science; Florida State University; Tallahassee FL 32306-4295 USA
| |
Collapse
|
18
|
van Tuinen M, Torres CR. Potential for bias and low precision in molecular divergence time estimation of the Canopy of Life: an example from aquatic bird families. Front Genet 2015; 6:203. [PMID: 26106406 PMCID: PMC4459087 DOI: 10.3389/fgene.2015.00203] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 05/25/2015] [Indexed: 11/13/2022] Open
Abstract
Uncertainty in divergence time estimation is frequently studied from many angles but rarely from the perspective of phylogenetic node age. If appropriate molecular models and fossil priors are used, a multi-locus, partitioned analysis is expected to equally minimize error in accuracy and precision across all nodes of a given phylogeny. In contrast, if available models fail to completely account for rate heterogeneity, substitution saturation and incompleteness of the fossil record, uncertainty in divergence time estimation may increase with node age. While many studies have stressed this concern with regard to deep nodes in the Tree of Life, the inference that molecular divergence time estimation of shallow nodes is less sensitive to erroneous model choice has not been tested explicitly in a Bayesian framework. Because of available divergence time estimation methods that permit fossil priors across any phylogenetic node and the present increase in efficient, cheap collection of species-level genomic data, insight is needed into the performance of divergence time estimation of shallow (<10 MY) nodes. Here, we performed multiple sensitivity analyses in a multi-locus data set of aquatic birds with six fossil constraints. Comparison across divergence time analyses that varied taxon and locus sampling, number and position of fossil constraint and shape of prior distribution showed various insights. Deviation from node ages obtained from a reference analysis was generally highest for the shallowest nodes but determined more by temporal placement than number of fossil constraints. Calibration with only the shallowest nodes significantly underestimated the aquatic bird fossil record, indicating the presence of saturation. Although joint calibration with all six priors yielded ages most consistent with the fossil record, ages of shallow nodes were overestimated. This bias was found in both mtDNA and nDNA regions. Thus, divergence time estimation of shallow nodes may suffer from bias and low precision, even when appropriate fossil priors and best available substitution models are chosen. Much care must be taken to address the possible ramifications of substitution saturation across the entire Tree of Life.
Collapse
Affiliation(s)
- Marcel van Tuinen
- Department of Biology and Marine Biology, University of North Carolina at WilmingtonWilmington, NC, USA
- Centre of Evolutionary and Ecological Studies, Marine Evolution and Conservation Group, University of GroningenGroningen, Netherlands
| | - Christopher R. Torres
- Department of Biology and Marine Biology, University of North Carolina at WilmingtonWilmington, NC, USA
- National Evolutionary Synthesis CenterDurham, NC, USA
- Department of Integrative Biology, University of Texas at AustinAustin, TX, USA
| |
Collapse
|
19
|
Gascuel F, Ferriere R, Aguilee R, Lambert A. How Ecology and Landscape Dynamics Shape Phylogenetic Trees. Syst Biol 2015; 64:590-607. [DOI: 10.1093/sysbio/syv014] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 03/09/2015] [Indexed: 01/21/2023] Open
|
20
|
Fuchs J, Johnson JA, Mindell DP. Rapid diversification of falcons (Aves: Falconidae) due to expansion of open habitats in the Late Miocene. Mol Phylogenet Evol 2015; 82 Pt A:166-82. [DOI: 10.1016/j.ympev.2014.08.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 07/22/2014] [Accepted: 08/10/2014] [Indexed: 10/24/2022]
|
21
|
Rolland J, Jiguet F, Jønsson KA, Condamine FL, Morlon H. Settling down of seasonal migrants promotes bird diversification. Proc Biol Sci 2014; 281:20140473. [PMID: 24759866 PMCID: PMC4043101 DOI: 10.1098/rspb.2014.0473] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 03/25/2014] [Indexed: 12/19/2022] Open
Abstract
How seasonal migration originated and impacted diversification in birds remains largely unknown. Although migratory behaviour is likely to affect bird diversification, previous studies have not detected any effect. Here, we infer ancestral migratory behaviour and the effect of seasonal migration on speciation and extinction dynamics using a complete bird tree of life. Our analyses infer that sedentary behaviour is ancestral, and that migratory behaviour evolved independently multiple times during the evolutionary history of birds. Speciation of a sedentary species into two sedentary daughter species is more frequent than speciation of a migratory species into two migratory daughter species. However, migratory species often diversify by generating a sedentary daughter species in addition to the ancestral migratory one. This leads to an overall higher migratory speciation rate. Migratory species also experience lower extinction rates. Hence, although migratory species represent a minority (18.5%) of all extant birds, they have a higher net diversification rate than sedentary species. These results suggest that the evolution of seasonal migration in birds has facilitated diversification through the divergence of migratory subpopulations that become sedentary, and illustrate asymmetrical diversification as a mechanism by which diversification rates are decoupled from species richness.
Collapse
Affiliation(s)
- Jonathan Rolland
- Centre de Mathématiques Appliquées (Ecole Polytechnique), CNRS, UMR 7641 Route de Saclay, 91128 Palaiseau, France
- Muséum National d'Histoire Naturelle, UMR 7204 MNHN-CNRS-UPMC, Centre d'Ecologie et des Sciences de la Conservation, CP51, 55 rue Buffon, 75005 Paris, France
- Institut de Biologie de l’École Normale Supérieure, CNRS UMR 8197, École Normale Supérieure, 46 rue d'Ulm, 75005 Paris
| | - Frédéric Jiguet
- Muséum National d'Histoire Naturelle, UMR 7204 MNHN-CNRS-UPMC, Centre d'Ecologie et des Sciences de la Conservation, CP51, 55 rue Buffon, 75005 Paris, France
| | - Knud Andreas Jønsson
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Fabien L. Condamine
- Centre de Mathématiques Appliquées (Ecole Polytechnique), CNRS, UMR 7641 Route de Saclay, 91128 Palaiseau, France
| | - Hélène Morlon
- Centre de Mathématiques Appliquées (Ecole Polytechnique), CNRS, UMR 7641 Route de Saclay, 91128 Palaiseau, France
- Institut de Biologie de l’École Normale Supérieure, CNRS UMR 8197, École Normale Supérieure, 46 rue d'Ulm, 75005 Paris
| |
Collapse
|
22
|
Moen D, Morlon H. Why does diversification slow down? Trends Ecol Evol 2014; 29:190-7. [DOI: 10.1016/j.tree.2014.01.010] [Citation(s) in RCA: 198] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 01/24/2014] [Accepted: 01/27/2014] [Indexed: 01/22/2023]
|
23
|
Tran LAP. The role of ecological opportunity in shaping disparate diversification trajectories in a bicontinental primate radiation. Proc Biol Sci 2014; 281:20131979. [PMID: 24598417 DOI: 10.1098/rspb.2013.1979] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Exceptional species and phenotypic diversity commonly are attributed to ecological opportunity (EO). The conventional EO model predicts that rates of lineage diversification and phenotypic evolution are elevated early in a radiation only to decline later in response to niche availability. Foregut fermentation is hypothesized to be a key innovation that allowed colobine monkeys (subfamily Colobinae), the only primates with this trait, to successfully colonize folivore adaptive zones unavailable to other herbivorous species. Therefore, diversification rates also are expected to be strongly linked with the evolution of traits related to folivory in these monkeys. Using dated molecular phylogenies and a dataset of feeding morphology, I test predictions of the EO model to evaluate the role of EO conferred by foregut fermentation in shaping the African and Asian colobine radiations. Findings from diversification methods coupled with colobine biogeographic history provide compelling evidence that decreasing availability of new adaptive zones during colonization of Asia together with constraints presented by dietary specialization underlie temporal changes in diversification in the Asian but not African clade. Additionally, departures from the EO model likely reflect iterative diversification events in Asia.
Collapse
Affiliation(s)
- Lucy A P Tran
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, , 1109 Geddes Avenue, Ann Arbor, MI 48109-1079, USA
| |
Collapse
|
24
|
Yessoufou K, Bamigboye SO, Daru BH, van der Bank M. Evidence of constant diversification punctuated by a mass extinction in the African cycads. Ecol Evol 2013; 4:50-8. [PMID: 24455160 PMCID: PMC3894887 DOI: 10.1002/ece3.880] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 10/12/2013] [Accepted: 10/14/2013] [Indexed: 11/29/2022] Open
Abstract
The recent evidence that extant cycads are not living fossils triggered a renewed search for a better understanding of their evolutionary history. In this study, we investigated the evolutionary diversification history of the genus Encephalartos, a monophyletic cycad endemic to Africa. We found an antisigmoidal pattern with a plateau and punctual explosive radiation. This pattern is typical of a constant radiation with mass extinction. The rate shift that we found may therefore be a result of a rapid recolonization of niches that have been emptied owing to mass extinction. Because the explosive radiation occurred during the transition Pliocene–Pleistocene, we argued that the processes might have been climatically mediated.
Collapse
Affiliation(s)
- Kowiyou Yessoufou
- African Centre for DNA Barcoding, Department of Botany and Plant Biotechnology, University of Johannesburg P. O. Box 524, Auckland Park, Johannesburg, 2006, South Africa
| | - Samuel O Bamigboye
- African Centre for DNA Barcoding, Department of Botany and Plant Biotechnology, University of Johannesburg P. O. Box 524, Auckland Park, Johannesburg, 2006, South Africa
| | - Barnabas H Daru
- African Centre for DNA Barcoding, Department of Botany and Plant Biotechnology, University of Johannesburg P. O. Box 524, Auckland Park, Johannesburg, 2006, South Africa
| | - Michelle van der Bank
- African Centre for DNA Barcoding, Department of Botany and Plant Biotechnology, University of Johannesburg P. O. Box 524, Auckland Park, Johannesburg, 2006, South Africa
| |
Collapse
|
25
|
|
26
|
Bristol RM, Fabre PH, Irestedt M, Jønsson KA, Shah NJ, Tatayah V, Warren BH, Groombridge JJ. Molecular phylogeny of the Indian Ocean Terpsiphone paradise flycatchers: Undetected evolutionary diversity revealed amongst island populations. Mol Phylogenet Evol 2013; 67:336-47. [DOI: 10.1016/j.ympev.2013.01.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 01/23/2013] [Accepted: 01/30/2013] [Indexed: 11/25/2022]
|
27
|
Stoeckle MY, Coffran C. TreeParser-aided Klee diagrams display taxonomic clusters in DNA barcode and nuclear gene datasets. Sci Rep 2013; 3:2635. [PMID: 24022383 PMCID: PMC3769653 DOI: 10.1038/srep02635] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/23/2013] [Indexed: 01/08/2023] Open
Abstract
Indicator vector analysis of a nucleotide sequence alignment generates a compact heat map, called a Klee diagram, with potential insight into clustering patterns in evolution. However, so far this approach has examined only mitochondrial cytochrome c oxidase I (COI) DNA barcode sequences. To further explore, we developed TreeParser, a freely-available web-based program that sorts a sequence alignment according to a phylogenetic tree generated from the dataset. We applied TreeParser to nuclear gene and COI barcode alignments from birds and butterflies. Distinct blocks in the resulting Klee diagrams corresponded to species and higher-level taxonomic divisions in both groups, and this enabled graphic comparison of phylogenetic information in nuclear and mitochondrial genes. Our results demonstrate TreeParser-aided Klee diagrams objectively display taxonomic clusters in nucleotide sequence alignments. This approach may help establish taxonomy in poorly studied groups and investigate higher-level clustering which appears widespread but not well understood.
Collapse
Affiliation(s)
- Mark Y. Stoeckle
- Program for the Human Environment, The Rockefeller University, New York, NY 10065
| | - Cameron Coffran
- Program for the Human Environment, The Rockefeller University, New York, NY 10065
| |
Collapse
|
28
|
Holt BG, Lessard JP, Borregaard MK, Fritz SA, Araújo MB, Dimitrov D, Fabre PH, Graham CH, Graves GR, Jønsson KA, Nogués-Bravo D, Wang Z, Whittaker RJ, Fjeldså J, Rahbek C. An Update of Wallace’s Zoogeographic Regions of the World. Science 2012; 339:74-8. [PMID: 23258408 DOI: 10.1126/science.1228282] [Citation(s) in RCA: 516] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Modern attempts to produce biogeographic maps focus on the distribution of species, and the maps are typically drawn without phylogenetic considerations. Here, we generate a global map of zoogeographic regions by combining data on the distributions and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals. We identify 20 distinct zoogeographic regions, which are grouped into 11 larger realms. We document the lack of support for several regions previously defined based on distributional data and show that spatial turnover in the phylogenetic composition of vertebrate assemblages is higher in the Southern than in the Northern Hemisphere. We further show that the integration of phylogenetic information provides valuable insight on historical relationships among regions, permitting the identification of evolutionarily unique regions of the world.
Collapse
Affiliation(s)
- Ben G Holt
- Center for Macroecology, Evolution, and Climate, Department of Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Etienne RS, Haegeman B. A Conceptual and Statistical Framework for Adaptive Radiations with a Key Role for Diversity Dependence. Am Nat 2012; 180:E75-89. [DOI: 10.1086/667574] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
30
|
Morrison ML, Collier BA, Mathewson HA, Groce JE, Wilkins RN. The prevailing paradigm as a hindrance to conservation. WILDLIFE SOC B 2012. [DOI: 10.1002/wsb.170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
31
|
Snell-Rood EC. The effect of climate on acoustic signals: does atmospheric sound absorption matter for bird song and bat echolocation? THE JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA 2012; 131:1650-1658. [PMID: 22352535 DOI: 10.1121/1.3672695] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The divergence of signals along ecological gradients may lead to speciation. The current research tests the hypothesis that variation in sound absorption selects for divergence in acoustic signals along climatic gradients, which has implications for understanding not only diversification, but also how organisms may respond to climate change. Because sound absorption varies with temperature, humidity, and the frequency of sound, individuals or species may vary signal structure with changes in climate over space or time. In particular, signals of lower frequency, narrower bandwidth, and longer duration should be more detectable in environments with high sound absorption. Using both North American wood warblers (Parulidae) and bats of the American Southwest, this work found evidence of associations between signal structure and sound absorption. Warbler species with higher mean absorption across their range were more likely to have narrow bandwidth songs. Bat species found in higher absorption habitats were more likely to have lower frequency echolocation calls. In addition, bat species changed echolocation call structure across seasons, using longer duration, lower frequency calls in the higher absorption rainy season. These results suggest that signals may diverge along climatic gradients due to variation in sound absorption, although the effects of absorption are modest.
Collapse
Affiliation(s)
- Emilie C Snell-Rood
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 East Lowell Street, Tucson, Arizona 85721, USA.
| |
Collapse
|
32
|
Campagna L, Benites P, Lougheed SC, Lijtmaer DA, Di Giacomo AS, Eaton MD, Tubaro PL. Rapid phenotypic evolution during incipient speciation in a continental avian radiation. Proc Biol Sci 2011; 279:1847-56. [PMID: 22130601 DOI: 10.1098/rspb.2011.2170] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Adaptive radiations have helped shape how we view animal speciation, particularly classic examples such as Darwin's finches, Hawaiian fruitflies and African Great Lakes cichlids. These 'island' radiations are comparatively recent, making them particularly interesting because the mechanisms that caused diversification are still in motion. Here, we identify a new case of a recent bird radiation within a continentally distributed species group; the capuchino seedeaters comprise 11 Sporophila species originally described on the basis of differences in plumage colour and pattern in adult males. We use molecular data together with analyses of male plumage and vocalizations to understand species limits of the group. We find marked phenotypic variation despite lack of mitochondrial DNA monophyly and few differences in other putatively neutral nuclear markers. This finding is consistent with the group having undergone a recent radiation beginning in the Pleistocene, leaving genetic signatures of incomplete lineage sorting, introgressive hybridization and demographic expansions. We argue that this apparent uncoupling between neutral DNA homogeneity and phenotypic diversity is expected for a recent group within the framework of coalescent theory. Finally, we discuss how the ecology of open habitats in South America during the Pleistocene could have helped promote this unique and ongoing radiation.
Collapse
Affiliation(s)
- Leonardo Campagna
- División de Ornitología, Museo Argentino de Ciencias Naturales Bernardino Rivadavia, Avenida Ángel Gallardo 470, Ciudad de Buenos Aires C1405DJR, Buenos Aires, Argentina.
| | | | | | | | | | | | | |
Collapse
|
33
|
Etienne RS, Haegeman B, Stadler T, Aze T, Pearson PN, Purvis A, Phillimore AB. Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record. Proc Biol Sci 2011; 279:1300-9. [PMID: 21993508 DOI: 10.1098/rspb.2011.1439] [Citation(s) in RCA: 249] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The branching times of molecular phylogenies allow us to infer speciation and extinction dynamics even when fossils are absent. Troublingly, phylogenetic approaches usually return estimates of zero extinction, conflicting with fossil evidence. Phylogenies and fossils do agree, however, that there are often limits to diversity. Here, we present a general approach to evaluate the likelihood of a phylogeny under a model that accommodates diversity-dependence and extinction. We find, by likelihood maximization, that extinction is estimated most precisely if the rate of increase in the number of lineages in the phylogeny saturates towards the present or first decreases and then increases. We demonstrate the utility and limits of our approach by applying it to the phylogenies for two cases where a fossil record exists (Cetacea and Cenozoic macroperforate planktonic foraminifera) and to three radiations lacking fossil evidence (Dendroica, Plethodon and Heliconius). We propose that the diversity-dependence model with extinction be used as the standard model for macro-evolutionary dynamics because of its biological realism and flexibility.
Collapse
Affiliation(s)
- Rampal S Etienne
- Community and Conservation Ecology, Centre for Ecological and Evolutionary Studies, PO Box 11103, 9700 CC, Groningen, The Netherlands.
| | | | | | | | | | | | | |
Collapse
|
34
|
Winger BM, Lovette IJ, Winkler DW. Ancestry and evolution of seasonal migration in the Parulidae. Proc Biol Sci 2011; 279:610-8. [PMID: 21752818 DOI: 10.1098/rspb.2011.1045] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Seasonal migration in birds is known to be highly labile and subject to rapid change in response to selection, such that researchers have hypothesized that phylogenetic relationships should neither predict nor constrain the migratory behaviour of a species. Many theories on the evolution of bird migration assume a framework that extant migratory species have evolved repeatedly and relatively recently from sedentary tropical or subtropical ancestors. We performed ancestral state reconstructions of migratory behaviour using a comprehensive, well-supported phylogeny of the Parulidae (the 'wood-warblers'), a large family of Neotropical and Nearctic migratory and sedentary songbirds, and examined the rates of gain and loss of migration throughout the Parulidae. Counter to traditional hypotheses, our results suggest that the ancestral wood-warbler was migratory and that losses of migration have been at least as prevalent as gains throughout the history of Parulidae. Therefore, extant sedentary tropical radiations in the Parulidae represent losses of latitudinal migration and colonization of the tropics from temperate regions. We also tested for phylogenetic signal in migratory behaviour, and our results indicate that although migratory behaviour is variable within some wood-warbler species and clades, phylogeny significantly predicts the migratory distance of species in the Parulidae.
Collapse
Affiliation(s)
- Benjamin M Winger
- Museum of Vertebrates and Department of Ecology and Evolutionary Biology, Corson Hall, Cornell University, Ithaca, NY 14853, USA.
| | | | | |
Collapse
|
35
|
Alström P, Fregin S, Norman JA, Ericson PG, Christidis L, Olsson U. Multilocus analysis of a taxonomically densely sampled dataset reveal extensive non-monophyly in the avian family Locustellidae. Mol Phylogenet Evol 2011; 58:513-26. [DOI: 10.1016/j.ympev.2010.12.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 12/17/2010] [Accepted: 12/20/2010] [Indexed: 11/29/2022]
|
36
|
Major global radiation of corvoid birds originated in the proto-Papuan archipelago. Proc Natl Acad Sci U S A 2011; 108:2328-33. [PMID: 21262814 DOI: 10.1073/pnas.1018956108] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A central paradigm in island biogeography has been the unidirectional "downstream" colonization of islands from continents (source to sink) based on the idea that less-diverse island communities are easier to invade than biologically more-diverse continental communities. Recently, several cases of "upstream" colonization (from islands to continents) have been documented, challenging the traditional view. However, all these cases have involved individual island species that have colonized mainland regions. Here, using molecular phylogenetic data, divergence time estimates, lineage diversity distributions, and ancestral area analyses, we reconstruct the spread of a species-rich (>700 species) passerine bird radiation (core Corvoidea) from its late Eocene/Oligocene origin in the emerging proto-Papuan archipelago north of Australia, including multiple colonizations from the archipelago to Southeast Asia. Thus, islands apparently provided the setting for the initiation of a major songbird radiation that subsequently invaded all other continents. Morphological and behavioral adaptations of the core Corvoidea as generalist feeders in open habitats, which facilitated dispersal and colonization, apparently evolved in the descendants of sedentary forest birds that invaded the proto-Papuan archipelago. The archipelago evidently provided islands of the right size, number, and proximity to continental areas to support the adaptation and diversification of vagile colonizers that went on to increase avian diversity on a global scale.
Collapse
|
37
|
Rowe KC, Aplin KP, Baverstock PR, Moritz C. Recent and Rapid Speciation with Limited Morphological Disparity in the Genus Rattus. Syst Biol 2011; 60:188-203. [PMID: 21239388 DOI: 10.1093/sysbio/syq092] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Kevin C. Rowe
- Museum of Vertebrate Zoology
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720-3160, USA
- Centre for Animal Conservation Genetics, School of Environmental Science and Management, Southern Cross University, PO Box 157, Lismore, NSW 2480, Australia
| | - Ken P. Aplin
- Australian National Wildlife Collection, CSIRO Division of Sustainable Ecosystems, GPO Box 284, Canberra, ACT 2601, Australia
| | - Peter R. Baverstock
- Centre for Animal Conservation Genetics, School of Environmental Science and Management, Southern Cross University, PO Box 157, Lismore, NSW 2480, Australia
| | - Craig Moritz
- Museum of Vertebrate Zoology
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720-3160, USA
| |
Collapse
|
38
|
Fordyce JA. Host shifts and evolutionary radiations of butterflies. Proc Biol Sci 2010; 277:3735-43. [PMID: 20610430 PMCID: PMC2992698 DOI: 10.1098/rspb.2010.0211] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Accepted: 06/16/2010] [Indexed: 11/12/2022] Open
Abstract
Ehrlich and Raven proposed a model of coevolution where major host plant shifts of butterflies facilitate a burst of diversification driven by their arrival to a new adaptive zone. One prediction of this model is that reconstructions of historical diversification of butterflies should indicate an increase in diversification rate following major host shifts. Using reconstructed histories of 15 butterfly groups, I tested this prediction and found general agreement with Ehrlich and Raven's model. Butterfly lineages with an inferred major historical host shift showed evidence of diversification rate variation, with a significant acceleration following the host shift. Lineages without an inferred major host shift generally agreed with a constant-rate model of diversification. These results are consistent with the view that host plant associations have played a profound role in the evolutionary history of butterflies, and show that major shifts to chemically distinct plant groups leave a historical footprint that remains detectable today.
Collapse
Affiliation(s)
- James A Fordyce
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA.
| |
Collapse
|
39
|
SHAFER AARONBA, CULLINGHAM CATHERINEI, CÔTÉ STEEVED, COLTMAN DAVIDW. Of glaciers and refugia: a decade of study sheds new light on the phylogeography of northwestern North America. Mol Ecol 2010; 19:4589-621. [PMID: 20849561 DOI: 10.1111/j.1365-294x.2010.04828.x] [Citation(s) in RCA: 260] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- AARON B. A. SHAFER
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - CATHERINE I. CULLINGHAM
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - STEEVE D. CÔTÉ
- Département de Biologie and Centre for Northern Studies, Université Laval, Québec, Québec G1V 0A6, Canada
| | - DAVID W. COLTMAN
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| |
Collapse
|
40
|
Mahler DL, Revell LJ, Glor RE, Losos JB. ECOLOGICAL OPPORTUNITY AND THE RATE OF MORPHOLOGICAL EVOLUTION IN THE DIVERSIFICATION OF GREATER ANTILLEAN ANOLES. Evolution 2010; 64:2731-45. [DOI: 10.1111/j.1558-5646.2010.01026.x] [Citation(s) in RCA: 338] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
41
|
Lovette IJ, Pérez-Emán JL, Sullivan JP, Banks RC, Fiorentino I, Córdoba-Córdoba S, Echeverry-Galvis M, Barker FK, Burns KJ, Klicka J, Lanyon SM, Bermingham E. A comprehensive multilocus phylogeny for the wood-warblers and a revised classification of the Parulidae (Aves). Mol Phylogenet Evol 2010; 57:753-70. [PMID: 20696258 DOI: 10.1016/j.ympev.2010.07.018] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Revised: 06/22/2010] [Accepted: 07/28/2010] [Indexed: 10/19/2022]
Abstract
The birds in the family Parulidae-commonly termed the New World warblers or wood-warblers-are a classic model radiation for studies of ecological and behavioral differentiation. Although the monophyly of a 'core' wood-warbler clade is well established, no phylogenetic hypothesis for this group has included a full sampling of wood-warbler species diversity. We used parsimony, maximum likelihood, and Bayesian methods to reconstruct relationships among all genera and nearly all wood-warbler species, based on a matrix of mitochondrial DNA (5840 nucleotides) and nuclear DNA (6 loci, 4602 nucleotides) characters. The resulting phylogenetic hypotheses provide a highly congruent picture of wood-warbler relationships, and indicate that the traditional generic classification of these birds recognizes many non-monophyletic groups. We recommend a revised taxonomy in which each of 14 genera (Seiurus, Helmitheros, Mniotilta, Limnothlypis, Protonotaria, Parkesia, Vermivora, Oreothlypis, Geothlypis, Setophaga, Myioborus, Cardellina, Basileuterus, Myiothlypis) corresponds to a well-supported clade; these nomenclatural changes also involve subsuming a number of well-known, traditional wood-warbler genera (Catharopeza, Dendroica, Ergaticus, Euthlypis, Leucopeza, Oporornis, Parula, Phaeothlypis, Wilsonia). We provide a summary phylogenetic hypothesis that will be broadly applicable to investigations of the historical biogeography, processes of diversification, and evolution of trait variation in this well studied avian group.
Collapse
Affiliation(s)
- Irby J Lovette
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, 159 Sapsucker Woods Road, Ithaca, NY 14950, USA.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
McCormack JE, Heled J, Delaney KS, Peterson AT, Knowles LL. CALIBRATING DIVERGENCE TIMES ON SPECIES TREES VERSUS GENE TREES: IMPLICATIONS FOR SPECIATION HISTORY OF APHELOCOMA JAYS. Evolution 2010; 65:184-202. [DOI: 10.1111/j.1558-5646.2010.01097.x] [Citation(s) in RCA: 210] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|
43
|
Vilaça ST, Santos FR. Biogeographic history of the species complex Basileuterus culicivorus (Aves, Parulidae) in the Neotropics. Mol Phylogenet Evol 2010; 57:585-97. [PMID: 20659571 DOI: 10.1016/j.ympev.2010.07.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 04/27/2010] [Accepted: 07/21/2010] [Indexed: 10/19/2022]
Abstract
The taxonomic status of Basileuterus culicivorus complex has been under debate for a long time. There are uncertainties about the relationships among recognized species (B. culicivorus and B. hypoleucus), and whether B. culicivorus can be considered as a single species. In order to elucidate the phylogenetic relationships among these species and their biogeographic history we used a broad geographic sampling from Mexico to Argentina of B. culicivorus and B. hypoleucus. Using a mitochondrial gene, a nuclear intron and microsatellites we identified highly structured groups according to their spatial distribution. The known subspecies of B. culicivorus formed monophyletic groups, except two ones from Brazil and Paraguay. Basileuterus hypoleucus sequences did not form a monophyletic clade, being more related to B. culicivorus from Brazil and Paraguay. The divergence time analysis indicated that the deep separation of the basal lineages of B. culicivorus occurred in Late Pliocene. Contrasting with the other geographically structured populations from Central and South America, the clade of birds from Brazil, Paraguay and Argentina showed a remarkably high population growth starting in the mid-Pleistocene, according to the most plausible evolutionary scenario expected for parulid birds of a range expansion directed southwards.
Collapse
Affiliation(s)
- Sibelle Torres Vilaça
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil.
| | | |
Collapse
|
44
|
Cusimano N, Renner SS. Slowdowns in Diversification Rates from Real Phylogenies May Not be Real. Syst Biol 2010; 59:458-64. [DOI: 10.1093/sysbio/syq032] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Natalie Cusimano
- Systematic Botany and Mycology, Department of Biology, University of Munich, D-80638 Munich, Germany;
| | - Susanne S. Renner
- Systematic Botany and Mycology, Department of Biology, University of Munich, D-80638 Munich, Germany;
| |
Collapse
|
45
|
Ricklefs RE. Host-pathogen coevolution, secondary sympatry and species diversification. Philos Trans R Soc Lond B Biol Sci 2010; 365:1139-47. [PMID: 20194175 DOI: 10.1098/rstb.2009.0279] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The build-up of species locally within a region by allopatric speciation depends on geographically separated (allopatric) sister populations becoming reproductively incompatible followed by secondary sympatry. Among birds, this has happened frequently in remote archipelagos, spectacular cases including the Darwin's finches (Geospizinae) and Hawaiian honeycreepers (Drepanidinae), but similar examples are lacking in archipelagos nearer to continental landmasses. Of the required steps in the speciation cycle, achievement of secondary sympatry appears to be limiting in near archipelagos and, by extension, in continental regions. Here, I suggest that secondary sympatry might be prevented by apparent competition mediated through pathogens that are locally coevolved with one population of host and are pathogenic in sister populations. The absence of numerous pathogens in remote archipelagos might, therefore, allow sister populations to achieve secondary sympatry more readily and thereby accelerate diversification. By similar reasoning, species should accumulate relatively slowly within continental regions. In this essay, I explore the assumptions and some implications of this model for species diversification.
Collapse
Affiliation(s)
- Robert E Ricklefs
- Department of Biology, University of Missouri-St Louis, One University Boulevard, St Louis, MO 63121-4499, USA.
| |
Collapse
|
46
|
Evolutionary diversification, coevolution between populations and their antagonists, and the filling of niche space. Proc Natl Acad Sci U S A 2010; 107:1265-72. [PMID: 20080597 DOI: 10.1073/pnas.0913626107] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The population component of a species' niche corresponds to the distribution of individuals across environments within a region. As evolutionary clades of species diversify, they presumably fill niche space, and, consequently, the rate of increase in species numbers slows. Total niche space and species numbers appear to be relatively stable over long periods, and so an increase in the species richness of one clade must be balanced by decrease in others. However, in several analyses, the total population niche space occupied per clade is independent of the number of species, suggesting that species in more diverse clades overlap more in niche space. This overlap appears to be accommodated by variation in the populations of each species, including their absence, within suitable niche space. I suggest that the uneven filling of niche space results from localized outcomes of the dynamic coevolutionary interactions of populations with their pathogens or other antagonists. Furthermore, I speculate that relationships with pathogens might constrain diversification if pathogen diversity increased with host diversity and resulted in more frequent host switching and emergent disease. Many indirect observations are consistent with these scenarios. However, the postulated influence of pathogens on the filling of niche space and diversification of clades primarily highlights our lack of knowledge concerning the space and time dimensions of coevolutionary interactions and their influence on population distribution and species diversification.
Collapse
|
47
|
Burbrink FT, Pyron RA. HOW DOES ECOLOGICAL OPPORTUNITY INFLUENCE RATES OF SPECIATION, EXTINCTION, AND MORPHOLOGICAL DIVERSIFICATION IN NEW WORLD RATSNAKES (TRIBE LAMPROPELTINI)? Evolution 2009; 64:934-43. [DOI: 10.1111/j.1558-5646.2009.00888.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
48
|
Rabosky DL. Heritability of Extinction Rates Links Diversification Patterns in Molecular Phylogenies and Fossils. Syst Biol 2009; 58:629-40. [DOI: 10.1093/sysbio/syp069] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
- Fuller Evolutionary Biology Program, Cornell Laboratory of Ornithology, 159 Sapsucker Woods Road, Ithaca, NY 14850, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| |
Collapse
|
49
|
Crisp MD, Cook LG. EXPLOSIVE RADIATION OR CRYPTIC MASS EXTINCTION? INTERPRETING SIGNATURES IN MOLECULAR PHYLOGENIES. Evolution 2009; 63:2257-65. [DOI: 10.1111/j.1558-5646.2009.00728.x] [Citation(s) in RCA: 140] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
50
|
Sridhar H, Beauchamp G, Shanker K. Why do birds participate in mixed-species foraging flocks? A large-scale synthesis. Anim Behav 2009. [DOI: 10.1016/j.anbehav.2009.05.008] [Citation(s) in RCA: 222] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|