1
|
Wang S, Wu L, Zhu Q, Wu J, Tang S, Zhao Y, Cheng Y, Zhang D, Qiao G, Zhang R, Lei F. Trait Variation and Spatiotemporal Dynamics across Avian Secondary Contact Zones. BIOLOGY 2024; 13:643. [PMID: 39194581 DOI: 10.3390/biology13080643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/16/2024] [Accepted: 08/20/2024] [Indexed: 08/29/2024]
Abstract
A secondary contact zone (SCZ) is an area where incipient species or divergent populations may meet, mate, and hybridize. Due to the diverse patterns of interspecific hybridization, SCZs function as field labs for illuminating the on-going evolutionary processes of speciation and the establishment of reproductive isolation. Interspecific hybridization is widely present in avian populations, making them an ideal system for SCZ studies. This review exhaustively summarizes the variations in unique traits within avian SCZs (vocalization, plumage, beak, and migratory traits) and the various movement patterns of SCZs observed in previous publications. It also highlights several potential future research directions in the genomic era, such as the relationship between phenotypic and genomic differentiation in SCZs, the genomic basis of trait differentiation, SCZs shared by multiple species, and accurate predictive models for forecasting future movements under climate change and human disturbances. This review aims to provide a more comprehensive understanding of speciation processes and offers a theoretical foundation for species conservation.
Collapse
Affiliation(s)
- Shangyu Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Wu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qianghui Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiahao Wu
- University of Chinese Academy of Sciences, Beijing 100049, China
- Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Shiyu Tang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yifang Zhao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yalin Cheng
- College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Gexia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Runzhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
2
|
Liu A, Geraldes A, Taylor EB. Historical and contemporary processes driving the origin and structure of an admixed population within a contact zone between subspecies of a north temperate diadromous fish. Mol Ecol 2024; 33:e17459. [PMID: 38994921 DOI: 10.1111/mec.17459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/23/2024] [Accepted: 04/30/2024] [Indexed: 07/13/2024]
Abstract
Hybridization between divergent lineages can result in losses of distinct evolutionary taxa. Alternatively, hybridization can lead to increased genetic variability that may fuel local adaptation and the generation of novel traits and/or taxa. Here, we examined single-nucleotide polymorphisms generated using genotyping-by-sequencing in a population of Dolly Varden char (Pisces: Salmonidae) that is highly admixed within a contact zone between two subspecies (Salvelinus malma malma, Northern Dolly Varden [NDV] and S. m. lordi, Southern Dolly Varden [SDV]) in southwestern Alaska to assess the spatial distribution of hybrids and to test hypotheses on the origin of the admixed population. Ancestry analysis revealed that this admixed population is composed of advanced generation hybrids between NDV and SDV or advanced backcrosses to SDV; no F1 hybrids were detected. Coalescent-based demographic modelling supported the origin of this population about 55,000 years ago by secondary contact between NDV and SDV with low levels of contemporary gene flow. Ancestry in NDV and SDV varies within the watershed and ancestry in NDV was positively associated with distance upstream from the sea, contingent on habitat-type sampled, and negatively associated with the number of migrations that individual fish made to the sea. Our results suggest that divergence between subspecies over hundreds of thousands of years may not be associated with significant reproductive isolation, but that elevated diversity owing to hybridization may have contributed to adaptive divergence in habitat use and life history.
Collapse
Affiliation(s)
- Amy Liu
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Armando Geraldes
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eric B Taylor
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Beaty Biodiversity Museum, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
3
|
Monjaraz-Ruedas R, Starrett J, Leavitt D, Hedin M. Broken Ring Speciation in California Mygalomorph Spiders (Nemesiidae, Calisoga). Am Nat 2024; 204:55-72. [PMID: 38857341 DOI: 10.1086/730262] [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] [Indexed: 06/12/2024]
Abstract
AbstractIdealized ring species, with approximately continuous gene flow around a geographic barrier but singular reproductive isolation at a ring terminus, are rare in nature. A broken ring species model preserves the geographic setting and fundamental features of an idealized model but accommodates varying degrees of gene flow restriction over complex landscapes through evolutionary time. Here we examine broken ring species dynamics in Calisoga spiders, which, like the classic ring species Ensatina salamanders, are distributed around the Central Valley of California. Using nuclear and mitogenomic data, we test key predictions of common ancestry, ringlike biogeography, biogeographic timing, population connectivity, and terminal overlap. We show that a ring complex of populations shares a single common ancestor, and from an ancestral area in the Sierra Nevada mountains, two distributional and phylogenomic arms encircle the Central Valley. Isolation by distance occurs along these distributional arms, although gene flow restriction is also evident. Where divergent lineages meet in the South Coast Ranges, we find rare lineage sympatry, without evidence for nuclear gene flow and with clear evidence for morphological and ecological divergence. We discuss general insights provided by broken ring species and how such a model could be explored and extended in other systems and future studies.
Collapse
|
4
|
Askelson KK, Spellman GM, Irwin D. Genomic divergence and introgression between cryptic species of a widespread North American songbird. Mol Ecol 2023; 32:6839-6853. [PMID: 37916530 DOI: 10.1111/mec.17169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 09/20/2023] [Indexed: 11/03/2023]
Abstract
Analysis of genomic variation among related populations can sometimes reveal distinct species that were previously undescribed due to similar morphological appearances, and close examination of such cases can provide much insight regarding speciation. Genomic data can also reveal the role of reticulate evolution in differentiation and speciation. White-breasted nuthatches (Sitta carolinensis) are widely distributed North American songbirds that are currently classified as a single species but have been suspected to represent a case of cryptic speciation. Previous genetic analyses suggested four divergent groups, but it was unclear whether these represented multiple reproductively isolated species. Using extensive genomic sampling of over 350 white-breasted nuthatches from across North America and a new chromosome-level reference genome, we asked if white-breasted nuthatches are comprised of multiple species and whether introgression has occurred between divergent populations. Genomic variation of over 300,000 loci revealed four highly differentiated populations (Pacific, n = 45; Eastern, n = 23; Rocky Mountains North, n = 138; and Rocky Mountains South, n = 150) with geographic ranges that are adjacent. We observed a moderate degree of admixture between Rocky Mountain populations but only a small number of hybrids between the Rockies and the Eastern population. The rarity of hybrids together with high levels of differentiation between populations is supportive of populations having some level of reproductive isolation. Between populations, we show evidence for introgression from a divergent ghost lineage of white-breasted nuthatches into the Rocky Mountains South population, which is otherwise closely related to Rocky Mountains North. We conclude that white-breasted nuthatches are best considered at least three species and that ghost lineage introgression has contributed to differentiation between the two Rocky Mountain populations. White-breasted nuthatches provide a dramatic case of morphological similarity despite high genomic differentiation, and the varying levels of reproductive isolation among the four groups provide an example of the speciation continuum.
Collapse
Affiliation(s)
- Kenneth K Askelson
- Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Garth M Spellman
- Department of Zoology, Denver Museum of Nature & Science, Denver, Colorado, USA
| | - Darren Irwin
- Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
5
|
Maldonado-Coelho M, Dos Santos SS, Isler ML, Svensson-Coelho M, Sotelo-Muñoz M, Miyaki CY, Ricklefs RE, Blake JG. Evolutionary and Ecological Processes Underlying Geographic Variation in Innate Bird Songs. Am Nat 2023; 202:E31-E52. [PMID: 37531273 DOI: 10.1086/725016] [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] [Indexed: 08/04/2023]
Abstract
AbstractEcological and evolutionary processes underlying spatial variation in signals involved in mate recognition and reproductive isolation are crucial to understanding the causes of population divergence and speciation. Here, to test hypotheses concerning the causes of song divergence, we examine how songs of two sister species of Atlantic Forest suboscine birds with innate songs, the Pyriglena fire-eye antbirds, vary across their ranges. Specifically, we evaluated the influence of isolation by distance and introgressive hybridization, as well as morphological and environmental variation, on geographic variation in male songs. Analyses based on 496 male vocalizations from 63 locations across a 2,200-km latitudinal transect revealed clinal changes in the structure of songs and showed that introgressive hybridization increases both the variability and the homogenization of songs in the contact zone between the two species. We also found that isolation by distance, morphological constraints, the environment, and genetic introgression independently predicted song variation across geographic space. Our study shows the importance of an integrative approach that investigates the roles of distinct ecological and evolutionary processes that influence acoustic signal evolution.
Collapse
|
6
|
Nikelski E, Rubtsov AS, Irwin D. High heterogeneity in genomic differentiation between phenotypically divergent songbirds: a test of mitonuclear co-introgression. Heredity (Edinb) 2023; 130:1-13. [PMID: 36463372 PMCID: PMC9814147 DOI: 10.1038/s41437-022-00580-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 12/05/2022] Open
Abstract
Comparisons of genomic variation among closely related species often show more differentiation in mitochondrial DNA (mtDNA) and sex chromosomes than in autosomes, a pattern expected due to the differing effective population sizes and evolutionary dynamics of these genomic components. Yet, introgression can cause species pairs to deviate dramatically from general differentiation trends. The yellowhammer (Emberiza citrinella) and pine bunting (E. leucocephalos) are hybridizing avian sister species that differ greatly in appearance and moderately in nuclear DNA, but that show no mtDNA differentiation. This discordance is best explained by adaptive mtDNA introgression-a process that can select for co-introgression at nuclear genes with mitochondrial functions (mitonuclear genes). To better understand these discordant differentiation patterns and characterize nuclear differentiation in this system, we investigated genome-wide differentiation between allopatric yellowhammers and pine buntings and compared it to what was seen previously in mtDNA. We found significant nuclear differentiation that was highly heterogeneous across the genome, with a particularly wide differentiation peak on the sex chromosome Z. We further investigated mitonuclear gene co-introgression between yellowhammers and pine buntings and found support for this process in the direction of pine buntings into yellowhammers. Genomic signals indicative of co-introgression were common in mitonuclear genes coding for subunits of the mitoribosome and electron transport chain complexes. Such introgression of mitochondrial DNA and mitonuclear genes provides a possible explanation for the patterns of high genomic heterogeneity in genomic differentiation seen among some species groups.
Collapse
Affiliation(s)
- Ellen Nikelski
- Department of Zoology, and Biodiversity Research Centre, 6270 University Blvd., University of British Columbia, Vancouver, BC, Canada.
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.
| | | | - Darren Irwin
- Department of Zoology, and Biodiversity Research Centre, 6270 University Blvd., University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
7
|
Lucati F, Miró A, Bosch J, Caner J, Jowers MJ, Rivera X, Donaire-Barroso D, Rebelo R, Ventura M. New insights on patterns of genetic admixture and phylogeographic history in Iberian high mountain populations of midwife toads. PLoS One 2022; 17:e0277298. [PMID: 36454960 PMCID: PMC9714896 DOI: 10.1371/journal.pone.0277298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 10/24/2022] [Indexed: 12/05/2022] Open
Abstract
Multiple Quaternary glacial refugia in the Iberian Peninsula, commonly known as "refugia within refugia", allowed diverging populations to come into contact and admix, potentially boosting substantial mito-nuclear discordances. In this study, we employ a comprehensive set of mitochondrial and nuclear markers to shed light onto the drivers of geographical differentiation in Iberian high mountain populations of the midwife toads Alytes obstetricans and A. almogavarii from the Pyrenees, Picos de Europa and Guadarrama Mountains. In the three analysed mountain regions, we detected evidence of extensive mito-nuclear discordances and/or admixture between taxa. Clustering analyses identified three major divergent lineages in the Pyrenees (corresponding to the eastern, central and central-western Pyrenees), which possibly recurrently expanded and admixed during the succession of glacial-interglacial periods that characterised the Late Pleistocene, and that currently follow a ring-shaped diversification pattern. On the other hand, populations from the Picos de Europa mountains (NW Iberian Peninsula) showed a mitochondrial affinity to central-western Pyrenean populations and a nuclear affinity to populations from the central Iberian Peninsula, suggesting a likely admixed origin for Picos de Europa populations. Finally, populations from the Guadarrama Mountain Range (central Iberian Peninsula) were depleted of genetic diversity, possibly as a consequence of a recent epidemic of chytridiomycosis. This work highlights the complex evolutionary history that shaped the current genetic composition of high mountain populations, and underscores the importance of using a multilocus approach to better infer the dynamics of population divergence.
Collapse
Affiliation(s)
- Federica Lucati
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & Global Change and Sustainability Institute (CHANGE), Faculty of Sciences, University of Lisbon, Lisbon, Portugal
- Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Catalonia, Spain
- Sociodemography Research Group (DemoSoc), University Pompeu Fabra (UPF), Barcelona, Spain
| | - Alexandre Miró
- Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Catalonia, Spain
| | - Jaime Bosch
- IMIB-Research Unit of Biodiversity (CSIC/UO/PA), Universidad de Oviedo, Mieres, Spain
- Centro de Investigación, Seguimiento y Evaluación, Parque Nacional Sierra de Guadarrama, Rascafría, Spain
| | - Jenny Caner
- Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Catalonia, Spain
| | - Michael Joseph Jowers
- Departamento de Zoología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
- National Institute of Ecology (NIE), Maseo-myeon, Seocheon-gun, Republic of Korea
| | - Xavier Rivera
- Catalan Society of Herpetology, Museu Blau, Barcelona, Catalonia, Spain
| | | | - Rui Rebelo
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & Global Change and Sustainability Institute (CHANGE), Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Marc Ventura
- Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Catalonia, Spain
| |
Collapse
|
8
|
Natola L, Seneviratne SS, Irwin D. Population genomics of an emergent tri-species hybrid zone. Mol Ecol 2022; 31:5356-5367. [PMID: 35951007 DOI: 10.1111/mec.16650] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/03/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022]
Abstract
Isolating barriers that drive speciation are commonly studied in the context of two-species hybrid zones. There is, however, evidence that more complex introgressive relationships are common in nature. Here, we use field observations and genomic analysis, including the sequencing and assembly of a novel reference genome, to study an emergent hybrid zone involving two colliding hybrid zones of three woodpecker species: red-breasted, red-naped, and yellow-bellied sapsuckers (Sphyrapicus ruber, S. nuchalis, and S. varius). Surveys of the area surrounding Prince George, British Columbia, Canada, show that all three species are sympatric, and Genotyping-by-Sequencing identifies hybrids from each species pair and birds with ancestry from all three species. Observations of phenotypes and genotypes of mated pairs provide evidence for assortative mating, though there is some heterospecific pairing. Hybridization is more extensive in this tri-species hybrid zone than in two di-species hybrid zones. However, there is no evidence of a hybrid swarm and admixture is constrained to contact zones, so we classify this region as a tension zone and invoke selection against hybrids as a likely mechanism maintaining species boundaries. Analysis of sapsucker age classes does not show disadvantages in hybrid survival to adulthood, so we speculate the selection upholding the tension zone may involve hybrid fecundity. Gene flow among all sapsuckers in di-species hybrid zones suggests introgression probably occurred before the formation of this tri-species hybrid zone, and might result from bridge hybridization, vagrancies, or other three-species interactions.
Collapse
Affiliation(s)
- Libby Natola
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada.,Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sampath S Seneviratne
- Avian Sciences and Conservation, Department of Zoology, University of Colombo, Colombo, Sri Lanka
| | - Darren Irwin
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada.,Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
9
|
Gilbert KJ, Moinet A, Peischl S. Gene surfing of underdominant alleles promotes formation of hybrid zones. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210006. [PMID: 35067089 PMCID: PMC8784928 DOI: 10.1098/rstb.2021.0006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 07/28/2021] [Indexed: 11/12/2022] Open
Abstract
The distribution of genetic diversity over geographical space has long been investigated in population genetics and serves as a useful tool to understand evolution and history of populations. Within some species or across regions of contact between two species, there are instances where there is no apparent ecological determinant of sharp changes in allele frequencies or divergence. To further understand these patterns of spatial genetic structure and potential species divergence, we model the establishment of clines that occur due to the surfing of underdominant alleles during range expansions. We provide analytical approximations for the fixation probability of underdominant alleles at expansion fronts and demonstrate that gene surfing can lead to clines in one-dimensional range expansions. We extend these results to multiple loci via a mixture of analytical theory and individual-based simulations. We study the interaction between the strength of selection against heterozygotes, migration rates, and local recombination rates on the formation of stable hybrid zones. Clines created by surfing at different loci can attract each other and align after expansion, if they are sufficiently close in space and in terms of recombination distance. Our findings suggest that range expansions can set the stage for parapatric speciation due to the alignment of multiple selective clines, even in the absence of ecologically divergent selection. This article is part of the theme issue 'Species' ranges in the face of changing environments (part I)'.
Collapse
Affiliation(s)
- Kimberly J. Gilbert
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern 3013, Switzerland
| | - Antoine Moinet
- Interfaculty Bioinformatics Unit, University of Bern, Baltzerstrasse 6, Bern 3012, Switzerland
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, Bern 3012, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Stephan Peischl
- Interfaculty Bioinformatics Unit, University of Bern, Baltzerstrasse 6, Bern 3012, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| |
Collapse
|
10
|
Cumer T, Machado AP, Dumont G, Bontzorlos V, Ceccherelli R, Charter M, Dichmann K, Kassinis N, Lourenço R, Manzia F, Martens HD, Prévost L, Rakovic M, Roque I, Siverio F, Roulin A, Goudet J. Landscape and climatic variations shaped secondary contacts amid barn owls of the Western Palearctic. Mol Biol Evol 2021; 39:6454100. [PMID: 34893883 PMCID: PMC8789042 DOI: 10.1093/molbev/msab343] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The combined actions of climatic variations and landscape barriers shape the history of natural populations. When organisms follow their shifting niches, obstacles in the landscape can lead to the splitting of populations, on which evolution will then act independently. When two such populations are reunited, secondary contact occurs in a broad range of admixture patterns, from narrow hybrid zones to the complete dissolution of lineages. A previous study suggested that barn owls colonized the Western Palearctic after the last glaciation in a ring-like fashion around the Mediterranean Sea, and conjectured an admixture zone in the Balkans. Here, we take advantage of whole-genome sequences of 94 individuals across the Western Palearctic to reveal the complex history of the species in the region using observational and modeling approaches. Even though our results confirm that two distinct lineages colonized the region, one in Europe and one in the Levant, they suggest that it predates the last glaciation and identify a secondary contact zone between the two in Anatolia. We also show that barn owls recolonized Europe after the glaciation from two distinct glacial refugia: a previously identified western one in Iberia and a new eastern one in Italy. Both glacial lineages now communicate via eastern Europe, in a wide and permeable contact zone. This complex history of populations enlightens the taxonomy of Tyto alba in the region, highlights the key role played by mountain ranges and large water bodies as barriers and illustrates the power of population genomics in uncovering intricate demographic patterns.
Collapse
Affiliation(s)
- Tristan Cumer
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Ana Paula Machado
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Guillaume Dumont
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Vasileios Bontzorlos
- Green Fund, Kifisia, Athens, Greece.,"TYTO" - Organization for the Management and Conservation of Biodiversity in Agricultural Ecosystems, Larisa, Greece
| | | | - Motti Charter
- Shamir Research Institute, University of Haifa, Katzrin, Israel.,Department of Geography and Environmental Sciences, University of Haifa, Haifa, Israel
| | | | | | - Rui Lourenço
- MED Mediterranean Institute for Agriculture, Environment and Development, Laboratory of Ornithology, IIFA, University of Évora, Évora, Portugal
| | | | | | - Laure Prévost
- Association C.H.E.N.E, Centre d'Hébergement et d'Etude sur la Nature et l'Environnement, Allouville-Bellefosse, 76190, France
| | - Marko Rakovic
- Natural History Museum of Belgrade, Belgrade, Serbia
| | - Inês Roque
- MED Mediterranean Institute for Agriculture, Environment and Development, Laboratory of Ornithology, IIFA, University of Évora, Évora, Portugal
| | - Felipe Siverio
- Canary Islands' Ornithology and Natural History Group (GOHNIC), 38480 Buenavista del Norte, Tenerife, Canary Islands, Spain
| | - Alexandre Roulin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| |
Collapse
|
11
|
Wolfgramm H, Martens J, Töpfer T, Vamberger M, Pathak A, Stuckas H, Päckert M. Asymmetric allelic introgression across a hybrid zone of the coal tit ( Periparus ater) in the central Himalayas. Ecol Evol 2021; 11:17332-17351. [PMID: 34938512 PMCID: PMC8668783 DOI: 10.1002/ece3.8369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/26/2021] [Accepted: 11/02/2021] [Indexed: 11/07/2022] Open
Abstract
In the Himalayas, a number of secondary contact zones have been described for vicariant vertebrate taxa. However, analyses of genetic divergence and admixture are missing for most of these examples. In this study, we provide a population genetic analysis for the coal tit (Periparus ater) hybrid zone in Nepal. Intermediate phenotypes between the distinctive western "spot-winged tit" (P. a. melanolophus) and Eastern Himalayan coal tits (P. a. aemodius) occur across a narrow range of <100 km in western Nepal. As a peculiarity, another distinctive cinnamon-bellied form is known from a single population so far. Genetic admixture of western and eastern mitochondrial lineages was restricted to the narrow zone of phenotypically intermediate populations. The cline width was estimated 46 km only with a center close to the population of the cinnamon-bellied phenotype. In contrast, allelic introgression of microsatellite loci was asymmetrical from eastern P. a. aemodius into far western populations of phenotypic P. a. melanolophus but not vice versa. Accordingly, the microsatellite cline was about 3.7 times wider than the mitochondrial one.
Collapse
Affiliation(s)
- Hannes Wolfgramm
- Senckenberg Natural History Collections DresdenDresdenGermany
- Present address:
Department of Functional GenomicsInterfaculty Institute of Genetics and Functional GenomicsUniversity Medicine GreifswaldGreifswaldGermany
| | - Jochen Martens
- Institute of Organismic and Molecular Evolution (iomE)Johannes Gutenberg UniversityMainzGermany
| | - Till Töpfer
- Leibniz Institute for the Analysis of Biodiversity ChangeZoological Research Museum Alexander KoenigBonnGermany
| | | | - Abhinaya Pathak
- Department of National Parks and Wildlife ConservationKathmanduNepal
| | - Heiko Stuckas
- Senckenberg Natural History Collections DresdenDresdenGermany
| | - Martin Päckert
- Senckenberg Natural History Collections DresdenDresdenGermany
| |
Collapse
|
12
|
Distant but related: genetic structure in the circum-boreal bumblebee Bombus jonellus (Kirby, 1802). Polar Biol 2021. [DOI: 10.1007/s00300-021-02937-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
13
|
Wenzell KE, McDonnell AJ, Wickett NJ, Fant JB, Skogen KA. Incomplete reproductive isolation and low genetic differentiation despite floral divergence across varying geographic scales in Castilleja. AMERICAN JOURNAL OF BOTANY 2021; 108:1270-1288. [PMID: 34289081 DOI: 10.1002/ajb2.1700] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/18/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Divergence depends on the strength of selection and frequency of gene flow between taxa, while reproductive isolation relies on mating barriers and geographic distance. Less is known about how these processes interact at early stages of speciation. Here, we compared population-level differentiation in floral phenotype and genetic sequence variation among recently diverged Castilleja to explore patterns of diversification under different scenarios of reproductive isolation. METHODS Using target enrichment enabled by the Angiosperms353 probe set, we assessed genetic distance among 50 populations of four Castilleja species. We investigated whether patterns of genetic divergence are explained by floral trait variation or geographic distance in two focal groups: the widespread C. sessiliflora and the more restricted C. purpurea species complex. RESULTS We document that C. sessiliflora and the C. purpurea complex are characterized by high diversity in floral color across varying geographic scales. Despite phenotypic divergence, groups were not well supported in phylogenetic analyses, and little genetic differentiation was found across targeted Angiosperms353 loci. Nonetheless, a principal coordinate analysis of single nucleotide polymorphisms revealed differentiation within C. sessiliflora across floral morphs and geography and less differentiation among species of the C. purpurea complex. CONCLUSIONS Patterns of genetic distance in C. sessiliflora suggest species cohesion maintained over long distances despite variation in floral traits. In the C. purpurea complex, divergence in floral color across narrow geographic clines may be driven by recent selection on floral color. These contrasting patterns of floral and genetic differentiation reveal that divergence can arise via multiple eco-evolutionary paths.
Collapse
Affiliation(s)
- Katherine E Wenzell
- Program in Plant Biology and Conservation, Northwestern University, O.T. Hogan Hall, Room 6-140B, 2205 Tech Drive, Evanston, IL, 60208, USA
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL, 60022, USA
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Angela J McDonnell
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL, 60022, USA
| | - Norman J Wickett
- Program in Plant Biology and Conservation, Northwestern University, O.T. Hogan Hall, Room 6-140B, 2205 Tech Drive, Evanston, IL, 60208, USA
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL, 60022, USA
| | - Jeremie B Fant
- Program in Plant Biology and Conservation, Northwestern University, O.T. Hogan Hall, Room 6-140B, 2205 Tech Drive, Evanston, IL, 60208, USA
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL, 60022, USA
| | - Krissa A Skogen
- Program in Plant Biology and Conservation, Northwestern University, O.T. Hogan Hall, Room 6-140B, 2205 Tech Drive, Evanston, IL, 60208, USA
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL, 60022, USA
| |
Collapse
|
14
|
Mikkelsen EK, Irwin D. Ongoing production of low-fitness hybrids limits range overlap between divergent cryptic species. Mol Ecol 2021; 30:4090-4102. [PMID: 34101940 DOI: 10.1111/mec.16015] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 05/13/2021] [Accepted: 05/26/2021] [Indexed: 01/23/2023]
Abstract
Contact zones between recently diverged taxa provide opportunities to examine the causes of reproductive isolation and the processes that determine whether two species can coexist over a broad region. The Pacific wren (Troglodytes pacificus) and winter wren (Troglodytes hiemalis) are two morphologically similar songbirds that started diverging about 4 million years ago, older than most sister species pairs of temperate songbirds. The ranges of these species come into narrow contact in western Canada, where the two species remain distinct. To assess evidence for differentiation, hybridization and introgression in this system, we examined variation in over 250,000 single nucleotide polymorphism markers distributed across the genome. The two species formed highly divergent genetic clusters, consistent with long-term differentiation. In a set of 75 individuals, two first-generation hybrids (i.e., F1 's) were detected, indicating only moderate levels of assortative mating between these taxa. We found no recent backcrosses or other evidence of recent breeding success of F1 's, indicating very low or zero fitness of F1 hybrids. Examination of genomic variation shows evidence for only a single backcrossing event many generations ago. The moderate rate of hybridization combined with very low F1 hybrid fitness is expected to result in a population sink in the contact zone, largely explaining the narrow overlap of the two species. If such dynamics are common in nature, they could explain the narrow range overlap often observed between pairs of closely related species.
Collapse
Affiliation(s)
- Else K Mikkelsen
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Darren Irwin
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
15
|
Climate Change Impacts on Himalayan Biodiversity: Evidence-Based Perception and Current Approaches to Evaluate Threats Under Climate Change. J Indian Inst Sci 2021. [DOI: 10.1007/s41745-021-00237-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
16
|
Wang Y, Feijó A, Cheng J, Xia L, Wen Z, Ge D, Sun J, Lu L, Li S, Yang Q. Ring distribution patterns-diversification or speciation? Comparative phylogeography of two small mammals in the mountains surrounding the Sichuan Basin. Mol Ecol 2021; 30:2641-2658. [PMID: 33817880 DOI: 10.1111/mec.15913] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 03/15/2021] [Accepted: 03/24/2021] [Indexed: 01/26/2023]
Abstract
Studying the genetic differentiation in a unique geographical area contributes to understanding the process of speciation. Here, we explore the spatial genetic structure and underlying formation mechanism of two congeneric small mammal species (Apodemus draco and A. chevrieri), which are mainly distributed in the mountains surrounding the lowland Sichuan Basin, southwest China. We applied a set of comparative phylogeographical analyses to determine their genetic diversification patterns, combining mitochondrial (Cytb and COI) and nuclear (microsatellite loci) markers, with dense sampling throughout the range (411 A. draco from 21 sites and 191 A. chevrieri from 22 sites). Moreover, we performed three complementary statistical methods to investigate the correlation between genotype and geographical and environmental components, and predicted the potential suitable distributional range under the present and historical climate conditions. Our results suggest that both species have experienced allopatric differentiation and admixture in historical periods, resulting in a ring-shape diversification, under the barrier effect of the Sichuan Basin. We infer that the tectonic events of the Qinghai-Tibetan Plateau and climatic oscillations during the Quaternary played an important role on the genetic divergence of the two species by providing environmental heterogeneity and geographical variation. Our study reveals a case of two sympatric small mammals following a ring-shaped diversification pattern and provides insight into the process of differentiation.
Collapse
Affiliation(s)
- Yanqun Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,School of Animal Science, Xichang College, Xichang, Sichuan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Anderson Feijó
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jian Sun
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Liang Lu
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Centre for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Song Li
- Chinese Academy of Sciences, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
17
|
Mohammadi Z, Ghorbani F, Kami HG, Khajeh A, Olsson U. Molecular Phylogeny of the Subgenus Karstomys Reveals Genetic Signature of Post-Glacial Colonization of Apodemus mystacinus (Rodentia: Muridae) in the Zagros Mountains from Different Refugia. Zoolog Sci 2021; 38:72-81. [PMID: 33639721 DOI: 10.2108/zs200065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 09/10/2020] [Indexed: 11/17/2022]
Abstract
Eastern broad-toothed field mouse, Apodemus mystacinus, is a rocky habitat dwelling rodent distributed in Asia Minor, the Levant, the Caucasus, and the Zagros Mountains. In this study, we investigated the phylogenetic relationship between different populations of A. mystacinus throughout its range, based on the mitochondrial cytb marker. Phylogenetic analyses revealed the existence of five separately evolving lineages within A. mystacinus, of which two previously unrecognized lineages were identified in the Zagros Mountains and the Levant. Divergence between two major clades of the subgenus Karstomys, corresponding to A. mystacinus and Apodemus epimelas, is inferred to coincide with the Messinian Salinity Crisis (Late Miocene), whereas the splits between major lineages of A. mystacinus are inferred to have occurred during the Pleistocene. Colonization of the Zagros may have occurred from different refugia via eastward migration of the Turkish population and then again by a more recent colonization from the Caucasus, after reopening of the land corridor between the Caucasus and the Zagros Mountains during the Holocene drought.
Collapse
Affiliation(s)
- Zeinolabedin Mohammadi
- Department of Biology, Faculty of Sciences, Golestan University, Gorgan, 39361-79142, Golestan, Iran, .,Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
| | - Fatemeh Ghorbani
- Department of Biology, Faculty of Sciences, Golestan University, Gorgan, 39361-79142, Golestan, Iran
| | - Haji Gholi Kami
- Department of Biology, Faculty of Sciences, Golestan University, Gorgan, 39361-79142, Golestan, Iran
| | - Asghar Khajeh
- Department of Crop Productions Technology, Faculty of Agriculture, Higher Educational Complex of Saravan, Saravan 99516-34145, Iran
| | - Urban Olsson
- University of Gothenburg, Department of Biology and Environmental Sciences, Systematics and Biodiversity, SE-405 30 Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, SE-405 30 Göteborg, Sweden
| |
Collapse
|
18
|
Choi JY, Purugganan M, Stacy EA. Divergent Selection and Primary Gene Flow Shape Incipient Speciation of a Riparian Tree on Hawaii Island. Mol Biol Evol 2020; 37:695-710. [PMID: 31693149 PMCID: PMC7038655 DOI: 10.1093/molbev/msz259] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A long-standing goal of evolutionary biology is to understand the mechanisms underlying the formation of species. Of particular interest is whether or not speciation can occur in the presence of gene flow and without a period of physical isolation. Here, we investigated this process within Hawaiian Metrosideros, a hypervariable and highly dispersible woody species complex that dominates the Hawaiian Islands in continuous stands. Specifically, we investigated the origin of Metrosideros polymorpha var. newellii (newellii), a riparian ecotype endemic to Hawaii Island that is purportedly derived from the archipelago-wide M. polymorpha var. glaberrima (glaberrima). Disruptive selection across a sharp forest-riparian ecotone contributes to the isolation of these varieties and is a likely driver of newellii's origin. We examined genome-wide variation of 42 trees from Hawaii Island and older islands. Results revealed a split between glaberrima and newellii within the past 0.3-1.2 My. Admixture was extensive between lineages within Hawaii Island and between islands, but introgression from populations on older islands (i.e., secondary gene flow) did not appear to contribute to the emergence of newellii. In contrast, recurrent gene flow (i.e., primary gene flow) between glaberrima and newellii contributed to the formation of genomic islands of elevated absolute and relative divergence. These regions were enriched for genes with regulatory functions as well as for signals of positive selection, especially in newellii, consistent with divergent selection underlying their formation. In sum, our results support riparian newellii as a rare case of incipient ecological speciation with primary gene flow in trees.
Collapse
Affiliation(s)
- Jae Young Choi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY
| | - Michael Purugganan
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY.,Center for Genomics and Systems Biology, NYU Abu Dhabi Research Institute, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Elizabeth A Stacy
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV
| |
Collapse
|
19
|
Deviatkin AA, Kholodilov IS, Belova OA, Bugmyrin SV, Bespyatova LA, Ivannikova AY, Vakulenko YA, Lukashev AN, Karganova GG. Baltic Group Tick-Borne Encephalitis Virus Phylogeography: Systemic Inconsistency Pattern between Genetic and Geographic Distances. Microorganisms 2020; 8:microorganisms8101589. [PMID: 33076346 PMCID: PMC7602664 DOI: 10.3390/microorganisms8101589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/07/2020] [Accepted: 10/13/2020] [Indexed: 10/26/2022] Open
Abstract
Tick-Borne Encephalitis Virus (TBEV) is a dangerous arbovirus widely distributed in Northern Eurasia. The area of this pathogen changes over time. At the beginning of the 2000s, the Ixodes tick populations in Karelia increased. At the same time, the area of I. persulcatus, the main vector of the Siberian TBEV subtype, also expanded. Herein, we sequenced 10 viruses isolated from ticks collected in three locations from the Karelia region in 2008-2018. PCR positive samples were passaged in suckling mice or pig embryo kidney cells (PEK). After the second passage in suckling, mice viral RNA was isolated and E-gene fragment was sequenced. Viral sequences were expected to be similar or nearly identical. Instead, there was up to a 4.8% difference in nucleotide sequence, comparable with the most diverse viruses belonging to the Baltic subgroup in Siberian TBEV subtype (Baltic TBEV-Sib). To reveal whether this was systemic or incidental, a comprehensive phylogeographical analysis was conducted. Interestingly, viruses within each geographic region demonstrated comparable diversity to the whole Baltic TBEV-Sib. Moreover, Baltic TBEV-Sib has a distribution area limited by three ecological regions. This means that active virus mixing occurs in the vast geographic area forming one common virus pool. The most plausible explanation is the involvement of flying animals in the TBEV spread.
Collapse
Affiliation(s)
- Andrei A. Deviatkin
- Laboratory of Molecular Biology and Biochemistry, Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119048 Moscow, Russia;
- Correspondence: (A.A.D.); (G.G.K.)
| | - Ivan S. Kholodilov
- Laboratory of Biology of Arboviruses, Chumakov Institute of Poliomyelitis and Viral Encephalitides (FSBSI “Chumakov FSC R&D IBP RAS), 108819 Moscow, Russia; (I.S.K.); (O.A.B.); (A.Y.I.)
| | - Oxana A. Belova
- Laboratory of Biology of Arboviruses, Chumakov Institute of Poliomyelitis and Viral Encephalitides (FSBSI “Chumakov FSC R&D IBP RAS), 108819 Moscow, Russia; (I.S.K.); (O.A.B.); (A.Y.I.)
| | - Sergey V. Bugmyrin
- Laboratory for Animal and Plant Parasitology, Institute of Biology of the Karelian Research Centre of the Russian Academy of Sciences (IB KarRC RAS), 185910 Petrozavodsk, Russia; (S.V.B.); (L.A.B.)
| | - Lubov A. Bespyatova
- Laboratory for Animal and Plant Parasitology, Institute of Biology of the Karelian Research Centre of the Russian Academy of Sciences (IB KarRC RAS), 185910 Petrozavodsk, Russia; (S.V.B.); (L.A.B.)
| | - Anna Y. Ivannikova
- Laboratory of Biology of Arboviruses, Chumakov Institute of Poliomyelitis and Viral Encephalitides (FSBSI “Chumakov FSC R&D IBP RAS), 108819 Moscow, Russia; (I.S.K.); (O.A.B.); (A.Y.I.)
| | - Yulia A. Vakulenko
- Department of Virology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia
| | - Alexander N. Lukashev
- Laboratory of Molecular Biology and Biochemistry, Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119048 Moscow, Russia;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia
| | - Galina G. Karganova
- Laboratory of Biology of Arboviruses, Chumakov Institute of Poliomyelitis and Viral Encephalitides (FSBSI “Chumakov FSC R&D IBP RAS), 108819 Moscow, Russia; (I.S.K.); (O.A.B.); (A.Y.I.)
- Department of Organization and Technology of Immunobiological Preparations, Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- Correspondence: (A.A.D.); (G.G.K.)
| |
Collapse
|
20
|
Cronemberger ÁA, Aleixo A, Mikkelsen EK, Weir JT. Postzygotic isolation drives genomic speciation between highly crypticHypocnemisantbirds from Amazonia. Evolution 2020; 74:2512-2525. [DOI: 10.1111/evo.14103] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 08/28/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Áurea A. Cronemberger
- Department of Ecology and Evolutionary Biology University of Toronto Toronto Canada
- Department of Biological Sciences University of Toronto Scarborough Toronto Canada
- Pós‐graduação em Biodiversidade e Evolução Museu Paraense Emílio Goeldi Belém Brazil
| | - Alexandre Aleixo
- Pós‐graduação em Biodiversidade e Evolução Museu Paraense Emílio Goeldi Belém Brazil
- Finnish Museum of Natural History University of Helsinki Helsinki Finland
| | - Else K. Mikkelsen
- Department of Ecology and Evolutionary Biology University of Toronto Toronto Canada
- Department of Biological Sciences University of Toronto Scarborough Toronto Canada
| | - Jason T. Weir
- Department of Ecology and Evolutionary Biology University of Toronto Toronto Canada
- Department of Biological Sciences University of Toronto Scarborough Toronto Canada
- Department of Natural History Royal Ontario Museum Toronto Canada
| |
Collapse
|
21
|
Wilkins MR, Odom KJ, Benedict L, Safran RJ. Analysis of female song provides insight into the evolution of sex differences in a widely studied songbird. Anim Behav 2020. [DOI: 10.1016/j.anbehav.2020.07.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
22
|
Xiao JH, Ding X, Li L, Ma H, Ci XQ, van der Merwe M, Conran JG, Li J. Miocene diversification of a golden-thread nanmu tree species ( Phoebe zhennan, Lauraceae) around the Sichuan Basin shaped by the East Asian monsoon. Ecol Evol 2020; 10:10543-10557. [PMID: 33072279 PMCID: PMC7548194 DOI: 10.1002/ece3.6710] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 01/04/2023] Open
Abstract
Understanding the role of climate changes and geography as drivers of population divergence and speciation is a long‐standing goal of evolutionary biology and can inform conservation. In this study, we used restriction site‐associated DNA sequencing (RAD‐seq) to evaluate genetic diversity, population structure, and infer demographic history of the endangered tree, Phoebe zhennan which is distributed around the Sichuan Basin. Genomic patterns revealed two distinct clusters, each largely confined to the West and East. Despite sympatry of the two genomic clusters at some sites, individuals show little or no evidence of genomic introgression. Demographic modeling supported an initial divergence time between the West and East lineages at ~15.08 Ma with further diversification within the West lineage at ~7.12 Ma. These times largely coincide with the two independent intensifications of the East Asian monsoon that were initiated during the middle (Langhian) and late Miocene (Messinian), respectively. These results suggest that the Miocene intensification phases of the East Asian monsoon played a pivotal role in shaping the current landscape‐level patterns of genetic diversity within P. zhennan, as has been found for the interspecific divergence of other subtropical Chinese plants. Based on isolation‐by‐distance and species distribution modeling, we hypothesize that P. zhennan followed a ring diversification which was facilitated by the Sichuan Basin acting as barrier to gene flow. In situ and ex situ conservation management plans should consider the results obtained in this study to help secure the future of this beautiful and culturally significant endangered tree.
Collapse
Affiliation(s)
- Jian-Hua Xiao
- Plant Phylogenetics and Conservation Group Centre for Integrative Conservation Xishuangbanna Tropical Botanical Garden Chinese Academy of Sciences Kunming China.,University of Chinese Academy of Sciences Beijing China
| | - Xin Ding
- Department of Landscape Architecture Guangdong Eco-engineering Polytechnic Guangzhou China
| | - Lang Li
- Plant Phylogenetics and Conservation Group Centre for Integrative Conservation Xishuangbanna Tropical Botanical Garden Chinese Academy of Sciences Kunming China.,Center of Conservation Biology Core Botanical Gardens Chinese Academy of Sciences Mengla China
| | - Hui Ma
- Plant Phylogenetics and Conservation Group Centre for Integrative Conservation Xishuangbanna Tropical Botanical Garden Chinese Academy of Sciences Kunming China
| | - Xiu-Qin Ci
- Plant Phylogenetics and Conservation Group Centre for Integrative Conservation Xishuangbanna Tropical Botanical Garden Chinese Academy of Sciences Kunming China.,Center of Conservation Biology Core Botanical Gardens Chinese Academy of Sciences Mengla China
| | - Marlien van der Merwe
- Research Centre for Ecological Resilience Australian Institute of Botanical Science The Royal Botanic Garden Sydney Sydney NSW Australia
| | - John G Conran
- Australian Centre for Evolutionary Biology and Biodiversity (ACEBB) Sprigg Geobiology Centre (SGC) School of Biological Sciences The University of Adelaide Adelaide SA Australia
| | - Jie Li
- Plant Phylogenetics and Conservation Group Centre for Integrative Conservation Xishuangbanna Tropical Botanical Garden Chinese Academy of Sciences Kunming China.,Center of Conservation Biology Core Botanical Gardens Chinese Academy of Sciences Mengla China
| |
Collapse
|
23
|
Mason NA, Fletcher NK, Gill BA, Funk WC, Zamudio KR. Coalescent-based species delimitation is sensitive to geographic sampling and isolation by distance. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1730475] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Nicholas A. Mason
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, New York 14853, USA
| | - Nicholas K. Fletcher
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, New York 14853, USA
| | - Brian A. Gill
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - W. Chris Funk
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Kelly R. Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, New York 14853, USA
| |
Collapse
|
24
|
Rheindt FE, Prawiradilaga DM, Ashari H, Suparno, Gwee CY, Lee GWX, Wu MY, Ng NSR. A lost world in Wallacea: Description of a montane archipelagic
avifauna. Science 2020; 367:167-170. [DOI: 10.1126/science.aax2146] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 11/21/2019] [Indexed: 12/16/2022]
Abstract
Birds are the best-known animal class, with only about five or six new
species descriptions per year since 1999. Integrating genomic and phenotypic
research with arduous fieldwork in remote regions, we describe five new songbird
species and five new subspecies from a small area near Sulawesi, Indonesia, all
collected in a single 6-week expedition. Two factors contributed to the
description of this large number of species from such a small geographic area: (i)
Knowledge of Quaternary Period land connections helped pinpoint isolated islands
likely to harbor substantial endemism and (ii) studying accounts of historic
collectors such as Alfred Wallace facilitated the identification of undercollected
islands. Our findings suggest that humans’ understanding of biogeographically
complex regions such as Wallacea remains incomplete.
Collapse
Affiliation(s)
- Frank E. Rheindt
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543
| | - Dewi M. Prawiradilaga
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor KM 46, Cibinong Science Center, Cibinong 16911, Indonesia
| | - Hidayat Ashari
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor KM 46, Cibinong Science Center, Cibinong 16911, Indonesia
| | - Suparno
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor KM 46, Cibinong Science Center, Cibinong 16911, Indonesia
| | - Chyi Yin Gwee
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543
| | - Geraldine W. X. Lee
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543
| | - Meng Yue Wu
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543
| | - Nathaniel S. R. Ng
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543
- Department of Conservation and Research, Wildlife Reserves Singapore, 80 Mandai Lake Road, Singapore 729826
| |
Collapse
|
25
|
Hofmann S, Baniya CB, Litvinchuk SN, Miehe G, Li J, Schmidt J. Phylogeny of spiny frogs Nanorana (Anura: Dicroglossidae) supports a Tibetan origin of a Himalayan species group. Ecol Evol 2019; 9:14498-14511. [PMID: 31938536 PMCID: PMC6953589 DOI: 10.1002/ece3.5909] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/09/2019] [Accepted: 11/18/2019] [Indexed: 11/29/2022] Open
Abstract
Recent advances in the understanding of the evolution of the Asian continent challenge the long-held belief of a faunal immigration into the Himalaya. Spiny frogs of the genus Nanorana are a characteristic faunal group of the Himalaya-Tibet orogen (HTO). We examine the phylogeny of these frogs to explore alternative biogeographic scenarios for their origin in the Greater Himalaya, namely, immigration, South Tibetan origin, strict vicariance. We sequenced 150 Nanorana samples from 62 localities for three mitochondrial (1,524 bp) and three nuclear markers (2,043 bp) and complemented the data with sequence data available from GenBank. We reconstructed a gene tree, phylogenetic networks, and ancestral areas. Based on the nuDNA, we also generated a time-calibrated species tree. The results revealed two major clades (Nanorana and Quasipaa), which originated in the Lower Miocene from eastern China and subsequently spread into the HTO (Nanorana). Five well-supported subclades are found within Nanorana: from the East, Central, and Northwest Himalaya, the Tibetan Plateau, and the southeastern Plateau margin. The latter subclade represents the most basal group (subgenus Chaparana), the Plateau group (Nanorana) represents the sister clade to all species of the Greater Himalaya (Paa). We found no evidence for an east-west range expansion of Paa along the Himalaya, nor clear support for a strict vicariance model. Diversification in each of the three Himalayan subclades has probably occurred in distinct areas. Specimens from the NW Himalaya are placed basally relative to the highly diverse Central Himalayan group, while the lineage from the Tibetan Plateau is placed within a more terminal clade. Our data indicate a Tibetan origin of Himalayan Nanorana and support a previous hypothesis, which implies that a significant part of the Himalayan biodiversity results from primary diversification of the species groups in South Tibet before this part of the HTO was uplifted to its recent heights.
Collapse
Affiliation(s)
- Sylvia Hofmann
- Department of Conservation BiologyUFZ – Helmholtz Centre for Environmental ResearchLeipzigGermany
| | | | | | - Georg Miehe
- Faculty of GeographyPhilipps University MarburgMarburgGermany
| | - Jia‐Tang Li
- Department of HerpetologyChengdu Institute of BiologyChinese Academy of SciencesChengduChina
| | - Joachim Schmidt
- Institute of Biosciences, General and Systematic ZoologyUniversity of RostockRostockGermany
| |
Collapse
|
26
|
Wang S, Rohwer S, Delmore K, Irwin DE. Cross-decades stability of an avian hybrid zone. J Evol Biol 2019; 32:1242-1251. [PMID: 31430391 DOI: 10.1111/jeb.13524] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 08/06/2019] [Accepted: 08/13/2019] [Indexed: 01/04/2023]
Abstract
Hybrid zones are particularly valuable for understanding the evolution of partial reproductive isolation between differentiated populations. An increasing number of hybrid zones have been inferred to move over time, but in most such cases zone movement has not been tested with long-term genomic data. The hybrid zone between Townsend's Warblers (Setophaga townsendi) and Hermit Warblers (S. occidentalis) in the Washington Cascades was previously inferred to be moving from northern S. townsendi southwards towards S. occidentalis, based on plumage and behavioural patterns as well as a 2000-km genetic wake of hermit mitochondrial DNA (mtDNA) in coastal Townsend's Warblers. We directly tested whether hybrid zone position has changed over 2-3 decades by tracking plumage, mtDNA and nuclear genomic variation across the hybrid zone over two sampling periods (1987-94 and 2015-16). Surprisingly, there was no significant movement in genomic or plumage cline centres between the two time periods. Plumage cline widths were narrower than expected by neutral diffusion, consistent with a 'tension zone' model, in which selection against hybrids is balanced by movement of parental forms into the zone. Our results indicate that this hybrid zone is either stable in its location or moving at a rate that is not detectable over 2-3 decades. Despite considerable gene flow, the stable clines in multiple phenotypic and genotypic characters over decades suggest evolutionary stability of this young pair of sister species, allowing divergence to continue. We propose a novel biogeographic scenario to explain these patterns: rather than the hybrid zone having moved thousands of kilometres to its current position, inland Townsend's met coastal Hermit Warbler populations along a broad front of the British Columbia and Alaska coast and hybridization led to replacement of the Hermit Warbler plumage with Townsend's Warbler plumage patterns along this coastline. Hence, hybrid zones along British Columbia and Alaska moved only a short distance from the inland to the coast, whereas the Hermit Warbler phenotype appears stable in Washington and further south. This case provides an example of the complex biogeographic processes that have led to the distribution of current phenotypes within and among closely related species.
Collapse
Affiliation(s)
- Silu Wang
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Sievert Rohwer
- Department of Biology and Burke Museum, University of Washington, Seattle, WA, USA
| | - Kira Delmore
- Department of Biology, Texas A & M, College Station, TX, USA
| | - Darren E Irwin
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
27
|
Martinet B, Lecocq T, Brasero N, Gerard M, Urbanová K, Valterová I, Gjershaug JO, Michez D, Rasmont P. Integrative taxonomy of an arctic bumblebee species complex highlights a new cryptic species (Apidae: Bombus). Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz041] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractBumblebees have been the focus of much research, but the taxonomy of many species groups is still unclear, especially for circumpolar species. Delimiting species based on multisource datasets provides a solution to overcome current systematic issues of closely related populations. Here, we use an integrative taxonomic approach based on new genetic and eco-chemical datasets to resolve the taxonomic status of Bombus lapponicus and Bombus sylvicola. Our results support the conspecific status of B. lapponicus and B. sylvicola and that the low gradual divergence around the Arctic Circle between Fennoscandia and Alaska does not imply speciation in this species complex. Therefore, based on our molecular and morphological analyses, we propose to assign them subspecific status: Bombus lapponicus lapponicus from Fennoscandia and West Siberia and Bombus lapponicus sylvicola comb. nov. from Alaska and Yukon. In addition, our analyses reveal a cryptic species in the B. lapponicus complex from Alaska, which we describe here as new: Bombus (Pyrobombus) interacti sp. nov.
Collapse
Affiliation(s)
- Baptiste Martinet
- University of Mons, Research Institute of Biosciences, Laboratory of Zoology, Place du Parc, Mons, Belgium
| | - Thomas Lecocq
- University of Mons, Research Institute of Biosciences, Laboratory of Zoology, Place du Parc, Mons, Belgium
- Université de Lorraine, INRA, URAFPA, Nancy, France
| | - Nicolas Brasero
- University of Mons, Research Institute of Biosciences, Laboratory of Zoology, Place du Parc, Mons, Belgium
| | - Maxence Gerard
- University of Mons, Research Institute of Biosciences, Laboratory of Zoology, Place du Parc, Mons, Belgium
| | - Klára Urbanová
- Czech University of Life Sciences, Faculty of Tropical AgriSciences, Department of Sustainable Technologies, Kamýcká, Prague, Czech Republic
| | - Irena Valterová
- Academy of Sciences of the Czech Republic, Institute of Organic Chemistry and Biochemistry, Flemingovo nám, Prague, Czech Republic
- Czech University of Life Sciences, Faculty of Tropical AgriSciences, Department of Sustainable Technologies, Kamýcká, Prague, Czech Republic
| | | | - Denis Michez
- University of Mons, Research Institute of Biosciences, Laboratory of Zoology, Place du Parc, Mons, Belgium
| | - Pierre Rasmont
- University of Mons, Research Institute of Biosciences, Laboratory of Zoology, Place du Parc, Mons, Belgium
| |
Collapse
|
28
|
A Multireference-Based Whole Genome Assembly for the Obligate Ant-Following Antbird, Rhegmatorhina melanosticta (Thamnophilidae). DIVERSITY-BASEL 2019. [DOI: 10.3390/d11090144] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Current generation high-throughput sequencing technology has facilitated the generation of more genomic-scale data than ever before, thus greatly improving our understanding of avian biology across a range of disciplines. Recent developments in linked-read sequencing (Chromium 10×) and reference-based whole-genome assembly offer an exciting prospect of more accessible chromosome-level genome sequencing in the near future. We sequenced and assembled a genome of the Hairy-crested Antbird (Rhegmatorhina melanosticta), which represents the first publicly available genome for any antbird (Thamnophilidae). Our objectives were to (1) assemble scaffolds to chromosome level based on multiple reference genomes, and report on differences relative to other genomes, (2) assess genome completeness and compare content to other related genomes, and (3) assess the suitability of linked-read sequencing technology for future studies in comparative phylogenomics and population genomics studies. Our R. melanosticta assembly was both highly contiguous (de novo scaffold N50 = 3.3 Mb, reference based N50 = 53.3 Mb) and relatively complete (contained close to 90% of evolutionarily conserved single-copy avian genes and known tetrapod ultraconserved elements). The high contiguity and completeness of this assembly enabled the genome to be successfully mapped to the chromosome level, which uncovered a consistent structural difference between R. melanosticta and other avian genomes. Our results are consistent with the observation that avian genomes are structurally conserved. Additionally, our results demonstrate the utility of linked-read sequencing for non-model genomics. Finally, we demonstrate the value of our R. melanosticta genome for future researchers by mapping reduced representation sequencing data, and by accurately reconstructing the phylogenetic relationships among a sample of thamnophilid species.
Collapse
|
29
|
Zhang D, Tang L, Cheng Y, Hao Y, Xiong Y, Song G, Qu Y, Rheindt FE, Alström P, Jia C, Lei F. 'Ghost introgression' as a cause of deep mitochondrial divergence in a bird species complex. Mol Biol Evol 2019; 36:2375-2386. [PMID: 31364717 DOI: 10.1093/molbev/msz170] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 05/15/2019] [Accepted: 07/08/2019] [Indexed: 12/19/2022] Open
Abstract
In the absence of nuclear-genomic differentiation between two populations, deep mitochondrial divergence (DMD) is a form of mito-nuclear discordance. Such instances of DMD are rare and might variably be explained by unusual cases of female-linked selection, by male-biased dispersal, by 'speciation reversal' or by mitochondrial capture through genetic introgression. Here we analyze DMD in an Asian Phylloscopus leaf warbler (Aves: Phylloscopidae) complex. Bioacoustic, morphological and genomic data demonstrate close similarity between the taxa affinis and occisinensis, even though DMD previously led to their classification as two distinct species. Using population genomic and comparative genomic methods on 45 whole genomes, including historical reconstructions of effective population size, genomic peaks of differentiation and genomic linkage, we infer that the form affinis is likely the product of a westward expansion in which it replaced a now-extinct congener that was the donor of its mtDNA and small portions of its nuclear genome. This study provides strong evidence of 'ghost introgression' as the cause of DMD, and we suggest that 'ghost introgression' may be a widely overlooked phenomenon in nature.
Collapse
Affiliation(s)
- Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Linfang Tang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ying Xiong
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore, Republic of Singapore
| | - Per Alström
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, Uppsala, Sweden.,Swedish Species Information Centre, Swedish University of Agricultural Sciences, Box 7007, Uppsala, Sweden
| | - Chenxi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| |
Collapse
|
30
|
Cacho NI, Monteverde-Suárez MJ, McIntyre PJ. Convergent evolution in floral morphology in a plant ring species, the Caribbean Euphorbia tithymaloides. AMERICAN JOURNAL OF BOTANY 2019; 106:1032-1045. [PMID: 31281963 DOI: 10.1002/ajb2.1318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 04/15/2019] [Indexed: 06/09/2023]
Abstract
PREMISE Ring species have long fascinated evolutionary biologists for their potential insights into lineage divergence and speciation across space. Few studies have investigated the potential for convergent or parallel evolution along the diverging fronts of ring species. We investigated a potential case of parallel floral variation in the Caribbean spurge Euphorbia tithymaloides, the only plant system with molecular support as a ring species. The terminal populations of each front, despite being the most divergent, exhibit such similar floral traits that they were originally considered each other's closest relative. METHODS We evaluated convergence in floral and leaf traits in relation to geography across 95 populations spanning the distribution of E. tithymaloides. We also reanalyzed available genetic data (from previous phylogenetic analyses) in an explicitly spatial framework. RESULTS Floral morphology appears to have shifted in a convergent fashion along both geographic fronts of E. tithymaloides, resulting in shorter and more compact inflorescences in Antillean populations compared to the typical elongate "slipper-like" cyathia characteristic of the area of origin. Patterns of spatial genetic variation were more consistent with a two-fronted invasion of the Caribbean than with a simpler model of isolation-by-distance. CONCLUSIONS Floral divergence in E. tithymaloides is consistent with convergent evolution along the two fronts of a ring species. We outline several (not mutually exclusive) mechanisms that could be driving patterns in morphology, including shifts toward generalized pollination with reduced reliance on hummingbirds, shifts in floral structure closely matching available hummingbird bill traits, and shifts toward increased selfing.
Collapse
Affiliation(s)
- N Ivalú Cacho
- Instituto de Biología, Universidad Nacional Autónoma de México, CDMX 04510, Mexico
| | | | - Patrick J McIntyre
- NatureServe, Western Regional Office, 1680 38th St., Suite 120, Boulder, Colorado, 80301, USA
| |
Collapse
|
31
|
Irwin DE. A tree of tree frogs around the Black Sea. Mol Ecol 2019; 25:4093-6. [PMID: 27616352 DOI: 10.1111/mec.13760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 07/05/2016] [Indexed: 11/30/2022]
Abstract
Speciation, the process by which one species evolves into two or more, is a major focus of ongoing debate, particularly regarding the geographic context in which it occurs. Geographic models of speciation tend to fall into discrete categories, typically referred to as allopatric, parapatric and sympatric speciation, according to whether two groups evolve reproductive isolation while geographically isolated, differentiated but connected by gene flow, or completely co-occurring. Yet molecular studies indicate that full development of reproductive isolation can take very long compared with the timescale at which climatic oscillations occur, such that the geographic context of differentiating forms might change often during the long process to full species. Studies of genetic relationships across the ranges of organisms with low-dispersal distances have the potential to reveal these complex histories. In a particularly elegant example in this issue, Dufresnes et al. () use genetic variation and ecological niche modelling to show that a ring of populations of the eastern tree frog (Hyla orientalis) surrounding the Black Sea had a complex history of geographic differentiation. Alternating phases of geographic fragmentation and phases of gene flow between neighbouring populations have produced a pattern of gradual genetic change connecting the western, southern and eastern sides of the ring, with the northwestern and northeastern forms being most differentiated. In the north, a population in Crimea appears to have been produced through mixture of the two extreme forms. The overall genetic relationships are reminiscent of those found in ring species, which have been used as prime demonstrations of the process of speciation. The difference, however, is that the terminal forms appear to have mixed rather than be reproductively isolated, although more research is needed to infer whether there might be some reproductive isolation on the northern side of the ring.
Collapse
Affiliation(s)
- Darren E Irwin
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| |
Collapse
|
32
|
Geraldes A, Askelson KK, Nikelski E, Doyle FI, Harrower WL, Winker K, Irwin DE. Population genomic analyses reveal a highly differentiated and endangered genetic cluster of northern goshawks ( Accipiter gentilis laingi) in Haida Gwaii. Evol Appl 2019; 12:757-772. [PMID: 30976308 PMCID: PMC6439496 DOI: 10.1111/eva.12754] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 01/10/2023] Open
Abstract
Accurate knowledge of geographic ranges and genetic relationships among populations is important when managing a species or population of conservation concern. Along the western coast of Canada, a subspecies of the northern goshawk (Accipiter gentilis laingi) is legally designated as Threatened. The range and distinctness of this form, in comparison with the broadly distributed North American subspecies (Accipiter gentilis atricapillus), is unclear. Given this morphological uncertainty, we analyzed genomic relationships in thousands of single nucleotide polymorphisms identified using genotyping-by-sequencing of high-quality genetic samples. Results revealed a genetically distinct population of northern goshawks on the archipelago of Haida Gwaii and subtle structuring among other North American sampling regions. We then developed genotyping assays for ten loci that are highly differentiated between the two main genetic clusters, allowing inclusion of hundreds of low-quality samples and confirming that the distinct genetic cluster is restricted to Haida Gwaii. As the laingi form was originally described as being based on Haida Gwaii (where the type specimen is from), further morphological analysis may result in this name being restricted to the Haida Gwaii genetic cluster. Regardless of taxonomic treatment, the distinct Haida Gwaii genetic cluster along with the small and declining population size of the Haida Gwaii population suggests a high risk of extinction of an ecologically and genetically distinct form of northern goshawk. Outside of Haida Gwaii, sampling regions along the coast of BC and southeast Alaska (often considered regions inhabited by laingi) show some subtle differentiation from other North American regions. These results will increase the effectiveness of conservation management of northern goshawks in northwestern North America. More broadly, other conservation-related studies of genetic variation may benefit from the two-step approach we employed that first surveys genomic variation using high-quality samples and then genotypes low-quality samples at particularly informative loci.
Collapse
Affiliation(s)
- Armando Geraldes
- Biodiversity Research CentreUniversity of British ColumbiaVancouverBritish ColumbiaCanada
- Department of ZoologyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Kenneth K. Askelson
- Biodiversity Research CentreUniversity of British ColumbiaVancouverBritish ColumbiaCanada
- Department of ZoologyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Ellen Nikelski
- Biodiversity Research CentreUniversity of British ColumbiaVancouverBritish ColumbiaCanada
- Department of ZoologyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Frank I. Doyle
- Wildlife Dynamics ConsultingTerraceBritish ColumbiaCanada
| | - William L. Harrower
- Biodiversity Research CentreUniversity of British ColumbiaVancouverBritish ColumbiaCanada
- Department of ZoologyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
- Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverBritish ColumbiaCanada
- Department of BiologyUniversity of VictoriaVictoriaBritish ColumbiaCanada
| | | | - Darren E. Irwin
- Biodiversity Research CentreUniversity of British ColumbiaVancouverBritish ColumbiaCanada
- Department of ZoologyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| |
Collapse
|
33
|
Wang Q, Lu W, Yang J, Jiang L, Zhang Q, Kan X, Yang X. Comparative transcriptomics in three Passerida species provides insights into the evolution of avian mitochondrial complex I. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 28:27-36. [DOI: 10.1016/j.cbd.2018.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 06/04/2018] [Accepted: 06/13/2018] [Indexed: 02/02/2023]
|
34
|
Qiao L, Wen G, Qi Y, Lu B, Hu J, Song Z, Fu J. Evolutionary melting pots and reproductive isolation: A ring-shaped diversification of an odorous frog (Odorrana margaratea
) around the Sichuan Basin. Mol Ecol 2018; 27:4888-4900. [DOI: 10.1111/mec.14899] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 09/04/2018] [Accepted: 10/03/2018] [Indexed: 01/17/2023]
Affiliation(s)
- Liang Qiao
- Chengdu Institute of Biology; Chinese Academy of Sciences; Chengdu Sichuan China
| | - Guannan Wen
- Chengdu Institute of Biology; Chinese Academy of Sciences; Chengdu Sichuan China
| | - Yin Qi
- Chengdu Institute of Biology; Chinese Academy of Sciences; Chengdu Sichuan China
| | - Bin Lu
- Chengdu Institute of Biology; Chinese Academy of Sciences; Chengdu Sichuan China
| | - Junhua Hu
- Chengdu Institute of Biology; Chinese Academy of Sciences; Chengdu Sichuan China
| | - Zhaobin Song
- College of Life Sciences; Sichuan University; Chengdu Sichuan China
| | - Jinzhong Fu
- Chengdu Institute of Biology; Chinese Academy of Sciences; Chengdu Sichuan China
- Department of Integrative Biology; University of Guelph; Guelph Ontario Canada
| |
Collapse
|
35
|
Distributional patterns of endemic southern South American freshwater aeglids (Crustacea: Decapoda: Anomura: Aeglidae). ZOOL ANZ 2018. [DOI: 10.1016/j.jcz.2018.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
36
|
Ng NSR, Prawiradilaga DM, Ng EYX, Suparno, Ashari H, Trainor C, Verbelen P, Rheindt FE. A striking new species of leaf warbler from the Lesser Sundas as uncovered through morphology and genomics. Sci Rep 2018; 8:15646. [PMID: 30353148 PMCID: PMC6199301 DOI: 10.1038/s41598-018-34101-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 09/27/2018] [Indexed: 11/09/2022] Open
Abstract
Leaf warblers (Aves; Phylloscopidae) are a diverse clade of insectivorous, canopy-dwelling songbirds widespread across the Old World. The taxonomy of Australasian leaf warblers is particularly complex, with multiple species-level divergences between island taxa in the region requiring further scrutiny. We use a combination of morphology, bioacoustics, and analysis of thousands of genome-wide markers to investigate and describe a new species of Phylloscopus leaf warbler from the island of Rote in the Lesser Sundas, Indonesia. We show that this new Rote Leaf Warbler is morphologically and genomically highly distinct from its congenerics, but do not find vocal differentiation between different island taxa. We discuss the behaviour and ecology of this highly distinctive new species, and make recommendations about its conservation status. We believe this constitutes the first description of a novel bird species that is partly based on insights from massive amounts of genome-wide DNA markers.
Collapse
Affiliation(s)
- Nathaniel S R Ng
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 129801, Singapore
| | - Dewi M Prawiradilaga
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor KM 46, Cibinong Science Center, Cibinong, 16911, Indonesia
| | - Elize Y X Ng
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 129801, Singapore
| | - Suparno
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor KM 46, Cibinong Science Center, Cibinong, 16911, Indonesia
| | - Hidayat Ashari
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor KM 46, Cibinong Science Center, Cibinong, 16911, Indonesia
| | - Colin Trainor
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, 0909, Australia
| | | | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 129801, Singapore.
| |
Collapse
|
37
|
Scordato ESC. Male competition drives song divergence along an ecological gradient in an avian ring species. Evolution 2018; 72:2360-2377. [DOI: 10.1111/evo.13604] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 08/07/2018] [Accepted: 08/21/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Elizabeth S. C. Scordato
- Committee on Evolutionary Biology The University of Chicago Chicago Illinois 60637
- Current Address: Department of Biological Sciences California State Polytechnic University Pomona California 91768
| |
Collapse
|
38
|
Irwin DE, Milá B, Toews DPL, Brelsford A, Kenyon HL, Porter AN, Grossen C, Delmore KE, Alcaide M, Irwin JH. A comparison of genomic islands of differentiation across three young avian species pairs. Mol Ecol 2018; 27:4839-4855. [PMID: 30187980 DOI: 10.1111/mec.14858] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 07/10/2018] [Accepted: 07/14/2018] [Indexed: 02/06/2023]
Abstract
Detailed evaluations of genomic variation between sister species often reveal distinct chromosomal regions of high relative differentiation (i.e., "islands of differentiation" in FST ), but there is much debate regarding the causes of this pattern. We briefly review the prominent models of genomic islands of differentiation and compare patterns of genomic differentiation in three closely related pairs of New World warblers with the goal of evaluating support for the four models. Each pair (MacGillivray's/mourning warblers; Townsend's/black-throated green warblers; and Audubon's/myrtle warblers) consists of forms that were likely separated in western and eastern North American refugia during cycles of Pleistocene glaciations and have now come into contact in western Canada, where each forms a narrow hybrid zone. We show strong differences between pairs in their patterns of genomic heterogeneity in FST , suggesting differing selective forces and/or differing genomic responses to similar selective forces among the three pairs. Across most of the genome, levels of within-group nucleotide diversity (πWithin ) are almost as large as levels of between-group nucleotide distance (πBetween ) within each pair, suggesting recent common ancestry and/or gene flow. In two pairs, a pattern of the FST peaks having low πBetween suggests that selective sweeps spread between geographically differentiated groups, followed by local differentiation. This "sweep-before-differentiation" model is consistent with signatures of gene flow within the yellow-rumped warbler species complex. These findings add to our growing understanding of speciation as a complex process that can involve phases of adaptive introgression among partially differentiated populations.
Collapse
Affiliation(s)
- Darren E Irwin
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - David P L Toews
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.,Cornell Lab of Ornithology & Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
| | - Alan Brelsford
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, California
| | - Haley L Kenyon
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Biology, Queen's University, Biosciences Complex, Kingston, Ontario, Canada
| | - Alison N Porter
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christine Grossen
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Kira E Delmore
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.,Max Planck Institute for Evolutionary Biology, Behavioural Genomics, Plön, Germany
| | - Miguel Alcaide
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jessica H Irwin
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
39
|
Richards EJ, Poelstra JW, Martin CH. Don't throw out the sympatric speciation with the crater lake water: fine-scale investigation of introgression provides equivocal support for causal role of secondary gene flow in one of the clearest examples of sympatric speciation. Evol Lett 2018; 2:524-540. [PMID: 30283699 PMCID: PMC6145409 DOI: 10.1002/evl3.78] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 07/13/2018] [Accepted: 07/18/2018] [Indexed: 12/19/2022] Open
Abstract
Genomic data has revealed complex histories of colonization and repeated gene flow previously unrecognized in some of the most celebrated examples of sympatric speciation and radiation. However, much of the evidence for secondary gene flow into these radiations comes from summary statistics calculated from sparse genomic sampling without knowledge of which specific genomic regions introgressed. This tells us little about how gene flow potentially influenced sympatric diversification. Here, we investigated whole genomes of Barombi Mbo crater lake cichlids for fine-scale patterns of introgression with neighboring riverine cichlid populations. We found evidence of secondary gene flow into the radiation scattered across <0.24% of the genome; however, from our analyses, it is not clear if the functional diversity in these regions contributed to the ecological, sexual, and morphological diversity found in the lake. Unlike similar studies, we found no obvious candidate genes for adaptive introgression and we cannot rule out that secondary gene flow was predominantly neutral with respect to the diversification process. We also found evidence for differential assortment of ancestral polymorphisms found in riverine populations between sympatric sister species, suggesting the presence of an ancestral hybrid swarm. Although the history of gene flow and colonization is more complicated than previously assumed, the lack of compelling evidence for secondary gene flow's role in species diversification suggests that we should not yet rule out one of the most celebrated examples of sympatric speciation in nature without a more thorough investigation of the timing and functional role of each introgressed region.
Collapse
Affiliation(s)
- Emilie J. Richards
- Biology DepartmentUniversity of North Carolina at Chapel HillChapel HillNorth Carolina27599
| | - Jelmer W. Poelstra
- Biology DepartmentUniversity of North Carolina at Chapel HillChapel HillNorth Carolina27599
- Biology DepartmentDuke UniversityDurhamNorth Carolina27710
| | - Christopher H. Martin
- Biology DepartmentUniversity of North Carolina at Chapel HillChapel HillNorth Carolina27599
| |
Collapse
|
40
|
Monotilla AP, Nishimura T, Adachi M, Tanii Y, Largo DB, Hiraoka M. Examination of prezygotic and postzygotic isolating barriers in tropical Ulva (Ulvophyceae, Chlorophyta): evidence for ongoing speciation. JOURNAL OF PHYCOLOGY 2018; 54:539-549. [PMID: 29846951 DOI: 10.1111/jpy.12755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 05/10/2018] [Indexed: 06/08/2023]
Abstract
Phylogenetic clades based on DNA sequences such as the chloroplast rbcL gene and the nuclear ITS region are frequently used to delimit algal species. However, these molecular markers cannot accurately delimit boundaries among some Ulva species. Although Ulva reticulata and Ulva ohnoi occasionally bloom in tropical to warm-temperate regions and are clearly distinguishable by their reticulate or plain blade morphology, they have few or no sequence divergences in these molecular markers and form a monophyletic clade. In this study, to clarify the speciation and species delimitation in the U. reticulata-ohnoi complex clade, reproductive relationships among several sexual strains from the Philippines and Japan including offspring that originated from the type specimen of U. ohnoi were examined by culturing and hybridization in addition to the ITS-based analysis. As a result, both prezygotic and postzygotic reproductive isolation were revealed to occur between genetically perforated U. reticulata and imperforate U. ohnoi. They were also separated on the basis of sequence analysis of the ITS region. That strongly supports that the two taxa are independent biological species. Although no prezygotic barrier among the Philippine and Japanese strains of U. reticulata was observed, unexpectedly zoospores produced by hybrid sporophytes in some of their combinations mostly failed to develop, indicating partial formation of a postzygotic barrier despite a 0.2% divergence in the ITS sequence. These findings suggest speciation is still ongoing in U. reticulata.
Collapse
Affiliation(s)
- Alvin P Monotilla
- Graduate School of Kuroshio Science, Kochi University, 2-5-1 Akebono, Kochi, 780-8520, Japan
| | - Tomohiro Nishimura
- Laboratory of Aquatic Environmental Science (LAQUES), Faculty of Agriculture and Marine Science, Kochi University, Otsu-200, Nankoku, Kochi, 783-8502, Japan
| | - Masao Adachi
- Laboratory of Aquatic Environmental Science (LAQUES), Faculty of Agriculture and Marine Science, Kochi University, Otsu-200, Nankoku, Kochi, 783-8502, Japan
| | - Yuta Tanii
- Laboratory of Aquatic Environmental Science (LAQUES), Faculty of Agriculture and Marine Science, Kochi University, Otsu-200, Nankoku, Kochi, 783-8502, Japan
| | - Danilo B Largo
- Biology Department, University of San Carlos, Nasipit, Talamban, Cebu City, 6000, Philippines
| | - Masanori Hiraoka
- Usa Marine Biological Institute, Kochi University, Inoshiri 194, Usa, Tosa, Kochi, 781-1164, Japan
| |
Collapse
|
41
|
Brelsford A, Toews DPL, Irwin DE. Admixture mapping in a hybrid zone reveals loci associated with avian feather coloration. Proc Biol Sci 2018; 284:rspb.2017.1106. [PMID: 29118129 DOI: 10.1098/rspb.2017.1106] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 10/10/2017] [Indexed: 12/30/2022] Open
Abstract
Identifying the genetic bases for colour patterns has provided important insights into the control and expression of pigmentation and how these characteristics influence fitness. However, much more is known about the genetic bases for traits based on melanin pigments than for traits based on another major class of pigments, carotenoids. Here, we use natural admixture in a hybrid zone between Audubon's and myrtle warblers (Setophaga coronata auduboni/S. c. coronata) to identify genomic regions associated with both types of pigmentation. Warblers are known for rapid speciation and dramatic differences in plumage. For each of five plumage coloration traits, we found highly significant associations with multiple single-nucleotide polymorphisms (SNPs) across the genome and these were clustered in discrete regions. Regions near significantly associated SNPs were enriched for genes associated with keratin filaments, fibrils that make up feathers. A carotenoid-based trait that differs between the taxa-throat colour-had more than a dozen genomic regions of association. One cluster of SNPs for this trait overlaps the Scavenger Receptor Class F Member 2 (SCARF2) gene. Other scavenger receptors are presumed to be expressed at target tissues and involved in the selective movement of carotenoids into the target cells, making SCARF2 a plausible new candidate for carotenoid processing. In addition, two melanin-based plumage traits-colours of the eye line and eye spot-show very strong associations with a single genomic region mapping to chromosome 20 in the zebra finch. These findings indicate that only a subset of the genomic regions differentiated between these two warblers are associated with the plumage differences between them and demonstrate the utility of reduced-representation genomic scans in hybrid zones.
Collapse
Affiliation(s)
- Alan Brelsford
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, Canada V6T 1Z4.,Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,Evolution, Ecology, and Organismal Biology Department, University of California Riverside, Riverside, CA, 92521, USA
| | - David P L Toews
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, Canada V6T 1Z4 .,Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, 159 Sapsucker Woods Road, Ithaca, NY 14850, USA
| | - Darren E Irwin
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, Canada V6T 1Z4
| |
Collapse
|
42
|
Alström P, Rheindt FE, Zhang R, Zhao M, Wang J, Zhu X, Gwee CY, Hao Y, Ohlson J, Jia C, Prawiradilaga DM, Ericson PGP, Lei F, Olsson U. Complete species-level phylogeny of the leaf warbler (Aves: Phylloscopidae) radiation. Mol Phylogenet Evol 2018; 126:141-152. [PMID: 29631054 DOI: 10.1016/j.ympev.2018.03.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/24/2018] [Accepted: 03/28/2018] [Indexed: 10/17/2022]
Abstract
The leaf warbler radiation (Aves: Phylloscopidae) has undergone a c. 50% increase in the number of recognised species over the last three decades, mainly as a result of analyses of vocalisations and DNA. Using a multilocus dataset for all of the species in this family, and multispecies coalescent-based as well as concatenation methods, we provide the first complete species-level phylogeny for this important group, as well as an estimate of the timing of diversification. The most recent common ancestor for the family was dated at 11.7 million years ago (mya) (95% highest posterior density 9.8-13.7 mya), and divergence times between sister species ranged from 0.5 mya (0.3-0.8 mya) to 6.1 mya (4.8-7.5 mya). Based on our results, we support synonymising Seicercus with Phylloscopus, which results in a monogeneric Phylloscopidae. We discuss the pros and cons of this treatment,and we argue againstproliferation of taxonomic names,and conclude that a large monogeneric Phylloscopidae leads to the fewest taxonomic changes compared to traditional classifications. We briefly discuss morphological evolution in the light of the phylogeny. The time calibrated phylogeny is a major improvement compared to previous studies based on a smaller number of species and loci and can provide a basis for future studies of other aspects of phylloscopid evolution.
Collapse
Affiliation(s)
- Per Alström
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden; Swedish Species Information Centre, Swedish University of Agricultural Sciences (SLU), Box 7007, Uppsala SE-750 07, Sweden; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, 117558 Singapore, Singapore
| | - Ruiying Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Min Zhao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaojia Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chyi Yin Gwee
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, 117558 Singapore, Singapore
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jan Ohlson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, Stockholm SE-10405, Sweden
| | - Chenxi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dewi M Prawiradilaga
- Research Centre for Biology, Indonesian Institute of Sciences (LIPI), Cibinong Science Centre, Jalan Raya Jakarta Bogor KM 46, Bogor 16911, Indonesia
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, Stockholm SE-10405, Sweden
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Urban Olsson
- Department of Biology and Environmental Science, University of Gothenburg, Box 463, SE-405 30 Gothenburg, Sweden
| |
Collapse
|
43
|
Puncher GN, Cariani A, Maes GE, Van Houdt J, Herten K, Cannas R, Rodriguez-Ezpeleta N, Albaina A, Estonba A, Lutcavage M, Hanke A, Rooker J, Franks JS, Quattro JM, Basilone G, Fraile I, Laconcha U, Goñi N, Kimoto A, Macías D, Alemany F, Deguara S, Zgozi SW, Garibaldi F, Oray IK, Karakulak FS, Abid N, Santos MN, Addis P, Arrizabalaga H, Tinti F. Spatial dynamics and mixing of bluefin tuna in the Atlantic Ocean and Mediterranean Sea revealed using next-generation sequencing. Mol Ecol Resour 2018; 18:620-638. [PMID: 29405659 DOI: 10.1111/1755-0998.12764] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/06/2018] [Accepted: 01/19/2018] [Indexed: 01/05/2023]
Abstract
The Atlantic bluefin tuna is a highly migratory species emblematic of the challenges associated with shared fisheries management. In an effort to resolve the species' stock dynamics, a genomewide search for spatially informative single nucleotide polymorphisms (SNPs) was undertaken, by way of sequencing reduced representation libraries. An allele frequency approach to SNP discovery was used, combining the data of 555 larvae and young-of-the-year (LYOY) into pools representing major geographical areas and mapping against a newly assembled genomic reference. From a set of 184,895 candidate loci, 384 were selected for validation using 167 LYOY. A highly discriminatory genotyping panel of 95 SNPs was ultimately developed by selecting loci with the most pronounced differences between western Atlantic and Mediterranean Sea LYOY. The panel was evaluated by genotyping a different set of LYOY (n = 326), and from these, 77.8% and 82.1% were correctly assigned to western Atlantic and Mediterranean Sea origins, respectively. The panel revealed temporally persistent differentiation among LYOY from the western Atlantic and Mediterranean Sea (FST = 0.008, p = .034). The composition of six mixed feeding aggregations in the Atlantic Ocean and Mediterranean Sea was characterized using genotypes from medium (n = 184) and large (n = 48) adults, applying population assignment and mixture analyses. The results provide evidence of persistent population structuring across broad geographic areas and extensive mixing in the Atlantic Ocean, particularly in the mid-Atlantic Bight and Gulf of St. Lawrence. The genomic reference and genotyping tools presented here constitute novel resources useful for future research and conservation efforts.
Collapse
Affiliation(s)
- Gregory N Puncher
- Department of Biological, Geological and Environmental Sciences/Laboratory of Genetics and Genomics of Marine Resources and Environment (GenoDREAM), University of Bologna, Ravenna, Italy.,Department of Biology, Marine Biology Research Group, Ghent University, Ghent, Belgium.,Department of Biology, University of New Brunswick, Saint John, NB, Canada
| | - Alessia Cariani
- Department of Biological, Geological and Environmental Sciences/Laboratory of Genetics and Genomics of Marine Resources and Environment (GenoDREAM), University of Bologna, Ravenna, Italy
| | - Gregory E Maes
- Centre for Sustainable Tropical Fisheries and Aquaculture, Comparative Genomics Centre, College of Science and Engineering, James Cook University, Townsville, Qld, Australia.,Centre for Human Genetics, Genomics Core, KU Leuven - UZ Leuven, Leuven, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven (KU Leuven), Leuven, Belgium
| | - Jeroen Van Houdt
- Centre for Human Genetics, Genomics Core, KU Leuven - UZ Leuven, Leuven, Belgium
| | - Koen Herten
- Centre for Human Genetics, Genomics Core, KU Leuven - UZ Leuven, Leuven, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven (KU Leuven), Leuven, Belgium
| | - Rita Cannas
- Department of Life & Environmental Sciences (DISVA), University of Cagliari, Cagliari, Italy
| | | | - Aitor Albaina
- Laboratory of Genetics Faculty of Science & Technology, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain.,Environmental Studies Centre (CEA), Vitoria-Gasteiz City Council, Vitoria-Gasteiz, Spain
| | - Andone Estonba
- Laboratory of Genetics Faculty of Science & Technology, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Molly Lutcavage
- School for the Environment and Large Pelagics Research Center, University of Massachusetts, Boston, Gloucester, MA, USA
| | - Alex Hanke
- Fisheries and Oceans Canada, St. Andrews Biological Station, St. Andrews, NB, Canada
| | - Jay Rooker
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX, USA.,Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, USA
| | - James S Franks
- Gulf Coast Research Laboratory, Center for Fisheries Research and Development, University of Southern Mississippi, Ocean Springs, MS, USA
| | - Joseph M Quattro
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Gualtiero Basilone
- National Research Council, Institute for Marine and Coastal Environment, Detached Unit of Capo Granitola, Trapani, Italy
| | - Igaratza Fraile
- Marine Research Division, AZTI Tecnalia, Pasaia, Gipuzkoa, Spain
| | - Urtzi Laconcha
- Marine Research Division, AZTI Tecnalia, Pasaia, Gipuzkoa, Spain.,Laboratory of Genetics Faculty of Science & Technology, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Nicolas Goñi
- Marine Research Division, AZTI Tecnalia, Pasaia, Gipuzkoa, Spain
| | - Ai Kimoto
- National Research Institute of Far Seas Fisheries, Shizuoka, Japan
| | - David Macías
- Instituto Español de Oceanografía, Centro Oceanográfico de Baleares, Palma, Spain
| | - Francisco Alemany
- Instituto Español de Oceanografía, Centro Oceanográfico de Baleares, Palma, Spain
| | - Simeon Deguara
- Federation of Maltese Aquaculture Producers (FMAP), Valletta, Malta
| | - Salem W Zgozi
- Marine Biology Research Center, Tripoli-Tajura, Libya
| | - Fulvio Garibaldi
- Department of Earth, Environmental and Life Sciences, University of Genoa, Genova, Italy
| | - Isik K Oray
- Faculty of Fisheries, Istanbul University, Laleli-Istanbul, Turkey
| | | | - Noureddine Abid
- National Institute of Fisheries Research, Regional Centre of Tangier, Tanger, Morocco
| | | | - Piero Addis
- Department of Life & Environmental Sciences (DISVA), University of Cagliari, Cagliari, Italy
| | | | - Fausto Tinti
- Department of Biological, Geological and Environmental Sciences/Laboratory of Genetics and Genomics of Marine Resources and Environment (GenoDREAM), University of Bologna, Ravenna, Italy
| |
Collapse
|
44
|
|
45
|
Blackburn GS, Brunet BMT, Muirhead K, Cusson M, Béliveau C, Levesque RC, Lumley LM, Sperling FAH. Distinct sources of gene flow produce contrasting population genetic dynamics at different range boundaries of aChoristoneurabudworm. Mol Ecol 2017; 26:6666-6684. [DOI: 10.1111/mec.14386] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 09/26/2017] [Accepted: 10/07/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Gwylim S. Blackburn
- Department of Biological Sciences; CW405 Biosciences Centre; University of Alberta; Edmonton AB Canada
- Laurentian Forestry Centre; Natural Resources Canada; Canadian Forest Service; Quebec City QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Bryan M. T. Brunet
- Department of Biological Sciences; CW405 Biosciences Centre; University of Alberta; Edmonton AB Canada
| | - Kevin Muirhead
- Department of Biological Sciences; CW405 Biosciences Centre; University of Alberta; Edmonton AB Canada
| | - Michel Cusson
- Laurentian Forestry Centre; Natural Resources Canada; Canadian Forest Service; Quebec City QC Canada
| | - Catherine Béliveau
- Laurentian Forestry Centre; Natural Resources Canada; Canadian Forest Service; Quebec City QC Canada
| | - Roger C. Levesque
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Lisa M. Lumley
- Department of Biological Sciences; CW405 Biosciences Centre; University of Alberta; Edmonton AB Canada
- Laurentian Forestry Centre; Natural Resources Canada; Canadian Forest Service; Quebec City QC Canada
| | - Felix A. H. Sperling
- Department of Biological Sciences; CW405 Biosciences Centre; University of Alberta; Edmonton AB Canada
| |
Collapse
|
46
|
Scordato ESC, Wilkins MR, Semenov G, Rubtsov AS, Kane NC, Safran RJ. Genomic variation across two barn swallow hybrid zones reveals traits associated with divergence in sympatry and allopatry. Mol Ecol 2017; 26:5676-5691. [DOI: 10.1111/mec.14276] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 07/19/2017] [Accepted: 07/24/2017] [Indexed: 12/31/2022]
Affiliation(s)
| | - Matthew R. Wilkins
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
- School of Biological Sciences University of Nebraska‐Lincoln Lincoln NE USA
| | - Georgy Semenov
- Department of Ecology & Evolutionary Biology University of Arizona Tucson AZ USA
- Institute of Systematics and Ecology of Animals Novosibirsk Russia
| | | | - Nolan C. Kane
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
| | - Rebecca J. Safran
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
| |
Collapse
|
47
|
Molecular Phylogenies indicate a Paleo-Tibetan Origin of Himalayan Lazy Toads (Scutiger). Sci Rep 2017; 7:3308. [PMID: 28607415 PMCID: PMC5468327 DOI: 10.1038/s41598-017-03395-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/27/2017] [Indexed: 01/02/2023] Open
Abstract
The Himalaya presents an outstanding geologically active orogen and biodiversity hotspot. However, our understanding of the historical biogeography of its fauna is far from comprehensive. Many taxa are commonly assumed to have originated from China-Indochina and dispersed westward along the Himalayan chain. Alternatively, the “Tibetan-origin hypothesis” suggests primary diversification of lineages in Paleo-Tibet, and secondary diversification along the slopes of the later uplifted Greater Himalaya. We test these hypotheses in high-mountain megophryid anurans (Scutiger). Extensive sampling from High Asia, and analyses of mitochondrial (2839 bp) and nuclear DNA (2208 bp), using Bayesian and Maximum likelihood phylogenetics, suggest that the Himalayan species form a distinct clade, possibly older than those from the eastern Himalaya-Tibet orogen. While immigration from China-Indochina cannot be excluded, our data may indicate that Himalayan Scutiger originated to the north of the Himalaya by colonization from Paleo-Tibet and then date back to the Oligocene. High intraspecific diversity of Scutiger implies limited migration across mountains and drainages along the Himalaya. While our study strengthens support for a “Tibetan-origin hypothesis”, current sampling (10/22 species; 1 revalidated: S. occidentalis) remains insufficient to draw final conclusions on Scutiger but urges comparative phylogeographers to test alternative, geologically supported hypotheses for a true future understanding of Himalayan biogeography.
Collapse
|
48
|
Soltani GG, Bénon D, Alvarez N, Praz CJ. When different contact zones tell different stories: putative ring species in the Megachile concinna species complex (Hymenoptera: Megachilidae). Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
49
|
Scordato ES. Geographical variation in male territory defence strategies in an avian ring species. Anim Behav 2017. [DOI: 10.1016/j.anbehav.2017.01.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
50
|
Hou B, Luo J, Zhang Y, Niu Z, Xue Q, Ding X. Iteration expansion and regional evolution: phylogeography of Dendrobium officinale and four related taxa in southern China. Sci Rep 2017; 7:43525. [PMID: 28262789 PMCID: PMC5337965 DOI: 10.1038/srep43525] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 01/27/2017] [Indexed: 11/24/2022] Open
Abstract
The genus Dendrobium was used as a case study to elucidate the evolutionary history of Orchidaceae in the Sino-Japanese Floristic Region (SJFR) and Southeast Asia region. These evolutionary histories remain largely unknown, including the temporal and spatial distribution of the evolutionary events. The present study used nuclear and plastid DNA to determine the phylogeography of Dendrobium officinale and four closely related taxa. Plastid DNA haplotype and nuclear data were shown to be discordant, suggesting reticulate evolution drove the species' diversification. Rapid radiation and genetic drift appeared to drive the evolution of D. tosaense and D. flexicaule, whereas introgression or hybridization might have been involved in the evolution of D. scoriarum and D. shixingense. The phylogeographical structure of D. officinale revealed that core natural distribution regions might have served as its glacial refuges. In recent years, human disturbances caused its artificial migration and population extinction. The five taxa may have originated from the Nanling Mountains and the Yungui Plateau and then migrated northward or eastward. After the initial iteration expansion, D. officinale populations appeared to experience the regional evolutionary patterns in different regions and follow the sequential or rapid decline in gene exchange.
Collapse
Affiliation(s)
- Beiwei Hou
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
- Nanjing Institute for Comprehensive Utilization of Wild Plants, Nanjing 210042, China
| | - Jing Luo
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yusi Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
- Jiangsu Industrial Technology Research Institute, Nanjing 210042, China
| | - Zhitao Niu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Qingyun Xue
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Xiaoyu Ding
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| |
Collapse
|