1
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Myers BM, Burns KJ, Clark CJ, Brelsford A. Sampling affects population genetic inference: A case study of the Allen's (Selasphorus sasin) and rufous hummingbird (Selasphorus rufus). J Hered 2023; 114:625-636. [PMID: 37455658 DOI: 10.1093/jhered/esad044] [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: 11/05/2022] [Accepted: 07/12/2023] [Indexed: 07/18/2023] Open
Abstract
Gene flow can affect evolutionary inference when species are undersampled. Here, we evaluate the effects of gene flow and geographic sampling on demographic inference of 2 hummingbirds that hybridize, Allen's hummingbird (Selasphorus sasin) and rufous hummingbird (Selasphorus rufus). Using whole-genome data and extensive geographic sampling, we find widespread connectivity, with introgression far beyond the Allen's × rufous hybrid zone, although the Z chromosome resists introgression beyond the hybrid zone. We test alternative hypotheses of speciation history of Allen's, rufous, and Calliope (S. calliope) hummingbird and find that rufous hummingbird is the sister taxon to Allen's hummingbird, and Calliope hummingbird is the outgroup. A model treating the 2 subspecies of Allen's hummingbird as a single panmictic population fit observed genetic data better than models treating the subspecies as distinct populations, in contrast to morphological and behavioral differences and analyses of spatial population structure. With additional sampling, our study builds upon recent studies that came to conflicting conclusions regarding the evolutionary histories of these 2 species. Our results stress the importance of thorough geographic sampling when assessing demographic history in the presence of gene flow.
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Affiliation(s)
- Brian M Myers
- Department of Biological Sciences, San Diego State University, San Diego, CA, United States
| | - Kevin J Burns
- Department of Biological Sciences, San Diego State University, San Diego, CA, United States
| | - Christopher J Clark
- Department of Evolution, Ecology, and Organismal Biology, Speith Hall, University of California, Riverside, CA, United States
| | - Alan Brelsford
- Department of Evolution, Ecology, and Organismal Biology, Speith Hall, University of California, Riverside, CA, United States
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2
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Hirst MA, Rodas-Martínez AZ, Milich KM, Cortés-Ortiz L. Differences in sperm morphology between Alouatta palliata and Alouatta pigra are consistent with the intensity of sperm competition in each species. Am J Primatol 2023; 85:e23538. [PMID: 37487624 PMCID: PMC10528854 DOI: 10.1002/ajp.23538] [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: 11/22/2022] [Revised: 07/03/2023] [Accepted: 07/08/2023] [Indexed: 07/26/2023]
Abstract
The intensity of sperm competition, in which sperm compete within the female reproductive tract to reach and fertilize her eggs, varies in species with different mating systems. Sperm competition is more intense in species where males cannot monopolize access to reproductive females and females mate with multiple males. In this scenario, a morphological change that increases the ability of sperm to reach and fertilize eggs should rapidly spread in the population, leading to sperm morphological differences between closely related species. Differences in sperm morphology have been reported among primate species with different mating systems. However, due to the inherent logistical and ethical difficulties to sample sperm from wild primates, the extent of variation in sperm morphology within species and among closely related species remains understudied. Here, we compared sperm morphological traits from two sister howler monkey species (Alouatta palliata and Alouatta pigra) that have different mating systems to investigate the effect of sperm competition on sperm morphological traits. We predicted that sperm from A. palliata, where females have more opportunities to mate with multiple males, would show differences in traits associated with increase sperm competitiveness compared to A. pigra where females mostly mate with the central male. We used linear mixed models to determine species differences in sperm morphology, controlling for individual variation. We found that midpieces and heads in A. palliata sperm were on average 26.2% and 11.0% longer, respectively, than those of A. pigra. Differences in these traits are important for sperm speed and hydrodynamic movement in other species and can affect fertilization success. This study provides empirical evidence of sperm morphological traits that evolved through sexual selection in sister primate species with different mating systems.
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Affiliation(s)
- Molly A. Hirst
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 N. University Ave., Ann Arbor, MI, USA 48109
| | - Alba Z. Rodas-Martínez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, km 0.5 Carr. Villahermosa-Cárdenas S/N, entroque a Bosques de Saloya, 86039 Villahermosa, Tabasco, México
| | - Krista M. Milich
- Department of Anthropology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, USA 63130
| | - Liliana Cortés-Ortiz
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 N. University Ave., Ann Arbor, MI, USA 48109
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3
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Markviriya D, Asensio N, Brockelman WY, Jeratthitikul E, Kongrit C. Genetic analysis of hybridization between white-handed (Hylobates lar) and pileated (Hylobates pileatus) gibbons in a contact zone in Khao Yai National Park, Thailand. Primates 2021; 63:51-63. [PMID: 34716489 DOI: 10.1007/s10329-021-00958-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 10/17/2021] [Indexed: 10/20/2022]
Abstract
Natural hybridization has played various roles in the evolutionary history of primates. Its consequences range from genetic introgression between taxa, formation of hybrid zones, and formation of new lineages. Hylobates lar, the white-handed gibbon, and Hylobates pileatus, the pileated gibbon, are largely allopatric species in Southeast Asia with a narrow contact zone in Khao Yai National Park, Thailand, which contains both parental types and hybrids. Hybrid individuals in the zone are recognizable by their intermediate pelage and vocal patterns, but have not been analyzed genetically. We analyzed mitochondrial and microsatellite DNA of 52 individuals to estimate the relative genetic contributions of the parental species to each individual, and the amount of introgression into the parental species. We obtained fecal samples from 33 H. lar, 15 H. pileatus and four phenotypically intermediate individuals in the contact zone. Both mitochondrial and microsatellite markers confirmed distinct differences between these taxa. Both H. lar and H. pileatus contributed to the maternal lineages of the hybrids based on mitochondrial analysis; hybrids were viable and present in socially normal reproductive pairs. The microsatellite analysis identified ten admixed individuals, four F1 hybrids, which corresponded to phenotypic hybrids, and six H. lar-like backcrosses. All 15 H. pileatus samples were identified as originating from genetically H. pileatus individuals with no H. lar admixture; hence, backcrossing is biased toward H. lar. A relatively low number of phenotypic hybrids and backcrossed individuals along with a high number of parental types indicates a bimodal hybrid zone, which suggests relatively strong bias in mate selection between the species.
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Affiliation(s)
- Darunee Markviriya
- Animal Systematics and Molecular Ecology Laboratory, Department of Biology, Faculty of Science, Mahidol University, Ratchathewi, Bangkok, 10400, Thailand
| | - Norberto Asensio
- Faculty of Environment and Resource Studies, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand.,Department of Clinical and Health Psychology and Research Methodology, Faculty of Psychology, University of the Basque Country, 20018, Donostia, Gipuzkoa, Spain
| | - Warren Y Brockelman
- Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand.,National Biobank of Thailand, National Science and Technology Development Agency, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Ekgachai Jeratthitikul
- Animal Systematics and Molecular Ecology Laboratory, Department of Biology, Faculty of Science, Mahidol University, Ratchathewi, Bangkok, 10400, Thailand
| | - Chalita Kongrit
- Animal Systematics and Molecular Ecology Laboratory, Department of Biology, Faculty of Science, Mahidol University, Ratchathewi, Bangkok, 10400, Thailand.
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4
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Baiz MD, Tucker PK, Mueller JL, Cortés-Ortiz L. X-Linked Signature of Reproductive Isolation in Humans is Mirrored in a Howler Monkey Hybrid Zone. J Hered 2021; 111:419-428. [PMID: 32725191 PMCID: PMC7525826 DOI: 10.1093/jhered/esaa021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Indexed: 12/13/2022] Open
Abstract
Reproductive isolation is a fundamental step in speciation. While sex chromosomes have been linked to reproductive isolation in many model systems, including hominids, genetic studies of the contribution of sex chromosome loci to speciation for natural populations are relatively sparse. Natural hybrid zones can help identify genomic regions contributing to reproductive isolation, like hybrid incompatibility loci, since these regions exhibit reduced introgression between parental species. Here, we use a primate hybrid zone (Alouatta palliata × Alouatta pigra) to test for reduced introgression of X-linked SNPs compared to autosomal SNPs. To identify X-linked sequence in A. palliata, we used a sex-biased mapping approach with whole-genome re-sequencing data. We then used genomic cline analysis with reduced-representation sequence data for parental A. palliata and A. pigra individuals and hybrids (n = 88) to identify regions with non-neutral introgression. We identified ~26 Mb of non-repetitive, putatively X-linked genomic sequence in A. palliata, most of which mapped collinearly to the marmoset and human X chromosomes. We found that X-linked SNPs had reduced introgression and an excess of ancestry from A. palliata as compared to autosomal SNPs. One outlier region with reduced introgression overlaps a previously described "desert" of archaic hominin ancestry on the human X chromosome. These results are consistent with a large role for the X chromosome in speciation across animal taxa and further, suggest shared features in the genomic basis of the evolution of reproductive isolation in primates.
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Affiliation(s)
- Marcella D Baiz
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI.,Department of Biology, Pennsylvania State University, University Park, PA
| | - Priscilla K Tucker
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Jacob L Mueller
- Department of Human Genetics, University of Michigan, Ann Arbor, MI
| | - Liliana Cortés-Ortiz
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI
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5
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Pazhenkova EA, Lukhtanov VA. Genomic introgression from a distant congener in the Levant fritillary butterfly, Melitaea acentria. Mol Ecol 2021; 30:4819-4832. [PMID: 34288183 DOI: 10.1111/mec.16085] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022]
Abstract
Introgressive hybridization is more common in nature than previously thought, and its role and creative power in evolution is hotly discussed but not completely understood. Introgression occurs more frequently in sympatry between recently diverged taxa, or when the speciation process has not yet been completed. However, there are relatively few documented cases of hybridization that erodes reproductive barriers between distantly related species. Here, we use whole genome and mitochondrial data to examine how introgression from a distant congener affects pattern of genetic differentiation in the Levant fritillary butterfly Melitaea acentria. We show that this local taxon has evolved as a peripatric geographic isolate of the widespread Melitaea persea, and that there has been significant unidirectional gene flow from the sympatric, nonclosely related Melitaea didyma to M. acentria. We found direct evidence of ongoing sporadic hybridization between M. didyma and M. acentria, which are separated by at least 5 million years of independent evolution. Elevated differentiation and lower level of introgression on the sex Z chromosome compared to autosomes suggest that the Z chromosome has accumulated loci acting as intrinsic postzygotic barriers. Our results show that introgression from M. didyma has been an additional source of nucleotide diversity in the M. acentria population, providing material for drift and selection.
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Affiliation(s)
- Elena A Pazhenkova
- Department of Entomology, St. Petersburg State University, St. Petersburg, Russia.,Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, St. Petersburg, Russia
| | - Vladimir A Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, St. Petersburg, Russia
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6
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Affiliation(s)
- Liliana Cortes-Ortiz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL, USA.
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7
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Guo K, Zhong J, Xie F, Zhu L, Qu Y, Ji X. Climate warming will increase chances of hybridization and introgression between two Takydromus lizards (Lacertidae). Ecol Evol 2021; 11:8573-8584. [PMID: 34257917 PMCID: PMC8258214 DOI: 10.1002/ece3.7671] [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: 01/22/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 11/06/2022] Open
Abstract
Coexisting species may experience population and range changes alone or jointly in response to environmental change. Here, we used six climate variables and ten modeling algorithms to predict the distribution of two Takydromus species (T. septentrionalis and T. sexlineatus) in China. We identified the sympatric and allopatric areas by comparing projections between the two species based on habitat suitability under present and future climate scenarios. We constructed the hypervolumes of six climate variables for the two species and then evaluated overlaps between hypervolumes. From this study, we know the following. First, minimum temperature of coldest month contributes the most to the prediction of habitat suitability. Second, habitats suitable for the two species will shift northward in response to climate warming. Third, the range of T. sexlineatus will expand across the four future time intervals before 2,100, namely the 2021-2040, 2041-2060, 2061-2080, and 2081-2100 intervals, under both Shared socioeconomic pathway (SSP) 245 and SSP585 scenarios, and the range of T. septentrionalis will also expand in the future except at the 2081-2100 interval under the SSP585 scenario. Fourth, the sympatric areas will contract or expand under the SSP245 scenario and expand across the four future time intervals before 2,100 under the SSP585 scenario. Fifth, the niche hypervolumes of the two species partially overlapped, and the differences in niche centroid show some degree of niche differentiation between the two species. These results allow to conclude that climate warming will not only drive the northward drift of sympatric areas but also increase the size of these areas if nothing is done to limit the emission of greenhouse gases. Given the existence of hybridization and introgression between T. septentrionalis and T. sexlineatus in the field where they coexist, we also conclude that climate warming will increase chances of hybridization and introgression between the two species.
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Affiliation(s)
- Kun Guo
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
- College of Life and Environmental SciencesWenzhou UniversityWenzhouChina
| | - Jun Zhong
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
- College of Life and Environmental SciencesWenzhou UniversityWenzhouChina
| | - Fan Xie
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
| | - Lin Zhu
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
| | - Yan‐Fu Qu
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
| | - Xiang Ji
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
- College of Life and Environmental SciencesWenzhou UniversityWenzhouChina
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8
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Melander SL, Mueller RL. Comprehensive Analysis of Salamander Hybridization Suggests a Consistent Relationship between Genetic Distance and Reproductive Isolation across Tetrapods. COPEIA 2020. [DOI: 10.1643/ch-19-319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Scott Lucas Melander
- Department of Biology, Colorado State University, 251 W Pitkin Street, Fort Collins, Colorado 80523; (SLM) ; and (RLM) . Send reprint requests to SLM
| | - Rachel Lockridge Mueller
- Department of Biology, Colorado State University, 251 W Pitkin Street, Fort Collins, Colorado 80523; (SLM) ; and (RLM) . Send reprint requests to SLM
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9
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Cong Q, Zhang J, Shen J, Cao X, Brévignon C, Grishin NV. Speciation in North American Junonia from a genomic perspective. SYSTEMATIC ENTOMOLOGY 2020; 45:803-837. [PMID: 34744257 PMCID: PMC8570557 DOI: 10.1111/syen.12428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Delineating species boundaries in phylogenetic groups undergoing recent radiation is a daunting challenge akin to discretizing continuity. Here, we propose a general approach exemplified by American butterflies from the genus Junonia Hübner notorious for the variety of similar phenotypes, ease of hybridization, and the lack of consensus about their classification. We obtain whole-genome shotgun sequences of about 200 specimens. We reason that discreteness emerges from continuity by means of a small number of key players, and search for the proteins that diverged markedly between sympatric populations of different species, while keeping low polymorphism within these species. Being 0.25% of the total number, these three dozen 'speciation' proteins indeed partition pairs of Junonia populations into two clusters with a prominent break in between, while all proteins taken together fail to reveal this discontinuity. Populations with larger divergence from each other, comparable to that between two sympatric species, form the first cluster and correspond to different species. The other cluster is characterized by smaller divergence, similar to that between allopatric populations of the same species and comprise conspecific pairs. Using this method, we conclude that J. genoveva (Cramer), J. litoralis Brévignon, J. evarete (Cramer), and J. divaricata C. & R. Felder are restricted to South America. We find that six species of Junonia are present in the United States, one of which is new: Junonia stemosa Grishin, sp.n. (i), found in south Texas and phenotypically closest to J. nigrosuffusa W. Barnes & McDunnough (ii) in its dark appearance. In the pale nudum of the antennal club, these two species resemble J. zonalis C. & R. Felder (iii) from Florida and the Caribbean Islands. The pair of sister species, J. grisea Austin & J. Emmel (iv) and J. coenia Hübner (v), represent the classic west/east U.S.A. split. The mangrove feeder (as caterpillar), dark nudum J. neildi Brévignon (vi) enters south Texas as a new subspecies Junonia neildi varia Grishin ssp.n. characterized by more extensive hybridization with and introgression from J. coenia, and, as a consequence, more variable wing patterns compared with the nominal J. n. neildi in Florida. Furthermore, a new mangrove-feeding species from the Pacific Coast of Mexico is described as Junonia pacoma Grishin sp.n. Finally, genomic analysis suggests that J. nigrosuffusa may be a hybrid species formed by the ancestors of J. grisea and J. stemosa sp.n.
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Affiliation(s)
- Qian Cong
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, U.S.A
| | - Jing Zhang
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, U.S.A
| | - Jinhui Shen
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, U.S.A
| | - Xiaolong Cao
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, U.S.A
| | - Christian Brévignon
- Villa A7 Rochambeau, Matoury, French Guiana, University of Texas Southwestern Medical Center, Dallas, TX, U.S.A
| | - Nick V Grishin
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, U.S.A
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, U.S.A
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10
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Toni P, Gall GEC, Clutton-Brock TH, Manser MB. Signalling adjustments to direct and indirect environmental effects on signal perception in meerkats. PLoS One 2020; 15:e0238313. [PMID: 32853231 PMCID: PMC7451564 DOI: 10.1371/journal.pone.0238313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 08/13/2020] [Indexed: 11/19/2022] Open
Abstract
The efficiency of communication between animals is determined by the perception range of signals. With changes in the environment, signal transmission between a sender and a receiver can be influenced both directly, where the signal's propagation quality itself is affected, and indirectly where the senders or receivers' behaviour is impaired, impacting for example the distance between them. Here we investigated how meerkats (Suricata suricatta) in the Kalahari Desert adjust to these challenges in the context of maintaining group cohesion through contact calls. We found that meerkats changed their calling rate when signal transmission was affected indirectly due to increased dispersion of group members as during a drought, but not under typical wet conditions, when signal transmission was directly affected due to higher vegetation density. Instead under these wetter conditions, meerkats remained within proximity to each other. Overall, both direct and indirect environmental effects on signal perception resulted in an increased probability of groups splitting. In conclusion, we provide evidence that social animals can flexibly adjust their vocal coordination behaviour to cope with direct and indirect effects of the environment on signal perception, but these adjustments have limitations.
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Affiliation(s)
- Pauline Toni
- Kalahari Meerkat Project, Kuruman River Reserve, Northern Cape, South Africa
| | - Gabriella E. C. Gall
- Kalahari Meerkat Project, Kuruman River Reserve, Northern Cape, South Africa
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- * E-mail:
| | - Tim H. Clutton-Brock
- Kalahari Meerkat Project, Kuruman River Reserve, Northern Cape, South Africa
- LARG, Department of Zoology, Cambridge, United Kingdom
- Mammal Research Institute, University of Pretoria, Pretoria, South Africa
| | - Marta B. Manser
- Kalahari Meerkat Project, Kuruman River Reserve, Northern Cape, South Africa
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Mammal Research Institute, University of Pretoria, Pretoria, South Africa
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11
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McElroy K, Black A, Dolman G, Horton P, Pedler L, Campbell CD, Drew A, Joseph L. Robbery in progress: Historical museum collections bring to light a mitochondrial capture within a bird species widespread across southern Australia, the Copperback Quail-thrush Cinclosoma clarum. Ecol Evol 2020; 10:6785-6793. [PMID: 32724551 PMCID: PMC7381587 DOI: 10.1002/ece3.6403] [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: 02/20/2020] [Revised: 04/17/2020] [Accepted: 04/21/2020] [Indexed: 01/01/2023] Open
Abstract
We surveyed mitochondrial, autosomal, and Z chromosome diversity within and between the Copperback Quail-thrush Cinclosoma clarum and Chestnut Quail-thrush C. castanotum, which together span the arid and semi-arid zones of southern Australia, and primarily from specimens held in museum collections. We affirm the recent taxonomic separation of the two species and then focus on diversity within the more widespread of the two species, C. clarum. To guide further study of the system and what it offers to understanding the genomics of the differentiation and speciation processes, we develop and present a hypothesis to explain mitonuclear discordance that emerged in ourdata. Following a period of historical allopatry, secondary contact has resulted in an eastern mitochondrial genome replacing the western mitochondrial genome in western populations. This is predicted under a population-level invasion in the opposite direction, that of the western population invading the range of the eastern one. Mitochondrial captures can be driven by neutral, demographic processes, or adaptive mechanisms, and we favor the hypothesized capture being driven by neutral means. We cannot fully reject the adaptive process but suggest how these alternatives may be further tested. We acknowledge an alternative hypothesis, which finds some support in phenotypic data published elsewhere, namely that outcomes of secondary contact have been more complex than our current genomic data suggest. Discriminating and reconciling these two alternative hypotheses, which may not be mutually exclusive, could be tested with closer sampling at levels of population, individual, and nucleotide than has so far been possible. This would be further aided by knowledge of the genetic basis to phenotypic variation described elsewhere.
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Affiliation(s)
- Kerensa McElroy
- Australian National Wildlife CollectionCSIRO National Research Collections AustraliaCanberraACTAustralia
| | | | - Gaynor Dolman
- Molecular Systematics UnitWestern Australian MuseumWAAustralia
- University of AdelaideAdelaideSAAustralia
| | | | - Lynn Pedler
- South Australian MuseumAdelaideSAAustralia
- KoolungaSAAustralia
| | - Catriona D. Campbell
- Australian National Wildlife CollectionCSIRO National Research Collections AustraliaCanberraACTAustralia
| | - Alex Drew
- Australian National Wildlife CollectionCSIRO National Research Collections AustraliaCanberraACTAustralia
| | - Leo Joseph
- Australian National Wildlife CollectionCSIRO National Research Collections AustraliaCanberraACTAustralia
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12
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Melo-Carrillo A, Dunn JC, Cortés-Ortiz L. Low genetic diversity and limited genetic structure across the range of the critically endangered Mexican howler monkey (Alouatta palliata mexicana). Am J Primatol 2020; 82:e23160. [PMID: 32557717 DOI: 10.1002/ajp.23160] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 06/01/2020] [Accepted: 06/07/2020] [Indexed: 11/08/2022]
Abstract
Genetic diversity provides populations with the possibility to persist in ever-changing environments, where selective regimes change over time. Therefore, the long-term survival of a population may be affected by its level of genetic diversity. The Mexican howler monkey (Alouatta palliata mexicana) is a critically endangered primate restricted to southeast Mexico. Here, we evaluate the genetic diversity and population structure of this subspecies based on 83 individuals from 31 groups sampled across the distribution range of the subspecies, using 29 microsatellite loci. Our results revealed extremely low genetic diversity (HO = 0.21, HE = 0.29) compared to studies of other A. palliata populations and to other Alouatta species. Principal component analysis, a Bayesian clustering method, and analyses of molecular variance did not detect strong signatures of genetic differentiation among geographic populations of this subspecies. Although we detect small but significant FST values between populations, they can be explained by a pattern of isolation by distance. These results and the presence of unique alleles in different populations highlight the importance of implementing conservation efforts in multiple populations across the distribution range of A. p. mexicana to preserve its already low genetic diversity. This is especially important given current levels of population isolation due to the extreme habitat fragmentation across the distribution range of this primate.
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Affiliation(s)
- Adrián Melo-Carrillo
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - Jacob C Dunn
- Behavioural Ecology Research Group, School of Life Sciences, Anglia Ruskin University, Cambridge, UK.,Biological Anthropology, Department of Archaeology, University of Cambridge, Cambridge, UK.,Department of Cognitive Biology, University of Vienna, Vienna, Austria
| | - Liliana Cortés-Ortiz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
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13
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Flores-Escobar E, Sanpera C, Jover L, Cortés-Ortiz L, Rangel-Negrín A, Canales-Espinosa D, Dias PAD. Isotopic niche partitioning in two sympatric howler monkey species. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 172:438-446. [PMID: 32091131 DOI: 10.1002/ajpa.24028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 01/10/2020] [Accepted: 02/10/2020] [Indexed: 01/20/2023]
Abstract
OBJECTIVES Ecological similarity between species can lead to interspecific trophic competition. However, when ecologically similar species coexist, they may differ in foraging strategies and habitat use, which can lead to niche partitioning. As the body tissues of consumers contain a stable isotope signature that reflects the isotopic composition of their diet, stable isotope analysis is a useful tool to study feeding behavior. We measured the isotopic niche width, which is a proxy for trophic niche width, of mantled (Alouatta palliata) and black (A. pigra) howler monkeys. Specifically, studied populations in allopatry and sympatry to assess whether these species showed niche partitioning. MATERIALS AND METHODS Between 2008 and 2012, we collected hair samples from 200 subjects (113 black and 87 mantled howler monkeys) and used continuous flow isotope ratio mass spectrometry to estimate δ13 C and δ15 N. We described the isotopic niche width of each species in allopatry and sympatry with the Bayesian estimation of the standard ellipse areas. RESULTS In allopatry, isotopic niche width and isotopic variation were similar in both species. In sympatry, black howler monkeys had a significantly broader isotopic niche, which was mainly determined by high δ15 N values, and included the majority of mantled howler monkeys' isotopic niche. The isotopic niche of mantled howler monkeys did not differ between sympatry and allopatry. CONCLUSIONS The coexistence of these ecologically similar species may be linked to trophic niche adjustments by one species, although the particular features of such adjustments (e.g., dietary, spatial, or sensory partitioning) remain to be addressed.
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Affiliation(s)
- Elizabeth Flores-Escobar
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.,Primate Behavioral Ecology Lab, Instituto de Neuroetología, Universidad Veracruzana, Xalapa, Mexico
| | - Carolina Sanpera
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Lluís Jover
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Liliana Cortés-Ortiz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - Ariadna Rangel-Negrín
- Primate Behavioral Ecology Lab, Instituto de Neuroetología, Universidad Veracruzana, Xalapa, Mexico
| | - Domingo Canales-Espinosa
- Primate Behavioral Ecology Lab, Instituto de Neuroetología, Universidad Veracruzana, Xalapa, Mexico
| | - Pedro Américo D Dias
- Primate Behavioral Ecology Lab, Instituto de Neuroetología, Universidad Veracruzana, Xalapa, Mexico
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14
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Ackermann RR, Arnold ML, Baiz MD, Cahill JA, Cortés-Ortiz L, Evans BJ, Grant BR, Grant PR, Hallgrimsson B, Humphreys RA, Jolly CJ, Malukiewicz J, Percival CJ, Ritzman TB, Roos C, Roseman CC, Schroeder L, Smith FH, Warren KA, Wayne RK, Zinner D. Hybridization in human evolution: Insights from other organisms. Evol Anthropol 2019; 28:189-209. [PMID: 31222847 PMCID: PMC6980311 DOI: 10.1002/evan.21787] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 01/30/2019] [Accepted: 04/30/2019] [Indexed: 12/14/2022]
Abstract
During the late Pleistocene, isolated lineages of hominins exchanged genes thus influencing genomic variation in humans in both the past and present. However, the dynamics of this genetic exchange and associated phenotypic consequences through time remain poorly understood. Gene exchange across divergent lineages can result in myriad outcomes arising from these dynamics and the environmental conditions under which it occurs. Here we draw from our collective research across various organisms, illustrating some of the ways in which gene exchange can structure genomic/phenotypic diversity within/among species. We present a range of examples relevant to questions about the evolution of hominins. These examples are not meant to be exhaustive, but rather illustrative of the diverse evolutionary causes/consequences of hybridization, highlighting potential drivers of human evolution in the context of hybridization including: influences on adaptive evolution, climate change, developmental systems, sex-differences in behavior, Haldane's rule and the large X-effect, and transgressive phenotypic variation.
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Affiliation(s)
- Rebecca R. Ackermann
- Department of Archaeology, University of Cape Town, Rondebosch, South Africa
- Human Evolution Research Institute, University of Cape Town, Rondebosch, South Africa
| | | | - Marcella D. Baiz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - James A. Cahill
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California
| | - Liliana Cortés-Ortiz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - Ben J. Evans
- Biology Department, Life Sciences Building, McMaster University, Hamilton, Canada
| | - B. Rosemary Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey
| | - Peter R. Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey
| | - Benedikt Hallgrimsson
- Department of Cell Biology and Anatomy and the Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Robyn A. Humphreys
- Department of Archaeology, University of Cape Town, Rondebosch, South Africa
- Human Evolution Research Institute, University of Cape Town, Rondebosch, South Africa
| | - Clifford J. Jolly
- Center for the Study of Human Origins, Department of Anthropology, New York University, and NYCEP, New York, New York
| | - Joanna Malukiewicz
- Biodesign Institute, Arizona State University, Tempe, Arizona
- Federal University of Vicosa, Department of Animal Biology, Brazil
| | - Christopher J. Percival
- Department of Cell Biology and Anatomy and the Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
- Department of Anthropology, Stony Brook University, New York
| | - Terrence B. Ritzman
- Department of Archaeology, University of Cape Town, Rondebosch, South Africa
- Human Evolution Research Institute, University of Cape Town, Rondebosch, South Africa
- Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri
- Department of Anthropology, Washington University, St. Louis, Missouri
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center (DPZ), Leibniz Institute for Primate Research, Göttingen, Germany
| | - Charles C. Roseman
- Department of Animal Biology, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Lauren Schroeder
- Human Evolution Research Institute, University of Cape Town, Rondebosch, South Africa
- Department of Anthropology, University of Toronto Mississauga, Mississauga, Canada
| | - Fred H. Smith
- Department of Sociology and Anthropology, Illinois State University, Normal, Illinois
| | - Kerryn A. Warren
- Department of Archaeology, University of Cape Town, Rondebosch, South Africa
- Human Evolution Research Institute, University of Cape Town, Rondebosch, South Africa
| | | | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center (DPZ), Leibniz Institute for Primate Research, Göttingen, Germany
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15
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Cortés-Ortiz L, Espinosa DC, Dias PD, Bergman T, Kitchen DM. From Mexico to Michigan and back: An international collaboration investigating primate behavior, ecology, and evolution from multiple perspectives. Am J Primatol 2019; 81:e22992. [PMID: 31183883 DOI: 10.1002/ajp.22992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 11/07/2022]
Abstract
Evolutionary research benefits form the integration of laboratory and field components to determine factors and processes that affect the evolutionary trajectories of species. Our shared interest in understanding hybridization with genetic admixture as a process that may impact social, behavioral, and ecological features of primates, brought us together in a collaborative project aimed at addressing how vocal variation in two species of howler monkeys in Mexico affects and is affected by hybridization. To achieve this goal, we joined our academic expertise in studying primate genetics, ecology, and behavior under different natural and experimental conditions. We took advantage of decades of experience studying and handing wild howler monkeys for translocation projects to safely sample and study wild populations for this project. Here, we describe the history of our collaboration highlighting how our different perspectives, academic realities, and individual strengths built the foundation for our successful collaboration. We also share our perspectives on how this collaboration opened up new academic venues, broadened our individual perspectives on the integration of different research approaches to address a complex topic, and allowed us to recognize the strength of international collaboration.
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Affiliation(s)
- Liliana Cortés-Ortiz
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 N. University, Ann Arbor, Michigan
| | - Domingo Canales Espinosa
- Primate Behavioral Ecology Lab, Instituto de Neuroetología, Universidad Veracruzana, Xalapa, Veracruz, Mexico
| | - Pedro D Dias
- Primate Behavioral Ecology Lab, Instituto de Neuroetología, Universidad Veracruzana, Xalapa, Veracruz, Mexico
| | - Thore Bergman
- Department of Psychology, University of Michigan, Ann Arbor, Michigan
| | - Dawn M Kitchen
- Department of Anthropology, The Ohio State University, Mansfield, Ohio
- Department of Anthropology, The Ohio State University, Columbus, Ohio
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16
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Baiz MD, Tucker PK, Cortés-Ortiz L. Multiple forms of selection shape reproductive isolation in a primate hybrid zone. Mol Ecol 2019; 28:1056-1069. [PMID: 30582763 PMCID: PMC6888905 DOI: 10.1111/mec.14966] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 10/22/2018] [Indexed: 01/02/2023]
Abstract
Speciation occurs when populations diverge and become reproductively isolated from each other. Natural selection is commonly accepted to play a large role in this process, and it has been widely assumed that reproductive isolation often results as a by-product of divergence driven by adaptation in allopatry. When such populations come into secondary contact, reinforcement can act to strengthen reproductive isolation, but the frequency and importance of this process are still unknown. Here, we explored genomic signatures of selection in allopatry and sympatry for loci associated with reproductive isolation using a natural primate hybrid zone. By analysing reduced-representation sequencing data, we quantified admixture and population structure across a howler monkey hybrid zone and examined the relationship between locus-specific differentiation and introgression. We detected extensive admixture that was mostly limited to the narrow contact zone. Loci with reduced introgression into the heterospecific genomic background (the pattern expected for loci associated with reproductive isolation due to selection against hybrids) were significantly more differentiated between allopatric parental populations than loci with neutral and increased introgression, supporting the hypothesis that reproductive isolation is a by-product of divergence in allopatry. Further, loci with reduced introgression showed greater differentiation in sympatry than in allopatry, suggesting a role for reinforcement. Thus, our results reflect multiple forms of selection that have shaped reproductive isolation in this system. We conclude that reproductive isolation may have initially been driven by divergence in allopatry, but later reinforced by divergent selection in sympatry.
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Affiliation(s)
- Marcella D Baiz
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - Priscilla K Tucker
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - Liliana Cortés-Ortiz
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
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17
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Cortés-Ortiz L, Roos C, Zinner D. Introduction to Special Issue on Primate Hybridization and Hybrid Zones. INT J PRIMATOL 2019. [DOI: 10.1007/s10764-019-00076-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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