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Judson BJ, Kristjánsson BK, Leblanc CA, Ferguson MM. The role of neutral and adaptive evolutionary processes on patterns of genetic diversity across small cave-dwelling populations of Icelandic Arctic charr ( Salvelinus alpinus). Ecol Evol 2024; 14:e11363. [PMID: 38770124 PMCID: PMC11103641 DOI: 10.1002/ece3.11363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 05/22/2024] Open
Abstract
Understanding the adaptability of small populations in the face of environmental change is a central problem in evolutionary biology. Solving this problem is challenging because neutral evolutionary processes that operate on historical and contemporary timescales can override the effects of selection in small populations. We assessed the effects of isolation by colonization (IBC), isolation by dispersal limitation (IBDL) as reflected by a pattern of isolation by distance (IBD), and isolation by adaptation (IBA) and the roles of genetic drift and gene flow on patterns of genetic differentiation among 19 cave-dwelling populations of Icelandic Arctic charr (Salvelinus alpinus). We detected evidence of IBC based on the genetic affinity of nearby cave populations and the genetic relationships between the cave populations and the presumed ancestral population in the lake. A pattern of IBD was evident regardless of whether high-level genetic structuring (IBC) was taken into account. Genetic signatures of bottlenecks and lower genetic diversity in smaller populations indicate the effect of drift. Estimates of gene flow and fish movement suggest that gene flow is limited to nearby populations. In contrast, we found little evidence of IBA as patterns of local ecological and phenotypic variation showed little association with genetic differentiation among populations. Thus, patterns of genetic variation in these small populations likely reflect localized gene flow and genetic drift superimposed onto a larger-scale structure that is largely a result of colonization history. Our simultaneous assessment of the effects of neutral and adaptive processes in a tractable and replicated system has yielded novel insights into the evolution of small populations on both historical and contemporary timescales and over a smaller spatial scale than is typically studied.
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Affiliation(s)
- Braden J. Judson
- Department of Integrative BiologyUniversity of GuelphGuelphOntarioCanada
| | | | | | - Moira M. Ferguson
- Department of Integrative BiologyUniversity of GuelphGuelphOntarioCanada
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Sidlauskas BL, Mathur S, Aydoğan H, Monzyk FR, Black AN. Genetic approaches reveal a healthy population and an unexpectedly recent origin for an isolated desert spring fish. BMC Ecol Evol 2024; 24:2. [PMID: 38177987 PMCID: PMC10765885 DOI: 10.1186/s12862-023-02191-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/17/2023] [Indexed: 01/06/2024] Open
Abstract
Foskett Spring in Oregon's desert harbors a historically threatened population of Western Speckled Dace (Rhinichthys klamathensis). Though recently delisted, the dace's recruitment depends upon regular removal of encroaching vegetation. Previous studies assumed that Foskett Dace separated from others in the Warner Valley about 10,000 years ago, thereby framing an enigma about the population's surprising ability to persist for so long in a tiny habitat easily overrun by plants. To investigate that persistence and the effectiveness of interventions to augment population size, we assessed genetic diversity among daces inhabiting Foskett Spring, a refuge at Dace Spring, and three nearby streams. Analysis revealed a robust effective population size (Ne) of nearly 5000 within Foskett Spring, though Ne in the Dace Spring refuge is just 10% of that value. Heterozygosity is slightly lower than expected based on random mating at all five sites, indicating mild inbreeding, but not at a level of concern. These results confirm the genetic health of Foskett Dace. Unexpectedly, genetic differentiation reveals closer similarity between Foskett Dace and a newly discovered population from Nevada's Coleman Creek than between Foskett Dace and dace elsewhere in Oregon. Demographic modeling inferred Coleman Creek as the ancestral source of Foskett Dace fewer than 1000 years ago, much more recently than previously suspected and possibly coincident with the arrival of large herbivores whose grazing may have maintained open water suitable for reproduction. These results solve the enigma of persistence by greatly shortening the duration over which Foskett Dace have inhabited their isolated spring.
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Affiliation(s)
- Brian L Sidlauskas
- Department of Fisheries, Wildlife and Conservation Sciences, Oregon State University, 104 Nash Hall, Corvallis, OR, 97331, USA.
| | - Samarth Mathur
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 318 W 12th Ave, Columbus, OH, 43210, USA
| | - Hakan Aydoğan
- Department of Fisheries, Wildlife and Conservation Sciences, Oregon State University, 104 Nash Hall, Corvallis, OR, 97331, USA
| | - Fred R Monzyk
- Oregon Department of Fish and Wildlife, Corvallis Research Lab, 28655 OR-34, Corvallis, OR, 97333, USA
| | - Andrew N Black
- Center for Quantitative Life Sciences, Oregon State University, 2750 SW Campus Way, Corvallis, OR, 97331, USA
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Mossop KD, Lemmon AR, Moriarty Lemmon E, Eytan R, Adams M, Unmack PJ, Smith Date K, Morales HE, Hammer MP, Wong BBM, Chapple DG. Phylogenomics and biogeography of arid-adapted Chlamydogobius goby fishes. Mol Phylogenet Evol 2023; 182:107757. [PMID: 36925090 DOI: 10.1016/j.ympev.2023.107757] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 02/01/2023] [Accepted: 03/07/2023] [Indexed: 03/17/2023]
Abstract
The progressive aridification of the Australian continent from ∼ 20 million years ago posed severe challenges for the persistence of its resident biota. A key question involves the role of refugial habitats - specifically, their ability to mediate the effects of habitat loss and fragmentation, and their potential to shape opportunities for allopatric speciation. With freshwater species, for example, the patchiness, or absence, of water will constrain distributions. However, aridity may not necessarily isolate populations if disjunct refugia experience frequent hydrological connections. To investigate this potential dichotomy, we explored the evolutionary history of the Chlamydogobius gobies (Gobiiformes: Gobiidae), an arid-adapted genus of six small, benthic fish species that exploit all types of waterbodies (i.e. desert springs, waterholes and bore-fed wetlands, coastal estuarine creeks and mangroves) across parts of central and northern Australia. We used Anchored Phylogenomics to generate a highly resolved phylogeny of the group from sequence data for 260 nuclear loci. Buttressed by companion allozyme and mtDNA datasets, our molecular findings infer the diversification of Chlamydogobius in arid Australia, and provide a phylogenetic structure that cannot be simply explained by invoking allopatric speciation events reflecting current geographic proximity. Our findings are generally consistent with the existing morphological delimitation of species, with one exception: at the shallowest nodes of phylogenetic reconstruction, the molecular data do not fully support the current dichotomous delineation of C. japalpa from C. eremius in Kati Thanda-Lake Eyre-associated waterbodies. Together these findings illustrate the ability of structural (hydrological) connections to generate patterns of connectivity and isolation for an ecologically moderate disperser in response to ongoing habitat aridification. Finally, we explore the implications of these results for the immediate management of threatened (C. gloveri) and critically endangered (C. micropterus, C. squamigenus) congeners.
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Affiliation(s)
- Krystina D Mossop
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, USA
| | | | - Ron Eytan
- Marine Biology Department, Texas A&M University at Galveston, Galveston, TX 77554, USA; Peabody Museum of Natural History, Yale University, New Haven, CT, USA
| | - Mark Adams
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, SA 5000, Australia; School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Peter J Unmack
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia; Centre for Applied Water Science, Institute for Applied Ecology, University of Canberra, ACT 2617, Australia
| | - Katie Smith Date
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia; Museum Victoria, Sciences Department, GPO Box 666, Melbourne, VIC 3001, Australia
| | - Hernán E Morales
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia; Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Michael P Hammer
- Natural Sciences, Museum and Art Gallery of the Northern Territory, Darwin, NT 0801, Australia
| | - Bob B M Wong
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - David G Chapple
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia.
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Gates K, Sandoval-Castillo J, Brauer CJ, Unmack PJ, Laporte M, Bernatchez L, Beheregaray LB. Environmental selection, rather than neutral processes, best explain regional patterns of diversity in a tropical rainforest fish. Heredity (Edinb) 2023:10.1038/s41437-023-00612-x. [PMID: 36997655 DOI: 10.1038/s41437-023-00612-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 03/14/2023] [Accepted: 03/14/2023] [Indexed: 03/31/2023] Open
Abstract
AbstractTo conserve the high functional and genetic variation in hotspots such as tropical rainforests, it is essential to understand the forces driving and maintaining biodiversity. We asked to what extent environmental gradients and terrain structure affect morphological and genomic variation across the wet tropical distribution of an Australian rainbowfish, Melanotaenia splendida splendida. We used an integrative riverscape genomics and morphometrics framework to assess the influence of these factors on both putative adaptive and non-adaptive spatial divergence. We found that neutral genetic population structure was largely explainable by restricted gene flow among drainages. However, environmental associations revealed that ecological variables had a similar power to explain overall genetic variation, and greater power to explain body shape variation, than the included neutral covariables. Hydrological and thermal variables were the strongest environmental predictors and were correlated with traits previously linked to heritable habitat-associated dimorphism in rainbowfishes. In addition, climate-associated genetic variation was significantly associated with morphology, supporting heritability of shape variation. These results support the inference of evolved functional differences among localities, and the importance of hydroclimate in early stages of diversification. We expect that substantial evolutionary responses will be required in tropical rainforest endemics to mitigate local fitness losses due to changing climates.
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Hay AC, Sandoval-Castillo J, Cooke GM, Chao NL, Beheregaray LB. Riverscape Genomics Clarifies Neutral and Adaptive Evolution in an Amazonian Characin Fish (Triportheus albus). Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.825406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Understanding the role of natural selection in the evolution of wild populations is challenging due to the spatial complexity of natural systems. The richest diversity of freshwater fishes in the world is found in the Amazon Basin, a system where marked hydrochemical differences exist at the interface of major rivers with distinct “water colors” (i.e., black, white, and clear water). We hypothesize that divergent natural selection associated with these “aquatic ecotones” influences population-level adaptive divergence in the non-migratory Amazonian fish fauna. This hypothesis was tested using a landscape genomics framework to compare the relative contribution of environmental and spatial factors to the evolutionary divergence of the Amazonian characin fish Triportheus albus. The framework was based on spatial data, in situ hydrochemical measurements, and 15,251 filtered SNPs (single nucleotide polymorphisms) for T. albus sampled from three major Amazonian rivers. Gradient Forest, redundancy analysis (RDA) and BayPass analyses were used to test for signals of natural selection, and model-based and model-free approaches were used to evaluate neutral population differentiation. After controlling for a signal of neutral hierarchical structure which was consistent with the expectations for a dendritic system, variation in turbidity and pH were key factors contributing to adaptive divergence. Variation in genes involved in acid-sensitive ion transport pathways and light-sensitive photoreceptor pathways was strongly associated with pH and turbidity variability. This study improves our understanding of how natural selection and neutral evolution impact on the distribution of aquatic biodiversity from the understudied and ecologically complex Amazonia.
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Rayne A, Blair S, Dale M, Flack B, Hollows J, Moraga R, Parata RN, Rupene M, Tamati‐Elliffe P, Wehi PM, Wylie MJ, Steeves TE. Weaving place‐based knowledge for culturally significant species in the age of genomics: Looking to the past to navigate the future. Evol Appl 2022; 15:751-772. [PMID: 35603033 PMCID: PMC9108313 DOI: 10.1111/eva.13367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 02/16/2022] [Accepted: 02/24/2022] [Indexed: 11/28/2022] Open
Abstract
Relationships with place provide critical context for characterizing biocultural diversity. Yet, genetic and genomic studies are rarely informed by Indigenous or local knowledge, processes, and practices, including the movement of culturally significant species. Here, we show how place‐based knowledge can better reveal the biocultural complexities of genetic or genomic data derived from culturally significant species. As a case study, we focus on culturally significant southern freshwater kōura (crayfish) in Aotearoa me Te Waipounamu (New Zealand, herein Aotearoa NZ). Our results, based on genotyping‐by‐sequencing markers, reveal strong population genetic structure along with signatures of population admixture in 19 genetically depauperate populations across the east coast of Te Waipounamu. Environment association and differentiation analyses for local adaptation also indicate a role for hydroclimatic variables—including temperature, precipitation, and water flow regimes—in shaping local adaptation in kōura. Through trusted partnerships between community and researchers, weaving genomic markers with place‐based knowledge has both provided invaluable context for the interpretation of data and created opportunities to reconnect people and place. We envisage such trusted partnerships guiding future genomic research for culturally significant species in Aotearoa NZ and beyond.
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Affiliation(s)
- Aisling Rayne
- University of Canterbury School of Biological Sciences Christchurch New Zealand
| | | | - Matthew Dale
- Waterscape Connections Ltd Dunedin New Zealand
- Te Rūnanga o Ngāi Tahu Dunedin New Zealand
| | - Brendan Flack
- Kāti Huirapa Rūnaka ki Puketeraki Karitane New Zealand
| | | | - Roger Moraga
- Tea Break Bioinformatics Ltd Palmerston North New Zealand
| | | | - Makarini Rupene
- University of Canterbury Ngāi Tahu Research Centre Christchurch New Zealand
- Environment Canterbury Christchurch New Zealand
| | | | - Priscilla M Wehi
- University of Otago, Centre for Sustainability Dunedin New Zealand
| | - Matthew J Wylie
- Kāti Huirapa Rūnaka ki Puketeraki Karitane New Zealand
- The New Zealand Institute for Plant and Food Research Limited Nelson New Zealand
| | - Tammy E Steeves
- University of Canterbury School of Biological Sciences Christchurch New Zealand
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