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Shen Y, Gong Y, Solovyeva D, Wang L, Li M, Hu M, Jiang Y, Vartanyan S, Wang H. Genetic diversity and shallow genetic differentiation of the endangered scaly-sided merganser Mergus squamatus. Ecol Evol 2024; 14:e70011. [PMID: 38983702 PMCID: PMC11233196 DOI: 10.1002/ece3.70011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 06/10/2024] [Accepted: 07/02/2024] [Indexed: 07/11/2024] Open
Abstract
Examining patterns of genetic diversity are crucial for conservation planning on endangered species, while inferring the underlying process of recent anthropogenic habitat modifications in the context potential long-term demographic changes remains challenging. The globally endangered scaly-sided merganser (SSME), Mergus squamatus, is endemic to a narrow range in Northeast Asia, and its population has recently been contracted into two main breeding areas. Although low genetic diversity has been suggested in the Russian population, the genetic status and demographic history of these individuals have not been fully elucidated. We therefore examined the genetic diversity and structure of the breeding populations of the SSME and investigated the relative importance of historical and recent demographic changes to the present-day pattern of genetic diversity. Using 10 nuclear microsatellite (SSR) markers and mitochondrial DNA (mtDNA) control region sequences, we found limited female-inherited genetic diversity and a high level of nuclear genetic diversity. In addition, analysis of both markers consistently revealed significant but weak divergence between the breeding populations. Inconsistent demographic history parameters calculated from mtDNA and bottleneck analysis results based on SSR suggested a stable historical effective population size. By applying approximate Bayesian computation, it was estimated that populations started to genetically diverge from each other due to recent fragmentation events caused by anthropogenic effects rather than isolation during Last Glacial Maximum (LGM) and post-LGM recolonization. These results suggest that limited historical population size and shallow evolutionary history may be potential factors contributing to the contemporary genetic diversity pattern of breeding SSME populations. Conservation efforts should focus on protecting the current breeding habitats from further destruction, with priority given to both the Russian and Chinese population, as well as restoring the connected suitable breeding grounds.
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Affiliation(s)
- Yulong Shen
- School of Life Sciences Northeast Normal University Changchun China
| | - Ye Gong
- School of Life Sciences Northeast Normal University Changchun China
| | - Diana Solovyeva
- Institute of Biological Problems of the North FEB RAS Magadan Russia
| | - Lin Wang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences Changchun China
| | - Mu Li
- School of Life Sciences Northeast Normal University Changchun China
| | - Mengxuan Hu
- School of Life Sciences Northeast Normal University Changchun China
| | - Yiwei Jiang
- School of Life Sciences Northeast Normal University Changchun China
| | - Sergey Vartanyan
- North-East Interdisciplinary Scientific Research Institute n. a. N. A. Shilo, Far East Branch, Russian Academy of Sciences Magadan Russia
| | - Haitao Wang
- School of Life Sciences Northeast Normal University Changchun China
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2
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Garrido-Bautista J, Comas M, Jowers MJ, Smith S, Penn DJ, Bakkali M, Moreno-Rueda G. Fine-scale genetic structure and phenotypic divergence of a passerine bird population inhabiting a continuous Mediterranean woodland. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240601. [PMID: 39253402 PMCID: PMC11382889 DOI: 10.1098/rsos.240601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 05/04/2024] [Accepted: 05/08/2024] [Indexed: 09/11/2024]
Abstract
Genetic differentiation between populations inhabiting ecologically different habitats might appear because of limited dispersal and gene flow, which may lead to patterns of phenotypic divergence and local adaptation. In this study, we use dispersal, genotypic (24 microsatellite loci) and phenotypic (body size and clutch size) data to analyse patterns of genetic structuring and phenotypic divergence in a blue tit (Cyanistes caeruleus) population inhabiting a continuous and heterogeneous woodland along a valley. The two slopes of the valley differ in their forest formations and environmental conditions. Findings showed that most blue tits reproduced within their natal slope. Accordingly, microsatellite analyses revealed that populations of blue tits established in the two slopes show subtle genetic differentiation. The two genetic populations diverged in clutch size, exceeding the level of differentiation expected based on genetic drift, hence suggesting divergent selection (or other processes promoting divergence) on this life-history trait. Our findings reveal that restricted dispersal and spatial heterogeneity may lead to genetic differentiation among bird populations at a surprisingly small scale. In this respect, it is worth highlighting that such differentiation occurs for an organism with high dispersal capacity and within a continuous woodland. Moreover, we show that small-scale ecological differences, together with limited gene flow, can result in selection favouring different phenotypes even within the same continuum population.
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Affiliation(s)
| | - Mar Comas
- Department of Zoology, University of Granada, Granada 18071, Spain
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA
| | - Michael J Jowers
- Department of Zoology, University of Granada, Granada 18071, Spain
| | - Steve Smith
- Department of Interdisciplinary Life Sciences, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine Vienna, Vienna 1160, Austria
| | - Dustin J Penn
- Department of Interdisciplinary Life Sciences, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine Vienna, Vienna 1160, Austria
| | - Mohammed Bakkali
- Department of Genetics, Faculty of Sciences, University of Granada, Granada 18071, Spain
| | - Gregorio Moreno-Rueda
- Department of Zoology, University of Granada, Granada 18071, Spain
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA
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Benham PM, Cicero C, Escalona M, Beraut E, Fairbairn C, Marimuthu MPA, Nguyen O, Sahasrabudhe R, King BL, Thomas WK, Kovach AI, Nachman MW, Bowie RCK. Remarkably High Repeat Content in the Genomes of Sparrows: The Importance of Genome Assembly Completeness for Transposable Element Discovery. Genome Biol Evol 2024; 16:evae067. [PMID: 38566597 PMCID: PMC11088854 DOI: 10.1093/gbe/evae067] [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: 11/02/2023] [Revised: 03/01/2024] [Accepted: 03/23/2024] [Indexed: 04/04/2024] Open
Abstract
Transposable elements (TE) play critical roles in shaping genome evolution. Highly repetitive TE sequences are also a major source of assembly gaps making it difficult to fully understand the impact of these elements on host genomes. The increased capacity of long-read sequencing technologies to span highly repetitive regions promises to provide new insights into patterns of TE activity across diverse taxa. Here we report the generation of highly contiguous reference genomes using PacBio long-read and Omni-C technologies for three species of Passerellidae sparrow. We compared these assemblies to three chromosome-level sparrow assemblies and nine other sparrow assemblies generated using a variety of short- and long-read technologies. All long-read based assemblies were longer (range: 1.12 to 1.41 Gb) than short-read assemblies (0.91 to 1.08 Gb) and assembly length was strongly correlated with the amount of repeat content. Repeat content for Bell's sparrow (31.2% of genome) was the highest level ever reported within the order Passeriformes, which comprises over half of avian diversity. The highest levels of repeat content (79.2% to 93.7%) were found on the W chromosome relative to other regions of the genome. Finally, we show that proliferation of different TE classes varied even among species with similar levels of repeat content. These patterns support a dynamic model of TE expansion and contraction even in a clade where TEs were once thought to be fairly depauperate and static. Our work highlights how the resolution of difficult-to-assemble regions of the genome with new sequencing technologies promises to transform our understanding of avian genome evolution.
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Affiliation(s)
- Phred M Benham
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Carla Cicero
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Colin Fairbairn
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA 95616, USA
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA 95616, USA
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA 95616, USA
| | - Benjamin L King
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA
| | - W Kelley Thomas
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Adrienne I Kovach
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH 03824, USA
| | - Michael W Nachman
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
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Klein JD, Maduna SN, Dicken ML, da Silva C, Soekoe M, McCord ME, Potts WM, Hagen SB, Bester‐van der Merwe AE. Local adaptation with gene flow in a highly dispersive shark. Evol Appl 2024; 17:e13628. [PMID: 38283610 PMCID: PMC10810256 DOI: 10.1111/eva.13628] [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: 08/23/2023] [Revised: 11/06/2023] [Accepted: 11/27/2023] [Indexed: 01/30/2024] Open
Abstract
Adaptive divergence in response to environmental clines are expected to be common in species occupying heterogeneous environments. Despite numerous advances in techniques appropriate for non-model species, gene-environment association studies in elasmobranchs are still scarce. The bronze whaler or copper shark (Carcharhinus brachyurus) is a large coastal shark with a wide distribution and one of the most exploited elasmobranchs in southern Africa. Here, we assessed the distribution of neutral and adaptive genomic diversity in C. brachyurus across a highly heterogeneous environment in southern Africa based on genome-wide SNPs obtained through a restriction site-associated DNA method (3RAD). A combination of differentiation-based genome-scan (outflank) and genotype-environment analyses (redundancy analysis, latent factor mixed models) identified a total of 234 differentiation-based outlier and candidate SNPs associated with bioclimatic variables. Analysis of 26,299 putatively neutral SNPs revealed moderate and evenly distributed levels of genomic diversity across sites from the east coast of South Africa to Angola. Multivariate and clustering analyses demonstrated a high degree of gene flow with no significant population structuring among or within ocean basins. In contrast, the putatively adaptive SNPs demonstrated the presence of two clusters and deep divergence between Angola and all other individuals from Namibia and South Africa. These results provide evidence for adaptive divergence in response to a heterogeneous seascape in a large, mobile shark despite high levels of gene flow. These results are expected to inform management strategies and policy at the national and regional level for conservation of C. brachyurus populations.
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Affiliation(s)
- Juliana D. Klein
- Molecular Breeding and Biodiversity Research Group, Department of GeneticsStellenbosch UniversityStellenboschSouth Africa
| | - Simo N. Maduna
- Department of Ecosystems in the Barents Region, Svanhovd Research StationNorwegian Institute of Bioeconomy Research—NIBIOSvanvikNorway
| | - Matthew L. Dicken
- KwaZulu‐Natal Sharks BoardUmhlanga RocksSouth Africa
- Institute for Coastal and Marine Research (CMR), Ocean Sciences CampusNelson Mandela UniversityGqeberhaSouth Africa
| | - Charlene da Silva
- Department of Forestry, Fisheries and EnvironmentRogge BaySouth Africa
| | - Michelle Soekoe
- Division of Marine ScienceReel Science CoalitionCape TownSouth Africa
| | - Meaghen E. McCord
- South African Shark ConservancyHermanusSouth Africa
- Canadian Parks and Wilderness SocietyVancouverBritish ColumbiaCanada
| | - Warren M. Potts
- Department of Ichthyology and Fisheries ScienceRhodes UniversityMakhandaSouth Africa
- South African Institute for Aquatic BiodiversityMakhandaSouth Africa
| | - Snorre B. Hagen
- Department of Ecosystems in the Barents Region, Svanhovd Research StationNorwegian Institute of Bioeconomy Research—NIBIOSvanvikNorway
| | - Aletta E. Bester‐van der Merwe
- Molecular Breeding and Biodiversity Research Group, Department of GeneticsStellenbosch UniversityStellenboschSouth Africa
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Carbeck K, Arcese P, Lovette I, Pruett C, Winker K, Walsh J. Candidate genes under selection in song sparrows co-vary with climate and body mass in support of Bergmann's Rule. Nat Commun 2023; 14:6974. [PMID: 37935683 PMCID: PMC10630373 DOI: 10.1038/s41467-023-42786-2] [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: 01/10/2023] [Accepted: 10/19/2023] [Indexed: 11/09/2023] Open
Abstract
Ecogeographic rules denote spatial patterns in phenotype and environment that may reflect local adaptation as well as a species' capacity to adapt to change. To identify genes underlying Bergmann's Rule, which posits that spatial correlations of body mass and temperature reflect natural selection and local adaptation in endotherms, we compare 79 genomes from nine song sparrow (Melospiza melodia) subspecies that vary ~300% in body mass (17 - 50 g). Comparing large- and smaller-bodied subspecies revealed 9 candidate genes in three genomic regions associated with body mass. Further comparisons to the five smallest subspecies endemic to California revealed eight SNPs within four of the candidate genes (GARNL3, RALGPS1, ANGPTL2, and COL15A1) associated with body mass and varying as predicted by Bergmann's Rule. Our results support the hypothesis that co-variation in environment, body mass and genotype reflect the influence of natural selection on local adaptation and a capacity for contemporary evolution in this diverse species.
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Affiliation(s)
- Katherine Carbeck
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, T6T 1Z4, Canada.
| | - Peter Arcese
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, T6T 1Z4, Canada
| | - Irby Lovette
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14850, USA
| | - Christin Pruett
- Department of Biology, Ouachita Baptist University, Arkadelphia, AR, 71998, USA
| | - Kevin Winker
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - Jennifer Walsh
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, USA
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6
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Maduna SN, Jónsdóttir ÓDB, Imsland AKD, Gíslason D, Reynolds P, Kapari L, Hangstad TA, Meier K, Hagen SB. Genomic Signatures of Local Adaptation under High Gene Flow in Lumpfish-Implications for Broodstock Provenance Sourcing and Larval Production. Genes (Basel) 2023; 14:1870. [PMID: 37895225 PMCID: PMC10606024 DOI: 10.3390/genes14101870] [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: 08/21/2023] [Revised: 09/20/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
Aquaculture of the lumpfish (Cyclopterus lumpus L.) has become a large, lucrative industry owing to the escalating demand for "cleaner fish" to minimise sea lice infestations in Atlantic salmon mariculture farms. We used over 10K genome-wide single nucleotide polymorphisms (SNPs) to investigate the spatial patterns of genomic variation in the lumpfish along the coast of Norway and across the North Atlantic. Moreover, we applied three genome scans for outliers and two genotype-environment association tests to assess the signatures and patterns of local adaptation under extensive gene flow. With our 'global' sampling regime, we found two major genetic groups of lumpfish, i.e., the western and eastern Atlantic. Regionally in Norway, we found marginal evidence of population structure, where the population genomic analysis revealed a small portion of individuals with a different genetic ancestry. Nevertheless, we found strong support for local adaption under high gene flow in the Norwegian lumpfish and identified over 380 high-confidence environment-associated loci linked to gene sets with a key role in biological processes associated with environmental pressures and embryonic development. Our results bridge population genetic/genomics studies with seascape genomics studies and will facilitate genome-enabled monitoring of the genetic impacts of escapees and allow for genetic-informed broodstock selection and management in Norway.
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Affiliation(s)
- Simo Njabulo Maduna
- Department of Ecosystems in the Barents Region, Svanhovd Research Station, Norwegian Institute of Bioeconomy Research, 9925 Svanvik, Norway;
| | | | - Albert Kjartan Dagbjartarson Imsland
- Akvaplan-Niva Iceland Office, Akralind 6, 201 Kópavogur, Iceland; (Ó.D.B.J.); (A.K.D.I.)
- Department of Biological Sciences, High Technology Centre, University of Bergen, 5020 Bergen, Norway
| | | | | | - Lauri Kapari
- Akvaplan-Niva, Framsenteret, 9296 Tromsø, Norway;
| | | | | | - Snorre B. Hagen
- Department of Ecosystems in the Barents Region, Svanhovd Research Station, Norwegian Institute of Bioeconomy Research, 9925 Svanvik, Norway;
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7
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Powell DM. Losing the forest for the tree? On the wisdom of subpopulation management. Zoo Biol 2023; 42:591-604. [PMID: 37218348 DOI: 10.1002/zoo.21776] [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: 07/19/2022] [Revised: 03/24/2023] [Accepted: 04/26/2023] [Indexed: 05/24/2023]
Abstract
Animal habitats are changing around the world in many ways, presenting challenges to the survival of species. Zoo animal populations are also challenged by small population sizes and limited genetic diversity. Some ex situ populations are managed as subpopulations based on presumed subspecies or geographic locality and related concerns over genetic purity or taxonomic integrity. However, these decisions can accelerate the loss of genetic diversity and increase the likelihood of population extinction. Here I challenge the wisdom of subpopulation management, pointing out significant concerns in the literature with delineation of species, subspecies, and evolutionarily significant units. I also review literature demonstrating the value of gene flow for preserving adaptive potential, the often-misunderstood role of hybridization in evolution, and the likely overstated concerns about outbreeding depression, and preservation of local adaptations. I argue that the most effective way to manage animal populations for the long term be they in human care, in the wild, or if a captive population is being managed for reintroduction, is to manage for maximum genetic diversity rather than managing subpopulations focusing on taxonomic integrity, genetic purity, or geographic locale because selection in the future, rather than the past, will determine what genotypes and phenotypes are the most fit. Several case studies are presented to challenge the wisdom of subpopulation management and stimulate thinking about the preservation of genomes rather than species, subspecies, or lineages because those units evolved in habitats that are likely very different from those habitats today and in the future.
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Affiliation(s)
- David M Powell
- Department of Reproductive & Behavioral Sciences, Saint Louis Zoo, Saint Louis, Missouri, USA
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