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Massip-Veloso Y, Hoagstrom CW, McMahan CD, Matamoros WA. Biogeography of Greater Antillean freshwater fishes, with a review of competing hypotheses. Biol Rev Camb Philos Soc 2024; 99:901-927. [PMID: 38205676 DOI: 10.1111/brv.13050] [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: 05/29/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024]
Abstract
In biogeography, vicariance and long-distance dispersal are often characterised as competing scenarios. However, they are related concepts, both relying on collective geological, ecological, and phylogenetic evidence. This is illustrated by freshwater fishes, which may immigrate to islands either when freshwater connections are temporarily present and later severed (vicariance), or by unusual means when ocean gaps are crossed (long-distance dispersal). Marine barriers have a strong filtering effect on freshwater fishes, limiting immigrants to those most capable of oceanic dispersal. The roles of vicariance and dispersal are debated for freshwater fishes of the Greater Antilles. We review three active hypotheses [Cretaceous vicariance, Greater Antilles-Aves Ridge (GAARlandia), long-distance dispersal] and propose long-distance dispersal to be an appropriate model due to limited support for freshwater fish use of landspans. Greater Antillean freshwater fishes have six potential source bioregions (defined from faunal similarity): Northern Gulf of México, Western Gulf of México, Maya Terrane, Chortís Block, Eastern Panamá, and Northern South America. Faunas of the Greater Antilles are composed of taxa immigrating from many of these bioregions, but there is strong compositional disharmony between island and mainland fish faunas (>90% of Antillean species are cyprinodontiforms, compared to <10% in Northern Gulf of México and Northern South America, and ≤50% elsewhere), consistent with a hypothesis of long-distance dispersal. Ancestral-area reconstruction analysis indicates there were 16 or 17 immigration events over the last 51 million years, 14 or 15 of these by cyprinodontiforms. Published divergence estimates and evidence available for each immigration event suggests they occurred at different times and by different pathways, possibly with rafts of vegetation discharged from rivers or washed to sea during storms. If so, ocean currents likely provide critical pathways for immigration when flowing from one landmass to another. On the other hand, currents create dispersal barriers when flowing perpendicularly between landmasses. In addition to high salinity tolerance, cyprinodontiforms collectively display a variety of adaptations that could enhance their ability to live with rafts (small body size, viviparity, low metabolism, amphibiousness, diapause, self-fertilisation). These adaptations likely also helped immigrants establish island populations after arrival and to persist long term thereafter. Cichlids may have used a pseudo bridge (Nicaragua Rise) to reach the Greater Antilles. Gars (Lepisosteidae) may have crossed the Straits of Florida to Cuba, a relatively short crossing that is not a barrier to gene flow for several cyprinodontiform immigrants. Indeed, widespread distributions of Quaternary migrants (Cyprinodon, Gambusia, Kryptolebias), within the Greater Antilles and among neighbouring bioregions, imply that long-distance dispersal is not necessarily inhibitory for well-adapted species, even though it appears to be virtually impossible for all other freshwater fishes.
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Affiliation(s)
- Yibril Massip-Veloso
- Programa de Doctorado en Ciencias en Biodiversidad y Conservación de Ecosistemas Tropicales, Instituto de Ciencias Biológicas, Universidad de Ciencias y Artes de Chiapas, Libramiento Norte Poniente 1150, C.P. 29039, Tuxtla Gutiérrez, Chiapas, Mexico
| | | | | | - Wilfredo A Matamoros
- Programa de Doctorado en Ciencias en Biodiversidad y Conservación de Ecosistemas Tropicales, Instituto de Ciencias Biológicas, Universidad de Ciencias y Artes de Chiapas, Libramiento Norte Poniente 1150, C.P. 29039, Tuxtla Gutiérrez, Chiapas, Mexico
- Field Museum of Natural History, Chicago, IL, 60605, USA
- Laboratorio de Diversidad Acuática y Biogeografía, Instituto de Ciencias Biológicas, Universidad de Ciencias y Artes de Chiapas, Libramiento Norte Poniente 1150, C.P. 29039, Tuxtla Gutiérrez, Chiapas, Mexico
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Turba R, Richmond JQ, Fitz-Gibbon S, Morselli M, Fisher RN, Swift CC, Ruiz-Campos G, Backlin AR, Dellith C, Jacobs DK. Genetic structure and historic demography of endangered unarmoured threespine stickleback at southern latitudes signals a potential new management approach. Mol Ecol 2022; 31:6515-6530. [PMID: 36205603 PMCID: PMC10092051 DOI: 10.1111/mec.16722] [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: 03/24/2022] [Revised: 09/05/2022] [Accepted: 09/29/2022] [Indexed: 01/13/2023]
Abstract
Habitat loss, flood control infrastructure, and drought have left most of southern California and northern Baja California's native freshwater fish near extinction, including the endangered unarmoured threespine stickleback (Gasterosteus aculeatus williamsoni). This subspecies, an unusual morph lacking the typical lateral bony plates of the G. aculeatus complex, occurs at arid southern latitudes in the eastern Pacific Ocean and survives in only three inland locations. Managers have lacked molecular data to answer basic questions about the ancestry and genetic distinctiveness of unarmoured populations. These data could be used to prioritize conservation efforts. We sampled G. aculeatus from 36 localities and used microsatellites and whole genome data to place unarmoured populations within the broader evolutionary context of G. aculeatus across southern California/northern Baja California. We identified three genetic groups with none consisting solely of unarmoured populations. Unlike G. aculeatus at northern latitudes, where Pleistocene glaciation has produced similar historical demographic profiles across populations, we found markedly different demographics depending on sampling location, with inland unarmoured populations showing steeper population declines and lower heterozygosity compared to low armoured populations in coastal lagoons. One exception involved the only high elevation population in the region, where the demography and alleles of unarmoured fish were similar to low armoured populations near the coast, exposing one of several cases of artificial translocation. Our results suggest that the current "management-by-phenotype" approach, based on lateral plates, is incidentally protecting the most imperilled populations; however, redirecting efforts toward evolutionary units, regardless of phenotype, may more effectively preserve adaptive potential.
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Affiliation(s)
- Rachel Turba
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
| | | | - Sorel Fitz-Gibbon
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
| | - Marco Morselli
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, USA
| | | | - Camm C Swift
- Emeritus, Section of Fishes, Natural History Museum of Los Angeles County, Los Angeles, California, USA
| | - Gorgonio Ruiz-Campos
- Ichthyological Collection, Facultad de Ciencias, Universidad Autónoma de Baja California, Ensenada, Baja California, Mexico
| | - Adam R Backlin
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station-Santa Ana Office, Santa Ana, California, USA
| | - Chris Dellith
- U.S. Fish and Wildlife Service, Ventura, California, USA
| | - David K Jacobs
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
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3
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Integrating Earth–life systems: a geogenomic approach. Trends Ecol Evol 2022; 37:371-384. [DOI: 10.1016/j.tree.2021.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/04/2021] [Accepted: 12/08/2021] [Indexed: 12/26/2022]
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Dolby GA. Towards a unified framework to study causality in Earth-life systems. Mol Ecol 2021; 30:5628-5642. [PMID: 34427004 PMCID: PMC9292314 DOI: 10.1111/mec.16142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 07/17/2021] [Accepted: 08/20/2021] [Indexed: 01/04/2023]
Abstract
There is considerable interest in better understanding how earth processes shape the generation and distribution of life on Earth. This question, at its heart, is one of causation. In this article I propose that at a regional level, earth processes can be thought of as behaving somewhat deterministically and may have an organized effect on the diversification and distribution of species. However, the study of how landscape features shape biology is challenged by pseudocongruent or collinear variables. I demonstrate that causal structures can be used to depict the cause–effect relationships between earth processes and biological patterns using recent examples from the literature about speciation and species richness in montane settings. This application shows that causal diagrams can be used to better decipher the details of causal relationships by motivating new hypotheses. Additionally, the abstraction of this knowledge into structural equation metamodels can be used to formulate theory about relationships within Earth–life systems more broadly. Causal structures are a natural point of collaboration between biologists and Earth scientists, and their use can mitigate against the risk of misassigning causality within studies. My goal is that by applying causal theory through application of causal structures, we can build a systems‐level understanding of what landscape features or earth processes most shape the distribution and diversification of species, what types of organisms are most affected, and why.
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Affiliation(s)
- Greer A Dolby
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA.,Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA
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Dolby GA. The hidden landscape: Evidence that sea-level change shaped the present population genomic patterns of marginal marine species. Mol Ecol 2021; 30:1357-1360. [PMID: 33545743 DOI: 10.1111/mec.15826] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 01/28/2021] [Indexed: 11/29/2022]
Abstract
Oftentimes, to understand the genetic relatedness and diversity of today's populations requires considering the ancient landscape on which those populations evolved. Nowhere is this clearer than along Earth's coastline, which has been in its present-day configuration for only about 6.5% of the past 800,000 years (Dolby et al., 2020; Miller et al., 2005). During ice ages when glaciers expanded in the Northern Hemisphere, they stored enough of the planet's water to drop global sea level by ~120 m below present levels ("lowstand", Figure 1a), and there have been at least eight of these 100,000-year cycles preceding today. When glaciers melted, ocean water reflooded shorelines, shifting and re-forming marginal marine habitats globally and shaping the relatedness of populations (Dolby et al., 2016). In a From the Cover article in this issue of Molecular Ecology, Stiller et al. (2020) integrate population genomic analysis of leafy seadragons in southern Australia with estimates of available seabed area to reveal that the expansion of habitat that accompanied this reflooding led to strong demographic expansions. With statistical models, they also show that western populations were eliminated and then recolonized because the continental shelf there is narrow, leaving little available habitat when sea level was low (Figure 1b). Their results document the dynamic and interrelated nature of a hidden, changing landscape and the evolution of species inhabiting it.
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Affiliation(s)
- Greer A Dolby
- Center for Mechanisms of Evolution, Biodesign Institute, School of Life Sciences, Arizona State University, Tempe, AZ, USA
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Stiller J, da Fonseca RR, Alfaro ME, Faircloth BC, Wilson NG, Rouse GW. Using ultraconserved elements to track the influence of sea-level change on leafy seadragon populations. Mol Ecol 2021; 30:1364-1380. [PMID: 33217068 DOI: 10.1111/mec.15744] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 09/08/2020] [Accepted: 11/06/2020] [Indexed: 12/12/2022]
Abstract
During the Last Glacial Maximum (LGM), global sea levels were 120-130 m lower than today, resulting in the emergence of most continental shelves and extirpation of subtidal organisms from these areas. During the interglacial periods, rapid inundation of shelf regions created a dynamic environment for coastal organisms, such as the charismatic leafy seadragon (Phycodurus eques, Syngnathidae), a brooder with low dispersal ability inhabiting kelp beds in temperate Australia. Reconstructions of the palaeoshoreline revealed that the increase of shallow areas since the LGM was not uniform across the species' range and we investigated the effects of these asymmetries on genetic diversity and structuring. Using targeted capture of 857 variable ultraconserved elements (UCEs, 2,845 single nucleotide polymorphisms) in 68 individuals, we found that the regionally different shelf topographies were paralleled by contrasting population genetic patterns. In the west, populations may not have persisted through sea-level lows because shallow seabed was very limited. Shallow genetic structure, weak expansion signals and a westward cline in genetic diversity indicate a postglacial recolonization of the western part of the range from a more eastern location following sea-level rise. In the east, shallow seabed persisted during the LGM and increased considerably after the flooding of large bays, which resulted in strong demographic expansions, deeper genetic structure and higher genetic diversity. This study suggests that postglacial flooding with rising sea levels produced locally variable signatures in colonizing populations.
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Affiliation(s)
- Josefin Stiller
- Scripps Institution of Oceanography, University of California San Diego, San Diego, CA, USA
- Centre for Biodiversity Genomics, Section for Ecology and Evolution, University of Copenhagen, Kobenhavn, Denmark
| | | | | | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - Nerida G Wilson
- Scripps Institution of Oceanography, University of California San Diego, San Diego, CA, USA
- Collections & Research, Western Australian Museum, Welshpool and School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - Greg W Rouse
- Scripps Institution of Oceanography, University of California San Diego, San Diego, CA, USA
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Chen W, Li C, Chen F, Li Y, Yang J, Li J, Li X. Phylogeographic analyses of a migratory freshwater fish (Megalobrama terminalis) reveal a shallow genetic structure and pronounced effects of sea-level changes. Gene 2020; 737:144478. [PMID: 32061762 DOI: 10.1016/j.gene.2020.144478] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/30/2020] [Accepted: 02/11/2020] [Indexed: 10/25/2022]
Abstract
Different types of fish taxa generally seem to present diverse phylogeographic structures and show different responses to environmental changes. In southern China, however, a large number of phylogeographic studies have been employed for small and/or benthic fish species, while phylogeographic patterns of larger and migratory species are not well understood. In this study, we chose Megalobrama terminalis, an endemic cyprinid from Southern China with a median size and relatively high migratory potential as a candidate to explore the phylogeographic structure and to seek the relevant driving forces using a multilocus approach (two mitochondrial markers and three nuclear markers). Our results show that M. terminalis exhibits three mtDNA genetic groups, each presenting genetic structure to the local geography, but the differentiation level was much weaker than that of small and/or benthic fish species reported in earlier studies. Nuclear loci did not observe pronounced genetic group subdivision, but did examine noteworthy genetic differentiation between the Hainan Island population and the mainland populations. Divergence time estimation and demographic analyses suggest that sea-level changes associated with the Late Pleistocene glacial cycles have exerted pronounced effects on the divergence of the three groups and the expansion of M. terminalis populations. Above all, our study provides important knowledge that can be used to improve monitoring programs and develop a conservation strategy for this endemic organism.
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Affiliation(s)
- Weitao Chen
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
| | - Ce Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
| | - Fangcan Chen
- Guangzhou Qianjiang Water Ecological Technology Co. LTD, China
| | - Yuefei Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
| | - Jiping Yang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
| | - Jie Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
| | - Xinhui Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China.
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Thomaz AT, Knowles LL. Common barriers, but temporal dissonance: Genomic tests suggest ecological and paleo‐landscape sieves structure a coastal riverine fish community. Mol Ecol 2020; 29:783-796. [DOI: 10.1111/mec.15357] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 01/02/2020] [Accepted: 01/13/2020] [Indexed: 12/28/2022]
Affiliation(s)
- Andréa T. Thomaz
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor MI USA
- Biodiversity Research Centre and Department of Zoology University of British Columbia Vancouver BC Canada
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor MI USA
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Beichman AC, Koepfli KP, Li G, Murphy W, Dobrynin P, Kliver S, Tinker MT, Murray MJ, Johnson J, Lindblad-Toh K, Karlsson EK, Lohmueller KE, Wayne RK. Aquatic Adaptation and Depleted Diversity: A Deep Dive into the Genomes of the Sea Otter and Giant Otter. Mol Biol Evol 2019; 36:2631-2655. [PMID: 31212313 PMCID: PMC7967881 DOI: 10.1093/molbev/msz101] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Despite its recent invasion into the marine realm, the sea otter (Enhydra lutris) has evolved a suite of adaptations for life in cold coastal waters, including limb modifications and dense insulating fur. This uniquely dense coat led to the near-extinction of sea otters during the 18th-20th century fur trade and an extreme population bottleneck. We used the de novo genome of the southern sea otter (E. l. nereis) to reconstruct its evolutionary history, identify genes influencing aquatic adaptation, and detect signals of population bottlenecks. We compared the genome of the southern sea otter with the tropical freshwater-living giant otter (Pteronura brasiliensis) to assess common and divergent genomic trends between otter species, and with the closely related northern sea otter (E. l. kenyoni) to uncover population-level trends. We found signals of positive selection in genes related to aquatic adaptations, particularly limb development and polygenic selection on genes related to hair follicle development. We found extensive pseudogenization of olfactory receptor genes in both the sea otter and giant otter lineages, consistent with patterns of sensory gene loss in other aquatic mammals. At the population level, the southern sea otter and the northern sea otter showed extremely low genomic diversity, signals of recent inbreeding, and demographic histories marked by population declines. These declines may predate the fur trade and appear to have resulted in an increase in putatively deleterious variants that could impact the future recovery of the sea otter.
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Affiliation(s)
- Annabel C Beichman
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
| | - Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Gang Li
- College of Life Science, Shaanxi Normal University, Xi’an, Shaanxi, China
| | - William Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX
| | - Pasha Dobrynin
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Sergei Kliver
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Martin T Tinker
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA
| | | | - Jeremy Johnson
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Kerstin Lindblad-Toh
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, MA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Elinor K Karlsson
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, MA
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
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Sawyer YE, MacDonald SO, Lessa EP, Cook JA. Living on the edge: Exploring the role of coastal refugia in the Alexander Archipelago of Alaska. Ecol Evol 2019; 9:1777-1797. [PMID: 30847072 PMCID: PMC6392352 DOI: 10.1002/ece3.4861] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 11/27/2018] [Accepted: 12/04/2018] [Indexed: 12/14/2022] Open
Abstract
Although islands are of long-standing interest to biologists, only a handful of studies have investigated the role of climatic history in shaping evolutionary diversification in high-latitude archipelagos. In this study of the Alexander Archipelago (AA) of Southeast Alaska, we address the impact of glacial cycles on geographic genetic structure for three mammals co-distributed along the North Pacific Coast. We examined variation in mitochondrial and nuclear loci for long-tailed voles (Microtus longicaudus), northwestern deermice (Peromyscus keeni), and dusky shrews (Sorex monticola), and then tested hypotheses derived from Species Distribution Models, reconstructions of paleoshorelines, and island area and isolation. In all three species, we identified paleoendemic clades that likely originated in coastal refugia, a finding consistent with other paleoendemic lineages identified in the region such as ermine. Although there is spatial concordance at the regional level for endemism, finer scale spatial and temporal patterns are less clearly defined. Demographic expansion across the region for these distinctive clades is also evident and highlights the dynamic history of Late Quaternary contraction and expansion that characterizes high-latitude species.
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Affiliation(s)
- Yadéeh E. Sawyer
- Department of Biology and Museum of Southwestern BiologyUniversity of New MexicoAlbuquerqueNew Mexico
| | - Stephen O. MacDonald
- Department of Biology and Museum of Southwestern BiologyUniversity of New MexicoAlbuquerqueNew Mexico
| | - Enrique P. Lessa
- Departamento de Ecología y Evolución, Facultad de CienciasUniversidad de la RepúblicaMontevideoUruguay
| | - Joseph A. Cook
- Department of Biology and Museum of Southwestern BiologyUniversity of New MexicoAlbuquerqueNew Mexico
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