1
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Musher LJ. The biogeographic and genomic signatures of dynamic river networks for terrestrial species in Amazonia. Biol Rev Camb Philos Soc 2025. [PMID: 40420553 DOI: 10.1111/brv.70042] [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: 06/24/2024] [Revised: 05/14/2025] [Accepted: 05/19/2025] [Indexed: 05/28/2025]
Abstract
Amazonia contains Earth's largest freshwater basin, largest contiguous stretch of tropical forest, and most species-rich terrestrial biota on Earth. Rivers are key geographic features that drive diversification of the Amazonian biota, but they are also dynamic, which challenges their role as long-term barriers to dispersal and gene flow. The impacts of such river dynamics on organismal evolution have only recently been explored in detail. Here I examine biodiversity patterns and processes in Amazonia to elucidate how taxa diversify in the context of river network dynamics. I borrow the River Capture Hypothesis from ichthyology, and draw on evidence from speciation genomics, hybrid zones, and community assembly to demonstrate the effects of river network evolution on biodiversification. The idea is simple: populations of organisms whose dispersal is restricted by rivers become semi-isolated by rivers. Drift and selection against introgression drive divergence, but as rivers move, previously isolated populations come into secondary contact, facilitating lineage fusions or the migration of hybrid zones to other rivers. The basin's unique macroecological patterns and rich biota thus may have resulted from repeated divergences, lineage fusions, and range expansions around a network of non-stationary extrinsic barriers with variable results depending on the degree of intrinsic reproductive isolation that accumulates during this process. The evolutionary consequences of dynamic landscapes extend beyond Amazonia as "fission-fusion-fission" cycles modulate the diversification and spatial patterning of life on Earth in general.
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Affiliation(s)
- Lukas J Musher
- The Academy of Natural Sciences of Drexel University, 1900 Benjamin Franklin Blvd, Philadelphia, Pennsylvania, 19103, USA
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2
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Zong S, Liu H, Xu L, Yang D, Zhang J. The Intertidal North-South Split: Oceanographic Features and Life History Shape the Phylogeography of Chiton Acanthochitona rubrolineata. Evol Appl 2025; 18:e70095. [PMID: 40171542 PMCID: PMC11955844 DOI: 10.1111/eva.70095] [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: 08/02/2024] [Revised: 03/09/2025] [Accepted: 03/17/2025] [Indexed: 04/03/2025] Open
Abstract
The genetic structure and demographic history of marine organisms are shaped by a variety of factors including biological and ecological characteristics, ocean currents, and the palaeogeological effects of sea-level fluctuations. Here we present a comprehensive method combining population genomics, laboratory experiments, and ocean modelling in 13 populations of the chiton Acanthochitona rubrolineata along the coast of China. Based on demographic and population genomic analyses, significant divergence was observed between the Northern and Southern population groups, which are separated by the Yangtze River Estuary. The numerical circulation model simulation showed that gene flow and population connectivity were strongly influenced by ocean currents and the larval dispersal ability of chiton A. rubrolineata. These data thus clearly revealed the presence of two separately evolving lineages in chiton-A. rubrolineata northern and A. rubrolineata southern. Our study highlights that a robust understanding of organisms in the intertidal zone requires a comprehensive consideration of factors that influence gene flow and genetic structure, including the life-history traits, coastal currents, geographic isolation, and habitat suitability. The life history of marine organisms, together with local oceanographic features, could ultimately drive the population divergence and lead to speciation. These findings provide a guideline for future analyses of non-model and potentially threatened species and will aid in the conservation of biodiversity.
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Affiliation(s)
- Shaobing Zong
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and ConservationInstitute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Huijie Liu
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and ConservationInstitute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Lingjing Xu
- CAS Key Laboratory of Ocean Circulation and WavesInstitute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Dezhou Yang
- CAS Key Laboratory of Ocean Circulation and WavesInstitute of Oceanology, Chinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Junlong Zhang
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and ConservationInstitute of Oceanology, Chinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
- Marine Biological MuseumChinese Academy of SciencesQingdaoChina
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3
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Li YX, Ip JCH, Chen C, Xu T, Zhang Q, Sun Y, Ma PZ, Qiu JW. Phylogenomics of Bivalvia Using Ultraconserved Elements Reveal New Topologies for Pteriomorphia and Imparidentia. Syst Biol 2025; 74:16-33. [PMID: 39283716 DOI: 10.1093/sysbio/syae052] [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: 02/16/2024] [Revised: 08/05/2024] [Accepted: 09/03/2024] [Indexed: 02/11/2025] Open
Abstract
Despite significant advances in phylogenetics over the past decades, the deep relationships within Bivalvia (phylum Mollusca) remain inconclusive. Previous efforts based on morphology or several genes have failed to resolve many key nodes in the phylogeny of Bivalvia. Advances have been made recently using transcriptome data, but the phylogenetic relationships within Bivalvia historically lacked consensus, especially within Pteriomorphia and Imparidentia. Here, we inferred the relationships of key lineages within Bivalvia using matrices generated from specifically designed ultraconserved elements (UCEs) with 16 available genomic resources and 85 newly sequenced specimens from 55 families. Our new probes (Bivalve UCE 2k v.1) for target sequencing captured an average of 849 UCEs with 1085 bp in mean length from in vitro experiments. Our results introduced novel schemes from 6 major clades (Protobranchina, Pteriomorphia, Palaeoheterodonta, Archiheterodonta, Anomalodesmata, and Imparidentia), though some inner nodes were poorly resolved, such as paraphyletic Heterodonta in some topologies potentially due to insufficient taxon sampling. The resolution increased when analyzing specific matrices for Pteriomorphia and Imparidentia. We recovered 3 Pteriomorphia topologies different from previously published trees, with the strongest support for ((Ostreida + (Arcida + Mytilida)) + (Pectinida + (Limida + Pectinida))). Limida were nested within Pectinida, warranting further studies. For Imparidentia, our results strongly supported the new hypothesis of (Galeommatida + (Adapedonta + Cardiida)), while the possible non-monophyly of Lucinida was inferred but poorly supported. Overall, our results provide important insights into the phylogeny of Bivalvia and show that target enrichment sequencing of UCEs can be broadly applied to study both deep and shallow phylogenetic relationships.
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Affiliation(s)
- Yi-Xuan Li
- Department of Biology, Hong Kong Baptist University, 224 Wateroo Road, Kowloon Tong, Kowloon, Hong Kong SAR, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou, Guangdong 511458, China
| | - Jack Chi-Ho Ip
- Science Unit, Lingnan University, 8 Castle Peak Road, Tuen Mun, Hong Kong SAR, China
| | - Chong Chen
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Ting Xu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou, Guangdong 511458, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Qian Zhang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, MNR, 6 Xianxialing Road, Laoshan District, Qingdao 266100, China
| | - Yanan Sun
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, 8 Nanhai Road, Shinan District, Qingdao 266071, China
| | - Pei-Zhen Ma
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao 266071, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, 224 Wateroo Road, Kowloon Tong, Kowloon, Hong Kong SAR, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou, Guangdong 511458, China
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Ochoa‐Zavala M, Mar‐Silva AF, Pérez‐Rodríguez R, Palacios‐Barreto P, Adams DH, Blanco‐Parra MDP, Díaz‐Jaimes P. Mitochondrial DNA patterns describe the evolutionary history of the bonnethead shark Sphyrna tiburo (Linneus 1758) complex in the western Atlantic Ocean. JOURNAL OF FISH BIOLOGY 2025; 106:403-419. [PMID: 39404156 PMCID: PMC11842186 DOI: 10.1111/jfb.15961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 09/11/2024] [Accepted: 09/20/2024] [Indexed: 02/22/2025]
Abstract
The apparent lack of physical barriers in the marine realm has created the conception that many groups have a constant gene flow. However, changes in ocean circulation patterns, glacial cycles, temperature, and salinity gradients are responsible for vicariant events in many fish species, including sharks. The bonnethead shark, Sphyrna tiburo, is an endangered small coastal shark species. Although considerable efforts have recently been undertaken, little remains known about the possible biogeographic scenario that can explain its actual distribution within the western Atlantic (WA). Here, we used 599 mitochondrial sequences to assess the phylogeographic structure and implement Bayesian phylogenetic analyses to obtain divergence times and reconstruct the ancestral geographic range. This allowed us to infer processes responsible for the diversification of S. tiburo into major divergent lineages. Our results indicated that S. tiburo in the WA represents three independent lineages, with Brazilian samples differentiated into a distinct genetic cluster. The posterior probability of ancestral range analysis indicated that the species likely originated in the northern region (Carolina Province and the southern Gulf of Mexico), where it colonized southward through the uplifting of the Central American Isthmus (CAI). The Northern and Caribbean genetic clusters appear to have arisen from the intensification of the Loop Current, which currently flows northward passing the Yucatan Peninsula, Gulf of Mexico, and east Florida. Following initial colonization, the Northeastern Brazil group differentiated from the Caribbean region due to the sediment and freshwater discharge of the Amazon-Orinoco Plume. Thus, the evolutionary history of the S. tiburo complex can be explained by a combination of dispersal and vicariance events that occurred over the last ~5 million years (MY). We established and confirmed the species and population limits, demonstrating that the Amazon-Orinoco Plume constitutes a significant dispersal barrier for coastal sharks. Finally, we discuss some recommendations for the conservation of the bonnethead shark.
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Affiliation(s)
- Maried Ochoa‐Zavala
- Escuela Nacional de Estudios Superiores, unidad Morelia, Laboratorio de Genética Evolutiva de Organismos TropicalesUniversidad Nacional Autónoma de MéxicoMoreliaMexico
| | - Adan Fernando Mar‐Silva
- Unidad Académica de Ecología y Biodiversidad AcuáticaInstituto de Ciencias del Mar y Limnología. Universidad Nacional Autónoma de MéxicoCiudad de MexicoMexico
| | - Rodolfo Pérez‐Rodríguez
- Universidad Michoacana de San Nicolás de HidalgoLaboratorio de Biología AcuáticaMoreliaMexico
| | - Paola Palacios‐Barreto
- Fundación colombiana para la Investigación y Conservación de Tiburones y Rayas, SQUALUSCaliColombia
| | - Douglas H. Adams
- Fish & Wildlife Research Institute, Florida Fish & Wildlife Conservation CommissionIndian River Field LabMelbourneFloridaUSA
| | | | - Píndaro Díaz‐Jaimes
- Unidad Académica de Ecología y Biodiversidad AcuáticaInstituto de Ciencias del Mar y Limnología. Universidad Nacional Autónoma de MéxicoCiudad de MexicoMexico
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Naughton I, Tsutsui ND, Ward PS, Holway DA. An assemblage-level comparison of genetic diversity and population genetic structure between island and mainland ant populations. Evolution 2024; 78:1685-1698. [PMID: 38981009 DOI: 10.1093/evolut/qpae103] [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: 10/25/2023] [Revised: 06/05/2024] [Accepted: 07/07/2024] [Indexed: 07/11/2024]
Abstract
Island biotas provide unparalleled opportunities to examine evolutionary processes. Founder effects and bottlenecks, e.g., typically decrease genetic diversity in island populations, while selection for reduced dispersal can increase population structure. Given that support for these generalities mostly comes from single-species analyses, assemblage-level comparisons are needed to clarify how (i) colonization affects the gene pools of interacting insular organisms, and (ii) patterns of genetic differentiation vary within assemblages of organisms. Here, we use genome-wide sequence data from ultraconserved elements (UCEs) to compare the genetic diversity and population structure of mainland and island populations of nine ant species in coastal southern California. As expected, island populations (from Santa Cruz Island) had lower expected heterozygosity and Watterson's theta compared to mainland populations (from the Lompoc Valley). Island populations, however, exhibited smaller genetic distances among samples, indicating less population subdivision. Within the focal assemblage, pairwise Fst values revealed pronounced interspecific variation in mainland-island differentiation, which increases with gyne body size. Our results reveal population differences across an assemblage of interacting species and illuminate general patterns of insularization in ants. Compared to single-species studies, our analysis of nine conspecific population pairs from the same island-mainland system offers a powerful approach to studying fundamental evolutionary processes.
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Affiliation(s)
- Ida Naughton
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
| | - Neil D Tsutsui
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
| | - Philip S Ward
- Department of Entomology and Nematology, University of California, Davis, Davis, CA, United States
| | - David A Holway
- Department of Ecology, Behavior, and Evolution, University of California, San Diego, La Jolla, CA, United States
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6
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Stiller J, Wilson NG, Rouse GW. Range-wide population genomics of common seadragons shows secondary contact over a former barrier and insights on illegal capture. BMC Biol 2023; 21:129. [PMID: 37248474 DOI: 10.1186/s12915-023-01628-9] [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: 01/26/2023] [Accepted: 05/16/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND Common seadragons (Phyllopteryx taeniolatus, Syngnathidae) are an emblem of the diverse endemic fauna of Australia's southern rocky reefs, the newly recognized "Great Southern Reef." A lack of assessments spanning this global biodiversity hotspot in its entirety is currently hampering an understanding of the factors that have contributed to its diversity. The common seadragon has a wide range across Australia's entire temperate south and includes a geogenetic break over a former land bridge, which has called its status as a single species into question. As a popular aquarium display that sells for high prices, common seadragons are also vulnerable to illegal capture. RESULTS Here, we provide range-wide nuclear sequences (986 variable Ultraconserved Elements) for 198 individuals and mitochondrial genomes for 140 individuals to assess species status, identify genetic units and their diversity, and trace the source of two poached individuals. Using published data of the other two seadragon species, we found that lineages of common seadragons have diverged relatively recently (< 0.63 Ma). Within common seadragons, we found pronounced genetic structure, falling into three major groups in the western, central, and eastern parts of the range. While populations across the Bassian Isthmus were divergent, there is also evidence for secondary contact since the passage opened. We found a strong cline of genetic diversity from the range center tapering symmetrically towards the range peripheries. Based on their genetic similarities, the poached individuals were inferred to have originated from around Albany in southwestern Australia. CONCLUSIONS We conclude that common seadragons constitute a single species with strong geographic structure but coherence through gene flow. The low genetic diversity on the east and west coasts is concerning given that these areas are projected to face fast climate change. Our results suggest that in addition to their life history, geological events and demographic expansions have all played a role in shaping populations in the temperate south. These insights are an important step towards understanding the historical determinants of the diversity of species endemic to the Great Southern Reef.
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Affiliation(s)
- Josefin Stiller
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, 92093 , USA.
- Centre for Biodiversity Genomics, University of Copenhagen, 2100, Copenhagen, Denmark.
| | - Nerida G Wilson
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, 92093 , USA
- Research & Collections, Western Australian Museum, Perth, Western Australia, 6106, Australia
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, 6009, Australia
| | - Greg W Rouse
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, 92093 , USA.
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Qu M, Zhang Y, Gao Z, Zhang Z, Liu Y, Wan S, Wang X, Yu H, Zhang H, Liu Y, Schneider R, Meyer A, Lin Q. The genetic basis of the leafy seadragon's unique camouflage morphology and avenues for its efficient conservation derived from habitat modeling. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-022-2317-6. [PMID: 37204606 DOI: 10.1007/s11427-022-2317-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/03/2023] [Indexed: 05/20/2023]
Abstract
The leafy seadragon certainly is among evolution's most "beautiful and wonderful" species aptly named for its extraordinary camouflage mimicking its coastal seaweed habitat. However, limited information is known about the genetic basis of its phenotypes and conspicuous camouflage. Here, we revealed genomic signatures of rapid evolution and positive selection in core genes related to its camouflage, which allowed us to predict population dynamics for this species. Comparative genomic analysis revealed that seadragons have the smallest olfactory repertoires among all ray-finned fishes, suggesting adaptations to the highly specialized habitat. Other positively selected and rapidly evolving genes that serve in bone development and coloration are highly expressed in the leaf-like appendages, supporting a recent adaptive shift in camouflage appendage formation. Knock-out of bmp6 results in dysplastic intermuscular bones with a significantly reduced number in zebrafish, implying its important function in bone formation. Global climate change-induced loss of seagrass beds now severely threatens the continued existence of this enigmatic species. The leafy seadragon has a historically small population size likely due to its specific habitat requirements that further exacerbate its vulnerability to climate change. Therefore, taking climate change-induced range shifts into account while developing future protection strategies.
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Affiliation(s)
- Meng Qu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingyi Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zexia Gao
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhixin Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
- Global Ocean and Climate Research Center, South China Sea Institute of Oceanology, Guangzhou, 510301, China
| | - Yali Liu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shiming Wan
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xin Wang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
| | - Haiyan Yu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
| | - Huixian Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
| | - Yuhong Liu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
| | - Ralf Schneider
- Marine Evolutionary Ecology, Zoological Institute, Kiel University, 24118, Kiel, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, 78464, Konstanz, Germany.
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China.
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Sinclair EA, Hovey RK, Krauss SL, Anthony JM, Waycott M, Kendrick GA. Historic and contemporary biogeographic perspectives on range-wide spatial genetic structure in a widespread seagrass. Ecol Evol 2023; 13:e9900. [PMID: 36950371 PMCID: PMC10025079 DOI: 10.1002/ece3.9900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/26/2023] [Indexed: 03/22/2023] Open
Abstract
Historical and contemporary processes drive spatial patterns of genetic diversity. These include climate-driven range shifts and gene flow mediated by biogeographical influences on dispersal. Assessments that integrate these drivers are uncommon, but critical for testing biogeographic hypotheses. Here, we characterize intraspecific genetic diversity and spatial structure across the entire distribution of a temperate seagrass to test marine biogeographic concepts for southern Australia. Predictive modeling was used to contrast the current Posidonia australis distribution to its historical distribution during the Last Glacial Maximum (LGM). Spatial genetic structure was estimated for 44 sampled meadows from across the geographical range of the species using nine microsatellite loci. Historical and contemporary distributions were similar, with the exception of the Bass Strait. Genetic clustering was consistent with the three currently recognized biogeographic provinces and largely consistent with the finer-scale IMCRA bioregions. Discrepancies were found within the Flindersian province and southwest IMCRA bioregion, while two regions of admixture coincided with transitional IMCRA bioregions. Clonal diversity was highly variable but positively associated with latitude. Genetic differentiation among meadows was significantly associated with oceanographic distance. Our approach suggests how shared seascape drivers have influenced the capacity of P. australis to effectively track sea level changes associated with natural climate cycles over millennia, and in particular, the recolonization of meadows across the Continental Shelf following the LGM. Genetic structure associated with IMCRA bioregions reflects the presence of stable biogeographic barriers, such as oceanic upwellings. This study highlights the importance of biogeography to infer the role of historical drivers in shaping extant diversity and structure.
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Affiliation(s)
- Elizabeth A. Sinclair
- School of Biological SciencesUniversity of Western AustraliaCrawleyWestern AustraliaAustralia
- Oceans Institute, University of Western AustraliaCrawleyWestern AustraliaAustralia
- Kings Park Science, Department of Biodiversity Conservation and AttractionsKings ParkWestern AustraliaAustralia
| | - Renae K. Hovey
- School of Biological SciencesUniversity of Western AustraliaCrawleyWestern AustraliaAustralia
- Oceans Institute, University of Western AustraliaCrawleyWestern AustraliaAustralia
| | - Siegfried L. Krauss
- School of Biological SciencesUniversity of Western AustraliaCrawleyWestern AustraliaAustralia
- Kings Park Science, Department of Biodiversity Conservation and AttractionsKings ParkWestern AustraliaAustralia
| | - Janet M. Anthony
- School of Biological SciencesUniversity of Western AustraliaCrawleyWestern AustraliaAustralia
- Kings Park Science, Department of Biodiversity Conservation and AttractionsKings ParkWestern AustraliaAustralia
| | - Michelle Waycott
- School of Biological SciencesUniversity of Adelaide and State Herbarium of South AustraliaAdelaideSouth AustraliaAustralia
| | - Gary A. Kendrick
- School of Biological SciencesUniversity of Western AustraliaCrawleyWestern AustraliaAustralia
- Oceans Institute, University of Western AustraliaCrawleyWestern AustraliaAustralia
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9
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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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10
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Petersen HC, Hansen BW, Knott KE, Banta GT. Species and genetic diversity relationships in benthic macroinvertebrate communities along a salinity gradient. BMC Ecol Evol 2022; 22:125. [PMID: 36324063 PMCID: PMC9632067 DOI: 10.1186/s12862-022-02087-6] [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: 09/24/2021] [Accepted: 10/26/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Species- and genetic diversity can change in parallel, resulting in a species-genetic diversity correlation (SGDC) and raising the question if the same drivers influence both biological levels of diversity. The SGDC can be either positive or negative, depending on whether the species diversity and the genetic diversity of the measured species respond in the same or opposite way to drivers. Using a traditional species diversity approach together with ultra-conserved elements and high throughput sequencing, we evaluated the SGDCs in benthic macrofauna communities in the Baltic Sea, a geologically young brackish water sea characterised by its steep salinity gradient and low species richness. Assessing SGDCs from six focal marine invertebrate species from different taxonomic groups and with differing life histories and ecological functions on both a spatial and temporal scale gives a more comprehensive insight into the community dynamics of this young ecosystem and the extrinsic factors that might drive the SGDCs. RESULTS No significant correlations between species diversity and genetic diversity were found for any of the focal species. However, both negative and positive trends of SGDCs for the individual focal species were observed. When examining the environmental drivers, no common trends between the species were found, even when restricting the analysis to specific taxonomic classes. Additionally, there were no common environmental factors driving the diversity relationships for species sharing the same SGDC trend (positive or negative). Local population dynamics, together with the invasion history of the individual species and their unique adaptation to the distinctive environment of the Baltic Sea, are expected to be of major influence on the outcome of the SGDCs. CONCLUSIONS The present results highlight the importance of assessing SGDCs using multiple species, not just a single indicator species. This emphasises a need to pay attention to the ecology and life history of the focal species. This study also provides insight into the large differences in both patterns and drivers of genetic diversity, which is important when including genetic biodiversity in conservation plans. We conclude that the effects of environmental and biological factors and processes that affects diversity patterns at both the community and genetic levels are likely species dependent, even in an environment such as the Baltic Sea with strong environmental gradients.
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Affiliation(s)
- H. Cecilie Petersen
- grid.11702.350000 0001 0672 1325Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark ,grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science, University of Jyväskylä, 40014 Jyväskylä, Finland
| | - Benni W. Hansen
- grid.11702.350000 0001 0672 1325Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark
| | - K. Emily Knott
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science, University of Jyväskylä, 40014 Jyväskylä, Finland
| | - Gary T. Banta
- grid.10825.3e0000 0001 0728 0170Department of Biology, University of Southern Denmark, 5238 Odense M, Denmark
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Melo BF, de Pinna MCC, Rapp Py-Daniel LH, Zuanon J, Conde-Saldaña CC, Roxo FF, Oliveira C. Paleogene emergence and evolutionary history of the Amazonian fossorial fish genus Tarumania (Teleostei: Tarumaniidae). Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.924860] [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
Tarumania walkerae is a rare fossorial freshwater fish species from the lower Rio Negro, Central Amazonia, composing the monotypic and recently described family Tarumaniidae. The family has been proposed as the sister group of Erythrinidae by both morphological and molecular studies despite distinct arrangements of the superfamily Erythrinoidea within Characiformes. Recent phylogenomic studies and time-calibrated analyses of characoid fishes have not included specimens of Tarumania in their analyses. We obtained genomic data for T. walkerae and constructed a phylogeny based on 1795 nuclear loci with 488,434 characters of ultraconserved elements (UCEs) for 108 terminals including specimens of all 22 characiform families. The phylogeny confirms the placement of Tarumaniidae as sister to Erythrinidae but differs from the morphological hypothesis in the placement of the two latter families as sister to the clade with Hemiodontidae, Cynodontidae, Serrasalmidae, Parodontidae, Anostomidae, Prochilodontidae, Chilodontidae, and Curimatidae. The phylogeny calibrated with five characoid fossils indicates that Erythrinoidea diverged from their relatives during the Late Cretaceous circa 90 Ma (108–72 Ma), and that Tarumania diverged from the most recent common ancestor of Erythrinidae during the Paleogene circa 48 Ma (66–32 Ma). The occurrence of the erythrinoid-like †Tiupampichthys in the Late Cretaceous–Paleogene formations of the El Molino Basin of Bolivia supports our hypothesis for the emergence of the modern Erythrinidae and Tarumaniidae during the Paleogene.
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Small CM, Healey HM, Currey MC, Beck EA, Catchen J, Lin ASP, Cresko WA, Bassham S. Leafy and weedy seadragon genomes connect genic and repetitive DNA features to the extravagant biology of syngnathid fishes. Proc Natl Acad Sci U S A 2022; 119:e2119602119. [PMID: 35733255 PMCID: PMC9245644 DOI: 10.1073/pnas.2119602119] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 04/13/2022] [Indexed: 12/18/2022] Open
Abstract
Seadragons are a remarkable lineage of teleost fishes in the family Syngnathidae, renowned for having evolved male pregnancy. Comprising three known species, seadragons are widely recognized and admired for their fantastical body forms and coloration, and their specific habitat requirements have made them flagship representatives for marine conservation and natural history interests. Until recently, a gap has been the lack of significant genomic resources for seadragons. We have produced gene-annotated, chromosome-scale genome models for the leafy and weedy seadragon to advance investigations of evolutionary innovation and elaboration of morphological traits in seadragons as well as their pipefish and seahorse relatives. We identified several interesting features specific to seadragon genomes, including divergent noncoding regions near a developmental gene important for integumentary outgrowth, a high genome-wide density of repetitive DNA, and recent expansions of transposable elements and a vesicular trafficking gene family. Surprisingly, comparative analyses leveraging the seadragon genomes and additional syngnathid and outgroup genomes revealed striking, syngnathid-specific losses in the family of fibroblast growth factors (FGFs), which likely involve reorganization of highly conserved gene regulatory networks in ways that have not previously been documented in natural populations. The resources presented here serve as important tools for future evolutionary studies of developmental processes in syngnathids and hold value for conservation of the extravagant seadragons and their relatives.
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Affiliation(s)
- Clayton M. Small
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403
- Presidential Initiative in Data Science, University of Oregon, Eugene, OR 97403
| | - Hope M. Healey
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403
| | - Mark C. Currey
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403
| | - Emily A. Beck
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403
- Presidential Initiative in Data Science, University of Oregon, Eugene, OR 97403
| | - Julian Catchen
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Angela S. P. Lin
- Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, OR 97403
| | - William A. Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403
- Presidential Initiative in Data Science, University of Oregon, Eugene, OR 97403
| | - Susan Bassham
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403
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13
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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: 2.7] [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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Rieseberg L, Warschefsky E, O'Boyle B, Taberlet P, Ortiz-Barrientos D, Kane NC, Sibbett B. Editorial 2022. Mol Ecol 2021; 31:1-30. [PMID: 34957606 DOI: 10.1111/mec.16328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 12/10/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Loren Rieseberg
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Univ. Grenoble Alpes, Grenoble Cedex 9, France
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences, The University of Queenland, St. Lucia, Queensland, Australia
| | - Nolan C Kane
- University of Colorado at Boulder, Boulder, Colorado, USA
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Sousa R, Vasconcelos J, Vera-Escalona I, Pinto AR, Hawkins SJ, Freitas M, Delgado J, González JA, Riera R. Pleistocene expansion, anthropogenic pressure and ocean currents: Disentangling the past and ongoing evolutionary history of Patella aspera Röding, 1798 in the archipelago of Madeira. MARINE ENVIRONMENTAL RESEARCH 2021; 172:105485. [PMID: 34715642 DOI: 10.1016/j.marenvres.2021.105485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 09/12/2021] [Accepted: 09/18/2021] [Indexed: 06/13/2023]
Abstract
AIMS Rising sea-level following the Last Glacial Maximum lead to fragmentation of coastal limpet populations between islands of the Archipelago of Madeira. This fragmentation is reinforced by recent heavy exploitation reducing effective population size on Madeira Island. We use the limpet P. aspera to understand how the role of processes at different time scales (i.e. changes in the sea level and overexploitation) can influence the genetic composition of an extant species, relating these processes to reproductive phenology and seasonal shifts in ocean currents. LOCATION Madeira Island, Porto Santo and Desertas (Archipelago of Madeira, NE Atlantic Ocean). TAXON The limpet Patella aspera. METHODS Twelve microsatellite genetic markers were used. A power analysis was used to evaluate the power of the microsatellite markers to detect a signal of population differentiation. Long-term past migrations were assessed using a Bayesian Markov Montecarlo approach in the software MIGRATE-n to estimate mutation-scaled migration rates (M = m/μ; m, probability of a lineage immigrating per generation; μ, mutation rate). Two scenarios were evaluated using an Approximate Bayesian Computation (ABC) in the software DIYABC 2.1 (i) Scenario 1: considered a population scenario from a reduced Ne at time t3 to a higher Ne at time t2; and (ii) Scenario 2 considering a reduction of Ne from a time t3 to a time t2. RESULTS Colonization of the archipelago by Portuguese settlers six centuries ago probably led to an important decrease in the genetic diversity of the species (Ne). Contemporary gene flow strongly support a pattern of high asymmetric connectivity explained by the reproductive phenology of the species and spatio-temporal seasonal changes in the ocean currents. Spatio-temporal reconstructions using Bayesian methods, including coalescent and Approximate Bayesian Computation (ABC) approaches, suggest changes in the migration patterns from highly symmetric to highly asymmetric connectivity with subtle population differentiation as consequence of post-glacial maximum sea level rise during the Holocene. MAIN CONCLUSIONS Our results suggest that anthropogenic activity could have had serious effects on the genetic diversity of heavily exploited littoral species since the end of the Pleistocene, probably accelerating in recent years.
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Affiliation(s)
- Ricardo Sousa
- Observatório Oceânico da Madeira, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (OOM/ARDITI) - Edifício Madeira Tecnopolo, Funchal, Madeira, Portugal; Direção Regional do Mar (DRM)/ Direção de Serviços de Monitorização, Estudos e Investigação do Mar (DSEIMar), 9004-562, Funchal, Madeira, Portugal; MARE - Marine and Environmental Sciences Centre, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI), Edifício Madeira Tecnopolo Piso 0, Caminho da Penteada, 9020-105, Funchal, Madeira, Portugal
| | - Joana Vasconcelos
- MARE - Marine and Environmental Sciences Centre, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI), Edifício Madeira Tecnopolo Piso 0, Caminho da Penteada, 9020-105, Funchal, Madeira, Portugal; Faculdade de Ciências de Vida, Universidade da Madeira, Campus Universitário da Madeira, Caminho da Penteada, 9020-020, Funchal, Madeira, Portugal; Departamento de Ecología, Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Casilla 297, Concepción, Chile
| | - Iván Vera-Escalona
- CIBAS, Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Casilla 297, Concepción, Chile; IU-ECOAQUA, Group of Biodiversity and Conservation (BIOCON), Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Ana Rita Pinto
- Direção Regional do Mar (DRM)/ Direção de Serviços de Monitorização, Estudos e Investigação do Mar (DSEIMar), 9004-562, Funchal, Madeira, Portugal
| | - S J Hawkins
- Marine Biological Association of the UK, Plymouth, PL1 2PB, UK; School of Ocean and Earth Science, University of Southampton, National Oceanography Centre, Southampton, SO14 3ZH, UK
| | - Mafalda Freitas
- Observatório Oceânico da Madeira, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (OOM/ARDITI) - Edifício Madeira Tecnopolo, Funchal, Madeira, Portugal; Direção Regional do Mar (DRM)/ Direção de Serviços de Monitorização, Estudos e Investigação do Mar (DSEIMar), 9004-562, Funchal, Madeira, Portugal; MARE - Marine and Environmental Sciences Centre, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI), Edifício Madeira Tecnopolo Piso 0, Caminho da Penteada, 9020-105, Funchal, Madeira, Portugal
| | - João Delgado
- Direção Regional do Mar (DRM)/ Direção de Serviços de Monitorização, Estudos e Investigação do Mar (DSEIMar), 9004-562, Funchal, Madeira, Portugal; Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Porto, Portugal
| | - José A González
- Ecología Marina Aplicada y Pesquerías (i-UNAT), Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Rodrigo Riera
- Departamento de Ecología, Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Casilla 297, Concepción, Chile; IU-ECOAQUA, Group of Biodiversity and Conservation (BIOCON), Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain.
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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: 0.5] [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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