The evolution of microendemism in a reef fish (<i>Hypoplectrus maya</i>)

Moran, Ben; Hench, Kosmas; Waples, Robin S.; Höppner, Marc P.; Baldwin, Carole C.; McMillan, W. Owen; Puebla, Oscar

doi:10.1111/mec.15110

Cited by 13 publications

(25 citation statements)

References 92 publications

(131 reference statements)

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“…3 B ). These results are consistent with previous analyses using a different approach that does not rely on phasing ( 45 ). Alternatively, gene flow among sympatric species may have obliterated the signature of older demographic events, which could be complex and involve several cycles of “fission–fusion–fission” ( 46 ).…”

Section: Resultssupporting

confidence: 93%

“…This parallels what has been observed in Heliconius butterflies ( 66 ) and Ficedula flycatchers ( 38 ) and indicates that divergence hitchhiking does not play the prominent role in the buildup of genomic differences that is implied by the genic view of speciation in these groups. In the hamlets, this finding is consistent with the rapid decay of linkage disequilibrium along chromosomes ( 25 , 45 ).…”

Section: Discussionsupporting

confidence: 82%

“… 25 , and 10 are from ref. 45 . All new tissue samples were available from previous studies ( 13 , 19 ), except for sample #28393, which was collected in 2017 in Bocas del Toro (Panama) under the Smithsonian Tropical Research Institute Institutional Animal Care and Use Committee protocol 2017-0101-2020-2, the Panamanian Ministry of Environment permits SC/A-53-16 and SEX/A-35-17, and the Access and Benefit-Sharing Clearing-House identifier ABSCH-IRCC-PA-241203-1.…”

Section: Methodsmentioning

confidence: 99%

“…This analysis was based on the phased SNPs only dataset, which was prepared following the MSMC2 authors recommendations ( 91 ) as detailed in ref. 45 . This included masking the data on the basis of mappability to the reference genome and the occurrence of indels.…”

Section: Methodsmentioning

confidence: 99%

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Rapid radiation in a highly diverse marine environment

Hench

Helmkampf

McMillan

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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Rapid diversification is often observed when founding species invade isolated or newly formed habitats that provide ecological opportunity for adaptive radiation. However, most of the Earth’s diversity arose in diverse environments where ecological opportunities appear to be more constrained. Here, we present a striking example of a rapid radiation in a highly diverse marine habitat. The hamlets, a group of reef fishes from the wider Caribbean, have radiated into a stunning diversity of color patterns but show low divergence across other ecological axes. Although the hamlet lineage is ∼26 My old, the radiation appears to have occurred within the last 10,000 generations in a burst of diversification that ranks among the fastest in fishes. As such, the hamlets provide a compelling backdrop to uncover the genomic elements associated with phenotypic diversification and an excellent opportunity to build a broader comparative framework for understanding the drivers of adaptive radiation. The analysis of 170 genomes suggests that color pattern diversity is generated by different combinations of alleles at a few large-effect loci. Such a modular genomic architecture of diversification has been documented before in Heliconius butterflies, capuchino finches, and munia finches, three other tropical radiations that took place in highly diverse and complex environments. The hamlet radiation also occurred in a context of high effective population size, which is typical of marine populations. This allows for the accumulation of new variants through mutation and the retention of ancestral genetic variation, both of which appear to be important in this radiation.

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Section: Resultssupporting

confidence: 93%

Section: Discussionsupporting

confidence: 82%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Rapid radiation in a highly diverse marine environment

Hench

Helmkampf

McMillan

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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“…The greatest concentration of range-restricted species occur in Belize and Curaçao followed by the Bahamas and Honduras. Belize and the Honduran Bay Islands are known hotspots of microendemism for Caribbean marine species that may have risen from isolating oceanographic conditions in that region (Moran et al, 2019).…”

Section: Hotspots Of Potential Invasion Impact In the Invaded Caribbeanmentioning

confidence: 99%

Trait‐based vulnerability reveals hotspots of potential impact for a global marine invader

Linardich

Green

2021

Global Change Biology

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Predation from the invasive Indo‐Pacific lionfish is likely to amplify declines in marine fishes observed in multiple ocean basins. As the invasion intensifies and expands, there is an urgent need to identify species that are most at risk for extirpation—and possible extinction—from this added threat. To address this gap and inform conservation plans, we develop and apply a quantitative framework for classifying the relative vulnerability of fishes based on morphological and behavioural traits known to influence susceptibility to lionfish predation (e.g. body shape, water column position and aggregation behaviour), habitat overlap with lionfish, and degree of geographic range restriction. Applying the framework to fishes across the invaded Caribbean Sea and ahead of the invasion front in the southwestern Atlantic revealed the identity of at least 77 fishes with relatively small ranges that are likely to be most affected by lionfish predation. Trait‐based vulnerability scores significantly predict the probability of fishes appearing within the diets of lionfish across the invaded region. Spatial richness analyses reveal hotspots of vulnerable species in the Bahamas, Belize and Curaçao. Crucially, our framework identifies 29 vulnerable fishes endemic to Brazil, which has not yet been colonized by lionfish. Of these, we suggest reefs around offshore island groups occupied by a dozen highly vulnerable and range‐restricted species as priorities for intervention should lionfish spread to the region. Observations of the rate of lionfish spread across the invaded range suggest that an average of 5 years (with a median of nearly 2 years) elapses from first sighting to maximum observed densities. This lag may allow managers to mobilize plans to suppress lionfish ahead of an invasion front in priority locations. Our framework also provides a method for assessing the relative vulnerability of cryptobenthic and/or deep‐reef fishes, for which population‐monitoring data are limited.

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Whole‐genome resequencing reveals the pleistocene temporal dynamics of Branchiostoma belcheri and Branchiostoma floridae populations

Lü

Huang

et al. 2020

Ecology and Evolution

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Global climatic fluctuations governed the ancestral demographic histories of species and contributed to place the current population status into a more extensive ecological and evolutionary context. Genetic variations will leave unambiguous signatures in the patterns of intraspecific genetic variation in extant species since the genome of each individual is an imperfect mosaic of the ancestral genomes. Here, we report the genome sequences of 20 Branchiostoma individuals by whole‐genome resequencing strategy. We detected over 140 million genomic variations for each Branchiostoma individual. In particular, we applied the pairwise sequentially Markovian coalescent (PSMC) method to estimate the trajectories of changes in the effective population size ( N e ) of Branchiostoma population during the Pleistocene. We evaluated the threshold of sequencing depth for proper inference of demographic histories using PSMC was ≥25×. The PSMC results highlight the role of historical global climatic fluctuations in the long‐term population dynamics of Branchiostoma . The inferred ancestral N e of the Branchiostoma belcheri populations from Zhanjiang and Xiamen (China) seawaters was different in amplitude before the first (mutation rate = 3 × 10 −9 ) or third glaciation (mutation rate = 9 × 10 −9 ) of the Pleistocene, indicating that the two populations most probably started to evolve in isolation in their respective seas after the first or third glaciation of the Pleistocene. A pronounced population bottleneck coinciding with the last glacial maximum was observed in all Branchiostoma individuals, followed by a population expansion occurred during the late Pleistocene. Species that have experienced long‐term declines may be especially vulnerable to recent anthropogenic activities. Recently, the industrial pollution and the exploitation of sea sand have destroyed the harmonious living environment of amphioxus species. In the future, we need to protect the habitat of Branchiostoma and make full use of these detected genetic variations to facilitate the functional study of Branchiostoma for adaptation to local environments.

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The evolution of microendemism in a reef fish (Hypoplectrus maya)

Cited by 13 publications

References 92 publications

Rapid radiation in a highly diverse marine environment

Rapid radiation in a highly diverse marine environment

Trait‐based vulnerability reveals hotspots of potential impact for a global marine invader

Whole‐genome resequencing reveals the pleistocene temporal dynamics of Branchiostoma belcheri and Branchiostoma floridae populations

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