Speciation with gene flow via cycles of isolation and migration: insights from multiple mangrove taxa

AbstractAllopatric speciation requiring an unbroken period of geographical isolation has been the standard model of neo-Darwinism. While doubts have been repeatedly raised, strict allopatry without any gene flow remains a plausible mechanism in most cases. To rigorously reject strict allopatry, genomic sequences superimposed on the geological records of a well-delineated geographical barrier will be necessary. The Strait of Malacca, narrowly connecting the Pacific and Indian Ocean coasts, serves at different times either as a geographical barrier or a conduit of gene flow for coastal/marine species. We surveyed 1,700 plants from 29 populations of five common mangrove species by large scale DNA sequencing and added several whole-genome assemblies. Speciation between the two oceans is driven by cycles of isolation and gene flow due to the fluctuations in sea level leading to the opening/closing of the Strait to ocean currents. Because the time required for speciation in mangroves is longer than the isolation phases, speciation in these mangroves has proceeded through many cycles of mixing-isolation-mixing, or MIM cycles. The MIM mechanism, by relaxing the condition of no gene flow, can promote speciation in many more geographical features than strict allopatry can. Finally, the MIM mechanism of speciation is also efficient, potentially yielding mn (m>1) species after n cycles.Significance statementMechanisms of species formation have always been a conundrum. Speciation between populations that are fully geographically isolated, or allopatric speciation, has been the standard solution in the last 50 years. Complete geographical isolation with no possibility of gene flow, however, is often untenable and is inefficient in generating the enormous biodiversity. By studying mangroves on the Indo-Malayan coasts, a global hotspot of coastal biodiversity, we were able to combine genomic data with geographical records on the Indo-Pacific barrier that separates Pacific and Indian Ocean coasts. We discovered a novel mechanism of speciation, that we call mixing-isolation-mixing (MIM) cycles. By permitting intermittent gene flow during speciation, MIM can potentially generate species at an exponential rate, thus combining speciation and biodiversity in a unified framework.

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Expansion of the mangrove species Rhizophora mucronata in the Western Indian Ocean launched contrasting genetic patterns

Scientific Reports ◽

10.1038/s41598-021-84304-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Ludwig Triest ◽

Tom Van der Stocken ◽

Dennis De Ryck ◽

Marc Kochzius ◽

Sophie Lorent ◽

...

Keyword(s):

Gene Flow ◽

Indian Ocean ◽

Large Scale ◽

Geographic Distance ◽

Western Indian Ocean ◽

Coastal Current ◽

Rhizophora Mucronata ◽

East African ◽

Mangrove Species ◽

Mozambique Channel

AbstractEstimates of population structure and gene flow allow exploring the historical and contemporary processes that determine a species’ biogeographic pattern. In mangroves, large-scale genetic studies to estimate gene flow have been conducted predominantly in the Indo-Pacific and Atlantic region. Here we examine the genetic diversity and connectivity of Rhizophora mucronata across a > 3,000 km coastal stretch in the Western Indian Ocean (WIO) including WIO islands. Based on 359 trees from 13 populations and using 17 polymorphic microsatellite loci we detected genetic breaks between populations of the (1) East African coastline, (2) Mozambique Channel Area (3) granitic Seychelles, and (4) Aldabra and northern Madagascar. Genetic structure, diversity levels, and patterns of inferred connectivity, aligned with the directionality of major ocean currents, driven by bifurcation of the South Equatorial Current, northward into the East African Coastal Current and southward into the Mozambique Channel Area. A secondary genetic break between nearby populations in the Delagoa Bight coincided with high inbreeding levels and fixed loci. Results illustrate how oceanographic processes can connect and separate mangrove populations regardless of geographic distance.

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Ancient globetrotters—connectivity and putative native ranges of two cosmopolitan biofouling amphipods

PeerJ ◽

10.7717/peerj.9613 ◽

2020 ◽

Vol 8 ◽

pp. e9613

Author(s):

Jan Beermann ◽

Allison K. Hall-Mullen ◽

Charlotte Havermans ◽

Joop WP Coolen ◽

Richard PMA Crooijmans ◽

...

Keyword(s):

Dna Sequences ◽

Marine Species ◽

Genetic Connectivity ◽

Native Range ◽

Species Dispersal ◽

Migration Rates ◽

Coastal Marine ◽

The World ◽

Geographic Populations ◽

And Migration

The geographic distributions of some coastal marine species have appeared as cosmopolitan ever since they were first scientifically documented. In particular, for many benthic species that are associated with anthropogenic substrata, there is much speculation as to whether or not their broad distributions can be explained by natural mechanisms of dispersal. Here, we focused on two congeneric coastal crustaceans with cosmopolitan distributions—the tube-dwelling amphipods Jassa marmorata and Jassa slatteryi. Both species are common elements of marine biofouling on nearly all kinds of artificial hard substrata in temperate to warm seas. We hypothesized that the two species’ modern occurrences across the oceans are the result of human shipping activities that started centuries ago. Mitochondrial DNA sequences of the CO1 fragment of specimens from distinct marine regions around the world were analysed, evaluating genetic structure and migration models and making inferences on putative native ranges of the two Jassa species. Populations of both species exhibited considerable genetic diversity with differing levels of geographic structure. For both species, at least two dominant haplotypes were shared among several geographic populations. Rapid demographic expansion and high migration rates between geographically distant regions support a scenario of ongoing dispersal all over the world. Our findings indicate that the likely former native range of J. marmorata is the Northwest Atlantic, whereas the likely former native range of J. slatteryi is the Northern Pacific region. As corroborated by the genetic connectivity between populations, shipping still appears to be the more successful vector of the two species’ dispersal when compared to natural mechanisms. Historical invasion events that likely started centuries ago, along with current ongoing dispersal, confirm these species’ identities as true “neocosmopolitans”.

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Genomic Biorepository of Coastal Marine Species in Estero Padre Ramos and Estero Real, Nicaragua

Encuentro ◽

10.5377/encuentro.v0i93.908 ◽

2012 ◽

pp. 6-18

Author(s):

Jorge A. Huete-Pérez ◽

Eduardo Mendoza-Ramírez ◽

Lucía Páiz-Medina

Keyword(s):

Marine Species ◽

Coi Gene ◽

Marine Biodiversity ◽

Land Bridge ◽

Coastal Marine ◽

The Pacific ◽

Biodiversity Database ◽

Northern Pacific ◽

Sandy Sediments ◽

The University

Nicaragua, located in southern Mesoamerica between the Caribbean Sea and the Pacific Ocean, has acted as a land bridge for flora and fauna migrating between North and South America during the last 3 million years. Because of Nicaragua’s location and history, it is rich in terrestrial and aquatic biodiversity. To study this biodiversity and preserve it for the future, Nicaragua’s Molecular Biology Center at the University of Central America (CBM-UCA) created the Genomic Biorepository Project. The Project collects and catalogs coastal marine biodiversity in the Estero Real and Padre Ramos estuaries, located in Nicaragua’s northern Pacific region.The biorepository holds more than three thousand tissue and genomic specimens, comprising 1,049 samples (714 specimens from Estero Padre Ramos and 335 from Estero Real) belonging to 100 species and 54 families, genomic extracts in triplicates for every sample collected and environmental sandy sediments representing 60 different sites. Changes in the biological composition of the region were documentedas compared to previous sampling. Of the 1,049 samples obtained from the two estuaries, 30 new residents were recorded in Estero Real, and 19 in Estero Padre Ramos. The Cytochrome Oxidase I (COI) gene was sequenced for a number of species, including 19 fish species, and published to public databases (BOLD SYSTEMS). The records contained in the genomic biorepository here described lay the foundation for the most complete marine biodiversity database in Nicaragua and is made available to national and international specialists, facilitating knowledge of Nicaraguan biodiversity.

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The role of the Andean uplift as an asymmetrical barrier to gene flow in the Neotropical leaf-cutting ant Atta cephalotes

10.1101/2021.03.24.436865 ◽

2021 ◽

Author(s):

Vanessa Muñoz-Valencia ◽

Glever Alexander Velez-Matinez ◽

James Montoya-Lerma ◽

Fernando Diaz

Keyword(s):

Gene Flow ◽

South America ◽

Management Strategies ◽

Atta Cephalotes ◽

Geographical Barrier ◽

History Of ◽

Andean Uplift ◽

Leaf Cutting ◽

And Migration

Neotropical diversification by the Andean uplift is typically addressed on a large evolutionary scale (e.g. speciation), even though many species are still distributed in both sides of the mountains. The three parallel mountain ranges in the northern Andes (Colombia) impose a major geographical barrier to species' migration from South to Central America. How important these barriers are for conspecific diversification of cross-Andean species such as the leaf-cutting ants remains largely unknown. To answer this question, we studied the mtCOI gene of Atta cephalotes, the most widely distributed leaf-cutting ant species. Our hierarchical analyzes evidenced substantial genetic structure among regions and populations, suggesting a more complex biogeographical history of Andean populations than previously thought. These mountains seem to isolate Central American and Western Colombian populations from the rest of A. cephalotes in South America. Population and migration modelling are consistent with the origin of this species in South America and a major role of the Eastern cordillera as a geographical barrier to historical gene flow, restricting dispersion from north to south. These findings provide insights into the role of the Andean uplift as barrier to gene flow and, eventually, implications for monitoring and designing management strategies for leaf-cutting ants.

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Tsunami-driven rafting: Transoceanic species dispersal and implications for marine biogeography

Science ◽

10.1126/science.aao1498 ◽

2017 ◽

Vol 357 (6358) ◽

pp. 1402-1406 ◽

Cited By ~ 110

Author(s):

James T. Carlton ◽

John W. Chapman ◽

Jonathan B. Geller ◽

Jessica A. Miller ◽

Deborah A. Carlton ◽

...

Keyword(s):

Climate Change ◽

Marine Species ◽

Species Dispersal ◽

Marine Biogeography ◽

Species Invasions ◽

Coastal Marine ◽

Coastal Species ◽

Plastic Materials ◽

The Pacific ◽

The Pacific Ocean

The 2011 East Japan earthquake generated a massive tsunami that launched an extraordinary transoceanic biological rafting event with no known historical precedent. We document 289 living Japanese coastal marine species from 16 phyla transported over 6 years on objects that traveled thousands of kilometers across the Pacific Ocean to the shores of North America and Hawai‘i. Most of this dispersal occurred on nonbiodegradable objects, resulting in the longest documented transoceanic survival and dispersal of coastal species by rafting. Expanding shoreline infrastructure has increased global sources of plastic materials available for biotic colonization and also interacts with climate change–induced storms of increasing severity to eject debris into the oceans. In turn, increased ocean rafting may intensify species invasions.

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Direct evidence of aeolian deposition of marine diatoms to an ice sheet

Antarctic Science ◽

10.1017/s0954102012000235 ◽

2012 ◽

Vol 24 (5) ◽

pp. 527-535 ◽

Cited By ~ 4

Author(s):

A.L. Budgeon ◽

D. Roberts ◽

M. Gasparon ◽

N. Adams

Keyword(s):

Large Scale ◽

Source Region ◽

Ice Sheet ◽

Ice Cores ◽

Open Water ◽

Marine Species ◽

Marine Diatoms ◽

Coastal Marine ◽

Westerly Winds ◽

Antarctic Snow

AbstractAntarctic snow samples collected from the Wilkins Runway, c. 50 km inland from the Windmill Islands, East Antarctica, contain aeolian-derived diatoms. The diatom assemblage preserved is exclusively of marine origin. As diatoms are excellent indicators of source conditions, we are able to confirm that an unusual weather event, with anomalous north-westerly winds blowing at around 10 m s-1, resulted in the deposition of coastal marine species at the Wilkins Runway. The composition of the floral assemblage collected indicate that the parent water mass was from a coastal marine region undergoing typical Antarctic summer conditions with periods of both consolidated sea ice and open water. On inspection of available satellite imagery, these conditions were found upwind of the deposition site. This study provides a methodology for diatoms found within ice cores to be identified and the source region to be determined. It also provides evidence for a large-scale aeolian deposition of marine diatoms to an ice sheet, which may have implications for the interpretation of controversial marine diatoms found in sediments that have been used as evidence for the retreat of the East Antarctic Ice Sheet.

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Systematics, Biogeography, and Morphological Character Evolution of the Hemiepiphytic Subfamily Monsteroideae (Araceae)

Annals of the Missouri Botanical Garden ◽

10.3417/2018269 ◽

2019 ◽

Vol 104 (1) ◽

pp. 33-48 ◽

Cited By ~ 4

Author(s):

Alejandro Zuluaga ◽

Martin Llano ◽

Ken Cameron

Keyword(s):

Dna Sequences ◽

Pacific Islands ◽

R Package ◽

Morphological Characters ◽

Ancestral State ◽

Seed Shape ◽

Long Distance ◽

The Pacific ◽

And Migration ◽

The Tropics

The subfamily Monsteroideae (Araceae) is the third richest clade in the family, with ca. 369 described species and ca. 700 estimated. It comprises mostly hemiepiphytic or epiphytic plants restricted to the tropics, with three intercontinental disjunctions. Using a dataset representing all 12 genera in Monsteroideae (126 taxa), and five plastid and two nuclear markers, we studied the systematics and historical biogeography of the group. We found high support for the monophyly of the three major clades (Spathiphylleae sister to Heteropsis Kunth and Rhaphidophora Hassk. clades), and for six of the genera within Monsteroideae. However, we found low rates of variation in the DNA sequences used and a lack of molecular markers suitable for species-level phylogenies in the group. We also performed ancestral state reconstruction of some morphological characters traditionally used for genera delimitation. Only seed shape and size, number of seeds, number of locules, and presence of endosperm showed utility in the classification of genera in Monsteroideae. We estimated ancestral ranges using a dispersal-extinction-cladogenesis model as implemented in the R package BioGeoBEARS and found evidence for a Gondwanan origin of the clade. One tropical disjunction (Monstera Adans. sister to Amydrium Schott–Epipremnum Schott) was found to be the product of a previous Boreotropical distribution. Two other disjunctions are more recent and likely due to long-distance dispersal: Spathiphyllum Schott (with Holochlamys Engl. nested within) represents a dispersal from South America to the Pacific Islands in Southeast Asia, and Rhaphidophora represents a dispersal from Asia to Africa. Future studies based on stronger phylogenetic reconstructions and complete morphological datasets are needed to explore the details of speciation and migration within and among areas in Asia.

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Statistical and machine learning models for optimizing energy in parallel applications

The International Journal of High Performance Computing Applications ◽

10.1177/1094342019842915 ◽

2019 ◽

Vol 33 (6) ◽

pp. 1079-1097 ◽

Cited By ~ 2

Author(s):

Mark Endrei ◽

Chao Jin ◽

Minh Ngoc Dinh ◽

David Abramson ◽

Heidi Poxon ◽

...

Keyword(s):

Machine Learning ◽

Energy Efficiency ◽

High Performance ◽

Large Scale ◽

Energy Use ◽

Parallel Applications ◽

Learning Models ◽

Trade Off ◽

Time Required ◽

Machine Learning Models

Rising power costs and constraints are driving a growing focus on the energy efficiency of high performance computing systems. The unique characteristics of a particular system and workload and their effect on performance and energy efficiency are typically difficult for application users to assess and to control. Settings for optimum performance and energy efficiency can also diverge, so we need to identify trade-off options that guide a suitable balance between energy use and performance. We present statistical and machine learning models that only require a small number of runs to make accurate Pareto-optimal trade-off predictions using parameters that users can control. We study model training and validation using several parallel kernels and more complex workloads, including Algebraic Multigrid (AMG), Large-scale Atomic Molecular Massively Parallel Simulator, and Livermore Unstructured Lagrangian Explicit Shock Hydrodynamics. We demonstrate that we can train the models using as few as 12 runs, with prediction error of less than 10%. Our AMG results identify trade-off options that provide up to 45% improvement in energy efficiency for around 10% performance loss. We reduce the sample measurement time required for AMG by 90%, from 13 h to 74 min.

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Social Media in and Around a Temporary Large-Scale Refugee Shelter in the Netherlands

Social Media + Society ◽

10.1177/20563051211024961 ◽

2021 ◽

Vol 7 (2) ◽

pp. 205630512110249

Author(s):

Peer Smets ◽

Younes Younes ◽

Marinka Dohmen ◽

Kees Boersma ◽

Lenie Brouwer

Keyword(s):

Social Media ◽

The Netherlands ◽

Crisis Communication ◽

Asylum Seekers ◽

Large Scale ◽

State Policies ◽

Refugee Crisis ◽

Top Down ◽

And Migration

During the 2015 refugee crisis in Europe, temporary refugee shelters arose in the Netherlands to shelter the large influx of asylum seekers. The largest shelter was located in the eastern part of the country. This shelter, where tents housed nearly 3,000 asylum seekers, was managed with a firm top-down approach. However, many residents of the shelter—mainly Syrians and Eritreans—developed horizontal relations with the local receiving society, using social media to establish contact and exchange services and goods. This case study shows how various types of crisis communication played a role and how the different worlds came together. Connectivity is discussed in relation to inclusion, based on resilient (non-)humanitarian approaches that link society with social media. Moreover, we argue that the refugee crisis can be better understood by looking through the lens of connectivity, practices, and migration infrastructure instead of focusing only on state policies.

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