Physiological diversity enhanced by recurrent divergence and secondary gene flow within a grass species

C 4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this species encompasses C 4 and non-C 4 populations. Using phylogenomics and population genomics, we infer the history of dispersal and secondary gene flow before, during and after photosynthetic divergence in A. semialata . We further analyse the genome composition of individuals with varied ploidy levels to establish the origins of polyploids in this species. Detailed organelle phylogenies indicate limited seed dispersal within the mountainous region of origin and the emergence of a C 4 lineage after dispersal to warmer areas of lower elevation. Nuclear genome analyses highlight repeated secondary gene flow. In particular, the nuclear genome associated with the C 4 phenotype was swept into a distantly related maternal lineage probably via unidirectional pollen flow. Multiple intraspecific allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types. Overall, our results show that limited dispersal and isolation allowed lineage divergence, with photosynthetic innovation happening after migration to new environments, and pollen-mediated gene flow led to the rapid spread of the derived C 4 physiology away from its region of origin.

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Recombination-aware phylogenomics unravels the complex divergence of hybridizing species.

10.1101/485904 ◽

2018 ◽

Cited By ~ 1

Author(s):

Gang Li ◽

Henrique V. Figueiro ◽

Eduardo Eizirik ◽

William J. Murphy

Keyword(s):

Gene Flow ◽

Evolutionary History ◽

Phylogenetic Signal ◽

Selective Sweeps ◽

A Genome ◽

Chromosome Recombination ◽

History Of ◽

Lineage Divergence ◽

Recurrent Patterns ◽

Ancient Gene

Current phylogenomic approaches implicitly assume that the predominant phylogenetic signal within a genome reflects the true evolutionary history of organisms, without assessing the confounding effects of gene flow that result in a mosaic of phylogenetic signals that interact with recombinational variation. Here we tested the validity of this assumption with a recombination-aware analysis of whole genome sequences from 27 species of the cat family. We found that the prevailing phylogenetic signal within the autosomes is not always representative of speciation history, due to ancient hybridization throughout felid evolution. Instead, phylogenetic signal was concentrated within large, conserved X-chromosome recombination deserts that exhibited recurrent patterns of strong genetic differentiation and selective sweeps across mammalian orders. By contrast, regions of high recombination were enriched for signatures of ancient gene flow, and these sequences inflated crown-lineage divergence times by ~40%. We conclude that standard phylogenomic approaches to infer the Tree of Life may be highly misleading without considering the genomic partitioning of phylogenetic signal relative to recombination rate, and its interplay with historical hybridization.

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Spintharus flavidus in the Caribbean – a 30 million year biogeographical history and radiation of a ‘widespread species’

10.7287/peerj.preprints.1332v1 ◽

2015 ◽

Author(s):

Austin Dziki ◽

Greta Binford ◽

Jonathan A Coddington ◽

Ingi Agnarsson

Keyword(s):

Single Species ◽

Caribbean Region ◽

Dispersal Ability ◽

Widespread Species ◽

Caribbean Islands ◽

Island Endemics ◽

Molecular Phylogenetic ◽

Limited Dispersal ◽

History Of ◽

The Caribbean

The Caribbean island biota is characterized by high levels of endemism, the result of an interplay between colonization opportunities on islands and effective oceanic barriers among them. A relatively small percentage of the biota is represented by ‘widespread species’, presumably taxa for which oceanic barriers are ineffective. Few studies have explored in detail the genetic structure of widespread Caribbean taxa. The cobweb spider Spintharus flavidus Hentz, 1850 (Theridiidae) is one of two described Spintharus species and is unique in being widely distributed from northern N. America to Brazil and throughout the Caribbean. As a taxonomic hypothesis, Spintharus “flavidus” predicts maintenance of gene flow among Caribbean islands, a prediction that seems contradicted by known S. flavidus biology, which suggests limited dispersal ability. As part of an extensive survey of Caribbean arachnids (project CarBio), we conducted the first molecular phylogenetic analysis of S. flavidus with the primary goal of testing the ‘widespread species’ hypothesis. Our results, while limited to three molecular loci, reject the hypothesis of a single widespread species. Instead this lineage seems to represent a radiation with at least 16 species in the Caribbean region. Nearly all are short range endemics with several distinct mainland groups and others being single island endemics. While limited taxon sampling, with a single specimen from S. America, constrains what we can infer about the biogeographical history of the lineage, clear patterns still emerge. Consistent with limited overwater dispersal, we find evidence for a single colonization of the Caribbean about 30 million years ago, coinciding with the timing of the GAARLandia landbridge hypothesis. In sum, S. “flavidus” is not a single species capable of frequent overwater dispersal, but rather a 30 my old radiation of single island endemics that provides preliminary support for a complex and contested geological hypothesis.

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Spintharus flavidus in the Caribbean – a 30 million year biogeographical history and radiation of a ‘widespread species’

10.7287/peerj.preprints.1332 ◽

2015 ◽

Author(s):

Austin Dziki ◽

Greta Binford ◽

Jonathan A Coddington ◽

Ingi Agnarsson

Keyword(s):

Single Species ◽

Caribbean Region ◽

Dispersal Ability ◽

Widespread Species ◽

Caribbean Islands ◽

Island Endemics ◽

Molecular Phylogenetic ◽

Limited Dispersal ◽

History Of ◽

The Caribbean

The Caribbean island biota is characterized by high levels of endemism, the result of an interplay between colonization opportunities on islands and effective oceanic barriers among them. A relatively small percentage of the biota is represented by ‘widespread species’, presumably taxa for which oceanic barriers are ineffective. Few studies have explored in detail the genetic structure of widespread Caribbean taxa. The cobweb spider Spintharus flavidus Hentz, 1850 (Theridiidae) is one of two described Spintharus species and is unique in being widely distributed from northern N. America to Brazil and throughout the Caribbean. As a taxonomic hypothesis, Spintharus “flavidus” predicts maintenance of gene flow among Caribbean islands, a prediction that seems contradicted by known S. flavidus biology, which suggests limited dispersal ability. As part of an extensive survey of Caribbean arachnids (project CarBio), we conducted the first molecular phylogenetic analysis of S. flavidus with the primary goal of testing the ‘widespread species’ hypothesis. Our results, while limited to three molecular loci, reject the hypothesis of a single widespread species. Instead this lineage seems to represent a radiation with at least 16 species in the Caribbean region. Nearly all are short range endemics with several distinct mainland groups and others being single island endemics. While limited taxon sampling, with a single specimen from S. America, constrains what we can infer about the biogeographical history of the lineage, clear patterns still emerge. Consistent with limited overwater dispersal, we find evidence for a single colonization of the Caribbean about 30 million years ago, coinciding with the timing of the GAARLandia landbridge hypothesis. In sum, S. “flavidus” is not a single species capable of frequent overwater dispersal, but rather a 30 my old radiation of single island endemics that provides preliminary support for a complex and contested geological hypothesis.

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A snapshot of progenitor-derivative speciation in action in Iberodes (Boraginaceae)

10.1101/823641 ◽

2019 ◽

Author(s):

Ana Otero ◽

Pablo Vargas ◽

Virginia Valcárcel ◽

Mario Fernández-Mazuecos ◽

Pedro Jiménez-Mejías ◽

...

Keyword(s):

Gene Flow ◽

Distribution Patterns ◽

Common Mechanism ◽

List Type ◽

Niche Modelling ◽

Climatic Niche ◽

Ideal System ◽

Integrative Study ◽

History Of ◽

Parapatric Speciation

SUMMARYTraditional classification of speciation modes has focused on physical barriers to gene flow. While allopatry has been viewed as the most common mechanism of speciation, parapatry and sympatry, both entail speciation in the face of ongoing gene flow and thus both are far more difficult to detect and demonstrate. Iberodes (Boraginaceae, NW Europe) with a small number of recently derived species (five) and contrasting morphological traits, habitats and distribution patterns constitutes an ideal system in which to study drivers of lineage divergence and differentiation.To reconstruct the evolutionary history of the genus, we undertook an integrative study entailing: (i) phylogenomics based on restriction-site associated DNA sequencing (RAD-seq), (ii) morphometrics, and (iii) climatic niche modelling.Key results revealed a history of repeated progenitor-derivative speciation, manifesting in paraphyletic pattern within Iberodes. Climatic niche analyses, together with the morphometric data and species distributions, suggest that ecological and geographical differentiation have interacted to shape the diversity of allopatric and parapatric distributions observed in Iberodes.Our integrative study has enabled to overcome previous barriers to understanding parapatric speciation by demonstrating the recurrence of progenitor-derivative speciation in plants with gene flow and ecological differentiation, explaining observed parapatry and paraphyly.

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Population genetic structure and evolutionary history of Psammochloa villosa (Trin.) Bor (Poaceae) revealed by AFLP marker

10.22541/au.161362620.02434922/v1 ◽

2021 ◽

Author(s):

Xu Su ◽

Ting Lv

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Evolutionary History ◽

In Situ Conservation ◽

Grass Species ◽

Sustainable Utilization ◽

Mongolian Plateau ◽

Quaternary Period ◽

Genetic Diversity And Structure ◽

History Of

We sought to generate a preliminary demographic framework for Psammochloa villosa to support of future studies of this ecologically important desert grass species, its conservation, and sustainable utilization. Psammochloa villosa occurs in the Inner Mongolian Plateau where it is frequently the dominant species and is involved in sand stabilization and wind breaking. Here, we characterized the genetic diversity and structure of 210 individuals from 43 natural populations of P. villosa using amplified fragment length polymorphism (AFLP) markers. We obtained 1728 well-defined amplified bands from eight pairs of primers, of which 1654 bands (95.72%) were polymorphic.All these values indicate that there is abundant genetic diversity, but limited gene flow in P. villosa. However, an analysis of molecular variance (AMOVA) showed that genetic variation mainly exists within 43 populations of the species (64.16%), and we found that the most genetically similar populations were often not geographically adjacent. Thus, this suggests that the mechanisms of gene flow are surprisingly complex in the species and may occur over long distances. In addition, we predicted the distribution dynamics of P. villosa based on the spatial distribution modeling and found that its range has contracted continuously since the last inter-glacial period. We speculate that dry, cold climates have been critical in determining the geographic distribution of P. villosa during the Quaternary period. Our study provides new insights into the population genetics and evolutionary history of P. villosa in the Inner Mongolian Plateau, which can be used to design in-situ conservation actions and to prioritize sustainable utilization of germplasm resources.

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Geography is more important than life history in the recent diversification of the tiger salamander complex

10.1101/2020.07.10.197624 ◽

2020 ◽

Author(s):

Kathryn M. Everson ◽

Levi N. Gray ◽

Angela G. Jones ◽

Nicolette M. Lawrence ◽

Mary E. Foley ◽

...

Keyword(s):

Life History ◽

Gene Flow ◽

Life History Strategies ◽

Conservation Priorities ◽

Tiger Salamander ◽

Life History Variation ◽

Wide Range ◽

History Of ◽

Lineage Divergence ◽

Salamander Species

AbstractThe North American tiger salamander species complex, including its flagship species the axolotl, has long been a source of biological fascination. The complex exhibits a wide range of variation in developmental life history strategies, including populations and individuals that undergo metamorphosis and those able to forego metamorphosis and retain a larval, aquatic lifestyle (i.e., paedomorphosis). Such disparate life history strategies are assumed to cause populations to become reproductively isolated, but the degree to which they have actually shaped population- and species-level boundaries is poorly understood. Using a large multi-locus dataset from hundreds of samples across North America, we identified genetic clusters with clear signs of admixture across the geographic range of the tiger salamander complex. Population clusters often contain a mixture of paedomorphic and metamorphic taxa, and we conclude that geography has played a large role in driving lineage divergence relative to obligate paedomorphosis in this system. This conclusion is bolstered by model-based analyses demonstrating gene flow between metamorphic and paedomorphic populations. Even the axolotl, a paedomorphic species with an isolated native range, apparently has a history of gene flow with its neighboring populations. This fine-scale genetic perspective on life-history variation establishes a framework for understanding how plasticity, local adaptation, and gene flow contribute to lineage divergence. The axolotl is currently used as the vertebrate model system in regenerative biology, and our findings chart a course for more informed use of these and other tiger salamander species in experimental and field research, including conservation priorities.Significance StatementPopulation structure and speciation are shaped by a variety of biotic and abiotic factors. In the tiger salamander complex, one factor that may influence diversification is life history: some taxa are obligately paedomorphic–a condition where adults maintain an aquatic, larval phenotype–while others are facultatively paedomorphic or entirely metamorphic. Using a large multi-locus dataset, we found evidence of gene flow and/or panmixia between obligately and facultatively paedomorphic taxa, suggesting that an obligately paedomorphic life history is not a strong driver of speciation in the tiger salamander complex. We also recovered a history of gene flow between the critically endangered axolotl and its neighboring populations, providing important information for its conservation and captive management.

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Spintharus flavidusin the Caribbean—a 30 million year biogeographical history and radiation of a ‘widespread species’

PeerJ ◽

10.7717/peerj.1422 ◽

2015 ◽

Vol 3 ◽

pp. e1422 ◽

Cited By ~ 16

Author(s):

Austin Dziki ◽

Greta J. Binford ◽

Jonathan A. Coddington ◽

Ingi Agnarsson

Keyword(s):

Single Species ◽

Caribbean Region ◽

Dispersal Ability ◽

Widespread Species ◽

Caribbean Islands ◽

Island Endemics ◽

Molecular Phylogenetic ◽

Limited Dispersal ◽

History Of ◽

The Caribbean

The Caribbean island biota is characterized by high levels of endemism, the result of an interplay between colonization opportunities on islands and effective oceanic barriers among them. A relatively small percentage of the biota is represented by ‘widespread species,’ presumably taxa for which oceanic barriers are ineffective. Few studies have explored in detail the genetic structure of widespread Caribbean taxa. The cobweb spiderSpintharus flavidusHentz, 1850 (Theridiidae) is one of two describedSpintharusspecies and is unique in being widely distributed from northern N. America to Brazil and throughout the Caribbean. As a taxonomic hypothesis,Spintharus “flavidus”predicts maintenance of gene flow among Caribbean islands, a prediction that seems contradicted by knownS. flavidusbiology, which suggests limited dispersal ability. As part of an extensive survey of Caribbean arachnids (project CarBio), we conducted the first molecular phylogenetic analysis ofS. flaviduswith the primary goal of testing the ‘widespread species’ hypothesis. Our results, while limited to three molecular loci, reject the hypothesis of a single widespread species. Instead this lineage seems to represent a radiation with at least 16 species in the Caribbean region. Nearly all are short range endemics with several distinct mainland groups and others are single island endemics. While limited taxon sampling, with a single specimen from S. America, constrains what we can infer about the biogeographical history of the lineage, clear patterns still emerge. Consistent with limited overwater dispersal, we find evidence for a single colonization of the Caribbean about 30 million years ago, coinciding with the timing of the GAARLandia landbridge hypothesis. In sum,S. “flavidus”is not a single species capable of frequent overwater dispersal, but rather a 30 my old radiation of single island endemics that provides preliminary support for a complex and contested geological hypothesis.

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The Relevance of Old World Archaeology to the First Entry of Man into New Worlds: Colonization Seen from the Antipodes

Quaternary Research ◽

10.1016/0033-5894(77)90060-6 ◽

1977 ◽

Vol 8 (1) ◽

pp. 128-148 ◽

Cited By ~ 24

Author(s):

Sylvia J. Hallam

Keyword(s):

Demographic Data ◽

Ecological Zones ◽

The North ◽

Technological Potential ◽

The Pacific ◽

Peopling Of The Americas ◽

Rapid Spread ◽

History Of ◽

Economic Innovation ◽

Considerable Complexity

Following several discussions in recent numbers of Quaternary Research on the peopling of the Americas, this paper suggests that movements into the New World should be viewed in the wider context of subsistence, technology, and movement around the western littorals of the Pacific, resulting in the colonization not of one but of two new continents by men out of Asia. Specific points which have been raised by these recent papers are reviewed in the light of Australian, Wallacian, and East Asian data.(1) The earliness of watercraft is evidenced by chronology of the human diaspora through Wallacia and Greater Australia.(2) The simplistic nomenclature of chopper-flake traditions masks considerable complexity and technological potential, revealed in detailed Antipodean studies.(3) These traditions also have great potential for adapting to differing ecological zones, evidenced within Greater Australia; and for technological and economic innovation there, through Southeast Asia, and to Japan and the north Asian littoral.(4) The history of discovery and the nature of the evidence from Australia cannot validly be used to controvert early dates in the Americas.(5) Demographic data from Australia suggest that total commitment to a rapid-spread “bowwave” model for the peopling of new continents may be unwise.

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Linking morphological and molecular sources to disentangle the case of Xylodon australis

Scientific Reports ◽

10.1038/s41598-020-78399-8 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Javier Fernández-López ◽

M. Teresa Telleria ◽

Margarita Dueñas ◽

Mara Laguna-Castro ◽

Klaus Schliep ◽

...

Keyword(s):

New Zealand ◽

Phylogenetic Analyses ◽

Single Species ◽

R Package ◽

Molecular Data ◽

Historical Collections ◽

Close Relationship ◽

Kinship Relations ◽

History Of ◽

Different Sources

AbstractThe use of different sources of evidence has been recommended in order to conduct species delimitation analyses to solve taxonomic issues. In this study, we use a maximum likelihood framework to combine morphological and molecular traits to study the case of Xylodon australis (Hymenochaetales, Basidiomycota) using the locate.yeti function from the phytools R package. Xylodon australis has been considered a single species distributed across Australia, New Zealand and Patagonia. Multi-locus phylogenetic analyses were conducted to unmask the actual diversity under X. australis as well as the kinship relations respect their relatives. To assess the taxonomic position of each clade, locate.yeti function was used to locate in a molecular phylogeny the X. australis type material for which no molecular data was available using morphological continuous traits. Two different species were distinguished under the X. australis name, one from Australia–New Zealand and other from Patagonia. In addition, a close relationship with Xylodon lenis, a species from the South East of Asia, was confirmed for the Patagonian clade. We discuss the implications of our results for the biogeographical history of this genus and we evaluate the potential of this method to be used with historical collections for which molecular data is not available.

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