Species delimitation with gene flow: A methodological comparison and population genomics approach to elucidate cryptic species boundaries in Malaysian Torrent Frogs

Chrysomyxa rusts are fungal pathogens widely distributed in the Northern hemisphere, causing spruce needle and cone rust diseases, and they are responsible for significant economic losses in China. Taxonomic delimitation and precise species identification are difficult within this genus because some characters often overlap in several species. Adequate species delimitation, enhanced by the use of DNA-based methodologies, will help to establish well-supported species boundaries and enable the identification of cryptic species. Here, we explore the cryptic species diversity in the rust genus Chrysomyxa from China. Species delimitation analyses are conducted using a distance-based method (ABGD) and three tree-based methods (GMYC, bPTP, and mPTP) based on combined LSU and ITS sequences of over 60 specimens. Although there is some incongruence among species delimitation methods, two new species and three putative cryptic species are identified. The key to 20 Chrysomyxa species distributed in China is presented. These results suggest that a significant level of undiscovered cryptic diversity is likely to be found in Chrysomyxa from China. Future studies should consider multiple analytical methods when dealing with multi-locus datasets.

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A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals

10.1101/523936 ◽

2019 ◽

Author(s):

Andrea M. Quattrini ◽

Tiana Wu ◽

Keryea Soong ◽

Ming-Shiou Jeng ◽

Yehuda Benayahu ◽

...

Keyword(s):

Cryptic Species ◽

Species Delimitation ◽

Incomplete Lineage Sorting ◽

Dna Barcode ◽

Species Boundaries ◽

Future Research ◽

Species Trees ◽

Lineage Sorting ◽

Evolutionary Diversification

AbstractBackgroundOur ability to investigate processes shaping the evolutionary diversification of corals (Cnidaria: Anthozoa) is limited by a lack of understanding of species boundaries. Discerning species has been challenging due to a multitude of factors, including homoplasious and plastic morphological characters and the use of molecular markers that are either not informative or have not completely sorted. Hybridization can also blur species boundaries by leading to incongruence between morphology and genetics. We used traditional DNA barcoding and restriction-site associated DNA sequencing combined with coalescence-based and allele-frequency methods to elucidate species boundaries and simultaneously examine the potential role of hybridization in a speciose genus of octocoral, Sinularia.ResultsSpecies delimitations using two widely used DNA barcode markers, mtMutS and 28S rDNA, were incongruent with one another and with the morphospecies identifications, likely due to incomplete lineage sorting. In contrast, 12 of the 15 morphospecies examined formed well-supported monophyletic clades in both concatenated RAxML phylogenies and SNAPP species trees of >6,000 RADSeq loci. DAPC and Structure analyses also supported morphospecies assignments, but indicated the potential for two additional cryptic species. Three morphologically distinct species pairs could not, however, be distinguished genetically. ABBA-BABA tests demonstrated significant admixture between some of those species, suggesting that hybridization may confound species delimitation in Sinularia.ConclusionsA genomic approach can help to guide species delimitation while simultaneously elucidating the processes generating diversity in corals. Results support the hypothesis that hybridization is an important mechanism in the evolution of Anthozoa, including octocorals, and future research should examine the contribution of this mechanism in generating diversity across the coral tree of life.

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Incorporating the speciation process into species delimitation

PLoS Computational Biology ◽

10.1371/journal.pcbi.1008924 ◽

2021 ◽

Vol 17 (5) ◽

pp. e1008924

Author(s):

Jeet Sukumaran ◽

Mark T. Holder ◽

L. Lacey Knowles

Keyword(s):

Gene Flow ◽

Species Delimitation ◽

Subsequent Development ◽

Genetic Data ◽

Distinct Species ◽

Species Boundaries ◽

Multispecies Coalescent ◽

Speciation Process ◽

Other Information ◽

Species Population

The “multispecies” coalescent (MSC) model that underlies many genomic species-delimitation approaches is problematic because it does not distinguish between genetic structure associated with species versus that of populations within species. Consequently, as both the genomic and spatial resolution of data increases, a proliferation of artifactual species results as within-species population lineages, detected due to restrictions in gene flow, are identified as distinct species. The toll of this extends beyond systematic studies, getting magnified across the many disciplines that rely upon an accurate framework of identified species. Here we present the first of a new class of approaches that addresses this issue by incorporating an extended speciation process for species delimitation. We model the formation of population lineages and their subsequent development into independent species as separate processes and provide for a way to incorporate current understanding of the species boundaries in the system through specification of species identities of a subset of population lineages. As a result, species boundaries and within-species lineages boundaries can be discriminated across the entire system, and species identities can be assigned to the remaining lineages of unknown affinities with quantified probabilities. In addition to the identification of species units in nature, the primary goal of species delimitation, the incorporation of a speciation model also allows us insights into the links between population and species-level processes. By explicitly accounting for restrictions in gene flow not only between, but also within, species, we also address the limits of genetic data for delimiting species. Specifically, while genetic data alone is not sufficient for accurate delimitation, when considered in conjunction with other information we are able to not only learn about species boundaries, but also about the tempo of the speciation process itself.

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DNA-based approaches uncover cryptic diversity in the European Lepidocyrtus lanuginosus species group (Collembola: Entomobryidae)

Invertebrate Systematics ◽

10.1071/is18068 ◽

2019 ◽

Cited By ~ 1

Author(s):

Bing Zhang ◽

Ting-Wen Chen ◽

Eduardo Mateos ◽

Stefan Scheu ◽

Ina Schaefer

Keyword(s):

Cryptic Species ◽

Species Delimitation ◽

Phylogenetic Trees ◽

Sequence Data ◽

Full Range ◽

Accurate Determination ◽

Nuclear Gene ◽

Species Group ◽

Species Boundaries ◽

Cryptic Diversity

DNA sequence data and phylogenies are useful tools for species delimitation, especially in taxa comprising cryptic species. The Lepidocyrtus lanuginosus species group (Collembola: Entomobryidae) comprises three morphospecies and distinct cryptic species. We applied three DNA-based methods to delimit species boundaries in the L. lanuginosus species group across central and southern Europe. Using cytochrome c oxidase subunit I and II, we identified gaps of genetic distances that indicate species boundaries and found 10 and 9 distinct genetic lineages in L. cyaneus and L. lanuginosus, respectively. The nuclear gene elongation factor 1-α delimited 89% of the lineages but 28S rDNA (D1–2 domain) was too conserved for this purpose. The phylogenetic trees showed that L. cyaneus and L. lanuginosus are polyphyletic, suggesting that body colour is insufficient for delimiting species in the L. lanuginosus species group. Our study challenges the current morphology-based species delimitation in the L. lanuginosus species group and suggests that molecular approaches are needed for fast and accurate determination of Collembola species in both taxonomic and ecological studies. Overall, the results suggest that wide geographic sampling combined with molecular phylogenetic approaches is needed to delimit species and to understand the full range of cryptic diversity in Collembola.

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Natural selection maintains species despite widespread hybridization in the desert shrub Encelia

10.1101/2020.01.23.917021 ◽

2020 ◽

Cited By ~ 1

Author(s):

Christopher D DiVittorio ◽

Sonal Singhal ◽

Adam B Roddy ◽

Felipe Zapata ◽

David D Ackerly ◽

...

Keyword(s):

Gene Flow ◽

Natural Selection ◽

Field Experiments ◽

Population Genomics ◽

Coastal Dunes ◽

Species Boundaries ◽

Hybrid Zones ◽

Desert Shrubs ◽

Species Complexes ◽

Species Pairs

ABSTRACTNatural selection is an important driver of genetic and phenotypic differentiation between species. A powerful way to test the role of natural selection in the formation and maintenance of species is to study species complexes in which potential gene flow is high but realized gene flow is low. For a recent radiation of New World desert shrubs (Encelia: Asteraceae), we use fine-scale geographic sampling and population genomics to determine patterns of gene flow across two hybrid zones formed between two independent pairs of species with parapatric distributions. After finding evidence for extremely strong selection at both hybrid zones, we use a combination of field experiments, high-resolution imaging, and physiological measurements to determine the ecological basis for selection at one of the hybrid zones. Our results identify multiple ecological mechanisms of selection (drought, salinity, herbivory, and burial) that together are sufficient to maintain species boundaries despite high rates of hybridization. Given that multiple pairs of species hybridize at ecologically divergent parapatric boundaries in the adaptive radiation of Encelia, such mechanisms may maintain species boundaries throughout this group.SIGNIFICANCE STATEMENTIn Baja California, the deserts meet the coastal dunes in a narrow transition visible even from satellite images. We study two species pairs of desert shrubs (Encelia) that occur across this transition. Although these species can interbreed, they remain distinct. Using a combination of genetics, field experiments, 3D-imaging, and physiological measurements, we show that natural selection counteracts the homogenizing effects of gene exchange. The different habitats of these species create multiple mechanisms of selection - drought, salinity, herbivory, and burial, which together maintain these species in their native habitats and their hybrids in intermediate habitats. This study illustrates how environmental factors influence traits and fitness and how this in turn maintain species, highlighting the importance of natural selection in speciation.

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Natural selection maintains species despite frequent hybridization in the desert shrub Encelia

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2001337117 ◽

2020 ◽

Vol 117 (52) ◽

pp. 33373-33383

Author(s):

Christopher T. DiVittorio ◽

Sonal Singhal ◽

Adam B. Roddy ◽

Felipe Zapata ◽

David D. Ackerly ◽

...

Keyword(s):

Gene Flow ◽

Natural Selection ◽

Field Experiments ◽

Population Genomics ◽

Species Boundaries ◽

Hybrid Zones ◽

Phenotypic Differentiation ◽

Desert Shrubs ◽

Resolution Imaging ◽

Ecological Mechanisms

Natural selection is an important driver of genetic and phenotypic differentiation between species. For species in which potential gene flow is high but realized gene flow is low, adaptation via natural selection may be a particularly important force maintaining species. For a recent radiation of New World desert shrubs (Encelia: Asteraceae), we use fine-scale geographic sampling and population genomics to determine patterns of gene flow across two hybrid zones formed between two independent pairs of species with parapatric distributions. After finding evidence for extremely strong selection at both hybrid zones, we use a combination of field experiments, high-resolution imaging, and physiological measurements to determine the ecological basis for selection at one of the hybrid zones. Our results identify multiple ecological mechanisms of selection (drought, salinity, herbivory, and burial) that together are sufficient to maintain species boundaries despite high rates of hybridization. Given that multiple pairs of Encelia species hybridize at ecologically divergent parapatric boundaries, such mechanisms may maintain species boundaries throughout Encelia.

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Gene Flow Dependent Introgression and Species Delimitation

Plant Diversity and Resources ◽

10.3724/sp.j.1143.2012.11187 ◽

2012 ◽

Vol 34 (3) ◽

pp. 257 ◽

Cited By ~ 2

Author(s):

Fang DU ◽

Fang XU

Keyword(s):

Gene Flow ◽

Species Delimitation

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Introgression between non-sister species of honeyeaters (Aves: Meliphagidae) several million years after speciation

Biological Journal of the Linnean Society ◽

10.1093/biolinnean/blz129 ◽

2019 ◽

Vol 128 (3) ◽

pp. 583-591

Author(s):

Leo Joseph ◽

Alex Drew ◽

Ian J Mason ◽

Jeffrey L Peters

Keyword(s):

Gene Flow ◽

Reproductive Isolation ◽

Sex Chromosomes ◽

Common Ancestor ◽

Sister Species ◽

Species Boundaries ◽

North Eastern ◽

The City

Abstract We reassessed whether two parapatric non-sister Australian honeyeater species (Aves: Meliphagidae), varied and mangrove honeyeaters (Gavicalis versicolor and G. fasciogularis, respectively), that diverged from a common ancestor c. 2.5 Mya intergrade in the Townsville area of north-eastern Queensland. Consistent with a previous specimen-based study, by using genomics methods we show one-way gene flow for autosomal but not Z-linked markers from varied into mangrove honeyeaters. Introgression barely extends south of the area of parapatry in and around the city of Townsville. While demonstrating the long-term porosity of species boundaries over several million years, our data also suggest a clear role of sex chromosomes in maintaining reproductive isolation.

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The Use of Protein Electrophoresis for Determining Species Boundaries in Amphipods

Crustaceana ◽

10.1163/156854093x00603 ◽

1993 ◽

Vol 65 (2) ◽

pp. 265-277 ◽

Cited By ~ 13

Author(s):

Barbara A. Stewart

Keyword(s):

Gene Flow ◽

Genetic Differentiation ◽

Morphological Variation ◽

Protein Electrophoresis ◽

Species Boundaries ◽

Allopatric Populations ◽

A Value ◽

Electrophoretic Data

AbstractThe use of protein electrophoretic data for determining species boundaries in amphipods is addressed. Analysis of published literature on genetic differentiation in amphipods showed that pairs of allopatric populations which have genetic identities (I) above a value of 0.85 probably represent intraspecific populations, whereas pairs of populations which have genetic identities below about 0.45 probably represent different species. It was recommended that if I values fall between 0.45 and 0.85, additional factors such as evidence of a lack of gene flow between the populations, and concordant morphological variation should be considered.

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