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69 results for “Candidate species”
Genome-wide analysis resolves the radiation of New Zealand's freshwater Galaxias vulgaris complex and reveals a candidate species obscured by mitochondrial capture
<p>Aim: Freshwater fish radiations are often characterized by multiple closely-related species in close proximity, which can lead to introgression and associated discordance of mitochondrial and nuclear characterizations of species diversity. As a case in point, single locus nuclear versus mitochondrial analyses of New Zealand's stream-resident <em>Galaxias vulgaris</em> complex have yielded conflicting phylogenies. Our goal is to use genome-wide divergence patterns among these fishes to evaluate the potential role of mitochondrial capture in obscuring species diversity and to understand how ancient and anthropogenic drainage modification explains this diversity.</p> <p>Location: Freshwater ecosystems of New Zealand. Methods: We generate and analyze a genome-wide data set comprising 52,352 SNPs across 187 <em>Galaxias</em> specimens to resolve the phylogeny of this recent fish radiation. We conduct phylogenetic, PCA, STRUCTURE, and ABBA-BABA analyses to evaluate the evolutionary relationships of lineages in the context of natural and anthropogenic river drainage alterations.</p> <p>Results: In addition to the 11 previously recognized stream-resident lineages, genome-wide data reveal a twelfth candidate species (<em>G</em>. 'Pomahaka'), apparently obscured by introgressive mitochondrial capture. We identify additional examples of mito-nuclear discordance and putative mitochondrial capture, likely mediated by geological and anthropogenic modification of drainage boundaries.</p> <p>Main conclusions: Our study highlights the need for genome-wide approaches for delimiting freshwater biodiversity. Genetic data also reveal the influence of drainage history on freshwater biodiversity, including the rapid divergence of recently fragmented fish populations, and the conservation genetic risks of anthropogenic translocations events.</p>
Fig 1 in Development of Microplitis similis (Hymenoptera: Braconidae) on two candidate host species, Spodoptera litura and Spodoptera exigua (Lepidoptera: Noctuidae)
Fig 1. Age–stage specific survival rates (Sx) of Micropletis similis that developed in Spodoptera exigua (A) and in S. litura (B).
Fig 2 in Development of Microplitis similis (Hymenoptera: Braconidae) on two candidate host species, Spodoptera litura and Spodoptera exigua (Lepidoptera: Noctuidae)
Fig 2. Daily body weight of parasitized and non-parasitized Spodoptera exigua (A) and S. litura (B). Each datum is shown as a mean ± SE.
Genome-wide analysis resolves the radiation of New Zealand’s freshwater Galaxias vulgaris complex and reveals a candidate species obscured by mitochondrial capture
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Data from: Phylogenomic data reveal reticulation and incongruence among mitochondrial candidate species in Dusky Salamanders (Desmognathus)
<p>Gene flow between evolutionarily distinct lineages is increasingly recognized as a common occurrence. Such processes distort our ability to diagnose and delimit species, as well as confound attempts to estimate phylogenetic relationships. A conspicuous example is Dusky Salamanders (<i>Desmognathus</i>), a common model-system for ecology, evolution, and behavior. Only 22 species are described; 7 in the last 40 years. However, mitochondrial datasets indicate the presence of up to 45 "candidate species" presenting a complex history of reticulation. Some authors have even suggested that the search for species boundaries in the group may be in vain. Here, we analyze nuclear and mitochondrial data containing 161 individuals from at least 49 distinct evolutionary lineages that we treat as candidate species. Concatenated and species-tree methods fail to provide satisfactory resolution for relationships among these taxa. Comparing topologies and applying methods for estimating phylogenetic networks, we find strong support for numerous instances of hybridization throughout the history of the group. We suggest that these processes may be more common than previously thought across the phylogeography-phylogenetics continuum, and that while the search for species boundaries in <i>Desmognathus</i> may not be in vain, it will be complicated by factors such as crypsis, parallelism, and gene-flow.</p>
Data from: Candidate gene SNP variation in floodplain populations of pedunculate oak (Quercus robur L.) near the species' southern range margin: weak differentiation yet distinct associations with water availability
<p>Populations residing near species' low-latitude range margins (LLM) often occur in warmer and drier environments than those in the core range. Thus, their genetic composition could be shaped by climatic drivers that differ from those occurring at higher latitudes, resulting in potentially adaptive variants of conservation value. Such variants could facilitate the adaptation of populations from other portions of the geographic range to similar future conditions anticipated under ongoing climate change. However, very few studies have assessed standing genetic variation at potentially adaptive loci in natural LLM populations. We investigated standing genetic variation at SNPs located within 117 candidate genes and its links to putative climatic selection pressures across 19 pedunculate oak (Quercus robur L.) populations distributed along a regional climatic gradient near the species' southern range margin in southeastern Europe. These populations are restricted to floodplain forests along large lowland rivers, whose hydric regime is undergoing significant shifts under modern rapid climate change. The populations showed very weak geographic structure, suggesting extensive genetic connectivity and gene flow or shared ancestry. We identified eight (6.2%) positive FST-outlier loci, and genotype-environment association analyses revealed consistent associations between SNP allele frequencies and several climatic variables linked to water availability. A total of 61 associations involving 37 SNPs (28.5%) from 35 annotated genes provided important insights into putative functional mechanisms in our system. Our findings provide empirical support for the role of LLM populations as sources of potentially adaptive variation that could enhance species' resilience to climate change-related pressures.</p>
Data from: Genomic islands of differentiation in two songbird species reveal candidate genes for hybrid female sterility
Hybrid sterility is a common first step in the evolution of postzygotic reproductive isolation. According to Haldane's Rule it affects predominantly the heterogametic sex. While the genetic basis of hybrid male sterility in organisms with heterogametic males has been studied for decades, the genetic basis of hybrid female sterility in organisms with heterogametic females has received much less attention. We investigated the genetic basis of reproductive isolation in two closely related avian species, the Common Nightingale (Luscinia megarhynchos) and the Thrush Nightingale (L. luscinia), that hybridize in a secondary contact zone and produce viable hybrid progeny. In accordance with Haldane's Rule, hybrid females are sterile, while hybrid males are fertile, allowing gene flow to occur between the species. Using transcriptomic data from multiple individuals of both nightingale species we identified genomic islands of high differentiation (FST) and of high divergence (Dxy), and we analyzed gene content and patterns of molecular evolution within these islands. Interestingly, we found that these islands were enriched for genes related to female meiosis and metabolism. The islands of high differentiation and divergence were also characterized by higher levels of linkage disequilibrium than the rest of the genome in both species indicating that they might be situated in genomic regions of low recombination. This study provides one of the first insights into genetic basis of hybrid female sterility in organisms with heterogametic females.
Candidate-species delimitation in Desmognathus salamanders reveals gene flow across lineage boundaries, confounding phylogenetic estimation and clarifying hybrid zones
Dusky Salamanders (genus Desmognathus) currently comprise only 22 described, extant species. However, recent mitochondrial and nuclear estimates indicate the presence of up to 49 candidate species based on ecogeographic sampling. Previous studies also suggest a complex history of hybridization between these lineages. Studies in other groups suggest that disregarding admixture may affect both phylogenetic inference and clustering-based species-delimitation. With a dataset comprising 233 Anchored Hybrid Enrichment (AHE) loci sequenced for 896 Desmognathus specimens from all 49 candidate species, we test three hypotheses regarding i) species-level diversity, ii) hybridization and admixture, and iii) misleading phylogenetic inference. Using phylogenetic and population-clustering analyses considering gene flow, we find support for at least 47 candidate species in the phylogenomic dataset, some of which are newly characterized here while others represent combinations of previously named lineages that are collapsed in the current dataset. Within these, we observe significant phylogeographic structure, with up to 64 total geographic genetic lineages, many of which hybridize either narrowly at contact zones or extensively across ecological gradients. We find strong support for both recent admixture between terminal lineages and ancient hybridization across internal branches. This signal appears to distort concatenated phylogenetic inference, wherein more heavily admixed terminal specimens occupy apparently artifactual early diverging topological positions, occasionally to the extent of forming false clades of intermediate hybrids. Additional geographic and genetic sampling and more robust computational approaches will be needed to clarify taxonomy, and to reconstruct a network topology to display evolutionary relationships in a manner that is consistent with their complex history of reticulation. --
Data from: Phylogenomic data reveal reticulation and incongruence among mitochondrial candidate species in Dusky Salamanders (Desmognathus)
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Data from: Genomic islands of differentiation in two songbird species reveal candidate genes for hybrid female sterility
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Data from: Candidate gene SNP variation in floodplain populations of pedunculate oak (Quercus robur L.) near the species' southern range margin: weak differentiation yet distinct associations with water availability
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Candidate-species delimitation in Desmognathus salamanders reveals gene flow across lineage boundaries, confounding phylogenetic estimation and clarifying hybrid zones
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Several candidate size metrics explain vital rates across multiple populations throughout a widespread species' range
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Data from: Plotting for change: an analytic framework to aid decisions on which lineages are candidate species in phylogenomic species discovery
<p>A recent study argued that coalescent-based models of species delimitation mostly delineate population structure not species, and called for the validation of candidate species using biological information additional to the genetic information, such as phenotypic or ecological data. Here we introduce a framework to interrogate genomic datasets and coalescent-based species trees for the presence of candidate species in situations where additional biological data are unavailable, unobtainable, or uninformative. For <i>de novo</i> genomic studies of species boundaries, we propose six steps: (a) visualize genetic affinities among individuals to identify both discrete and admixed genetic groups from first principles, and to hold aside individuals involved in contemporary admixture for independent consideration; (b) apply phylogenetic techniques to identify lineages; (c) assess diagnosability of those lineages as potential candidate species; (d) interpret the diagnosable lineages in a geographic context (sympatry, parapatry, allopatry); (e) assess significance of difference or trends in the context of sampling intensity; and (f) adopt a holistic approach to available evidence to inform decisions on species status in the difficult cases of allopatry. We use this approach to distinguish candidate species from within-species lineages for a widespread species complex of Australian freshwater fishes (<i>Retropinna</i> spp.). Our framework addresses two cornerstone issues in systematics that are often not explicitly discussed in genomic species discovery: diagnosability and how to determine it, and what criteria should be used to decide whether diagnosable lineages are conspecific or represent different species.</p>
Data from: The last bastion? X chromosome genotyping of Anopheles gambiae species pair males from a hybrid zone reveals complex recombination within the major candidate 'genomic island of speciation'
Speciation with gene flow may be aided by reduced recombination helping to build linkage between genes involved in the early stages of reproductive isolation. Reduced recombination on chromosome X has been implicated in speciation within the Anopheles gambiae complex, species of which represent the major Afrotropical malaria vectors. The most recently diverged, morphologically indistinguishable, species pair, A. gambiae and Anopheles coluzzii, ubiquitously displays a 'genomic island of divergence' spanning over 4 Mb from chromosome X centromere, which represents a particularly promising candidate region for reproductive isolation genes, in addition to containing the diagnostic markers used to distinguish the species. Very low recombination makes the island intractable for experimental recombination studies, but an extreme hybrid zone in Guinea Bissau offers the opportunity for natural investigation of X-island recombination. SNP analysis of chromosome X hemizygous males revealed: (i) strong divergence in the X-island despite a lack of autosomal divergence; (ii) individuals with multiple-recombinant genotypes, including likely double crossovers and localized gene conversion; (iii) recombination-driven discontinuity both within and between the molecular species markers, suggesting that the utility of the diagnostics is undermined under high hybridization. The largely, but incompletely protected nature of the X centromeric genomic island is consistent with a primary candidate area for accumulation of adaptive variants driving speciation with gene flow, while permitting some selective shuffling and removal of genetic variation.
Data from: Genome-wide SNPs resolve a key conflict between sequence and allozyme data to confirm another threatened candidate species of river blackfishes (Teleostei: Percichthyidae: Gadopsis)
Conflicting results from different molecular datasets have long confounded our ability to characterise species boundaries. Here we use genome-wide SNP data and an expanded allozyme dataset to resolve conflicting systematic hypotheses on an enigmatic group of fishes (Gadopsis, river blackfishes, Percichthyidae) restricted to southeastern Australia. Previous work based on three sets of molecular markers: mtDNA, nuclear intron DNA and 51 allozyme loci was unable to clearly resolve the status of a putative fifth candidate species (SWV) within Gadopsis marmoratus. Resolving the taxonomic status of candidate species SWV is particularly critical as based on IUCN criteria this taxon would be considered Critically Endangered. After all filtering steps we retained a subset of 10,862 putatively unlinked SNP loci for population genetic and phylogenomic analyses. Analyses of SNP loci based on maximum likelihood, fastSTRUCTURE and DAPC were all consistent with the previous and updated allozyme results supporting the validity of the candidate Gadopsis species SWV. Immediate conservation actions should focus on preventing take by anglers, protection of water resources to sustain perennial reaches and drought refuge pools, and aquatic and riparian habitat protection and improvement. In addition, a formal morphological taxonomic review of the genus Gadopsis is urgently required.
Data from: Digging for gold nuggets: uncovering novel candidate genes for variation in gastrointestinal nematode burden in a wild bird species
The extent to which genotypic variation at a priori identified candidate genes can explain variation in complex phenotypes is a major debate in evolutionary biology. Whereas some high-profile genes such as the MHC or MC1R clearly do account for variation in ecologically relevant characters, many complex phenotypes such as response to parasite infection may well be underpinned by a large number of genes, each of small and effectively undetectable effect. Here, we characterize a suite of novel candidate genes for variation in gastrointestinal nematode (Trichostrongylus tenuis) burden among red grouse (Lagopus lagopus scotica) individuals across a network of moors in north-east Scotland. We test for associations between parasite load and genotypic variation in twelve genes previously identified to be differentially expressed in experimentally infected red grouse or genetically differentiated among red grouse populations with overall different parasite loads. These genes are associated with a broad physiological response including immune system processes. Based on individual-level generalized linear models, genotypic variants in nine genes were significantly associated with parasite load, with effect sizes accounting for differences of 514–666 worms per bird. All but one of these variants were synonymous or untranslated, suggesting that these may be linked to protein-coding variants or affect regulatory processes. In contrast, population-level analyses revealed few and inconsistent associations with parasite load, and little evidence of signatures of natural selection. We discuss the broader significance of these contrasting results in the context of the utility of population genomics and landscape genomics approaches in detecting adaptive genomic signatures.
Data from: Integrating phylogenomic and morphological data to assess candidate species-delimitation models in brown and red-bellied snakes (Storeria)
Systematics at the species level is still marked by theoretical and empirical tensions amongst the desires to identify geographical lineages, delimit species, and estimate their relationships. These goals are often confounded because each relies, at least to some extent, on the others being known. However, recently developed methods can simultaneously address all three. Furthermore, next-generation genomic sequencing allows us to generate large-scale molecular data sets to examine variation within species at a fine scale. Finally, a renaissance in morphological species validation allows us to integrate historical species definitions with coalescent models for species delimitation. Here, we investigate the applicability of these methods in an empirical case, in the Nearctic snake genus Storeria. Integrating trait data into species delimitation reduces the number of species delimited from molecular data alone. Whereas molecular data support eight distinct species-level lineages, including morphological data reduces this to four. The taxa Storeria dekayi, Storeria occipitomaculata, Storeria storerioides, and Storeria victa are considered distinct, monotypic species, with no subspecies recognized. We highlight the need for careful assessment of species delimitation, combining both computational genetic methods as well as traditional character-based descriptions. It is now possible to identify phylogeographical lineages, delimit species using molecular and morphological data, and estimate their relationships in a single coherent set of analyses. Moving forward, this will allow for more rapid and objective assessments of cryptic diversity at the species level.
Figure 2 in Integrating phylogenomic and morphological data to assess candidate species-delimitation models in brown and red-bellied snakes (Storeria)
Figure 2. Map of Storeria ranges and sampling locations, showing geographical extent of populations, and range of former species with respect to re-delimited taxa. A, previous geographical extent of Storeria occipitomaculata is shown in red; circles indicate sampling localities. The asterisk indicates the sample of Storeria 'hidalgoensis' examined for morphology, with the range of this subpopulation, now considered part of S. occipitomaculata, indicated in pink. The range of Storeria storerioides is indicated in blue, with the sampling locality indicated by a square. B, previous geographical extent of Storeria dekayi is shown in yellow, with pentagons indicating sampling localities of S. dekayi, triangles indicating Storeria victa, and a line drawn to approximate the range boundary. The asterisk in the Central American population indicates the collection location of the specimen of Storeria 'tropica' examined for morphology, which is now considered part of S. dekayi.
Assessing candidate DNA barcodes for Chinese and internationally traded timber species
<p>Accurate identification of species from timber is an essential step to help control illegal logging and forest loss. However, current approaches to timber identification based on morphological and anatomical characteristics have limited species resolution. DNA barcoding is a proven tool for plant species identification, but there is a need to build reliable reference data across broad taxonomic and spatial scales. Here, we construct a species barcoding library consisting of 1,550 taxonomically diverse timber species from 656 genera and 124 families, representing a comprehensive genetic reference data set for Chinese timber species and international commercial traded timber species, using four barcodes (<i>rbc</i>L, <i>mat</i>K, <i>trn</i>H–<i>psb</i>A, and ITS2). The ITS2 fragment was found to be the most efficient locus for Chinese timber species identification among the four barcodes tested, both at the species and genus level, despite its low recovery rate. Nevertheless, the barcode combination <i>mat</i>K+<i>trn</i>H–<i>psb</i>A+ITS2 was required as a complementary barcode to distinguish closely related species in complex datasets involving internationally traded timber species. Comparative analyses of family-level discrimination and species/genus ratios indicated that the inclusion of closely related species is an important factor affecting the resolution ability of barcodes for timber species verification. Our study indicates that although nuclear ITS2 is the most efficient single barcode for timber species authentication in China, complementary combinations like <i>mat</i>K+<i>trn</i>H–<i>psb</i>A+ITS2 are required to provide broader discrimination power. These newly-generated sequences enrich the existing publicly available databases, especially for tropical and subtropical evergreen timber trees and this current timber species barcode reference library can serve as an important genetic resource for forestry monitoring, illegal logging prosecution and biodiversity projects.</p>
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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