The genomic revolution and species delimitation in birds (and other organisms): Why phenotypes should not be overlooked

Ornithology, Journal Year: 2021, Volume and Issue: 138(2)

Published: March 1, 2021

Abstract Given the availability of genomic data to identify separately evolving groups organisms, many researchers establish species limits based on assessments extent gene flow among populations and often use analytical approaches in which is explicitly disallowed. Strictly considering lack of—or limited—gene as main or only criterion delimit involves two complications practice. First, used analyze genome-wide cannot by themselves distinguish from within-species population structure, particularly allopatric organisms. Second, recognizing those lineages one can using such fails embrace role other evolutionary forces (i.e. various forms selection) defining lineages. Using examples birds, we call for importance additional delimitation explain why commonly taxonomic studies may be insufficient properly uncover limits. By processes that structure genotypic phenotypic variation during speciation, argue rigorous analyses remain crucial genomics era because phenotypes uniquely inform us about selection maintaining cohesion Evolutionary theory describing roles flow, genetic drift natural sexual origin maintenance calls an integration with phenomics avian delimitation.

Language: Английский

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Introgression and Species Delimitation in the Longear Sunfish Lepomis megalotis (Teleostei: Percomorpha: Centrarchidae)

Systematic Biology, Journal Year: 2021, Volume and Issue: 71(2), P. 273 - 285

Published: April 29, 2021

Abstract Introgression and hybridization are major impediments to genomic-based species delimitation because many implementations of the multispecies coalescent framework assume no gene flow among species. The sunfish genus Lepomis, one world’s most popular groups freshwater sport fish, has a complicated taxonomic history. results ddRAD phylogenomic analyses do not provide support for current taxonomy that recognizes two species, Lepomis megalotis peltastes, in L. complex. Instead, evidence from phylogenomics phenotype warrants recognizing six relatively ancient evolutionary lineages introgressed hybridizing populations complex localized appear be result secondary contact or rare events between nonsister Segregating admixed our identifies with moderate high genealogical divergence, whereas including drives all but lineage below threshold divergence. Segregation individuals also helps reveal phenotypic distinctiveness morphological traits used by ichthyologists discover delimit over last centuries. Our protocols allow identification accommodation introgression delimitation. Genomic-based validated multiple lines provides path towards discovery new biodiversity resolving long-standing problems.[ddRAD; divergence index; hybridization; integrative delimitation; phylogeny; contact; systematics; taxonomy.]

Language: Английский

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Were Neanderthals and Homo sapiens ‘good species’?

Quaternary Science Reviews, Journal Year: 2023, Volume and Issue: 303, P. 107975 - 107975

Published: Jan. 28, 2023

Prior to the advent of whole-genome sequencing in ancient humans, likelihood that Homo sapiens and Neanderthals admixed has long been debated, mostly on basis phenotypic assessments alone. Today, evidence for archaic hominin admixture is being documented an increasing number studies, expanding evidential debate whether merit separate specific taxonomic status. Here we argue while new provided us with a finer-grained picture intra- intergroup demographic dynamics, it does not yet justify merging expanded concept or abandoning taxonomies. We approach this issue apparent conflict between molecular morphology-based taxonomies from diachronic perspective lineage divergence, highlighting how different properties are expected arise at points time, integrative species conceptions delimitation criteria. light similar "invasions" genome among other animal taxa, full reproductive isolation as final, litmus test distinct status should be rather considered biologically misplaced expectation. Therefore, suggest nomenclature perceived embarrassment but justifiably applied human paleogenomic publications, maintaining congruence zoological literature. then briefly consider problematize recent suggestions evolutionary diversification now best represented by 'braided stream" network. conclude putting our paleoanthropological case study broader context genomic era.

Language: Английский

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Incomplete lineage sorting and ancient admixture, and speciation without morphological change in ghost-worm cryptic species

PeerJ, Journal Year: 2021, Volume and Issue: 9, P. e10896 - e10896

Published: Feb. 9, 2021

Morphologically similar species, that is cryptic may be or quasi-similar owing to the deceleration of morphological evolution and stasis. While factors underlying stasis in species remain unknown, decades research field paleontology on punctuated equilibrium have originated clear hypotheses. Species are expected morphologically identical scenarios shared genetic variation, such as hybridization incomplete lineage sorting, where bottlenecks reduce variation constrain morphology. Here, focusing three

Language: Английский

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Indo-Pacific Eels (Anguilla marmorata) from the Caroline Islands Belong to the Micronesia Population Based on Total Number of Vertebrae Counts

Pacific Science, Journal Year: 2025, Volume and Issue: 78(2)

Published: Jan. 6, 2025

The Indo-Pacific eel, Anguilla marmorata Quoy & Gaimard, has the widest geographic distribution of anguillid eels. At least four populations (North Pacific, Micronesia, Indian Ocean and South Pacific) this species were estimated to exist by previous morphological molecular genetic studies. Recent mitochondrial control region haplotype analysis A. eels from eastern Caroline Islands Guam grouped them in two separated lineages with Pacific western Ocean. To examine composition possible Micronesia population that may mostly be found Mariana (Guam) (Palau, Yap, Chuuk, Pohnpei, Kosrae) islands relation other region, we statistically compared total number vertebrae (TV) specimens collected throughout most range including 32 Kosrae Pohnpei islands. TV for 1298 combined data 15 localities ranged 100 110. mean (107.95, 108.03) (105–110) clearly higher than localities. post hoc multiple pairwise comparisons 105 pairs single showed there 57 significant differences between each locality. all 13 statistical pooled regional data, various studies, general geography indicate are likely six spawning marmorata. This study indicates included population, but further research is needed understand area life history seems live on a relatively small Oceania.

Language: Английский

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Common names for all species and subspecies of the genus Anguilla

Environmental Biology of Fishes, Journal Year: 2020, Volume and Issue: 103(8), P. 985 - 991

Published: June 19, 2020

Abstract Scientific naming rules of animals are strictly defined by the International Code Zoological Nomenclature, while those for common names vague and not well defined. Specifically, freshwater eels genus Anguilla have become confused among scientific papers, pictorial books, online resources in recent years. This disordered use demonstrates urgent need standardization these species. In addition, eel populations drastically decreased worldwide over past few decades, resulting their listing as endangered present study, we following five eels: to (1) a representative locality name geographic distribution species or subspecies, (2) distinguish two sympatric subspecies longfin shortfin, (3) select that would enable be easily recalled, (4) value longstanding former if they adhere above three rules, (5) shortest possible. Based on current knowledge proposed 22 all known 19 genus. As result, 21, 6, 13, 3 were named based Rules (1), (2), (3), (4), respectively.

Language: Английский

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Phylogenomic Assessment of Biodiversity Using a Reference-Based Taxonomy: An Example With Horned Lizards (Phrynosoma)

Frontiers in Ecology and Evolution, Journal Year: 2021, Volume and Issue: 9

Published: July 26, 2021

Phylogenomic investigations of biodiversity facilitate the detection fine-scale population genetic structure and demographic histories species populations. However, determining whether or not divergence measured among populations reflects species-level differentiation remains a central challenge in delimitation. One potential solution is to compare between putative new with other closely related species, sometimes referred as reference-based taxonomy. To be described should at least divergent species. Here, we develop taxonomy for Horned Lizards ( Phrynosoma ; 17 species) using phylogenomic data (ddRADseq data) provide framework delimiting Greater Short-horned Lizard complex P. hernandesi ). Previous delimitation studies this have produced conflicting results, morphological suggesting that consists five whereas mitochondrial DNA support anywhere from 1 10 + help address conflict, first estimated time-calibrated tree close relatives SNP data. These results paraphyly hernandesi; recommend recognition two promote consistent monophyly. There strong evidence three within , modeling admixture analyses suggest these are reproductively isolated, which previous hybridization could common. Finally, characterize population-species boundary by quantifying levels all 18 Genetic measures western southern failed exceed those but relatively small size northern causes it appear comparisons underscore difficulties associated putting approach into practice. Nevertheless, offers promising assessment clades organisms similar life ecological traits.

Language: Английский

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Anthropogenic Contaminants Shape the Fitness of the Endangered European Eel: A Machine Learning Approach

Fishes, Journal Year: 2022, Volume and Issue: 7(5), P. 274 - 274

Published: Oct. 5, 2022

European eel is thought to be a symbol of the effects global change on aquatic biodiversity. The species has persisted for millions years and faced drastic environmental fluctuations thanks its phenotypic plasticity. However, recently declined historically low levels under synergistic human pressures. Sublethal chemical contamination been shown alter reproductive capacity, but impacts required actions are not fully addressed by conservation plans. This paper proposes modelling approach quantify sublethal anthropogenic pollutants expression life history traits related fitness critically endangered eel. Material Methods: We sampled female silver eels from eight different catchments across Europe previously representative spectrum variability contamination. measured 11 fitness-related within four main categories: fecundity, adaptability plasticity, migratory readiness, spawning potential. used machine learning in models explore reaction (expression these traits) according geographical parameters, parasite burdens (the introduced nematode Anguillicoloides crassus) contaminants (persistent organic (POPs) muscular tissue trace elements (TEs) gonads, livers muscles). Finally, we simulated, two management scenarios—contamination reduction increase—on fecundity recruitment. Results: Contamination our sampling was have stronger control than do geographic factors that currently described literature. modelled scenarios assess benefit mitigation: suggest reducing concentrations lowest values occurred design would double compared current situation. Discussion: Remediation could represent viable option increasing resilience populations, with much more solely fishing mortality. More broadly, work provides an innovative way quantitative assessment norms species’ biological inorganic pollutions thus opening new pathways revert erosion

Language: Английский

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For R-eel?! Investigating international sales of critically endangered species in freshwater eel products with DNA barcoding

Food Control, Journal Year: 2023, Volume and Issue: 150, P. 109752 - 109752

Published: March 15, 2023

The growing popularity of Japanese cuisine worldwide has caused an increasing demand for freshwater eels (family Anguillidae), usually termed 'unagi' and commonly utilised in sushi donburi dishes. trade the Critically Endangered European eel (Anguilla anguilla) is now restricted this resulted illegal trade. Here, DNA barcoding was used to identify species sold processed products worldwide, including a focus on Europe North America. For first time, traditional jellied stewed from UK are also barcoded. A total 114 novel samples were analysed alongside previously published data evaluate differences composition between locations, over time unagi versus more products. results revealed East Asia than japonica) – demonstrating stark contrast native those sale (although variation product type recruitment influence this). This suggests thousands food miles potentially hidden Considering limitations export eel, numbers identified outside its natural range bring into question legality supply. An increased prevalence endangered American rostrata) shown globally. Future efforts should implementing robust traceability systems, using genetic methods, deter within industry.

Language: Английский

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Genome‐wide methylation in the panmictic European eel (Anguilla anguilla)

Molecular Ecology, Journal Year: 2022, Volume and Issue: 31(16), P. 4286 - 4306

Published: June 29, 2022

The role of methylation in adaptive, developmental and speciation processes has attracted considerable interest, but interpretation results is complicated by diffuse boundaries between genetic non-genetic variation. We studied whole genome variation the European eel, distributed from subarctic to subtropical environments, with panmixia precluding genetically based local adaptation beyond single-generation responses. Overall was 70.9%, hypomethylation predominantly found promoters first exons. Redundancy analyses involving juvenile glass eels showed 0.06% 0.03% variance at SNPs be explained localities environmental variables, respectively, GO terms genes associated outliers primarily neural system functioning. For CpGs 2.98% 1.36% variables. Differentially methylated regions particularly included involved processes, Hox clusters featuring prominently. Life stage (adult versus eels) most important source inter-individual methylation, probably reflecting both ageing processes. Demethylation transposable elements relative pure eel observed X American hybrids, possibly representing postzygotic barriers this characterized prolonged ongoing gene flow. Whereas data are consistent a selective responses, underpin importance epigenetics life cycle suggest interactions development phenotypic mediated Eels remarkable having retained eight clusters, roles for adaptive

Language: Английский

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