Towards the next generation of species delimitation methods: an overview of Machine Learning applications DOI Creative Commons
Matheus Salles, Fabrícius Maia Chaves Bicalho Domingos

Published: Dec. 7, 2023

Species delimitation is the process of distinguishing between populations same species and distinct a particular group organisms. Various methods exist for inferring limits, with most them being rooted in Coalescent Theory. Their primary goal to identify independently evolving lineages that should represent separate species. models have improved by enabling explicit testing hypotheses regarding evolutionary independence among lineages. However, they some limitations, especially complex scenarios, large datasets, varying genetic data types. In this context, machine learning (ML) can be considered as promising analytical tool, clearly provides an effective way explore dataset structures when species-level divergences are hypothesised. review, we examine use ML provide overview critical appraisal existing workflows. We also simple explanations on how main types approaches operate, which help researchers students interested field. While current designed infer limits analytically powerful, present specific limitations not definitive alternatives traditional coalescent delimitation. For instance, there clear utilisation simulated data, supervised deep approaches, type representation used each approach. then discuss strengths weaknesses pipelines, propose best practices delimitation, offer insights into potential future applications. Generative adversarial networks domain adaptation techniques, could partially address misspecification issue related simulating data. Besides, integrating hypothesis process, alongside available coalescent-based methods, enable more comprehensive exploration parameters, improving accuracy biological interpretability analyses. Additionally, suggest guidelines enhancing accessibility, effectiveness, objectivity processes, aiming transformative perspective subject.

Language: Английский

Phylogenomics of the rarest animals: a second species of Micrognathozoa identified by machine learning DOI Creative Commons
Shoyo Sato,

Cecilie Appeldorff,

Owen S. Wangensteen

et al.

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2025, Volume and Issue: 292(2041)

Published: Feb. 1, 2025

The latest animal phylum to be discovered, Micrognathozoa, constitutes a rare group of limnic meiofauna. These microscopic 'jaw animals' are among the smallest metazoans yet possess highly complex jaw structures. single species Limnognathia maerski Kristensen and Funch, 2000, was first described from Greenland, later reported remote Subantarctic island more recently discovered in Pyrenees on European continent. Successful collections these three known populations facilitated investigations intraphylum relationships limits within for time. Through detailed anatomical comparisons, we substantiate lack morphological differences between geographically disjunct populations. With transcriptomic data specimens, conducted phylogenetic analyses extensively tested hypotheses using standard approaches novel machine learning methods. Analyses clearly delimited population, here as desmeti sp. nov., second but did not definitively split Greenland separate species. Divergence dating analysis suggests distribution Micrognathozoa is human mediated result long-distance dispersal raising questions about their capabilities potential undiscovered

Language: Английский

Citations

1
Morphological Species Delimitation in The Western Pond Turtle (Actinemys): Can Machine Learning Methods Aid in Cryptic Species Identification? DOI Creative Commons
Robert W. Burroughs, James F. Parham, Bryan L. Stuart

et al.

Integrative Organismal Biology, Journal Year: 2024, Volume and Issue: 6(1)

Published: Jan. 1, 2024

As the discovery of cryptic species has increased in frequency, there been an interest whether geometric morphometric data can detect fine-scale patterns variation that be used to morphologically diagnose such species. We a combination and ensemble five supervised machine learning methods (MLMs) investigate plastron shape differentiate two putative turtle species, Actinemys marmorata pallida. focus considerable research due its biogeographic distribution conservation status. Despite this work, reliable morphological diagnoses for are still lacking. validated our approach on datasets, one consisting eight disparate emydid other subspecies Trachemys (T. scripta scripta, T. elegans). The validation tests returned near-perfect classification rates, demonstrating is effective means distinguishing taxonomic groups emydids via MLMs. In contrast, same did not return high rates set alternative phylogeographic binning schemes Actinemys. All hypotheses performed poorly relative datasets no single hypothesis was unequivocally supported Two had performance marginally better than remaining hypotheses. both cases, those favored two-species split between A. pallida specimens, lending tentative support However, results also underscore as whole lower levels plastral turtles within Emydidae, but reason conservatism unclear.

Language: Английский

Citations

3
River Drainage Reorganization and Reticulate Evolution in the Two-Lined Salamander (Eurycea bislineata) Species Complex DOI
Todd W. Pierson, Kenneth H. Kozak, Travis C. Glenn

et al.

Systematic Biology, Journal Year: 2023, Volume and Issue: 73(1), P. 26 - 35

Published: Oct. 16, 2023

Abstract The origin and eventual loss of biogeographic barriers can create alternating periods allopatry secondary contact, facilitating gene flow among distinct metapopulations generating reticulate evolutionary histories that are not adequately described by a bifurcating tree. One such example may exist in the two-lined salamander (Eurycea bislineata) species complex, where discordance morphological molecular datasets has created “vexing taxonomic challenge.” Previous phylogeographic analyses mitochondrial DNA (mtDNA) suggested reorganization Miocene paleodrainages drove vicariance dispersal, but inherent limitations single-locus dataset precluded evaluation subsequent flow. Here, we generate triple-enzyme restriction site-associated sequencing (3RAD) data for > 100 individuals representing all major mtDNA lineages use suite complementary methods to demonstrate earlier is best explained history influenced river drainage reorganization. Systematics groups should acknowledge these complex relationships strictly hierarchical. [Amphibian; hybridization; introgression; Plethodontidae; stream capture.]

Language: Английский

Citations

5
Discerning structure versus speciation in phylogeographic analysis of Seepage Salamanders (Desmognathus aeneus) using demography, environment, geography, and phenotype DOI Open Access
R. Alexander Pyron, Anvith Kakkera, David A. Beamer

et al.

Molecular Ecology, Journal Year: 2023, Volume and Issue: 33(2)

Published: Nov. 28, 2023

Abstract Numerous mechanisms can drive speciation, including isolation by adaptation, distance, and environment. These forces promote genetic phenotypic differentiation of local populations, the formation phylogeographic lineages, ultimately, completed speciation. However, conceptually similar may also result in stabilizing rather than diversifying selection, leading to lineage integration long‐term persistence population structure within genetically cohesive species. Processes that maintenance geographic diversity while facilitating high rates migration limiting thereby is not accompanied reproductive isolation. We suggest this framework be applied more broadly address classic dilemma “structure” versus “species” when evaluating diversity, unifying genetics, species delimitation, underlying study demonstrate one such instance Seepage Salamander ( Desmognathus aeneus ) from southeastern United States. Recent studies estimated up 6.3% mitochondrial divergence four phylogenomic lineages with broad admixture across hybrid zones, which could potentially represent distinct supported our species‐delimitation analyses. limited dispersal promotes substantial microhabitat specificity appears yield selection on a single, uniform, ecologically mediated phenotype. As result, climatic cycles recurrent contact between repeated instances through time. Subsequent hybridization apparently counteracted adaptive introgression, leaving single unified deeply divergent nonetheless do appear incipient

Language: Английский

Citations

2
“Alstroemeria maxima (Alstroemeriaceae, Alstroemerieae), a hidden giant” revealed through integrative taxonomy DOI
Nicolás Villalobos, Carlos M. Baeza, Víctor L. Finot

et al.

Revista Brasileira de Botânica, Journal Year: 2024, Volume and Issue: 47(3), P. 649 - 669

Published: May 25, 2024

Language: Английский

Citations

0
The limits of the metapopulation: Lineage fragmentation in a widespread terrestrial salamander (Plethodon cinereus) DOI
Brian P. Waldron, Emily F. Watts,

Donald J Morgan

et al.

Systematic Biology, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 7, 2024

Abstract In vicariant species formation, divergence results primarily from periods of allopatry and restricted gene flow. Widespread harboring differentiated, geographically distinct sublineages offer a window into what may be common mode whereby originates, spreads across the landscape, then fragments multiple units. However, incipient lineages usually lack reproductive barriers that prevent their fusion upon secondary contact, blurring boundaries between single, large metapopulation-level lineage independent species. Here, we explore this model formation in Eastern Red-backed Salamander (Plethodon cinereus), widespread terrestrial vertebrate with at least 6 divergent mitochondrial clades throughout its range. Using anchored hybrid enrichment data, applied phylogenomic population genomic approaches to investigate patterns divergence, flow, contact. Genomic data broadly match most groups but reveal introgression extensive admixture several contact zones. While delimitation analyses Bayesian Phylogenetics Phylogeography supported 5 P. cinereus, genealogical indices (gdi) were highly sensitive inclusion admixed samples geographic representation candidate species, increasing support for when removing or limiting sampling single locality per group. An analysis morphometric revealed differences body size limb proportions among groups, reduction forelimb length warmer drier localities consistent increased fossoriality. We conclude cinereus is one structured component various degrees independence.

Language: Английский

Citations

0
Understanding species limits through the formation of phylogeographic lineages DOI Creative Commons
Frank T. Burbrink, Edward A. Myers, R. Alexander Pyron

et al.

Ecology and Evolution, Journal Year: 2024, Volume and Issue: 14(10)

Published: Oct. 1, 2024

The outcomes of speciation across organismal dimensions (e.g., ecological, genetic, phenotypic) are often assessed using phylogeographic methods. At one extreme, reproductively isolated lineages represent easily delimitable species differing in many or all dimensions, and at the other, geographically distinct genetic segments introgress broad environmental gradients with limited phenotypic disparity. In ambiguous gray zone speciation, where genetically but still interacting ecologically, it is expected that these context ontology evolutionary concept when they maintained over time well-defined hybrid zones, particularly intersection environments. As a result, structure correlated differences not space alone, subset genes fail to zones as underlying genomic accumulate. We present set tests synthesize delimitation process. can thereby assess historical demographics diversification processes while understanding how through by exploring spatial genome clines, genotype-environment interactions, scans for selected loci. Employing eight lineage-pairs snakes North America, we show six pairs 12 "good" two local adaptation regional population structure. have signature divergence before near mid-Pleistocene, low migration, stable varying size, loci showing selection on alleles corresponding transitions between ecoregions. Locally adapted populations younger, exhibit higher less ecological differentiation. Our results demonstrate be delimited methods properly integrate spatial, temporal, data.

Language: Английский

Citations

0
Estudio taxonómico del complejo Alstroemeria pulchra (Alstroemeriaceae) desde una perspectiva integrativa. DOI Open Access
Nicolás Villalobos

Published: March 31, 2024

Esta tesis doctoral se centró en la caracterización detallada del complejo Alstroemeria pulchra, utilizando un enfoque integrativo que combinó análisis morfo-colorimétricos, citológicos, moleculares y ecológicos para discernir unidades taxonómicas discretas. A través de métodos avanzados morfometría geométrica colorimétricos, logró una cuantificación comparación precisa morfología coloración florales, destacando diferenciación pulchra var. maxima A. subsp. lavandulacea pulchra. Los discriminantes destacaron capacidad estos caracteres diferenciar taxones, especialmente con sus características morfológicas colorimétricas distintivas. Además, inclusión estudios citológicos proporcionó comprensión más profunda estructura genética evolución complejo. La variabilidad encontrada magnifica magenta sugiere existencia procesos adaptativos recientes o activos, resaltando importancia futuros incluyan especies poblaciones explorar eventos hibridación dentro género. Este trabajo contribuye al conocimiento taxonómico Alstroemeria, enfatizando necesidad enfoques multidisciplinarios taxonomía botánica fundamentada, proporcionando bases sólidas conservación biodiversidad este género endémico alto interés ecológico ornamental.

Citations

0
The genetic origins of species boundaries at subtropical and temperate ecoregions in the North American racers (Coluber constrictor) DOI Creative Commons
Frank T. Burbrink, Edward A. Myers

Heredity, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 28, 2024

Abstract Phylogeographically structured lineages are a common outcome of range-wide population genetic studies. In the southeastern United States, disconnection between populations found at intersection coastal plains peninsular Florida and adjacent continent is readily apparent among many plants animals. However, timing maintenance species boundaries these distinctly different subtropical temperate regions remains unknown for all organisms studied there. Using genome-scale data, we examine origins, gene flow, movement genes under selection in unique ecoregions within North American racers ( Coluber constrictor ). Isolation-migration models along with tests genome-wide selection, locus-environment associations, spatial genomic clines demonstrate that two unrecognized present contact boundary ecoregions. We show several loci associated environments have maintained despite constant levels flow over thousands generations. This research provides new avenue to speciation processes poorly biodiversity hotspots.

Language: Английский

Citations

0
Towards the next generation of species delimitation methods: an overview of Machine Learning applications DOI Creative Commons
Matheus Salles, Fabrícius Maia Chaves Bicalho Domingos

Published: Dec. 7, 2023

Species delimitation is the process of distinguishing between populations same species and distinct a particular group organisms. Various methods exist for inferring limits, with most them being rooted in Coalescent Theory. Their primary goal to identify independently evolving lineages that should represent separate species. models have improved by enabling explicit testing hypotheses regarding evolutionary independence among lineages. However, they some limitations, especially complex scenarios, large datasets, varying genetic data types. In this context, machine learning (ML) can be considered as promising analytical tool, clearly provides an effective way explore dataset structures when species-level divergences are hypothesised. review, we examine use ML provide overview critical appraisal existing workflows. We also simple explanations on how main types approaches operate, which help researchers students interested field. While current designed infer limits analytically powerful, present specific limitations not definitive alternatives traditional coalescent delimitation. For instance, there clear utilisation simulated data, supervised deep approaches, type representation used each approach. then discuss strengths weaknesses pipelines, propose best practices delimitation, offer insights into potential future applications. Generative adversarial networks domain adaptation techniques, could partially address misspecification issue related simulating data. Besides, integrating hypothesis process, alongside available coalescent-based methods, enable more comprehensive exploration parameters, improving accuracy biological interpretability analyses. Additionally, suggest guidelines enhancing accessibility, effectiveness, objectivity processes, aiming transformative perspective subject.

Language: Английский

Citations

0