Integrating coalescent species delimitation with analysis of host specificity reveals extensive cryptic diversity despite minimal mitochondrial divergence in the malaria parasite genus Leucocytozoon DOI Creative Commons
Spencer C. Galen,

Renato Nunes,

Paul R. Sweet

и другие.

BMC Evolutionary Biology, Год журнала: 2018, Номер 18(1)

Опубликована: Авг. 30, 2018

Coalescent methods that use multi-locus sequence data are powerful tools for identifying putatively reproductively isolated lineages, though this approach has rarely been used the study of microbial groups likely to harbor many unrecognized species. Among symbionts, integrating genetic species delimitation with trait could indicate reproductive isolation, such as host specificity data, despite its potential inform limits. Here we test ability an integrative combining and delimit within avian malaria parasite genus Leucocytozoon in central Alaska. We sequenced seven nuclear loci 69 samples multiple (GMYC BPP models), tested differences infection patterns among putative based on 406 individual infections, characterized morphology. found cryptic morphology masked a highly diverse assemblage, most recovering support at least 21 separate occur sympatrically have divergent patterns. Reproductive isolation appears evolved low mtDNA divergence, one instance two cytb haplotypes differed by single base pair (~ 0.2% divergence) were supported However, there was no consistent association between divergence three pairs observed idiosyncratic ecological haplotype be either conspecific, specificity, or specialization. Integrating non-traditional types provide novel view diversity parasites missed previously using barcodes. Species show is species-rich Alaska, extraordinary species-level worldwide. will important understanding evolutionary history symbionts moving forward.

Язык: Английский

Multispecies coalescent delimits structure, not species DOI Open Access
Jeet Sukumaran, L. Lacey Knowles

Proceedings of the National Academy of Sciences, Год журнала: 2017, Номер 114(7), С. 1607 - 1612

Опубликована: Янв. 30, 2017

Significance Despite its widespread application to the species delimitation problem, our study demonstrates that what multispecies coalescent actually delimits is structure. The current implementations of under do not provide any way for distinguishing between structure due population-level processes and boundaries. overinflation misidentification general genetic boundaries has profound implications understanding generation dynamics biodiversity, because ecological or evolutionary studies rely on as their fundamental units will be impacted, well very existence this conservation planning undermined isolated populations incorrectly being treated distinct species.

Язык: Английский

Процитировано

805
Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent DOI
Graham Jones

Journal of Mathematical Biology, Год журнала: 2016, Номер 74(1-2), С. 447 - 467

Опубликована: Июнь 10, 2016

Язык: Английский

Процитировано

277
A biologist’s guide to Bayesian phylogenetic analysis DOI
Fabrícia F. Nascimento, Mario dos Reis, Ziheng Yang

и другие.

Nature Ecology & Evolution, Год журнала: 2017, Номер 1(10), С. 1446 - 1454

Опубликована: Сен. 13, 2017

Язык: Английский

Процитировано

190
Minimalist revision and description of 403 new species in 11 subfamilies of Costa Rican braconid parasitoid wasps, including host records for 219 species DOI Creative Commons
Michael J. Sharkey, Daniel H. Janzen, Winnie Hallwachs

и другие.

ZooKeys, Год журнала: 2021, Номер 1013, С. 1 - 665

Опубликована: Фев. 2, 2021

Three new genera are described:

Язык: Английский

Процитировано

173
Species delimitation 4.0: integrative taxonomy meets artificial intelligence DOI Creative Commons
Kevin Karbstein, Lara M. Kösters, Ladislav Hodač

и другие.

Trends in Ecology & Evolution, Год журнала: 2024, Номер 39(8), С. 771 - 784

Опубликована: Июнь 6, 2024

Although species are central units for biological research, recent findings in genomics raising awareness that what we call can be ill-founded entities due to solely morphology-based, regional descriptions. This particularly applies groups characterized by intricate evolutionary processes such as hybridization, polyploidy, or asexuality. Here, challenges of current integrative taxonomy (genetics/genomics + morphology ecology, etc.) become apparent: different favored concepts, lack universal characters/markers, missing appropriate analytical tools processes, and highly subjective ranking fusion datasets. Now, combined with artificial intelligence under a unified concept enable automated feature learning data integration, thus reduce subjectivity delimitation. approach will likely accelerate revising unraveling eukaryotic biodiversity.

Язык: Английский

Процитировано

30
The Multispecies Coalescent Over-Splits Species in the Case of Geographically Widespread Taxa DOI Open Access
E. Anne Chambers, David M. Hillis

Systematic Biology, Год журнала: 2019, Номер 69(1), С. 184 - 193

Опубликована: Июнь 5, 2019

Many recent species delimitation studies rely exclusively on limited analyses of genetic data analyzed under the multispecies coalescent (MSC) model, and results from these often are regarded as conclusive support for taxonomic changes. However, most MSC-based methods have well-known unmet assumptions. Uncritical application genetic-based approaches (without due consideration sampling design, effects a priori group designations, isolation by distance, cytoplasmic-nuclear mismatch, population structure) can lead to over-splitting species. Here, we argue that in many common biological scenarios, researchers must be particularly cautious regarding limitations, especially cases well-studied, geographically variable, parapatrically distributed complexes. We consider points with respect historically controversial group, American milksnakes (Lampropeltis triangulum complex), using analysis (Ruane et al. 2014). show over-reliance program Bayesian Phylogenetics Phylogeography, without adequate its assumptions resulted this study. Several hypothesized instead appear represent arbitrary slices continuous geographic clines. conclude best available evidence supports three, rather than seven, within complex. More generally, recommend coalescent-based incorporate thorough variation carefully examine putative contact zones among delimited before making

Язык: Английский

Процитировано

145
Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics DOI Creative Commons
Gustavo A. Bravo, Alexandre Antonelli, Christine D. Bacon

и другие.

PeerJ, Год журнала: 2019, Номер 7, С. e6399 - e6399

Опубликована: Фев. 14, 2019

Building the Tree of Life (ToL) is a major challenge modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing many heterogeneous genomic signals emerging from first decade large-scale phylogenetic analysis spawned high-throughput sequencing (HTS). Such include those most commonly encountered phylogenomic datasets, such as incomplete lineage sorting, but also reticulate processes with greater frequency, recombination introgression. Here focus specifically on how methods can accommodate heterogeneity incurred population genetic processes; do not discuss ignore processes, concatenation or supermatrix approaches supertrees. We suggest acquisition types markers used will remain restricted until posteriori marker choice are made possible routine whole-genome taxa interest. limitations potential extensions model supporting innovation today, multispecies coalescent (MSC). Macroevolutionary models use phylogenies, character mapping, often which building phylogenies increasingly rely assimilating an important goal moving forward. Finally, integrative cyberinfrastructure linking all steps process ToL, specimen field publication tracking data, well culture values contributors at each step, essential for progress.

Язык: Английский

Процитировано

134
Sky island diversification meets the multispecies coalescent – divergence in the spruce‐fir moss spider (Microhexura montivaga, Araneae, Mygalomorphae) on the highest peaks of southern Appalachia DOI
Marshal Hedin, David E. Carlson,

Fred Coyle

и другие.

Molecular Ecology, Год журнала: 2015, Номер 24(13), С. 3467 - 3484

Опубликована: Май 25, 2015

Abstract Microhexura montivaga is a miniature tarantula‐like spider endemic to the highest peaks of southern Appalachian mountains and known only from six allopatric, highly disjunct montane populations. Because severe declines in spruce‐fir forest late 20th century, M. was formally listed as US federally endangered species 1995. Using DNA sequence data one mitochondrial seven nuclear genes, patterns multigenic genetic divergence were assessed for Independent discovery analyses reveal obvious fragmentation both within among populations, with five primary lineages recovered. Multispecies coalescent validation [guide tree unguided Bayesian Phylogenetics Phylogeography ( BPP ), Bayes factor delimitation BFD )] using nuclear‐only congruently recover or distinct lineages; combined plus favour eight lineages. In stark contrast this clear fragmentation, survey secondary sexual features available males indicates morphological conservatism across While it certainly possible that morphologically cryptic speciation has occurred taxon, system may alternatively represent case where extreme population structuring (but not speciation) leads an oversplitting lineage diversity by multispecies methods. Our results have conservation implications taxon illustrate methodological issue expected become more common genomic‐scale sets are gathered taxa found naturally fragmented habitats.

Язык: Английский

Процитировано

98
iTaxoTools 0.1: Kickstarting a specimen-based software toolkit for taxonomists DOI Creative Commons
Miguel Vences, Aurélien Miralles,

Sophie Brouillet

и другие.

Megataxa, Год журнала: 2021, Номер 6(2)

Опубликована: Июль 23, 2021

While powerful and user-friendly software suites exist for phylogenetics, an impressive cybertaxomic infrastructure of online species databases has been set up in the past two decades, targeted explicitly at facilitating alpha-taxonomic work, i.e., delimiting diagnosing species, is still its infancy. Here we present a project to develop bioinformatic toolkit taxonomy, based on open-source Python code, including tools focusing delimitation diagnosis centered around specimen identifiers. At core iTaxoTools user-friendliness, with numerous autocorrect options data files intuitive graphical user interfaces. Assembled standalone executables all or suite launcher window will be distributed Windows, Linux, Mac OS systems, future also implemented web server. The initial version (iTaxoTools 0.1) this paper (https://github.com/iTaxoTools/iTaxoTools-Executables) contains interface (GUI) versions six programs (ABGD, ASAP, DELINEATE, GMYC, PTP, tr2) simple threshold-clustering tool. There are new implementations existing algorithms, compute pairwise DNA distances, ultrametric time trees non-parametric rate smoothing, species-diagnostic nucleotide positions, standard morphometric analyses. Other utilities convert among different formats molecular sequences, geographical coordinates, units; merge, split prune sequence files, tables partition files; perform statistical tests. As perspective, envisage become part pipeline next-generation taxonomy that accelerates inventory life while maintaining high-quality hypotheses. open source code binaries available from Github (https://github.com/iTaxoTools) further information website (http://itaxotools.org).

Язык: Английский

Процитировано

98
A Plea for Standardized Nuclear Markers in Metazoan DNA Taxonomy DOI
Jonas Eberle, Dirk Ahrens, Christoph Mayer

и другие.

Trends in Ecology & Evolution, Год журнала: 2020, Номер 35(4), С. 336 - 345

Опубликована: Янв. 15, 2020

Язык: Английский

Процитировано

81