Integrative taxonomy and geographic sampling underlie successful species delimitation

The Auk ◽  
2021 ◽  
Author(s):  
Carla Cicero ◽  
Nicholas A Mason ◽  
Rosa Alicia Jiménez ◽  
Daniel R Wait ◽  
Cynthia Y Wang-Claypool ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Population Level ◽  
Integrative Taxonomy ◽  
Species Level ◽  
Level Variation ◽  
Multiple Traits ◽  
Guiding Principle ◽  
Environmental Space ◽  
Exciting Time ◽  
Access To Data

Abstract Species delimitation requires a broad assessment of population-level variation using multiple lines of evidence, a process known as integrative taxonomy. More specifically, studies of species limits must address underlying questions of what limits the distribution of populations, how traits vary in association with different environments, and whether the observed trait differences may lead to speciation through reproductive isolation. While genomic data have revolutionized the process of delimiting species, such data should be analyzed along with phenotypic, behavioral, and ecological traits that shape individuals across geographic and environmental space. The integration of multiple traits promotes taxonomic stability and should be a major guiding principle for species delimitation. Equally important, however, is thorough geographic sampling to adequately represent population-level variation—both in allopatry and across putative contact zones. We discuss the importance of both of these factors in the context of species concepts and traits and present different examples from birds that illustrate criteria for species delimitation. In addition, we review a decade of proposals for species-level taxonomic revisions considered by the American Ornithological Society’s North American Classification Committee, and summarize the basis for decisions on whether to split or lump species. Finally, we present recommendations and discuss challenges (specifically permits, time, and funding) for species delimitation studies. This is an exciting time to be studying species delimitation in birds: many species-level questions remain, and methodological advances along with increased access to data enable new approaches to studying age-old problems in avian taxonomy.

scholarly journals Molecular Species Delimitation of Larks (Aves: Alaudidae), and Integrative Taxonomy of the Genus Calandrella, with the Description of a Range-Restricted African Relic Taxon

Diversity ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 428
Author(s):  
Martin Stervander ◽  
Bengt Hansson ◽  
Urban Olsson ◽  
Mark F. Hulme ◽  
Ulf Ottosson ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Molecular Species ◽  
Species Delimitation ◽  
Integrative Taxonomy ◽  
West African ◽  
Northwest Africa ◽  
Sub Saharan ◽  
Plateau State ◽  
Avian Family ◽  
Relic Population

Larks constitute an avian family of exceptional cryptic diversity and striking examples of convergent evolution. Therefore, traditional morphology-based taxonomy has recurrently failed to reflect evolutionary relationships. While taxonomy ideally should integrate morphology, vocalizations, behaviour, ecology, and genetics, this can be challenging for groups that span several continents including areas that are difficult to access. Here, we combine morphometrics and mitochondrial DNA to evaluate the taxonomy of Calandrella larks, with particular focus on the African C. cinerea and the Asian C. acutirostris complexes. We describe a new range-restricted West African taxon, Calandrella cinerea rufipecta ssp. nov. (type locality: Jos, Plateau State, Nigeria), with an isolated relic population 3000 km from its closest relative in the Rift Valley. We performed molecular species delimitation, employing coalescence-based multi-rate Poisson Tree Processes (mPTP) on cytochrome b sequences across 52 currently recognized lark species, including multiple taxa currently treated as subspecies. Three species-level splits were inferred within the genus Calandrella and another 13 across other genera, primarily among fragmented sub-Saharan taxa and taxa distributed from Northwest Africa to Arabia or East Africa. Previously unknown divergences date back as far as to the Miocene, indicating the presence of currently unrecognized species. However, we stress that taxonomic decisions should not be based on single datasets, such as mitochondrial DNA, although analyses of mitochondrial DNA can be a good indicator of taxa in need of further integrative taxonomic assessment.

scholarly journals Identification of medicinal plant Schisandra chinensis using a potential DNA barcode ITS2

2013 ◽  
Vol 82 (4) ◽  
pp. 283-288 ◽  
Author(s):  
Xian-kuan Li ◽  
Bing Wang ◽  
Rong-chun Han ◽  
Yan-chao Zheng ◽  
Hai-bo Yin Yin ◽  
...  
Keyword(s):  
Dna Barcode ◽  
Population Level ◽  
Species Level ◽  
Its2 Region ◽  
Schisandra Chinensis ◽  
Success Rates ◽  
Wild Populations ◽  
Efficient Tool ◽  
Different Populations ◽  
Cultivated Populations

To test whether the internal transcribed spacer 2 (ITS2) region is an effective marker for using in authenticating of the <em>Schisandra chinensis</em> at the species and population levels, separately. And the results showed that the wild populations had higher percentage of individuals that had substitution of C→A at site 86-bp than the cultivated populations. At sites 10-bp, 37-bp, 42-bp and 235-bp, these bases of the <em>Schisandra sphenanthera</em> samples differed from that of <em>S. chinensis</em>. Two species showed higher levels of inter-specific divergence than intra-specific divergence within ITS2 sequences. However, 24 populations did not demonstrate much difference as inter-specific and intra-specific divergences were concerned. Both <em>S. chinensis</em> and <em>S. sphenanthera</em> showed monophyly at species level, yet the samples of different populations shown polyphyly at population level. ITS2 performed well when using BLAST1 method. ITS2 obtained 100% identification success rates at the species level for <em>S. chinensis</em>, with no ambiguous identification at the genus level for ITS2 alone. The ITS2 region could be used to identify <em>S. chinensis</em> and <em>S. sphenanthera</em> in the “Chinese Pharmacopoeia”. And it could also correctly distinguish 100% of species and 100% of genera from the 193 sequences of <em>S. chinensis</em>. Hence, the ITS2 is a powerful and efficient tool for species identification of <em>S. chinensis</em>.

scholarly journals Colouration, chaetotaxy and molecular data provide species-level resolution in a species complex of Dicranocentrus (Collembola : Entomobryidae)

2018 ◽  
Vol 32 (6) ◽  
pp. 1298 ◽  
Author(s):  
Feng Zhang ◽  
Daoyuan Yu ◽  
Mark I. Stevens ◽  
Yinhuan Ding
Keyword(s):  
Species Complex ◽  
Instar Larva ◽  
Molecular Data ◽  
Integrative Taxonomy ◽  
Species Level ◽  
Integrative Approach ◽  
Gene Markers ◽  
Late Neogene ◽  
Taxonomic Approach ◽  
Colour Patterns

Integrative taxonomic approaches are increasingly providing species-level resolution to ‘cryptic’ diversity. In the absence of an integrative taxonomic approach, formal species validation is often lacking because of inadequate morphological diagnoses. Colouration and chaetotaxy are the most commonly used characters in collembolan taxonomy but can cause confusion in species diagnoses because these characters often have large intraspecific variation. Here, we take an integrative approach to the genus Dicranocentrus in China where four species have been previously recognised, but several members of the genus have been morphologically grouped as a species complex based on having paired outer teeth on unguis and seven colour patterns. Molecular delimitations based on distance- and evolutionary models recovered four candidate lineages from three gene markers and revealed that speciation events likely occurred during the late Neogene (4–13million years ago). Comparison of intact dorsal chaetotaxy, whose homologies were erected on the basis of first instar larva, further validated these candidates as formal species: D. gaoligongensis, sp. nov., D. similis, sp. nov., D. pallidus, sp. nov. and D. varicolor, sp. nov., and increase the number of Dicranocentrus species from China to eight. Our study further highlights the importance of adequate taxonomy in linking morphological and molecular characters within integrative taxonomy.

scholarly journals Does segregating variation in sexual or microhabitat preferences lead to non-random mating within a population of Drosophila melanogaster ?

2009 ◽  
Vol 6 (1) ◽  
pp. 102-105 ◽  
Author(s):  
Brad R. Foley ◽  
Anne Genissel ◽  
Harmon L. Kristy ◽  
Sergey V. Nuzhdin
Keyword(s):  
Recombinant Inbred Lines ◽  
Random Mating ◽  
Population Level ◽  
Inbred Lines ◽  
Male Mating ◽  
Complex Environment ◽  
Level Variation ◽  
Group Preference ◽  
Female Genotype ◽  
Microhabitat Preferences

Variation in female choice for mates has implications for the maintenance of genetic variation and the evolution of male traits. Yet, estimates of population-level variation in male mating success owing to female genotype are rare. Here, we used a panel of recombinant inbred lines to estimate the strength of selection at many genetic loci in a single generation and attempt to assess differences between females with respect to the males they mated with. We performed selection assays in a complex environment to allow differences in habitat or social group preference to be expressed. We detected directional selection at loci across the genome, but are unable to provide support for differential male success because of variation in female genotype.

scholarly journals Transcribed enhancers in the human brain identify novel disease risk mechanisms

2021 ◽  
Author(s):  
Pengfei Dong ◽  
Gabriel E. Hoffman ◽  
Pasha Apontes ◽  
Jaroslav Bendl ◽  
Samir Rahman ◽  
...  
Keyword(s):  
Human Brain ◽  
Disease Risk ◽  
Association Studies ◽  
Population Level ◽  
Cell Type ◽  
Level Variation ◽  
Functional Interpretation ◽  
Neuropsychiatric Diseases ◽  
Order Of Magnitude ◽  
Cell Type Specific

Enhancer RNAs (eRNAs) constitute an important tissue- and cell-type-specific layer of the regulome. Identification of risk variants for neuropsychiatric diseases within enhancers underscores the importance of understanding the population-level variation of eRNAs in the human brain. We jointly analyzed cell type-specific transcriptome and regulome data to identify 30,795 neuronal and 23,265 non-neuronal eRNAs, expanding the catalog of known human brain eRNAs by an order of magnitude. Examination of the population-level variation of the transcriptome and regulome in 1,382 brain samples identified reproducible changes affecting cis- and trans-co-regulation of eRNA-gene modules in schizophrenia. We show that 13% of schizophrenia heritability is jointly mediated in cis by brain gene and eRNA expression. Inclusion of eRNAs in transcriptome-wide association studies facilitated fine-mapping and functional interpretation of disease loci. Overall, our study characterizes the eRNA-gene regulome and genetic mechanisms in the human cortex in both healthy and disease states.

Species delimitation in the Lepraria isidiata-L. santosii group: a population study in the Mediterranean-Macaronesian region

2009 ◽  
Vol 41 (1) ◽  
pp. 1-15 ◽  
Author(s):  
Mauro Tretiach ◽  
Lucia Muggia ◽  
Laurence Baruffo
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Variability ◽  
Species Delimitation ◽  
Carbonate Rocks ◽  
Morphological Study ◽  
Species Level ◽  
Siliceous Rocks ◽  
Group A ◽  
The Mediterranean ◽  
Mineral Soils

AbstractA thorough chemical, molecular and morphological study has been carried out on a problematic group in the genus Lepraria characterized by lobed, granular thalli with a raised rim and a preference for mosses, rocks and mineral soils in exposed, xeric habitats. The material examined was collected in seven countries of the Mediterranean-Macaronesian region, from chalk, carbonate rocks and derived soils (A-thalli), and from siliceous rocks and derived soils (B-thalli). The results of a phylogenetic analysis based on 93 ITS sequences (29 of which newly obtained) support the identification and the segregation of two taxa at species level, provisionally identified as Lepraria isidiata s. lat., (most of the A-thalli), and L. santosii s. lat. (B-thalli plus the remaining A-thalli), as the observed genetic variability is quite high. Three chemotypes were detected in L. isidiata s. lat., and seven in L. santosii s. lat. The two taxa are morphologically well characterized: in L. isidiata s. lat. the thallus is thicker and the propagules larger than in L. santosii s. lat. The first stages of thallus development from single propagules are described in both species. Some critical remarks are made about the increasing use of the species rank for taxa of Lepraria, which are morphologically and genetically scarcely characterized.

scholarly journals Species level variation in coccolithophores

2004 ◽  
pp. 327-366 ◽  
Author(s):  
Markus Geisen ◽  
Jeremy R. Young ◽  
Ian Probert ◽  
Alberto G. Sáez ◽  
Karl-Heinz Baumann ◽  
...  
Keyword(s):  
Species Level ◽  
Level Variation

scholarly journals The dynamics of trait variance in multi-species communities

2020 ◽  
Vol 7 (8) ◽  
pp. 200321
Author(s):  
Jan Martin Nordbotten ◽  
Folmer Bokma ◽  
Jo Skeie Hermansen ◽  
Nils Chr. Stenseth
Keyword(s):  
Differential Equations ◽  
Blow Up ◽  
Adaptive Dynamics ◽  
Population Level ◽  
Species Level ◽  
Density Distributions ◽  
Formal Stability ◽  
Speciation Event ◽  
Trait Variance ◽  
Level Model

In this paper, we establish the explicit connection between deterministic trait-based population-level models (in the form of partial differential equations) and species-level models (in the form of ordinary differential equations), in the context of eco-evolutionary systems. In particular, by starting from a population-level model of density distributions in trait space, we derive what amounts to an extension of the typical models at the species level known from adaptive dynamics literature, to account not only for abundance and mean trait values, but also explicitly for trait variances. Thus, we arrive at an explicitly polymorphic model at the species level. The derivations make precise the relationship between the parameters in the two classes of models and allow us to distinguish between notions of fitness on the population and species levels. Through a formal stability analysis, we see that exponential growth of an eigenvalue in the trait covariance matrix corresponds to a breakdown of the underlying assumptions of the species-level model. In biological terms, this may be interpreted as a speciation event: that is, we obtain an explicit notion of the blow-up of the variance of (possibly a linear combination of) traits as a precursor to speciation. Moreover, since evolutionary volatility of the mean trait value is proportional to trait variance, this provides a notion that species at the cusp of speciation are also the most adaptive. We illustrate these concepts and considerations using a numerical simulation.

Detecting density dependence from spatial patterns in a heterogeneous subtropical forest of central China

2015 ◽  
Vol 45 (6) ◽  
pp. 710-720 ◽  
Author(s):  
Yili Guo ◽  
Zhijun Lu ◽  
Qinggang Wang ◽  
Junmeng Lu ◽  
Yaozhan Xu ◽  
...  
Keyword(s):  
Population Structure ◽  
Density Dependence ◽  
Habitat Heterogeneity ◽  
Species Traits ◽  
Subtropical Forest ◽  
Species Level ◽  
Central China ◽  
Life Stages ◽  
Natural Forests ◽  
Level Variation

Accumulating evidence suggests that density dependence, whether at early or late life stages, is an important mechanism regulating plant population structure. However, the opposing effects of habitat heterogeneity and species-level variation might have confounded the prevalence of density dependence in natural forests. These compatible ideas were rarely considered simultaneously. In this study, we applied a spatial statistical technique to examine (i) the prevalence of density dependence at late life stages after controlling for habitat heterogeneity and (ii) the relationships between species traits and the strength of density dependence in a newly established, 25 ha subtropical mountain forest plot in central China. Of the 88 (75%) tree species analyzed, 66 were found to exhibit density dependence predominantly at very close distances among neighbors in the species-rich subtropical forest. In addition, the strength of density dependence was associated with species traits. Our findings identified strong density dependence among trees that had greater stature and were rarer. We concluded that density dependence was a prevalent mechanism for regulating the population structure of most tree species and both habitat heterogeneity and species-level variation played crucial roles in shaping the strength of density dependence in natural forests.

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