scholarly journals Phylogenomic Analyses Clarify True Species within the Butterfly Genus Speyeria despite Evidence of a Recent Adaptive Radiation

Insects ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 209
Author(s):  
Erin Thompson ◽  
Jason Baumsteiger ◽  
Ryan I. Hill
Keyword(s):  
Adaptive Radiation ◽  
North American ◽  
Incomplete Lineage Sorting ◽  
Legal Protection ◽  
Evolutionary Model ◽  
Morphological Characters ◽  
Anthropogenic Factors ◽  
Lineage Sorting ◽  
The North ◽  
Phylogenetic Resolution

When confronted with an adaptive radiation, considerable evidence is needed to resolve the evolutionary relationships of these closely related lineages. The North American genus Speyeria is one especially challenging radiation of butterflies due to potential signs of incomplete lineage sorting, ongoing hybridization, and similar morphological characters between species. Previous studies have found species to be paraphyletic and have been unable to disentangle taxa, often due to a lack of data and/or incomplete sampling. As a result, Speyeria remains unresolved. To achieve phylogenetic resolution of the genus, we conducted phylogenomic and population genomic analyses of all currently recognized North American Speyeria species, as well as several subspecies, using restriction-site-associated DNA sequencing (RADseq). Together, these analyses confirm the 16 canonical species, and clarify many internal relationships. However, a few relationships within Speyeria were poorly supported depending on the evolutionary model applied. This lack of resolution among certain taxa corroborates Speyeria is experiencing an ongoing adaptive radiation, with incomplete lineage sorting and lack of postzygotic reproductive barriers contributing to hybridization and further ambiguity. Given that many Speyeria taxa are under duress from anthropogenic factors, their legal protection must be viewed cautiously and on a case by case basis in order to properly conserve the diversity being generated.

The North American Allies of Hylobius piceus (De Geer) (Coleoptera: Curculionidae)

1957 ◽  
Vol 89 (1) ◽  
pp. 37-43 ◽  
Author(s):  
Stephen L. Wood
Keyword(s):  
North American ◽  
Distinct Species ◽  
Morphological Characters ◽  
North American Species ◽  
Winged Form ◽  
The North ◽  
The Status ◽  
Field Workers ◽  
Dimorphic Species ◽  
Biological Differences

While investigating the biology of the North American species of Hypomolyx, field workers in Manitoba found a vestigial, or short-winged, and a long-winged form under apparently identical conditions in about equal numbers. Although biological differences were nor then apparent, there was doubt as to whether they were dealing with one dimorphic species or with two distinct species, A search for morphological characters brought to light numerous differences between the two forms, supporting the view that two species were present. These differences, a description the previously unrecognized species, and notes concerning the status of the genera Hylobius and Hypomolyx are reported below.

scholarly journals The choices we make and the impacts they have: Machine learning and species delimitation in North American box turtles (Terrapene spp.)

2020 ◽  
Author(s):  
Bradley T. Martin ◽  
Tyler K. Chafin ◽  
Marlis R. Douglas ◽  
John S. Placyk ◽  
Roger D. Birkhead ◽  
...  
Keyword(s):  
Machine Learning ◽  
North American ◽  
Species Delimitation ◽  
Species Concept ◽  
Incomplete Lineage Sorting ◽  
Signal To Noise Ratio ◽  
Lineage Sorting ◽  
Biogeographic History ◽  
Box Turtles ◽  
A Minor

AbstractModel-based approaches that attempt to delimit species are hampered by computational limitations as well as the unfortunate tendency by users to disregard algorithmic assumptions. Alternatives are clearly needed, and machine-learning (M-L) is attractive in this regard as it functions without the need to explicitly define a species concept. Unfortunately, its performance will vary according to which (of several) bioinformatic parameters are invoked. Herein, we gauge the effectiveness of M-L-based species-delimitation algorithms by parsing 64 variably-filtered versions of a ddRAD-derived SNP dataset involving North American box turtles (Terrapene spp.). Our filtering strategies included: (A) minor allele frequencies (MAF) of 5%, 3%, 1%, and 0% (=none), and (B) maximum missing data per-individual/per-population at 25%, 50%, 75%, and 100% (=none). We found that species-delimitation via unsupervised M-L impacted the signal-to-noise ratio in our data, as well as the discordance among resolved clades. The latter may also reflect biogeographic history, gene flow, incomplete lineage sorting, or combinations thereof (as corroborated from previously observed patterns of differential introgression). Our results substantiate M-L as a viable species-delimitation method, but also demonstrate how commonly observed patterns of phylogenetic discord can seriously impact M-L-classification.

scholarly journals Genomic data reveals potential for hybridization, introgression, and incomplete lineage sorting to confound phylogenetic relationships in an adaptive radiation of narrow-mouth frogs

Evolution ◽  
2016 ◽  
Vol 71 (2) ◽  
pp. 475-488 ◽  
Author(s):  
Alana M. Alexander ◽  
Yong-Chao Su ◽  
Carl H. Oliveros ◽  
Karen V. Olson ◽  
Scott L. Travers ◽  
...  
Keyword(s):  
Adaptive Radiation ◽  
Phylogenetic Relationships ◽  
Incomplete Lineage Sorting ◽  
Genomic Data ◽  
Lineage Sorting

scholarly journals Detailed description and illustration of larva, pupa and imago of Holorusia mikado (Westwood, 1876) (Diptera: Tipulidae) from Japan

2021 ◽  
Vol 9 ◽  
Author(s):  
Levente-Péter Kolcsár ◽  
Takeyuki Nakamura ◽  
Daichi Kato ◽  
Kozo Watanabe
Keyword(s):  
Leaf Litter ◽  
North American ◽  
Morphological Characters ◽  
Wide Distribution ◽  
Female Genitalia ◽  
Immature Stages ◽  
Aquatic Habitats ◽  
Male And Female ◽  
The North ◽  
First Time

Holorusia Loew, 1863 (Diptera: Tipulidae) is a relatively large crane fly genus with a wide distribution in the Afrotropic, Australasian–Oceanian, Eastern Palearctic, Oriental and Nearctic Regions. Although the genus is well known to include the largest crane fly species, the immature stages are, thus far, only described for the larva and pupa of the North American Holorusia hesperea Arnaud & Byers, 1990. In this study, we describe for the first time the egg, larva and pupae of the Japanese Holorusia mikado (Westwood, 1876). Larvae were collected from semi-aquatic habitats, from slow flowing areas of streams and small waterfalls where leaf litter accumulates; the larvae are detritivores and feed on wet, decomposing leaves. The larvae were reared to adults in the laboratory. Morphological characters of immature stages discussed with comparison with the North American H. hespera. Male and female genitalia are illustrated and described in detail for the first time.

scholarly journals Intra- and interpopulation variability of Solidago canadensis L. s. l. in Belarus

2019 ◽  
pp. 67-78
Author(s):  
Valery N. Tikhomirov ◽  
Iryna A. Ravenskaya
Keyword(s):  
North American ◽  
Spontaneous Mutation ◽  
Morphological Characters ◽  
North American Species ◽  
Point Of View ◽  
Solidago Canadensis ◽  
The North ◽  
Ray Florets ◽  
The Republic ◽  
Average Plant

The study of the variability of 22 morphological characters in 5 populations of Solidago canadensis L. s. l., growing in the city of Minsk and its environs, was carried out. Comparison of the obtained data with previously published information on the nature and range of variability of the North American taxa Solidago subsect. Triplinerviae showed that plants growing on the territory of the Republic of Belarus cannot be unambiguously assigned to any of the North American species by the combination of morphological characters. Compared to North American taxa, the plants of the studied populations have a significantly more powerful habitus (a large average plant height, longer and in many populations broader mid stem leaves, most often a larger inflorescence), intermediate in comparison with S. canadensis s. str. and S. altissima s. str. and significantly different from both North American species, the length of involucres and the length of tubular flowers, significantly longer outer phyllaries, shorter straps of ray florets, larger ovaries of ray florets, but their shorter pappus, a significantly smaller number of disc florets. The disc florets have significantly larger teeth compared to S. canadensis s. str. and S. altissima s. str. The data obtained confirm the point of view of Hildemar Scholz, according to which the invasive goldenrod, which is currently widely distributed throughout Europe, are of European origin. Most likely, they are either stabilized hybrids that arose during breeding due to the crossing of several North American species, or arose as a result of spontaneous mutation and further selection under natural conditions.

Molecular systematics and phylogeography of a widespread Neotropical avian lineage: evidence for cryptic speciation with protracted gene flow throughout the Late Quaternary

2020 ◽  
Author(s):  
Leonardo S Miranda ◽  
Bernardo O Prestes ◽  
Alexandre Aleixo
Keyword(s):  
Gene Flow ◽  
Incomplete Lineage Sorting ◽  
Late Quaternary ◽  
Integrative Approach ◽  
Lineage Sorting ◽  
Distribution Models ◽  
The North ◽  
History Of ◽  
Andean South America ◽  
Spatio Temporal

Abstract Here we use an integrative approach, including coalescent-based methods, isolation–migration and species distribution models, to infer population structure, divergence times and diversification in the two species of the genus Cymbilaimus (Aves, Thamnophilidae). Our results support a recent and rapid diversification with both incomplete lineage sorting and gene flow shaping the evolutionary history of Cymbilaimus. The spatio-temporal pattern of cladogenesis suggests that Cymbilaimus originated in the north/western portion of cis-Andean South America and then diversified into the Brazilian Shield and Central America after consolidation of the modern Amazonian drainage and the Andean range. This evolutionary scenario is explained by cycles of range expansion and dispersal, followed by isolation, and recurrent gene flow, during the last 1.2 Myr. Our results agree with those recently reported for other closely related suboscine lineages, whereby the window of introgression between closely related taxa remains open for up to a few million years after their original split. In Cymbilaimus, introgression was recurrent between C. lineatus and C. sanctaemariae, even after they acquired vocal and ecological differentiation, supporting the claim that at least in Neotropical suboscines, full reproductive compatibility may take millions of years to evolve and cannot be interpreted as synonymous with a lack of speciation.

The separation of Carex disticha and Carex sartwellii and the status of Carex disticha in North America

1988 ◽  
Vol 66 (11) ◽  
pp. 2323-2330 ◽  
Author(s):  
P. M. Catling ◽  
A. A. Reznicek ◽  
B. S. Brookes
Keyword(s):  
North American ◽  
Principal Component ◽  
Small Region ◽  
Morphological Characters ◽  
Scatter Diagram ◽  
The North ◽  
The Status ◽  
Beak Length ◽  
The Relationship ◽  
Distinguishing Features

To clarify the relationship between the Eurasian Carex disticha and the North American Carex sartwellii, 38 morphological characters were measured in 30 specimens of each. Various qualitative features were also scored. Through analysis of variance (ANOVA), a reduced number of 10 important continuous characters was obtained and the sample of each taxon was increased to 50. ANOVA of these 10 characters revealed that perigynium length and perigynium beak length were the most important discriminating characters, but in a scatter diagram of these two, 15% of the sample occupied a region of overlap. Principal-component analysis and discriminant analysis using the 10 characters resulted in a separation of the two groups, but a small region of overlap existed in both cases. The two taxa are distinct by virtue of accumulation of small morphological and other differences in a number of characters, rather than by sharp differentiation in a few characters. Carex disticha has larger perigynia with beaks (0.8–)1–1.5(–2.3) mm long, whereas C. sartwellii has smaller perigynia with beaks 0.4–1(–1.2) mm long. All distinguishing features are discussed and a key is provided. Immature vouchers for the occurrence of C. disticha in southwestern Quebec are confirmed on the basis of features of the inflorescence. The only other North American station of C. disticha, discovered in Simcoe Co., Ontario, in 1972 and extant in 1986, is also confirmed in the numerical analyses.

scholarly journals A phylogenomic study of Steganinae fruit flies (Diptera: Drosophilidae): strong gene tree heterogeneity and evidence for monophyly

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Guilherme Rezende Dias ◽  
Eduardo Guimarães Dupim ◽  
Thyago Vanderlinde ◽  
Beatriz Mello ◽  
Antonio Bernardo Carvalho
Keyword(s):  
Gene Annotation ◽  
Incomplete Lineage Sorting ◽  
Branching Processes ◽  
Gene Tree ◽  
Morphological Characters ◽  
Species Tree ◽  
Small Sample ◽  
Gene Trees ◽  
Species Trees ◽  
Lineage Sorting

Abstract Background The Drosophilidae family is traditionally divided into two subfamilies: Drosophilinae and Steganinae. This division is based on morphological characters, and the two subfamilies have been treated as monophyletic in most of the literature, but some molecular phylogenies have suggested Steganinae to be paraphyletic. To test the paraphyletic-Steganinae hypothesis, here, we used genomic sequences of eight Drosophilidae (three Steganinae and five Drosophilinae) and two Ephydridae (outgroup) species and inferred the phylogeny for the group based on a dataset of 1,028 orthologous genes present in all species (> 1,000,000 bp). This dataset includes three genera that broke the monophyly of the subfamilies in previous works. To investigate possible biases introduced by small sample sizes and automatic gene annotation, we used the same methods to infer species trees from a set of 10 manually annotated genes that are commonly used in phylogenetics. Results Most of the 1,028 gene trees depicted Steganinae as paraphyletic with distinct topologies, but the most common topology depicted it as monophyletic (43.7% of the gene trees). Despite the high levels of gene tree heterogeneity observed, species tree inference in ASTRAL, in PhyloNet, and with the concatenation approach strongly supported the monophyly of both subfamilies for the 1,028-gene dataset. However, when using the concatenation approach to infer a species tree from the smaller set of 10 genes, we recovered Steganinae as a paraphyletic group. The pattern of gene tree heterogeneity was asymmetrical and thus could not be explained solely by incomplete lineage sorting (ILS). Conclusions Steganinae was clearly a monophyletic group in the dataset that we analyzed. In addition to ILS, gene tree discordance was possibly the result of introgression, suggesting complex branching processes during the early evolution of Drosophilidae with short speciation intervals and gene flow. Our study highlights the importance of genomic data in elucidating contentious phylogenetic relationships and suggests that phylogenetic inference for drosophilids based on small molecular datasets should be performed cautiously. Finally, we suggest an approach for the correction and cleaning of BUSCO-derived genomic datasets that will be useful to other researchers planning to use this tool for phylogenomic studies.

scholarly journals Population Structure and Mitochondrial Polyphyly in North American Gadwalls (Anas Strepera)

The Auk ◽  
2007 ◽  
Vol 124 (2) ◽  
pp. 444-462 ◽  
Author(s):  
Jeffrey L. Peters ◽  
Kevin E. Omland
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
North America ◽  
North American ◽  
Incomplete Lineage Sorting ◽  
Population Expansion ◽  
Lineage Sorting ◽  
Clade B ◽  
Base Pair Fragment ◽  
Anas Strepera

Abstract We examined population genetic structure in Gadwalls (Anas strepera) to test the prediction that female philopatry and fidelity to migratory flyways have contributed to the partitioning of mitochondrial variation across North America. Sequencing a 658–659 base-pair fragment of the mitochondrial DNA (mtDNA) control region from 348 Gadwalls, we found two distinct clades that were broadly intermixed across both breeding and nonbreeding populations. Clade A was abundant in North America as well as among published sequences from Eurasia. Clade B was sequenced from 5.5% of North American Gadwalls and was more similar to Asian Falcated Duck (A. falcata) haplotypes than to clade A haplotypes. Maximum likelihood indicated that Gadwall clade B haplotypes were a monophyletic group nested within Falcated Duck haplotypes, which suggests mtDNA introgression of clade B into Gadwalls. However, that topology was weakly supported, and we could not reject topologies that were consistent with incomplete lineage-sorting as the cause of mitochondrial polyphyly. Migratory flyways did not contribute significantly to population structure and, in general, we found a lack of genetic structure among most populations. However, Gadwalls sampled in Alaska and Washington were well differentiated from other populations. Coalescent analyses supported a historical population expansion for clade A, and this expansion could have contributed to the high genetic similarity among some populations but the strong differentiation of others. Female-mediated gene flow, along with both historical and contemporary population and range expansions, has likely contributed to the overall weak mtDNA structure in North American Gadwalls. Estructura Poblacional y Polifilia Mitocondrial en Anas strepera

A new species within the Eurytemora affinis complex (Copepoda: Calanoida) from the Atlantic Coast of USA, with observations on eight morphologically different European populations

Zootaxa ◽  
2011 ◽  
Vol 2767 (1) ◽  
pp. 41 ◽  
Author(s):  
VICTOR R. ALEKSEEV ◽  
ANISSA SOUISSI
Keyword(s):  
New Species ◽  
North American ◽  
Atlantic Coast ◽  
River Estuary ◽  
Morphological Characters ◽  
Cylindrical Shape ◽  
Eurytemora Affinis ◽  
Lawrence Estuary ◽  
The North ◽  
Caudal Rami

Eurytemora carolleeae sp. nov. (Crustacea: Copepoda: Calaniformes) is described from the Chesapeake Bay, USA. The new species belongs to the Atlantic clade of the Eurytemora affinis complex outlined by previously published molecular work but poorly characterized morphologically. To discriminate E. carolleeae we compare specimens from the Atlantic USA clade with specimens from the type population of E. affinis (Poppe, 1880) from the Elbe River Estuary (Germany), as well as with eight other European coastal populations. Several important morphological characters clearly separate the North American E. cf. affinis from the European clade that include both sexes: a large outside orientated dent on the mandible, and clearly observable seta segmentation in the caudal rami and swimming legs. Unlike E. affinis, the newly described species possesses wing-like outgrowths on the genital double-somite and a very small spine near the distal seta insertion point in P5 in females. In males, the specific characters include naked dorsal and ventral sides of the caudal rami, and a cylindrical shape of exopod on the left P5, in contrast to a triangular shape of the segment in E. affinis. The new species was also found in Canada (St. Lawrence Estuary) and as an invasive species in the Baltic Sea. Eurytemora carolleeae is possibly widely distributed along the North American Atlantic coast, as well as in inland waters from Great Lakes to Mexico.

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