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

2021 ◽  
Vol 9 ◽  
Author(s):  
Adam D. Leaché ◽  
Hayden R. Davis ◽  
Sonal Singhal ◽  
Matthew K. Fujita ◽  
Megan E. Lahti ◽  
...  
Keyword(s):  
New Species ◽  
Genetic Divergence ◽  
Species Delimitation ◽  
Life Histories ◽  
Species Complex ◽  
Small Population ◽  
Morphological Data ◽  
Lizard Species ◽  
Horned Lizards ◽  
Close Relatives

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

scholarly journals Species delimitation in the Stenocereus griseus (Cactaceae) species complex reveals a new species, S. huastecorum

PLoS ONE ◽  
2018 ◽  
Vol 13 (1) ◽  
pp. e0190385 ◽  
Author(s):  
Hernán Alvarado-Sizzo ◽  
Alejandro Casas ◽  
Fabiola Parra ◽  
Hilda Julieta Arreola-Nava ◽  
Teresa Terrazas ◽  
...  
Keyword(s):  
New Species ◽  
Species Delimitation ◽  
Species Complex ◽  
A New Species

Taxonomic revision of the Square-tailed Drongo species complex (Passeriformes: Dicruridae) with description of a new species from western Africa

Zootaxa ◽  
2018 ◽  
Vol 4438 (1) ◽  
pp. 105 ◽  
Author(s):  
JÉRÔME FUCHS ◽  
MORY DOUNO ◽  
RAURI C.K. BOWIE ◽  
JON FJELDSÅ
Keyword(s):  
New Species ◽  
Genetic Divergence ◽  
Species Complex ◽  
Morphological Character ◽  
Taxonomic Revision ◽  
Genetic Data ◽  
Sister Species ◽  
Western Africa ◽  
Gallery Forests ◽  
A New Species

We describe a new species of drongo in the Square-tailed Drongo (Dicrurus ludwigii) complex using a combination of biometric and genetic data. The new species differs from previously described taxa in the Square-tailed Drongo complex by possessing a significantly heavier bill and via substantial genetic divergence (6.7%) from its sister-species D. sharpei. The new species is distributed across the gallery forests of coastal Guinea, extending to the Niger and Benue Rivers of Nigeria. We suspect that this taxon was overlooked by previous avian systematists because they either lacked comparative material from western Africa or because the key diagnostic morphological character (bill characteristics) was not measured. We provide an updated taxonomy of the Square-tailed Drongo species complex. 

scholarly journals Establishment of six new Rhabdoblatta species (Blattodea, Blaberidae, Epilamprinae) from China

ZooKeys ◽  
2019 ◽  
Vol 851 ◽  
pp. 27-69
Author(s):  
Rong Yang ◽  
Zhenzhen Wang ◽  
Yanshuang Zhou ◽  
Zongqing Wang ◽  
Yanli Che
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Molecular Species ◽  
Species Delimitation ◽  
Female Genitalia ◽  
Morphological Data ◽  
Coi Sequences ◽  
First Time

This study examined 504 Rhabdoblatta specimens sampled from China, of which, 86 Rhabdoblatta specimens were used for COI sequencing. A phylogenetic analysis using the ML method and MOTUs estimations by ABGD and GMYC based on COI sequences was performed. Eighteen Rhabdoblatta species were identified when these data were combined with morphological data. Six new species were established among these samples, i.e., Rh.similsinuatasp. n., Rh.densimaculatasp. n., Rh.gyroflexasp. n., Rh.chaulformissp. n., Rh.maculatasp. n., and Rh.ecarinatasp. n. For the first time, females including female genitalia of 14 known Rhabdoblatta species are described worldwide. Our study shows that combining molecular species delimitation methods with morphological data helps to delimit species and understand cockroach biodiversity.

scholarly journals Ottelia fengshanensis, a new bisexual species of Ottelia (Hydrocharitaceae) from southwestern China

PhytoKeys ◽  
2019 ◽  
Vol 135 ◽  
pp. 1-10
Author(s):  
Zhi-Zhong Li ◽  
Shuang Wu ◽  
Chun-Yu Zhou ◽  
Yan Liu ◽  
Guang-Wan Hu ◽  
...  
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Species Delimitation ◽  
Southwest China ◽  
Morphological Features ◽  
Bisexual Species ◽  
Molecular Phylogenetic ◽  
Dark Green ◽  
Close Relatives ◽  
A New Species

Ottelia fengshanensis, a new species (Hydrocharitaceae) from southwest China is here described and illustrated. Comparing its morphological features to putative close relatives O. guanyangensis, it has 3–4 flowers (vs. 2–5) each spathe, hexagonal-cylindric fruit, white styles (vs. yellow), green leaves (vs. dark green) and fruit tiny winged (vs. winged obviously). Molecular phylogenetic investigation of four DNA sequences (ITS, rbcL, trnK5’ intron and trnS-trnG) and the Poisson Tree Processes model for species delimitation (PTP) analysis, further resolves O. fengshanensis as a new species that is close to O. guanyangensis with distinct support.

Discovery of a new species of Anolis lizards from Brazil and its implications for the historical biogeography of montane Atlantic Forest endemics

2020 ◽  
Vol 41 (1) ◽  
pp. 87-103 ◽  
Author(s):  
Ivan Prates ◽  
Paulo Roberto Melo-Sampaio ◽  
Kevin de Queiroz ◽  
Ana Carolina Carnaval ◽  
Miguel Trefaut Rodrigues ◽  
...  
Keyword(s):  
New Species ◽  
Atlantic Forest ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Time Estimation ◽  
Molecular Data ◽  
Morphological Data ◽  
Lizard Species ◽  
Divergence Time Estimation ◽  
The City

Abstract Recent biological discoveries have changed our understanding of the distribution and evolution of neotropical biotas. In the Brazilian Atlantic Forest, the discovery of closely related species isolated on distant mountains has led to the hypothesis that the ancestors of montane species occupied and dispersed through lowland regions during colder periods. This process may explain the distribution of an undescribed Anolis lizard species that we recently discovered at a montane site in the Serra dos Órgãos National Park, a popular tourist destination close to the city of Rio de Janeiro. To investigate whether this species is closely related to other Atlantic Forest montane anoles, we implement phylogenetic analyses and divergence time estimation based on molecular data. We infer the new species nested within the Dactyloa clade of Anolis, forming a clade with A. nasofrontalis and A. pseudotigrinus, two species restricted to montane sites about 400 km northeast of Serra dos Órgãos. The new species diverged from its sister A. nasofrontalis around 5.24 mya, suggesting a cold-adapted lowland ancestor during the early Pliocene. Based on the phylogenetic results, we emend the definitions of the series taxa within Dactyloa, recognizing a clade containing the new species and several of its relatives as the nasofrontalis series. Lastly, we provide morphological data supporting the recognition of the new species and give it a formal scientific name. Future studies are necessary to assess how park visitors, pollutants, and shrinking montane habitats due to climate change will affect this previously overlooked anole species.

Two new species of the genus Crangonyx Bate, 1859 (Amphipoda: Crangonyctidae) from the St. Marks River Basin with notes on the “Crangonyx floridanus complex”

Zootaxa ◽  
2019 ◽  
Vol 4691 (4) ◽  
pp. 301-332 ◽  
Author(s):  
ANDREW G. CANNIZZARO ◽  
THOMAS R. SAWICKI
Keyword(s):  
New Species ◽  
Related Species ◽  
Species Delimitation ◽  
Species Complex ◽  
Morphological Characteristics ◽  
Molecular Data ◽  
Closely Related Species ◽  
Leon County ◽  
Two New Species ◽  
Morphological And Molecular Data

Crangonyx ephemerus n. sp. and Crangonyx pseudoephemerus n. sp. are described from the headwaters of the St. Marks River in Leon County, Florida, based on detailed morphological and molecular comparisons with the closely related species Crangonyx floridanus Bousfield, 1963. The morphological and molecular data, including three species delimitation models, lend support to the hypothesis that the taxon C. floridanus sensu lato represents a species complex. Diagnostic morphological characteristics are highlighted and discussed within this group to assist in future morphological analyses. 

Revision of the subgenus Phortica (sensu stricto) (Diptera, Drosophilidae) from East Asia, with assessment of species delimitation using DNA barcodes

Zootaxa ◽  
2019 ◽  
Vol 4678 (1) ◽  
pp. 1-75
Author(s):  
JIA HUANG ◽  
LU GONG ◽  
SHUN-CHERN TSAUR ◽  
LIN ZHU ◽  
KEYING AN ◽  
...  
Keyword(s):  
New Species ◽  
Cytochrome C Oxidase ◽  
Species Delimitation ◽  
Species Complex ◽  
Dna Barcode ◽  
Sensu Stricto ◽  
Coi Gene ◽  
Mitochondrial Cytochrome ◽  
Dna Barcodes ◽  
New Synonyms

A total of 50 (43 known and seven new) species in the subgenus Phortica (sensu stricto) were surveyed and (re)described from China: P. bicornuta (Chen & Toda, 1997); P. bipartita (Toda & Peng, 1992); P. biprotrusa (Chen & Toda, 1998); P. cardua (Okada, 1977); P. chi (Toda & Sidorenko, 1996); P. conifera (Okada, 1977); P. eparmata (Okada, 1977); P. eugamma (Toda & Peng, 1990); P. excrescentiosa (Toda & Peng, 1990); P. fangae (Máca, 1993); P. flexuosa (Zhang & Gan, 1986); P. foliata (Chen & Toda, 1997); P. gamma (Toda & Peng, 1990); P. gigas (Okada, 1977); P. glabtabula Chen & Gao, 2005; P. hainanensis (Chen & Toda, 1998); P. hongae (Máca, 1993); P. huazhii Cheng & Chen, 2008; P. iota (Toda & Sidorenko, 1996); P. jadete Zhu, Cao & Chen, 2018; P. kappa (Máca, 1977); P. lambda (Toda & Peng, 1990); P. latifoliacea Chen & Watabe, 2008; P. magna (Okada, 1960); P. okadai (Máca, 1977); P. omega (Okada, 1977); P. orientalis (Hendel, 1914); P. pangi Chen & Wen, 2005; P. paramagna (Okada, 1971); P. perforcipata (Máca & Lin, 1993); P. pi (Toda & Peng, 1990); P. protrusa (Zhang & Shi, 1997); P. pseudopi (Toda & Peng, 1990); P. pseudotau (Toda & Peng, 1990); P. psi (Zhang & Gan, 1986); P. rhagolobos Chen & Gao, 2008; P. saeta (Zhang & Gan, 1986); P. setitabula Chen & Gao, 2005; P. subradiata (Okada, 1977); P. tau (Toda & Peng, 1990); P. uncinata Chen & Gao, 2005; P. unipetala Chen & Wen, 2005; P. allomega Gong & Chen, sp. nov.; P. archikappa Gong & Chen, sp. nov.; P. dianzangensis Gong & Chen, sp. nov.; P. imbacilia Gong & Chen, sp. nov.; P. liukuni Gong & Chen, sp. nov.; P. tibeta Gong & Chen, sp. nov.; and P. xianfui Gong & Chen, sp. nov. In addition, seven new synonyms were recognized: P. acongruens (Zhang & Shi, 1997), syn. nov.; P. antillaria (Chen & Toda, 1997), syn. nov.; P. kukuanensis Máca, 2003, syn. nov.; P. linae (Máca & Chen, 1993), syn. nov.; P. shillongensis (Singh & Gupta, 1979), syn. nov.; P. takadai (Okada, 1977), syn. nov.; and P. watanabei (Máca & Lin, 1993), syn. nov. A key to all Asian species (except for the eparmata species complex) of this subgenus was provided. All currently available DNA barcode (partial mitochondrial cytochrome c oxidase subunit I (COI) gene) sequences of this subgenus (217 sequences of 54 species) are employed in a molecular analysis using different species delimitation methods. The results indicate that approximately 68.5% (37 of 54 spp.) of Phortica (s. str.) species could be clearly distinguished from closely related morphospecies or cryptic species. 

scholarly journals Ceratozamia aurantiaca (Zamiaceae): A New Cycad Species from the Northern Rainforests of Oaxaca, Mexico

Taxonomy ◽  
2021 ◽  
Vol 1 (3) ◽  
pp. 243-255
Author(s):  
Miguel Angel Pérez-Farrera ◽  
José Said Gutiérrez-Ortega ◽  
Jody L. Haynes ◽  
Jeff Chemnick ◽  
Silvia H. Salas-Morales ◽  
...  
Keyword(s):  
New Species ◽  
Species Delimitation ◽  
Species Complex ◽  
Tropical Rainforests ◽  
Orange Color

Ceratozamia aurantiaca, a new cycad species from Oaxaca, Mexico, is described. The new species is endemic to lowland karst tropical rainforests of the northern mountains (Sierra Norte region). This species is related to C. subroseophylla and C. robusta, together considered part of the C. robusta species complex due to their shared characteristics: robust, upright trunk; large and long leaves with densely armed petioles and linear to subfalcate leaflets; and large megastrobili. Ceratozamia aurantiaca, as the epithet suggests, is easily distinguished from other species by the orange color of its emerging leaves, a trait unique in the genus. Additionally, C. aurantiaca is distinguished from C. subroseophylla and C. robusta by having significantly shorter petioles, wider spacing between leaflets, and wider median leaflets. The taxonomic recognition of this species represents a step toward clarifying species delimitation in the C. robusta complex.

scholarly journals A revision of the Triodia basedowii species complex and close relatives (Poaceae: Chloridoideae)

2017 ◽  
Vol 30 (3) ◽  
pp. 197 ◽  
Author(s):  
Benjamin M. Anderson ◽  
Kevin R. Thiele ◽  
Matthew D. Barrett
Keyword(s):  
New Species ◽  
Western Australia ◽  
Related Species ◽  
Species Complex ◽  
Perennial Grasses ◽  
Key To Species ◽  
Molecular Studies ◽  
Close Relatives ◽  
Current Species ◽  
Species Taxonomy

Perennial grasses commonly known as ‘spinifex’ (Triodia R.Br.) are iconic Australian plants, predominantly found in the arid interior of the continent. In some areas, such as the economically important Pilbara region of Western Australia, current species taxonomy does not account for observed diversity. Previous morphological and molecular studies of Triodia basedowii E.Pritz. and related species have revealed multiple unnamed lineages requiring taxonomic recognition. Here, we describe and name eight new species of Triodia, including T. birriliburu B.M.Anderson, T. chichesterensis B.M.Anderson, T. glabra B.M.Anderson & M.D.Barrett, T. infesta B.M.Anderson & M.D.Barrett, T. mallota B.M.Anderson & M.D.Barrett, T. nana B.M.Anderson, T. scintillans B.M.Anderson & M.D.Barrett, and T. vanleeuwenii B.M.Anderson & M.D.Barrett. We also provide recircumscriptions and revised descriptions for T. basedowii, T. lanigera Domin, T. concinna N.T.Burb. and T. plurinervata N.T.Burb. A key to species and photographs are included.

Three morphologically and genetically confirmed new Pleurota species from Morocco (Lepidoptera: Gelechioidea: Oecophoridae: Pleurotinae)

Zootaxa ◽  
2019 ◽  
Vol 4624 (3) ◽  
pp. 442-450
Author(s):  
JUKKA TABELL ◽  
MARKO MUTANEN ◽  
PASI SIHVONEN
Keyword(s):  
New Species ◽  
Life Histories ◽  
Species Complex ◽  
Index Number ◽  
Wing Pattern ◽  
Dna Barcodes ◽  
Adult Males ◽  
Males And Females

Three new Pleurota species (Oecophoridae: Pleurotinae) from Morocco, which form a species complex, are described: P. variocolor Tabell, sp. nov., P. azrouensis Tabell, sp. nov., and P. ternaria Tabell, sp. nov. Species are diagnosable by wing pattern and they have distinct genetic divergences in DNA barcodes, while genitalia structures are uniform and less informative. DNA barcodes of the new species are compared with those of all other Pleurotinae available in BOLD database. Each of the newly described species has a unique BIN (Barcode Index Number). Adult males and females, and their genitalia, are illustrated. Life histories of new species are unknown, but two of those were collected during daytime. 

Sign in / Sign up

Export Citation Format

Share Document