scholarly journals Cryptic diversity among Yazoo Darters (Percidae: Etheostoma raneyi) in disjunct watersheds of northern Mississippi

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9014
Author(s):  
Ken A. Sterling ◽  
Stuart V. Nielsen ◽  
Andrew J. Brown ◽  
Melvin L. Warren, Jr. ◽  
Brice P. Noonan
Keyword(s):  
Phylogenetic Analyses ◽  
Relevant Literature ◽  
Suitable Habitat ◽  
Cryptic Diversity ◽  
Glacial Cycles ◽  
River Drainage ◽  
Yazoo River Basin ◽  
River Drainages ◽  
Two Populations ◽  
High Support

The Yazoo Darter, Etheostoma raneyi (Percidae), is an imperiled freshwater fish species endemic to tributaries of the Yocona and Little Tallahatchie rivers of the upper Yazoo River basin, in northern Mississippi, USA. The two populations are allopatric, isolated by unsuitable lowland habitat between the two river drainages. Relevant literature suggests that populations in the Yocona River represent an undescribed species, but a lack of data prevents a thorough evaluation of possible diversity throughout the range of the species. Our goals were to estimate phylogenetic relationships of the Yazoo Darter across its distribution and identify cryptic diversity for conservation management purposes. Maximum likelihood (ML) phylogenetic analyses of the mitochondrial cytochrome b (cytb) gene returned two reciprocally monophyletic clades representing the two river drainages with high support. Bayesian analysis of cytb was consistent with the ML analysis but with low support for the Yocona River clade. Analyses of the nuclear S7 gene yielded unresolved relationships among individuals in the Little Tallahatchie River drainage with mostly low support, but returned a monophyletic clade for individuals from the Yocona River drainage with high support. No haplotypes were shared between the drainages for either gene. Additional cryptic diversity within the two drainages was not indicated. Estimated divergence between Yazoo Darters in the two drainages occurred during the Pleistocene (<1 million years ago) and was likely linked to repeated spatial shifts in suitable habitat and changes in watershed configurations during glacial cycles. Individuals from the Yocona River drainage had lower genetic diversity consistent with the literature. Our results indicate that Yazoo Darters in the Yocona River drainage are genetically distinct and that there is support for recognizing Yazoo Darter populations in the Yocona River drainage as a new species under the unified species concept.

Genetic diversity and species delimitation in Rhamdia (Siluriformes: Heptapteridae) in South America, with a redescription of R. quelen (Quoy & Gaimard, 1824)

Zootaxa ◽  
2020 ◽  
Vol 4801 (1) ◽  
pp. 85-104
Author(s):  
RAFAEL COSTA ANGRIZANI ◽  
LUIZ ROBERTO MALABARBA
Keyword(s):  
Species Delimitation ◽  
Species Complex ◽  
Phylogenetic Analyses ◽  
Gene Tree ◽  
The Andes ◽  
In Cis ◽  
River Drainages ◽  
High Support ◽  
Large Distribution ◽  
Eleven Species

More than 100 species have been referred to Rhamdia since its description, but in the last revision of the genus more than two decades ago, only eleven species have been considered as valid. Rhamdia quelen was then redefined to include 47 junior synonyms, resulting in a species with a large distribution in the Neotropics, from Mexico to Argentina. Populations of Rhamdia from west of the Andes have been recently removed from the synonymy of R. quelen, and currently there are 27 species recognized in the genus. Most cis-Andean populations, however, remain referred to the R. quelen species complex. In this paper, we use species delimitation methods and multilocus phylogenetic analyses to delimit the species contained in the R. quelen species complex in cis-Andean river drainages. Eighteen MOTUs in the gene tree were recovered with high support. We further demonstrate that the previous designation of a neotype for R. quelen is invalid, and has to be replaced by the proper designation of a neotype from the type locality of the species. The neotype is designated herein and R. quelen is diagnosed and redescribed. 

scholarly journals Densely sampled phylogenetic analyses of the Lesser Short‐toed Lark ( Alaudala rufescens ) — Sand Lark ( A. raytal ) species complex (Aves, Passeriformes) reveal cryptic diversity

2020 ◽  
Vol 49 (4) ◽  
pp. 427-439 ◽  
Author(s):  
Fatemeh Ghorbani ◽  
Mansour Aliabadian ◽  
Ruiying Zhang ◽  
Martin Irestedt ◽  
Yan Hao ◽  
...  
Keyword(s):  
Species Complex ◽  
Phylogenetic Analyses ◽  
Cryptic Diversity

Molecular identification of cyst-forming nematodes (Heteroderidae) from Iran and a phylogeny based on ITS-rDNA sequences

Nematology ◽  
2003 ◽  
Vol 5 (1) ◽  
pp. 99-111 ◽  
Author(s):  
Zahra Tanha Maafi ◽  
Sergei Subbotin ◽  
Maurice Moens
Keyword(s):  
Phylogenetic Analyses ◽  
Species Level ◽  
Its Rdna ◽  
Heterodera Avenae ◽  
Published Data ◽  
Rdna Sequences ◽  
First Time ◽  
Group Species ◽  
High Support ◽  
Different Parts

Abstract RFLP and sequences of ITS-rDNA of 45 populations of cyst-forming nematodes collected from different parts of Iran were analysed and identified as representatives of 21 species. Eight enzymes generated RFLP for all studied populations. Comparison of RFLP profiles and sequences of the ITS regions with published data confirmed the presence of Heterodera avenae, H. filipjevi, H. glycines, H. hordecalis, H. latipons, H. schachtii and H. trifolii in Iran. RFLP patterns and ITS sequences for H. elachista, H. turcomanica, H. mothi and C. cacti were obtained for the first time in this study. Heterodera humuli, H. goettingiana, H. fici, H. elachista, H. turcomanica and Cactodera cacti are recorded for the first time in Iran. These results correspond with morphological and morphometric identification of the populations. Several populations were not identified at the species level and are attributed to Heterodera sp.; some of these may correspond to new species. Twenty-one new sequences from Iranian cyst-forming nematodes and 36 known sequences were used for the phylogenetic analyses. The cyst-forming nematodes formed several clades corresponding to their morphological features. Heterodera mothi and H. elachista clustered with high support with other Cyperi group species and H. turcomanica formed a moderately to highly supported clade with the Humuli group.

Molecular and morphological characterisation of Cryptaphelenchus baujardi n. sp. (Nematoda: Ektaphelenchinae), a new species based on two populations from Iran

Nematology ◽  
2019 ◽  
Vol 21 (1) ◽  
pp. 45-56 ◽  
Author(s):  
Farzad Aliramaji ◽  
Esmaeil Miraeiz ◽  
Ebrahim Pourjam ◽  
Ramin Heydari
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Lsu Rdna ◽  
New Taxon ◽  
Male Body ◽  
Northern Iran ◽  
Lateral Field ◽  
Rdna Sequences ◽  
Strong Resemblance ◽  
Two Populations

Summary Cryptaphelenchus baujardi n. sp. is described and illustrated based on two populations from Golestan province, northern Iran. The new species is characterised by female and male body length of 224 (190-261) and 215 (195-229) μm, respectively, offset cephalic region with a shallow constriction, delicate stylet 6.6 (6.0-7.0) μm long, four incisures in the lateral field, presence of a rudimentary post-uterine sac in the female gonoduct, elongate-conoid female tail ending in an acute to finely rounded terminus, male tail conical, male with seven caudal papillae and delicate spicules. The new species shows a strong resemblance to C. varicaudatus and C. iranicus, but has a sclerotised mass near the tip of the spicule and an indistinct spermatheca. Phylogenetic analyses based on both partial SSU and LSU rDNA sequences confirm its status as a new taxon.

The enigmatic groundwater amphipod Awacaris kawasawai revisited: synonymisation of the genus Sternomoera, with molecular phylogenetic analyses of Awacaris and Sternomoera species (Crustacea : Amphipoda : Pontogeneiidae)

2017 ◽  
Vol 31 (2) ◽  
pp. 125 ◽  
Author(s):  
Ko Tomikawa ◽  
Masaki Kyono ◽  
Keiko Kuribayashi ◽  
Takafumi Nakano
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
28S Rrna ◽  
Ancestral State ◽  
Cryptic Diversity ◽  
Japanese Archipelago ◽  
Molecular Phylogenetic ◽  
The Japanese Archipelago ◽  
Kochi Prefecture

Amphipod crustaceans are dominant in subterranean habitats, and members of eight genera are endemic to groundwater environments in the Japanese Archipelago. The taxonomic status of two of these genera remains unclear, because their original descriptions were incomplete. The descriptions of the enigmatic subterranean monotypic genus Awacaris and its type species, A. kawasawai Uéno, 1971, are revisited here. Awacaris kawasawai was originally described based on specimens from a subterranean stream at Himise Cave, Tokushima Prefecture, Shikoku, Japan. Recently, a new population of A. kawasawai was found at Saruta Cave, Kochi Prefecture, Shikoku. Detailed observation of the newly collected specimens reveals the presence of sternal gills, which is the diagnostic character of the pontogeneiid genus Sternomoera, making the validity of Sternomoera open to question. Phylogenetic analyses using nuclear 28S rRNA and mitochondrial cytochrome c oxidase subunit I markers demonstrate that A. kawasawai forms a well-supported clade with the subterranean S. morinoi Tomikawa and Ishimaru, 2014. In addition, phylogenetic analysis reveals cryptic diversity in epigean species of Sternomoera. Ancestral state reconstruction suggests that catadromous Sternomoera species have evolved from freshwater ancestors. Based on our morphological and phylogenetic analysis of Awacaris and Sternomoera species, it is concluded here that Sternomoera should be treated as a subjective junior synonym of Awacaris.

scholarly journals Phylogeography of the widespread white-eared hummingbird (Hylocharis leucotis): pre-glacial expansion and genetic differentiation of populations separated by the Isthmus of Tehuantepec

2020 ◽  
Vol 130 (2) ◽  
pp. 247-267
Author(s):  
Luz E Zamudio-Beltrán ◽  
Yuyini Licona-Vera ◽  
Blanca E Hernández-Baños ◽  
John Klicka ◽  
Juan Francisco Ornelas
Keyword(s):  
Genetic Differentiation ◽  
Haplotype Network ◽  
Suitable Habitat ◽  
Glacial Cycles ◽  
Niche Modelling ◽  
Climatic Fluctuations ◽  
History Of ◽  
Genetic Differentiation Of Populations ◽  
Isthmus Of Tehuantepec ◽  
Glacial Expansion

Abstract The Pleistocene glacial cycles had a strong influence on the demography and genetic structure of many species, particularly on northern-latitude taxa. Here we studied the phylogeography of the white-eared hummingbird (Hylocharis leucotis), a widely distributed species of the highlands of Mexico and Central America. Analysis of mitochondrial DNA (mtDNA) sequences was combined with ecological niche modelling (ENM) to infer the demographic and population differentiation scenarios under present and past conditions. Analyses of 108 samples from 11 geographic locations revealed population structure and genetic differentiation among populations separated by the Isthmus of Tehuantepec (IT) and the Motagua-Polochic-Jocotán (MPJ) fault barriers. ENM predicted a widespread distribution of suitable habitat for H. leucotis since the Last Inter Glacial (LIG), but this habitat noticeably contracted and fragmented at the IT. Models for historical dispersal corridors based on population genetics data and ENM revealed the existence of corridors among populations west of the IT; however, the connectivity of populations across the IT has changed little since the LIG. The shallow geographic structure on either side of the isthmus and a star-like haplotype network, combined with the long-term persistence of populations across time based on genetic data and potential dispersal routes, support a scenario of divergence with migration and subsequent isolation and differentiation in Chiapas and south of the MPJ fault. Our findings corroborate the profound effects of Pleistocene climatic fluctuations on the evolutionary history of montane taxa but challenge the generality of expanded suitable habitat (pine-oak forests) during glacial cycles.

Lobocriconema iranense (Van den Berg, Eskandari, Tiedt & Karegar, 2010) n. comb. and description of L. nokandense n. sp. (Nematoda: Criconematidae) from Iran

Nematology ◽  
2019 ◽  
Vol 21 (10) ◽  
pp. 1043-1061 ◽  
Author(s):  
Farahnaz Jahanshahi Afshar ◽  
Ebrahim Pourjam ◽  
Majid Pedram
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
The Body ◽  
Entire Body ◽  
Mazandaran Province ◽  
Northern Iran ◽  
Close Relatives ◽  
Two Populations ◽  
Small Annulus

Summary Two populations of Lobocriconema were recovered from the rhizosphere of Parrotia persica in Rango forest, Gorgan, and Nargesi forest, Nokandeh, Golestan province, northern Iran. Both of the recovered populations were characterised using morphological (light and scanning electron microscopy), morphometric and molecular data based upon small, partial large and internal transcribed spacer 1 ribosomal RNA (SSU, LSU D2-D3, ITS1 rDNA) and the mitochondrial cytochrome c subunit oxidase I (COI mtDNA) gene sequences. The first examined population, recovered from Gorgan, was mainly characterised by having 34-39 retrorse body annuli 11-16 μm thick at mid-body with crenate, dentate and lobulate margins, longitudinal cuticular scratches on entire body on both lateral regions, sometimes one or two anastomoses along the body, a single labial annulus with smooth margin and smaller than the first body annulus, four distinct submedian lobes, simple open vulva with no overhang, and a terminal anus. This population was almost identical to Neolobocriconema iranense, a close examination of a topotype population recovered in this study confirming that they were conspecific. The second population, L. nokandense n. sp., was recovered from the Nokandeh and looked similar to the first population but was morphologically separated from it by a slightly crenate labial annulus under SEM (vs smooth), longer tail (13-21 vs 6-10 μm) and smaller ratio c (23.6-32.4 vs 44.7-86.0). In molecular phylogenetic analyses, the two populations formed a clade in both SSU and LSU phylogenies. In ITS1 and COI phylogenies, the Nokandeh population (the new species) formed a separate sister clade to the N. iranense clade. Detailed observations using SEM data revealed a small annulus between the submedian lobes and the single labial annulus, an open vulva and a slightly ornamented cuticle in all three studied populations (the newly recovered populations from Golestan and the topotype population of N. iranense from Mazandaran province and the new species), corroborating their placement under Lobocriconema. As a result, N. iranense was transferred to Lobocriconema as L. iranense n. comb. (= N. iranense). The new species was morphologically compared with its close relatives L. iranense n. comb., L. pauperum, L. incrassatum, and L. nasuense, all of which having the aforementioned small annulus between the submedian lobes and the first labial annulus. The phylogeny of the genus is discussed.

Molecular characterisation of, and new data on, two populations of Xiphinema ingens Luc & Dalmasso, 1964 (Nematoda: Longidoridae) from Iran

Nematology ◽  
2015 ◽  
Vol 17 (2) ◽  
pp. 125-138
Author(s):  
Sohrab Mirzaei ◽  
Ebrahim Pourjam ◽  
Majid Pedram
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Morphological Variation ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
28S Rdna ◽  
Molecular Characterisation ◽  
Morphometric Data ◽  
Two Populations

Two populations of Xiphinema ingens were recovered and characterised based on morphological, morphometric and molecular data. Interesting morphological variation was observed on the nature of differentiation in uterus of females between both populations, i.e. one population had only a pseudo-Z-organ in the shape of globular bodies, whilst the second population had a similar pseudo-Z-organ but also had crystalloids which varied in size and number and were located near the pseudo-Z-globules or sometimes at some distance from them towards the vagina. Variation was also observed in the shape of tail of juveniles within each population as well as between two recovered populations. Both populations had the same range of morphometric data and formed a fully supported clade in both Bayesian inference (BI) and maximum likelihood (ML) methods of phylogenetic analyses using partial sequences of 28S rDNA D2-D3 and ITS1 regions. The two populations of X. ingens formed a clade with another Xiphinema species native to Iran (X. castilloi) in 28S and two species, X. macroacanthum and X. bernardi, in ITS1 trees.

scholarly journals Genomic signatures of rapid adaptive divergence in a tropical montane species

2021 ◽  
Vol 17 (7) ◽  
pp. 20210089
Author(s):  
Per G. P. Ericson ◽  
Martin Irestedt ◽  
Huishang She ◽  
Yanhua Qu
Keyword(s):  
Environmental Heterogeneity ◽  
Adaptive Divergence ◽  
Glacial Cycles ◽  
Genomic Signatures ◽  
Tropical Mountain ◽  
Population Genomic ◽  
Allopatric Divergence ◽  
Suitable Habitats ◽  
Genomic Regions ◽  
Two Populations

Mountain regions contain extraordinary biodiversity. The environmental heterogeneity and glacial cycles often accelerate speciation and adaptation of montane species, but how these processes influence the genomic differentiation of these species is largely unknown. Using a novel chromosome-level genome and population genomic comparisons, we study allopatric divergence and selection in an iconic bird living in a tropical mountain region in New Guinea, Archbold's bowerbird ( Amblyornis papuensis ). Our results show that the two populations inhabiting the eastern and western Central Range became isolated ca 11 800 years ago, probably because the suitable habitats for this cold-tolerating bird decreased when the climate got warmer. Our genomic scans detect that genes in highly divergent genomic regions are over-represented in developmental processes, which is probably associated with the observed differences in body size between the populations. Overall, our results suggest that environmental differences between the eastern and western Central Range probably drive adaptive divergence between them.

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