scholarly journals The biogeography of Elaphe sauromates (Pallas, 1814), with a description of a new rat snake species

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6944 ◽  
Author(s):  
Daniel Jablonski ◽  
Oleg V. Kukushkin ◽  
Aziz Avcı ◽  
Sabina Bunyatova ◽  
Yusuf Kumlutaş ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Morphological Variation ◽  
Molecular Genetic ◽  
Glacial Refugia ◽  
Morphological Data ◽  
Meristic Characters ◽  
Climatic Oscillations ◽  
The Balkans ◽  
Haplotype Networks ◽  
Rat Snake

Background The rat snake genus Elaphe once comprised several dozens of species distributed in temperate through tropical zones of the New and Old World. Based on molecular-genetic analyses in early 2000s, the genus was split into several separate genera, leaving only 15 Palearctic and Oriental species as its members. One of the three species also occurring in Europe is Elaphe sauromates, a robust snake from the Balkans, Anatolia, Caucasus, Ponto-Caspian steppes, and Levant that has been suspected to be composed of two or more genetically diverse populations. Here, we studied the genetic structure and morphological variation of E. sauromates, aiming to better understand its inter-population relationships and biogeography, and subsequently revise its taxonomy. Methods We reconstructed the phylogeography and analyzed the genetic structure of E. sauromates populations originating from most of its geographic range using both mitochondrial (COI, ND4) and nuclear (C-MOS, MC1R, PRLR, RAG1) DNA gene fragments. We employed Maximum likelihood and Bayesian inference methods for the phylogenetic tree reconstructions, supplemented with species delimitation methods, analysis of haplotype networks, and calculation of uncorrected p-distances. Morphological variation in 15 metric and 18 meristic characters was studied using parametric univariate tests as well as multivariate general linearized models. In total, we analyzed sequences originating from 63 specimens and morphological data from 95 specimens of E. sauromates sensu lato. Results The molecular phylogeny identified two clearly divergent sister lineages within E. sauromates, with both forming a lineage sister to E. quatuorlineata. The genetic distance between them (5.80–8.24% in mtDNA) is similar to the distances among several other species of the genus Elaphe. Both lineages are also moderately morphologically differentiated and, while none of the characters are exclusively diagnostic, their combination can be used for confident lineage identification. Here, following the criteria of genetic and evolutionary species concepts, we describe the lineage from eastern Anatolia and parts of the Lesser and Great Caucasus as a new species E. urartica sp. nov. Discussion Elaphe urartica sp. nov. represents a cryptic species whose ancestors presumably diverged from their common ancestor with E. sauromates around the Miocene-Pliocene boundary. The intraspecific genetic structure indicates that the recent diversity of both species has been predominantly shaped by Pleistocene climatic oscillations, with glacial refugia mainly located in the Balkans, Crimea, and/or Anatolia in E. sauromates and Anatolia and/or the Caucasus in E. urartica sp. nov.

scholarly journals Morphological and genetic differentiation in the anguid lizard Pseudopus apodus supports the existence of an endemic subspecies in the Levant

2021 ◽  
Vol 71 ◽  
pp. 175-200
Author(s):  
Daniel Jablonski ◽  
Marco Antônio Ribeiro-Júnior ◽  
Shai Meiri ◽  
Erez Maza ◽  
Oleg V. Kukushkin ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Eastern Mediterranean ◽  
Glacial Refugia ◽  
Mediterranean Coast ◽  
New Subspecies ◽  
Climatic Oscillations ◽  
The Balkans ◽  
Western Palearctic ◽  
Independent Evolutionary History

The Levant represents one of the most important reptile diversity hotspots and centers of endemism in the Western Palearctic. The region harbored numerous taxa in glacial refugia during the Pleistocene climatic oscillations. Due to the hostile arid conditions in the warmer periods they were not always able to spread or come into contact with populations from more distant regions. One large and conspicuous member of the Levantine herpetofauna is the legless anguid lizard Pseudopus apodus. This species is distributed from the Balkans to Central Asia with a portion of its range running along the eastern Mediterranean coast. Mitochondrial and nuclear DNA sequences, microsatellite genotypes, and morphology show that populations in this region differ from the two named subspecies and presumably had a long independent evolutionary history during the Quaternary. Here we describe the Levantine population as a new subspecies and present biogeographic scenarios for its origin and diversification. The new subspecies is genetically highly diverse, and it forms a sister lineage to Pseudopus from the remaining parts of the range according to mtDNA. It is the largest-bodied of the three subspecies, but occupies the smallest range.

scholarly journals Population Genetic Structure Analysis Reveals Decreased but Moderate Diversity for the Oriental Fire-Bellied Toad Introduced to Beijing after 90 Years of Independent Evolution

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1429
Author(s):  
Yang Teng ◽  
Jing Yang ◽  
Guofen Zhu ◽  
Fuli Gao ◽  
Yingying Han ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Structure Analysis ◽  
Phylogenetic Trees ◽  
Molecular Genetic ◽  
Genetic Research ◽  
Haplotype Diversity ◽  
Botanical Garden ◽  
Source Population ◽  
Independent Evolution ◽  
Loop Region

Detailed molecular genetic research on amphibian populations has a significant role in understanding the genetic adaptability to local environments. The oriental fire-bellied toads (Bombina orientalis) were artificially introduced to Beijing from Shandong Province in 1927, and since then, this separated population went through an independent evolution. To explore the differentiation of the introduced population with its original population, this study analyzed the genetic structure of the oriental fire-bellied toad, based on the mitochondrial genome control region and six microsatellite sites. The results showed that the haplotype diversity and nucleotide diversity of the mitochondrial D-loop region partial sequences of the Beijing Botanical Garden population and the Baiwangshan population were lower than those of the Shangdong Kunyushan population. Microsatellite marker analysis also showed that the observed heterozygosity and expected heterozygosity of the Beijing populations were lower than those of the Kunyushan population. The phylogenetic trees and network diagrams of haplotypes indicated that the three populations were not genetically separated. However, the structure analysis showed a genetic differentiation and categorized the sampling individuals into Beijing and Shandong genetic clusters, which indicated a tendency for isolated evolution in the Beijing population. Although the Beijing populations showed a decline in genetic diversity, it was still at a moderate level, which could maintain the survival of the population. Thus, there is no need to reintroduce new individuals from the Kunyushan source population.

scholarly journals The influence of climatic oscillations during the Quaternary Era on the genetic structure of Asian black bears in Japan

Heredity ◽  
2009 ◽  
Vol 102 (6) ◽  
pp. 579-589 ◽  
Author(s):  
N Ohnishi ◽  
R Uno ◽  
Y Ishibashi ◽  
H B Tamate ◽  
T Oi
Keyword(s):  
Genetic Structure ◽  
Black Bears ◽  
Climatic Oscillations

scholarly journals Revisiting the Issue of the Molecular-genetic Structure of the Causative Agent of the Bovine Leukemia Virus in the Russian Federation

2016 ◽  
Vol 9 (42) ◽  
Author(s):  
Irina Mikhailovna Donnik ◽  
Maksim Valeryevich Petropavlovsky ◽  
Anna Sergeevna Krivonogova ◽  
Irina Alekseevna Shkuratova ◽  
Marzena Rola-Łuszczak ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Russian Federation ◽  
Causative Agent ◽  
Bovine Leukemia Virus ◽  
Leukemia Virus ◽  
Molecular Genetic ◽  
The Russian Federation

scholarly journals Population genetic structure and variability in Lindera glauca (Lauraceae) indicates low levels of genetic diversity and skewed sex ratios in natural populations in mainland China

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8304 ◽  
Author(s):  
Biao Xiong ◽  
Limei Zhang ◽  
Shubin Dong ◽  
Zhixiang Zhang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Isolation By Distance ◽  
Sex Ratios ◽  
Mainland China ◽  
Small Sample ◽  
Chloroplast Microsatellites ◽  
Wild Populations ◽  
Haplotype Networks ◽  
Low Levels

Lindera glauca (Lauraceae) is a tree of economic and ecological significance that reproduces sexually and asexually via apomictic seeds. It is widely distributed in the low-altitude montane forests of East Asia. Despite the potential implications of a mixed reproductive system in terms of genetic diversity, few studies have focused on this aspect. In this study, the genetic structure of wild populations of L. glauca was investigated via genetic analyses. Overall, 13 nuclear microsatellites (nSSRs) and five chloroplast microsatellites (cpSSRs) were used to genotype 300 individual plants, taken from 20 wild populations (a small sample size in some wild populations is due to the limitation of its specific reproduction, leading to certain limitations in the results of this study) and two cultivated populations ranging across nearly the entire natural distribution of mainland China. The populations exhibited low levels of genetic diversity (nSSR: AR = 1.75, Ho = 0.32, He = 0.36; cpSSR: Nb = 2.01, Hrs = 0.40), and no significant effect of isolation by distance between populations existed, regardless of marker type (nSSR: R2 = 0.0401, P = 0.068; cpSSR: R2 = 0.033, P = 0.091). Haplotype networks showed complex relationships among populations, and the H12 haplotype was predominant in most populations. Analyses of molecular variance obtained with nuclear markers (Fsc = 0.293, FST = 0.362) and chloroplast markers (Fsc = 0.299, FST = 0.312) were similar. The migration ratio of pollen flow versus seed flow in this study was negative (r = −1.149). Results suggest that weak barriers of dispersal between populations and/or the similarity of founders shared between neighbors and distant populations are indicative of the gene flow between populations more likely involving seeds. Wild L. glauca in mainland China was inferred to have highly skewed sex ratios with predominant females. In addition, some populations experienced a recent bottleneck effect, especially in Gujianshan, Chongqing, and southwest China (population GJS). It is suggested that few wild male individuals should be conserved in order to maintain overall genetic diversity in the wild populations of this species. These findings provide important information for the sustainable utilization and preservation of the overall genetic diversity of L. glauca.

scholarly journals Lobster Fishery Connectivity and Management in Indonesia Waters

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Waluyo Waluyo ◽  
Taslim Arifin
Keyword(s):  
Genetic Structure ◽  
Fishery Management ◽  
Marine Organism ◽  
Molecular Genetic ◽  
Three Dimensional ◽  
Geographical Information ◽  
Biophysical Model ◽  
Complex Life Cycle ◽  
Biophysical Modeling ◽  
The Individual

The distribution of lobsters in Indonesia waters is very wide, even lobster species in Indonesia are also scattered in the tropical waters of the western Pacific Ocean, the Indian Ocean, Africa to Japanese waters.Indonesia waters are divided into 11 (eleven) Fishery Management Zone (FMZ). Lobsters in Indonesia may come from various water areas, both national and regional waters zone, it’s called the sink population, its spread is influenced by the movement of the current. Lobster seed is nurtured by nature through oceancurrents from Australia, East Indonesia, Japan, then back to Australia. Lobsters have a complex life cycle,where adult lobsters inhabit coral reefs as a place to lay eggs, then hatch into planktonic larvae, and grow up in open seas and carry out diurnal and ontogenetic vertical migrations before returning to nurseries in shallow coastal areas and reefs. coral, as well as habitat by the type of species. Literature research had used at leasttwo methodologies to estimate the distribution and connection sensitivity matrices of marine organism larvae.The two most common approaches are using genetic markers and numerical biophysical modeling. Thus, this research uses molecular genetic techniques to explain the genetic structure of lobster populations using a biophysical model approach that can explain the genetic structure of lobsters, as well as the distribution base on regional oceanographic synthesis data and lobster biology known in Indonesia waters. This model has four components, namely: 1) a benthic module based on a Geographical Information System (GIS) which is a lobster habitat in the spawning and recruitment process, 2) a physical oceanography module containing daily velocity in the form of a three-dimensional hydrodynamic model, 3) a larva biology module that describes larval life history characteristics, and 4) a Lagrangian Stochastic module that tracks the individual trajectories of larvae.

scholarly journals Variations in genetic structure and male genitalia suggest recent lineage diversification in the Neotropical dung beetle complex Canthon cyanellus (Scarabaeidae: Scarabaeinae)

2020 ◽  
Vol 131 (3) ◽  
pp. 505-520
Author(s):  
Janet Nolasco-Soto ◽  
Mario E Favila ◽  
Alejandro Espinosa De Los Monteros ◽  
Jorge González-Astorga ◽  
Gonzalo Halffter ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Morphological Variation ◽  
Male Genitalia ◽  
Morphological Variability ◽  
Dung Beetle ◽  
Morphological Characters ◽  
Taxonomic Assignment ◽  
Morphometric Variation ◽  
Evolutionary Forces ◽  
Significant Genetic Structure

Abstract We analysed the genetic divergence and morphology of the aedeagus (i.e. phallobase and parameres) in Canthon cyanellus at different geographical levels. The results from both approaches were compared with the current taxonomic assignment of the C. cyanellus complex, which includes three subspecies. We found a high variation in all the morphological characters of the aedeagus in the populations analysed; the morphometric variation was not geographically structured, either by population or by region. The genealogical analysis indicates a significant genetic structure that does not match either the morphological variation in the male genitalia or the previous subspecific taxonomic classification. Our results suggest that the morphological variation of the aedeagus is seemingly not an isolating reproductive barrier and that the intra- and interpopulation morphological variability of the aedeagus in the C. cyanellus complex does not permit the division into several species. We suggest that other evolutionary forces, such as genetic drift and sexual selection, have influenced the evolution of the male genitalia and the incipient differentiation of this species complex.

scholarly journals Records of regalecid fishes in Argentine waters

Zootaxa ◽  
2010 ◽  
Vol 2509 (1) ◽  
pp. 62
Author(s):  
ANA E. RUIZ ◽  
ATILA E. GOSZTONYI
Keyword(s):  
Fish Fauna ◽  
Morphological Data ◽  
Body Measurements ◽  
Meristic Characters ◽  
Argentine Sea ◽  
The Pacific

The first two specimens of Regalecus glesne Ascanius, 1788, collected in the Argentine Sea, at Playa Unión beach, 43º 18' S, 65º 02' W are reported. Body measurements, meristic characters and morphological data are given. The most important differences with two other regalecid species, R. russelii Cuvier and R. kinoi Castro-Aguirre et al. 1991, from the Pacific coasts of Mexico, are considered. Also, a specimen caught at 43° 03’ S, 59° 14’ W, at 993 m depth, previously identified as Agrostichthys sp. is rediagnosed as Agrostichthys parkeri Benham, 1904. The distribution of R. glesne is extended to the Argentine Sea, adding a regalecid species to its fish fauna.

Genetic relationships among napiergrass (Pennisetum purpureum Schum.) nursery accessions using AFLP markers

2009 ◽  
Vol 8 (1) ◽  
pp. 63-70 ◽  
Author(s):  
Karen Harris ◽  
William Anderson ◽  
Ravindra Malik
Keyword(s):  
Genetic Relatedness ◽  
Pennisetum Glaucum ◽  
Genetic Relationships ◽  
Molecular Genetic ◽  
Perennial Grass ◽  
Morphological Data ◽  
Pennisetum Purpureum ◽  
Group Method ◽  
Heterotic Groups ◽  
Arithmetic Average

Pennisetum purpureum Schum. (napiergrass) is a perennial grass used for forage especially in South America and Africa. Over the last 30 years, a USDA–ARS nursery containing accessions collected from all over the world has been established in Tifton, Georgia. The study reported here was conducted to assess the molecular genetic variation and genetic relatedness among 89 accessions from the Tifton nursery using amplified fragment length polymorphism markers, morphological data and ploidy level. Using 218 polymorphic markers from eight selective primer combinations, the 89 accessions were clustered into five groups using a principal components analysis and a dendrogram based on Dice similarity estimates and unweighted pair group method with arithmetic average clustering. These five groups include three groups collected from Kenya, a group from Puerto Rico, and accessions derived from the cultivar Merkeron. This research provides the first molecular characterization of the Tifton nursery, displays the relationships between accessions, and provides potential heterotic groups for napiergrass and pearl millet (Pennisetum glaucum (L.) R. Br.) breeding improvement.

A Paedomorphocline in Eucalyptus: Natural Variation in the E. risdonii/E. tenuiramis Complex

1991 ◽  
Vol 39 (6) ◽  
pp. 545 ◽  
Author(s):  
RJE Wiltshire ◽  
BM Potts ◽  
JB Reid
Keyword(s):  
Morphological Variation ◽  
Natural Variation ◽  
Natural Populations ◽  
Morphological Data ◽  
Closely Related Species ◽  
Leaf Habit ◽  
Juvenile Leaf ◽  
Adult Leaf ◽  
Morphological Differences ◽  
Fruit Characters

Ontogenetic and morphological variation in 40 natural populations of the closely related species, E. risdonii and E. tenuiramis, were assessed in a multivariate study of juvenile and adult leaf and fruit characters. The present taxonomic separation of the two taxa is based mainly on ontogenetic differences, but this study reveals that the variation between the two taxa in the retention of the juvenile leaf habit is continuous and may represent a paedomorphocline. The morphological data suggest that at least four phenetic groups are required to summarise the morphological variation in the E. risdonii/ E. tenuiramis complex. When ontogenetic variation is removed, the morphological variation between some E. risdonii and some E. tenuiramis populations is also continuous and much smaller than the morphological differences within E. tenuiramis. This suggests that E. risdonii may be the product of relatively recent changes in developmental timing (heterochrony) from E. tenuiramis.

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