Mitochondrial phylogeography of the Mediterranean horseshoe bat on the Balkan Peninsula

The Balkan Peninsula is identified as one of the major glacial refugia in Europe during the Pleistocene, and it has served as a genetic source for post-glacial recolonization for many temperate species. The aim of this study was to investigate the genetic diversity and phylogeographic patterns of the Mediterranean horseshoe bat, Rhinolophus euryale Blasius 1853, on the Balkan Peninsula. We also analyzed its demographic history and tested the hypothesis that this region was a glacial refugium for this species. We collected 82 samples from 20 localities in the Balkans and Italy and sequenced the mitochondrial D-loop region. Our results revealed low nucleotide but high haplotype diversity, with 20 out of 24 haplotypes reported for the first time. All Balkan and Italian samples belonged to a single genetic clade in the phylogenetic reconstruction, where they clustered together with previously published samples from Turkey, southern France and North Africa. The haplotype network had a star-like pattern that is indicative of recent population expansion. Both mismatch distribution and shallow genetic differentiation also supported the scenario of a sudden demographic expansion. We estimated that expansion within this lineage commenced in the Late Pleistocene. We suggest that the Balkan Peninsula was a glacial refugium for R. euryale.

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Population genetic structure of Marbled Rockfish, Sebastiscus marmoratus (Cuvier, 1829), in the northwestern Pacific Ocean

ZooKeys ◽

10.3897/zookeys.830.30586 ◽

2019 ◽

Vol 830 ◽

pp. 127-144 ◽

Cited By ~ 2

Author(s):

Lu Liu ◽

Xiumei Zhang ◽

Chunhou Li ◽

Hui Zhang ◽

Takashi Yanagimoto ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Population Genetic ◽

Fishery Management ◽

Demographic History ◽

Haplotype Diversity ◽

Population Expansion ◽

Northwestern Pacific ◽

Distribution Analysis ◽

Recent Population Expansion

Sebastiscusmarmoratus is an ovoviviparous fish widely distributed in the northwestern Pacific. To examine the gene flow and test larval dispersal strategy of S.marmoratus in Chinese and Japanese coastal waters, 421 specimens were collected from 22 localities across its natural distribution. A 458 base-pair fragment of the mitochondrial DNA (mtDNA) control region was sequenced to examine genetic diversity and population structure. One-hundred-six variable sites defined 166 haplotypes. The populations of S.marmoratus showed high haplotype diversity with a range from 0.8587 to 0.9996, indicating a high level of intrapopulation genetic diversity. Low non-significant genetic differentiation was estimated among populations except those of Hyogo, Behai, and Niiigata, which showed significant genetic differences from the other populations. The demographic history examined by neutrality tests, mismatch distribution analysis, and Bayesian skyline analysis suggested a sudden population expansion dating to the late Pleistocene. Recent population expansion in the last glacial period, wide dispersal of larvae by coastal currents, and the homogeneity of the environment may have important influences on the population genetic pattern. Knowledge of genetic diversity and genetic structure will be crucial to establish appropriate fishery management of S.marmoratus.

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Genetic Diversity in the mtDNA control region and population structure of Chrysichthys nigrodigitatus from selected Nigerian rivers: Implications for conservation and aquaculture

Archives of Polish Fisheries ◽

10.1515/aopf-2016-0010 ◽

2016 ◽

Vol 24 (2) ◽

pp. 85-97 ◽

Cited By ~ 2

Author(s):

Sylvanus A. Nwafili ◽

Tian-Xiang Gao

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Control Region ◽

Haplotype Diversity ◽

Population Expansion ◽

Mitochondrial Control Region ◽

Recent Population Expansion ◽

Base Pair Fragment ◽

Population Structures ◽

High Level

Abstract The genetic diversity and population structure of Chrysichthys nigrodigitatus were evaluated using a 443 base pair fragment of the mitochondrial control region. Among the eight populations collected comprising 129 individuals, a total of 89 polymorphic sites defined 57 distinct haplotypes. The mean haplotype diversity and nucleotide diversity of the eight populations were 0.966±0.006 and 0.0359±0.004, respectively. Analysis of molecular variance showed significant genetic differentiation among the eight populations (FST =0.34; P < 0.01). The present results revealed that C. nigrodigitatus populations had a high level of genetic diversity and distinct population structures. We report the existence of two monophyletic matrilineal lineages with mean genetic distance of 10.5% between them. Non-significant negative Tajima’s D and Fu’s Fs for more than half the populations suggests that the wild populations of C. nigrodigitatus underwent a recent population expansion, although a weak one since the late Pleistocene.

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Population Genetic Structure of Ornate Threadfin Bream (Nemipterus hexodon) in Thailand

Tropical Life Sciences Research ◽

10.21315/tlsr2021.32.1.4 ◽

2021 ◽

Vol 32 (1) ◽

pp. 61-80

Author(s):

Verakiat Supmee ◽

◽

Apirak Songrak ◽

Juthamas Suppapan ◽

Pradit Sangthong ◽

...

Keyword(s):

Genetic Structure ◽

Population Genetic Structure ◽

Genetic Information ◽

Population Genetic ◽

Demographic History ◽

Haplotype Diversity ◽

Population Expansion ◽

Andaman Sea ◽

Gulf Of Thailand ◽

The Gulf Of Thailand

Ornate threadfin bream (Nemipterus hexodon) is an economically important fishery species in Southeast Asia. In Thailand, N. hexodon decreased dramatically due to overexploitation for commercial purposes. To construct an effective sustainable management plan, genetic information is necessary. Thus, in our study, the population genetic structure and demographic history of N. hexodon were investigated using 419 bp of the mitochondrial DNA sequence in cytochrome oxidase subunit I gene (mtDNA COI). A total of 142 samples was collected from nine localities in the Gulf of Thailand (Chonburi, Samut Songkhram, Surat Thani, Nakhon Si Thammarat, Songkhla), and the Andaman Sea (Satun, Trang, Krabi, Phang Nga). Fourteen polymorphic sites defined 18 haplotypes, revealing a high haplotype diversity and low nucleotide diversity among nine localities. The Analysis of molecular variance (AMOVA) analysis, pairwise FST, and minimum spanning network result revealed that the genetic structure of N. hexodon was separated into two populations: the Gulf of Thailand and the Andaman Sea population. The genetic structure of N. hexodon can be explained by a disruption of gene flow from the geographic barrier and the Pleistocene isolation of the marine basin hypothesis. Neutrality tests, Bayesian skyline analysis, mismatch distribution, and the estimated values of population growth suggested that N. hexodon had experienced a population expansion. The genetic information would certainly help us gain insight into the population genetic structure of N. hexodon living on the coast of Thailand.

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Genetic Structure and Diversity of Banana Bunchy Top Virus (BBTV) in the Philippines

10.1101/2021.05.11.442582 ◽

2021 ◽

Author(s):

Jay-Vee S. Mendoza ◽

Fe M. Dela Cueva ◽

Cris Q. Cortaga ◽

Anand Noel C. Manohar ◽

Roanne R. Gardoce ◽

...

Keyword(s):

Genetic Structure ◽

Phylogenetic Analyses ◽

Infected Plant ◽

Haplotype Diversity ◽

Population Expansion ◽

The Philippines ◽

Recent Population Expansion ◽

Banana Bunchy Top Virus ◽

Reference Sequences ◽

Genetic Structure And Diversity

Banana bunchy top virus (BBTV) is an important disease of banana in the Philippines and in other banana-producing countries. This study was conducted to investigate the genetic structure and diversity of Philippine BBTV isolates which remain unexplored in the country. BBTV-infected plant tissues were sampled from banana-growing provinces (i.e., Cagayan, Isabela, Quirino, Batangas, Laguna, Rizal, Quezon, Palawan, Cebu, Leyte, and Davao del Sur) and the partial DNA-R gene of BBTV was sequenced. Analysis of all local BBTV isolates showed a nucleotide diversity (π) of 0.00721, average number of nucleotide differences (k) of 5.51984, and haplotype diversity (hd) of 0.971. Neutrality tests using Fu′s Fs and Tajima′s D showed significant and highly negative values which suggest an excess number of rare alleles due to recent population expansion or from genetic hitchhiking. Haplotype network and phylogenetic analyses revealed that the local BBTV isolates were closely related to Southeast Asian (SEA) group and exhibited a monophyletic clade with distinct haplotype grouping from other SEA sequences. However, some Indonesian and Indian reference sequences were also clustered within the Philippine BBTV group suggesting sequence homology. Results also showed that the local BBTV isolates may be categorized into three major haplotype groups (HA, HB, and HC) but only the HC group remained distinct upon comparison with other Philippine and SEA reference sequences. BBTV isolates from Quezon were the most diverse while isolates from Palawan displayed low genetic diversity indices and belonged only in the HC group. The assessment of the degree of variability among Philippine BBTV isolates will provide a reference towards the development of high-throughput BBTV detection systems as well as enable to devise plant breeding strategies to manage the current BBTV spread and variations.

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Demographic history of the fragmented yellowthroated bulbul (Pycnonotus xantholaemus) population in the Deccan Peninsula, India

Endangered Species Research ◽

10.3354/esr01062 ◽

2020 ◽

Vol 43 ◽

pp. 199-207

Author(s):

A Jha ◽

K Vasudevan

Keyword(s):

Demographic History ◽

Population Decline ◽

Haplotype Diversity ◽

Population Expansion ◽

Mitochondrial Control Region ◽

Haplotype Network ◽

Genetic Connectivity ◽

Founder Population ◽

Effective Population ◽

Genetic Structuring

The yellow-throated bulbul (YTB) is an endemic passerine restricted to scrub forests along hill slopes with exposed rocky outcrops in the Deccan Peninsula, India. It is found in small, discontinuous populations and is vulnerable to extinction due to ongoing habitat loss and subsequent population decline. To assess the genetic connectivity and past demography, we sequenced 1050 nucleotide base pairs of the mitochondrial control region of 60 individuals that represent distinct populations in the geographic range of the species. We recovered 39 haplotypes defined by 81 variable sites. Haplotype diversity was high with low nucleotide diversity, suggesting rapid population growth from a founder population with a small effective population size. The negative values of Tajima’s D and Fu’s Fs and small positive value of Ramos-Onsins and Rozas’ R2 suggest deviation from neutrality and population expansion. The haplotype network and demographic expansion parameters further suggest historical population expansion. Mismatch analysis statistics and Bayesian skyline plots estimate population expansion during the late Pleistocene. Although the species presently occurs in small, disconnected we found no structuring of the population. Dispersal events are the most likely explanation for the absence of genetic structuring in the YTB population. These results represent important data for the design of a conservation plan for this endemic and globally threatened species.

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Recent population expansion of longtail tuna Thunnus tonggol (Bleeker, 1851) inferred from the mitochondrial DNA markers

PeerJ ◽

10.7717/peerj.9679 ◽

2020 ◽

Vol 8 ◽

pp. e9679

Author(s):

Noorhani Syahida Kasim ◽

Tun Nurul Aimi Mat Jaafar ◽

Rumeaida Mat Piah ◽

Wahidah Mohd Arshaad ◽

Siti Azizah Mohd Nor ◽

...

Keyword(s):

Mitochondrial Dna ◽

Pacific Ocean ◽

Goodness Of Fit ◽

Demographic History ◽

Population Expansion ◽

Seasonal Migration ◽

Likelihood Method ◽

Recent Population Expansion ◽

D Loop ◽

Longtail Tuna

The population genetic diversity and demographic history of the longtail tuna Thunnus tonggol in Malaysian waters was investigated using mitochondrial DNA D-loop and NADH dehydrogenase subunit 5 (ND5). A total of 203 (D-loop) and 208 (ND5) individuals of T. tonggol were sampled from 11 localities around the Malaysian coastal waters. Low genetic differentiation between populations was found, possibly due to the past demographic history, dispersal potential during egg and larval stages, seasonal migration in adults, and lack of geographical barriers. The gene trees, constructed based on the maximum likelihood method, revealed a single panmictic population with unsupported internal clades, indicating an absence of structure among the populations studied. Analysis on population pairwise comparison ФST suggested the absence of limited gene flow among study sites. Taken all together, high haplotype diversity (D-loop = 0.989–1.000; ND5 = 0.848–0.965), coupled with a low level of nucleotide diversity (D-loop = 0.019–0.025; ND5 = 0.0017–0.003), “star-like” haplotype network, and unimodal mismatch distribution, suggests a recent population expansion for populations of T. tonggol in Malaysia. Furthermore, neutrality and goodness of fit tests supported the signature of a relatively recent population expansion during the Pleistocene epoch. To provide additional insight into the phylogeographic pattern of the species within the Indo-Pacific Ocean, we included haplotypes from GenBank and a few samples from Taiwan. Preliminary analyses suggest a more complex genetic demarcation of the species than an explicit Indian Ocean versus Pacific Ocean delineation.

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Mitochondrial DNA variation of the ruffed grouse (Bonasa umbellus)

BMC Research Notes ◽

10.1186/s13104-019-4607-3 ◽

2019 ◽

Vol 12 (1) ◽

Cited By ~ 2

Author(s):

Rodney L. Honeycutt ◽

Glenn A. Proudfoot ◽

Nova J. Silvy

Keyword(s):

Mitochondrial Dna ◽

Demographic History ◽

Haplotype Diversity ◽

Population Expansion ◽

The United States ◽

Mitochondrial Haplotype ◽

Ruffed Grouse ◽

Bonasa Umbellus ◽

Long Distance ◽

Mtdna Variation

Abstract Objective The ruffed grouse, Bonasa umbellus, is broadly distributed across North America and displays considerable taxonomic diversity. Except for a genetic study of some western populations of ruffed grouse, nothing is known about genetic variation in other regions of Canada and the United States. Our objective is to examine patterns of mitochondrial DNA (mtDNA) variation in the ruffed grouse across western, central, and eastern parts of its distribution. We compare patterns of mtDNA variation to those characterized by morphology and ecology. Additionally, we evaluate the demographic history of the species based on mitochondrial haplotype diversity. Results Patterns of mtDNA variation revealed geographic subdivision, with populations of ruffed grouse subdivided into 3 to 4 genetically distinct groups. This subdivision partially coincided with the ranges of described subspecies. Behavioral traits prohibiting long-distance movement and barriers to dispersal in response to physiography and unsuitable habitat help explain these patterns of subdivision. Historically, the ruffed grouse probably experienced a population expansion, possibly in response to changes during the Pleistocene.

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Genetic Diversity and Population Structure of Rhododendron rex Subsp. rex Inferred from Microsatellite Markers and Chloroplast DNA Sequences

Plants ◽

10.3390/plants9030338 ◽

2020 ◽

Vol 9 (3) ◽

pp. 338 ◽

Cited By ~ 1

Author(s):

Xue Zhang ◽

Yuan-Huan Liu ◽

Yue-Hua Wang ◽

Shi-Kang Shen

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Microsatellite Markers ◽

Chloroplast Dna ◽

Dna Sequences ◽

Demographic History ◽

Population Decline ◽

Population Expansion ◽

Distribution Models ◽

Recent Population Expansion

Genetic diversity is vital to the sustainable utilization and conservation of plant species. Rhododendron rex subsp. rex Lévl. is an endangered species endemic to the southwest of China. Although the natural populations of this species are facing continuous decline due to the high frequency of anthropogenic disturbance, the genetic information of R. rex subsp. rex is not yet elucidated. In the present study, 10 pairs of microsatellite markers (nSSRs) and three pairs of chloroplast DNA (cpDNAs) were used in the elucidation of the genetic diversity, population structure, and demographic history of 11 R. rex subsp. rex populations. A total of 236 alleles and 12 haplotypes were found. A moderate genetic diversity within populations (HE = 0.540 for nSSRs, Hd = 0.788 for cpDNA markers), high historical and low contemporary gene flows, and moderate genetic differentiation (nSSR: FST = 0.165***; cpDNA: FST = 0.841***) were detected among the R. rex subsp. rex populations. Genetic and geographic distances showed significant correlation (p < 0.05) determined by the Mantel test. The species exhibited a conspicuous phylogeographical structure among the populations. Using the Bayesian skyline plot and species distribution models, we found that R. rex subsp. rex underwent a population demography contraction approximately 50,000–100,000 years ago. However, the species did not experience a recent population expansion event. Thus, habitat loss and destruction, which result in a population decline and species inbreeding depression, should be considered in the management and conservation of R. rex subsp. rex.

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Mitochondrial D-loop Sequence Variability in Three Native Insular Griffon Vulture (Gyps fulvus) Populations from the Mediterranean Basin

BioMed Research International ◽

10.1155/2019/2073919 ◽

2019 ◽

Vol 2019 ◽

pp. 1-8

Author(s):

Paolo Mereu ◽

Monica Pirastru ◽

Valentina Satta ◽

Gian Nicola Frongia ◽

Nicolaos Kassinis ◽

...

Keyword(s):

Mediterranean Basin ◽

Haplotype Diversity ◽

Evolutionary Process ◽

Essential Elements ◽

Mediterranean Islands ◽

Griffon Vulture ◽

Loop Region ◽

D Loop ◽

The Mediterranean ◽

The Mediterranean Basin

The islands of Sardinia, Crete, and Cyprus are hosting the last native insular griffon populations in the Mediterranean basin. Their states have been evaluated from “vulnerable” to “critically endangered”. The sequence analysis of molecular markers, particularly the mtDNA D-loop region, provides useful information in studying the evolution of closely related taxa and the conservation of endangered species. Therefore, a study of D-loop region sequence was carried out to estimate the genetic diversity and phylogenetic relationship within and among these three populations. Among 84 griffon specimens (44 Sardinian, 33 Cretan, and 7 Cypriot), we detected four haplotypes including a novel haplotype (HPT-D) that was exclusively found in the Cretan population with a frequency of 6.1%. When considered as a unique population, haplotype diversity (Hd) and nucleotide diversity (π) were high at 0.474 and 0.00176, respectively. A similar level of Hd and π was found in Sardinian and Cretan populations, both showing three haplotypes. The different haplotype frequencies and exclusivity detected were in accordance with the limited matrilineal gene flow (FST = 0.07097), probably related to the species reluctance to fly over sea masses. The genetic variability we observe today would therefore be the result of an evolutionary process strongly influenced by isolation leading to the appearance of island variants which deserve to be protected. Furthermore, since nesting sites and food availability are essential elements for colony settlement, we may infer that the island's colonization began when the first domestic animals were transferred by humans during the Neolithic. In conclusion, our research presents a first contribution to the genetic characterization of the griffon vulture populations in the Mediterranean islands of Sardinia, Crete and Cyprus and lays the foundation for conservation and restocking programs.

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Population Genetics of the Black Citrus Aphid Aphis aurantii (Hemiptera, Aphididae) in China

Frontiers in Ecology and Evolution ◽

10.3389/fevo.2021.702178 ◽

2021 ◽

Vol 9 ◽

Author(s):

Hong-Ling Liu ◽

Zhi-Teng Chen ◽

Chao Liu ◽

Xing-Long Wu ◽

Ke-Jun Xiao ◽

...

Keyword(s):

Isolation By Distance ◽

Genetic Difference ◽

Geographic Distance ◽

Flow Analysis ◽

Haplotype Diversity ◽

Population Expansion ◽

Population Diversity ◽

Recent Population Expansion ◽

High Positive Correlation ◽

Local Populations

The black citrus aphid, Aphis aurantiiBoyer de Fonscolombe, 1841, is one of the most destructive pests in commercial tea plantations and gardens in China. In this study, we investigated the population genetic structure of A. aurantii based on the concatenated sequences of two mitochondrial genes, cytochrome c oxidase I (cox1) and cytochrome b (cytb). A total of 166 haplotypes were identified from 177 individuals collected at 11 locations in China. The whole Chinese A. aurantii population showed a low nucleotide diversity (0.00968) and a high population diversity (haplotype diversity; 0.9991). The haplotypes of the 11 local populations were widely distributed in the neighbor-joining phylogenetic tree and haplotype network diagram, whereas no apparent lineages were detected. Gene flow analysis showed gene exchanges among local populations. The pairwise Fst values revealed a certain amount of genetic difference among local populations. Analysis of molecular variance (AMOVA) reflected genetic differences both within and among populations. The isolation by distance (IBD) analysis revealed a high positive correlation between the geographic distance and genetic distance of the different populations. Neutral test and mismatch distribution suggested that A. aurantii may have experienced recent population expansion events.

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