scholarly journals Conservative plumage masks extraordinary phylogenetic diversity in the Grallaria rufula (Rufous Antpitta) complex of the humid Andes

The Auk ◽  
2020 ◽  
Vol 137 (3) ◽  
Author(s):  
R Terry Chesser ◽  
Morton L Isler ◽  
Andrés M Cuervo ◽  
C Daniel Cadena ◽  
Spencer C Galen ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Genetic Divergence ◽  
Phylogenetic Diversity ◽  
Biological Species ◽  
Cryptic Speciation ◽  
Species Groups ◽  
River Valleys ◽  
Prime Location

Abstract The Grallaria rufula complex is currently considered to consist of 2 species, G. rufula (Rufous Antpitta) and G. blakei (Chestnut Antpitta). However, it has been suggested that the complex, populations of which occur in humid montane forests from Venezuela to Bolivia, comprises a suite of vocally distinct yet morphologically cryptic species. We sequenced nuclear and mitochondrial DNA for 80 individuals from across the distribution of the complex to determine the extent of genetic variation between and within described taxa. Our results revealed 18 geographically coherent clades separated by substantial genetic divergence: 14 within rufula, 3 within blakei, and 1 corresponding to G. rufocinerea (Bicolored Antpitta), a species with distinctive plumage found to be nested within the complex. Neither G. rufula nor G. blakei as presently defined was monophyletic. Although 6 of the 7 recognized subspecies of G. rufula were monophyletic, several subspecies contained substantial genetic differentiation. Genetic variation was largely partitioned across recognized geographic barriers, especially across deep river valleys in Peru and Colombia. Coalescent modeling identified 17 of the 18 clades as significantly differentiated lineages, whereas analyses of vocalizations delineated 16 biological species within the complex. The G. rufula complex seems unusually diverse even among birds of the humid Andes, a prime location for cryptic speciation; however, the extent to which other dispersal-limited Andean species groups exhibit similar degrees of cryptic differentiation awaits further study.

scholarly journals Low genetic divergence and variation in coastal dune populations of the widespread terrestrial orchid Epipactis helleborine

2020 ◽  
Vol 193 (3) ◽  
pp. 419-430 ◽  
Author(s):  
Hans Jacquemyn ◽  
Hanne De Kort ◽  
An Vanden Broeck ◽  
Rein Brys
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Genetic Divergence ◽  
Coastal Dune ◽  
Terrestrial Orchid ◽  
Colonization Event ◽  
History Of ◽  
Epipactis Helleborine ◽  
Seed Introduction

Abstract Reconstructing the early history of species divergence and quantifying the level of standing genetic variation in diverging populations are central to our understanding of ecotype formation and ultimately speciation. In this study, we used single nucleotide polymorphisms to reconstruct the evolutionary history of species divergence in coastal dune populations of the widespread terrestrial orchid Epipactis helleborine and to investigate the level of standing genetic variation in 29 coastal dune populations in a fragmented dune landscape along the Belgian and French coast. Additionally, we used seed introduction experiments to assess the potential for gene flow into existing populations after long-distance seed dispersal and the ability to colonize vacant sites. Our results showed that coastal dune populations diverged only recently from inland populations, went through a significant bottleneck and were most probably the result of a single colonization event. Current levels of population genetic diversity are low and not related to population size or spatial isolation. The sampled dune populations also showed little genetic differentiation, and no apparent spatial genetic structure was observed. Seed introduction experiments showed that seeds of coastal dune populations germinated easily in both occupied and unoccupied sites in dune habitat, indicating that the availability of suitable mycorrhizal fungi is not limiting the distribution of coastal dune populations and that gene flow through seeds has probably contributed to the observed low levels of genetic differentiation. Overall, these results are consistent with a process of genetic divergence after a single, recent colonization event, followed by extensive gene flow among populations.

scholarly journals Patterns of morphological and genetic variation in the Mentocrex kioloides complex (Aves: Gruiformes: Rallidae) from Madagascar, with the description of a new species

Zootaxa ◽  
2011 ◽  
Vol 2776 (1) ◽  
pp. 49 ◽  
Author(s):  
STEVEN M. GOODMAN ◽  
MARIE JEANNE RAHERILALAO ◽  
NICHOLAS L. BLOCK
Keyword(s):  
Genetic Variation ◽  
New Species ◽  
Genetic Differentiation ◽  
Genetic Divergence ◽  
Molecular Genetic ◽  
Plumage Coloration ◽  
Karst Areas ◽  
A New Species

We examine patterns of morphological and molecular genetic differentiation in the endemic Mentocrex kioloides complex of Madagascar. This forest-dwelling rail (often placed in Canirallus) is known from two subspecies: M. k. kioloides, which occurs in the island’s humid central and eastern forests; and M. k. berliozi, which occurs in the transitional dry deciduoushumid forests of the northwest. Two new specimens (an adult and a downy young) recently became available from limestone karst areas of the lowland central west, the adult of which is notably different in size and plumage coloration, as well as showing considerable genetic divergence, from the two recognized subspecies of M. kioloides. The central west animals are herein named as a species new to science, Mentocrex beankaensis, sp. nov.

scholarly journals Population genetic variation analysis of bitter gourd wilt caused by Fusarium oxysporum f. sp. momordicae in China using inter simple sequence repeats (ISSR) molecular markers

2021 ◽  
Author(s):  
Rui Zang ◽  
Ying Zhao ◽  
Kangdi Guo ◽  
Kunqi Hong ◽  
Huijun Xi ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genetic Differentiation ◽  
Fusarium Oxysporum ◽  
Diversity Index ◽  
Gene Diversity ◽  
Pcr Amplification ◽  
Bitter Gourd ◽  
Diseased Plant ◽  
Variation Analysis ◽  
Group I

AbstractBitter gourd wilt caused by Fusarium oxysporum f. sp. momordicae (FOM) is a devastating crop disease in China. A total of 173 isolates characteristic of typical Fusarium oxysporum with abundant microconidia and macroconidia on white or ruby colonies were obtained from diseased plant tissues. BLASTn analysis of the rDNA-ITS of the isolates showed 99% identity with F. oxysporum species. Among the tested isolates, three were infectious toward tower gourd and five were pathogenic to bottle gourd. However, all of the isolates were pathogenic to bitter gourd. For genetic differences analysis, 40 ISSR primers were screened and 11 primers were used for ISSR-PCR amplification. In total, 127 loci were detected, of which 76 were polymorphic at a rate of 59.84%. POPGENE analysis showed that Nei’s gene diversity index (H) and Shannon’s information index (I) were 0.09 and 0.15, respectively, which indicated that the genetic diversity of the 173 isolates was low. The coefficient of gene differentiation (Gst = 0.33 > 0.15) indicated that genetic differentiation was mainly among populations. The strength of gene flow (Nm = 1.01 > 1.0) was weak, indicating that the population differentiation caused by gene drift was blocked to some degree. The dendrogram based on ISSR markers showed that the nine geographical populations were clustered into two groups at the threshold of genetic similarity coefficient of 0.96. The Shandong and Henan populations were clustered into Group I, while the Guangdong, Hainan, Guangxi, Fujian, Jiangxi, and Hubei populations constituted Group II. Results of the genetic variation analysis showed that the Hunan and Guangxi populations had the highest degree of genetic differentiation, while the Hubei population had the lowest genetic differentiation. Our findings enrich the knowledge of the genetic variation characteristics of FOM populations with the goal of developing effective disease-management programs and resistance breeding programs.

scholarly journals Genetic Diversities and Historical Dynamics of Native Ethiopian Horse Populations (Equus caballus) Inferred from Mitochondrial DNA Polymorphisms

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 155
Author(s):  
Kefena Effa ◽  
Sonia Rosenbom ◽  
Jianlin Han ◽  
Tadelle Dessie ◽  
Albano Beja-Pereira
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Genetic Differentiation ◽  
Sequence Divergence ◽  
Dna Polymorphisms ◽  
Base Pairs ◽  
Feral Horses ◽  
Domestic Horses ◽  
D Loop ◽  
Diversity Estimates

Matrilineal genetic diversity and relationship were investigated among eight morphologically identified native Ethiopian horse populations using polymorphisms in 46 mtDNA D-loop sequences (454 base pairs). The horse populations identified were Abyssinian, Bale, Borana, Horro, Kafa, Kundido feral horses, Ogaden and Selale. Mitochondrial DNA D-loop sequences were characterized by 15 variable sites that defined five different haplotypes. All genetic diversity estimates, including Reynolds’ linearized genetic distance, genetic differentiation (FST) and nucleotide sequence divergence (DA), revealed a low genetic differentiation in native Ethiopian horse populations. However, Kundido feral and Borana domestic horses were slightly diverged from the rest of the Ethiopian horse populations. We also tried to shed some light on the matrilineal genetic root of native Ethiopian horses from a network constructed by combining newly generated haplotypes and reference haplotypes deposited in the GenBank for Eurasian type Turkish Anatolian horses that were used as a genetic conduit between Eurasian and African horse populations. Ninety-two haplotypes were generated from the combined Ethio-Eurasian mtDNA D-loop sequences. A network reconstructed from the combined haplotypes using Median-Joining algorithm showed that haplotypes generated from native Ethiopian horses formed separate clusters. The present result encourages further investigation of the genetic origin of native African horses by retrieving additional mtDNA sequences deposited in the GenBank for African and Eurasian type horses.

Restriction fragment length polymorphisms demonstrate single origin of infection centers in Phellinus weirii

1994 ◽  
Vol 72 (4) ◽  
pp. 440-447 ◽  
Author(s):  
Hanhong Bae ◽  
Everett M. Hansen ◽  
Steven H. Strauss
Keyword(s):  
Mitochondrial Dna ◽  
Restriction Fragment ◽  
Ribosomal Dna ◽  
Fragment Length ◽  
Host Species ◽  
Root Rot ◽  
Biological Species ◽  
Douglas Fir ◽  
Dna Probes ◽  
Restriction Fragment Length

Restriction fragment length polymorphism (RFLP) markers were used to study genetic variation in the basidiomycete fungus Phellinus weirii (Murr.) Gilbertson, the cause of laminated root rot of conifers. In an initial study, three isolates each from the Douglas-fir type and the cedar-type biological species were surveyed with 12 restriction enzymes and 20 random, mitochondrial, and nuclear-ribosomal gene probes. The two biological species were distinct with most probe–enzyme combinations (91%). Variation within biological species was detected for the random and ribosomal DNA probes but not for the mitochondrial DNA probes. In a subsequent study 65 probe–enzyme combinations (13 × 5) that had detected variation within the Douglas-fir type biological species were used to analyze 27 isolates derived from six infection centers, two host species, and two geographic areas in western Oregon. Infection centers differed from one another in numerous probe–enzyme combinations but were nearly genetically uniform within. Isolates from the two host species, Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) and mountain hemlock (Tsuga mertensiana (Bong.) Carr.), showed few RFLP differences. Initiation of infection centers, and subsequent vegetative or basdiospore initiated immigration, appear to be rare events. Key words: ribosomal DNA, mitochondrial DNA, RFLP, root rot, conifer.

scholarly journals ANALYSIS OF GENETIC VARIABILITY AT MITOCHONDRIAL DNA LEVEL IN SOME ROUMANIAN PHYTOPHTHORA INFESTANS ACCESSIONS

1970 ◽  
Vol 63 ◽  
Author(s):  
C. Botez ◽  
V. Florian ◽  
I. Oroian ◽  
G. Morar ◽  
Meda Lucaci
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Variability ◽  
Genetic Differentiation ◽  
Phytophthora Infestans ◽  
Restriction Enzymes ◽  
Molecular Polymorphism ◽  
Caps Markers

Analysis of secondary molecular polymorphism at the level of amplified mitochondrial DNA, digested by restriction enzymes (CAPS markers), revealed genetic differentiation among ten Phytophthora infestans accessions. Mitochondrial DNA was amplified with four pairs of primers (H1,H2,H3 and H4) and after that the products of amplification were digested with Hha I (for H1 products of amplification), Msp I (for H2 products of amplification) and Eco R I (for H3 and H4 products of amplification) restriction enzymes. On this basis we have established that the ten Phytophthora infestans accessions belongs to two haplotypes, one accession belongs to Ia haplotyp and the others belong to IIa haplotype.

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