scholarly journals Climatic Refugia and Geographical Isolation Contribute to the Speciation and Genetic Divergence in Himalayan-Hengduan Tree Peonies (Paeonia delavayi and Paeonia ludlowii)

2021 ◽  
Vol 11 ◽  
Author(s):  
Yu-Juan Zhao ◽  
Gen-Shen Yin ◽  
Yue-Zhi Pan ◽  
Bo Tian ◽  
Xun Gong
Keyword(s):  
Genetic Variation ◽  
Late Quaternary ◽  
Demographic History ◽  
Nuclear Gene ◽  
Genetic Distances ◽  
Population Divergence ◽  
Widespread Species ◽  
Isolation With Migration ◽  
Isolation By Environment ◽  
Paeonia Delavayi

Himalaya and Hengduan Mountains (HHM) is a biodiversity hotspot, and very rich in endemic species. Previous phylogeographical studies proposed different hypotheses (vicariance and climate-driven speciation) in explaining diversification and the observed pattern of extant biodiversity, but it is likely that taxa are forming in this area in species-specific ways. Here, we reexplored the phylogenetic relationship and tested the corresponding hypotheses within Paeonia subsect. Delavayanae composed of one widespread species (Paeonia delavayi) and the other geographically confined species (Paeonia ludlowii). We gathered genetic variation data at three chloroplast DNA fragments and one nuclear gene from 335 individuals of 34 populations sampled from HHM. We performed a combination of population genetic summary statistics, isolation-with-migration divergence models, isolation by environment, and demographic history analyses. We found evidence for the current taxonomic treatment that P. ludlowii and P. delavayi are two different species with significant genetic differentiation. The significant isolation by environment was revealed within all sampled populations but genetic distances only explained by geographical distances within P. delavayi populations. The results of population divergence models and demographic history analyses indicated a progenitor–derivative relationship and the Late Quaternary divergence without gene flow between them. The coalescence of all sampled cpDNA haplotypes could date to the Late Miocene, and P. delavayi populations probably underwent a severe bottleneck in population size during the last glacial period. Genetic variation in Paeonia subsect. Delavayanae is associated with geographical and environmental distances. These findings point to the importance of geological and climatic changes as causes of the speciation event and lineage diversification within Paeonia subsect. Delavayanae.

scholarly journals Genetic Diversity and Population Divergence of a Rare, Endemic Grass (Elymus breviaristatus) in the Southeastern Qinghai-Tibetan Plateau

2019 ◽  
Vol 11 (20) ◽  
pp. 5863 ◽  
Author(s):  
Qingqing Yu ◽  
Qian Liu ◽  
Yi Xiong ◽  
Yanli Xiong ◽  
Zhixiao Dong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Tibetan Plateau ◽  
Isolation By Distance ◽  
Genetic Distances ◽  
Conservation Strategy ◽  
Conservation Strategies ◽  
Grass Species ◽  
Population Divergence ◽  
High Genetic Diversity ◽  
Widespread Species

Elymus breviaristatus is a grass species only distributed in the southeast of Qinghai-Tibetan Plateau (QTP), which has suffered from serious habitat fragmentation. Therefore, understanding patterns of genetic diversity within and among natural E. breviaristatus populations could provide insight for future conservation strategies. In this study, sequence-related amplified polymorphism markers were employed to investigate the genetic diversity and hierarchical structure of seven E. breviaristatus populations from QTP, China. Multiple measures of genetic diversity indicated that there is low to moderate genetic variation within E. breviaristatus populations, consistent with its presumed mating system. In spite of its rarity, E. breviaristatus presented high genetic diversity that was equivalent to or even higher than that of widespread species. Bayesian clustering approaches, along with clustering analysis and principal coordinate analysis partitioned the studied populations of E. breviaristatus into five genetic clusters. Differentiation coefficients (Fst, GST, etc.) and AMOVA analysis revealed considerable genetic divergence among different populations. BARRIER analyses indicated that there were two potential barriers to gene flow among the E. breviaristatus populations. Despite these patterns of differentiation, genetic distances between populations were independent of geographic distances (r = 0.2197, p = 0.2534), indicating little isolation by distance. Moreover, despite detecting a common outlier by two methods, bioclimatic factors (altitude, annual mean temperature, and annual mean precipitation) were not related to diversity parameters, indicating little evidence for isolation caused by the environment. These patterns of diversity within and between populations are used to propose a conservation strategy for E. breviaristatus.

scholarly journals Genetic variation of the Chilean endemic long-haired mouse Abrothrix longipilis (Rodentia, Supramyomorpha, Cricetidae) in a geographical and environmental context

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9517 ◽  
Author(s):  
Lourdes Valdez ◽  
Marcial Quiroga-Carmona ◽  
Guillermo D’Elía
Keyword(s):  
Genetic Variation ◽  
Isolation By Distance ◽  
Demographic History ◽  
Mitochondrial Gene ◽  
General Pattern ◽  
Mediterranean Ecosystem ◽  
Gene Genealogy ◽  
Quaternary Climate ◽  
Mitochondrial Cytochrome B ◽  
Isolation By Environment

Quaternary climate and associated vegetational changes affected the fauna of the Chilean Mediterranean ecosystem. Here we studied the genetic variation of the long-haired mouse, Abrothrix longipilis, a sigmodontine rodent endemic to this area. Within an environmentally explicit context, we examined the geographic distribution of the genetic diversity and demographic history of the species based on sequences of the mitochondrial Cytochrome-b gene of 50 individuals from 13 localities and a large panel of single nucleotide polymorphisms of 17 individuals from 6 localities. The gene genealogy of A. longipilis revealed three intraspecific lineages that are allopatric and latitudinally segregated (northern, central, and southern lineages) with an estimated crown age for the whole species clade of 552.3 kyr B.P. A principal component analysis based on 336,596 SNP loci is in line with the information given by the the mitochondrial gene genealogy. Along its complete distributional range, A. longipilis showed patterns of isolation by distance and also isolation by environment. The general pattern of historical demography showed stability for most intraspecific lineages of A. longipilis. Northern and central lineages showed signals of historical demographic stability, while the southern lineage showed contrasting signals. In agreement with this, the niche models performed showed that in the northern range of A. longipilis, areas of high suitability for this species increased towards the present time; areas of central range would have remained relatively stable, while southern areas would have experienced more change through time. In summary, our study shows three distinct allopatric lineages of A. longipilis, each showing slightly different demographic history.

scholarly journals Evolutionary history of a relict conifer, Pseudotaxus chienii (Taxaceae), in south-east China during the late Neogene: old lineage, young populations

2019 ◽  
Vol 125 (1) ◽  
pp. 105-117 ◽  
Author(s):  
Yixuan Kou ◽  
Li Zhang ◽  
Dengmei Fan ◽  
Shanmei Cheng ◽  
Dezhu Li ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Genetic Divergence ◽  
Evolutionary History ◽  
Isolation By Distance ◽  
Demographic History ◽  
East China ◽  
Population Divergence ◽  
Isolation By Environment ◽  
Late Neogene ◽  
History Of

Abstract Background and Aims Many monotypic gymnosperm lineages in south-east China paradoxically remain in relict status despite long evolutionary histories and ample opportunities for allopatric speciation, but this paradox has received little attention and has yet to be resolved. Here, we address this issue by investigating the evolutionary history of a relict conifer, Pseudotaxus chienii (Taxaceae). Methods DNA sequences from two chloroplast regions and 14 nuclear loci were obtained for 134 samples. The demographic history was inferred and the contribution of isolation by environment (IBE) in patterning genetic divergence was compared with that of isolation by distance (IBD). Key Results Three genetic clusters were identified. Approximate Bayesian computation analyses showed that the three clusters diverged in the late Pliocene (~3.68 Ma) and two admixture events were detected. Asymmetric gene flow and similar population divergence times (~ 3.74 Ma) were characterized using the isolation with migration model. Neither IBD nor IBE contributed significantly to genetic divergence, and the contribution of IBE was much smaller than that of IBD. Conclusions These results suggest that several monotypic relict gymnosperm lineages like P. chienii in south-east China did not remain in situ and undiversified for millions of years. On the contrary, they have been evolving and the extant populations have become established more recently, having insufficient time to speciate. Our findings provide a new perspective for understanding the formation and evolution of the relict gymnosperm flora of China as well as of the Sino-Japanese Flora.

scholarly journals Genetic, Morphological, and Environmental Differentiation of an Arid-Adapted Oak with a Disjunct Distribution

Forests ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 465
Author(s):  
Bethany A. Zumwalde ◽  
Ross A. McCauley ◽  
Ian J. Fullinwider ◽  
Drew Duckett ◽  
Emma Spence ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Large Scale ◽  
Niche Overlap ◽  
The United States ◽  
Disjunct Distribution ◽  
Population Divergence ◽  
Environmental Niche ◽  
Widespread Species ◽  
Precipitation Seasonality ◽  
Bioclimatic Variables

The patterns of genetic and morphological diversity of a widespread species can be influenced by environmental heterogeneity and the degree of connectivity across its geographic distribution. Here, we studied Quercus havardii Rydb., a uniquely adapted desert oak endemic to the Southwest region of the United States, using genetic, morphometric, and environmental datasets over various geographic scales to quantify differentiation and understand forces influencing population divergence. First, we quantified variation by analyzing 10 eastern and 13 western populations from the disjunct distribution of Q. havardii using 11 microsatellite loci, 17 morphological variables, and 19 bioclimatic variables. We then used regressions to examine local and regional correlations of climate with genetic variation. We found strong genetic, morphological and environmental differences corresponding with the large-scale disjunction of populations. Additionally, western populations had higher genetic diversity and lower relatedness than eastern populations. Levels of genetic variation in the eastern populations were found to be primarily associated with precipitation seasonality, while levels of genetic variation in western populations were associated with lower daily temperature fluctuations and higher winter precipitation. Finally, we found little to no observed environmental niche overlap between regions. Our results suggest that eastern and western populations likely represent two distinct taxonomic entities, each associated with a unique set of climatic variables potentially influencing local patterns of diversity.

scholarly journals Molecular biogeography and host relations of a parasitoid fly

2019 ◽  
Author(s):  
David A. Gray ◽  
Henry D. Kunerth ◽  
Marlene Zuk ◽  
William H. Cade ◽  
Susan L. Balenger
Keyword(s):  
Genetic Variation ◽  
Range Expansion ◽  
Host Species ◽  
Host Finding ◽  
Molecular Techniques ◽  
Host Specialization ◽  
Population Divergence ◽  
New Host ◽  
Widespread Species ◽  
Gravid Females

AbstractSuccessful geographic range expansion by parasites and parasitoids may also require host range expansion. Thus the evolutionary advantages of host specialization may trade off against the ability to exploit new host species encountered in new geographic regions. Here we use molecular techniques and confirmed host records to examine biogeography, population divergence, and host flexibility of the parasitoid fly, Ormia ochracea (Bigot). Gravid females of this fly find their cricket hosts acoustically by eavesdropping on male cricket calling songs; these songs vary greatly among the known host species of crickets. Using both nuclear and mitochondrial genetic markers, we (1) describe the geographical distribution and sub-division of genetic variation in O. ochracea from across the continental United States, the Mexican states of Sonora and Oaxaca, and populations introduced to Hawaii; (2) demonstrate that the distribution of genetic variation among fly populations is consistent with a single widespread species with regional host specialization, rather than locally differentiated cryptic species, (3) identify the more-probable source populations for the flies introduced to the Hawaiian islands; (4) examine genetic variation and sub-structure within Hawaii; and (5) discuss specialization and lability in host-finding behavior in light of the diversity of cricket songs serving as host cues in different geographically separate populations.

scholarly journals Biases in demographic modelling affect our understanding of recent divergence

2021 ◽  
Author(s):  
Paolo Momigliano ◽  
Ann-Britt Florin ◽  
Juha Merilä
Keyword(s):  
Baltic Sea ◽  
Demographic History ◽  
Divergence Time ◽  
Model Organisms ◽  
Secondary Contact ◽  
Population Divergence ◽  
Model Choice ◽  
Isolation With Migration ◽  
Divergence Time Estimates ◽  
Demographic Modelling

Abstract Testing among competing demographic models of divergence has become an important component of evolutionary research in model and non-model organisms. However, the effect of unaccounted demographic events on model choice and parameter estimation remains largely unexplored. Using extensive simulations, we demonstrate that under realistic divergence scenarios, failure to account for population size (Ne) changes in daughter and ancestral populations leads to strong biases in divergence time estimates as well as model choice. We illustrate these issues reconstructing the recent demographic history of North Sea and Baltic Sea turbots (Schopthalmus maximus) by testing 16 Isolation with Migration (IM) and 16 Secondary Contact (SC) scenarios, modelling changes in Ne as well as the effects of linked selection and barrier loci. Failure to account for changes in Ne resulted in selecting SC models with long periods of isolation and divergence times preceding the formation of the Baltic Sea. In contrast, models accounting for Ne changes suggest recent (<6 kya) divergence with constant gene flow. We further show how interpreting genomic landscapes of differentiation can help discerning among competing models. For example, in the turbots data islands of differentiation show signatures of recent selective sweeps, rather than old divergence resisting secondary introgression. The results have broad implications for the study of population divergence by high-lighting the potential effects of unmodeleld changes in Ne on demographic inference. Tested models should aim at representing realistic divergence scenarios for the target taxa, and extreme caution should always be exercised when interpreting results of demographic modelling.

Molecular phylogeny and taxonomic evaluation of the genus Asaccus Dixon and Anderson, 1973 (Reptilia: Phyllodactylidae) in Iran

2020 ◽  
pp. 207-214
Author(s):  
Akbar Fattahi
Keyword(s):  
Molecular Phylogeny ◽  
Nuclear Gene ◽  
Genetic Distances ◽  
Genetic Lineage ◽  
New Taxon ◽  
Zagros Mountains ◽  
Relict Species ◽  
Taxonomical Revision ◽  
Two Populations ◽  
Taxonomic Evaluation

The Iranian species of the phyllodactylid geckos of the genus Asaccus are found only in the valleys of the Zagros Mountains, a region which represents an important area of endemism in western Iran. Recently, many relict species have been described from the central and southern parts of the Zagros Mountains, which were previously known as A. elisae. The recent descriptions of species within this complex suggest that diversity within the genus may be higher than expected and that its taxonomy and systematics should be revised. In the present study, phylogenetic relationships within the genus Asaccus were evaluated using two mitochondrial and one nuclear gene. Genetically, the genus shows high levels of variability. The molecular phylogeny of the genus suggests the presence of three main clades along the Zagros Mountains with the southern population (from the Hormozgan province) and one clade (A. sp8 and A. sp9) being sister taxon to A. montanus from UAE. The remaining samples are separated into two reciprocally monophyletic groups: the northern (Kurdistan, Kermanshah and Ilam provinces) and the central (Lorestan, Khuzestan, Kohgilouye-Bouyer Ahmad and Fars provinces) Zagros groups. The results of the present study suggest that populations attributed to A. elisae in Iran correspond to distinct lineages with high genetic distances. In brief, our results suggest that the genus needs a major taxonomical revision The Arabian origin of the genus has not been confirmed, because two populations from Zagros were located within the A. montanus, A. gallagheri and A. platyrhynchus clade. Further morphological analyses are needed to systematically define each genetic lineage as a new taxon.

Population Genetics ofCaenorhabditis elegans: The Paradox of Low Polymorphism in a Widespread Species

Genetics ◽  
2003 ◽  
Vol 163 (1) ◽  
pp. 147-157 ◽  
Author(s):  
Arjun Sivasundar ◽  
Jody Hey
Keyword(s):  
Genetic Variation ◽  
Microsatellite Loci ◽  
Population Expansion ◽  
Widespread Species ◽  
C Elegans ◽  
Model Research ◽  
The World ◽  
Natural Isolates ◽  
History Of ◽  
Low Levels

AbstractCaenorhabditis elegans has become one of the most widely used model research organisms, yet we have little information on evolutionary processes and recent evolutionary history of this widespread species. We examined patterns of variation at 20 microsatellite loci in a sample of 23 natural isolates of C. elegans from various parts of the world. One-half of the loci were monomorphic among all strains, and overall genetic variation at microsatellite loci was low, relative to most other species. Some population structure was detected, but there was no association between the genetic and geographic distances among different natural isolates. Thus, despite the nearly worldwide occurrence of C. elegans, little evidence was found for local adaptation in strains derived from different parts of the world. The low levels of genetic variation within and among populations suggest that recent colonization and population expansion might have occurred. However, the patterns of variation are not consistent with population expansion. A possible explanation for the observed patterns is the action of background selection to reduce polymorphism, coupled with ongoing gene flow among populations worldwide.

scholarly journals Czechoslovakian Wolfdog Genomic Divergence from Its Ancestors Canis lupus, German Shepherd Dog, and Different Sheepdogs of European Origin

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 832
Author(s):  
Nina Moravčíková ◽  
Radovan Kasarda ◽  
Radoslav Židek ◽  
Luboš Vostrý ◽  
Hana Vostrá-Vydrová ◽  
...  
Keyword(s):  
Demographic History ◽  
Genome Structure ◽  
Principal Component ◽  
Genetic Distances ◽  
Nucleotide Polymorphisms ◽  
German Shepherd ◽  
German Shepherd Dog ◽  
Genome Wide ◽  
Scale Population ◽  
History Effect

This study focused on the genomic differences between the Czechoslovakian wolfdog (CWD) and its ancestors, the Grey wolf (GW) and German Shepherd dog. The Saarloos wolfdog and Belgian Shepherd dog were also included to study the level of GW genetics retained in the genome of domesticated breeds. The dataset consisted of 131 animals and 143,593 single nucleotide polymorphisms (SNPs). The effects of demographic history on the overall genome structure were determined by screening the distribution of the homozygous segments. The genetic variance distributed within and between groups was quantified by genetic distances, the FST index, and discriminant analysis of principal components. Fine-scale population stratification due to specific morphological and behavioural traits was assessed by principal component and factorial analyses. In the CWD, a demographic history effect was manifested mainly in a high genome-wide proportion of short homozygous segments corresponding to a historical load of inbreeding derived from founders. The observed proportion of long homozygous segments indicated that the inbreeding events shaped the CWD genome relatively recently compared to other groups. Even if there was a significant increase in genetic similarity among wolf-like breeds, they were genetically separated from each other. Moreover, this study showed that the CWD genome carries private alleles that are not found in either wolves or other dog breeds analysed in this study.

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