Correction to: Genetic differentiation and overexploitation history of the critically endangered Lehmann’s Poison Frog: Oophaga lehmanni

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.

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Phylogenomic Reconstruction of the Neotropical Poison Frogs (Dendrobatidae) and Their Conservation

Diversity ◽

10.3390/d11080126 ◽

2019 ◽

Vol 11 (8) ◽

pp. 126 ◽

Cited By ~ 5

Author(s):

Wilson X. Guillory ◽

Morgan R. Muell ◽

Kyle Summers ◽

Jason L. Brown

Keyword(s):

Bayesian Methods ◽

Evolutionary History ◽

Conservation Status ◽

Nuclear Data ◽

Nuclear Markers ◽

Poison Frog ◽

Sequence Capture ◽

Genome Wide ◽

Frog Species ◽

History Of

The evolutionary history of the Dendrobatidae, the charismatic Neotropical poison frog family, remains in flux, even after a half-century of intensive research. Understanding the evolutionary relationships between dendrobatid genera and the larger-order groups within Dendrobatidae is critical for making accurate assessments of all aspects of their biology and evolution. In this study, we provide the first phylogenomic reconstruction of Dendrobatidae with genome-wide nuclear markers known as ultraconserved elements. We performed sequence capture on 61 samples representing 33 species across 13 of the 16 dendrobatid genera, aiming for a broadly representative taxon sample. We compare topologies generated using maximum likelihood and coalescent methods and estimate divergence times using Bayesian methods. We find most of our dendrobatid tree to be consistent with previously published results based on mitochondrial and low-count nuclear data, with notable exceptions regarding the placement of Hyloxalinae and certain genera within Dendrobatinae. We also characterize how the evolutionary history and geographic distributions of the 285 poison frog species impact their conservation status. We hope that our phylogeny will serve as a backbone for future evolutionary studies and that our characterizations of conservation status inform conservation practices while highlighting taxa in need of further study.

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Large-scale geographic survey provides insights into the colonization history of a major aphid pest on its cultivated apple host in Europe, North America and North Africa

10.1101/2020.12.11.421644 ◽

2020 ◽

Author(s):

S.G. Olvera-Vazquez ◽

C. Remoue ◽

A. Venon ◽

A. Rousselet ◽

O. Grandcolas ◽

...

Keyword(s):

Gene Flow ◽

North America ◽

Genetic Differentiation ◽

North Africa ◽

Large Scale ◽

Demographic History ◽

High Genetic Diversity ◽

The North ◽

The Us ◽

History Of

With frequent host shifts involving the colonization of new hosts across large geographical ranges, crop pests are good models for examining the mechanisms of rapid colonization. The microbial partners of pest insects may be involved or affected by colonization, which has been little studied so far. We investigated the demographic history of the rosy apple aphid, Dysaphis plantaginea, a major pest of the cultivated apple (Malus domestica) in Europe, North Africa and North America, as well as the diversity of its endosymbiotic bacterial community. We genotyped a comprehensive sample of 714 colonies from Europe, Morocco and the US using mitochondrial (CytB and CO1), bacterial (16s rRNA and TrnpB), and 30 microsatellite markers. We detected five populations spread across the US, Morocco, Western and Eastern Europe, and Spain. Populations showed weak genetic differentiation and high genetic diversity, except the Moroccan and the North American that are likely the result of recent colonization events. Coalescent-based inferences releaved high levels of gene flow among populations during the colonization, but did not allow determining the sequence of colonization of Europe, America and Morroco by D. plantaginea, likely because of the weak genetic differentiation and the occurrence of gene flow among populations. Finally, we found that D. plantaginea rarely hosts any other endosymbiotic bacteria than its obligate nutritional symbiont Buchnera aphidicola. This suggests that secondary endosymbionts did not play any role in the rapid spread of the rosy apple aphid. These findings have fundamental importance for understanding pest colonization processes and implications for sustainable pest control programs.

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Life history of the Critically Endangered largetooth sawfish: a compilation of data for population assessment and demographic modelling

Endangered Species Research ◽

10.3354/esr01090 ◽

2020 ◽

Author(s):

PM Kyne ◽

M Oetinger ◽

MI Grant ◽

P Feutry

Keyword(s):

Life History ◽

Critically Endangered ◽

Population Assessment ◽

History Of ◽

Demographic Modelling

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Genetic Differentiation of Reintroduced Père David’s Deer (Elaphurus davidianus) Based on Population Genomics Analysis

Frontiers in Genetics ◽

10.3389/fgene.2021.705337 ◽

2021 ◽

Vol 12 ◽

Author(s):

Shumiao Zhang ◽

Chao Li ◽

Yiping Li ◽

Qi Chen ◽

Defu Hu ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Genetic Differentiation ◽

Population Size ◽

Population Genomics ◽

Distribution Area ◽

History Of ◽

Père David’S Deer ◽

Free Ranging ◽

Elaphurus Davidianus

The reintroduction is an important conservation tool to restore a species in its historically distribution area, but the rate of reintroduction success varies across species or regions due to different reasons. Genetic evaluation is important to the conservation management of reintroduced species. Conservation concerns relate to genetic threats for species with a small population size or severely historically bottle-necked species, such as negative consequences associated with loss of genetic diversity and inbreeding. The last 40years have seen a rapid increasing of population size for Père David’s deer (Elaphurus davidianus), which originated from a limited founder population. However, the genetic structure of reintroduced Père David’s deer has not been investigated in terms of population genomics, and it is still not clear about the evolutionary history of Père David’s deer and to what extent the inbreeding level is. Conservation genomics methods were used to reconstruct the demographic history of Père David’s deer, evaluate genetic diversity, and characterize genetic structure among 18 individuals from the captive, free-ranging and wild populations. The results showed that 1,456,457 single nucleotide polymorphisms (SNPs) were obtained for Père David’s deer, and low levels of genome-wide genetic diversity were observed in Père David’s deer compared with Red deer (Cervus elaphus) and Sika deer (Cervus nippon). A moderate population genetic differentiation was detected among three populations of Père David’s deer, especially between the captive population in Beijing Père David’s deer park and the free-ranging population in Jiangsu Dafeng National Nature Reserve. The effective population size of Père David’s deer started to decline ~25.8ka, and the similar levels of three populations’ LD reflected the genetic impacts of long-term population bottlenecks in the Père David’s deer. The findings of this study could highlight the necessity of individual exchange between different facilities, and genetic management should generally be integrated into conservation planning with other management considerations.

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Genetic differentiation and introgression amongst Thylogale (pademelons) taxa in eastern Australia

Australian Journal of Zoology ◽

10.1071/zo11022 ◽

2011 ◽

Vol 59 (2) ◽

pp. 103 ◽

Cited By ~ 6

Author(s):

M. D. B. Eldridge ◽

K. Heckenberg ◽

L. E. Neaves ◽

C. J. Metcalfe ◽

S. Hamilton ◽

...

Keyword(s):

Genetic Differentiation ◽

Dispersal Ability ◽

Sympatric Populations ◽

Genetic Studies ◽

Eastern Australia ◽

Moist Forest ◽

Phylogeographic History ◽

History Of ◽

Wet Tropics ◽

Mtdna Markers

Although pademelons (Thylogale) are widespread and common in coastal eastern Australia, they have been largely neglected in population genetic studies. Here we use 10 microsatellite loci and the mitochondrial DNA (mtDNA) cytochrome b (Cytb) gene to examine genetic differentiation amongst populations of the red-necked (Thylogale thetis) and red-legged (T. stigmatica) pademelon in eastern Australia. Evidence of hybridisation was detected between subspecies of T. stigmatica in central Queensland. Specimens sampled between Eungella and Sarina were found to represent a broad (~90 km) zone of introgression, for both nuclear and mtDNA markers, between T. s. stigmatica (Wet Tropics) and T. s. wilcoxi (south-east Queensland). In addition, individuals sampled from around Proserpine were genetically T. s. stigmatica rather than T. s. wilcoxi, as had previously been assumed. This observation raises some intriguing questions about the dispersal ability of T. stigmatica and the phylogeographic history of moist forest taxa in eastern Australia. Only limited evidence of introgression was detected between sympatric populations of T. thetis and T. s. wilcoxi in south-east Queensland.

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