Species limits and phylogeographic structure in two genera of solitary African mole-rats Georychus and Heliophobius

2021 ◽  
pp. 107337
Author(s):  
M Uhrová ◽  
O Mikula ◽  
N.C Bennett ◽  
P Van Daele ◽  
L Piálek ◽  
...  
Keyword(s):  
Phylogeographic Structure ◽  
Species Limits

Species limits and cryptic biogeographic structure in a widespread complex of Australian monsoon tropics trees (broad-leaf paperbarks: Melaleuca, Myrtaceae)

2018 ◽  
Author(s):  
Robert D. Edwards ◽  
Michael D. Crisp ◽  
Lyn G. Cook
Keyword(s):  
Incomplete Lineage Sorting ◽  
Phylogeographic Structure ◽  
Lineage Sorting ◽  
Species Limits ◽  
Widespread Species ◽  
Australian Monsoon ◽  
Network Analyses ◽  
The North ◽  
Broad Leaf ◽  
Drying Trend

The Australian monsoon tropics are currently dominated by savanna and tropical woodland biomes that have arisen in response to a cooling and drying trend within the past ~3 million years. It is expected that organisms well adapted to these conditions have expanded into available habitats, leading to the differentiation of populations and species across this landscape, a process that could be magnified by the presence of several biogeographic barriers. The broad-leaved paperbark (Melaleuca leucadendra (L.) L.) complex is one such group of plants, with 14 poorly morphologically differentiated species occupying large overlapping distributions across the region, and across several recognised biogeographic barriers. Using phylogenetic and network analyses of nuclear and plastid sequences, we tested species limits among currently described species within the complex and for phylogeographic structure within species across seven of these barriers. Overall, our data suggested patterns of differentiation among species consistent with the early to middle stages of incomplete lineage sorting, and evidence for an idiosyncratic cryptic response of species to biogeographic barriers. Unexpectedly, we found a deep molecular split across all species, broadly coinciding with the northern part of the Great Dividing Range, a feature not typically considered to be a barrier to dispersal. Our study has offered one of the first insights into the dynamics within and among widespread species across the north of Australia, suggesting considerably more geographic structure than was previously recognised.

Joseph Sidebotham: vicissitudes of a Victorian collector

2015 ◽  
Vol 42 (2) ◽  
pp. 197-210 ◽  
Author(s):  
Laurence M. Cook
Keyword(s):  
Natural History ◽  
Species Limits ◽  
Clear Cut ◽  
Natural History Collections ◽  
As Species ◽  
Scientific World

Joseph Sidebotham (1824–1885) was a Manchester cotton baron whose natural history collections are now in the Manchester Museum. In addition to collecting he suggested a method for identifying and classifying Lepidoptera and investigated variation within species as well as species limits. With three close collaborators, he is credited with discovering many species new to Britain in both Lepidoptera and Coleoptera. A suspicion of fraud attaches to these claims. The evidence is not clear-cut in the Lepidoptera, but a possible reason is suggested why Sidebotham, as an amateur in the increasingly professional scientific world, might have engaged in deceit.

Differences between recent and historical records of upper species limits in the northern European Alps

Erdkunde ◽  
2013 ◽  
Vol 67 (4) ◽  
pp. 345-354
Author(s):  
Sebastian Schmidtlein ◽  
Ulrike Faude ◽  
Ole Rössler ◽  
Hannes Feilhauer ◽  
Jörg Ewald ◽  
...  
Keyword(s):  
European Alps ◽  
Historical Records ◽  
Species Limits ◽  
Northern European

scholarly journals Whole-Genome Sequencing and Characterization of Buffalo Genetic Resources: Recent Advances and Future Challenges

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 904
Author(s):  
Saif ur Rehman ◽  
Faiz-ul Hassan ◽  
Xier Luo ◽  
Zhipeng Li ◽  
Qingyou Liu
Keyword(s):  
Selective Breeding ◽  
Reference Genome ◽  
De Novo ◽  
Phenotypic Diversity ◽  
Molecular Data ◽  
Genomic Diversity ◽  
Production Performance ◽  
Phylogeographic Structure ◽  
Economic Significance ◽  
And Performance

The buffalo was domesticated around 3000–6000 years ago and has substantial economic significance as a meat, dairy, and draught animal. The buffalo has remained underutilized in terms of the development of a well-annotated and assembled reference genome de novo. It is mandatory to explore the genetic architecture of a species to understand the biology that helps to manage its genetic variability, which is ultimately used for selective breeding and genomic selection. Morphological and molecular data have revealed that the swamp buffalo population has strong geographical genomic diversity with low gene flow but strong phenotypic consistency, while the river buffalo population has higher phenotypic diversity with a weak phylogeographic structure. The availability of recent high-quality reference genome and genotyping marker panels has invigorated many genome-based studies on evolutionary history, genetic diversity, functional elements, and performance traits. The increasing molecular knowledge syndicate with selective breeding should pave the way for genetic improvement in the climatic resilience, disease resistance, and production performance of water buffalo populations globally.

scholarly journals Analysis of multiple chromosomal rearrangements in the genome of Willisornis vidua using BAC-FISH and chromosome painting on a supposed conserved karyotype

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Talita Fernanda Augusto Ribas ◽  
Julio Cesar Pieczarka ◽  
Darren K. Griffin ◽  
Lucas G. Kiazim ◽  
Cleusa Yoshiko Nagamachi ◽  
...  
Keyword(s):  
Chromosome Painting ◽  
Diploid Number ◽  
Chromosomal Rearrangements ◽  
Large Degree ◽  
Artificial Chromosome ◽  
Gallus Gallus ◽  
Phylogeographic Structure ◽  
Molecular Cytogenetic ◽  
Burhinus Oedicnemus ◽  
Intrachromosomal Rearrangements

Abstract Background Thamnophilidae birds are the result of a monophyletic radiation of insectivorous Passeriformes. They are a diverse group of 225 species and 45 genera and occur in lowlands and lower montane forests of Neotropics. Despite the large degree of diversity seen in this family, just four species of Thamnophilidae have been karyotyped with a diploid number ranging from 76 to 82 chromosomes. The karyotypic relationships within and between Thamnophilidae and another Passeriformes therefore remain poorly understood. Recent studies have identified the occurrence of intrachromosomal rearrangements in Passeriformes using in silico data and molecular cytogenetic tools. These results demonstrate that intrachromosomal rearrangements are more common in birds than previously thought and are likely to contribute to speciation events. With this in mind, we investigate the apparently conserved karyotype of Willisornis vidua, the Xingu Scale-backed Antbird, using a combination of molecular cytogenetic techniques including chromosome painting with probes derived from Gallus gallus (chicken) and Burhinus oedicnemus (stone curlew), combined with Bacterial Artificial Chromosome (BAC) probes derived from the same species. The goal was to investigate the occurrence of rearrangements in an apparently conserved karyotype in order to understand the evolutionary history and taxonomy of this species. In total, 78 BAC probes from the Gallus gallus and Taeniopygia guttata (the Zebra Finch) BAC libraries were tested, of which 40 were derived from Gallus gallus macrochromosomes 1–8, and 38 from microchromosomes 9–28. Results The karyotype is similar to typical Passeriformes karyotypes, with a diploid number of 2n = 80. Our chromosome painting results show that most of the Gallus gallus chromosomes are conserved, except GGA-1, 2 and 4, with some rearrangements identified among macro- and microchromosomes. BAC mapping revealed many intrachromosomal rearrangements, mainly inversions, when comparing Willisornis vidua karyotype with Gallus gallus, and corroborates the fissions revealed by chromosome painting. Conclusions Willisornis vidua presents multiple chromosomal rearrangements despite having a supposed conservative karyotype, demonstrating that our approach using a combination of FISH tools provides a higher resolution than previously obtained by chromosome painting alone. We also show that populations of Willisornis vidua appear conserved from a cytogenetic perspective, despite significant phylogeographic structure.

scholarly journals Morphology, vocalizations, and mitochondrial DNA suggest that the Graceful Prinia is two species

The Auk ◽  
2021 ◽  
Author(s):  
Per Alström ◽  
Pamela C Rasmussen ◽  
Canwei Xia ◽  
Lijun Zhang ◽  
Chengyi Liu ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Arabian Peninsula ◽  
Morphological Characters ◽  
Sensu Stricto ◽  
Species Limits ◽  
Mosaic Pattern ◽  
Coalescence Time ◽  
New Subspecies ◽  
Taxonomic Analysis ◽  
Potential Contact

Abstract Prinias (Cisticolidae: Prinia) are resident warblers of open areas across Africa and Asia and include many polytypic species whose species limits have not been seriously reevaluated recently. Based on an integrative taxonomic analysis of morphology, song, and mitochondrial DNA (mtDNA), we suggest that 2 species should be recognized in the Graceful Prinia (Prinia gracilis) complex. In addition, our morphological analyses show the existence of a well-marked undescribed form in southeastern Somalia, which we name herein as a new subspecies. Prinia gracilis is a small, drab, long-tailed species with streaking above and plain pale underparts that has been suggested to fall into 2 groups: the southwestern nominate group (from Egypt to Oman) and the northeastern lepida group (from Turkey through India). However, the characters presented to justify this grouping are variable and show a mosaic pattern, and whether genetic and vocal differences exist is unknown. We found consistent between-group song differences, with the nominate group giving consistently longer inter-phrase intervals, whereas the members of the lepida group sing an essentially continuous reel. An mtDNA tree suggests a deep split between the nominate and lepida groups, with a coalescence time between these clades of ~ 2.2 million years ago. Vocal and mtDNA analyses provided evidence that the northeastern Arabian Peninsula taxon carpenteri belongs to the lepida group. We found that, of all the morphological characters proposed, only proportions and tail barring and spotting relatively consistently distinguish the 2 groups. However, these characters strongly suggest that the eastern Arabian Peninsula is populated by taxa of both the gracilis and lepida groups, in different areas, but we lack genetic and bioacoustic data to corroborate this. Although further study is needed in potential contact zones, we suggest that 2 species should be recognized in the P. gracilis complex, and we propose the retention of the English name Graceful Prinia for P. gracilis sensu stricto, while we suggest that P. lepida be known as Delicate Prinia.

scholarly journals Phylogeographic Structure of White Oaks Throughout the European Continent

Genetics ◽  
1997 ◽  
Vol 146 (4) ◽  
pp. 1475-1487 ◽  
Author(s):  
S Dumolin-Lapègue ◽  
B Demesure ◽  
S Fineschi ◽  
V Le Come ◽  
R J Petit
Keyword(s):  
Statistical Approach ◽  
Restriction Analysis ◽  
Phylogeographic Structure ◽  
White Oak ◽  
European Continent ◽  
The Balkans ◽  
Left Behind ◽  
The Difference ◽  
Mantel’S Test ◽  
Very High

Patterns of chloroplast DNA (cpDNA) variation were studied in eight white oak species by sampling 345 populations throughout Europe. The detection of polymorphisms by restriction analysis of PCR-amplified cpDNA fragments allowed the identification of 23 haplotypes that were phylogenetically ordered. A systematic hybridization and introgression between the eight species studied is evident. The levels of subdivision for unordered (G  ST) and ordered (N  ST) alleles are very high and close (0.83 and 0.85). A new statistical approach to the quantitative study of phylogeography is presented, which relies on the coefficients of differentiation G  ST and N  ST and the Mantel's test. Based on pairwise comparisons between populations, the significance of the difference between both coefficients is evaluated at a global and a local scale. The mapped distribution of the haplotypes indicates the probable routes of postglacial recolonization followed by oak populations that had persisted in southern refugia, especially in the Iberian peninsula, Italy and the Balkans. Most cpDNA polymorphisms appear to be anterior to the befinnina of the last recolonization. A subset of the preexisting haplotypes have merely expanded north, while others were left behind in the south.

Performance of a points-based scoring system for assessing species limits in birds

The Auk ◽  
2021 ◽  
Author(s):  
Joseph A Tobias ◽  
Paul F Donald ◽  
Rob W Martin ◽  
Stuart H M Butchart ◽  
Nigel J Collar
Keyword(s):  
Strong Support ◽  
Molecular Data ◽  
Sympatric Species ◽  
Global Scale ◽  
Training Set ◽  
Species Limits ◽  
Phenotypic Data ◽  
Fast Tracking ◽  
Extinction Rates ◽  
Phenotypic Divergence

AbstractSpecies are fundamental to biology, conservation, and environmental legislation; yet, there is often disagreement on how and where species limits should be drawn. Even sophisticated molecular methods have limitations, particularly in the context of geographically isolated lineages or inadequate sampling of loci. With extinction rates rising, methods are needed to assess species limits rapidly but robustly. Tobias et al. devised a points-based system to compare phenotypic divergence between taxa against the level of divergence in sympatric species, establishing a threshold to guide taxonomic assessments at a global scale. The method has received a mixed reception. To evaluate its performance, we identified 397 novel taxonomic splits from 328 parent taxa made by application of the criteria (in 2014‒2016) and searched for subsequent publications investigating the same taxa with molecular and/or phenotypic data. Only 71 (18%) novel splits from 60 parent taxa have since been investigated by independent studies, suggesting that publication of splits underpinned by the criteria in 2014–2016 accelerated taxonomic decisions by at least 33 years. In the evaluated cases, independent analyses explicitly or implicitly supported species status in 62 (87.3%) of 71 splits, with the level of support increasing to 97.2% when excluding subsequent studies limited only to molecular data, and reaching 100% when the points-based criteria were applied using recommended sample sizes. Despite the fact that the training set used to calibrate the criteria was heavily weighted toward passerines, splits of passerines and non-passerines received equally strong support from independent research. We conclude that the method provides a useful tool for quantifying phenotypic divergence and fast-tracking robust taxonomic decisions at a global scale.

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