An Integrative Approach Using Phylogenomics and High-Resolution X-Ray Computed Tomography for Species Delimitation in Cryptic Taxa

Systematic Biology, Journal Year: 2019, Volume and Issue: unknown

Published: July 24, 2019

Morphologically cryptic taxa have proved to be a long-standing challenge for taxonomists. Lineages that show strong genomic structuring across the landscape but are phenotypically similar pose conundrum, with traditional morphological analyses of these lineages struggling keep up species delimitation advances. Micro X-ray computed tomography (CT) combined geometric morphometric provides promising avenue identification morphologically taxa, given its ability detect subtle differences in anatomical structures. However, this approach has yet used combination data comparative analytical framework distinguish taxa. We present an integrative incorporating and evidence assess grassland earless dragons (Tympanocryptis spp.) north-eastern Australia. Using mitochondrial nuclear genes (ND2 RAG1, respectively), along $>$8500 SNPs (nuclear single nucleotide polymorphisms), we evolutionary independence target several closely related species. then integrate phylogenomic osteological cranial variation between using landmark-based three-dimensional CT models. High levels differentiation three were uncovered, also supported by significant differences. By multiple lines evidence, provide support undescribed Tympanocryptis Australia warrant taxonomic review. Our demonstrates successful application approaches delimitation, which is broadly applicable vertebrates containing genetically distinct lineages. Additionally, review recent assessment how our can value-add research.

Language: Английский

---

Updating the Bibliography of Interbreeding among Canis in North America

Journal of Heredity, Journal Year: 2020, Volume and Issue: 111(3), P. 249 - 262

Published: Feb. 6, 2020

Abstract This bibliography provides a collection of references that documents the evolution studies evidencing interbreeding among Canis species in North America. Over past several decades, advances biology and genomic technology greatly improved our ability to detect characterize interbreeding, which has significance for understanding changing landscape as well endangered management. includes discussion within each category timeline developing evidence, review research conducted on experimental crosses. Research early 20th century is rich with detailed records photographs hybrid offspring development behavior. With progression molecular methods, can estimate historical demographic parameters chromosomal patterns ancestry. As these methods continue increase accessibility, field will gain deeper richer evolutionary history American Canis.

Language: Английский

---

Testing the effectiveness of genetic monitoring using genetic non‐invasive sampling

Ecology and Evolution, Journal Year: 2021, Volume and Issue: 12(1)

Published: Dec. 27, 2021

Abstract Effective conservation requires accurate data on population genetic diversity, inbreeding, and structure. Increasingly, scientists are adopting non‐invasive sampling (gNIS) as a cost‐effective population‐wide monitoring approach. gNIS has, however, known limitations which may impact the accuracy of downstream analyses. Here, using high‐quality single nucleotide polymorphism (SNP) from blood/tissue free‐ranging koala ( n = 430), we investigated how reduced SNP panel size call rate typical samples (derived experimental field trials) impacts measures, also effect intensity these measures. We found that at small sample sizes (14% population) can provide diversity but slightly underestimated inbreeding coefficients. Accurate measures internal relatedness required least 33% to be sampled. geographic spatial autocorrelation analysis between 28% 51% show low powerful tool aid decision‐making recommendations for researchers looking apply techniques systems.

Language: Английский

---

Phenotypic characterization and analysis of genetic diversity between commercial crossbred and indigenous chickens from three different agro-ecological zones using DArT-Seq technology

PLoS ONE, Journal Year: 2024, Volume and Issue: 19(5), P. e0297643 - e0297643

Published: May 2, 2024

Indigenous and were used to study genetic diversity population structure analyses. Polymorphism information content (PIC) values ranged from 0.0 0.5, with 21,285 SNP markers (35%) being in the lowest PIC value range (0 0.15) while 13,511 (commercial chickens have developed unique adaptations their environments, which may include nutrition, pathogens, thermal stress. Besides, environmental pressures artificial selection generated significant genome-wide divergence chickens, as those contribute a considerable evolutionary force phenotypic genotypic differentiation. Herein, we determined genomic of indigenous semi-deciduous rainforest (SDR), coastal savannah (CS) Guinea (GS) agro-ecological zones (AEZs) Ghana commercial crossbreds (CC) reared at Kwame Nkrumah University Science Technology (KNUST). We 82 (62 chicken ecotypes 26 crossbred ecotype) using DArT-Seq technology. A total 85,396 after filtering data, 58,353 21%) highest (0.45 0.50). The CC more genetically diverse than birds, expected heterozygosity 0.220. Between ecotypes, pairwise F ST estimated be 0.105 between CS, 0.096 SDF, 0.133 GS. Furthermore, PCA analysis showed that CC, SDF GS clustered together are distant crossbred. herein show AEZs studied can considered one population. However, due abundance agro-byproducts SDR compared CS GS, AEZ had better growth counterparts. It is suggested within local could form basis for improvement.

Language: Английский

---

Advancements in noninvasive koala monitoring through combining Chlamydia detection with a targeted koala genotyping assay

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Dec. 5, 2024

Wildlife diseases are major players in local and global extinctions. Effective disease surveillance, management conservation strategies require accurate estimates of pathogen prevalence. Yet detection wild animals remains challenging. Current gold standards often samples collected through veterinary examination, but this method is costly, intensive, invasive, requires specialised staff equipment. Collection non-invasive samples, such as scats, an effective monitoring tool which can be deployed at large scale, scats contain DNA both host pathogens. The koala (Phascolarctos cinereus) listed 'endangered' under the EPBC Act 1999, with chlamydial representing a threat. Here, we present new approach that combines restriction-enzyme associated sequencing targeted-sequence-capture genotyping, namely DArTcap, to detect Chlamydia pecorum scats. We found has similar accuracy current (qPCR swab samples), sensitivity 91.7% specificity 100%. This incorporated into existing genetic studies using marker panels, where population attributes estimated alongside C. presence, same scat option add further markers interest. Such one-stop-shop panel would considerably reduce processing times cost.

Language: Английский

---