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Species phylogeny of North Pacific albatrosses (Phoebastria spp.). Phoebastria nigripes and P. immutabilis are sister species, which cluster with P. albatrus to form a monophyletic clade. P. irrorata is the outgroup to this clade. Species tree inferred using (A) SNAPP based on SNPs. Topology is the same as MP-EST species trees based on UCEs, exons, and introns (supplementary fig. S1, Supplementary Material online). Diomedea exulans is included as outgroup. Scales are shown in coalescent units. (B) Phylogeny based on whole mitochondrial genomes. Individual IDs are in parentheses (see supplementary table S1, Supplementary Material online for sample information). Islands of origin are shown at right. Black circle indicates bootstrap support >90%. Illustrations reproduced with permission of Lynx Edicions.
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Throughout the Plio-Pleistocene, climate change has impacted tropical marine ecosystems substantially, with even more severe impacts predicted in the Anthropocene. Although many studies have clarified demographic histories of seabirds in polar regions, the history of keystone seabirds of the tropics is unclear, despite the prominence of albatrosses...
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... whole-genome phylogenomic analyses and a mitogenome tree, we determined the phylogenetic relationships of the four North Pacific albatross species. Our revised phylogeny places the three species breeding in the North Pacific ( fig. 2A and supplementary fig. S2, Supplementary Material online) in a monophyletic group to the exclusion of P. irrorata, which differs from earlier topologies inferred using only cytochrome b (cytb) sequences that lacks the power to resolve the relationship ( Nunn et al. 1996;Chambers et al. 2009). Colonization of the North Pacific Ocean was therefore likely a single ...
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... first mapping trial provided evidence for collapsed MHC class II gene copies in each albatross species (see supplementary fig. S20, Supplementary Material online), so we therefore mapped reads to a reference MHC region that contained a duplicated MHC class IIα/β gene pair to further corroborate this result. We generated this reference MHC region in silico by overlapping the MHC-containing scaffolds identified for P. nigripes and then mapped the 220 bp fragment ...
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... MHC class II α and β genes were shown to undergo duplication in each albatross species (supplementary fig. S20, Supplementary Material online) and therefore likely originated from a single ancestral duplication event. The duplicated α and β genes are adjacent to each other, separated by only ∼1.2 kb and flanked by the COL11A2 and BRD2 ...
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... from their genome assemblies and then aligned with those from other procellariiform species using MEGA7 ( Kumar et al. 2016). The 16 lineage-specific nucleotides used to differentiate DAB1 and DAB2 genes were inferred from Goebel et al. (2017). The duplicated MHC IIβ genes all belong to the DAB2 lineage as described by Goebel et al. (2017) (supplementary fig. S22, Supplementary Material online). No DAB1 lineage genes were found in albatross, in contrast to some other procellariiform seabirds (Dearborn et al. ...
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... To address these data gaps, we sourced 99 reference samples (Table S1) To enable evaluation of the three selected markers across all procellariiform species, we subsequently developed a custom reference DNA sequence database for each marker (COI_AP, Cytb_AP and CRBird_AP), using all available sequences from all 149 procellariiform species. These databases included all relevant procellariiform sequences from GenBank (families Diomedeidae, Hydrobatidae, Oceanitidae and Procellariidae; accessed July 2023), sequences extracted from the mitochondrial genomes of four North Pacific albatross species (genus Phoebastria) and for wandering albatross (D. exulans) as assembled by Huynh et al. (2023), and the new reference sequences generated in this study (described above). Two CR copy two sequences, previously unpublished by Rains, Weimerskirch, and Burg (2011), were also included (Table S1; Diomedea exulans; PP712121 and PP712122). ...
... For each of the three genetic markers, we accessed all relevant sequences available from GenBank for all procellariiform species (families Diomedeidae, Hydrobatidae, Oceanitidae and Procellariidae; accessed July 2023). We also extracted the relevant sequences of the mitochondrial genomes assembled for four North Pacific albatross species (genus Phoebastria) and for wandering albatross (D. exulans) by Huynh et al. (2023) and included the new reference sequences generated in this study (described above). ...
Incidental mortality in fisheries is a major driver of population declines for albatrosses and petrels globally. However, accurate identification of species can be difficult due to the poor condition of bycaught birds and/or visual similarities between closely related species. We assessed three genetic markers for their ability to distinguish the 36 albatross and petrel species listed in Annex 1 to the Agreement on the Conservation of Albatrosses and Petrels (ACAP) and in Australia's Threat Abatement Plan (TAP) for the bycatch of seabirds during oceanic longline fishing operations. We generated 275 new sequences, from 29 species, to improve the coverage of reference databases for these listed species. The combined use of the selected Cytochrome b and Control Region markers enabled the identification of 31 of 36 listed seabirds to species level and four to sister species. One petrel species could not be evaluated as no reference sequences were available. We tested these markers on 59 feathers from bycaught seabirds and compared these to onboard visual identification. We successfully assigned all procellariiforms to species (n = 58), whereas only two seabirds were correctly identified to species visually onboard, highlighting the difficulty of visual species assignment and the need for alternative methods. We assessed the utility of our two chosen markers for the assignment of all procellariiform species, with 74% of species with reference sequences identified to species or sister species level. However, a precautionary approach is needed for application beyond our listed species due to unvalidated reference sequences. The approach described here provides a streamlined framework for the molecular identification of seabird bycatch. This approach is recommended for use in fisheries within and outside Australian waters to improve the resolution of bycatch reporting and to corroborate logbook entries, observer reports and audits of images captured by electronic monitoring systems as well as help inform conservation efforts.
... Single nucleotide polymorphisms (SNPs) and microsatellites are two examples of molecular markers that have made it possible to precisely identify and characterize the genetic variety of chicken breeds [6]. These methods shed light on the genetic linkages, breeding histories, and evolutionary histories of various poultry populations [7]. Moreover, molecular methods make assessing genetic features easier and finding potential genes linked to phenotypic attributes like disease resistance, egg production, and meat quality. ...
Tukong chicken is called the rumples (no tailbone) chicken in Indonesia. This research was done to determine whether the D-loop in mitochondrial DNA might be used to distinguish between the Tukong chicken and other local chickens. The D-loop region’s first 630 base pairs were amplified and successfully sequenced. Our research displayed 34 nucleotide variants based on the alignment between the Tukong and GenBank of Gallus (25 accession number) sequences of Indonesian local chicken and several exotic chicken breeds. However, there were no specific mutations for Tukong chicken. The Tajima’s neutrality test showed that from 31 sequences and 34 total sites, the nucleotide diversity (π) was 0.013. The phylogenetic analysis by the maximum-likelihood method revealed that the Tukong chicken was in a different clade from the Araucana, Nunukan, and Piao chickens, which have similar rumples phenotypes. Meanwhile, the local chicken of Indonesia (Kampung Sumatera, Pelung, Cemani, and Bekikuk) and the Tukong chicken are closely related. It can be concluded that based on the partial D-loop sequences, the Tukong chicken is more closely related to Indonesian local chicken despite its different morphological appearance.
Understanding how population structure and demography are determined is a central theme in marine biogeography. While historical events, such as past climate change, are important determinants, the mechanisms by which they act are not well understood in many marine species. In this study, the population structure of the Japanese, marine intertidal gastropod Lunella correensis was investigated to determine whether it has been affected by past environmental changes. A genome-wide SNP analysis, L. correensis showed a genetic gradient along the coast and a weak genetic differentiation between sites in the Sea of Japan and the Pacific Ocean. Demographic inference suggests that the effective population size expanded and shrunk in response to periods of rapid warming and cooling due to past climate change. Further, ecological niche modelling suggests that the population size of L. correensis increased by advancing into the Sea of Japan during rapid warming after the Last Glacial Maximum. Notably, our analyses suggest that recent human activities may have influenced the effective population size of this species. Specifically, the period of reduction in the population size coincides with environmental changes and habitat loss associated with development along the Japanese coastal area. Thus, these results emphasize that the genetic structure and demography of marine species have been influenced by past environmental change around the Japanese Archipelago.
Island organisms often evolve phenotypes divergent from their mainland counterparts, providing a useful system for studying adaptation under differential selection. In the white-winged fairywren (Malurus leucopterus), subspecies on two islands have a black nuptial plumage whereas the subspecies on the Australian mainland has a blue nuptial plumage. The black subspecies have a feather nanostructure that could in principle produce a blue structural color, suggesting a blue ancestor. An earlier study proposed independent evolution of melanism on the islands based on the history of subspecies divergence. However, the genetic basis of melanism and the origin of color differentiation in this group are still unknown. Here, we used whole-genome resequencing to investigate the genetic basis of melanism by comparing the blue and black M. leucopterus subspecies to identify highly divergent genomic regions. We identified a well-known pigmentation gene ASIP and four candidate genes that may contribute to feather nanostructure development. Contrary to the prediction of convergent evolution of island melanism, we detected signatures of a selective sweep in genomic regions containing ASIP and SCUBE2 not in the black subspecies but in the blue subspecies, which possesses many derived SNPs in these regions, suggesting that the mainland subspecies has re-evolved a blue plumage from a black ancestor. This proposed re-evolution was likely driven by a pre-existing female preference. Our findings provide new insight into the evolution of plumage coloration in island versus continental populations, and, importantly, we identify candidate genes that likely play roles in the development and evolution of feather structural coloration.
