Spheniscidae (1 Viewer)

[Peter Kovalik]

Cole, T.L., C. Zhou, M. Fang, H. Pan, D.T. Ksepka, S.R. Fiddaman, C.A. Emerling, D.B. Thomas, X. Bi, Q. Fang, M.R. Ellegaard, S. Feng, A.L. Smith, T.A. Heath, A.J.D. Tennyson, P. García Borboroglu, J.R. Wood, P.W. Hadden, S. Grosser, C.-A. Bost, Y. Cherel, T. Mattern, T. Hart, M.-H.S. Sinding, L.D. Shepherd, R.A. Phillips, P. Quillfeldt, J.F. Masello, J.L. Bouzat, P.G. Ryan, D.R. Thompson, U. Ellenberg, P. Dann, G. Miller, P.D. Boersma, R. Zhao, M.T.P. Gilbert, H. Yang, D.-X. Zhang, and G. Zhang. 2022. Genomic insights into the secondary aquatic transition of penguins. Nature Communications 13: 3912. published 19 July 2022. Genomic insights into the secondary aquatic transition of penguins - Nature Communications

Abstract
Penguins lost the ability to fly more than 60 million years ago, subsequently evolving a hyper-specialized marine body plan. Within the framework of a genome-scale, fossil-inclusive phylogeny, we identify key geological events that shaped penguin diversification and genomic signatures consistent with widespread refugia/recolonization during major climate oscillations. We further identify a suite of genes potentially underpinning adaptations related to thermoregulation, oxygenation, diving, vision, diet, immunity and body size, which might have facilitated their remarkable secondary transition to an aquatic ecology. Our analyses indicate that penguins and their sister group (Procellariiformes) have the lowest evolutionary rates yet detected in birds. Together, these findings help improve our understanding of how penguins have transitioned to the marine environment, successfully colonizing some of the most extreme environments on Earth.

 

[Melanie]

Designation of a neotype for Eudyptula minor (Aves: Spheniscidae)​

No abstract

Designation of a neotype for Eudyptula minor (Aves: Spheniscidae) | Zootaxa

mapress.com

 

[albertonykus]

Herman, R.W., G. Clucas, J. Younger, J. Bates, B. Robinson, S. Reddy, J. Stepanuk, K. O'Brien, K. Veeramah, and H.J. Lynch (2024)
Whole genome sequencing reveals stepping-stone dispersal buffered against founder effects in a range expanding seabird
Molecular Ecology (advance online publication)
doi: 10.1111/mec.17282

Many species are shifting their ranges in response to climate-driven environmental changes, particularly in high-latitude regions. However, the patterns of dispersal and colonization during range shifting events are not always clear. Understanding how populations are connected through space and time can reveal how species navigate a changing environment. Here, we present a fine-scale population genomics study of gentoo penguins (Pygoscelis papua), a presumed site-faithful colonial nesting species that has increased in population size and expanded its range south along the Western Antarctic Peninsula. Using whole genome sequencing, we analysed 129 gentoo penguin individuals across 12 colonies located at or near the southern range edge. Through a detailed examination of fine-scale population structure, admixture, and population divergence, we inferred that gentoo penguins historically dispersed rapidly in a stepping-stone pattern from the South Shetland Islands leading to the colonization of Anvers Island, and then the adjacent mainland Western Antarctica Peninsula. Recent southward expansion along the Western Antarctic Peninsula also followed a stepping-stone dispersal pattern coupled with limited post-divergence gene flow from colonies on Anvers Island. Genetic diversity appeared to be maintained across colonies during the historical dispersal process, and range-edge populations are still growing. This suggests large numbers of migrants may provide a buffer against founder effects at the beginning of colonization events to maintain genetic diversity similar to that of the source populations before migration ceases post-divergence. These results coupled with a continued increase in effective population size since approximately 500–800 years ago distinguish gentoo penguins as a robust species that is highly adaptable and resilient to changing climate.

 

[albertonykus]

McComish, B.J., M.A. Charleston, M. Parks, C. Baroni, M.C. Salvatore, R. Li, G. Zhang, C.D. Millar, B.R. Holland, and D.M. Lambert (2024)
Ancient and modern genomes reveal microsatellites maintain a dynamic equilibrium through deep time
Genome Biology and Evolution 16: evae017
doi: 10.1093/gbe/evae017

Microsatellites are widely used in population genetics, but their evolutionary dynamics remain poorly understood. It is unclear whether microsatellite loci drift in length over time. This is important because the mutation processes that underlie these important genetic markers are central to the evolutionary models that employ microsatellites. We identify more than 27 million microsatellites using a novel and unique dataset of modern and ancient Adélie penguin genomes along with data from 63 published chordate genomes. We investigate microsatellite evolutionary dynamics over 2 timescales: one based on Adélie penguin samples dating to ∼46.5 ka and the other dating to the diversification of chordates aged more than 500 Ma. We show that the process of microsatellite allele length evolution is at dynamic equilibrium; while there is length polymorphism among individuals, the length distribution for a given locus remains stable. Many microsatellites persist over very long timescales, particularly in exons and regulatory sequences. These often retain length variability, suggesting that they may play a role in maintaining phenotypic variation within populations.

 

[Peter Kovalik]

Proposal (1001) to SACC

Treat Eudyptes filholi as a separate species from E. chrysocome

 

[Peter Kovalik]

Proposal (1001) to SACC

Treat Eudyptes filholi as a separate species from E. chrysocome

DID NOT PASS

 

[Peter Kovalik]

León, F., E. Pizarro, D. Noll, L. R. Pertierra, P. Parker, M. P. A. Espinaze, G. Luna-Jorquera, A. Simeone, E. Frere, G. Dantas, R. Cristofari, O. E. Cornejo, R. C. K. Bowie, and J. A. Vianna (2024) Comparative genomics supports ecologically induced selection as a putative driver of banded penguin diversification [Spheniscus]. Molecular Biology and Evolution: msae166, published online 16 August 2024.
Comparative genomics supports ecologically induced selection as a putative driver of banded penguin diversification

Abstract
The relative importance of genetic drift and local adaptation in facilitating speciation remains unclear. This is particularly true for seabirds, who can disperse over large geographic distances, providing opportunities for intermittent gene flow among distant colonies that span the temperature and salinity gradients of the oceans. Here, we delve into the genomic basis of adaptation and speciation of banded penguins, Galápagos (Spheniscus mendiculus), Humboldt (S. humboldti), Magellanic (S. magellanicus) and African penguins (S. demersus), by analyzing 114 genomes from the main 16 breeding colonies. We aim to identify the molecular mechanism and genomic adaptive traits that have facilitated their diversifications. Through positive selection and gene family expansion analyses, we identified candidate genes that may be related to reproductive isolation processes mediated by ecological thermal niche divergence. We recover signals of positive selection on key loci associated with spermatogenesis, especially during the recent peripatric divergence of the Galápagos penguin from the Humboldt penguin. High temperatures in tropical habitats may have favored selection on loci associated with spermatogenesis to maintain sperm viability, leading to reproductive isolation among young species. Our results suggest that genome-wide selection on loci associated with molecular pathways that underpin thermoregulation, osmoregulation, hypoxia, and social behavior appear to have been crucial in local adaptation of banded penguins. Overall, these results contribute to our understanding of how the complexity of biotic, but especially abiotic, factors, along with the high dispersal capabilities of these marine species, may promote both neutral and adaptive lineage divergence even in the presence of gene flow.

 

[albertonykus]

Wood, J.R., C. Zhou, T.L. Cole, M. Coleman, D.P. Anderson, P.O’B. Lyver, S. Tan, X. Xiang, X. Long, S. Luo, M. Lou, J.R. Southon, Q. Li, and G. Zhang (2025)
Sedimentary DNA insights into Holocene Adélie penguin (Pygoscelis adeliae) populations and ecology in the Ross Sea, Antarctica
Nature Communications 16: 1798
doi: 10.1038/s41467-025-56925-4

We report 156 sediment metagenomes from Adélie penguin (Pygoscelis adeliae) colonies dating back 6000 years along the Ross Sea coast, Antarctica, and identify marine and terrestrial eukaryotes, including locally occurring bird and seal species. The data reveal spatiotemporal patterns of Adélie penguin diet, including spatial patterns in consumption of cnidarians, a historically overlooked component of Adélie penguin diets. Relative proportions of Adélie penguin mitochondrial lineages detected at each colony are comparable to those previously reported from bones. Elevated levels of Adélie penguin mitochondrial nucleotide diversity in upper stratigraphic samples of several active colonies are consistent with recent population growth. Moreover, the highest levels of Adélie penguin mitochondrial nucleotide diversity recovered from surface sediment layers are from the two largest colonies, indicating that sedaDNA could provide estimates for the former size of abandoned colonies. SedaDNA also reveals prior occupation of the Cape Hallett Adélie penguin colony site by southern elephant seal (Mirounga leonina), demonstrating how terrestrial sedaDNA can detect faunal turnover events in Antarctica driven by past climate or sea ice conditions. Low rates of cytosine deamination indicate exceptional sedaDNA preservation within the region, suggesting there is high potential for recovering much older sedaDNA records from local Pleistocene terrestrial sediments.