Biology subjects

Salis, A. T.

Publications and source records attributed to Salis, A. T..

6 recordsLinked to original sources

bioRxiv2026

Ancient mitogenomes reveal unexpected diversity in Madagascar's extinct hippopotamuses

Madagascar's extinct hippopotamuses were a distinctive component of the island's recently lost megafauna, yet their origins, diversification history, and taxonomy have remained unresolved. Here, we recover the first ancient mitochondrial genomes from Malagasy hippopotamuses, obtaining phylogenetic data from 37 subfossil specimens across seven localities and all three named species, and integrate these data with morphology and total-evidence phylogenetic analyses. The 35 endemic specimens form a single clade most closely related to Hippopotamus amphibius, supporting a single colonization of Madagascar. Within this radiation, five deeply divergent and geographically structured mitochondrial lineages diversified across most regions of Madagascar during the Pleistocene. Tip-dating estimates a remarkably young crown age of ~1.41 Ma, following divergence from mainland Hippopotamus at ~3.24 Ma. These lineages do not map cleanly onto traditional taxonomy: material assigned to H. lemerleispans several divergent clades, while H. laloumena and H. madagascariensis are nested within this broader diversity. Morphology supports some lineage assignments but also points to previously unrecognized diversity, while ancestral-state reconstruction supports early body-size reduction followed by a secondary increase in H. laloumena. Malagasy hippopotamuses therefore represent an exceptionally recent radiation of large-bodied island mammals (and the youngest in Madagascar), showing that Madagascar continued to generate endemic mammalian diversity well into the Pleistocene. Their late-Holocene extinction erased the product of more than a million years of rapid insular diversification, the drivers of which remain enigmatic.

evolutionary biology↗

bioRxiv2026

Was the extinct Spectacled Cormorant part of the North Pacific kelp-associated fauna?

The coastal North Pacific kelp ecosystems are highly productive, supporting a rich faunal assemblage. Some historical aspects of this ecosystem remain poorly studied, as exemplified by the extinct Spectacled Cormorant Urile perspicillatus, whose Late Holocene distribution was apparently restricted to Bering Island. This cormorant's taxonomic relationships remain unresolved and little is known about its ecology. We use ancient-DNA to reconstruct the evolutionary history of the Spectacled Cormorant. Mitogenomes from five of the six known historical skins form a strongly supported clade within Urile cormorants. The ancestors of Spectacled Cormorant diverged from its closest relatives, the Pelagic (U. pelagicus) and Red-faced (U. urile) cormorants, ~6.98 Mya, and the population subsequently underwent a pronounced bottleneck. This divergence time is co-incident with the establishment of coastal kelp-forests. The Spectacled Cormorant may have been an integral part of the kelp-associated fauna as a large benthic-foraging predator. Similar to the sympatric Steller's sea cow (Hydrodamalis gigas), the historical relict distribution of the Spectacled Cormorant may be the result of trophic collapse of kelp-forest ecosystems and subsistence hunting. Future palaeogenomic and dietary isotopic research, and reassessment of North Pacific archaeological and fossil assemblages, should shed light on the evolution and palaeoecology of this enigmatic seabird.

evolutionary biology↗

bioRxiv2026

Historically Small Population Size Limits Purging of Deleterious Mutations in a Conservation-Reliant Species, the Kirtlands Warbler

Strong population contractions can leave a persistent genomic legacy that can influence populations long after their demographic recovery. While bottlenecks facilitate the removal of strongly deleterious mutations, the effectiveness of purging may be limited in historically small populations. The Kirtlands warbler (Setophaga kirtlandii) is a rare North American songbird with an ancestrally small population. After narrowly evading extinction, they are one of few species that have been delisted from federal protections in the USA. Despite their recovery, a previous study showed evidence for recent inbreeding and a high burden of deleterious mutations that may have not been purged despite strong bottlenecks. Historical DNA offers a unique opportunity to understand the consequences of recent demographic declines on genetic diversity. Here, we use DNA from over 100-year-old museum specimens to estimate changes in genetic load in the Kirtlands warblers pre- and post-bottleneck. We validate our results with forward-in-time genetic simulations and explore how sample size and missing data can affect estimates. Both empirical data and simulations suggest a reduced ability to purge deleterious mutations in this historically small population. Our simulations also highlight that limited sampling design and data quality can constrain the ability to detect changes.

evolutionary biology↗

bioRxiv2021

Rapid radiation of Southern Ocean shags in response to receding sea ice

AimUnderstanding how wild populations respond to climatic shifts is a fundamental goal of biological research in a fast-changing world. The Southern Ocean represents a fascinating system for assessing large-scale climate-driven biological change, as it contains extremely isolated island groups within a predominantly westerly, circumpolar wind and current system. The blue-eyed shags (Leucocarbo spp.) represent a paradoxical Southern Ocean seabird radiation; a circumpolar distribution implies strong dispersal capacity yet their speciose nature suggests local adaptation and isolation. Here we use genetic tools in an attempt to resolve this paradox. LocationSouthern Ocean. Taxa17 species and subspecies of blue-eyed shags (Leucocarbo spp.) across the geographical distribution of the genus. MethodsHere we use mitochondrial and nuclear sequence data to conduct the first global genetic analysis of this group using a temporal phylogenetic framework to test for rapid speciation. ResultsOur analysis reveals remarkably shallow evolutionary histories among island-endemic lineages, consistent with a recent high-latitude circumpolar radiation. This rapid sub-Antarctic expansion contrasts with significantly deeper lineages detected in more temperate regions such as South America and New Zealand that may have acted as glacial refugia. The dynamic history of high-latitude expansions is further supported by ancestral demographic and biogeographic reconstructions. Main conclusionsThe circumpolar distribution of blue-eyed shags, and their highly dynamic evolutionary history, potentially make Leucocarbo a strong sentinel of past and ongoing Southern Ocean ecosystem change given their sensitivity to climatic impacts.

evolutionary biology↗

bioRxiv2021

Ancient genomes reveal hybridisation between extinct short-faced bears and the extant spectacled bear (Tremarctos ornatus)

Two genera and multiple species of short-faced bear from the Americas went extinct during or toward the end of the Pleistocene, and all belonged to the endemic New World subfamily Tremarctinae [1-7]. Two of these species were giants, growing in excess of 1,000 kg [6, 8, 9], but it remains uncertain how these extinct bears were related to the sole surviving short-faced bear: the spectacled bear (Tremarctos ornatus). Ancient mitochondrial DNA has recently suggested phylogenetic relationships among these lineages that conflict with interpretations based on morphology [1, 10-12]. However, widespread hybridisation and incomplete lineage sorting among extant bears mean that the mitochondrial phylogeny frequently does not reflect the true species tree [13, 14]. Here we present ancient nuclear genome sequences from representatives of the two extinct short-faced bear genera, Arctotherium and Arctodus. Our new data support a third hypothesis for the relationships among short-faced bears, which conflicts with existing mitochondrial and morphological data. Based on genome-wide D-statistics, we suggest that the extant spectacled bear derives substantial ancestry from Pleistocene hybridisation with an extinct short-faced bear lineage, resulting in a discordant phylogenetic signal between the mitochondrion and portions of the nuclear genome.

evolutionary biology↗

bioRxiv2020

Lions and brown bears colonized North America in multiple synchronous waves of dispersal across the Bering Land Bridge

The Bering Land Bridge connecting North America and Eurasia was periodically exposed and inundated by oscillating sea levels during the Pleistocene glacial cycles. This land connection allowed the intermittent dispersal of animals, including humans, between Western Beringia (far north-east Asia) and Eastern Beringia (north-west North America), changing the faunal community composition of both continents. The Pleistocene glacial cycles also had profound impacts on temperature, precipitation, and vegetation, impacting faunal community structure and demography. While these paleoenvironmental impacts have been studied in many large herbivores from Beringia (e.g., bison, mammoths, horses), the Pleistocene population dynamics of the diverse guild of carnivorans present in the region are less well understood, due to their lower abundances. In this study, we analyze mitochondrial genome data from ancient brown bears (Ursus arctos; n = 103) and lions (Panthera spp.; n = 39), two megafaunal carnivorans that dispersed into North America during the Pleistocene. Our results reveal striking synchronicity in the population dynamics of Beringian lions and brown bears, with multiple waves of dispersal across the Bering Land Bridge coinciding with glacial periods of low sea levels, as well as synchronous local extinctions in Eastern Beringia during Marine Isotope Stage 3. The evolutionary histories of these two taxa underscore the crucial biogeographic role of the Bering Land Bridge in the distribution, turnover, and maintenance of megafaunal populations in North America.

evolutionary biology↗