Methodology Advances in Vertebrate Age Estimation

Age is a core metric in vertebrate management, and the correct estimation of the age of an individual plays a principal role in comprehending animal behavior, identifying genealogical information, and assessing the potential reproductive capacity of populations. Vertebrates have a vertebral column and a distinct head containing a developed brain; they have played an important role in the study of biological evolution. However, biological age estimations constantly exhibit large deviations due to the diversity of vertebrate taxon species, sample types, and determination methods. To systematically and comprehensively understand age estimation methods in different situations, we classify the degree of damage to vertebrates during sample collection, present the sample types and their applications, list commonly applied methods, present methodological recommendations based on the combination of accuracy and implementability, and, finally, predict future methods for vertebrate age assessments, taking into account the current level of research and requirements. Through comprehensive data gathering and compilation, this work serves as an introduction and summary for those who are eager to catch up on related fields and facilitates the rapid and accurate selection of an evaluation method for researchers engaged in related research. This is essential to promote animal conservation and guide the smooth implementation of conservation management plans.

Mercury accumulation, biomagnification, and relationships to δ13C, δ15N and δ34S of fishes and marine mammals in a coastal Arctic marine food web

Combining mercury and stable isotope data sets of consumers facilitates the quantification of whether contaminant variation in predators is due to diet, habitat use and/or environmental factors. We investigated inter-species variation in total Hg (THg) concentrations, trophic magnification slope between δ15N and THg, and relationships of THg with δ13C and δ34S in 15 fish and four marine mammal species (249 individuals in total) in coastal Arctic waters. Median THg concentration in muscle varied between species ranging from 0.08 ± 0.04 μg g-1 dw in capelin to 3.10 ± 0.80 μg g-1 dw in beluga whales. Both δ15N (r2 = 0.26) and δ34S (r2 = 0.19) best explained variation in log-THg across consumers. Higher THg concentrations occurred in higher trophic level species that consumed more pelagic-associated prey than consumers that rely on the benthic microbial-based food web. Our study illustrates the importance of using a multi-isotopic approach that includes δ34S when investigating trophic Hg dynamics in coastal marine systems.

Decadal migration phenology of a long-lived Arctic icon keeps pace with climate change

Animals migrate in response to seasonal environments, to reproduce, to benefit from resource pulses, or to avoid fluctuating hazards. Although climate change is predicted to modify migration, only a few studies to date have demonstrated phenological shifts in marine mammals. In the Arctic, marine mammals are considered among the most sensitive to ongoing climate change due to their narrow habitat preferences and long life spans. Longevity may prove an obstacle for species to evolutionarily respond. For species that exhibit high site fidelity and strong associations with migration routes, adjusting the timing of migration is one of the few recourses available to respond to a changing climate. Here, we demonstrate evidence of significant delays in the timing of narwhal autumn migrations with satellite tracking data spanning 21 y from the Canadian Arctic. Measures of migration phenology varied annually and were explained by sex and climate drivers associated with ice conditions, suggesting that narwhals are adopting strategic migration tactics. Male narwhals were found to lead the migration out of the summering areas, while females, potentially with dependent young, departed later. Narwhals are remaining longer in their summer areas at a rate of 10 d per decade, a similar rate to that observed for climate-driven sea ice loss across the region. The consequences of altered space use and timing have yet to be evaluated but will expose individuals to increasing natural changes and anthropogenic activities on the summering areas.

Evaluating the role of reference-genome phylogenetic distance on evolutionary inference

When a high-quality genome assembly of a target species is unavailable, an option to avoid the costly de novo assembly process is a mapping-based assembly. However, mapping shotgun data to a distant relative may lead to biased or erroneous evolutionary inference. Here, we used short-read data from a mammal (beluga whale) and a bird species (rowi kiwi) to evaluate whether reference genome phylogenetic distance can impact downstream demographic (Pairwise Sequentially Markovian Coalescent) and genetic diversity (heterozygosity, runs of homozygosity) analyses. We mapped to assemblies of species of varying phylogenetic distance (from conspecific to genome-wide divergence of >7%), and de novo assemblies created using cross-species scaffolding. We show that while reference genome phylogenetic distance has an impact on demographic analyses, it is not pronounced until using a reference genome with >3% divergence from the target species. When mapping to cross-species scaffolded assemblies, we are unable to replicate the original beluga demographic results, but are able with the rowi kiwi, presumably reflecting the more fragmented nature of the beluga assemblies. We find that increased phylogenetic distance has a pronounced impact on genetic diversity estimates; heterozygosity estimates deviate incrementally with increasing phylogenetic distance. Moreover, runs of homozygosity are largely undetectable when mapping to any nonconspecific assembly. However, these biases can be reduced when mapping to a cross-species scaffolded assembly. Taken together, our results show that caution should be exercised when selecting reference genomes. Cross-species scaffolding may offer a way to avoid a costly, traditional de novo assembly, while still producing robust, evolutionary inference.

Circumpolar phylogeography and demographic history of beluga whales reflect past climatic fluctuations

Several Arctic marine mammal species are predicted to be negatively impacted by rapid sea ice loss associated with ongoing ocean warming. However, consequences for Arctic whales remain uncertain. To investigate how Arctic whales responded to past climatic fluctuations, we analysed 206 mitochondrial genomes from beluga whales (Delphinapterus leucas) sampled across their circumpolar range, and four nuclear genomes, covering both the Atlantic and the Pacific Arctic region. We found four well-differentiated mitochondrial lineages, which were established before the onset of the last glacial expansion ~110 thousand years ago. Our findings suggested these lineages diverged in allopatry, reflecting isolation of populations during glacial periods when the Arctic sea-shelf was covered by multiyear sea ice. Subsequent population expansion and secondary contact between the Atlantic and Pacific Oceans shaped the current geographic distribution of lineages, and may have facilitated mitochondrial introgression. Our demographic reconstructions based on both mitochondrial and nuclear genomes showed markedly lower population sizes during the Last Glacial Maximum (LGM) compared to the preceding Eemian and current Holocene interglacial periods. Habitat modelling similarly revealed less suitable habitat during the LGM (glacial) than at present (interglacial). Together, our findings suggested the association between climate, population size, and available habitat in belugas. Forecasts for year 2100 showed that beluga habitat will decrease and shift northwards as oceans continue to warm, putatively leading to population declines in some beluga populations. Finally, we identified vulnerable populations which, if extirpated as a consequence of ocean warming, will lead to a substantial decline of species-wide haplotype diversity.

Detection of steroid and thyroid hormones in mammalian teeth

Endocrine tools can provide an avenue to better understand mammalian life histories and predict how individuals and populations may respond to environmental stressors; however, few options exist for studying long-term endocrine patterns in individual marine mammals. Here, we (i) determined whether hormones could be measured in teeth from four marine mammal species: narwhal (Monodon monoceros), beluga (Delphinapterus leucas), killer whale (Orcinus orca) and Atlantic walrus (Odobenus rosmarus rosmarus); (ii) validated commercially available enzyme immunoassay kits for use with tooth extracts; and (iii) conducted biological validations for each species to determine whether reproductive hormone concentrations in teeth correlated with age of sexual maturity. Tooth extracts from all species had measurable concentrations of progesterone, testosterone, 17β-estradiol, corticosterone, aldosterone and triiodothyronine (T3); however, cortisol was undetectable. Parallelism between the binding curves of assay kit standards and serially diluted pools of tooth extract for each species was observed for all measurable hormones. Slopes of accuracy tests ranged from 0.750 to 1.116, with r² values ranging from 0.977 to 1.000, indicating acceptable accuracy. Biological validations were inconsistent with predictions for each species, with the exception of female killer whales (n = 2), which assumed higher progesterone and testosterone concentrations in mature individuals than immature individuals. Instead, we observed a decline in progesterone and testosterone concentrations from infancy through adulthood in narwhal (n = 1) and walruses (n = 2) and higher reproductive hormone concentrations in immature individuals than mature individuals in belugas (n = 8 and 10, respectively) and male killer whales (n = 1 and 2, respectively). While unexpected, this pattern has been observed in other taxa; however, further analytical and biological validations are necessary before this technique can be used to assess individual mammalian endocrine patterns.

Influence of past climate change on phylogeography and demographic history of narwhals, Monodon monoceros

The Arctic is warming at an unprecedented rate, with unknown consequences for endemic fauna. However, Earth has experienced severe climatic oscillations in the past, and understanding how species responded to them might provide insight into their resilience to near-future climatic predictions. Little is known about the responses of Arctic marine mammals to past climatic shifts, but narwhals (Monodon monoceros) are considered one of the endemic Arctic species most vulnerable to environmental change. Here, we analyse 121 complete mitochondrial genomes from narwhals sampled across their range and use them in combination with species distribution models to elucidate the influence of past and ongoing climatic shifts on their population structure and demographic history. We find low levels of genetic diversity and limited geographic structuring of genetic clades. We show that narwhals experienced a long-term low effective population size, which increased after the Last Glacial Maximum, when the amount of suitable habitat expanded. Similar post-glacial habitat release has been a key driver of population size expansion of other polar marine predators. Our analyses indicate that habitat availability has been critical to the success of narwhals, raising concerns for their fate in an increasingly warming Arctic.

The longer the better: evidence that narwhal tusks are sexually selected

Once thought to be the magical horn of a unicorn, narwhal tusks are one of the most charismatic structures in biology. Despite years of speculation, little is known about the tusk's function, because narwhals spend most of their lives hidden underneath the Arctic ice. Some hypotheses propose that the tusk has sexual functions as a weapon or as a signal. By contrast, other hypotheses propose that the tusk functions as an environmental sensor. Since assessing the tusks function in nature is difficult, we can use the morphological relationships of tusk size with body size to understand this mysterious trait. To do so, we collected morphology data on 245 adult male narwhals over the course of 35 years. Based on the disproportional growth and large variation in tusk length we found, we provide the best evidence to date that narwhal tusks are indeed sexually selected. By combining our results on tusk scaling with known material properties of the tusk, we suggest that the narwhal tusk is a sexually selected signal that is used during male-male contests.

Asian elephants exhibit post-reproductive lifespans

BACKGROUND

The existence of extended post-reproductive lifespan is an evolutionary puzzle, and its taxonomic prevalence is debated. One way of measuring post-reproductive life is with post-reproductive representation, the proportion of adult years lived by females after cessation of reproduction. Analyses of post-reproductive representation in mammals have claimed that only humans and some toothed whale species exhibit extended post-reproductive life, but there are suggestions of a post-reproductive stage for false killer whales and Asian elephants. Here, we investigate the presence of post-reproductive lifespan in Asian elephants using an extended demographic dataset collected from semi-captive timber elephants in Myanmar. Furthermore, we investigate the sensitivity of post-reproductive representation values to availability of long-term data over 50 years.

RESULTS

We find support for the presence of an extended post-reproductive stage in Asian elephants, and that post-reproductive representation and its underlying demographic rates depend on the length of study period in a long-lived animal.

CONCLUSIONS

The extended post-reproductive lifespan is unlikely due to physiological reproductive cessation, and may instead be driven by mating preferences or condition-dependent fertility. Our results also show that it is crucial to revisit such population measures in long-lived species as more data is collected, and if the typical lifespan of the species exceeds the initial study period.

Narwhal Genome Reveals Long-Term Low Genetic Diversity despite Current Large Abundance Size

The narwhal (Monodon monoceros) is a highly specialized endemic Arctic cetacean, restricted to the Arctic seas bordering the North Atlantic. Low levels of genetic diversity have been observed across several narwhal populations using mitochondrial DNA and microsatellites. Despite this, the global abundance of narwhals was recently estimated at ∼170,000 individuals. However, the species is still considered vulnerable to changing climates due to its high specialization and restricted Arctic distribution. We assembled and annotated a genome from a narwhal from West Greenland. We find relatively low diversity at the genomic scale and show that this did not arise by recent inbreeding, but rather has been stable over an extended evolutionary timescale. We also find that the current large global abundance most likely reflects a recent rapid expansion from a much smaller founding population.

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Assembled and annotated narwhal nuclear genome

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Low genetic diversity despite large global abundance

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Lack of signs of inbreeding

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Demography is the driving force behind the low diversity

Evidence for a maximum "shelf-life" of oocytes in mammals suggests that human menopause may be an implication of meiotic arrest

There is an ongoing debate why a trait like human menopause should have evolved. Adaptive explanations explain menopause with fitness benefits of ceasing reproduction, whereas non-adaptive explanations view it as an epiphenomenon. Here we present data in support of non-adaptive explanations of menopause suggesting a maximum shelf-life of oocytes. By analyzing the association between lifespan and age at reproductive senescence across 49 mammal species, we find that the positive association levels off in long lived species, indicating that the age at reproductive senescence has an upper limit. Only in baleen whales there seems to be no evidence for reproductive senescence. We suggest that apart from the baleen whales, the confinement of reproductive senescence in long-lived species may be the result of physiological constraints imposed by the long period of time oocytes remain inactive in an arrested phase of meiosis from their production in utero until ovulation. We therefore conclude that menopause may be an implication of the long duration of meiotic arrest caused by semelgametogenesis together with long lifespan.

Analyses of ovarian activity reveal repeated evolution of post-reproductive lifespans in toothed whales

In most species the reproductive system ages at the same rate as somatic tissue and individuals continue reproducing until death. However, females of three species – humans, killer whales and short-finned pilot whales – have been shown to display a markedly increased rate of reproductive senescence relative to somatic ageing. In these species, a significant proportion of females live beyond their reproductive lifespan: they have a post-reproductive lifespan. Research into this puzzling life-history strategy is hindered by the difficulties of quantifying the rate of reproductive senescence in wild populations. Here we present a method for measuring the relative rate of reproductive senescence in toothed whales using published physiological data. Of the sixteen species for which data are available (which does not include killer whales), we find that three have a significant post-reproductive lifespan: short-finned pilot whales, beluga whales and narwhals. Phylogenetic reconstruction suggests that female post-reproductive lifespans have evolved several times independently in toothed whales. Our study is the first evidence of a significant post-reproductive lifespan in beluga whales and narwhals which, when taken together with the evidence for post-reproductive lifespan in killer whales, doubles the number of non-human mammals known to exhibit post-reproductive lifespans in the wild.

Spatial distribution of narwhal (Monodon monoceros) diving for Canadian populations helps identify important seasonal foraging areas

In Canada, narwhals (Monodon monoceros L., 1758) are divided into the Baffin Bay (BB) and northern Hudson Bay (NHB) populations. Satellite tracking of 21 narwhals from BB and NHB provided information on their diving behaviour and was used to identify foraging regions. Previous research from hunted narwhals indicated that narwhals in both populations depend on benthic prey to meet their dietary needs. To evaluate home ranges and define areas important for benthic foraging, we conducted kernel density analysis on narwhal locations and focused on areas where deep diving occurs, as a proxy for foraging, in the winter, spring, and migratory periods. These analyses revealed important areas for foraging for BB narwhals on the summer grounds in Eclipse Sound, and the winter grounds in Davis Strait, as well as on the migratory pathway between regions. Similarly, important areas were identified for the NHB narwhal population in northwestern Hudson Bay in summer, in NHB and Hudson Strait on the migration, and to the east of the entrance to Hudson Strait in the winter. This, along with an analysis of the absolute dive depths, provides information on seasons and regions important for foraging, which is particularly relevant with increasing industrial activities in the Arctic.