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The escape of DNA from mitochondria into the nuclear genome (nuclear mitochondrial DNA, NUMT) is an ongoing process. Although pervasively observed in eukaryotic genomes, their evolutionary trajectories in a mammal-wide context are poorly understood. The main challenge lies in the orthology assignment of NUMTs across species due to their fast evolution and chromosomal rearrangements over the past 200 million years. To address this issue, we systematically investigated the characteristics of NUMT insertions in 45 mammalian genomes and established a novel, synteny-based method to accurately predict orthologous NUMTs and ascertain their evolution across mammals. With a series of comparative analyses across taxa, we revealed that NUMTs may originate from nonrandom regions in mtDNA, are likely found in transposon-rich and intergenic regions, and unlikely code for functional proteins. Using our synteny-based approach, we leveraged 630 pairwise comparisons of genome-wide microsynteny and predicted the NUMT orthology relationships across 36 mammals. With the phylogenetic patterns of NUMT presence-and-absence across taxa, we constructed the ancestral state of NUMTs given the mammal tree using a coalescent method. We found support on the ancestral node of Fereuungulata within Laurasiatheria, whose subordinal relationships are still controversial. This study broadens our knowledge on NUMT insertion and evolution in mammalian genomes and highlights the merit of NUMTs as alternative genetic markers in phylogenetic inference. [ABSTRACT FROM AUTHOR]

Hibernation is linked with various hypotheses to explain the extended lifespan of hibernating mammals compared with their non-hibernating counterparts. Studies on telomeres, markers of ageing and somatic maintenance, suggest telomere shortening slows during hibernation, and lengthening may reflect self-maintenance with favourable conditions. Bats in temperate zones adjust body temperatures during winter torpor to conserve energy and exploit mild conditions for foraging. Climate change may impact the hibernation cycle of bats, but more research is needed regarding the role of telomeres in understanding their response to a changing climate. Here, relative telomere length (rTL) was measured in the long-lived greater horseshoe bat Rhinolophus ferrumequinum (n = 223 individuals) over three winters, considering climatic conditions. Cross-sectional analyses revealed between-individual variation in rTL with a strong year effect, likely linked to varying weather conditions and foraging success. Additionally, within-individual increases of rTL occurred in 51% of consecutive measurements, with evidence of increasing telomerase expression during hibernation in this species. These findings highlight the beneficial effects of hibernation on telomeres and potential consequences of changing climatic conditions for long-lived temperate bats. Understanding the interplay between hibernation, telomeres, and climate can provide insights into the adaptive capacity and survival of bat populations facing environmental challenges. [ABSTRACT FROM AUTHOR]

Horizontal transfer of transposable elements (TEs) is an important mechanism contributing to genetic diversity and innovation. Bats (order Chiroptera) have repeatedly been shown to experience horizontal transfer of TEs at what appears to be a high rate compared with other mammals. We investigated the occurrence of horizontally transferred (HT) DNA transposons involving bats. We found over 200 putative HT elements within bats; 16 transposons were shared across distantly related mammalian clades, and 2 other elements were shared with a fish and two lizard species. Our results indicate that bats are a hotspot for horizontal transfer of DNA transposons. These events broadly coincide with the diversification of several bat clades, supporting the hypothesis that DNA transposon invasions have contributed to genetic diversification of bats. [ABSTRACT FROM AUTHOR]

Over 20% of all living mammals are bats (order Chiroptera). Bats possess extraordinary adaptations including powered flight, laryngeal echolocation and a unique immune system that enables them to tolerate a diversity of viral infections without presenting clinical disease symptoms. They occupy multiple trophic niches and environments globally. Significant physiological and ecological diversity occurs across the order. Bats also exhibit extreme longevity given their body size with many species showing few signs of ageing. The molecular basis of this extended longevity has recently attracted attention. Telomere maintenance potentially underpins bats' extended healthspan, although functional studies are still required to validate the causative mechanisms. In this review, we detail the current knowledge on bat telomeres, telomerase expression, and how these relate to ecology, longevity and life‐history strategies. Patterns of telomere shortening and telomerase expression vary across species, and comparative genomic analyses suggest that alternative telomere maintenance mechanisms evolved in the longest‐lived bats. We discuss the unique challenges faced when working with populations of wild bats and highlight ways to advance the field including expanding long‐term monitoring across species that display contrasting life‐histories and occupy different environmental niches. We further review how new high quality, chromosome‐level genome assemblies can enable us to uncover the molecular mechanisms governing telomere dynamics and how phylogenomic analyses can reveal the adaptive significance of telomere maintenance and variation in bats. [ABSTRACT FROM AUTHOR]

Biologists are struggling to understand a recent emerging infectious disease, white-nose syndrome (WNS) (1), which potentially threatens >20% of all mammalian diversity (bats) (2). WNS is a deadly epidemic that [...]

Seven species of the Asian torrent frogs (genus Amolops) have previously been reported from the eastern Himalayan country of Bhutan. Species identifications from the region have been largely based on photographed animals with few voucher specimens available and no molecular sampling. Understanding the taxonomic status of Bhutan's torrent frogs has also been hampered by the poorly understood distributional limits of species from surrounding regions. Herein we utilised molecular phylogenetic and morphological data for vouchered specimens from Bhutan and provide a complete literature review of all Amolops populations reported from the country. Phylogenetic relationships were estimated by combining available sequence data (from GenBank) with newly generated sequences from recently collected Bhutanese Amolops populations. We also obtained archival DNA sequences from the type specimens of Amolops formosus, A. himalayanus, and A. kaulbacki, collected between 82 and 151 years ago. Our comparative analyses revealed a large, new (to science) species of the Amolops viridimaculatus group from eastern Bhutan. Morphological examinations of related taxa revealed that A. senchalensis from India is not a synonym of A. marmoratus. Molecular phylogenetic results supplemented by morphological data unambiguously demonstrate i) that A. himalayanus is present in eastern Nepal, ii) the presence of a previously undocumented population of A. nepalicus in eastern Nepal, iii) a 200 km range extention for A. kaulbacki into Yunnan, China, iv) that A. gyirongensis should be considered a junior subjective synonym of A. formosus, and v) that A. splendissimus from Vietnam should be considered a junior subjective synonym of A. viridimaculatus. Based on our results, we expand the Amolops viridimaculatus group to include nine species, including A. formosus, A. himalayanus, A. kaulbacki, and the new species described herein. We provisionally include a further three species in the viridimaculatus group based on morphology, A. longimanus, A. nidorbellus, and A. senchalensis. Combining our data with the literature review allowed us to identify several unidentified Amolops species from recent phylogenetic studies and remove nine frog species (including Hyla, Sylvirana, and seven Amolops species) from Bhutan's amphibian checklist. We recognise four species of Amolops in Bhutan, three of which cannot be confidently identified to the species level based on currently available data. [ABSTRACT FROM AUTHOR]

Relationships among laurasiatherian clades represent one of the most highly disputed topics in mammalian phylogeny. In this study, we attempt to disentangle laurasiatherian interordinal relationships using two independent genome-level approaches: (1) quantifying retrotransposon presence/absence patterns, and (2) comparisons of exon datasets at the levels of nucleotides and amino acids. The two approaches revealed contradictory phylogenetic signals, possibly due to a high level of ancestral incomplete lineage sorting. The positions of Eulipotyphla and Chiroptera as the first and second earliest divergences were consistent across the approaches. However, the phylogenetic relationships of Perissodactyla, Cetartiodactyla, and Ferae, were contradictory. While retrotransposon insertion analyses suggest a clade with Cetartiodactyla and Ferae, the exon dataset favoured Cetartiodactyla and Perissodactyla. Future analyses of hitherto unsampled laurasiatherian lineages and synergistic analyses of retrotransposon insertions, exon and conserved intron/intergenic sequences might unravel the conflicting patterns of relationships in this major mammalian clade. [ABSTRACT FROM AUTHOR]

Author(s): Emma C. Teeling [1, 2]; Mark Scally [1, 2]; Diana J. Kao [3]; Michael L. Romagnoli [3]; Mark S. Springer [3]; Michael J. Stanhope (corresponding author) [1, 2] Bats [...]

Comprising more than 1,400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent lineages, reducing the scope of inferences on gene family evolution across the Order Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat species, one generated in this study, encompassing a large number of lineages, with a particular emphasis on multi‐gene family evolution across immune and metabolic genes. In agreement with previous analyses, we found lineage‐specific expansions of the APOBEC3 and MHC‐I gene families, and loss of the proinflammatory PYHIN gene family. We inferred more than 1,000 gene losses unique to bats, including genes involved in the regulation of inflammasome pathways such as epithelial defence receptors, the natural killer gene complex and the interferon‐gamma induced pathway. Gene set enrichment analyses revealed genes lost in bats are involved in defence response against pathogen‐associated molecular patterns and damage‐associated molecular patterns. Gene family evolution and selection analyses indicate bats have evolved fundamental functional differences compared to other mammals in both innate and adaptive immune system, with the potential to enhance antiviral immune response while dampening inflammatory signalling. In addition, metabolic genes have experienced repeated expansions related to convergent shifts to plant‐based diets. Our analyses support the hypothesis that, in tandem with flight, ancestral bats had evolved a unique set of immune adaptations whose functional implications remain to be explored. [ABSTRACT FROM AUTHOR]

Telomeres are used increasingly in ecology and evolution as biomarkers for ageing and environmental stress, and are typically measured from DNA extracted from nonlethally sampled blood. However, obtaining blood is not always possible in field conditions and only limited amounts can be taken from small mammals, such as bats, which moreover lack nucleated red blood cells and hence yield relatively low amounts of DNA. As telomere length can vary within species according to age and tissue, it is important to determine which tissues serve best as a representation of the organism as a whole. Here, we investigated whether wing tissue biopsies, a rapid and relatively noninvasive tissue collection method, could serve as a proxy for other tissues when measuring relative telomere length (rTL) in the Egyptian fruit bat (Rousettus aegyptiacus). Telomeres were measured from blood, brain, heart, kidney, liver lung, muscle and wing, and multiple wing biopsies were taken from the same individuals to determine intra‐individual repeatability of rTL measured by using qPCR. Wing rTL correlated with rTL estimates from most tissues apart from blood. Blood rTL was not significantly correlated with rTL from any other tissue. Blood and muscle rTLs were significantly longer compared with other tissues, while lung displayed the shortest rTLs. Individual repeatability of rTL measures from wing tissue was high (>70%). Here we show the relationships between tissue telomere dynamics for the first time in a bat, and our results provide support for the use of wing tissue for rTL measurements. [ABSTRACT FROM AUTHOR]

Age‐related telomere shortening is considered a hallmark of the ageing process. However, a recent cross‐sectional ageing study of relative telomere length (rTL) in bats failed to detect a relationship between rTL and age in the long‐lived genus Myotis (M. myotis and M. bechsteinii), suggesting some other factors are responsible for driving telomere dynamics in these species. Here, we test if longitudinal rTL data show signatures of age‐associated telomere attrition in M. myotis and differentiate which intrinsic or extrinsic factors are likely to drive telomere length dynamics. Using quantitative polymerase chain reaction, rTL was measured in 504 samples from a marked population, from Brittany, France, captured between 2013 and 2016. These represent 174 individuals with an age range of 0 to 7+ years. We find no significant relationship between rTL and age (p =.762), but demonstrate that within‐individual rTL is highly variable from year to year. To investigate the heritability of rTL, a population pedigree (n = 1744) was constructed from genotype data generated from a 16‐microsatellite multiplex, designed from an initial, low‐coverage, Illumina genome for M. myotis. Heritability was estimated in a Bayesian, mixed model framework, and showed that little of the observed variance in rTL is heritable (h2 = 0.01–0.06). Rather, correlations of first differences, correlating yearly changes in telomere length and weather variables, demonstrate that, during the spring transition, average temperature, minimum temperature, rainfall and windspeed correlate with changes in longitudinal telomere dynamics. As such, rTL may represent a useful biomarker to quantify the physiological impact of various environmental stressors in bats. see also the Perspective by Luise A. Seeker. [ABSTRACT FROM AUTHOR]

is currently considered to be among the most widely dispersed species within the genus, however, recent studies have provided compelling evidence that this species represents a complex of morphologically similar, deeply divergent taxa. The focus of this paper is to take a closer look at species from Northeast India (NEI) and Bangladesh that are currently, or were until recently, considered to represent M. parva, now comprising the M. (Xenophrys) megacephala species group. We investigate their troublesome taxonomic histories, identify hidden cryptic species diversity using morphological and molecular data, and resolve many of the historical misidentifications that have led to a proliferation of taxonomic confusion in this group. Molecular analyses extend the geographic distribution of the M. (X.) megacephala species group east into northern Myanmar based on available sequence data. A detailed redescription of the paralectotypes of M. parva is provided to better define this poorly known species. The geographic distributions of the taxonomically obscure species, M. serchhipii and M. zunhebotoensis, are extended far beyond their respective type localities, and both are considerably better defined taxonomically based on detailed descriptions of referred specimens, and comparison with relevant congeners. Significant geographic range extensions are also provided for the recently described species M. oropedion and M. megacephala. Three new species from the Indian states of Nagaland and Manipur are identified using a combination of morphological characters, supported by significant genetic divergence. Examination of historical specimen collections and scrutiny of published literature provide sufficient evidence to remove M. parva and M. wuliangshanensis from the checklist of Indian species. Previous records of M. parva from Bangladesh are demonstrated to represent M. serchhipii. Recent reports of M. glandulosa and M. robusta from Meghalaya are also revised and are considered to be based on misidentifications of known species from the state. The revised distributions of NEI's small-sized horned frogs provide insights into the biogeography of the group. One of the newly described species known only from the high-elevation Dzükou Valley, Nagaland, might require immediate conservation action due to increased tourist activity at its type locality. [ABSTRACT FROM AUTHOR]