205 newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates

Mitochondrial DNA remains a cornerstone for molecular ecology, especially for study species from which high-quality tissue samples cannot be easily obtained. Methods using mitochondrial markers are usually reliant on reference databases, but these are often incomplete. Furthermore, available mitochondrial genomes often lack crucial metadata, such as sampling location, limiting their utility for many analyses. Here, we assembled 205 new mitochondrial genomes for platyrrhine primates, most from the Amazon and with known sampling locations. We present a dated mitogenomic phylogeny based on these samples along with additional published platyrrhine mitogenomes, and use this to assess support for the long-standing riverine barrier hypothesis (RBH), which proposes that river formation was a major driver of speciation in Amazonian primates. Along the Amazon, Negro, and Madeira rivers, we found mixed support for the RBH. While we identified divergences that coincide with a river barrier, only some occur synchronously and also overlap with the proposed dates of river formation. The most compelling evidence is for the Amazon river potentially driving speciation within bearded saki monkeys (Chiropotes spp.) and within the smallest extant platyrrhines, the marmosets and tamarins. However, we also found that even large rivers do not appear to be barriers for some primates, including howler monkeys (Alouatta spp.), uakaris (Cacajao spp.), sakis (Pithecia spp.), and robust capuchins (Sapajus spp.). Our results support a more nuanced, clade-specific effect of riverine barriers and suggest that other evolutionary mechanisms, besides the RBH and allopatric speciation, may have played an important role in the diversification of platyrrhines

The genomics of ecological flexibility, large brains, and long lives in capuchin monkeys revealed with fecalFACS

Ecological flexibility, extended lifespans, and large brains have long intrigued evolutionary biologists, and comparative genomics offers an efficient and effective tool for generating new insights into the evolution of such traits. Studies of capuchin monkeys are particularly well situated to shed light on the selective pressures and genetic underpinnings of local adaptation to diverse habitats, longevity, and brain development. Distributed widely across Central and South America, they are inventive and extractive foragers, known for their sensorimotor intelligence. Capuchins have among the largest relative brain size of any monkey and a lifespan that exceeds 50 y, despite their small (3 to 5 kg) body size. We assemble and annotate a de novo reference genome for Through high-depth sequencing of DNA derived from blood, various tissues, and feces via fluorescence-activated cell sorting (fecalFACS) to isolate monkey epithelial cells, we compared genomes of capuchin populations from tropical dry forests and lowland rainforests and identified population divergence in genes involved in water balance, kidney function, and metabolism. Through a comparative genomics approach spanning a wide diversity of mammals, we identified genes under positive selection associated with longevity and brain development. Additionally, we provide a technological advancement in the use of noninvasive genomics for studies of free-ranging mammals. Our intra- and interspecific comparative study of capuchin genomics provides insights into processes underlying local adaptation to diverse and physiologically challenging environments, as well as the molecular basis of brain evolution and longevity. [Abstract copyright: Copyright © 2021 the Author(s). Published by PNAS.

The population genomic legacy of the second plague pandemic

Human populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10%–40%.1 It is assumed that this high mortality affected the gene pools of these populations. First, local population crashes reduced genetic diversity. Second, a change in frequency is expected for sequence variants that may have affected survival or susceptibility to the etiologic agent (Yersinia pestis).2 Third, mass mortality might alter the local gene pools through its impact on subsequent migration patterns. We explored these factors using the Norwegian city of Trondheim as a model, by sequencing 54 genomes spanning three time periods: (1) prior to the plague striking Trondheim in 1,349 CE, (2) the 17th–19th century, and (3) the present. We find that the pandemic period shaped the gene pool by reducing long distance immigration, in particular from the British Isles, and inducing a bottleneck that reduced genetic diversity. Although we also observe an excess of large FST values at multiple loci in the genome, these are shaped by reference biases introduced by mapping our relatively low genome coverage degraded DNA to the reference genome. This implies that attempts to detect selection using ancient DNA (aDNA) datasets that vary by read length and depth of sequencing coverage may be particularly challenging until methods have been developed to account for the impact of differential reference bias on test statistics.publishedVersio

Body condition changes of Miniopterus schreibersii in autumn and winter

To prepare for hibernation, bats rapidly deposit large amounts of adipose tissue in early autumn that will be needed to sustain them during the dormancy period. The store of a small amount of body fat in autumn or high mass loss during winter can be critical. This study aims to investigate the autumn and winter body condition changes in 1998-99 of M. schreibersii and its interannual variability. We have studied bats from four Spanish shelters. Bats were weighed, sexed and their forearms measured. The samples were analysed by using calculation of residuals, one-way ANOVA and Scheffé test Interannual variability has been analysed by comparing the data obtained during winter 1998-99 to data obtained during winters 1984-85 and 1985-86. Body condition of M. schreibersii change significantly from October to March. M. schreibersii from NE Spain store reserves from October to mid-November. Bats increased their body mass of 31.5 % in just 29 days during autumn 1998, whereas they lost 23% of prehibemation body mass in 4 months approximately. We have proved the existence of interannual variability in M. schreibersii body condition at the beginning and at the end of hibernation (February), and we have also proved variability in mid-March. We have observed that hibernation in M. schreibersii is not a period of continuous torpidity. When hibemacula temperature was lower than 5 °C bats woke up and changed places inside the winter quarter or they even changed shelters. Arousals in winter can be one of the cause of the large loss of body condition rate during winter. The information obtained must contribute to a better protection of autumn shelters used to prepare hibernation and caves used as hibemacula for the recovery of endangered cavemicolous species.Pour préparer l’hibernation, les chauves-souris accumulent au début de l’automne d’importantes reserves graisseuses qui leur seront nécessaires durant ce sommeil hivernal. Une faible accumulation de graisse en automne ou une forte diminution de la masse corporelle en hiver peuvent être critiques pour leur survie. Notre travail a porté sur l’analyse des changements de la condition corporelle des Miniopterus schreibersii durant l’automne-hiver 1998-99 et sur l’étude de la variabilité interannuelle lors des hivers 1984-85, 1985-86 et 1998-99. L’étude a porté sur les chauves-souris de quatre refuges espagnols. Les minioptères ont été pesés, sexés et leurs avant-bras mesurés. Les échantillons ont été analysés en utilisant le calcul des résiduels, l’analyse de variance et le test de Scheffé. La condition corporelle de M. schreibersii change significativement d’octobre a mars. Les chauves-souris du nord-est de l’Espagne accumulent des reserves d’octobre à la mi-novembre. Pendant l’automne, leur masse corporelle s’accroît de 31,5 % en 29 jours seulement, tandis qu’elle décroît de 23 % en à peu près quatre mois durant l’hiver. Nous avons prouvé l’existence d’une variabilité interannuelle de la condition corporelle des M. schreibersii au debut et à la fin de l’hibernation (février) ainsi qu’à la mi-mars. Nous avons observé que l’hibernation de cette espèce ne constitue pas une période de torpeur continue. Quand la temperature du refuge d’hibernation est inférieure à 5 °C, les chauves-souris se réveillent et changent de place à l’intérieur du site hivernal ou bien elles changent de refuge. Les réveils peuvent être la cause d’importantes pertes de reserves pendant l’hiver. Les données obtenues devraient contribuer à mieux organiser la protection des refuges d’automne et des sites d’hivernage favorables à la sauvegarde des espèces cavernicoles menacées.Serra-Cobo J., López-Roig M., Marquès-Bonet T., Martínez-Rica J.P. Body condition changes of Miniopterus schreibersii in autumn and winter. In: Revue d'Écologie (La Terre et La Vie), tome 55, n°4, 2000. pp. 351-360

Analysis of structural diversity in wolf-like canids reveals post-domestication variants

Background: Although a variety of genetic changes have been implicated in causing phenotypic differences among dogs, the role of copy number variants (CNVs) and their impact on phenotypic variation is still poorly understood. Further, very limited knowledge exists on structural variation in the gray wolf, the ancestor of the dog, or other closely related wild canids. Documenting CNVs variation in wild canids is essential to identify ancestral states and variation that may have appeared after domestication. Results: In this work, we genotyped 1,611 dog CNVs in 23 wolf-like canids (4 purebred dogs, one dingo, 15 gray wolves, one red wolf, one coyote and one golden jackal) to identify CNVs that may have arisen after domestication. We have found an increase in GC-rich regions close to the breakpoints and around 1 kb away from them suggesting that some common motifs might be associated with the formation of CNVs. Among the CNV regions that showed the largest differentiation between dogs and wild canids we found 12 genes, nine of which are related to two known functions associated with dog domestication; growth (PDE4D, CRTC3 and NEB) and neurological function (PDE4D, EML5, ZNF500, SLC6A11, ELAVL2, RGS7 and CTSB). Conclusions: Our results provide insight into the evolution of structural variation in canines, where recombination is not regulated by PRDM9 due to the inactivation of this gene. We also identified genes within the most differentiated CNV regions between dogs and wolves, which could reflect selection during the domestication process.OR is a postdoctoral Researcher from the JAEdoc program cofounded by European Science Foundation. IO has a predoctoral fellowship from the Basque Government (DEUI). This work has been founded by Spanish Government Grants BFU2011-28549 (to TM-B) and BFU2012-34157 (to CL-F), Andalusian Government Grant “Programa de Captación del Conocimiento para Andalucía C2A” (to CV) and EU ERC Starting Grant 260372 (to TM-B

Analysis of structural diversity in wolf-like canids reveals post-domestication variants

Background: Although a variety of genetic changes have been implicated in causing phenotypic differences among dogs, the role of copy number variants (CNVs) and their impact on phenotypic variation is still poorly understood. Further, very limited knowledge exists on structural variation in the gray wolf, the ancestor of the dog, or other closely related wild canids. Documenting CNVs variation in wild canids is essential to identify ancestral states and variation that may have appeared after domestication. Results: In this work, we genotyped 1,611 dog CNVs in 23 wolf-like canids (4 purebred dogs, one dingo, 15 gray wolves, one red wolf, one coyote and one golden jackal) to identify CNVs that may have arisen after domestication. We have found an increase in GC-rich regions close to the breakpoints and around 1 kb away from them suggesting that some common motifs might be associated with the formation of CNVs. Among the CNV regions that showed the largest differentiation between dogs and wild canids we found 12 genes, nine of which are related to two known functions associated with dog domestication; growth (PDE4D, CRTC3 and NEB) and neurological function (PDE4D, EML5, ZNF500, SLC6A11, ELAVL2, RGS7 and CTSB). Conclusions: Our results provide insight into the evolution of structural variation in canines, where recombination is not regulated by PRDM9 due to the inactivation of this gene. We also identified genes within the most differentiated CNV regions between dogs and wolves, which could reflect selection during the domestication process.OR is a postdoctoral Researcher from the JAEdoc program cofounded by European Science Foundation. IO has a predoctoral fellowship from the Basque Government (DEUI). This work has been founded by Spanish Government Grants BFU2011-28549 (to TM-B) and BFU2012-34157 (to CL-F), Andalusian Government Grant “Programa de Captación del Conocimiento para Andalucía C2A” (to CV) and EU ERC Starting Grant 260372 (to TM-B

Genomic analysis of 18th-century Kazakh individuals and their oral microbiome

The Asian Central Steppe, consisting of current-day Kazakhstan and Russia, has acted as a highway for major migrations throughout history. Therefore, describing the genetic composition of past populations in Central Asia holds value to understanding human mobility in this pivotal region. In this study, we analyse paleogenomic data generated from five humans from Kuygenzhar, Kazakhstan. These individuals date to the early to mid-18th century, shortly after the Kazakh Khanate was founded, a union of nomadic tribes of Mongol Golden Horde and Turkic origins. Genomic analysis identifies that these individuals are admixed with varying proportions of East Asian ancestry, indicating a recent admixture event from East Asia. The high amounts of DNA from the anaerobic Gram-negative bacteria Tannerella forsythia, a periodontal pathogen, recovered from their teeth suggest they may have suffered from periodontitis disease. Genomic analysis of this bacterium identified recently evolved virulence and glycosylation genes including the presence of antibiotic resistance genes predating the antibiotic era. This study provides an integrated analysis of individuals with a diet mostly based on meat (mainly horse and lamb), milk, and dairy products and their oral microbiome.C.L.-F. is supported by a PGC2018-0955931-B-100 grant (MCIU/AEI/FEDER, UE) of Spain; T.M.-B. is supported by funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 864203), BFU2017-86471-P (MINECO/FEDER, UE), “Unidad de Excelencia María de Maeztu”, funded by the AEI (CEX2018-000792-M), Howard Hughes International Early Career, Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880). L.v.D. is supportd by a UCL Excellence Fellowship. The Ministry of the Education and Science of the Republic of Kazakhstan permitted and granted the research and the study (Grant number AP09261134). Additional financial contribution was provided by the ISMEO of Rome

Circular DNA intermediates in the generation of large human segmental duplications

Background: Duplications of large genomic segments provide genetic diversity in genome evolution. Despite their importance, how these duplications are generated remains uncertain, particularly for distant duplicated genomic segments. Results: Here we provide evidence of the participation of circular DNA intermediates in the single generation of some large human segmental duplications. A specific reversion of sequence order from A-B/C-D to B-A/D-C between duplicated segments and the presence of only microhomologies and short indels at the evolutionary breakpoints suggest a circularization of the donor ancestral locus and an accidental replicative interaction with the acceptor locus. Conclusions: This novel mechanism of random genomic mutation could explain several distant genomic duplications including some of the ones that took place during recent human evolution

The Earth BioGenome Project 2020: Starting the clock

November 2020 marked 2 y since the launch of the Earth BioGenome Project (EBP), which aims to sequence all known eukaryotic species in a 10-y timeframe. Since then, significant progress has been made across all aspects of the EBP roadmap, as outlined in the 2018 article describing the project's goals, strategies, and challenges (1). The launch phase has ended and the clock has started on reaching the EBP's major milestones. This Special Feature explores the many facets of the EBP, including a review of progress, a description of major scientific goals, exemplar projects, ethical legal and social issues, and applications of biodiversity genomics. In this Introduction, we summarize the current status of the EBP, held virtually October 5 to 9, 2020, including recent updates through February 2021. References to the nine Perspective articles included in this Special Feature are cited to guide the reader toward deeper understanding of the goals and challenges facing the EBP