The evolution of the ratite birds has been widely attributed to vicariant speciation, driven by the Cretaceous breakup of the supercontinent Gondwana. The early isolation of Africa and Madagascar ...implies that the ostrich and extinct Madagascan elephant birds (Aepyornithidae) should be the oldest ratite lineages. We sequenced the mitochondrial genomes of two elephant birds and performed phylogenetic analyses, which revealed that these birds are the closest relatives of the New Zealand kiwi and are distant from the basal ratite lineage of ostriches. This unexpected result strongly contradicts continental vicariance and instead supports flighted dispersal in all major ratite lineages. We suggest that convergence toward gigantism and flightlessness was facilitated by early Tertiary expansion into the diurnal herbivory niche after the extinction of the dinosaurs.
The near-simultaneous appearance of most modern animal body plans (phyla) ∼530 million years ago during the Cambrian explosion is strong evidence for a brief interval of rapid phenotypic and genetic ...innovation, yet the exact speed and nature of this grand adaptive radiation remain debated 1–12. Crucially, rates of morphological evolution in the past (i.e., in ancestral lineages) can be inferred from phenotypic differences among living organisms—just as molecular evolutionary rates in ancestral lineages can be inferred from genetic divergences 13. We here employed Bayesian 14 and maximum likelihood 15 phylogenetic clock methods on an extensive anatomical 16 and genomic 17 data set for arthropods, the most diverse phylum in the Cambrian and today. Assuming an Ediacaran origin for arthropods, phenotypic evolution was ∼4 times faster, and molecular evolution ∼5.5 times faster, during the Cambrian explosion compared to all subsequent parts of the Phanerozoic. These rapid evolutionary rates are robust to assumptions about the precise age of arthropods. Surprisingly, these fast early rates do not change substantially even if the radiation of arthropods is compressed entirely into the Cambrian (∼542 mega-annum Ma) or telescoped into the Cryogenian (∼650 Ma). The fastest inferred rates are still consistent with evolution by natural selection and with data from living organisms, potentially resolving “Darwin’s dilemma.” However, evolution during the Cambrian explosion was unusual (compared to the subsequent Phanerozoic) in that fast rates were present across many lineages.
Display omitted
•The Cambrian explosion (evolution’s “big bang”) is compatible with Darwinian evolution•Anatomical and genetic evolution occurred 5 times faster during the early Cambrian•Bayesian methods can infer evolutionary rates in deep time, using living taxa•This study concerns arthropods, but the results are likely applicable to most of life
Molecular evolutionary rate estimates have been shown to depend on the time period over which they are estimated. Factors such as demographic processes, calibration errors, purifying selection, and ...the heterogeneity of substitution rates among sites (RHAS) are known to affect the accuracy with which rates of evolution are estimated. We use mathematical modeling and Bayesian analyses of simulated sequence alignments to explore how mutational hotspots can lead to time-dependent rate estimates. Mathematical modeling shows that underestimation of molecular rates over increasing time scales is inevitable when RHAS is ignored. Although a gamma distribution is commonly used to model RHAS, we show that when the actual RHAS deviates from a gamma-like distribution, rates can either be under- or overestimated in a time-dependent manner. Simulations performed under different scenarios of RHAS confirm the mathematical modeling and demonstrate the impacts of time-dependent rates on estimates of divergence times. Most notably, erroneous rate estimates can have narrow credibility intervals, leading to false confidence in biased estimates of rates, and node ages. Surprisingly, large errors in estimates of overall molecular rate do not necessarily generate large errors in divergence time estimates. Finally, we illustrate the correlation between time-dependent rate patterns and differential saturation between quickly and slowly evolving sites. Our results suggest that data partitioning or simple nonparametric mixture models of RHAS significantly improve the accuracy with which node ages and substitution rates can be estimated.
The two living species of bison (European and American) are among the few terrestrial megafauna to have survived the late Pleistocene extinctions. Despite the extensive bovid fossil record in ...Eurasia, the evolutionary history of the European bison (or wisent, Bison bonasus) before the Holocene (<11.7 thousand years ago (kya)) remains a mystery. We use complete ancient mitochondrial genomes and genome-wide nuclear DNA surveys to reveal that the wisent is the product of hybridization between the extinct steppe bison (Bison priscus) and ancestors of modern cattle (aurochs, Bos primigenius) before 120 kya, and contains up to 10% aurochs genomic ancestry. Although undetected within the fossil record, ancestors of the wisent have alternated ecological dominance with steppe bison in association with major environmental shifts since at least 55 kya. Early cave artists recorded distinct morphological forms consistent with these replacement events, around the Last Glacial Maximum (LGM, ∼21-18 kya).
Haplogroup H dominates present-day Western European mitochondrial DNA variability (>40%), yet was less common (~19%) among Early Neolithic farmers (~5450 BC) and virtually absent in Mesolithic ...hunter-gatherers. Here we investigate this major component of the maternal population history of modern Europeans and sequence 39 complete haplogroup H mitochondrial genomes from ancient human remains. We then compare this 'real-time' genetic data with cultural changes taking place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. Our results reveal that the current diversity and distribution of haplogroup H were largely established by the Mid Neolithic (~4000 BC), but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers expanding out of Iberia in the Late Neolithic (~2800 BC). Dated haplogroup H genomes allow us to reconstruct the recent evolutionary history of haplogroup H and reveal a mutation rate 45% higher than current estimates for human mitochondria.
The Black Rat (Rattus rattus) spread out of Asia to become one of the world's worst agricultural and urban pests, and a reservoir or vector of numerous zoonotic diseases, including the devastating ...plague. Despite the global scale and inestimable cost of their impacts on both human livelihoods and natural ecosystems, little is known of the global genetic diversity of Black Rats, the timing and directions of their historical dispersals, and the risks associated with contemporary movements. We surveyed mitochondrial DNA of Black Rats collected across their global range as a first step towards obtaining an historical genetic perspective on this socioeconomically important group of rodents. We found a strong phylogeographic pattern with well-differentiated lineages of Black Rats native to South Asia, the Himalayan region, southern Indochina, and northern Indochina to East Asia, and a diversification that probably commenced in the early Middle Pleistocene. We also identified two other currently recognised species of Rattus as potential derivatives of a paraphyletic R. rattus. Three of the four phylogenetic lineage units within R. rattus show clear genetic signatures of major population expansion in prehistoric times, and the distribution of particular haplogroups mirrors archaeologically and historically documented patterns of human dispersal and trade. Commensalism clearly arose multiple times in R. rattus and in widely separated geographic regions, and this may account for apparent regionalism in their associated pathogens. Our findings represent an important step towards deeper understanding the complex and influential relationship that has developed between Black Rats and humans, and invite a thorough re-examination of host-pathogen associations among Black Rats.
Hotel quarantine for international travelers has been used to prevent coronavirus disease spread into Australia. A quarantine hotel–associated community outbreak was detected in South Australia. ...Real-time genomic sequencing enabled rapid confirmation tracking the outbreak to a recently returned traveler and linked 2 cases of infection in travelers at the same facility.
The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile ...by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages.
High‐throughput sequencing has dramatically fostered ancient DNA research in recent years. Shotgun sequencing, however, does not necessarily appear as the best‐suited approach due to the extensive ...contamination of samples with exogenous environmental microbial DNA. DNA capture‐enrichment methods represent cost‐effective alternatives that increase the sequencing focus on the endogenous fraction, whether it is from mitochondrial or nuclear genomes, or parts thereof. Here, we explored experimental parameters that could impact the efficacy of MYbaits in‐solution capture assays of ~5000 nuclear loci or the whole genome. We found that varying quantities of the starting probes had only moderate effect on capture outcomes. Starting DNA, probe tiling, the hybridization temperature and the proportion of endogenous DNA all affected the assay, however. Additionally, probe features such as their GC content, number of CpG dinucleotides, sequence complexity and entropy and self‐annealing properties need to be carefully addressed during the design stage of the capture assay. The experimental conditions and probe molecular features identified in this study will improve the recovery of genetic information extracted from degraded and ancient remains.
PDF
