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Abstract
Phylogeny and characteristics of ruminants
Ruminants are a diverse group of mammals that includes families containing well-known taxa such as deer, cows, and goats. However, their evolutionary relationships have been contentious, as have the origins of their distinctive digestive systems and headgear, including antlers and horns (see the Perspective by Ker and Yang). To understand the relationships among ruminants, L. Chen et al. sequenced 44 species representing 6 families and performed a phylogenetic analysis. From this analysis, they were able to resolve the phylogeny of many genera and document incomplete lineage sorting among major clades. Interestingly, they found evidence for large population reductions among many taxa starting at approximately 100,000 years ago, coinciding with the migration of humans out of Africa. Examining the bony appendages on the head—the so-called headgear—Wang et al. describe specific evolutionary changes in the ruminants and identify selection on cancer-related genes that may function in antler development in deer. Finally, Lin et al. take a close look at the reindeer genome and identify the genetic basis of adaptations that allow reindeer to survive in the harsh conditions of the Arctic.
Science , this issue p. eaav6202 , p. eaav6335 , p. eaav6312 ; see also p. 1130
... 2023, 24, 1165 2 of 18 of more than 3000 m; it has a typical cold climate [12]. The Tibetan antelope belongs to the family Pantholopinae, whereas the Siberian ibex belongs to the family Capridae [13]. Interestingly, due to these two species living in similar high-altitude, frigid environments, they co-evolved superfine cashmere features to withstand the cold. ...
... With the completion of high-quality genome assembly of more and more spec is possible to study the adaptive evolution of specific environmental and physiolo characteristics of species using comparative genomics methods. Our previously publ Ruminant Genome Project de novo assembled genomes of 44 ruminant species, w were better to understand their evolution [13]. For instance, the Chinese water deer dropotes inermis) and Forest musk deer (Moschus berezovskii) convergent pseudogeniz led to secondary loss of headgear [41], the Reindeer (Rangifer tarandus) biological ad tion in the Arctic regions [42] and the Giraffes (Giraffa camelopardalis) involved in elongation and cardiovascular adaptations [43]. ...
... With the completion of high-quality genome assembly of more and more species, it is possible to study the adaptive evolution of specific environmental and physiological characteristics of species using comparative genomics methods. Our previously published Ruminant Genome Project de novo assembled genomes of 44 ruminant species, which were better to understand their evolution [13]. For instance, the Chinese water deer (Hydropotes inermis) and Forest musk deer (Moschus berezovskii) convergent pseudogenization led to secondary loss of headgear [41], the Reindeer (Rangifer tarandus) biological adaptation in the Arctic regions [42] and the Giraffes (Giraffa camelopardalis) involved in neck elongation and cardiovascular adaptations [43]. ...
Convergent evolution provides powerful opportunities to investigate the genetic basis of complex traits. The Tibetan antelope (Pantholops hodgsonii) and Siberian ibex (Capra sibirica) belong to different subfamilies in Bovidae, but both have evolved similar superfine cashmere characteristics to meet the cold temperature in plateau environments. The cashmere traits of cashmere goats underwent strong artificial selection, and some traces of domestication also remained in the genome. Hence, we investigated the convergent genomic signatures of cashmere traits between natural and artificial selection. We compared the patterns of convergent molecular evolution between Tibetan antelope and Siberian ibex by testing positively selected genes, rapidly evolving genes and convergent amino acid substitutions. In addition, we analyzed the selected genomic features of cashmere goats under artificial selection using whole-genome resequencing data, and skin transcriptome data of cashmere goats were also used to focus on the genes involved in regulating cashmere traits. We found that molecular convergent events were very rare, but natural and artificial selection genes were convergent enriched in similar functional pathways (e.g., ECM-receptor interaction, focal adhesion, PI3K-Akt signaling pathway) in a variety of gene sets. Type IV collagen family genes (COL4A2, COL4A4, COL4A5, COL6A5, COL6A6) and integrin family genes (ITGA2, ITGA4, ITGA9, ITGB8) may be important candidate genes for cashmere formation and development. Our results provide a comprehensive approach and perspective for exploring cashmere traits and offer a valuable reference for subsequent in-depth research on the molecular mechanisms regulating cashmere development and fineness.
... The lack of suitable starting material limits the choice of sequencing technology and affects the quality of the obtained data. For example, in a comparative genomics study of ruminants, the genomes of several species, such as mountain nyala, common eland, bongo, and oribi, were assembled at the contig level due to degenerate DNA samples, which were not suitable for constructing mate-pair libraries (Chen et al., 2019). Another example of poor DNA involves studies of ancient DNA (aDNA; Stoneking & Krause, 2011), which mostly contains very short fragments between 44 and 172 bp (Sawyer et al., 2012). ...
... The mountain nyala (T. buxtoni) genome, which was generated with only paired-end reads from the degenerate samples, was not well-assembled (Chen et al., 2019). The quality of the draft genome generated without using in silico mate-pair libraries was unsatisfactory (N50: 3.5 kb, complete BUSCOs: 645; Note: Contiguity, accuracy, and BUSCO results of the Takifugu bimaculatus assemblies using the original in silico method (*) and optimized in silico method (**). ...
A combination of short-insert paired-ended and mate-pair libraries of large insert sizes is used as a standard method to generate genome assemblies with high contiguity. The third-generation sequencing techniques also are used to improve the quality of assembled genomes. However, both mate-pair libraries and the third-generation libraries require high-molecular-weight DNA, making the use of these libraries inappropriate for samples with only degraded DNA. An in silico method that generates mate-pair libraries using a reference genome was devised for the task of assembling target genomes. Although the contiguity and completeness of assembled genomes were significantly improved by this method, a high level of errors manifested in the assembly, further to which the methods for using reference genomes, was not optimized. Here, we tested different strategies for using reference genomes to generate in silico mate-pairs. The results showed that using a closely related reference genome from the same genus was more effective than using divergent references. Conservation of in silico mate-pairs by comparing two references and using those to guide genome assembly reduced the number of misassemblies (18.6%-46.1%) and increased the contiguity of assembled genomes (9.7%-70.7%), while maintaining gene completeness at a level that was either similar or marginally lower than that obtained via the current method. Finally, we developed a pipeline of the optimized in silico method and compared it with another reference-guided assembler, RagTag. We found that RagTag produced longer scaffolds (17.8 Mbp vs 3.0 Mbp), but resulted in a much higher misassembly rate (85.68%) than our optimized in silico mate-pair method. This optimized in silico pipeline developed in this study should facilitate further studies on genomics, population genetics, and conservation of endangered species.
... *Reported cases exist of sheep developing clinical signs of MCF [36][37][38]. Phylogenetic tree of ruminants adapted from ref. [39]. While various forms of MCF have been described, the clinical and pathological manifestations of both WD-MCF and sheep-associated MCF are similar. ...
Gammaherpesviruses (γHVs) include viruses that can induce lymphoproliferative diseases and tumors. These viruses can persist in the long term in the absence of any pathological manifestation in their natural host. Alcelaphine gammaherpesvirus 1 (AlHV-1) belongs to the genus Macavirus and asymptomatically infects its natural host, the wildebeest (Connochaetes spp.). However, when transmitted to several susceptible species belonging to the order Artiodactyla, AlHV-1 is responsible for the induction of a lethal lymphoproliferative disease, named wildebeest-derived malignant catarrhal fever (WD-MCF). Understanding the pathogenic mechanisms responsible for the induction of WD-MCF is important to better control the risks of transmission and disease development in susceptible species. The aim of this review is to synthesize the current knowledge on WD-MCF with a particular focus on the mechanisms by which AlHV-1 induces the disease. We discuss the potential mechanisms of pathogenesis from viral entry into the host to the maintenance of viral genomes in infected CD8+ T lymphocytes, and we present current hypotheses to explain how AlHV-1 infection induces a peripheral T cell lymphoma-like disease.
... The number of CNEs identified depends on the evolutionary divergence between the compared species and the thresholds used for similarity and sequence length (Harmston et al., 2013). Comparison of the bovine genome with more closely related species, for example, other members of the Bovidae, is likely to yield a much larger set of lineage-specific CNEs (Chen et al., 2019). An analysis of distantly related species, on the other hand, is expected to yield less CNEs but might increase the signal-tonoise ratio by filtering out slow-evolving neutral sequences (Woolfe et al., 2005). ...
Deer species were repeatedly overexploited and protected for their meat and fur and they had strong impacts on ecosystems and human society by damaging crops and planted trees, altering vegetation, deer vehicle collision, and increasing ticks that vector zoonosis. To accomplish appropriate population management, the historical demography and its main driver need to be clarified. In this study, we estimated the historical demography of effective population size (Ne) of sika deer (Cervus nippon Temminck) in Hokkaido and Hyogo Prefectures of the Japanese archipelago. We estimated Ne of >100 generations from present (2020) by folded single nucleotide polymorphisms (SNP) frequency spectra and, within 100 generations from present, by linkage disequilibrium between SNP. In Hokkaido, Ne drastically increased around 3.0 ky BP and decreased around 100–150 years ago with the assumption of their generation length as 4 or 9years. The Ne decreased by a 10th before the recent bottleneck. In Hyogo, Ne increased around 80 and 1ky BP and decreased around 100–250years ago. Ne decreased by a 100th before the recent bottleneck. After these recent bottlenecks, Ne of both regions recovered and the current Ne has nearly reaches the highest level of the last 100 ky BP. Literature survey and paleoclimate indicates that the decrease and increase of Ne of sika deer in Japanese archipelago may be caused by variations in the hunting activity of humans rather than climate change or the top predator extinction.
We describe here the Bovidae from the early Middle Miocene site of Maboko, Kenya, known for its rich and highly diverse assemblage of Primates. They are attributed to two taxa of slightly different sizes, Turcocerus africanus n.sp. and Kubanotragus pickfordi. In addition to Kenya, Turcocerus ranges through the Middle Miocene from Turkey to China; it might have originated in Africa but the lack of precise dating weakens any phylogeographic hypothesis. Kubanotragus has similar chronological and geographic ranges. Both Maboko species retain low levels of hypsodonty compared to their northern relatives and may have been less specialised for grazing than Eurasian taxa. The Maboko Bovidae illustrate an early diversification of the family in Africa that appears to pre-date the major diversification of Bovidae and appearance of the diverse clades that are characteristic of modern African pecoran faunas.
Pangolins form a group of scaly mammals that are trafficked at record numbers for their meat and medicinal properties. Despite their great conservation concern, knowledge of their evolution is limited by a paucity of genomic data. We aim to produce exhaustive genomic resources that include 3 238 orthologous genes and whole-genome polymorphisms to assess the evolution of all eight pangolin species. Robust orthologous gene-based phylogenies recovered the monophyly of the three genera of pangolins, and highlighted the existence of an undescribed species closely related to South-East Asian pangolins. Signatures of middle Miocene admixture between an extinct, possibly European, lineage and the ancestor of South-East Asian pangolins, provides new insights into the early evolutionary history of the group. Demographic trajectories and genome-wide heterozygosity estimates revealed contrasts between continental vs. island populations and species lineages, suggesting that conservation planning should consider intra-specific patterns. With the expected loss of genomic diversity from recent, extensive trafficking not yet been realized in pangolins, we recommend that populations are genetically surveyed to anticipate any deleterious impact of the illegal trade. Finally, we produce a complete set of genomic resources that will be integral for future conservation management and forensic endeavors required for conserving pangolins, including tracing their illegal trade. These include the completion of whole-genomes for pangolins through the first reference genome with long reads for the giant pangolin (Smutsia gigantea) and new draft genomes (~43x-77x) for four additional species, as well as a database of orthologous genes with over 3.4 million polymorphic sites.
The reduced costs of next-generation sequencing (NGS) has allowed researchers to generate nuclear and mitochondrial genome data to gain deeper insights into the phylogeography, evolutionary history, and biology of non-model species. While the Cape buffalo (Syncerus caffer caffer) has been well-studied across its range with traditional genetic markers over the last 25 years, researchers are building on this knowledge by generating whole genome, population-level datasets to improve understanding of its genetic composition and evolutionary history. Using publicly available NGS data, we assembled 40 Cape buffalo mitochondrial genomes (mitogenomes) from four protected areas in South Africa, expanding the geographical range and almost doubling the number of mitogenomes available for this species. Coverage of the mitogenomes ranged from 154-1,036X. Haplotype and nucleotide diversity for Kruger National Park (n = 15) and Mokala National Park (n = 5) were similar to diversity levels in southern and eastern Africa. Hluhluwe-iMfolozi Park (n = 15) had low levels of genetic diversity, with only four haplotypes detected, reflecting its past bottleneck. Addo Elephant National Park (n = 5) had the highest nucleotide diversity of all populations across Africa, which was unexpected, as it is known from previous studies to have low nuclear diversity. This diversity was driven by a highly divergent mitogenome from one sample, which was also identified in another sample via Sanger sequencing of cytochrome b. Using a fossil-calibrated phylogenetic analysis, we estimated that this mitogenome diverged from all other Cape buffalo approximately 2.15 million years ago. We discuss several potential sources of this mitogenome but propose that it most likely originated through introgressive hybridisation with the extinct long-horned buffalo, Syncerus (Pelorovis) antiquus. We conclude by discussing the conservation consequences of this finding for the Addo Elephant National Park population, proposing careful genetic management to prevent inbreeding depression while maintaining this highly unique diversity.
Polyomaviruses are oncogenic viruses that are generally thought to have co-evolved with their hosts. While primate and rodent polyomaviruses are increasingly well-studied, less is known about polyomaviruses that infect other mammals. In an effort to gain insight into polyomaviruses associated with carnivores, we surveyed fecal samples collected in the USA from bobcats (Lynx rufus), pumas (Puma concolor), Canada lynxes (Lynx canadensis), and grizzly bears (Ursus arctos). Using a viral metagenomic approach, we identified six novel polyomavirus genomes. Surprisingly, four of the six genomes showed a phylogenetic relationship to polyomaviruses found in prey animals. These included a putative rabbit polyomavirus from a bobcat fecal sample and two possible deer-trophic polyomaviruses from Canada lynx feces. One polyomavirus found in a grizzly bear sample was found to be phylogenetically distant from previously identified polyomaviruses. Further analysis of the grizzly bear fecal sample showed that it contained anelloviruses that are known to infect pigs, suggesting that the bear might have preyed on a wild or domestic pig. Interestingly, a polyomavirus genome identified in a puma fecal sample was found to be closely related both to raccoon polyomavirus 1 and to Lyon-IARC polyomavirus, the latter of which was originally identified in human saliva and skin swab specimens but has since been found in samples from domestic cats (Felis catus).
We present the latest version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which contains many sophisticated
methods and tools for phylogenomics and phylomedicine. In this major upgrade, MEGA has been optimized for use on 64-bit computing
systems for analyzing bigger datasets. Researchers can now explore and analyze tens of thousands of sequences in MEGA. The
new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict
gene duplication events in gene family trees. The 64-bit MEGA is made available in two interfaces: graphical and command line.
The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OSX. The command
line MEGA is available as native applications for Windows, Linux, and Mac OSX. They are intended for use in high-throughput
and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
Phylogeny and characteristics of ruminants
Ruminants are a diverse group of mammals that includes families containing well-known taxa such as deer, cows, and goats. However, their evolutionary relationships have been contentious, as have the origins of their distinctive digestive systems and headgear, including antlers and horns (see the Perspective by Ker and Yang). To understand the relationships among ruminants, L. Chen et al. sequenced 44 species representing 6 families and performed a phylogenetic analysis. From this analysis, they were able to resolve the phylogeny of many genera and document incomplete lineage sorting among major clades. Interestingly, they found evidence for large population reductions among many taxa starting at approximately 100,000 years ago, coinciding with the migration of humans out of Africa. Examining the bony appendages on the head—the so-called headgear—Wang et al. describe specific evolutionary changes in the ruminants and identify selection on cancer-related genes that may function in antler development in deer. Finally, Lin et al. take a close look at the reindeer genome and identify the genetic basis of adaptations that allow reindeer to survive in the harsh conditions of the Arctic.
Science , this issue p. eaav6202 , p. eaav6335 , p. eaav6312 ; see also p. 1130
Background:
Evolutionary histories can be discordant across the genome, and such discordances need to be considered in reconstructing the species phylogeny. ASTRAL is one of the leading methods for inferring species trees from gene trees while accounting for gene tree discordance. ASTRAL uses dynamic programming to search for the tree that shares the maximum number of quartet topologies with input gene trees, restricting itself to a predefined set of bipartitions.
Results:
We introduce ASTRAL-III, which substantially improves the running time of ASTRAL-II and guarantees polynomial running time as a function of both the number of species (n) and the number of genes (k). ASTRAL-III limits the bipartition constraint set (X) to grow at most linearly with n and k. Moreover, it handles polytomies more efficiently than ASTRAL-II, exploits similarities between gene trees better, and uses several techniques to avoid searching parts of the search space that are mathematically guaranteed not to include the optimal tree. The asymptotic running time of ASTRAL-III in the presence of polytomies is [Formula: see text] where D=O(nk) is the sum of degrees of all unique nodes in input trees. The running time improvements enable us to test whether contracting low support branches in gene trees improves the accuracy by reducing noise. In extensive simulations, we show that removing branches with very low support (e.g., below 10%) improves accuracy while overly aggressive filtering is harmful. We observe on a biological avian phylogenomic dataset of 14K genes that contracting low support branches greatly improve results.
Conclusions:
ASTRAL-III is a faster version of the ASTRAL method for phylogenetic reconstruction and can scale up to 10,000 species. With ASTRAL-III, low support branches can be removed, resulting in improved accuracy.
PhyloNet was released in 2008 as a software package for representing and analyzing phylogenetic networks. At the time of its release, the main functionalities in PhyloNet consisted of measures for comparing network topologies and a single heuristic for reconciling gene trees with a species tree. Since then, PhyloNet has grown significantly. The software package now includes a wide array of methods for inferring phylogenetic networks from data sets of unlinked loci while accounting for both reticulation (e.g., hybridization) and incomplete lineage sorting. In particular, PhyloNet now allows for maximum parsimony, maximum likelihood, and Bayesian inference of phylogenetic networks from gene tree estimates. Furthermore, Bayesian inference directly from sequence data (sequence alignments or bi-allelic markers) is implemented. Maximum parsimony is based on an extension of the "minimizing deep coalescences" criterion to phylogenetic networks, whereas maximum likelihood and Bayesian inference are based on the multispecies network coalescent. All methods allow for multiple individuals per species. As computing the likelihood of a phylogenetic network is computationally hard, PhyloNet allows for evaluation and inference of networks using a pseudo-likelihood measure. PhyloNet summarizes the results of the various analyses, and generates phylogenetic networks in the extended Newick format that is readily viewable by existing visualization software.
Genetic engineering in livestock has been greatly enhanced through the use of artificial programmed nucleases such as the recently emerged clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) system. We recently reported our successful application of the CRISPR/Cas9 system to engineer the goat genome through micro-injection of Cas9 mRNA and sgRNAs targeting MSTN and FGF5 in goat embryos. The phenotypes induced by edited loss-of-function mutations of MSTN remain to be evaluated extensively. We demonstrate the utility of this approach by disrupting MSTN, resulting in enhanced body weight and larger muscle fiber size in Cas9-mediated gene-modified goats. The effects of genome modifications were further characterized by H&E staining, quantitative PCR, Western blotting and immunofluorescence staining. Morphological and genetic analyses indicated the occurrence of phenotypic and genotypic modifications. We further provide sufficient evidence, including breeding data, to demonstrate the transmission of the knockout alleles through the germline. By phenotypic and genotypic characterization, we demonstrated the merit of using the CRISPR/Cas9 approach for establishing genetically modified livestock with an enhanced production trait.
Background
Milu, also known as Père David's deer (Elaphurus davidianus), was widely distributed in East Asia but recently experienced a severe bottleneck. Only 18 survived by the end of the 19th century, and the current population of 4500 individuals was propagated from just 11 kept by the 11th British Duke of Bedford. This species is known for its distinguishable appearance, the driving force behind which is still a mystery. To aid efforts to explore these phenomena we constructed a draft genome of the species.
Findings
In total, we generated 321.86 gigabases (Gb) of raw DNA sequence from whole-genome sequencing of a male milu deer using an Illumina HiSeq 2000 platform. Assembly yielded a final genome with a scaffold N50 size of 3.03 megabases (Mb), and total length of 2.52 Gb. Moreover, we identified 20,125 protein-coding genes and 988.1 Mb of repetitive sequences. In addition, homology-based searches detected 280 rRNA, 1,335 miRNA, 1,441 snRNA and 893 tRNA sequences in the milu genome. The divergence time between E. davidianus and Bos taurus was estimated to be about 28.20 million years ago (Mya). We identified 167 species-specific genes and 293 expanded gene families in the milu lineage.
Conclusions
We report the first reference genome of milu, which will provide a valuable resource for studying the species’ demographic history of severely bottlenecked and genetic mechanism of special phenotypic evolution.
The peopling of Asia
In recent years, there has been increasing focus on the paleoanthropology of Asia, particularly the migration patterns of early modern humans as they spread out of Africa. Bae et al. review the current state of the Late Pleistocene Asian human evolutionary record from archaeology, hominin paleontology, geochronology, genetics, and paleoclimatology. They evaluate single versus multiple dispersal models and southern versus the northern dispersal routes across the Asian continent. They also review behavioral and environmental variability and how these may have affected modern human dispersals and interactions with indigenous populations.
Science , this issue p. eaai9067
