The origin, current diversity and future conservation of the modern lion (
            Panthera leo
            )

Understanding the phylogeographic processes affecting endangered species is crucial both to interpreting their evolutionary history and to the establishment of conservation strategies. Lions provide a key opportunity to explore such processes; however, a lack of genetic diversity and shortage of suitable samples has until now hindered such investigation. We used mitochondrial control region DNA (mtDNA) sequences to investigate the phylogeographic history of modern lions, using samples from across their entire range. We find the sub-Saharan African lions are basal among modern lions, supporting a single African origin model of modern lion evolution, equivalent to the ‘recent African origin’ model of modern human evolution. We also find the greatest variety of mtDNA haplotypes in the centre of Africa, which may be due to the distribution of physical barriers and continental-scale habitat changes caused by Pleistocene glacial oscillations. Our results suggest that the modern lion may currently consist of three geographic populations on the basis of their recent evolutionary history: North African–Asian, southern African and middle African. Future conservation strategies should take these evolutionary subdivisions into consideration.

Download Full-text

RIP mutated ITS genes in populations of Ophiocordyceps sinensis and their implications for molecular systematics

IMA Fungus ◽

10.1186/s43008-020-00040-0 ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Yi Li ◽

Lan Jiang ◽

Ke Wang ◽

Hai-Jun Wu ◽

Rui-Heng Yang ◽

...

Keyword(s):

Evolutionary History ◽

Large Scale ◽

Its Region ◽

Wide Distribution ◽

Specific Primers ◽

Ophiocordyceps Sinensis ◽

Single Genome ◽

History Of ◽

Geographic Populations ◽

Internal Transcribed Spacer Sequences

Abstract Different hypotheses have been proposed to interpret the observed unusual ITS (internal transcribed spacer) sequences in Ophiocordyceps sinensis. The coexistence of diverged ITS paralogs in a single genome was previously shown by amplifying the ITS region from mono-ascospore isolates using specific primers designed for different ITS paralog groups. Among those paralogs, are AT-biased ITS sequences which were hypothesized to result from repeat-induced point mutation (RIP). This is a process that detects and mutates repetitive DNA and frequently leads to epigenetic silencing, and these mutations have been interpreted as pseudogenes. Here we investigate the occurrence and frequency of ITS pseudogenes in populations of O. sinensis using large-scale sampling, and discusses the implications of ITS pseudogenes for fungal phylogenetic and evolutionary studies. Our results demonstrate a wide distribution of ITS pseudogenes amongst different geographic populations, and indicate how ITS pseudogenes can contribute to the reconstruction of the evolutionary history of the species.

Download Full-text

The evolutionary history of human spindle genes includes back-and-forth gene flow with Neandertals

10.1101/2021.11.29.470407 ◽

2021 ◽

Author(s):

Stéphane Peyrégne ◽

Janet Kelso ◽

Benjamin Marco Peter ◽

Svante Pääbo

Keyword(s):

Gene Flow ◽

Evolutionary History ◽

Common Ancestor ◽

Modern Human ◽

Modern Humans ◽

Ancestral Gene ◽

Cytoskeletal Structure ◽

Spindle Apparatus ◽

History Of ◽

Segregation Of Chromosomes

Proteins associated with the spindle apparatus, a cytoskeletal structure that ensures the proper segregation of chromosomes during cell division, experienced an unusual number of amino acid substitutions in modern humans after the split from the ancestors of Neandertals and Denisovans. Here, we analyze the history of these substitutions and show that some of the genes in which they occur may have been targets of positive selection. We also find that the two changes in the kinetochore scaffold 1 (KNL1) protein, previously believed to be specific to modern humans, were present in some Neandertals. We show that the KNL1 gene of these Neandertals shared a common ancestor with present-day Africans about 200,000 years ago due to gene flow from the ancestors (or relatives) of modern humans into Neandertals. Subsequently, some non-Africans inherited this modern human-like gene variant from Neandertals, but none inherited the ancestral gene variants. These results add to the growing evidence of early contacts between modern humans and archaic groups in Eurasia and illustrate the intricate relationships among these groups.

Download Full-text

Migration without interbreeding: evolutionary history of a highly selfing Mediterranean grass inferred from whole genomes

10.1101/2020.09.03.280842 ◽

2020 ◽

Author(s):

Christoph Stritt ◽

Elena L. Gimmi ◽

Michele Wyler ◽

Abdelmonaim H. Bakali ◽

Aleksandra Skalska ◽

...

Keyword(s):

Evolutionary History ◽

Brachypodium Distachyon ◽

Genotypic Diversity ◽

Plant Evolution ◽

Whole Genome ◽

Continental Scale ◽

Whole Genomes ◽

History Of ◽

Adaptive Phenotypic Plasticity ◽

Independent Expansion

AbstractWhole genome sequences and coalescence theory allow the study of plant evolution in unprecedented detail. In this study we extend the genomic resources for the wild Mediterranean grass Brachypodium distachyon to investigate the scale of population structure and its underlying history at whole-genome resolution. The analysis of 196 accessions, spanning the Mediterranean from Iberia to Iraq, shows that the interplay of high selfing and seed dispersal rates has shaped genetic structure. At the continental scale, evolution in B. distachyon is characterized by the independent expansion of three lineages during the Upper Pleistocene. Today, these lineages may occur in sympatry yet do not interbreed. At the local scale, dispersal and selfing interact to maintain high genotypic diversity. Our study lays a foundation for the study of microevolution in B. distachyon and identifies adaptive phenotypic plasticity and frequency-dependent selection as key themes to be addressed with this model system.

Download Full-text

Archaic Lineages in the History of Modern Humans

Genetics ◽

10.1093/genetics/156.2.799 ◽

2000 ◽

Vol 156 (2) ◽

pp. 799-808 ◽

Cited By ~ 2

Author(s):

Damian Labuda ◽

Ewa Ziętkiewicz ◽

Vania Yotova

Keyword(s):

Homo Sapiens ◽

Large Fraction ◽

Principal Component ◽

Distinct Group ◽

Dystrophin Gene ◽

Modern Human ◽

Genetic Admixture ◽

Human Populations ◽

History Of ◽

Sub Saharan

Abstract An important question in the ongoing debate on the origin of Homo sapiens is whether modern human populations issued from a single lineage or whether several, independently evolving lineages contributed to their genetic makeup. We analyzed haplotypes composed of 35 polymorphisms from a segment of the dystrophin gene. We find that the bulk of a worldwide sample of 868 chromosomes represents haplotypes shared by different continental groups. The remaining chromosomes carry haplotypes specific for the continents or for local populations. The haplotypes specific for non-Africans can be derived from the most frequent ones through simple recombination or a mutation. In contrast, chromosomes specific for sub-Saharan Africans represent a distinct group, as shown by principal component analysis, maximum likelihood tree, structural comparison, and summary statistics. We propose that African chromosomes descend from at least two lineages that have been evolving separately for a period of time. One of them underwent range expansion colonizing different continents, including Africa, where it mixed with another, local lineage represented today by a large fraction of African-specific haplotypes. Genetic admixture involving archaic lineages appears therefore to have occurred within Africa rather than outside this continent, explaining greater diversity of sub-Saharan populations observed in a variety of genetic systems.

Download Full-text

Reconstructing the past

Evolutionary Genetics ◽

10.1093/oso/9780198830917.003.0009 ◽

2019 ◽

pp. 214-249

Author(s):

Glenn-Peter Sætre ◽

Mark Ravinet

Keyword(s):

Phylogenetic Trees ◽

Evolutionary History ◽

Sequence Data ◽

Modern Human ◽

Evolutionary Relationships ◽

Human Populations ◽

Gene Trees ◽

Exciting Field ◽

History Of ◽

Life On Earth

How can genetics and genomics be used to understand the evolutionary history of organisms? This chapter focuses on such methods. First, the field of phylogenetics is introduced, as a way to visualize and quantify the evolutionary relationships among species. The chapter outlines how we go from aligning DNA sequence data to building gene trees and we argue that “tree-thinking” is fundamentally important for understanding evolution. The chapter also goes beyond phylogenetic trees to focus on phylogeography, i.e. the understanding of evolutionary relationships in a spatial context. More recently, the explosion of genomic data from ancient and modern human populations has made this an extremely exciting field which is transforming our understanding of our own evolutionary history. Before that, though, the chapter reviews how modern phylogenetics has arisen from historical efforts to classify life on Earth.

Download Full-text

Ketosis-Prone Type 2 Diabetes in Patients of Sub-Saharan African Origin: Clinical Pathophysiology and Natural History of -Cell Dysfunction and Insulin Resistance

Diabetes ◽

10.2337/diabetes.53.3.645 ◽

2004 ◽

Vol 53 (3) ◽

pp. 645-653 ◽

Cited By ~ 159

Author(s):

F. Mauvais-Jarvis ◽

E. Sobngwi ◽

R. Porcher ◽

J.-P. Riveline ◽

J.-P. Kevorkian ◽

...

Keyword(s):

Insulin Resistance ◽

Type 2 Diabetes ◽

Natural History ◽

African Origin ◽

Cell Dysfunction ◽

History Of ◽

Sub Saharan

Download Full-text

Over a Thousand Years of Evolutionary History of Domestic Geese from Russian Archaeological Sites, Analysed Using Ancient DNA

Genes ◽

10.3390/genes9070367 ◽

2018 ◽

Vol 9 (7) ◽

pp. 367 ◽

Cited By ~ 7

Author(s):

Johanna Honka ◽

Matti Heino ◽

Laura Kvist ◽

Igor Askeyev ◽

Dilyara Shaymuratova ◽

...

Keyword(s):

Ancient Dna ◽

Evolutionary History ◽

Early Period ◽

Mitochondrial Control Region ◽

Archaeological Sites ◽

Anser Anser ◽

Bean Goose ◽

Base Pair Fragment ◽

History Of ◽

Greylag Goose

The European domestic goose is a widely farmed species known to have descended from the wild greylag goose (Anser anser). However, the evolutionary history of this domesticate is still poorly known. Ancient DNA studies have been useful for many species, but there has been little such work on geese. We have studied temporal genetic variation among domestic goose specimens excavated from Russian archaeological sites (4th–18th centuries) using a 204 base pair fragment of the mitochondrial control region. Specimens fell into three different genetic clades: the domestic D-haplogroup, the F-haplogroup that includes both wild and domestic geese, and a clade comprising another species, the taiga bean goose. Most of the subfossil geese carried typical domestic D-haplotypes. The domestication status of the geese carrying F-haplotypes is less certain, as the haplotypes identified were not present among modern domestic geese and could represent wild geese (misclassified as domestics), introgression from wild geese, or local domestication events. The bones of taiga bean goose were most probably misidentified as domestic goose but the domestication of bean goose or hybridization with domestic goose is also possible. Samples from the 4th to 10th century were clearly differentiated from the later time periods due to a haplotype that was found only in this early period, but otherwise no temporal or geographical variation in haplotype frequencies was apparent.

Download Full-text

Ape Out of Water

Positive Evolutionary Psychology ◽

10.1093/oso/9780190647124.003.0003 ◽

2019 ◽

pp. 26-36

Author(s):

Glenn Geher ◽

Nicole Wedberg

Keyword(s):

Evolutionary Psychology ◽

Evolutionary History ◽

Social Groups ◽

Daily Basis ◽

Modern Human ◽

Social Worlds ◽

Core Concept ◽

African Savanna ◽

Evolutionary Mismatch ◽

History Of

A core concept in the discipline of positive evolutionary psychology pertains to evolutionary mismatch. Evolutionary mismatch exists when the current environment of an organism is somehow inconsistent with the ancestral conditions that existed during the evolutionary history of that organism. Modern human environments differ dramatically from the conditions that surrounded our nomadic ancestors, who spent thousands of generations in the African savanna in small social groups. This chapter describes the issue of evolutionary mismatch in detail and then provides several examples of mismatch that adversely affect life for so many of us on a daily basis. Such issues include mismatches regarding diet, exercise, and the nature of our modern social worlds.

Download Full-text

The evolutionary history of Neanderthal and Denisovan Y chromosomes

Science ◽

10.1126/science.abb6460 ◽

2020 ◽

Vol 369 (6511) ◽

pp. 1653-1656 ◽

Cited By ~ 5

Author(s):

Martin Petr ◽

Mateja Hajdinjak ◽

Qiaomei Fu ◽

Elena Essel ◽

Hélène Rougier ◽

...

Keyword(s):

Mitochondrial Dna ◽

Evolutionary History ◽

Genetic Load ◽

Modern Human ◽

Gene Pools ◽

Chromosomal Gene ◽

Human History ◽

Effective Population ◽

Y Chromosomes ◽

History Of

Ancient DNA has provided new insights into many aspects of human history. However, we lack comprehensive studies of the Y chromosomes of Denisovans and Neanderthals because the majority of specimens that have been sequenced to sufficient coverage are female. Sequencing Y chromosomes from two Denisovans and three Neanderthals shows that the Y chromosomes of Denisovans split around 700 thousand years ago from a lineage shared by Neanderthals and modern human Y chromosomes, which diverged from each other around 370 thousand years ago. The phylogenetic relationships of archaic and modern human Y chromosomes differ from the population relationships inferred from the autosomal genomes and mirror mitochondrial DNA phylogenies, indicating replacement of both the mitochondrial and Y chromosomal gene pools in late Neanderthals. This replacement is plausible if the low effective population size of Neanderthals resulted in an increased genetic load in Neanderthals relative to modern humans.

Download Full-text