Human Evolution in Polynesia: a Molecular Biological Study

<p>Human evolution is an extremely interesting and contentious topic that incorporates data from a wide variety of disciplines. Molecular studies are becoming increasingly important for reconstructing human history, as new techniques allow faster recovery of results, and genetic tests provide an independent test for colonisation theories that are usually based on archaeological and linguistic evidence. Mitochondrial DNA (mtDNA) is an extremely useful genetic marker that is widely used in molecular biology for establishing phylogenetic links between individuals and populations. In the current study the 3' Hypervariable Region (3' HVI) of mtDNA from human populations living in New Zealand (Aotearoa) was analysed. The HVI mtDNA diversity in the New Zealand Maori population was significantly reduced compared with Polynesian and Melanesian populations, with an extremely high frequency (~87%) of the 'Polynesian CGT motif' haplotype. Additionally, the 9-bp deletion, common in Polynesian populations, has reached fixation (100%) in the Maori samples. These results support a settlement scenario with repeated population bottlenecks. The mtDNA HVI haplotype frequencies in this study, combined with those from previous studies, were used in computer simulations to estimate the number of females required to found the current Maori population. Approximately 56 women, and an equal or greater number of men, were estimated to have been present in the founding waka. This estimate is too large to support any settlement models with a small number of founders and effectively rules out the possibility of 'accidental discovery', instead supporting a planned settlement of Aotearoa in agreement with traditional knowledge. Analysis of interdisciplinary data has allowed current theories for the origins of the Polynesians and proto-Austronesians to be consolidated by introducing a 'Synthetic Total Evidence Theory'. It is likely that once published this theory will stimulate intense discussion and debate and will continue to grow as further evidence is obtained and incorporated into this model.</p>

Human Evolution in Polynesia: a Molecular Biological Study

<p>Human evolution is an extremely interesting and contentious topic that incorporates data from a wide variety of disciplines. Molecular studies are becoming increasingly important for reconstructing human history, as new techniques allow faster recovery of results, and genetic tests provide an independent test for colonisation theories that are usually based on archaeological and linguistic evidence. Mitochondrial DNA (mtDNA) is an extremely useful genetic marker that is widely used in molecular biology for establishing phylogenetic links between individuals and populations. In the current study the 3' Hypervariable Region (3' HVI) of mtDNA from human populations living in New Zealand (Aotearoa) was analysed. The HVI mtDNA diversity in the New Zealand Maori population was significantly reduced compared with Polynesian and Melanesian populations, with an extremely high frequency (~87%) of the 'Polynesian CGT motif' haplotype. Additionally, the 9-bp deletion, common in Polynesian populations, has reached fixation (100%) in the Maori samples. These results support a settlement scenario with repeated population bottlenecks. The mtDNA HVI haplotype frequencies in this study, combined with those from previous studies, were used in computer simulations to estimate the number of females required to found the current Maori population. Approximately 56 women, and an equal or greater number of men, were estimated to have been present in the founding waka. This estimate is too large to support any settlement models with a small number of founders and effectively rules out the possibility of 'accidental discovery', instead supporting a planned settlement of Aotearoa in agreement with traditional knowledge. Analysis of interdisciplinary data has allowed current theories for the origins of the Polynesians and proto-Austronesians to be consolidated by introducing a 'Synthetic Total Evidence Theory'. It is likely that once published this theory will stimulate intense discussion and debate and will continue to grow as further evidence is obtained and incorporated into this model.</p>

PSXII-8 Mitochondrial DNA diversity within domestic reindeer in Russia

Domestic reindeer in Russia are a valuable resource of vital importance to the physical and cultural survival of the Northern indigenous minority. During the last decades, the mitochondrial (mt) genetic markers have been widely used as a molecular tool to investigate genetic structure and diversity of livestock species. Here we aimed at the assessing the mtDNA diversity of the domestic reindeer inhabiting the area from the Kola Peninsula in the west to the Chukotka region in the east. A complete cytochrome b (cytb) sequences (1,140 bp) from representatives of six populations, including Nenets (NEN, n = 16), Evenk (EVK, n = 12), Even (EVN, n = 6), Chukotka (CHU, n = 6), Chukotka-Khargin (CHUKH, n = 6) and Tuva (TUVA, n = 6) were obtained. Sequences’ alignment was conducted using MUSCLE algorithm in R package msa. In total, 34 haplotypes were identified. Median-joining network, constructed in PopART 1.7, revealed three major groups of haplotypes: the first one joined the samples of all the populations, the second one included NEN, EVN and CHUKH, and the third group was presented by the one sample of CHU. AMOVA, calculated in Arlequin 3.5.2.2, showed that only 9.58% of molecular variance could be explained by the differences between populations and 90.42% - within populations. Genetic diversity parameters calculated in DnaSP 6.12.03, demonstrated that average number of nucleotide differences (K) was highest in CHUKH (28.333) and EVN (27.409) and lowest in TUVA (4.533) and EVK (5.400). Nucleotide diversity (Pi) was 0.01238±0.00559, 0.00474±0.00091, 0.02404±0.00453, 0.01281±0.00464, 0.02485±0.00744, and 0.00398±0.00110 for NEN, EVK, EVN, CHU, CHUKH and TUVA, respectively. Our study demonstrated the lack of clear genetic structure of the studied reindeer populations in relation to cytb sequence. The level of genetic diversity was associated with census size and was lowest in the smallest Tuva population. This study was supported by RSF-21-16-00071 and Russian Ministry of Science and Higher Education-0445-2019-0024.

Mitogenome Phylogeny Including Data from Additional Subspecies Provides New Insights into the Historical Biogeography of the Eurasian lynx Lynx lynx

Previous molecular studies of the wide-ranging Eurasian lynx Lynx lynx focused mainly on its northern Palearctic populations, with the consequence that the reconstruction of this species’ evolutionary history did not include genetic variation present in its southern Palearctic distribution. We sampled a previously not considered Asian subspecies (L. l. dinniki), added published data from another Asian subspecies (L. l. isabellinus), and reassessed the Eurasian lynx mtDNA phylogeny along with previously published data from northern Palearctic populations. Our mitogenome-based analyses revealed the existence of three major clades (A: Central Asia, B: SE Europe/SW Asia, C: Europe and Northern Asia) and at least five lineages, with diversification in Lynx lynx commencing at least 28kyr earlier than hitherto estimated. The subspecies L. l. isabellinus harbors the most basal matriline, consistent with the origin of Lynx lynx in this subspecies’ current range. L. l. dinniki harbors the second most basal matriline, which is related to, and may be the source of, the mtDNA diversity of the critically endangered Balkan lynx L. l. balcanicus. Our results suggest that the Anatolian peninsula was a glacial refugium for Eurasian lynx, with previously unconsidered implications for the colonization of Europe by this species.

New evidence for distinctiveness of the island-endemic Príncipe giant tree frog (Arthroleptidae: Leptopelis palmatus)

The Príncipe giant tree frog Leptopelis palmatus is endemic to the small oceanic island of Príncipe in the Gulf of Guinea. For several decades, this charismatic but poorly known species was confused with another large tree frog species from continental Africa, L. rufus. Phylogenetic relationships within the African genus Leptopelis are poorly understood and consequently the evolutionary history of L. palmatus and its affinity to L. rufus remain unclear. In this study, we combined mitochondrial DNA (mtDNA), morphological, and acoustic data for L. palmatus and L. rufus to assess different axes of divergence between the species. Our mtDNA gene tree for the genus Leptopelis indicated that L. palmatus is not closely related to L. rufus or other large species of Leptopelis. Additionally, we found low mtDNA diversity in L. palmatus across its range on Príncipe. We found significant morphological differences between females of L. rufus and L. palmatus, but not between males. We characterised the advertisement call of L. palmatus for the first time, which is markedly distinct from L. rufus. Finally, we summarised our observations of L. palmatus habitats and additional notes on phenotypic variation and behaviour. Our study reinforces the distinctiveness of L. palmatus and provides information important for the conservation of this endangered species. A rã gigante de Príncipe, Leptopelis palmatus, é endêmica da pequena ilha oceânica de Príncipe no Golfo da Guiné. Por várias décadas, esta espécie carismática mas pouco conhecida foi confundida com outra espécie grande de rã da África continental, L. rufus. As relações filogenéticas dentro do gênero africano Leptopelis são mal compreendidas e, conseqüentemente, a história evolutiva de L. palmatus e sua afinidade com L. rufus permanecem obscuras. Neste estudo, combinamos dados de DNA mitocondrial (mtDNA), morfológicos e acústicos de L. palmatus e L. rufus para avaliar diferentes eixos de divergência entre as espécies. Nossa árvore de genes de mtDNA para o gênero Leptopelis indicou que L. palmatus não está proximamente relacionada a L. rufus ou outras espécies grandes de Leptopelis, e encontramos baixa diversidade de mtDNA em L. palmatus em toda a sua distribuição em Príncipe. Encontramos diferenças morfológicas significativas entre as fêmeas de L. rufus e L. palmatus, mas não entre os machos. Caracterizamos o canto reprodutor de L. palmatus pela primeira vez, que é marcadamente distinto do de L. rufus. Finalmente, resumimos nossas observações dos habitats de L. palmatus e notas adicionais sobre variação fenotípica e comportamento. Nosso estudo fornece informações importantes para a conservação dessa espécie ameaçada de extinção

Herded and hunted goat genomes from the dawn of domestication in the Zagros Mountains

The Aceramic Neolithic (∼9600 to 7000 cal BC) period in the Zagros Mountains, western Iran, provides some of the earliest archaeological evidence of goat (Capra hircus) management and husbandry by circa 8200 cal BC, with detectable morphological change appearing ∼1,000 y later. To examine the genomic imprint of initial management and its implications for the goat domestication process, we analyzed 14 novel nuclear genomes (mean coverage 1.13X) and 32 mitochondrial (mtDNA) genomes (mean coverage 143X) from two such sites, Ganj Dareh and Tepe Abdul Hosein. These genomes show two distinct clusters: those with domestic affinity and a minority group with stronger wild affinity, indicating that managed goats were genetically distinct from wild goats at this early horizon. This genetic duality, the presence of long runs of homozygosity, shared ancestry with later Neolithic populations, a sex bias in archaeozoological remains, and demographic profiles from across all layers of Ganj Dareh support management of genetically domestic goat by circa 8200 cal BC, and represent the oldest to-this-date reported livestock genomes. In these sites a combination of high autosomal and mtDNA diversity, contrasting limited Y chromosomal lineage diversity, an absence of reported selection signatures for pigmentation, and the wild morphology of bone remains illustrates domestication as an extended process lacking a strong initial bottleneck, beginning with spatial control, demographic manipulation via biased male culling, captive breeding, and subsequently phenotypic and genomic selection.

Origin and Genetic Diversity of Nepalese Indigenous Goats (Capra hircus)

Background: A very little study has been conducted on the phylogenetic diversity of Nepalese indigenous goats where four breeds, Khari, Chyangra, Terai and Sinhal, have been identified. Methods: The 625-bp long sequences of the mitochondrial DNA hyper-variable region obtained from 93 goats in this study revealed high haplotype diversity among breeds, which come under four haplogroups (A-D).Result: The study demonstrated a certain level of gene flow among the neighboring goat populations exhibiting no correspondence between the geographic regions of origin and relationships among breeds. The complex mtDNA diversity and structure identified among indigenous Nepalese goats can be explained by gene flow through ancient trading and the current ‘free’ movement of goats across the geographic vicinities in India and China. Furthermore, HapG B showed the southward direction of gene flow which does not cross the Himalayas, whereas HapG B1 revealed the South-West gene flow from the claimed domestication center for HapG B, China, to Nepal.

Species limits in birds: Australian perspectives on interrelated challenges of allopatry, introgression of mitochondrial DNA, recent speciation, and selection

Four main challenges that can underpin ongoing, intransigent debates about species limits in birds are reviewed: allopatry (population subdivision vs. speciation), geographically widespread introgression of mitochondrial DNA (mtDNA), recent speciation, and selection. Examples from birds of the Australian region show how these challenges, their interplay, and the molecular-phenotypic discordance they generate can clarify or mislead species limits. Examples of how phylogenetic frameworks help reject or retain hypotheses of species limits under these challenges are given. Although mtDNA’s strengths and limitations are well known, an underappreciated limitation of mtDNA is geographically widespread introgression that homogenizes mtDNA diversity across species, subspecies, or population boundaries and across hundreds of kilometers. The resulting discordance between mtDNA and phenotype can be profound. If undetected, the setting of species limits and evolutionarily significant units are misled. An example shows how recent genomic analyses can detect and solve the problem. Other examples concern legacy mtDNA-only datasets. These are often essentially unfinished studies leaving residual uncertainty in species limits. Examples illustrate when the possibility of large-scale introgression across species boundaries needs to be considered, and how genomic scale data offer solutions. Researchers must carefully parse 3 questions: has there been introgression of mtDNA and, if so, which population genetics-based driver has caused introgression, and do species limits need altering? Understanding of allopatry, mtDNA introgression, recent speciation, and selection must be properly integrated if species limits are to be robustly understood and applied with maximum benefit in downstream applications such as conservation and management.

Genetic Consequences of Fence Confinement in a Population of White-Tailed Deer

Fencing wildlife populations can aid wildlife management goals, but potential benefits may not always outweigh costs of confinement. Population isolation can erode genetic diversity and lead to the accumulation of inbreeding, reducing viability and limiting adaptive potential. We used microsatellite and mitochondrial DNA data collected from 640 white-tailed deer confined within a 1184 ha fence to quantify changes in genetic diversity and inbreeding over the first 12 years of confinement. Genetic diversity was sustained over the course of the study, remaining comparable to unconfined white-tailed deer populations. Uneroded genetic diversity suggests that genetic drift is mitigated by a low level of gene flow, which supports field observations that the fence is not completely impermeable. In year 9 of the study, we observed an unexpected influx of mtDNA diversity and drop in inbreeding as measured by FIS. A male harvest restriction imposed that year increased male survival, and more diverse mating may have contributed to the inbreeding reduction and temporary genetic diversity boost we observed. These data add to our understanding of the long-term impacts of fences on wildlife, but also highlight the importance of continued monitoring of confined populations.