Runs of Homozygosity and Population History of Three Horse Breeds With Small Population Size

Abstract Eumops floridanus (Allen, 1932) is a molossid commonly called the Florida bonneted bat or the Florida mastiff bat. Eumops floridanus is the largest species of bat in Florida and is one of 16 species in the genus Eumops. With one of the smallest distributions of any bat in the United States, it is endemic to southern peninsular Florida where it roosts in cavities of live and dead trees and man-made structures. Eumops floridanus was formerly classified as a subspecies of E. glaucinus but has been elevated to species level based on morphology. Due primarily to its restricted distribution, small population size, and the continued loss of habitat, E. floridanus is federally listed as “Endangered” (EN) by the United States Fish and Wildlife Service.

Download Full-text

Clipperton Atoll as a model to study small marine populations: Endemism and the genomic consequences of small population size

PLoS ONE ◽

10.1371/journal.pone.0198901 ◽

2018 ◽

Vol 13 (6) ◽

pp. e0198901 ◽

Cited By ~ 4

Author(s):

Nicole L. Crane ◽

Juliette Tariel ◽

Jennifer E. Caselle ◽

Alan M. Friedlander ◽

D. Ross Robertson ◽

...

Keyword(s):

Population Size ◽

Small Population ◽

Small Population Size

Download Full-text

Small population size limits reproduction in an invasive grass through both demography and genetics

Oecologia ◽

10.1007/s00442-012-2465-y ◽

2012 ◽

Vol 172 (1) ◽

pp. 109-117 ◽

Cited By ~ 12

Author(s):

Jeffrey L. Firestone ◽

Marie Jasieniuk

Keyword(s):

Population Size ◽

Small Population ◽

Invasive Grass ◽

Small Population Size ◽

Size Limits

Download Full-text

Mobile elements reveal small population size in the ancient ancestors of Homo sapiens

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0909000107 ◽

2010 ◽

Vol 107 (5) ◽

pp. 2147-2152 ◽

Cited By ~ 27

Author(s):

Chad D. Huff ◽

Jinchuan Xing ◽

Alan R. Rogers ◽

David Witherspoon ◽

Lynn B. Jorde

Keyword(s):

Population Size ◽

Effective Population Size ◽

Dna Sequences ◽

Mobile Element ◽

Small Population ◽

Mobile Elements ◽

Population History ◽

Recent Common Ancestor ◽

Demographic Model ◽

Effective Population

The genealogies of different genetic loci vary in depth. The deeper the genealogy, the greater the chance that it will include a rare event, such as the insertion of a mobile element. Therefore, the genealogy of a region that contains a mobile element is on average older than that of the rest of the genome. In a simple demographic model, the expected time to most recent common ancestor (TMRCA) is doubled if a rare insertion is present. We test this expectation by examining single nucleotide polymorphisms around polymorphic Alu insertions from two completely sequenced human genomes. The estimated TMRCA for regions containing a polymorphic insertion is two times larger than the genomic average (P < <10−30), as predicted. Because genealogies that contain polymorphic mobile elements are old, they are shaped largely by the forces of ancient population history and are insensitive to recent demographic events, such as bottlenecks and expansions. Remarkably, the information in just two human DNA sequences provides substantial information about ancient human population size. By comparing the likelihood of various demographic models, we estimate that the effective population size of human ancestors living before 1.2 million years ago was 18,500, and we can reject all models where the ancient effective population size was larger than 26,000. This result implies an unusually small population for a species spread across the entire Old World, particularly in light of the effective population sizes of chimpanzees (21,000) and gorillas (25,000), which each inhabit only one part of a single continent.

Download Full-text

The abundance of false killer whale, Pseudorca crassidens (Artiodactyla: Delphinidae) in coastal waters of Golfo Dulce and Osa Peninsula, Costa Rica

Revista de Biología Tropical ◽

10.15517/rbt.v68i2.37196 ◽

2020 ◽

Vol 68 (2) ◽

Author(s):

Erika Sánchez Robledo ◽

Lenin Enrique Oviedo Correa ◽

David Herra-Miranda ◽

Juan Diego Pacheco-Polanco ◽

Sierra Goodman ◽

...

Keyword(s):

Costa Rica ◽

Population Size ◽

Killer Whale ◽

Small Population ◽

Killer Whales ◽

Apparent Survival ◽

Osa Peninsula ◽

Small Population Size ◽

False Killer Whale ◽

Pseudorca Crassidens

Introduction: False killer whale (Pseudorca crassidens) is a tropical and subtropical social species that live in groups with individuals of mixed ages and sex classes. False killer whales have been documented since the late 1990s in Southwestern Costa Rica. Objective: To estimate the abundance of false killer whales in Osa Peninsula waters. Methods: Cetacean surveys off the Osa Peninsula Waters (OPW), Costa Rica, yielded opportunistic encounters with false killer whales in Drake Bay and Caño Island (2001-2015) and observations during formal surveys in Golfo Dulce (2005-2015). Photo-identification data was analyzed using capture-mark-recapture models in the study area, through an open population (POPAN) framework, considering the effect of time on the parameters apparent survival and capture probability, producing an abundance estimate for a superpopulation in the entire study area. Results: False killer whale abundance in OPW is characterized by a small population size of no more than 100 individuals, complemented by a very low probability of encounter and a contrasting high apparent survival. Conclusions: This population estimate should be taken as conservative, however, the small population size of less than 100 individuals should be considered vulnerable, in contrast to the increasing anthropogenic impacts in the coastal seascape. We argue the potential occurrence of population units along the coastal seascape of the Pacific littoral and oceanic island-associated units at Isla del Coco.

Download Full-text

An Efficient Algorithm for Estimating Population History from Genetic Data

10.1101/2021.01.23.427922 ◽

2021 ◽

Author(s):

Alan R. Rogers

Keyword(s):

Population Size ◽

Efficient Algorithm ◽

Genetic Data ◽

Deterministic Algorithm ◽

Population History ◽

History Of

AbstractLegofit is a statistical package that uses genetic data to estimate the history of population size, subdivision, and admixture. This article describes a new deterministic algorithm, which makes Legofit orders of magnitude faster and more accurate.

Download Full-text

Detecting a Literary Future in the Historical Past: The Gibraltar Case

Armenian Folia Anglistika ◽

10.46991/afa/2015.11.2.123 ◽

2015 ◽

Vol 11 (2 (14)) ◽

pp. 123-134

Author(s):

John A. Stotesbury

Keyword(s):

Population Size ◽

Present Article ◽

Literary Culture ◽

Small Population ◽

Autonomous Community ◽

Literary Identity ◽

Small Population Size ◽

The Past ◽

British Colonial ◽

Historical Past

Until the present millennium, very little creative literary writing in either English or Spanish had been published in the British colonial enclave of Gibraltar. Given the small population size of the autonomous community of some 30,000 people, it was considered unlikely that a “national” literary culture could form. In the course of the past decade, a handful of dedicated writers have published a noticeable amount of fiction, all of which is concerned with establishing a recognized Gibraltarian literary identity. The present article, while not arguing for the permanence of a Gibraltarian national literary culture, attempts to trace some of the ways in which a small, unified, geopolitical territory has attempted to tell its own story.

Download Full-text

Diversity and Paleodemography of the Addax (Addax nasomaculatus), a Saharan Antelope on the Verge of Extinction

Genes ◽

10.3390/genes12081236 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1236

Author(s):

Elisabeth Hempel ◽

Michael V. Westbury ◽

José H. Grau ◽

Alexandra Trinks ◽

Johanna L. A. Paijmans ◽

...

Keyword(s):

Population Size ◽

Population History ◽

Phylogeographic Structure ◽

Recent Common Ancestor ◽

Mitochondrial Genomes ◽

Effective Population ◽

Mammal Species ◽

Human Disturbances ◽

Most Recent Common Ancestor ◽

History Of

Since the 19th century, the addax (Addax nasomaculatus) has lost approximately 99% of its former range. Along with its close relatives, the blue antelope (Hippotragus leucophaeus) and the scimitar-horned oryx (Oryx dammah), the addax may be the third large African mammal species to go extinct in the wild in recent times. Despite this, the evolutionary history of this critically endangered species remains virtually unknown. To gain insight into the population history of the addax, we used hybridization capture to generate ten complete mitochondrial genomes from historical samples and assembled a nuclear genome. We found that both mitochondrial and nuclear diversity are low compared to other African bovids. Analysis of mitochondrial genomes revealed a most recent common ancestor ~32 kya (95% CI 11–58 kya) and weak phylogeographic structure, indicating that the addax likely existed as a highly mobile, panmictic population across its Sahelo–Saharan range in the past. PSMC analysis revealed a continuous decline in effective population size since ~2 Ma, with short intermediate increases at ~500 and ~44 kya. Our results suggest that the addax went through a major bottleneck in the Late Pleistocene, remaining at low population size prior to the human disturbances of the last few centuries.

Download Full-text

Introgression makes waves in inferred histories of effective population size

10.1101/121483 ◽

2017 ◽

Author(s):

John Hawks

Keyword(s):

Gene Flow ◽

Population Size ◽

Effective Population Size ◽

Population History ◽

Human Populations ◽

Effective Population ◽

History Of ◽

Or Gene ◽

Time Of Origin ◽

Past Population

AbstractHuman populations have a complex history of introgression and of changing population size. Human genetic variation has been affected by both these processes, so that inference of past population size depends upon the pattern of gene flow and introgression among past populations. One remarkable aspect of human population history as inferred from genetics is a consistent “wave” of larger effective population size, prior to the bottlenecks and expansions of the last 100,000 years. Here I carry out a series of simulations to investigate how introgression and gene flow from genetically divergent ancestral populations affect the inference of ancestral effective population size. Both introgression and gene flow from an extinct, genetically divergent population consistently produce a wave in the history of inferred effective population size. The time and amplitude of the wave reflect the time of origin of the genetically divergent ancestral populations and the strength of introgression or gene flow. These results demonstrate that even small fractions of introgression or gene flow from ancient populations may have large effects on the inference of effective population size.

Download Full-text