scholarly journals Complex admixture preceded and followed the extinction of wisent in the wild

2016 ◽  
Author(s):  
Karolina Węcek ◽  
Stefanie Hartmann ◽  
Johanna L. A. Paijmans ◽  
Ulrike Taron ◽  
Georgios Xenikoudakis ◽  
...  
Keyword(s):  
Captive Breeding ◽  
Incomplete Lineage Sorting ◽  
Population History ◽  
Conservation Strategies ◽  
Lineage Sorting ◽  
Captive Breeding Program ◽  
Before And After ◽  
In The Wild ◽  
Population Processes ◽  
Using Data

AbstractRetracing complex population processes that precede extreme bottlenecks may be impossible using data from living individuals. The wisent (Bison bonasus), Europe’s largest terrestrial mammal, exemplifies such a population history, having gone extinct in the wild but subsequently restored by captive breeding efforts. Using low coverage genomic data from modern and historical individuals, we investigate population processes occurring before and after this extinction. Analysis of aligned genomes supports the division of wisent into two previously recognised subspecies, but almost half of the genomic alignment contradicts this population history as a result of incomplete lineage sorting and admixture. Admixture between subspecies populations occurred prior to extinction and subsequently during the captive breeding program. Admixture with the Bos cattle lineage is also widespread but results from ancient events rather than recent hybridisation with domestics. Our study demonstrates the huge potential of historical genomes for both studying evolutionary histories and for guiding conservation strategies.

scholarly journals Disentangling Population History and Character Evolution among Hybridizing Lineages

2020 ◽  
Vol 37 (5) ◽  
pp. 1295-1305 ◽  
Author(s):  
Sean P Mullen ◽  
Nicholas W VanKuren ◽  
Wei Zhang ◽  
Sumitha Nallu ◽  
Evan B Kristiansen ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
De Novo ◽  
Balancing Selection ◽  
Incomplete Lineage Sorting ◽  
Introgressive Hybridization ◽  
Character Evolution ◽  
Population History ◽  
Lineage Sorting ◽  
Evolutionary Origins ◽  
Whole Genome Resequencing

Abstract Understanding the origin and maintenance of adaptive phenotypic novelty is a central goal of evolutionary biology. However, both hybridization and incomplete lineage sorting can lead to genealogical discordance between the regions of the genome underlying adaptive traits and the remainder of the genome, decoupling inferences about character evolution from population history. Here, to disentangle these effects, we investigated the evolutionary origins and maintenance of Batesian mimicry between North American admiral butterflies (Limenitis arthemis) and their chemically defended model (Battus philenor) using a combination of de novo genome sequencing, whole-genome resequencing, and statistical introgression mapping. Our results suggest that balancing selection, arising from geographic variation in the presence or absence of the unpalatable model, has maintained two deeply divergent color patterning haplotypes that have been repeatedly sieved among distinct mimetic and nonmimetic lineages of Limenitis via introgressive hybridization.

Aspects of the life history and breeding biology of the Mountain Pygmy-possum (Burramys parvus), (Marsupialia: Burramyidae) in alpine Victoria.

1990 ◽  
Vol 13 (2) ◽  
pp. 179
Author(s):  
I.M. Mansergh ◽  
J. Scotts D
Keyword(s):  
Life History ◽  
Sex Ratio ◽  
Captive Breeding ◽  
Rare Event ◽  
Cycle Period ◽  
Differential Survival ◽  
Active Season ◽  
Captive Breeding Program ◽  
Fat Reserves ◽  
In The Wild

From February 1982 to November 1989, a trapping and captive breeding program was undertaken to examine the life history of the vulnerable Mountain Pygmy-possum (Burramys parvus), the only Australian mammal restricted to the alpine and subalpine region. During the active season (Oct.-Apr.) over 38 000 trapnights in the habitat throughout Victoria yielded over 900 individual B. parvus captured on over 3 800 occasions. Burramys parvus is a polyoestrous species (mean cycle period of 20.3 days) and produces supernumerary young, up to twice the number of available teats (4). In the wild, breeding is highly synchronised to spring and a single litter is carried p.a. (x = 3.6; mode = 4). Whilst B. parvus retains the capacity to produce a second litter, this is a rare event in the wild and would be selected against as there would be insufficient time to obtain fat reserves for hibernation. At birth and independence the sex ratio of the cohort is at parity, yet at any time the sex ratio of the B. parvus population is always biased toward females due to differential survival of the sexes (at breeding I M: 4-6 F). In autumn, females that would survive winter were on average > 12 % heavier than those not retrapped. One female was at least 11 years old whilst the oldest male recorded was 4 years. Burramys parvus is the longest lived small terrestrial mammal known. Aspects of the life histo ry are discussed in the context of adaptions to the alpine environment and are compared to other small mammals in the habitat and in other cold climates, and to other small marsupial diprotodonts.

scholarly journals Historical DNA analysis reveals living descendants of an extinct species of Galápagos tortoise

2008 ◽  
Vol 105 (40) ◽  
pp. 15464-15469 ◽  
Author(s):  
Nikos Poulakakis ◽  
Scott Glaberman ◽  
Michael Russello ◽  
Luciano B. Beheregaray ◽  
Claudio Ciofi ◽  
...  
Keyword(s):  
Dna Analysis ◽  
Captive Breeding ◽  
Charles Darwin ◽  
Critical Role ◽  
Museum Specimens ◽  
Galapagos Archipelago ◽  
Captive Breeding Program ◽  
Long Term Study ◽  
In The Wild

Giant tortoises, a prominent symbol of the Galápagos archipelago, illustrate the influence of geological history and natural selection on the diversification of organisms. Because of heavy human exploitation, 4 of the 15 known species (Geochelone spp.) have disappeared. Charles Darwin himself detailed the intense harvesting of one species, G. elephantopus, which once was endemic to the island of Floreana. This species was believed to have been exterminated within 15 years of Darwin's historic visit to the Galápagos in 1835. The application of modern DNA techniques to museum specimens combined with long-term study of a system creates new opportunities for identifying the living remnants of extinct taxa in the wild. Here, we use mitochondrial DNA and microsatellite data obtained from museum specimens to show that the population on Floreana was evolutionarily distinct from all other Galápagos tortoise populations. It was demonstrated that some living individuals on the nearby island of Isabela are genetically distinct from the rest of the island's inhabitants. Surprisingly, we found that these “non-native” tortoises from Isabela are of recent Floreana ancestry and closely match the genetic data provided by the museum specimens. Thus, we show that the genetic line of G. elephantopus has not been completely extinguished and still exists in an intermixed population on Isabela. With enough individuals to commence a serious captive breeding program, this finding may help reestablish a species that was thought to have gone extinct more than a century ago and illustrates the power of long-term genetic analysis and the critical role of museum specimens in conservation biology.

scholarly journals Rarely Observed Behaviors and Occurrences of Black-footed Ferrets Preconditioning for Wild Release 2014–2017

2018 ◽  
Vol 10 (1) ◽  
pp. 241-249
Author(s):  
Tyler N. Tretten
Keyword(s):  
Captive Breeding ◽  
Natural Habitat ◽  
Cynomys Ludovicianus ◽  
Intermediate Step ◽  
Prairie Dog ◽  
Mustela Nigripes ◽  
Crotalus Viridis ◽  
Captive Breeding Program ◽  
In The Wild ◽  
Endangered Status

Abstract Black-footed ferrets Mustela nigripes became extinct in the wild in 1987 when the last known wild animals were removed from a remnant population in an attempt to save the species by beginning a captive breeding program. Breeding efforts were successful, and since 1991 wildlife managers have annually released ferrets back into the wild at sites within the ferrets' historic range. Before their release into the wild, ferrets undergo a preconditioning stage in a quasi-natural habitat which better prepares them for life in the wild after a captive upbringing. Due to their nocturnal, fossorial, and largely solitary lifestyle, combined with their expansive habitat and endangered status, there are undoubtedly a multitude of behaviors ferrets exhibit that are not commonly observed. Here I detail multiple aspects of rarely described black-footed ferret ecology including black-tailed prairie dog Cynomys ludovicianus hunting stratagems, interactions with prairie rattlesnakes Crotalus viridis viridis, predation on birds, and sudden unexplained deaths of entire ferret family groups. The preconditioning setting that serves as an intermediate step between a captive and wild life for captive-reared ferrets allows for wildlife managers to witness ferret behaviors, though similar situations conceivably occur somewhat regularly in the wild.

Overcoming paralogy and incomplete lineage sorting to detect a phylogeographic signal: a GapC study of Armeria pungens

Botany ◽  
2009 ◽  
Vol 87 (2) ◽  
pp. 164-177 ◽  
Author(s):  
Rosalía Piñeiro ◽  
Andrea Costa ◽  
Javier Fuertes Aguilar ◽  
Gonzalo Nieto Feliner
Keyword(s):  
Allelic Variation ◽  
Incomplete Lineage Sorting ◽  
Direct Sequencing ◽  
Nuclear Gene ◽  
Amino Acid Sequences ◽  
Population History ◽  
Lineage Sorting ◽  
Genetic Lineages ◽  
Statistical Parsimony ◽  
Promising Source

Low-copy nuclear genes have been suggested as a promising source of independent phylogeographic markers in plants. However, the available studies at the intraspecific level have revealed that extracting information from them is frequently hampered by paralogy and lack of coalescence of alleles. It is thus relevant to test their utility with plants for which solid data from other markers are available. The aims of this study are to retrieve phylogeographic useful information in a low-copy nuclear gene by examining the congruence of the genetic variation with the geography, as well as with previous nuclear ribosomal, plastid, and amplified fragment length polymorphism (AFLP) markers. Seven combinations of primers have been assayed to characterize the structure of GapC (cytosolic glyceraldehyde 3-phosphate dehydrogenase) in Armeria pungens (Link) Hoffmanns. & Link, a linearly distributed Atlantic–Mediterranean disjunct sand-dune species. A matrix of 101 direct sequences from 71 individuals was analysed with statistical parsimony. To check the reliability of direct sequencing, 216 cloned sequences were also generated. Tests of recombination have also been attempted. By comparing nucleotide and amino acid sequences, three different paralogs (1, 2, 3) were identified of which paralog 2 was sampled for phylogeographic inference. Within this paralog, 13 alleles belonging in three different sequence types (I, II, III) were detected. These types are shown to correspond with lineages from the same locus whose splitting predates the origin of A. pungens, although type III could be a recent paralog. Allelic variation within types I and II followed a clear geographic trend supporting the two main genetic lineages detected in A. pungens with previous markers. This study suggests that information on the population history of a species can be retrieved, even if some uncertainty remains on the source of variation of low-copy nuclear gene sequences, either alleles from the same locus or paralogs.

scholarly journals The effect of captivity on the oral health of the critically endangered black-footed ferret (Mustela nigripes)

2016 ◽  
Vol 94 (1) ◽  
pp. 15-22 ◽  
Author(s):  
T.S. Antonelli ◽  
C.L. Leischner ◽  
J.J. Ososky ◽  
A. Hartstone-Rose
Keyword(s):  
Oral Health ◽  
Captive Breeding ◽  
Periodontal Diseases ◽  
Breeding Program ◽  
Prairie Dogs ◽  
Westward Expansion ◽  
Mustela Nigripes ◽  
Captive Breeding Program ◽  
Soft Diet ◽  
In The Wild

Black-footed ferrets (Mustela nigripes (Audubon and Bachman, 1851)), a North American species of mustelid, faced near extinction after westward expansion during the 20th century destroyed a majority of the population of prairie dogs (genus Cynomys Rafinesque, 1817), their primary food source. Fearing extinction of the black-footed ferret, the U.S. Fish and Wildlife Service captured the entire population between 1985 and 1987 and began a captive breeding program. While in captivity, the fertility and genetic diversity of the species was closely monitored; however, there is little information about other health consequences of this breeding program. For instance, the black-footed ferrets have been fed a diet that is very different than what they consume in the wild. How did the composition of this diet affect the oral health of these animals? An analysis of dentition of wild and captive black-footed ferrets reveals that calculus accumulation and periodontal diseases occurred with greater severity in captive black-footed ferrets, suggesting that such oral pathologies arose from the unnaturally soft diet fed to them. These findings offer insight into how mechanical properties of diet can affect oral health and how these dietary properties should be considered, not only in regard to the health of black-footed ferrets but also to the health of all mammals including humans.

scholarly journals Born to Be Wild: Evaluating the Zoo-Based Regent Honeyeater Breed for Release Program to Optimise Individual Success and Conservation Outcomes in the Wild

2021 ◽  
Vol 2 ◽  
Author(s):  
Joy S. Tripovich ◽  
Gordana Popovic ◽  
Andrew Elphinstone ◽  
Dean Ingwersen ◽  
Glen Johnson ◽  
...  
Keyword(s):  
Reproductive Success ◽  
Captive Breeding ◽  
Pedigree Information ◽  
Breeding Programs ◽  
Captive Breeding Program ◽  
Trade Offs ◽  
In The Wild ◽  
Release Program ◽  
Individual Success ◽  
The Impact

Evaluating the effectiveness of captive breeding programs is central to improving conservation outcomes in released animals. However, few studies have assessed the impact of the strategies and trade-offs involved in husbandry decisions and the selection of traits on the success of breeding programs. This study evaluated a range of husbandry features including an animal's environment, health, and traits of the released individual and its parents involved in the zoo-based Regent Honeyeater breed for release program to optimise individual reproductive success and survivability, leading to improved conservation outcomes in the wild. We analysed 285 birds using a penalised Cox proportional hazard model to assess survival and an ordinal logistic model to evaluate the reproductive success of zoo bred birds released to the wild. Key features identified by the study highlight the importance of having parents that are successful breeders and parents that have an overall higher lifetime reproductive output. However, there were associated quantity-quality trade-offs, as the success of young (i.e., released birds) produced by parents was negatively associated to the number of clutches per year (where one clutch per year was found optimal). The study demonstrated the importance of considering the parental effects on the traits of its offspring beyond its pedigree information and found there was an associated decline in fitness of its offspring with older fathers. Song tutoring using wild Regent Honeyeaters was also important for increased survival post-release. Other important factors are discussed within the review. In general, the study recommended that a multi-faceted approach in the assessment and evaluation of the captive breeding program, to identify markers that will improve conservation outcomes of future releases.

scholarly journals The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales

2020 ◽  
Author(s):  
Liming Cai ◽  
Zhenxiang Xi ◽  
Emily Moriarty Lemmon ◽  
Alan R Lemmon ◽  
Austin Mast ◽  
...  
Keyword(s):  
Gene Flow ◽  
Incomplete Lineage Sorting ◽  
Estimation Error ◽  
Gene Tree ◽  
Species Tree ◽  
Flowering Plant ◽  
Estimation Methods ◽  
Lineage Sorting ◽  
Tree Estimation ◽  
Perfect Storm

Abstract The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent (MSC) model and improved gene tree estimation methods can better accommodate gene tree heterogeneity caused by incomplete lineage sorting (ILS) and gene tree estimation error stemming from the short internal branches. However, the relative influence of these factors in species tree inference is not well understood. Using anchored hybrid enrichment, we generated a data set including 423 single-copy loci from 64 taxa representing 39 families to infer the species tree of the flowering plant order Malpighiales. This order includes nine of the top ten most unstable nodes in angiosperms, which have been hypothesized to arise from the rapid radiation during the Cretaceous. Here, we show that coalescent-based methods do not resolve the backbone of Malpighiales and concatenation methods yield inconsistent estimations, providing evidence that gene tree heterogeneity is high in this clade. Despite high levels of ILS and gene tree estimation error, our simulations demonstrate that these two factors alone are insufficient to explain the lack of resolution in this order. To explore this further, we examined triplet frequencies among empirical gene trees and discovered some of them deviated significantly from those attributed to ILS and estimation error, suggesting gene flow as an additional and previously unappreciated phenomenon promoting gene tree variation in Malpighiales. Finally, we applied a novel method to quantify the relative contribution of these three primary sources of gene tree heterogeneity and demonstrated that ILS, gene tree estimation error, and gene flow contributed to 10.0%, 34.8%, and 21.4% of the variation, respectively. Together, our results suggest that a perfect storm of factors likely influence this lack of resolution, and further indicate that recalcitrant phylogenetic relationships like the backbone of Malpighiales may be better represented as phylogenetic networks. Thus, reducing such groups solely to existing models that adhere strictly to bifurcating trees greatly oversimplifies reality, and obscures our ability to more clearly discern the process of evolution.

scholarly journals Morphological, Ecological, and Molecular Divergence of Conogethes pinicolalis from C. punctiferalis (Lepidoptera: Crambidae)

Insects ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 455
Author(s):  
Na Ra Jeong ◽  
Min Jee Kim ◽  
Sung-Soo Kim ◽  
Sei-Woong Choi ◽  
Iksoo Kim
Keyword(s):  
Phylogenetic Analysis ◽  
First Generation ◽  
Incomplete Lineage Sorting ◽  
Divergence Time ◽  
Sequence Divergence ◽  
Lineage Sorting ◽  
Mitochondrial Coi ◽  
Feeding Type ◽  
Pine Trees ◽  
Yellow Peach Moth

Conogethes pinicolalis has long been considered as a Pinaceae-feeding type of the yellow peach moth, C. punctiferalis, in Korea. In this study, the divergence of C. pinicolalis from the fruit-feeding moth C. punctiferalis was analyzed in terms of morphology, ecology, and genetics. C. pinicolalis differs from C. punctiferalis in several morphological features. Through field observation, we confirmed that pine trees are the host plants for the first generation of C. pinicolalis larvae, in contrast to fruit-feeding C. punctiferalis larvae. We successfully reared C. pinicolalis larvae to adults by providing them pine needles as a diet. From a genetic perspective, the sequences of mitochondrial COI of these two species substantially diverged by an average of 5.46%; moreover, phylogenetic analysis clearly assigned each species to an independent clade. On the other hand, nuclear EF1α showed a lower sequence divergence (2.10%) than COI. Overall, EF1α-based phylogenetic analysis confirmed each species as an independent clade, but a few haplotypes of EF1α indicated incomplete lineage sorting between these two species. In conclusion, our results demonstrate that C. pinicolalis is an independent species according to general taxonomic criteria; however, analysis of the EF1α sequence revealed a short divergence time.

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