Mixed Mating in a Multi-Origin Population Suggests High Potential for Genetic Rescue in North Island Brown Kiwi, Apteryx mantelli

Reinforcement translocations are increasingly utilised in conservation with the goal of achieving genetic rescue. However, concerns regarding undesirable results, such as genetic homogenisation or replacement, are widespread. One factor influencing translocation outcomes is the rate at which the resident and the introduced individuals interbreed. Consequently, post-release mate choice is a key behaviour to consider in conservation planning. Here we studied mating, and its consequences for genomic admixture, in the North Island brown kiwi Apteryx mantelli population on Ponui Island which was founded by two translocation events over 50 years ago. The two source populations used are now recognised as belonging to two separate management units between which birds differ in size and are genetically differentiated. We examined the correlation between male and female morphometrics for 17 known pairs and quantified the relatedness of 20 pairs from this admixed population. In addition, we compared the genetic similarity and makeup of 106 Ponui Island birds, including 23 known pairs, to birds representing the source populations for the original translocations. We found no evidence for size-assortative mating. On the contrary, genomic SNP data suggested that kiwi of one feather did not flock together, meaning that mate choice resulted in pairing between individuals that were less related than expected by random chance. Furthermore, the birds in the current Ponui Island population were found to fall along a gradient of genomic composition consistent with non-clustered representation of the two parental genomes. These findings indicate potential for successful genetic rescue in future Apteryx reinforcement translocations, a potential that is currently under utilised due to restrictive translocation policies. In light of our findings, we suggest that reconsideration of these policies could render great benefits for the future diversity of this iconic genus in New Zealand.

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Island life and isolation: The population genetics of Pacific Wrens on the North Pacific Rim

The Condor ◽

10.1650/condor-16-183.1 ◽

2017 ◽

Vol 119 (1) ◽

pp. 131-142

Author(s):

Christin L. Pruett ◽

Angela Ricono ◽

Cory Spern ◽

Kevin Winker

Keyword(s):

Genetic Diversity ◽

Island Population ◽

Genetic Rescue ◽

Conservation Units ◽

Widespread Species ◽

Island Populations ◽

The North ◽

Conservation Concern ◽

Lagopus Muta ◽

The North Pacific

Abstract Conservation of intraspecific variation is a growing focus of conservation biology. Island populations can make up a large portion of the variation of widespread species, as they are often isolated and exhibit differences in phenotype and genetic structure compared with mainland populations. We genotyped 169 Pacific Wrens (Troglodytes pacificus) from 9 locations and 6 subspecies in Alaska, USA, and British Columbia, Canada, to examine the population structure, genetic diversity, and likelihood of genetic rescue of island populations of conservation concern. We found that 25% of genetic variation was partitioned among conservation units delineated by subspecies, suggesting that the present framework of managing subspecies as separate units is warranted. Populations found farthest from possible mainland sources had the lowest genetic diversity. The Attu Island population, subspecies T. p. meligerus, had the lowest genetic diversity and highest genetic divergence of all sampled locations, a signal also found in Attu Island populations of Song Sparrow (Melospiza melodia) and Rock Ptarmigan (Lagopus muta). Currently, populations in western Alaska are unlikely to be connected to populations in mainland locations through dispersal, and thus are unlikely candidates for natural genetic or demographic rescue.

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Modified rescue and risk expectations for species with diverse mating systems and modes of inheritance

10.1093/oso/9780198783398.003.0008 ◽

2017 ◽

Author(s):

Richard Frankham ◽

Jonathan D. Ballou ◽

Katherine Ralls ◽

Mark D. B. Eldridge ◽

Michele R. Dudash ◽

...

Keyword(s):

Mating Systems ◽

Outbreeding Depression ◽

Mixed Mating ◽

Genetic Rescue ◽

Mode Of Inheritance

The risks of inbreeding and outbreeding depression, and the prospects for genetic rescue are often different in species with alternative mating systems and mode of inheritance (compared to outbreeding diploids), such as self-incompatible, self-fertilizing, mixed mating, non-diploid (haploid, haplodiploid and polyploid) and asexual.

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Genome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America

Scientific Reports ◽

10.1038/s41598-021-90325-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Kyung Seok Kim ◽

Kevin J. Roe

Keyword(s):

Phylogenetic Analyses ◽

Freshwater Mussel ◽

Conservation Strategies ◽

Nucleotide Polymorphisms ◽

Conservation Units ◽

Genetic Structuring ◽

The North ◽

Snp Data ◽

Genome Wide ◽

Significant Difference

AbstractDetailed information on species delineation and population genetic structure is a prerequisite for designing effective restoration and conservation strategies for imperiled organisms. Phylogenomic and population genomic analyses based on genome-wide double digest restriction-site associated DNA sequencing (ddRAD-Seq) data has identified three allopatric lineages in the North American freshwater mussel genus Cyprogenia. Cyprogenia stegaria is restricted to the Eastern Highlands and displays little genetic structuring within this region. However, two allopatric lineages of C. aberti in the Ozark and Ouachita highlands exhibit substantial levels (mean uncorrected FST = 0.368) of genetic differentiation and each warrants recognition as a distinct evolutionary lineage. Lineages of Cyprogenia in the Ouachita and Ozark highlands are further subdivided reflecting structuring at the level of river systems. Species tree inference and species delimitation in a Bayesian framework using single nucleotide polymorphisms (SNP) data supported results from phylogenetic analyses, and supports three species of Cyprogenia over the currently recognized two species. A comparison of SNPs generated from both destructively and non-destructively collected samples revealed no significant difference in the SNP error rate, quality and amount of ddRAD sequence reads, indicating that nondestructive or trace samples can be effectively utilized to generate SNP data for organisms for which destructive sampling is not permitted.

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Genome-wide sequence-based genotyping supports a nonhybrid origin of Castanea alabamensis

10.1101/680371 ◽

2019 ◽

Author(s):

M. Taylor Perkins ◽

Tetyana Zhebentyayeva ◽

Paul H. Sisco ◽

J. Hill Craddock

Keyword(s):

North American ◽

Distinct Group ◽

Morphological Diversity ◽

Hybrid Origin ◽

Putative Hybrid ◽

Eastern United States ◽

The North ◽

Snp Data ◽

Genome Wide ◽

Conservation Concern

AbstractThe genus Castanea in North America contains multiple tree and shrub taxa of conservation concern. The two species within the group, American chestnut (Castanea dentata) and chinquapin (C. pumila sensu lato), display remarkable morphological diversity across their distributions in the eastern United States and southern Ontario. Previous investigators have hypothesized that hybridization between C. dentata and C. pumila has played an important role in generating morphological variation in wild populations. A putative hybrid taxon, Castanea alabamensis, was identified in northern Alabama in the early 20th century; however, the question of its hybridity has been unresolved. We tested the hypothesized hybrid origin of C. alabamensis using genome-wide sequence-based genotyping of C. alabamensis, all currently recognized North American Castanea taxa, and two Asian Castanea species at >100,000 single-nucleotide polymorphism (SNP) loci. With these data, we generated a high-resolution phylogeny, tested for admixture among taxa, and analyzed population genetic structure of the study taxa. Bayesian clustering and principal components analysis provided no evidence of admixture between C. dentata and C. pumila in C. alabamensis genomes. Phylogenetic analysis of genome-wide SNP data indicated that C. alabamensis forms a distinct group within C. pumila sensu lato. Our results are consistent with the model of a nonhybrid origin for C. alabamensis. Our finding of C. alabamensis as a genetically and morphologically distinct group within the North American chinquapin complex provides further impetus for the study and conservation of the North American Castanea species.

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Multimodal signalling in the North American barn swallow: a phenotype network approach

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2015.1574 ◽

2015 ◽

Vol 282 (1816) ◽

pp. 20151574 ◽

Cited By ~ 33

Author(s):

Matthew R. Wilkins ◽

Daizaburo Shizuka ◽

Maxwell B. Joseph ◽

Joanna K. Hubbard ◽

Rebecca J. Safran

Keyword(s):

Mate Choice ◽

North American ◽

Communication Systems ◽

Animal Communication ◽

Complex Signal ◽

Network Approach ◽

Barn Swallow ◽

Complex Signals ◽

The North ◽

Phenotype Network

Complex signals, involving multiple components within and across modalities, are common in animal communication. However, decomposing complex signals into traits and their interactions remains a fundamental challenge for studies of phenotype evolution. We apply a novel phenotype network approach for studying complex signal evolution in the North American barn swallow ( Hirundo rustica erythrogaster ). We integrate model testing with correlation-based phenotype networks to infer the contributions of female mate choice and male–male competition to the evolution of barn swallow communication. Overall, the best predictors of mate choice were distinct from those for competition, while moderate functional overlap suggests males and females use some of the same traits to assess potential mates and rivals. We interpret model results in the context of a network of traits, and suggest this approach allows researchers a more nuanced view of trait clustering patterns that informs new hypotheses about the evolution of communication systems.

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New records of 45 bird species in the desert margins area of the North-West Province, South Africa

Koedoe ◽

10.4102/koedoe.v49i1.102 ◽

2006 ◽

Vol 49 (1) ◽

Author(s):

A. Hudson ◽

H. Bouwman

Keyword(s):

South Africa ◽

Conservation Planning ◽

New Records ◽

Bird Species ◽

North West ◽

Additional Information ◽

The North ◽

North West Province ◽

Human Habitation ◽

Number Of Visits

New records and possible range extensions are reported on 45 bird species (ca 25% of the 167 species recorded during surveys) in the Bophirima district of the North-West Province, South Africa. The findings were compared with data in The Atlas of Southern African Birds. The main reasons for these new records may be ascribed to the low number of visits during the atlas project, higher precipitation during the time of our observations versus that of the atlas project, and possibly an increased suitability of the area for some bird species due to human habitation. These new records also provide additional information that may be useful in conservation planning, especially in arid areas. Heuningvlei Pan in particular, should be considered for additional conservation measures.

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Genetic similarity and mate selection in Uruguay

Journal of Biosocial Science ◽

10.1017/s0021932000021374 ◽

1994 ◽

Vol 26 (3) ◽

pp. 285-289 ◽

Cited By ~ 9

Author(s):

M. Sans ◽

I. Alvarez ◽

S. M. Callegari-Jacques ◽

F. M. Salzano

Keyword(s):

Mate Choice ◽

Blood Group ◽

Genetic Markers ◽

Mate Selection ◽

Genetic Similarity ◽

Previous Sample ◽

Putative Father ◽

Blood Genetic Markers

SummaryIt has been suggested that average genetic similarity, as assessed by blood genetic markers, could influence mate choice in humans. In the present study, average genetic similarity was assessed in 183 couples submitting to paternity determinations in relation to six blood group systems and three HLA loci. Couples in which the putative father was excluded were compared with those in which such exclusion did not occur, and real couples were compared to random pairs. The differences were all statistically non-significant. Possible reasons for the different results found in the previous sample and in the present study are considered.

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Genetic diversity in natural and introduced island populations of koalas in Queensland

Australian Journal of Zoology ◽

10.1071/zo12075 ◽

2012 ◽

Vol 60 (5) ◽

pp. 303 ◽

Cited By ~ 13

Author(s):

Kristen E. Lee ◽

Jennifer M. Seddon ◽

Stephen Johnston ◽

Sean I. FitzGibbon ◽

Frank Carrick ◽

...

Keyword(s):

Genetic Diversity ◽

Allelic Richness ◽

Island Population ◽

Founder Effects ◽

Phascolarctos Cinereus ◽

Island Populations ◽

The North ◽

Mitochondrial Haplotypes ◽

Naturally Occurring ◽

Microsatellite Alleles

Island populations of animals are expected to show reduced genetic variation and increased incidence of inbreeding because of founder effects and the susceptibility of small populations to the effects of genetic drift. Koalas (Phascolarctos cinereus) occur naturally in a patchy distribution across much of the eastern Australian mainland and on a small number of islands near the Australian coast. We compared the genetic diversity of the naturally occurring population of koalas on North Stradbroke Island in south-east Queensland with other island populations including the introduced group on St Bees Island in central Queensland. The population on St Bees Island shows higher diversity (allelic richness 4.1, He = 0.67) than the North Stradbroke Island population (allelic richness 3.2, He = 0.55). Koalas on Brampton, Newry and Rabbit Islands possessed microsatellite alleles that were not identified from St Bees Island koalas, indicating that it is most unlikely that these populations were established by a sole secondary introduction from St Bees Island. Mitochondrial haplotypes on the central Queensland islands were more similar to a haplotype found at Springsure in central Queensland and the inland clades in south-east Queensland, rather than the coastal clade in south-east Queensland.

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The genomic signatures of natural selection in admixed human populations

10.1101/2021.09.01.458503 ◽

2021 ◽

Author(s):

Sebastian Cuadros-Espinoza ◽

Guillaume Laval ◽

Lluís Quintana-Murci ◽

Etienne Patin

Keyword(s):

Natural Selection ◽

Human Populations ◽

Genomic Signatures ◽

Local Environments ◽

Admixed Population ◽

Resistance To Infection ◽

Source Populations ◽

Neutral Mutations ◽

New Evidence

Admixture has been a pervasive phenomenon in human history, shaping extensively the patterns of population genetic diversity. There is increasing evidence to suggest that admixture can also facilitate genetic adaptation to local environments, i.e., admixed populations acquire beneficial mutations from source populations, a process that we refer to as adaptive admixture. However, the role of adaptive admixture in human evolution and the power to detect it are poorly characterized. Here, we use extensive computer simulations to evaluate the power of several neutrality statistics to detect natural selection in the admixed population, accounting for background selection and assuming different admixture scenarios. We show that two statistics based on admixture proportions, F_adm and LAD, show high power to detect mutations that are beneficial in the admixed population, whereas iHS and F_ST falsely detect neutral mutations that have been selected in the source populations only. By combining F_adm and LAD into a single statistic, we scanned the genomes of 15 worldwide, admixed populations for signatures of adaptive admixture. We confirm that lactase persistence and resistance to malaria have been under adaptive admixture in West Africa and in Madagascar, North Africa and South Asia, respectively. Our approach also uncovers new cases of adaptive admixture, including the APOL1 / MYH9 locus in the Fulani nomads and PKN2 in East Indonesians, involved in resistance to infection and metabolism, respectively. Collectively, our study provides new evidence that adaptive admixture has occurred in multiple human populations, whose genetic history is characterized by periods of isolation and spatial expansions resulting in increased gene flow.

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Systematic Conservation Planning at an Ocean Basin Scale: Identifying a Viable Network of Deep-Sea Protected Areas in the North Atlantic and the Mediterranean

Frontiers in Marine Science ◽

10.3389/fmars.2021.611358 ◽

2021 ◽

Vol 8 ◽

Author(s):

Magali Combes ◽

Sandrine Vaz ◽

Anthony Grehan ◽

Telmo Morato ◽

Sophie Arnaud-Haond ◽

...

Keyword(s):

Fish Species ◽

North Atlantic ◽

Conservation Planning ◽

Deep Sea ◽

Demersal Fish ◽

Systematic Conservation Planning ◽

The North ◽

Basin Scale ◽

The North Atlantic ◽

Conservation Network

Designing conservation networks requires a well-structured framework for achieving essential objectives such as connectivity, replication or viability, and for considering local management and socioeconomic stakes. Although systematic conservation planning (SCP) approaches are increasingly used to inform such networks, their application remains challenging in large and poorly researched areas. This is especially the case in the deep sea, where SCP has rarely been applied, although growing awareness of the vulnerability of deep-sea ecosystems urges the implementation of conservation measures from local to international levels. This study aims to structure and evaluate a framework for SCP applicable to the deep sea, focusing on the identification of conservation priority networks for vulnerable marine ecosystems (VMEs), such as cold-water coral reefs, sponge grounds, or hydrothermal vents, and for key demersal fish species. Based on multi-objective prioritization, different conservation scenarios were investigated, allowing the impact of key elements such as connectivity and conservation cost to be evaluated. Our results show that continental margin slopes, the Mid-Atlantic Ridge, and deeper areas of large and productive shelves housing fishing grounds appeared as crucial zones for preserving the deep-sea biodiversity of the North Atlantic, and within the limitations imposed by the data available, of the Mediterranean. Using biologically-informed connectivity led to a more continuous and denser conservation network, without increasing the network size. Even when minimizing the overlap with socioeconomic activities, the inclusion of exploited areas was necessary to fulfil conservation objectives. Such areas included continental shelf fishing grounds for demersal fish species, and areas covered by deep-sea mining exploration contracts for hydrothermal vent communities. Covering 17% of the study area and protecting 55% of each feature on average, the identified priority network held a high conservation potential. However, these areas still suffer from poor protection, with 30% of them benefiting from some form of recognition and 11% only from protection against trawling. Integrating them into current marine spatial planning (MSP) discussions could foster the implementation of a basin-scale conservation network for the deep sea. Overall, this work established a framework for developing large-scale systematic planning, useful for managing Areas Beyond National Jurisdiction (ABNJ).

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