Understanding Historical Demographic Processes to Inform Contemporary Conservation of an Arid Zone Specialist: The Yellow-Footed Rock-Wallaby

Little genetic research has been undertaken on mammals across the vast expanse of the arid biome in Australia, despite continuing species decline and need for conservation management. Here, we evaluate the contemporary and historical genetic connectivity of the yellow-footed rock-wallaby, Petrogale xanthopus xanthopus, a threatened macropodid which inhabits rocky outcrops across the disconnected mountain range systems of the southern arid biome. We use 17 microsatellite loci together with mitochondrial control region data to determine the genetic diversity of populations and the evolutionary processes shaping contemporary population dynamics on which to base conservation recommendations. Our results indicate the highly fragmented populations have reduced diversity and limited contemporary gene flow, with most populations having been through population bottlenecks. Despite limited contemporary gene flow, the phylogeographic relationships of the mitochondrial control region indicate a lack of structure and suggests greater historical connectivity. This is an emerging outcome for mammals across this arid region. On the basis of our results, we recommend augmentation of populations of P. x. xanthopus, mixing populations from disjunct mountain range systems to reduce the chance of continued diversity loss and inbreeding depression, and therefore maximize the potential for populations to adapt and survive into the future.

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Population genetic structure of long-tailed pygmy rice rats (Oligoryzomys longicaudatus) from Argentina and Chile based on the mitochondrial control region

Canadian Journal of Zoology ◽

10.1139/z09-115 ◽

2010 ◽

Vol 88 (1) ◽

pp. 23-35 ◽

Cited By ~ 13

Author(s):

Raúl E. González-Ittig ◽

Hernán J. Rossi-Fraire ◽

Gustavo E. Cantoni ◽

Eduardo R. Herrero ◽

Rosendo Benedetti ◽

...

Keyword(s):

Gene Flow ◽

Genetic Structure ◽

Control Region ◽

Phylogenetic Trees ◽

Mitochondrial Control Region ◽

The Andes ◽

Single Clade ◽

The Last Glacial Maximum ◽

Oligoryzomys Longicaudatus ◽

The Last Glacial

The rodent Oligoryzomys longicaudatus (Bennett, 1832) (Rodentia, Cricetidae) inhabits southern forests of Argentina and Chile, a region severely affected by glaciations during the Pleistocene–Holocene periods. We evaluate here the diversity of the mitochondrial control region to characterize the genetic structure of this species from forests and bushy areas of seven populations from Argentina and four populations from Chile. Statistical analyses showed shallow haplotype trees and mismatch distributions compatible with recent range expansions. The presence of “private” haplotypes indicates that current levels of gene flow among populations of each country would be low to moderate. Significant differences in haplotype frequencies were detected between eastern and western populations, indicating that the Andes mountains would be an effective geographic barrier for gene flow despite the existing valleys that could act as corridors for dispersion. A single clade containing all the haplotypes was recovered in the phylogenetic trees, suggesting postglacial dispersion from a single refugium during the Last Glacial Maximum. The higher effective size and levels of polymorphism in populations from Chile suggest that the refugium was located in this country. The asymmetric gene flow from Chile to Argentina may reflect a recent colonization of the eastern populations.

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Genetic Consequences of Forest Fragmentation in a Widespread Forest Bat (Natalus mexicanus, Chiroptera: Natalidae)

Diversity ◽

10.3390/d13040140 ◽

2021 ◽

Vol 13 (4) ◽

pp. 140

Author(s):

Ricardo López-Wilchis ◽

Aline Méndez-Rodríguez ◽

Javier Juste ◽

Alejandra Serrato-Díaz ◽

Flor Rodríguez-Gómez ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Habitat Fragmentation ◽

Natural Habitat ◽

Mitochondrial Control Region ◽

Genetic Structuring ◽

Forest Connectivity ◽

Contemporary Gene Flow ◽

Multiple Species ◽

Genetic Structure And Diversity

Recent historical and anthropogenic changes in the landscape causing habitat fragmentation can disrupt the connectivity of wild populations and pose a threat to the genetic diversity of multiple species. This study investigated the effect of habitat fragmentation on the structure and genetic diversity of the Mexican greater funnel-eared bat (Natalus mexicanus) throughout its distribution range in Mexico, whose natural habitat has decreased dramatically in recent years. Genetic structure and diversity were measured using the HVII hypervariable domain of the mitochondrial control region and ten nuclear microsatellite loci, to analyze historical and contemporary information, respectively. The mitochondrial and nuclear results pointed to a differential genetic structuring, derived mainly from philopatry in females. Our results also showed that genetic diversity was historically high and currently moderate; additionally, the contemporary gene flow between the groups observed was null. These findings confirm that the effects of habitat fragmentation have started to be expressed in populations and that forest loss is already building barriers to contemporary gene flow. The concern is that gene flow is a process essential to ensure that the genetic diversity of N. mexicanus populations (and probably of many other forest species) distributed in Mexico is preserved or increased in the long term by maintaining forest connectivity between locations.

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Testing concordance and conflict in spatial replication of landscape genetics inferences

10.1101/2021.06.21.449301 ◽

2021 ◽

Author(s):

Van Wishingrad ◽

Robert C Thomson

Keyword(s):

Gene Flow ◽

Genetic Differentiation ◽

Genetic Markers ◽

Sierra Nevada ◽

Landscape Genetics ◽

Species Range ◽

Genetic Connectivity ◽

Small Subset ◽

Mountain Range ◽

Spatial Replication

The field of landscape genetics relates habitat features and genetic information to infer dispersal and genetic connectivity between populations or individuals distributed across a landscape. Such studies usually focus on a small portion of a species range, and the degree to which these geographically restricted results can be extrapolated to different areas of a species range remains poorly understood. Studies that have focused on spatial replication in landscape genetics processes either evaluate a small number of sites, are informed by a small set of genetic markers, analyze only a small subset of environmental variables, or implement models that do not fully explore parameter space. Here, we used a broadly distributed ectothermic lizard (Sceloporus occidentalis, Western Fence lizard) as a model species to evaluate the full role of topography, climate, vegetation, and roads on dispersal and genetic differentiation. We conducted landscape genetics analyses in five areas within the Sierra Nevada mountain range, using thousands of ddRAD genetic markers distributed across the genome, implemented in the landscape genetics program ResistanceGA. Across study areas, we found a great deal of consistency in the variables impacting genetic connectivity, but also noted site-specific differences in the factors in each study area. High-elevation colder areas were consistently found to be barriers to gene flow, as were areas of high ruggedness and slope. High temperature seasonality and high precipitation during the winter wet season also presented a substantial barrier to gene flow in a majority of study areas. The effect of other landscape variables on genetic differentiation was more idiosyncratic and depended on specific attributes at each site. Vegetation type was found to substantially affect gene flow only in the southernmost Sequoia site, likely due to a higher proportion of desert habitat here, thereby fragmenting habitats that have lower costs to dispersal. The effect of roads also varied between sites and may be related to differences in road usage and amount of traffic in each area. Across study areas, canyons were always substantially implicated as facilitators to dispersal and key features linking populations and maintaining genetic connectivity across landscapes. We emphasize that spatial data layers are complex and multidimensional, and a careful consideration of associations between variables is vital to form sound conclusions about the critical factors affecting dispersal and genetic connectivity across space.

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Regional and Population-scale Influences on Genetic Diversity Partitioning within Costa Rican Populations of the Pioneer Tree Vochysia ferruginea Mart

Silvae Genetica ◽

10.1515/sg-2005-0037 ◽

2005 ◽

Vol 54 (1-6) ◽

pp. 258-264 ◽

Cited By ~ 12

Author(s):

S. Cavers ◽

C. Navarro ◽

P. Hopkins ◽

R. A. Ennos ◽

A. J. Lowe

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Isolation By Distance ◽

Costa Rican ◽

Population Diversity ◽

Mountain Range ◽

Pioneer Species ◽

Contemporary Gene Flow ◽

Sustainable Utilisation ◽

Vochysia Ferruginea

Abstract The neotropical pioneer species Vochysia ferruginea is locally important for timber and is being increasingly exploited. The sustainable utilisation of this species would benefit from an understanding of the level and partitioning of genetic diversity within remnant and secondary regrowth populations. We used data from total genome (amplified fragment length polymorphism, AFLP) and chloroplast genome markers to assay diversity levels within seven Costa Rican populations. Significant chloroplast differentiation between Atlantic and Pacific watersheds was observed, suggesting divergent historical origins for these populations. Contemporary gene flow, though extensive, is geographically constrained and a clear pattern of isolation by distance was detectable when an inter-population distance representing gene flow around the central Costa Rican mountain range was used. Overall population differentiation was low (FST = 0.15) and within-population diversity high, though variable (Hs = 0.16-0.32), which fits with the overall pattern of population genetic structure expected for a widespread, outcrossed tropical tree. However genetic diversity was significantly lower and differentiation higher for recently colonised and disturbed populations compared to that at more established sites. Such a pattern seems indicative of a pioneer species undergoing repeated cycles of colonisation and succession.

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A molecular characteristic of the Anatidae mitochondrial control region – a review

Annals of Animal Science ◽

10.1515/aoas-2017-0016 ◽

2018 ◽

Vol 18 (1) ◽

pp. 3-15 ◽

Cited By ~ 2

Author(s):

Joanna Warzecha ◽

Agnieszka Fornal ◽

Maria Oczkowicz ◽

Monika Bugno-Poniewierska

Keyword(s):

Phylogenetic Analysis ◽

Mitochondrial Dna ◽

Control Region ◽

Close Relationships ◽

Genetic Research ◽

Mitochondrial Control Region ◽

Coding Region ◽

Conserved Domain ◽

Control Region Sequences ◽

D Loop

Abstract Mitochondrial DNA (mtDNA) is a molecular tool that is very effective in genetic research, including phylogenetic analysis. The non-coding region is the most variable fragment of mtDNA, showing variability in length and nucleobase composition and containing three domains: two hypervariable peripheral regions and the conserved domain (D-loop) in the middle. The Anseriformes are amongst the best studied avian groups, including approximately 150 species and containing geese, swans, ducks (Anatidae), the Magpie goose (Anseranatidae) and screamers (Anhimidae). The most numerous family is the Anatidae, appearing in close relationships within the phylogenetic branches of the species. There are differences between the non-coding region of the Anatidae in comparison to other avian control regions. In the article presented below the control region sequences and the phylogeny of the Anatidae were reviewed.

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Mitochondrial Control Region Polymorphism Reveal High Amount of Gene Flow in Fennoscandian Willow Tits (Parus Montanus Borealis)

Hereditas ◽

10.1111/j.1601-5223.1998.00133.x ◽

2004 ◽

Vol 128 (2) ◽

pp. 133-143 ◽

Cited By ~ 22

Author(s):

Laura Kvist ◽

Minna Ruokonen ◽

Anna Thessing ◽

Jaakko Lumme ◽

Markku Orell

Keyword(s):

Gene Flow ◽

Control Region ◽

Mitochondrial Control Region ◽

Parus Montanus

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Genetic structure of raccoons in eastern North America based on mtDNA: implications for subspecies designation and rabies disease dynamics

Canadian Journal of Zoology ◽

10.1139/z08-072 ◽

2008 ◽

Vol 86 (9) ◽

pp. 947-958 ◽

Cited By ~ 27

Author(s):

C. I. Cullingham ◽

C. J. Kyle ◽

B. A. Pond ◽

B. N. White

Keyword(s):

Gene Flow ◽

North America ◽

Control Region ◽

Mississippi River ◽

Procyon Lotor ◽

Mitochondrial Control Region ◽

Sea Levels ◽

Central United States ◽

Rising Sea Levels ◽

Eastern Seaboard

Subspecific designations are useful for wildlife management when they represent real barriers to gene flow. In this study, we assess genetic partitioning of mitochondrial DNA control region variation to determine if the structuring is congruent with morphologically defined subspecies of the common raccoon (Procyon lotor (L., 1758)). Mitochondrial control region sequences were analyzed within and among four subspecies ( Procyon lotor elucus Bangs, 1898, Procyon lotor lotor (L., 1758), Procyon lotor hirtus Nelson and Goldman, 1930, and Procyon lotor varius Nelson and Goldman, 1930) that occur along the eastern seaboard of North America through to the central United States. This identified 76 haplotypes, 59 of which were specific to one of the four ranges, while only 1 haplotype was wide-spread. Phylogenetic analysis revealed three distinct lineages: one found primarily in Florida, one along the eastern seaboard, and the third predominantly to the west of the Mississippi River. These lineages likely diverged during the Pleistocene, as a result of rising sea levels creating barriers to gene flow. The range of P. l. elucus is still primarily one lineage supporting the subspecific designation; however, there is considerable lineage mixing across the ranges of P. l. hirtus, P. l. lotor, and P. l. varius, suggesting that they be synonymized to P. l. lotor. While some of these subspecies designations are not supported, we have found that landscape attributes affect gene flow, which can be of use in informing rabies management.

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