Geographic variation and genetic structure in the Bahama Oriole (Icterus northropi), a critically endangered synanthropic species

Bird species may exhibit unexpected population structuring over small distances, with gene flow restricted by geographic features such as water or mountains. The Bahama Oriole (Icterus northropi) is a critically endangered, synanthropic island endemic with a declining population of fewer than 300 individuals. It now remains only on Andros Island (The Bahamas), which is riddled with waterways that past studies assumed did not hinder gene flow. We examined 1,858 base pairs of mitochondrial DNA sequenced from four gene regions in 14 birds (roughly 5% of the remaining population) found on the largest land masses of Andros Island (North Andros and Mangrove Cay/South Andros). We sought to discern genetic structuring between the remaining subpopulations and its relationship to current conservation concerns. Four unique haplotypes were identified, with only one shared between the two subpopulations. Nucleotide and haplotype diversity were higher for the North Andros subpopulation than for the Mangrove Cay/South Andros subpopulation. Analysis of molecular variance (AMOVA) yielded a Wright’s fixation index (Fst) of 0.60 (PFst= 0.016), with 40.2% of the molecular variation explained by within-population differences and 59.8% by among-population differences. Based on the mitochondrial regions examined in this study, we suggest the extant subpopulations of Bahama Oriole exhibit significant population structuring over short distances, consistent with some other non-migratory tropical songbird species.

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Phylogeography of the American Woodcock (Scolopax Minor): Are Management Units Based on Band Recovery Data Reflected in Genetically Based Management Units?

The Auk ◽

10.1093/auk/122.4.1149 ◽

2005 ◽

Vol 122 (4) ◽

pp. 1149-1160

Author(s):

Judith M. Rhymer ◽

Daniel G. McAuley ◽

Heather L. Ziel

Keyword(s):

Gene Flow ◽

North America ◽

Haplotype Diversity ◽

Bird Species ◽

Population Expansion ◽

Phylogeographic Structure ◽

Eastern Region ◽

Management Units ◽

American Woodcock ◽

Scolopax Minor

Abstract Information on population connectivity throughout the annual cycle has become more crucial, because populations of many migratory birds are in decline. One such species is the American Woodcock (Scolopax minor), which inhabits early-successional forests in eastern North America. Although band recoveries have proved useful for dividing populations of this game bird species into an Eastern Region and Central Region for management purposes, these data do not provide enough detail to determine the breeding population of origin of birds recovered on stopover and wintering areas. To obtain more fine-scale data, we undertook a phylogeographic study of American Woodcock populations throughout their primary breeding range in the eastern United States and Canada using mitochondrial DNA (mtDNA) sequences from the hypervariable control region I (CRI) and ND6 gene. Despite high haplotype diversity, nucleotide diversity was low and there was no phylogeographic structure among American Woodcock populations across the species range, with birds from many states and provinces in both management regions sharing identical haplotypes. Results suggest recent or ongoing gene flow among populations, with asymmetric movement of birds between migration flyways. As has been demonstrated for several other avian species in North America, American Woodcock appear to have undergone a rapid population expansion following the late Pleistocene glacial retreat. Thus, a combination of historical demographic factors and recent or ongoing gene flow mask any population structure based on mtDNA that might accrue from philopatry to breeding areas observed in studies of marked birds. Phylogéographie de Scolopax minor: Est-ce que les Unités de Gestion Basées sur les Données de Retour de Bagues Reflètent les Unités de Gestion Basées sur la Génétique?

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Cryptic Population Structuring and the Role of the Isthmus of Tehuantepec as a Gene Flow Barrier in the Critically Endangered Central American River Turtle

PLoS ONE ◽

10.1371/journal.pone.0071668 ◽

2013 ◽

Vol 8 (9) ◽

pp. e71668 ◽

Cited By ~ 5

Author(s):

Gracia P. González-Porter ◽

Jesús E. Maldonado ◽

Oscar Flores-Villela ◽

Richard C. Vogt ◽

Axel Janke ◽

...

Keyword(s):

Gene Flow ◽

Central American ◽

Critically Endangered ◽

American River ◽

Population Structuring ◽

Isthmus Of Tehuantepec

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Population sizes and the status of endemic and restricted-range bird species on Sangihe Island, Indonesia

Bird Conservation International ◽

10.1017/s0959270902002046 ◽

2001 ◽

Vol 12 (1) ◽

pp. 53-78 ◽

Cited By ~ 9

Author(s):

Jon Riley

Keyword(s):

Endemic Species ◽

Bird Species ◽

Critically Endangered ◽

Primary Forest ◽

Restricted Range ◽

Lowland Forest ◽

Island Endemic ◽

The Status ◽

Secondary Habitats ◽

Primary Habitat

The island of Sangihe, Indonesia, was visited in 1998–99 with the aim of producing population estimates of the island's endemic and other restricted-range bird species, some of which were poorly known and thought to be at risk of extinction due to habitat change. The study focused on the last remaining patch of primary forest, on Mount Sahendaruman in southern Sangihe, home to three critically endangered endemic species: Cerulean Paradise-flycatcher Eutrichomyias rowleyi, Sangihe Shrike-thrush Colluricincla sanghirensis, and Sangihe White-eye Zosterops nehrkorni. Population densities were estimated from primary forest and secondary habitats across Sangihe to assess species dependency on primary habitat. Twenty of 24 restricted-range, globally threatened or endemic taxa were recorded and density estimates were calculated for 15 of these. The endemic Red-and-blue Lory Eos histrio is extinct on Sangihe as a result of lowland forest loss. Six species (Nicobar Pigeon Caloenas nicobarica, Sulawesi Dwarf Kingfisher Ceyx fallax, Golden Bulbul Ixos affinis, E. rowleyi, C. sanghirensis, and Z. nehrkorni) were either not recorded or have very small populations and are critically endangered on Sangihe; two species of Tanygnathus parrot are also facing local extinction on the island. The major threat to all these species is the destruction of primary forest; larger species are also threatened by hunting. The remaining endemic and restricted-range species (Blue-tailed Imperial Pigeon Ducula concinna, Sangihe Hanging-parrot Loriculus catamene, Sangihe Scops-owl Otus collari, Lilac-cheeked Kingfisher Cittura cyanotis and Elegant Sunbird Aethopyga duyvenbodei) were more widespread and occurred in secondary habitats. I recommend that L. catamene and A. duyvenbodei, currently treated as globally endangered, be reclassified as near-threatened and vulnerable respectively because of their large populations and tolerance of disturbed habitats. Species with wide global ranges that are represented by endemic subspecies have the greatest tolerance for disturbed habitat. The widespread deforestation of Sangihe has had serious consequences for many bird species and today the island supports the most threatened assemblage of single-island endemic species in Indonesia. Species-specific research to determine the status and ecology of E. rowleyi, C. sanghirensis and Z. nehrkorni, and monitoring of the Sahendaruman forest are desperately needed as a basis for future conservation efforts.

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Population genetic structure and phenotypic diversity of Aspidodera raillieti (Nematoda: Heterakoidea), a parasite of Didelphini marsupials in Brazil’s South and Southeast Atlantic Forest

10.21203/rs.3.rs-1192398/v1 ◽

2021 ◽

Author(s):

Karina Varella ◽

Roberto do Val Vilela ◽

Rosana Gentile ◽

Thiago dos Santos Cardoso ◽

Sócrates Fraga da Costa-Neto ◽

...

Keyword(s):

Gene Flow ◽

Genetic Structure ◽

Host Specificity ◽

Atlantic Forest ◽

Host Species ◽

Population Genetic ◽

Fixation Index ◽

The South ◽

Genetic Structuring ◽

Morphometric Variation

Abstract Background: Population genetics of parasites may be influenced by host specificity, life-cycle, geographical distance, evolutionary history, and host-populations structure. The nematode Aspidodera raillieti infects different marsupial and rodent hosts in the Nearctic and Neotropical regions, implying a presumably significant gene flow among populations. However, niche diversification of A. raillieti main hosts in superimposed areas may provide conditions for population genetic structuring within this parasite species. We examined the genetic structuring of A. raillieti infecting three marsupial species co-occurring along South and Southeast Brazilian Atlantic Forest, a hotspot of biodiversity.Methods: We employed morphometric analyses and partial mitochondrial cytochrome c oxidase I gene sequences (MT-CO1) to characterize populations via phylogenetic and phylogeographic analyses.Results: Among 175 A. raillieti specimens recovered from marsupial hosts Didelphis aurita, D. albiventris, and Philander quica, we identified 99 MT-CO1 haplotypes forming four groups in phylogenetic trees and networks. Clades I and II encompassed parasites of D. albiventris from the South region, Clade III comprised parasites of D. aurita from the South and Southeast regions, and Clade IV encompassed parasites of D. aurita and D. albiventris from the South and Southeast regions and parasites of Philander quica from the South region. High genetic differentiation between clades, with a high fixation index and greater genetic variation in the analysis of molecular variance (AMOVA), indicated low gene flow between clades. Haplotypes shared among host species revealed a lack of host specificity. Significant correlation in the Mantel test, suggested parasite isolation by distance, although there was no evidence of geographic structure between populations. Negative values in neutrality tests for Clades III and IV suggested recent population expansion. Morphometric differentiation between A. raillieti specimens recovered from different host species, as well as from different localities, was more evident in males.Conclusion: The genetic structure of A. raillieti populations in the South and Southeast Atlantic Forest resulted from historical events rather than from current geographical distribution or host specificity. We also demonstrate morphometric variation associated with host species and localities, suggesting phenotypic plasticity to host attributes and to spatial variables.

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Morphogenetic and population structure of two species marine bivalve (Ostreidae: Saccostrea cucullata and Crassostrea iredalei) in Aceh, Indonesia

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d190329 ◽

2018 ◽

Vol 19 (3) ◽

pp. 978-988 ◽

Cited By ~ 1

Author(s):

MUTIA RAMADHANIATY ◽

ISDRAJAD SETYOBUDIANDI ◽

HAWIS H. MADDUPPA

Keyword(s):

Population Structure ◽

Gene Flow ◽

Genetic Distance ◽

Haplotype Diversity ◽

Fixation Index ◽

Morphological Identification ◽

Marine Bivalve ◽

Geographical Distance ◽

Environmental Complexity ◽

Saccostrea Cucullata

Ramadhaniaty M, Setyobudiandi I, Madduppa HH. 2018. Morphogenetic and population structure of two species marine bivalve (Ostreidae: Saccostrea cucullata and Crassostrea iredalei) in Aceh, Indonesia. Biodiversitas 19: 978-988. Oysters (Family Ostreidae) are mollusks, with high levels of phenotypic plasticity and wide geographic distribution. Oysters are a challenging group for morphological identification and genetic populations study. Saccostrea cucullata and Crassostrea iredalei are oysters from bivalve class that lives in the intertidal area and mangrove ecosystem. To clarify the morphology, genetic diversity and population structure of the two forms of S. cucullata and C. iredalei, we collected and studied oysters from three locations along the coastal region of Aceh by using morphometric method and 16 S mtDNA sequences analysis. We also added more oysters sequences from China, Japan, and Thailand to determine the connectivity between all populations. Morphometric characteristics of the oyster showed a negative allometric growth pattern, which means the rate of length gain is faster than that of the weight gain. The genetic distance from S. cucullata was 0.0030.004 (Fst = 0.708) and C. iredalei was 0.000 (Fst = 0.971). The long genetic distance and high fixation index (Fst) in the oysters population are caused by the close geographical distance of the species in the three populations. The haplotype diversity value from S. cucullata and C. iredalei were 20 and 3, respectively. The haplotype showed the connectivity among the oyster populations which indicated by the gene flow pattern. The gene flow was affected by geographical distance and environmental complexity.

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Fine-scale genetic structure in the critically endangered red-fronted macaw in the absence of geographic and ecological barriers

Scientific Reports ◽

10.1038/s41598-020-79575-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Guillermo Blanco ◽

Francisco Morinha ◽

Séverine Roques ◽

Fernando Hiraldo ◽

Abraham Rojas ◽

...

Keyword(s):

Gene Flow ◽

Genetic Structure ◽

Critically Endangered ◽

Cognitive Capacity ◽

Ex Situ ◽

Fine Scale ◽

Genetic Structuring ◽

Long Distance ◽

Ecological Barriers ◽

Genetic Clusters

AbstractBehavioural and socio-cultural traits are recognized in the restriction of gene flow in species with high cognitive capacity and complex societies. This isolation by social barriers has been generally overlooked in threatened species by assuming disrupted gene flow due to population fragmentation and decline. We examine the genetic structure and ecology of the global population of the Critically Endangered red-fronted macaw (Ara rubrogenys), an endemic species to the inter-Andean valleys of Bolivia. We found a fine-scale genetic structuring in four genetic clusters. Genetic diversity was higher in wild compared to captive-bred macaws, but similar to that of captive wild-caught macaws. We found no clear evidence of severe genetic erosion in the population in recent decades, but it was patent in historic times, overlapping with drastic human habitat transformation and macaw persecution over millennia. We found no evidence of geographical and ecological barriers, owing to the high dispersal ability, nesting and foraging habits between genetic clusters. The lack of genetic intermixing despite long-distance foraging and seasonal movements suggests recruitment in natal colonies and other social factors reinforcing philopatry-related genetic structure. Conservation efforts should be specifically focussed on major threats in each genetic cluster as independent conservation units, and also considered in ex-situ management.

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Spatial Scale Patterns of Genetic Diversity and Gene Flow in Populations of Sweet Detar (Detarium microcarpum Guill. & Perr.; Fabaceae)

10.21203/rs.3.rs-879012/v1 ◽

2021 ◽

Author(s):

Relique Ignace AGBO ◽

Antoine Missihoun ◽

David Montcho ◽

Rollande Dagba ◽

Paulin Sédah ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Molecular Analysis ◽

Haplotype Diversity ◽

Fixation Index ◽

Chloroplast Microsatellite ◽

Evolutionary Forces ◽

Detarium Microcarpum ◽

Polymorphism Rate ◽

Amova Analysis

Abstract The main objective of this study is to investigate the patterns of genetic diversity and phylogenetic relationships within populations of Detarium microcarpum (Fabaceae) relative to different spatial conditions. Seventy-eight (78) accessions of D. microcarpum belonging to six populations (Phytogeographic districts) were sampled. In order to have very good quality DNA for molecular analysis, an optimization of the DNA isolation protocol was made. The molecular analysis of the accessions was carried out using 7 chloroplast microsatellite markers. The polymorphism rate (P) is 85.71% and the Polymorphism Information Content (PIC) was in the range of 0.43 (Ntcp_9) to 0.73 (Ccmp_2) with an average of 0.59. Allelic richness (A) ranged from 1.41 to 2.85 with an average of 2.04. The observed heterozygosity (Ho) ranged from 0.23 to 0.60 with an average of 0.39. The expected heterozygosity (He) ranged from 0.43 to 0.60 with a mean of 0.50. Wright's fixation index (FIS) ranged from − 0.17 to 0.47. The effective allele (Ae) is between 1.77 and 2.53 with an average of 2.02. Wright differentiation index (FST) was 0.024. Phylogenetic analysis revealed that the NST value was significantly higher than the GST value (NST = 0.452; GST = 0.190; P < 0.05). A relatively low hd haplotype diversity is obtained (Hd = 0.320). AMOVA analysis showed that 17.35% of the variation existed within populations but 45.80% among populations within the species. Neighbor-Joining phylogenetic tree of D. microcarpum revealed three non-distinct clusters haplotypes showing the existence of gene flow between populations of the species. Our findings of genetic structure and gene flow of D. microcarpum populations based on different spatial conditions is caused by evolutionary forces such as scattering and pollination.

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Endemic Cyprus Scops Owl Otus cyprius Readily Breeds in Artificial Nest Boxes

Animals ◽

10.3390/ani11061775 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1775

Author(s):

Savvas Iezekiel ◽

Reuven Yosef ◽

Constantinos Themistokleus ◽

Dimitrios E. Bakaloudis ◽

Christos G. Vlachos ◽

...

Keyword(s):

Rural Areas ◽

Habitat Preferences ◽

Bird Species ◽

Laying Date ◽

Artificial Nests ◽

Breeding Parameters ◽

Island Endemic ◽

Nest Boxes ◽

Ecological Requirements ◽

Old Trees

As is well-known, endemic island bird species are especially vulnerable to extinction from anthropogenic environmental change and reduced fitness compared with mainland taxa. The Cyprus Scops Owl, Otus cyprius, is a recently recognized island endemic species whose ecology and breeding biology have not been studied. It nests mainly in holes in trees and buildings, so the felling of old trees, modern architectural practices, and the renovation of old houses in villages may reduce nest site availability. Its population trend is also unknown. Therefore, to better determine its ecological requirements and habitat preferences we placed nest boxes in rural areas adjacent to the forest, in the forest, and in the ecotone between them, and used breeding success as our indicator of habitat suitability. We found that breeding parameters like laying date, clutch size, length of the incubation period, hatching day, hatching success, and number of nestlings did not differ between the three habitats. Despite the low level of nest box occupancy rate (5–11%) the endemic Cyprus Scops Owl readily breeds in artificial nests. Therefore, although we are unaware of any current threats to the Cyprus Scops Owl, we recommend that its conservation be prioritized, including studies, monitoring, habitat conservation, and the provision of nest boxes.

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Threatened birds of Guatemala: a random subset of the avifauna?

Bird Conservation International ◽

10.1017/s0959270911000517 ◽

2011 ◽

Vol 22 (3) ◽

pp. 348-353

Author(s):

ANDREA NÁJERA ◽

JAVIER A. SIMONETTI

Keyword(s):

Body Size ◽

Geographical Distribution ◽

Scientific Information ◽

Bird Species ◽

Critically Endangered ◽

Aquatic Species ◽

Random Subset ◽

The Pacific ◽

Taxonomic Affiliation

SummaryIdentifying attributes that affect the vulnerability of a species to extinction is important as it allows conservation efforts to be focused on more susceptible species. We assessed whether threatened birds of Guatemala are a random subset of the avifauna, considering their taxonomic affiliation, body size, diet and geographical distribution. We found that threatened bird species in Guatemala were neither taxonomically nor geographically randomly distributed. Large-bodied species and Psittaciformes, Galliformes, Falconiformes and Ciconiformes were among the most threatened groups, and the Pacific slopes of the country hosted more threatened birds than would be expected. Published scientific information regarding Critically Endangered bird species in Guatemala is scant and biased against nocturnal and aquatic species. Research and conservation efforts ought to be oriented toward these species and regions to safeguard the Guatemalan avifauna. This study allows an overall consideration on whether we are conserving the species and areas that are important for threatened birds.

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Y-chromosome STR variation in Ukrainian populations

Bulletin of Taras Shevchenko National University of Kyiv Series Biology ◽

10.17721/1728_2748.2015.70.55-61 ◽

2015 ◽

Vol 70 (2) ◽

pp. 55-61

Author(s):

O. Utevska ◽

L. Atramentova ◽

E. Balanovska ◽

O. Balanovsky

Keyword(s):

Y Chromosome ◽

Haplotype Diversity ◽

Allele Frequencies ◽

Forest Steppe ◽

Population Differences ◽

Match Probability ◽

Str Loci ◽

Carpathian Region ◽

Y Chromosome Str ◽

Forensic Parameters

The haplotype and allele frequencies for 17 STR loci of Y-chromosome were obtained for 1151 indigenous Ukrainians from 13 regional populations representing the major territorial subdivisions of Ukraine. There were no significant inter-population differences. The genetic subdivisions within Ukraine was revealed between Polesie, western and eastern forest-steppe populations. The highest microsatellite variability was observed along the edges of Ukrainian area – in the Carpathian region, Bukovina, Sloboda Ukraine; the lowest – in Polesie. The average haplotype diversity values are higher in the steppe and forest-steppe zones, than in Polesie and the Carpathians. Forensic parameters were calculated: total haplotype diversity HD = 0,998855, match probability MP = 0.00114508, the discrimination capacity DC = 0,89400521.

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