Shared mtDNA Haplotypes Research Articles

A critically endangered estuarine limpet’s only two populations are genomically and morphologically distinct

Abstract Seagrass habitats are declining worldwide, placing several seagrass‐associated animals at risk of extinction. The Critically Endangered limpet Siphonaria compressa is one of the rarest molluscs in Africa, and has been reported from only two disjunctive lagoons in South Africa. Being a highly specialized grazer that lives exclusively on the narrow blades of Cape eelgrass, Zostera capensis, which is itself listed as Endangered in the South African Red List and has decreased in abundance, conservation initiatives are urgently needed to ensure the long‐term survival of S. compressa. Molecular data (sequence data from the mitochondrial genome and single nucleotide polymorphism data of the nuclear genome) and morphological data were analysed to determine whether the two populations are conspecific, with implications for whether translocation between localities could be a viable management strategy to restore either population in the event of a collapse, or to maintain the genetic diversity of each population. Strong evidence emerged for the distinctness of the two populations, including a lack of shared mtDNA haplotypes that indicate an absence of contemporary gene flow, a divergence time that dates to the late Pleistocene, and a number of morphological characters that distinguish their shells. These findings indicate that the two populations are distinct cryptic subspecies. As the two populations occur in different temperature‐defined marine biogeographical regions, they are probably adapted to different thermal environments. Translocations are not recommended, as this management strategy has considerable potential to result in outbreeding depression and exacerbate the extinction risk. Instead, each population should be managed separately, and several alternative conservation measures are discussed, including the protection and restoration of seagrass beds.

Genetic examination of historical North Atlantic right whale (Eubalaena glacialis) bone specimens from the eastern North Atlantic: Insights into species history, transoceanic population structure, and genetic diversity

AbstractSpecies monitoring and conservation is increasingly challenging under current climate change scenarios. For the North Atlantic right whale (Eubalaena glacialis) this challenge is heightened by the added effects of complicated and uncertain past species demography. Right whales once had a much wider distribution across the North Atlantic Ocean, although the degree to which right whales in the western and eastern North Atlantic were genetically isolated remains unknown. We analyzed DNA from 24 4th–20th century (CE) right whale bone specimens that were collected from 10 historical and archaeological sites in Iceland, the Faroe Islands, and Scotland. Following mtDNA species identification, we obtained 15‐locus nuclear microsatellite profiles from a subset of eight specimens and compared these to contemporary data from animals remaining in the western North Atlantic population. While some specimens share mtDNA haplotypes with the contemporary population, several new haplotypes were found. Moderate mtDNA and nuclear differentiation between the two regions was identified (mtDNA: FST = 0.0423, ΦST = 0.041; nuclear DNA: FST = 0.024). Interpretation of the relationships between animals in the two regions is not simple, and this research highlights the difficulty in conducting such assessments in species with complex histories of unknown structure prior to extensive exploitation.

Systematics and conservation of an endemic radiation ofAccipiterhawks in the Caribbean islands

AbstractMore than one-third of the bird species found in the Caribbean are endemic to a set of neighboring islands or a single island. However, we have little knowledge of the evolutionary history of the Caribbean avifauna, and the lack of phylogenetic studies limits our understanding of the extent of endemism in the region. The Sharp-shinned Hawk (Accipiter striatus) occurs widely across the Americas and includes 3 endemic Caribbean taxa: venator on Puerto Rico, striatus on Hispaniola, and fringilloides on Cuba. These island populations have undergone extreme declines presumably due to ecosystem changes caused by anthropogenic factors, as well as due to severe hurricanes. Sharp-shinned Hawks, in general, and Caribbean Sharp-shinned Hawks, in particular, have not been placed in a modern phylogenetic context. However, the island taxa have historically been presumed to have some ongoing gene flow with mainland populations. Here we sequenced ultraconserved elements (UCEs) and their flanking regions from 38 samples, focusing on Caribbean taxa. Using a combination of UCEs, mitochondrial genome sequences, and single-nucleotide polymorphisms, we investigated the phylogenetic relationships among Caribbean lineages and their relationships to mainland taxa. We found that Caribbean Sharp-shinned Hawks are reciprocally monophyletic in all datasets with regard to mainland populations and among island taxa (with no shared mtDNA haplotypes) and that divergence in the NADH dehydrogenase 2 gene (ND2) between these mainland and island groups averaged 1.83%. Furthermore, sparse non-negative matrix factorization (sNMF) analysis indicated that Hispaniola, Puerto Rico, and mainland samples each form separate populations with limited admixture. We argue that our findings are consistent with the recognition of the 3 resident Caribbean populations as species-level taxa because nuclear and mitochondrial genetic data indicate reciprocal monophyly and have species-level divergences, there is no sharing of mitochondrial haplotypes among or between island taxa and those on the mainland; and they are diagnosable by plumage.

A New Species of Bridled Darter Endemic to the Etowah River System in Georgia (Percidae: Etheostomatinae: Percina)

Percina freemanorum, the Etowah Bridled Darter, is described as a new species endemic to the Etowah River system in Georgia, specifically in Long Swamp Creek, Amicalola Creek, and the upper portion of the Etowah River. The earliest collection records for Percina freemanorum date to 1948 and in 2007 the species was delimited as populations of Percina kusha. Our investigation into the systematics of Percina kusha is motivated by the uncertain status of populations in the Coosawattee River system and observed morphological disparity in several meristic traits between populations in the Conasauga and Etowah River systems. Our analyses of morphological divergence, nuclear genotypes, and mitochondrial DNA (mtDNA) haplotype networks confirm the distinctiveness of Percina freemanorum. Morphologically, Percina freemanorum is distinguished from Percina kusha through lower average numbers of lateral line scales (65.4 vs. 72.3); rows of transverse scales (18.0 vs. 21.4); scales around the caudal peduncle (22.1 vs. 24.9); and modally more pectoral fin rays (14 vs. 13). The two species are not reciprocally monophyletic in phylogenetic analysis of mtDNA sequences, but the two species do not share mtDNA haplotypes. Analysis of up to 158,000 double digest restriction-site associated DNA (ddRAD) sequencing loci resolve each of the two species as reciprocally monophyletic and genomic clustering analysis of single nucleotide polymorphisms identifies two genetic clusters that correspond to the morphologically delimited Percina freemanorum and Percina kusha.

Old divergence and restricted gene flow between torrent duck (Merganetta armata) subspecies in the Central and Southern Andes.

AimTo investigate the structure and rate of gene flow among populations of habitat‐specialized species to understand the ecological and evolutionary processes underpinning their population dynamics and historical demography, including speciation and extinction.LocationPeruvian and Argentine Andes.TaxonTwo subspecies of torrent duck (Merganetta armata).MethodsWe sampled 156 individuals in Peru (M. a. leucogenis; Chillón River, n = 57 and Pachachaca River, n = 49) and Argentina (M. a. armata; Arroyo Grande River, n = 33 and Malargüe River, n = 17), and sequenced the mitochondrial DNA (mtDNA) control region to conduct coarse and fine‐scale demographic analyses of population structure. Additionally, to test for differences between subspecies, and across genetic markers with distinct inheritance patterns, a subset of individuals (Peru, n = 10 and Argentina, n = 9) was subjected to partial genome resequencing, obtaining 4,027 autosomal and 189 Z‐linked double‐digest restriction‐associated DNA sequences.ResultsHaplotype and nucleotide diversities were higher in Peru than Argentina across all markers. Peruvian and Argentine subspecies showed concordant species‐level differences (ΦST mtDNA = 0.82; ΦST autosomal = 0.30; ΦST Z chromosome = 0.45), including no shared mtDNA haplotypes. Demographic parameters estimated for mtDNA using IM and IMa2 analyses, and for autosomal markers using ∂a∂i (isolation‐with‐migration model), supported an old divergence (mtDNA = 600,000 years before present (ybp), 95% HPD range = 1.2 Mya to 200,000 ybp; and autosomal ∂a∂i = 782,490 ybp), between the two subspecies, characteristic of deeply diverged lineages. The populations were well‐differentiated in Argentina but moderately differentiated in Peru, with low unidirectional gene flow in each country.Main conclusionsWe suggest that the South American Arid Diagonal was preexisting and remains a current phylogeographic barrier between the ranges of the two torrent duck subspecies, and the adult territoriality and breeding site fidelity to the rivers define their population structure.

Molecular and morphological differentiation among Torrent Duck (Merganetta armata) populations in the Andes

AbstractBirds living in riverine environments may show weak population structure because high dispersal abilities required to track habitat dynamics can result in gene flow over broad spatial scales. Alternatively, the configuration of river networks may result in restricted dispersal within river courses or basins, leading to high genetic structure. Although several bird species are riverine specialists in the Andes, no study has extensively evaluated the population genetic structure of any of them. We examined evidence from genetic and morphological data to address questions about the biogeography and taxonomy of the Torrent Duck (Merganetta armata), a riverine specialist bird with a broad distribution in Andean riverine habitats which certainly comprises different subspecies and may comprise more than one species. We found deep subdivisions of Torrent Duck populations from the northern, central and southern portions of the Andes. These lineages, which partly coincide with subspecies described based on plumage variation and body size, do not share mtDNA haplotypes, have private nuclear alleles and exhibit marked differences in morphometric traits. Some geographic barriers presumably restricting gene flow between groups partially coincide with those associated with major genetic breaks in forest species with similar distributions along the Andes, suggesting that bird assemblages including species occupying different habitats were likely affected by common biogeographical events. The three groups of Torrent Ducks may be considered different species under some species definitions and are distinct evolutionary lineages to be conserved and managed separately.

Molecular evidence for cryptic species in the common slug eating snake Duberrialutrixlutrix (Squamata, Lamprophiidae) from South Africa.

We examined the impact of climatic fluctuations on the phylogeographic structure of the common slug eating snake (Duberrialutrixlutrix) throughout its distribution in South Africa. The evolutionary history within the taxon was examined using partial DNA sequence data for two mitochondrial genes (ND4 + cyt b) in combination with a nuclear locus (SPTBN1). Phylogenetic relationships were investigated for both the combined mtDNA and total evidence DNA sequence data. In addition, population and demographic analyses together with divergence time estimations were conducted on the combined mtDNA data. Topologies derived from the combined mtDNA analyses and the total evidence analyses were congruent and retrieved five statistically well-supported clades, suggesting that Duberrial.lutrix represents a species complex. The five clades were generally allopatric, separated by altitudinal barriers and characterised by the absence of shared mtDNA haplotypes suggesting long term isolation. Divergence time estimations indicate that the diversification within the D.l.lutrix species complex occurred during the Plio/Pleistocene as a result of climatic fluctuations and habitat shifts for the species. A taxonomic revision of the D.l.lutrix species complex may be required to delineate possible species boundaries.

Population genetic structure and evolutionary history of Bale monkeys (Chlorocebus djamdjamensis) in the southern Ethiopian Highlands

BackgroundSpecies with a restricted geographic distribution, and highly specialized habitat and dietary requirements, are particularly vulnerable to extinction. The Bale monkey (Chlorocebus djamdjamensis) is a little-known arboreal, bamboo-specialist primate endemic to the southern Ethiopian Highlands. While most Bale monkeys inhabit montane forests dominated by bamboo, some occupy forest fragments where bamboo is much less abundant. We used mitochondrial DNA (mtDNA) sequences to analyse the genetic structure and evolutionary history of Bale monkeys covering the majority of their remaining distribution range. We analysed 119 faecal samples from their two main habitats, continuous forest (CF) and fragmented forests (FF), and sequenced 735 bp of the hypervariable region I (HVI) of the control region. We added 12 orthologous sequences from congeneric vervets (C. pygerythrus) and grivets (C. aethiops) as well as animals identified as hybrids, previously collected in southern Ethiopia.ResultsWe found strong genetic differentiation (with no shared mtDNA haplotypes) between Bale monkey populations from CF and FF. Phylogenetic analyses revealed two distinct and highly diverged clades: a Bale monkey clade containing only Bale monkeys from CF and a green monkey clade where Bale monkeys from FF cluster with grivets and vervets. Analyses of demographic history revealed that Bale monkey populations (CF and FF) have had stable population sizes over an extended period, but have all recently experienced population declines.ConclusionsThe pronounced genetic structure and deep mtDNA divergence between Bale monkey populations inhabiting CF and FF are likely to be the results of hybridization and introgression of the FF population with parapatric Chlorocebus species, in contrast to the CF population, which was most likely not impacted by hybridization. Hybridization in the FF population was probably enhanced by an alteration of the bamboo forest habitat towards a more open woodland habitat, which enabled the parapatric Chlorocebus species to invade the Bale monkey's range and introgress the FF population. We therefore propose that the CF and FF Bale monkey populations should be managed as separate units when developing conservation strategies for this threatened species.

Genetic Structure and Diversity Among Historic and Modern Populations of the Sumatran Rhinoceros (Dicerorhinus sumatrensis).

The Sumatran rhinoceros (Dicerorhinus sumatrensis), once widespread across Southeast Asia, now consists of as few as 30 individuals within Sumatra and Borneo. To aid in conservation planning, we sequenced 218 bp of control region mitochondrial (mt) DNA, identifying 17 distinct mitochondrial haplotypes across modern (N = 13) and museum (N = 26) samples. Museum specimens from Laos and Myanmar had divergent mtDNA, consistent with the placement of western mainland rhinos into the distinct subspecies D. s. lasiotis (presumed extinct). Haplotypes from Bornean rhinos were highly diverse, but dissimilar from those of other regions, supporting the distinctiveness of the subspecies D. s. harrissoni. Rhinos from Sumatra and Peninsular Malaysia shared mtDNA haplotypes, consistent with their traditional placement into a single subspecies D. s sumatrensis. Modern samples of D. s. sumatrensis were genotyped at 18 microsatellite loci. Rhinos within Sumatra formed 2 sub-populations, likely separated by the Barisan Mountains, though with only modest genetic differentiation between them. There are so few remaining Sumatran rhinoceros that separate management strategies for subspecies or subpopulations may not be viable, while each surviving rhino pedigree is likely to retain alleles found in no other individuals. Given the low population size and low reproductive potential of Sumatran rhinos, rapid genetic erosion is inevitable, though an under-appreciated concern is the potential for fixation of harmful genetic variants. Both concerns underscore 2 overriding priorities for the species: 1) translocation of wild rhinos to ex situ facilities, and 2) collection and storage of gametes and cell lines from every surviving captive and wild individual.

Geographic origins and post-introduction hybridization between strains of Trioxys pallidus introduced to western North America for the biological control of walnut and filbert aphids

Strains of the exotic parasitoid wasp Trioxys pallidus were introduced on multiple occasions to the western United States resulting in successful classical biological control of aphids in walnut and filbert orchard systems. However, breakdowns in biological control services have been reported in recent years in both orchard systems. To aid in potential plans to stabilize these important biological control programs we investigated the individual origins of each strain that was introduced to and established in the western United States, and examined whether post-introduction hybridization between strains has occurred. We collected individuals from the native and introduced ranges of T. pallidus, performed genetic clustering analyses using 15 polymorphic microsatellite loci, and reconstructed a phylogeny and estimated haplotype networks based on the mitochondrial (mtDNA) locus cytochrome oxidase I (COI). Based on microsatellite loci we find that T. pallidus individuals can be assigned to one of three distinct genetic clusters, and based on mtDNA haplotypes, to one of two distinct clades/networks. The majority of individuals from California were assigned to the same genetic cluster as individuals collected in Iran, also with shared mtDNA haplotypes, while the majority of individuals from Oregon were assigned to a genetic cluster represented by only a single individual collected near Bordeaux, France. Although we found some evidence of hybridization between the strains, the rates were so low that hybrid-breakdown is unlikely to be responsible for recent failures of biological control services in the western United States. We did find elevated levels of inbreeding within established populations, however, suggesting that inbreeding depression may have played an important role in these recent breakdowns.

Angelfishes, Paper Tigers, and the Devilish Taxonomy of the Centropyge flavissima Complex.

The pygmy angelfishes (genus Centropyge) provide numerous examples of discordance between color morphology, taxonomy, and evolutionary genetic lineages. This discordance is especially evident in the Centropyge flavissima complex, which includes three primary color morphs, three previously recognized species (C. flavissima, Centropyge eibli, and Centropyge vrolikii) and three distinct mitochondrial (mtDNA) lineages that do not align with species designations. Our previous research showed that the putative C. flavissima arose independently in the Indian and Pacific Oceans, and the three mtDNA lineages align with geography rather than species assignments. Here, we add 157 specimens to the previous dataset of 291 specimens, spread across a greater geographic range, to pinpoint the distribution of mtDNA lineages and color morphs. We found that the mtDNA lineages show remarkably strong geographic boundaries corresponding to the Indian Ocean, Central-West Pacific, and Central-South Pacific. We also test the validity of the "Black Tiger Centropyge" in the C. flavissima species complex, a taxonomic oddity that is restricted to shoals and atolls off the coast of northwestern Australia, and the newly named Centropyge cocosensis assigned to the C. flavissima lineage in the Indian Ocean. We conclude that the Black Tiger Centropyge is not a valid species but rather an intermediate between sympatric color morphs that correspond to the putative species C. eibli and C. vrolikii Our greater sampling efforts also do not support the genetic distinctiveness of C. cocosensis given shared mtDNA haplotypes with the sympatric C. eibli and C. vrolikii, but instead we find conflicting lines of evidence concerning the taxonomy of this group. We urge caution and taxonomic restraint until the true nature of this species complex can be revealed.

Do genes lie? Mitochondrial capture masks the Red Sea collector urchin’s true identity (Echinodermata: Echinoidea: Tripneustes)

Novel COI and bindin sequences of the Red Sea collector echinoid Tripneustes gratilla elatensis are used to show that (1) discordance between mitochondrial and nuclear loci exists in this echinoid genus, (2) Tripneustes gratilla as currently defined possibly comprises a complex of cryptic species, and (3) Red Sea Tripneustes form a genetically distinct clade in the bindin tree, which diverged from other Tripneustes clades at least 2–4million years ago. Morphological reassessment of T. gratilla elatensis shows perfect congruence between identification based on skeletal features and genetic data based on a nuclear marker sequence. Hence the Red Sea Tripneustes subspecies established by Dafni in 1983 is a distinct biological unit.All T. g. elatensis samples analyzed are highly similar to or share mtDNA haplotypes with Philippine T. g. gratilla, as do representatives from other edge-of-range occurrences. This lack of genetic structure in Indo-Pacific Tripneustes is interpreted as a result of wide-spread mitochondrial introgression. New fossil specimens from the Red Sea area confirm the sympatric occurrence of T. g. elatensis and T. g. gratilla in the northern Red Sea during Late Pleistocene, identifying a possible timing for the introgression. In addition, present-day distribution shows a contact zone in the Southern Red Sea (in the Dahlak Archipelago).T. g. elatensis, is yet another example of a Red Sea taxon historically identified as conspecific with its Indo-Pacific relatives, but which turned out to be a morphologically and genetically distinct endemic taxon, suggesting that the level of endemism in the Red Sea may still be underestimated.

Socio‐genetic structure of short‐beaked common dolphins in southern Australia

AbstractDelphinids show a wide range of social structures. However, studies investigating the influence of genetic relatedness and maternal kinship on school associations are limited to a small number of relatively well‐studied delphinid species. This study investigated biparental genetic relatedness and potential maternal kinship structure in schools of short‐beaked common dolphins Delphinus delphis from southern Australian waters. A total of 128 biopsy samples were obtained from free‐ranging individuals within 62 schools of common dolphins. Each sample was genotyped at 13 nuclear microsatellite markers, sequenced at 438 bp of the mitochondrial DNA control region, and used for genetic sexing. Pairwise analyses within and between schools showed that the average genetic relatedness between males was greater within schools than between schools. Pairs of individuals within schools were also more likely to share mtDNA haplotypes, for both pairs of males and of females. The results suggest that both biparental relatedness and potentially maternal kinship have an impact on school associations of short‐beaked common dolphins in southern Australia, similar to social traits reported of other dolphin species inhabiting shallow coastal environments. The information provided by this study contributes to our understanding of social evolution in delphinids. It also suggests that dolphin bycatch and deaths in fisheries from this region could lead to a reduction in the genetic diversity of this population, particularly if related individuals are simultaneously killed in the nets.

Mitochondrial DNA COI characterization of Helicoverpa armigera (Lepidoptera: Noctuidae) from Paraguay and Uruguay.

Since its detection in Brazil in 2013, the Old World cotton bollworm Helicoverpa armigera has been reported in Argentina, Paraguay, and Bolivia. Here we present evidence extending the South American range of H. armigera to Uruguay, using polymerase chain reaction and sequencing of the partial mitochondrial DNA (mtDNA) cytochrome oxidase I region. Molecular characterization of this gene region from individuals from Paraguay also supports previous morphological identification of H. armigera in Paraguay. Shared mtDNA haplotypes in H. armigera from Brazil, Uruguay, and Paraguay were identified. Additional surveying of populations in this region will be imperative to better monitor and understand factors that are underpinning its presence and successful adaptation in these South American regions. We discuss our findings with respect to the development of resistance pest management strategies of this invasive insect pest in a predominantly monoculture soybean crop landscape in the Southern Cone region.

Insights about the genetic diversity and population structure of an offshore group of common bottlenose dolphins (Tursiops truncatus) in the Mid-Atlantic.

Although the genus Tursiops has a worldwide distribution and is globally well-studied, some dolphin populations continue to face high risks of decline. Hence, it is necessary to assess the genetic diversity and structure of this genus to properly assess its conservation status and to implement appropriate management actions. In Brazil, genetic studies on this group remain rare, particularly for populations inhabiting offshore waters. Saint Peter and Saint Paul Archipelago (SPSPA) is a small group of islands located in the Mid- Atlantic Ridge, where recent studies of the Tursiops truncatus group indicate that individuals are resident throughout the year around the archipelago, exhibiting considerable site fidelity. A previous study with this group indicated that the individuals form an isolated population. To test this hypothesis, and describe the genetic diversity of SPSPA individuals, we assessed 12 microsatellite loci and a portion of the mitochondrial control region. Bayesian analysis revealed that SPSPA bottlenose dolphins form a unique population. In a phylogeographic perspective, we found that individuals from SPSPA shared mtDNA haplotypes with inshore and offshore individuals from North Atlantic, suggesting that they are not currently isolated from their conspecifics. Mirroring mtDNA findings, microsatellite analysis revealed that most of the pairs of individuals sampled seem to be unrelated (83.8%) and no indication of inbreeding, what would be expected if a small population such as SPSPA was reproductively isolated.

Genetic Variability of the Grey Wolf Canis lupus in the Caucasus in Comparison with Europe and the Middle East: Distinct or Intermediary Population?

Despite continuous historical distribution of the grey wolf (Canis lupus) throughout Eurasia, the species displays considerable morphological differentiation that resulted in delimitation of a number of subspecies. However, these morphological discontinuities are not always consistent with patterns of genetic differentiation. Here we assess genetic distinctiveness of grey wolves from the Caucasus (a region at the border between Europe and West Asia) that have been classified as a distinct subspecies C. l. cubanensis. We analysed their genetic variability based on mtDNA control region, microsatellite loci and genome-wide SNP genotypes (obtained for a subset of the samples), and found similar or higher levels of genetic diversity at all these types of loci as compared with other Eurasian populations. Although we found no evidence for a recent genetic bottleneck, genome-wide linkage disequilibrium patterns suggest a long-term demographic decline in the Caucasian population – a trend consistent with other Eurasian populations. Caucasian wolves share mtDNA haplotypes with both Eastern European and West Asian wolves, suggesting past or ongoing gene flow. Microsatellite data also suggest gene flow between the Caucasus and Eastern Europe. We found evidence for moderate admixture between the Caucasian wolves and domestic dogs, at a level comparable with other Eurasian populations. Taken together, our results show that Caucasian wolves are not genetically isolated from other Eurasian populations, share with them the same demographic trends, and are affected by similar conservation problems.

Tempo and mode of recurrent polyploidization in the Carassius auratus species complex (Cypriniformes, Cyprinidae)

Polyploidization is an evolutionarily rare but important mechanism in both plants and animals because it increases genetic diversity. Goldfish of the Carassius auratus species complex can be tetraploids, hexaploids and octaploids. Polyploidization events have occurred repeatedly in goldfish, yet the extent of this phenomenon and its phyletic history are poorly understood. We explore the origin, tempo and frequency of polyploidization in Chinese and Japanese goldfish using both mitochondrial (mtDNA) and nuclear DNA sequences from up to 1202 individuals including the outgroup taxon, Cyprinus carpio. Analyses of de novo nuclear gene data resolve two clusters of alleles and the pattern supports the prior hypothesis of an ancient allotetraploidization for Carassius. Alleles shared by tetraploid and hexaploid individuals indicate recent autoploidizations within the C. auratus complex. Sympatric tetraploids and hexaploids share mtDNA haplotypes and these frequently occur independently within six well-supported lineages and sublineages on a small spatial scale. Gene flow estimates (Fst values) indicate that hexaploids differ only slightly from sympatric tetraploids, if at all. In contrast, allopatric populations of tetraploids and hexaploids differ from one another to a far greater extent. Gene flow between sampled localities appears to be limited. Coalescence-based time estimations for hexaploids reveal that the oldest lineage within any sampled locality is around one million years old, which is very young. Sympatric, recurrent autoploidization occurs in all sampled populations of the C. auratus complex. Goldfish experience polyploidization events more frequently than any other vertebrate.

Phylogenetic relationships within Bothrops neuwiedi group (Serpentes, Squamata): Geographically highly-structured lineages, evidence of introgressive hybridization and Neogene/Quaternary diversification

Eight current species of snakes of the Bothrops neuwiedi group are widespread in South American open biomes from northeastern Brazil to southeastern Argentina. In this paper, 140 samples from 93 different localities were used to investigate species boundaries and to provide a hypothesis of phylogenetic relationships among the members of this group based on 1122bp of cyt b and ND4 from mitochondrial DNA and also investigate the patterns and processes occurring in the evolutionary history of the group. Combined data recovered the B. neuwiedi group as a highly supported monophyletic group in maximum parsimony, maximum likelihood and Bayesian analyses, as well as four major clades (Northeast I, Northeast II, East–West, West-South) highly-structured geographically. Monophyly was recovered only for B. pubescens. By contrast, B. diporus, B. lutzi, B. erythromelas, B. mattogrossensis, B. neuwiedi, B. marmoratus, and B. pauloensis, as currently defined on the basis of morphology, were polyphyletic. Sympatry, phenotypic intergrades and shared mtDNA haplotypes, mainly between B. marmoratus and B. pauloensis suggest recent introgressive hybridization and the possible occurrence of a narrow hybrid zone in Central Brazil. Our data suggest at least three candidate species: B. neuwiedi from Espinhaço Range, B. mattogrossensis (TM173) from Serra da Borda (MT) and B. diporus (PT3404) from Castro Barros, Argentina. Divergence estimates highlight the importance of Neogene events in the origin of B. neuwiedi group, and the origin of species and diversification of populations of the Neotropical fauna from open biomes during the Quaternary climate fluctuations. Data reported here represent a remarkable increase of the B. neuwiedi group sampling size, since representatives of all the current recognized species from a wide geographic range are included in this study, providing basic information for understanding the evolution and conservation of Neotropical biodiversity.

Genetic Structure of Pelagic and Littoral Cichlid Fishes from Lake Victoria

The approximately 700 species of cichlids found in Lake Victoria in East Africa are thought to have evolved over a short period of time, and they represent one of the largest known examples of adaptive radiation. To understand the processes that are driving this spectacular radiation, we must determine the present genetic structure of these species and elucidate how this structure relates to the ecological conditions that caused their adaptation. We analyzed the genetic structure of two pelagic and seven littoral species sampled from the southeast area of Lake Victoria using sequences from the mtDNA control region and 12 microsatellite loci as markers. Using a Bayesian model-based clustering method to analyze the microsatellite data, we separated these nine species into four groups: one group composed of pelagic species and another three groups composed mainly of rocky-shore species. Furthermore, we found significant levels of genetic variation between species within each group at both marker loci using analysis of molecular variance (AMOVA), although the nine species often shared mtDNA haplotypes. We also found significant levels of genetic variation between populations within species. These results suggest that initial groupings, some of which appear to have been related to habitat differences, as well as divergence between species within groups took place among the cichlid species of Lake Victoria.

Molecular phylogeny of the South American sheldgeese with implications for conservation of Falkland Islands (Malvinas) and continental populations of the Ruddy-headed GooseChloephaga rubidicepsand Upland GooseC. picta

SummarySheldgeese of the genusChloephagaare waterfowl (Anatidae) endemic to mainland South America and the Falkland Islands (Malvinas). Continental populations of three speciesC. picta,C. poliocephala, andC. rubidicepsbreed in Patagonia and Tierra del Fuego and migrate northwards to winter in central Argentina and Chile. These continental populations have declined by > 50% in the past 30 years due to direct hunting to control crop damage and by the introduction of the grey foxDusicyon griseusto their breeding grounds in Tierra del Fuego. The continental population ofC. rubidicepsis critically endangered, estimated to be < 1,000 individuals. While no historic population size estimates exist forC. rubidicepsin its wintering grounds, the breeding population in Tierra del Fuego was estimated to number several thousand individuals in the 1950s. In contrast, theC. rubidicepspopulation in the Falkland Islands (Malvinas) is non-migratory and stable with > 42,000 individuals, as is the Falkland Islands (Malvinas) population ofC. picta leucopterawith > 138,000 individuals. Here we use sequence data from the mitochondrial DNA control region to quantify genetic divergence between insular and continental populations of these two species of sheldgeese.Chloephaga rubidicepsandC. pictashowed significant intraspecific differentiation of 1.0% and 0.6%, respectively. In both cases, mainland and insular populations were reciprocally monophyletic and did not share mtDNA haplotypes. These results suggest that the insular and continental populations ofC. rubidicepsandC. pictaare genetically distinct and that female-mediated gene flow is restricted. We recommend a reevaluation of the threat category status of the continentalC. rubidicepspopulation, under IUCN guidelines. It is necessary to implement urgent actions for the conservation of this critically endangered population.