scholarly journals Population Genetics of New Zealand Scampi (Metanephrops challengeri)

2021 ◽  
Author(s):  
◽  
Alexander Verry
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
Population Structure ◽  
Gene Flow ◽  
New Zealand ◽  
Demographic History ◽  
Eastern Coast ◽  
Genetic Structuring ◽  
The North ◽  
Dispersal Potential

<p>A fundamental goal of fisheries management is sustainable harvesting and the preservation of properly functioning populations. Therefore, an important aspect of management is the identification of demographically independent populations (stocks), which is achieved by estimating the movement of individuals between areas. A range of methods have been developed to determine the level of connectivity among populations; some measure this directly (e.g. mark-recapture) while others use indirect measures (e.g. population genetics). Each species presents a different set of challenges for methods that estimate levels of connectivity. Metanephrops challengeri is a species of nephropid lobster that supports a commercial fishery and inhabits the continental shelf and slope of New Zealand. Very little research on population structure has been reported for this species and it presents a unique set of challenges compared to finfish species. M. challengeri have a short pelagic larval duration lasting up to five days which limits the dispersal potential of larvae, potentially leading to low levels of connectivity among populations. The aim of this study was to examine the genetic population structure of the New Zealand M. challengeri fishery.  DNA was extracted from M. challengeri samples collected from the eastern coast of the North Island (from the Bay of Plenty to the Wairarapa), the Chatham Rise, and near the Auckland Islands. DNA from the mitochondrial CO1 gene and nuclear ITS-1 region was amplified and sequenced. The aligned dataset of DNA sequences was then used to estimate levels of both genetic diversity and differentiation, and examine demographic history. Analyses of population structure indicate that M. challengeri from the Auckland Islands region are genetically distinct from M. challengeri inhabiting the Chatham Rise, and those collected from waters off the eastern coast of the North Island. There appears to be gene flow among the sampling sites off the eastern coast of the North Island and on the Chatham Rise, but some isolation by distance was detected. These results indicate that some of these populations may be demographically uncoupled. Genetic diversity estimates combined with Bayesian skyline plots and demographic history parameters suggest that M. challengeri populations have recently undergone a size expansion.  The genetic structuring between the Auckland Islands site and all others may be due to a putative habitat disjunction off the Otago shelf. In contrast, a largely continuously distributed population along the eastern coast of the North Island and the Chatham Rise most likely promotes gene flow as larvae can be transported limited distances by oceanic currents. Historical changes in climate may have influenced the patterns of present-day structure and genetic diversity of M. challengeri, by altering habitat availability and other characteristics of their environment. This study provides evidence that species which appear to have limited dispersal potential can still maintain connected populations, but there are situations where large breaks in suitable habitat appear to limit gene flow. The results of this study will help inform stock structure of the M. challengeri fishery, which will enable stock assessments to be more precisely aligned to natural population boundaries.</p>

scholarly journals Population Genetics of New Zealand Scampi (Metanephrops challengeri)

2021 ◽  
Author(s):  
◽  
Alexander Verry
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
Population Structure ◽  
Gene Flow ◽  
New Zealand ◽  
Demographic History ◽  
Eastern Coast ◽  
Genetic Structuring ◽  
The North ◽  
Dispersal Potential

<p>A fundamental goal of fisheries management is sustainable harvesting and the preservation of properly functioning populations. Therefore, an important aspect of management is the identification of demographically independent populations (stocks), which is achieved by estimating the movement of individuals between areas. A range of methods have been developed to determine the level of connectivity among populations; some measure this directly (e.g. mark-recapture) while others use indirect measures (e.g. population genetics). Each species presents a different set of challenges for methods that estimate levels of connectivity. Metanephrops challengeri is a species of nephropid lobster that supports a commercial fishery and inhabits the continental shelf and slope of New Zealand. Very little research on population structure has been reported for this species and it presents a unique set of challenges compared to finfish species. M. challengeri have a short pelagic larval duration lasting up to five days which limits the dispersal potential of larvae, potentially leading to low levels of connectivity among populations. The aim of this study was to examine the genetic population structure of the New Zealand M. challengeri fishery.  DNA was extracted from M. challengeri samples collected from the eastern coast of the North Island (from the Bay of Plenty to the Wairarapa), the Chatham Rise, and near the Auckland Islands. DNA from the mitochondrial CO1 gene and nuclear ITS-1 region was amplified and sequenced. The aligned dataset of DNA sequences was then used to estimate levels of both genetic diversity and differentiation, and examine demographic history. Analyses of population structure indicate that M. challengeri from the Auckland Islands region are genetically distinct from M. challengeri inhabiting the Chatham Rise, and those collected from waters off the eastern coast of the North Island. There appears to be gene flow among the sampling sites off the eastern coast of the North Island and on the Chatham Rise, but some isolation by distance was detected. These results indicate that some of these populations may be demographically uncoupled. Genetic diversity estimates combined with Bayesian skyline plots and demographic history parameters suggest that M. challengeri populations have recently undergone a size expansion.  The genetic structuring between the Auckland Islands site and all others may be due to a putative habitat disjunction off the Otago shelf. In contrast, a largely continuously distributed population along the eastern coast of the North Island and the Chatham Rise most likely promotes gene flow as larvae can be transported limited distances by oceanic currents. Historical changes in climate may have influenced the patterns of present-day structure and genetic diversity of M. challengeri, by altering habitat availability and other characteristics of their environment. This study provides evidence that species which appear to have limited dispersal potential can still maintain connected populations, but there are situations where large breaks in suitable habitat appear to limit gene flow. The results of this study will help inform stock structure of the M. challengeri fishery, which will enable stock assessments to be more precisely aligned to natural population boundaries.</p>

scholarly journals Speciation, Connectivity and Self-Recruitment  Among Mollusc Populations from  Isolated Oceanic Islands

2021 ◽  
Author(s):  
◽  
Céline Marie Olivia Reisser
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
New Zealand ◽  
Last Glacial Maximum ◽  
Genetic Homogeneity ◽  
Genetic Structuring ◽  
Subantarctic Islands ◽  
History Of ◽  
The Last Glacial Maximum ◽  
The Last Glacial

<p>The conventional view that marine populations are demographically ‘open’ and exchange migrants (juveniles or adults, but mostly larvae) has been challenged by recent genetic studies and the discovery of significant genetic subdivision among populations on small geographic scales. Despite the numerous publications on the matter, the extent to which some/all marine populations rely on self-recruitment and whether this reliance is stable in time and space currently remains unanswered. This is particularly true for populations from isolated oceanic archipelagos, such as the New Zealand (NZ) subantarctic islands and the Kermadec Islands. The specific objectives of this thesis were to: 1) assess the genetic diversity, phylogeography and contemporary levels of dispersal and self-recruitment in populations of the Cellana strigilis limpet complex, endemic to the NZ subantarctic islands; 2) conduct a morphometric analysis of the C. strigilis complex to complement its molecular investigation; 3) develop and optimize specific microsatellite markers for Nerita melanotragus, a marine gastropod of the Kermadec Islands and New Zealand North Island rocky shores; 4) assess the genetic structuring and levels of connectivity of N. melanotragus populations within the Kermadec Islands, within NZ North Island, and between the Kermadec Islands and NZ; and 5) compare the genetic structuring of N. melanotragus at the Kermadec Islands to that of NZ North Island populations, to test for any “island effect” on connectivity levels, and test for possible gene flow between the two groups. Genetic investigation of the C. strigilis complex confirmed the presence of two distinct lineages, separated by their sister species Cellana denticulata. Morphometric analyses were congruent with molecular analyses, and were used to provide a new taxonomic description of the C. strigilis limpet complex: two species were recognized, Cellana strigilis and Cellana oliveri. The role of the subantarctic islands during the last glacial maximum was highlighted, and the colonisation history of the islands by the two Cellana species was explained. Contemporary levels of connectivity (gene flow) among the different populations of the two lineages were low, or non-existant, revealing their high reliability on self-recruitment. However, the analysis detected a recent migration event in one of the two lineages. Considering the geographical distance of the islands and the life history of the Cellana species, the use of mediated dispersal means (e.g., rafting on a natural substrate such as kelp) seems very likely. Ten novel polymorphic microsatellite loci were developed for N. melanotragus, and seven of those were used to investigate the levels of connectivity and self-recruitment in six populations from the Kermadec Islands, and nine populations from the east coast of NZ North Island. According to what can be expected for a species with a long pelagic larval duration (PLD), genetic homogeneity was recorded for the Kermadec Islands populations. A lack of genetic structuring was also found for the nine populations on the NZ North Island, which is congruent with the literature in this geographic area. However, what was surprising was the high level of genetic homogeneity found between the Kermadec Islands and the NZ North Island, meaning that the two groups are effectively exchanging individuals. Hence, the Kermadec archipelago can be considered “open” at the scale of the South Pacific, for N. melanotragus populations. This Ph.D. highlights the importance of having the correct taxonomy for conservation and connectivity studies, and gives a better understanding of the historical and contemporary patterns of genetic connectivity in the NZ offshore islands. It illustrated how historical events, such as the last glacial maximum, can shape local genetic diversity, and how this historical pattern can be maintained because of limited contemporary gene exchange. Also, this thesis demonstrated that remote populations could be strongly connected to mainland populations, contributing to the resilience of both systems and confirming the necessity of integrating remote oceanic habitats in the creation of effective Marine Protected Areas (MPA) networks to protect the marine environment.</p>

scholarly journals Speciation, Connectivity and Self-Recruitment  Among Mollusc Populations from  Isolated Oceanic Islands

2021 ◽  
Author(s):  
◽  
Céline Marie Olivia Reisser
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
New Zealand ◽  
Last Glacial Maximum ◽  
Genetic Homogeneity ◽  
Genetic Structuring ◽  
Subantarctic Islands ◽  
History Of ◽  
The Last Glacial Maximum ◽  
The Last Glacial

<p>The conventional view that marine populations are demographically ‘open’ and exchange migrants (juveniles or adults, but mostly larvae) has been challenged by recent genetic studies and the discovery of significant genetic subdivision among populations on small geographic scales. Despite the numerous publications on the matter, the extent to which some/all marine populations rely on self-recruitment and whether this reliance is stable in time and space currently remains unanswered. This is particularly true for populations from isolated oceanic archipelagos, such as the New Zealand (NZ) subantarctic islands and the Kermadec Islands. The specific objectives of this thesis were to: 1) assess the genetic diversity, phylogeography and contemporary levels of dispersal and self-recruitment in populations of the Cellana strigilis limpet complex, endemic to the NZ subantarctic islands; 2) conduct a morphometric analysis of the C. strigilis complex to complement its molecular investigation; 3) develop and optimize specific microsatellite markers for Nerita melanotragus, a marine gastropod of the Kermadec Islands and New Zealand North Island rocky shores; 4) assess the genetic structuring and levels of connectivity of N. melanotragus populations within the Kermadec Islands, within NZ North Island, and between the Kermadec Islands and NZ; and 5) compare the genetic structuring of N. melanotragus at the Kermadec Islands to that of NZ North Island populations, to test for any “island effect” on connectivity levels, and test for possible gene flow between the two groups. Genetic investigation of the C. strigilis complex confirmed the presence of two distinct lineages, separated by their sister species Cellana denticulata. Morphometric analyses were congruent with molecular analyses, and were used to provide a new taxonomic description of the C. strigilis limpet complex: two species were recognized, Cellana strigilis and Cellana oliveri. The role of the subantarctic islands during the last glacial maximum was highlighted, and the colonisation history of the islands by the two Cellana species was explained. Contemporary levels of connectivity (gene flow) among the different populations of the two lineages were low, or non-existant, revealing their high reliability on self-recruitment. However, the analysis detected a recent migration event in one of the two lineages. Considering the geographical distance of the islands and the life history of the Cellana species, the use of mediated dispersal means (e.g., rafting on a natural substrate such as kelp) seems very likely. Ten novel polymorphic microsatellite loci were developed for N. melanotragus, and seven of those were used to investigate the levels of connectivity and self-recruitment in six populations from the Kermadec Islands, and nine populations from the east coast of NZ North Island. According to what can be expected for a species with a long pelagic larval duration (PLD), genetic homogeneity was recorded for the Kermadec Islands populations. A lack of genetic structuring was also found for the nine populations on the NZ North Island, which is congruent with the literature in this geographic area. However, what was surprising was the high level of genetic homogeneity found between the Kermadec Islands and the NZ North Island, meaning that the two groups are effectively exchanging individuals. Hence, the Kermadec archipelago can be considered “open” at the scale of the South Pacific, for N. melanotragus populations. This Ph.D. highlights the importance of having the correct taxonomy for conservation and connectivity studies, and gives a better understanding of the historical and contemporary patterns of genetic connectivity in the NZ offshore islands. It illustrated how historical events, such as the last glacial maximum, can shape local genetic diversity, and how this historical pattern can be maintained because of limited contemporary gene exchange. Also, this thesis demonstrated that remote populations could be strongly connected to mainland populations, contributing to the resilience of both systems and confirming the necessity of integrating remote oceanic habitats in the creation of effective Marine Protected Areas (MPA) networks to protect the marine environment.</p>

scholarly journals Range-Wide and Regional Patterns of Population Structure and Genetic Diversity in the Gopher Tortoise

2017 ◽  
Vol 8 (2) ◽  
pp. 497-512 ◽  
Author(s):  
D. Gaillard ◽  
J.R. Ennen ◽  
B.R. Kreiser ◽  
C.P. Qualls ◽  
S.C. Sweat ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Microsatellite Loci ◽  
Spatial Scales ◽  
Demographic History ◽  
Genetic Admixture ◽  
Gopher Tortoise ◽  
Regional Patterns ◽  
Genetic Groups

Abstract The gopher tortoise (Gopherus polyphemus) has experienced dramatic population declines throughout its distribution in the southeastern United States and is federally listed as threatened in the area west of the Tombigbee and Mobile rivers. While there is molecular support for recognizing the listed portion of the range as genetically distinct, other research has suggested that additional population structure exists at both range-wide and regional scales. In this study, we sought to comprehensively define genetic population structure at both spatial scales by doubling the data available in terms of the number of sampling sites, individuals, and microsatellite loci compared to previously published work. We also compared patterns of genetic diversity, gene flow, and demographic history across the range. We collected 933 individuals from 47 sampling sites across the range and genotyped them for 20 microsatellite loci. Our range-wide analyses supported the recognition of five genetic groups (or regions) delineated by the Tombigbee and Mobile rivers, Apalachicola and Chattahoochee rivers, and the transitional areas between several physiographic province sections of the Coastal Plains (i.e., Eastern Gulf, Sea Island, and Floridian). We found genetic admixture at sampling sites along the boundaries of these genetically defined groups. We detected some degree of additional genetic structure within each of the five regions. Notably, within the range listed as threatened under the Endangered Species Act, we found some support for two additional genetic groups loosely delineated by the Pascagoula and Chickasawhay rivers, and we detected four more genetic groups within the Florida region that seemed to reflect the influence of the local physiography. Additionally, our range-wide analysis found the periphery of the range had lower levels of genetic diversity relative to the core. We suggest that the five main genetic groups delineated in our study warrant recognition as management units in terms of conservation planning. Intraregional population structure also points to the potential importance of other barriers to gene flow at finer spatial scales, although additional work is needed to better delineate these genetic groups.

scholarly journals Inferring the late Quaternary phylogeography of Pseudopanax crassifolius using microsatellite analysis

2021 ◽  
Author(s):  
◽  
Michael Gemmell
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
New Zealand ◽  
Late Quaternary ◽  
Leading Edge ◽  
The South ◽  
Genetic Structuring ◽  
The North ◽  
Chloroplast Haplotypes ◽  
Patterns And Processes

<p>Geologic processes have shaped the New Zealand archipelago throughout its existence. The last major geologic event was the Pleistocene glaciations beginning around 2.5 million years ago. This cold period left its mark in the phylogeography (the geographic distribution of genetic variation) of New Zealand’s globally significant biota. Studies into the phylogeography of New Zealand have largely focused on species with limited distributions through rarity or ecological preferences. This study focuses on the ubiquitous species Pseudopanax crassifolius (Sol. Ex A. Cunn) K. Koch, also known commonly as Horoeka or Lancewood. This species is widespread and almost continuously distributed throughout New Zealand giving a broad scale look at the patterns and processes that have influenced the formation of New Zealand’s natural history.  Seven microsatellite loci and two rps4 chloroplast haplotypes were utilised to study 247 Pseudopanax crassifolius and nine P. chathamicus individuals sampled from populations from around New Zealand. Pseudopanax crassifolius was found to have levels of genetic diversity and overall differentiation consistent with common widespread trees. The genetic structuring suggests P. crassifolius is not a single homogenous population across a southern cluster. The geographic structuring of genetic variation within these clusters is poor.   The genetic patterns and the spatial distribution of these patterns may reflect the response of Pseudopanax crassifolius to changing environmental conditions during the late Quaternary following the maximum extent of the last glacial maximum (LGM) period. During the maximally cold periods of the LGM, P. crassifolius is likely to have been eliminated or at least greatly reduced in the south and west coast of the South Island. In the remainder of the South Island and throughout the North Island it remained widespread. The heterogeneous pattern of genetic variation with little geographic correlation in the northern cluster may reflect either the extent of the historic distribution of the species or the effect of gene flow between populations acting to inhibit population structuring from establishing. The reduction in genetic diversity and the homogeneity of structure in the south indicate a pattern of leading edge re-colonisation into southern areas as conditions became more favourable following the LGM. The leading edge mode is supported by asymmetric introgression of rps4 haplotype seen between P. crassifolius and P. ferox along the east coast of the South Island.  This study also investigated levels of differentiation between Pseudopanax crassifolius and P. chathamicus. There is limited evidence of differentiation based on microsatellite markers. There is therefore no strong genetic evidence for either the support or rejection of the current species delimitation of the crassifolius group of Pseudopanax species. The two species are morphologically different and geographically isolated. This, alongside evidence from previous studies suggest that P. chathamicus is possibly an example of a group undergoing incipient allopatric speciation. A recent founder event is proposed with enough potential diversity carried in two individual fruit to account for the diversity seen in P. chathamicus.</p>

scholarly journals Inferring the late Quaternary phylogeography of Pseudopanax crassifolius using microsatellite analysis

2021 ◽  
Author(s):  
◽  
Michael Gemmell
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
New Zealand ◽  
Late Quaternary ◽  
Leading Edge ◽  
The South ◽  
Genetic Structuring ◽  
The North ◽  
Chloroplast Haplotypes ◽  
Patterns And Processes

<p>Geologic processes have shaped the New Zealand archipelago throughout its existence. The last major geologic event was the Pleistocene glaciations beginning around 2.5 million years ago. This cold period left its mark in the phylogeography (the geographic distribution of genetic variation) of New Zealand’s globally significant biota. Studies into the phylogeography of New Zealand have largely focused on species with limited distributions through rarity or ecological preferences. This study focuses on the ubiquitous species Pseudopanax crassifolius (Sol. Ex A. Cunn) K. Koch, also known commonly as Horoeka or Lancewood. This species is widespread and almost continuously distributed throughout New Zealand giving a broad scale look at the patterns and processes that have influenced the formation of New Zealand’s natural history.  Seven microsatellite loci and two rps4 chloroplast haplotypes were utilised to study 247 Pseudopanax crassifolius and nine P. chathamicus individuals sampled from populations from around New Zealand. Pseudopanax crassifolius was found to have levels of genetic diversity and overall differentiation consistent with common widespread trees. The genetic structuring suggests P. crassifolius is not a single homogenous population across a southern cluster. The geographic structuring of genetic variation within these clusters is poor.   The genetic patterns and the spatial distribution of these patterns may reflect the response of Pseudopanax crassifolius to changing environmental conditions during the late Quaternary following the maximum extent of the last glacial maximum (LGM) period. During the maximally cold periods of the LGM, P. crassifolius is likely to have been eliminated or at least greatly reduced in the south and west coast of the South Island. In the remainder of the South Island and throughout the North Island it remained widespread. The heterogeneous pattern of genetic variation with little geographic correlation in the northern cluster may reflect either the extent of the historic distribution of the species or the effect of gene flow between populations acting to inhibit population structuring from establishing. The reduction in genetic diversity and the homogeneity of structure in the south indicate a pattern of leading edge re-colonisation into southern areas as conditions became more favourable following the LGM. The leading edge mode is supported by asymmetric introgression of rps4 haplotype seen between P. crassifolius and P. ferox along the east coast of the South Island.  This study also investigated levels of differentiation between Pseudopanax crassifolius and P. chathamicus. There is limited evidence of differentiation based on microsatellite markers. There is therefore no strong genetic evidence for either the support or rejection of the current species delimitation of the crassifolius group of Pseudopanax species. The two species are morphologically different and geographically isolated. This, alongside evidence from previous studies suggest that P. chathamicus is possibly an example of a group undergoing incipient allopatric speciation. A recent founder event is proposed with enough potential diversity carried in two individual fruit to account for the diversity seen in P. chathamicus.</p>

Genetic diversity, population structure and gene flow pattern among populations of Lasiurus sindicus Henr. - an endemic, C4 grass of Indian Thar desert

Plant Gene ◽  
2020 ◽  
Vol 21 ◽  
pp. 100206 ◽  
Author(s):  
Bhuwnesh Goswami ◽  
Rekha Rankawat ◽  
Wahlang Daniel Regie ◽  
Bhana Ram Gadi ◽  
Satyawada Rama Rao
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Flow Pattern ◽  
Thar Desert ◽  
C4 Grass

scholarly journals Population Genetics of the Red Rock Lobster,  Jasus edwardsii

2021 ◽  
Author(s):  
◽  
Luke Thomas
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
New Zealand ◽  
Genetic Differentiation ◽  
Microsatellite Markers ◽  
Rocky Reef ◽  
Rock Lobster ◽  
Wide Range ◽  
Jasus Edwardsii ◽  
Polymorphic Microsatellite

<p>Understanding patterns of gene flow across a species range is a vital component of an effective fisheries management strategy. The advent of highly polymorphic microsatellite markers has facilitated the detection of fine-scale patterns of genetic differentiation at levels below the resolving power of earlier techniques. This has triggered the wide-spread re-examination of population structure for a number of commercially targeted species. The aims of thesis were to re-investigate patterns of gene flow of the red rock lobster Jasus edwardsii throughout New Zealand and across the Tasman Sea using novel microsatellite markers. Jasus edwardsii is a keystone species of subtidal rocky reef system and supports lucrative export markets in both Australia and New Zealand. Eight highly polymorphic microsatellite markers were developed from 454 sequence data and screened across a Wellington south coast population to obtain basic diversity indices. All loci were polymorphic with the number of alleles per locus ranging from 6-39. Observed and expected heterozygosity ranged from 0.563-0.937 and 0.583-0.961, respectively. There were no significant deviations from Hardy-Weinberg equilibrium following standard Bonferroni corrections. The loci were used in a population analysis of J. edwardsii that spanned 10 degrees of latitude and stretched 3,500 km across the South Pacific. The analysis rejected the null-hypothesis of panmixia based on earlier mDNA analysis and revealed significant population structure (FST=0.011, RST=0.028) at a wide range of scales. Stewart Island was determined to have the highest levels of genetic differentiation of all populations sampled suggesting a high degree of reproductive isolation and self-recruitment. This study also identified high levels of asymmetric gene flow from Australia to New Zealand indicating a historical source-sink relationship between the two countries. Results from the genetic analysis were consistent with results from oceanographic dispersal models and it is likely that the genetic results reflect historical and contemporary patterns of Jasus edwardsii dispersal and recruitment throughout its range.</p>

scholarly journals Population structure and demographic history of the chukar partridge Alectoris chukar in China

2013 ◽  
Vol 59 (4) ◽  
pp. 458-474 ◽  
Author(s):  
Sen Song ◽  
Shijie Bao ◽  
Ying Wang ◽  
Xinkang Bao ◽  
Bei An ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
North America ◽  
Demographic History ◽  
Population Expansion ◽  
Northwest China ◽  
Population History ◽  
Extant Species ◽  
History Of ◽  
Chukar Partridge

Abstract Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. Although the effects of recent glacial cycles on genetic diversity have been well studied on species in Europe and North America, genetic legacy of species in the Pleistocene in north and northwest of China where glaciations was not synchronous with the ice sheet development in the Northern Hemisphere or or had little or no ice cover during the glaciations’ period, remains poorly understood. Here we used phylogeographic methods to investigate the genetic structure and population history of the chukar partridge Alec-toris chukar in north and northwest China. A 1,152 – 1,154 bp portion of the mtDNA CR were sequenced for all 279 specimens and a total number of 91 haplotypes were defined by 113 variable sites. High levels of gene flow were found and gene flow estimates were greater than 1 for most population pairs in our study. The AMOVA analysis showed that 81% and 16% of the total genetic variability was found within populations and among populations within groups, respectively. The demographic history of chukar was examined using neutrality tests and mismatch distribution analyses and results indicated Late Pleistocene population expansion. Results revealed that most populations of chukar experienced population expansion during 0.027 ? 0.06 Ma. These results are at odds with the results found in Europe and North America, where population expansions occurred after Last Glacial Maximum (LGM, 0.023 to 0.018 Ma). Our results are not consistent with the results from avian species of Tibetan Plateau, either, where species experienced population expansion following the retreat of the extensive glaciation period (0.5 to 0.175 Ma).

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